From b3f35ec19a2f9383feab1b3faf97109214bdc780 Mon Sep 17 00:00:00 2001
From: Galileo Sartor <galileo.sartor@gmail.com>
Date: Sat, 26 Jan 2019 17:52:37 +0100
Subject: [PATCH 001/184] Update snapcraft.yaml Move to snap folder

---
 .gitignore                                    |  12 ------
 .../snapcraft => snap/gui}/jabref.desktop     |   2 +-
 .../gui/jabref.png                            | Bin
 snap/snapcraft.yaml                           |  34 +++++++++++++++++
 snapcraft.yaml                                |  35 ------------------
 5 files changed, 35 insertions(+), 48 deletions(-)
 rename {buildres/snapcraft => snap/gui}/jabref.desktop (90%)
 rename buildres/snapcraft/JabRef-icon-256.png => snap/gui/jabref.png (100%)
 create mode 100644 snap/snapcraft.yaml
 delete mode 100644 snapcraft.yaml

diff --git a/.gitignore b/.gitignore
index eef074f6e45..7c7850841ea 100644
--- a/.gitignore
+++ b/.gitignore
@@ -23,18 +23,6 @@ ui/
 jabref.xml
 *.sonargraph
 
-# Snapcraft - JabRef places the files into buildres/snapcraft
-snap/
-
-
-
-
-
-
-
-
-
-
 # Created by https://www.gitignore.io/api/gradle,java,jabref,intellij,eclipse,netbeans,windows,linux,macos,node,snapcraft
 
 ### Eclipse ###
diff --git a/buildres/snapcraft/jabref.desktop b/snap/gui/jabref.desktop
similarity index 90%
rename from buildres/snapcraft/jabref.desktop
rename to snap/gui/jabref.desktop
index ef63a896d2d..3444b73fc8a 100644
--- a/buildres/snapcraft/jabref.desktop
+++ b/snap/gui/jabref.desktop
@@ -4,7 +4,7 @@ GenericName=BibTeX Editor
 Comment=JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.
 Type=Application
 Terminal=false
-Icon=${SNAP}/meta/gui/JabRef-icon-256.png
+Icon=${SNAP}/meta/gui/jabref.png
 Exec=jabref %U
 Keywords=bibtex;biblatex;latex;bibliography
 Categories=Office;
diff --git a/buildres/snapcraft/JabRef-icon-256.png b/snap/gui/jabref.png
similarity index 100%
rename from buildres/snapcraft/JabRef-icon-256.png
rename to snap/gui/jabref.png
diff --git a/snap/snapcraft.yaml b/snap/snapcraft.yaml
new file mode 100644
index 00000000000..6873178bf86
--- /dev/null
+++ b/snap/snapcraft.yaml
@@ -0,0 +1,34 @@
+name: jabref
+version: "git"
+version-script: cat build.gradle | grep "^version =" | cut -d'"' -f2
+#icon: snap/gui/icon.png
+summary: Bibliography manager
+description: JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.
+
+grade: devel
+confinement: strict
+
+apps:
+  jabref:
+    command: desktop-launch java -jar $SNAP/jar/JabRef-$SNAP_VERSION.jar
+    environment:
+      JAVA_OPTS: "-Djava.util.prefs.systemRoot=$SNAP_USER_DATA/.java -Djava.util.prefs.userRoot=$SNAP_USER_DATA/.java/.userPrefs"
+    plugs:
+      - desktop
+      - desktop-legacy
+      - wayland
+      - unity7
+      - home
+      - network-bind
+
+parts:
+  jabref:
+    plugin: gradle
+    source: .
+    stage-packages:
+      - openjdk-8-jre
+      - openjfx
+      - x11-utils
+    gradle-options: [snapJar]
+    gradle-output-dir: 'build/releases'
+    after: [desktop-gtk3]
diff --git a/snapcraft.yaml b/snapcraft.yaml
deleted file mode 100644
index 0daa48c83c4..00000000000
--- a/snapcraft.yaml
+++ /dev/null
@@ -1,35 +0,0 @@
-# based on https://github.com/snapcore/snapcraft/blob/master/demos/gradle/snap/snapcraft.yaml
-
-name: jabref
-
-# the version string 4.2-dev is replaced by scripts/run-snapcraft.sh with the current version provided in build.gradle
-version: '4.2-dev'
-
-summary: Bibliography manager
-icon: buildres/snapcraft/JabRef-icon-256.png
-description: JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.
-
-# only with the following set to stable + strict, we can do a full release
-
-# see https://snapcraft.io/docs/reference/channels
-# stable | devel
-grade: devel
-
-# see https://snapcraft.io/docs/reference/confinement
-# strict | devmode
-confinement: strict
-
-apps:
-   jabref:
-     command: desktop-launch java -jar $SNAP/jar/JabRef-4.2-dev.jar
-     plugs: [desktop, desktop-legacy, wayland, unity7, home, network-bind]
-     desktop: ../buildres/snapcraft/jabref.desktop
-
-parts:
-  jabref:
-    plugin: gradle
-    source: .
-    stage-packages: [default-jre, openjfx, x11-utils]
-    gradle-options: [snapJar]
-    gradle-output-dir: 'build/releases'
-    after: [desktop-gtk3]

From e18d236f42954efdc1e86e320db2ae7a45c76899 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sat, 26 Jan 2019 20:49:07 +0100
Subject: [PATCH 002/184] [WIP] Convert LibraryProperties to JavaFX

First part of view and viewmodel
---
 .../dbproperties/LibraryPropertiesDialog.fxml | 131 ++++++++++++++++++
 .../LibraryPropertiesDialogView.java          | 112 +++++++++++++++
 .../LibraryPropertiesDialogViewModel.java     |  75 ++++++++++
 3 files changed, 318 insertions(+)
 create mode 100644 src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml
 create mode 100644 src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java
 create mode 100644 src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java

diff --git a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml
new file mode 100644
index 00000000000..e344382c505
--- /dev/null
+++ b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml
@@ -0,0 +1,131 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.geometry.Insets?>
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.CheckBox?>
+<?import javafx.scene.control.ComboBox?>
+<?import javafx.scene.control.DialogPane?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.control.RadioButton?>
+<?import javafx.scene.control.Separator?>
+<?import javafx.scene.control.TextField?>
+<?import javafx.scene.control.ToggleGroup?>
+<?import javafx.scene.layout.ColumnConstraints?>
+<?import javafx.scene.layout.GridPane?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.RowConstraints?>
+<?import javafx.scene.layout.VBox?>
+
+
+<DialogPane prefHeight="516.0" prefWidth="922.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.dbproperties.LibraryPropertiesDialogView">
+   <content>
+      <VBox fx:id="contentVbox" prefHeight="200.0" prefWidth="100.0">
+         <children>
+            <GridPane>
+              <columnConstraints>
+                <ColumnConstraints hgrow="SOMETIMES" maxWidth="218.0" minWidth="10.0" prefWidth="200.0" />
+                <ColumnConstraints hgrow="SOMETIMES" maxWidth="797.0" minWidth="10.0" prefWidth="529.0" />
+                  <ColumnConstraints hgrow="SOMETIMES" maxWidth="797.0" minWidth="10.0" prefWidth="100.0" />
+              </columnConstraints>
+              <rowConstraints>
+                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                  <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+              </rowConstraints>
+               <children>
+                  <Label text="Library encoding" />
+                  <ComboBox fx:id="encoding" prefWidth="250.0" GridPane.columnIndex="1" GridPane.hgrow="ALWAYS" />
+                  <HBox alignment="CENTER" prefHeight="100.0" prefWidth="200.0" GridPane.columnSpan="2147483647" GridPane.rowIndex="1">
+                     <children>
+                        <Label alignment="BOTTOM_LEFT" text="Override default file directories" />
+                        <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
+                           <opaqueInsets>
+                              <Insets left="10.0" right="10.0" top="10.0" />
+                           </opaqueInsets>
+                           <HBox.margin>
+                              <Insets />
+                           </HBox.margin>
+                           <padding>
+                              <Insets left="10.0" />
+                           </padding>
+                        </Separator>
+                     </children>
+                     <GridPane.margin>
+                        <Insets />
+                     </GridPane.margin>
+                  </HBox>
+                  <Label text="General file directory" GridPane.rowIndex="2" />
+                  <TextField fx:id="generalFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="2" />
+                  <Button fx:id="browseGeneralFileDir" mnemonicParsing="false" onAction="#browseGeneralFileDirectory" text="Browse" GridPane.columnIndex="2" GridPane.rowIndex="2" />
+                  <Label text="User-specific file directory" GridPane.rowIndex="3" />
+                  <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
+                  <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
+               </children>
+            </GridPane>
+            <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
+               <children>
+                  <Label alignment="BOTTOM_LEFT" text="Save sort order" />
+                  <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
+                     <opaqueInsets>
+                        <Insets left="10.0" right="10.0" top="10.0" />
+                     </opaqueInsets>
+                     <HBox.margin>
+                        <Insets />
+                     </HBox.margin>
+                     <padding>
+                        <Insets left="10.0" />
+                     </padding>
+                  </Separator>
+               </children>
+            </HBox>
+            <VBox fx:id="saveOrdervbox">
+             <fx:define>
+              <ToggleGroup fx:id="saveOrderToggleGroup" />
+               </fx:define>
+               <children>
+                  <RadioButton fx:id="saveInOriginalOrder" mnemonicParsing="false" text="Save entries in their original order" toggleGroup="$saveOrderToggleGroup" />
+                  <RadioButton fx:id="saveInSpecifiedOrder" mnemonicParsing="false" text="Save entries ordered as specified" toggleGroup="$saveOrderToggleGroup" />
+               </children>
+            </VBox>
+            <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
+               <children>
+                  <Label alignment="BOTTOM_LEFT" text="Library protection" />
+                  <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
+                     <opaqueInsets>
+                        <Insets left="10.0" right="10.0" top="10.0" />
+                     </opaqueInsets>
+                     <HBox.margin>
+                        <Insets />
+                     </HBox.margin>
+                     <padding>
+                        <Insets left="10.0" />
+                     </padding>
+                  </Separator>
+               </children>
+            </HBox>
+            <CheckBox fx:id="protect" mnemonicParsing="false" text="Refuse to save the library before external changes have been reviewed" />
+            <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
+               <children>
+                  <Label alignment="BOTTOM_LEFT" text="Save actions" />
+                  <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
+                     <opaqueInsets>
+                        <Insets left="10.0" right="10.0" top="10.0" />
+                     </opaqueInsets>
+                     <HBox.margin>
+                        <Insets />
+                     </HBox.margin>
+                     <padding>
+                        <Insets left="10.0" />
+                     </padding>
+                  </Separator>
+               </children>
+            </HBox>
+         </children>
+      </VBox>
+   </content>
+  <buttonTypes>
+    <ButtonType fx:constant="CANCEL" />
+    <ButtonType fx:constant="OK" />
+  </buttonTypes>
+</DialogPane>
diff --git a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java
new file mode 100644
index 00000000000..d4715b07f99
--- /dev/null
+++ b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java
@@ -0,0 +1,112 @@
+package org.jabref.gui.dbproperties;
+
+import java.nio.charset.Charset;
+
+import javax.inject.Inject;
+
+import javafx.event.ActionEvent;
+import javafx.fxml.FXML;
+import javafx.scene.control.Button;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.ComboBox;
+import javafx.scene.control.RadioButton;
+import javafx.scene.control.TextField;
+import javafx.scene.control.ToggleGroup;
+import javafx.scene.layout.VBox;
+
+import org.jabref.gui.BasePanel;
+import org.jabref.gui.DialogService;
+import org.jabref.gui.SaveOrderConfigDisplay;
+import org.jabref.gui.cleanup.FieldFormatterCleanupsPanel;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.logic.cleanup.Cleanups;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.shared.DatabaseLocation;
+import org.jabref.model.metadata.SaveOrderConfig;
+import org.jabref.preferences.PreferencesService;
+
+import com.airhacks.afterburner.views.ViewLoader;
+
+public class LibraryPropertiesDialogView extends BaseDialog<Void> {
+
+    @FXML private VBox contentVbox;
+    @FXML private ComboBox<Charset> encoding;
+    @FXML private TextField generalFileDirectory;
+    @FXML private Button browseGeneralFileDir;
+    @FXML private TextField userSpecificFileDirectory;
+    @FXML private Button browseUserSpefiicFileDir;
+    @FXML private VBox saveOrdervbox;
+    @FXML private ToggleGroup saveOrderToggleGroup;
+    @FXML private RadioButton saveInOriginalOrder;
+    @FXML private RadioButton saveInSpecifiedOrder;
+    @FXML private CheckBox protect;
+    private SaveOrderConfigDisplay saveOrderPanel;
+    private BasePanel panel;
+    private LibraryPropertiesDialogViewModel viewModel;
+    private final DialogService dialogService;
+    @Inject private PreferencesService preferencesService;
+
+    public LibraryPropertiesDialogView(DialogService dialogService) {
+        this.dialogService = dialogService;
+        ViewLoader.view(this)
+                  .load()
+                  .setAsDialogPane(this);
+
+        setResultConverter(btn -> {
+
+            return null;
+        });
+
+        setTitle(Localization.lang("Library properties"));
+
+    }
+
+    @FXML
+    private void initialize() {
+        viewModel = new LibraryPropertiesDialogViewModel(dialogService, preferencesService.getWorkingDir());
+
+        generalFileDirectory.textProperty().bindBidirectional(viewModel.generalFileDirectoryPropertyProperty());
+        userSpecificFileDirectory.textProperty().bindBidirectional(viewModel.userSpecificFileDirectoryProperty());
+
+        encoding.valueProperty().bind(viewModel.selectedEncodingProperty());
+        saveOrderPanel = new SaveOrderConfigDisplay();
+        saveOrdervbox.getChildren().add(saveOrderPanel.getJFXPanel());
+        FieldFormatterCleanupsPanel fieldFormatterCleanupsPanel = new FieldFormatterCleanupsPanel(Localization.lang("Enable save actions"),
+                                                                                                  Cleanups.DEFAULT_SAVE_ACTIONS);
+
+        contentVbox.getChildren().add(fieldFormatterCleanupsPanel);
+        saveInOriginalOrder.selectedProperty().bindBidirectional(viewModel.saveInOriginalProperty());
+        saveInSpecifiedOrder.selectedProperty().bindBidirectional(viewModel.saveInSpecifiedOrderProperty());
+    }
+
+    public void updateEnableStatus() {
+        DatabaseLocation location = panel.getBibDatabaseContext().getLocation();
+        boolean isShared = (location == DatabaseLocation.SHARED);
+        encoding.setDisable(isShared); // the encoding of shared database is always UTF-8
+        saveInOriginalOrder.setDisable(isShared);
+        saveInSpecifiedOrder.setDisable(isShared);
+        saveOrderPanel.setEnabled(!isShared);
+        protect.setDisable(isShared);
+    }
+
+    private SaveOrderConfig getNewSaveOrderConfig() {
+        SaveOrderConfig saveOrderConfig = null;
+        if (saveInOriginalOrder.isSelected()) {
+            saveOrderConfig = SaveOrderConfig.getDefaultSaveOrder();
+        } else {
+            saveOrderConfig = saveOrderPanel.getSaveOrderConfig();
+            saveOrderConfig.setSaveInSpecifiedOrder();
+        }
+        return saveOrderConfig;
+    }
+
+    @FXML
+    public void browseGeneralFileDirectory(ActionEvent event) {
+        viewModel.browseGeneralDir();
+    }
+
+    @FXML
+    public void browseUserSpecificFileDirectory(ActionEvent event) {
+        viewModel.browseUserDir();
+    }
+}
diff --git a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java
new file mode 100644
index 00000000000..cc0c1f78c13
--- /dev/null
+++ b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java
@@ -0,0 +1,75 @@
+package org.jabref.gui.dbproperties;
+
+import java.nio.charset.Charset;
+import java.nio.file.Path;
+
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.ListProperty;
+import javafx.beans.property.ObjectProperty;
+import javafx.beans.property.SimpleBooleanProperty;
+import javafx.beans.property.SimpleListProperty;
+import javafx.beans.property.SimpleObjectProperty;
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
+import javafx.collections.FXCollections;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.util.DirectoryDialogConfiguration;
+import org.jabref.logic.l10n.Encodings;
+
+public class LibraryPropertiesDialogViewModel {
+
+    private final StringProperty generalFileDirectoryProperty = new SimpleStringProperty("");
+    private final StringProperty userSpecificFileDirectoryProperty = new SimpleStringProperty("");
+    private final ListProperty<Charset> encodingsProperty = new SimpleListProperty<>(FXCollections.observableArrayList(Encodings.getCharsets()));
+    private final ObjectProperty<Charset> selectedEncodingPropety = new SimpleObjectProperty<>(Encodings.getCharsets().get(0));
+    private final BooleanProperty saveInOriginalProperty = new SimpleBooleanProperty();
+    private final BooleanProperty saveInSpecifiedOrderProperty = new SimpleBooleanProperty();
+
+    private final DialogService dialogService;
+    private final DirectoryDialogConfiguration directoryDialogConfiguration;
+
+    public LibraryPropertiesDialogViewModel(DialogService dialogService, Path workingDir) {
+        this.dialogService = dialogService;
+
+        directoryDialogConfiguration = new DirectoryDialogConfiguration.Builder()
+                                                                                 .withInitialDirectory(workingDir).build();
+    }
+
+    public StringProperty generalFileDirectoryPropertyProperty() {
+        return this.generalFileDirectoryProperty;
+    }
+
+    public StringProperty userSpecificFileDirectoryProperty() {
+        return this.userSpecificFileDirectoryProperty;
+    }
+
+    public ListProperty<Charset> encodingsProperty() {
+        return this.encodingsProperty;
+    }
+
+    public ObjectProperty<Charset> selectedEncodingProperty() {
+        return this.selectedEncodingPropety;
+    }
+
+    public void browseGeneralDir() {
+        dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> generalFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
+    }
+
+    public void browseUserDir() {
+        dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> userSpecificFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
+
+    }
+
+    public BooleanProperty saveInOriginalProperty() {
+        return this.saveInOriginalProperty;
+    }
+
+    public BooleanProperty saveInSpecifiedOrderProperty() {
+        return this.saveInSpecifiedOrderProperty;
+    }
+
+    public void storeSettings() {
+        //TODO
+    }
+}

From dd537702493917ca5fcdc3aeb3046c11caea06ce Mon Sep 17 00:00:00 2001
From: Galileo Sartor <galileo.sartor@gmail.com>
Date: Sun, 27 Jan 2019 13:05:12 +0100
Subject: [PATCH 003/184] Fix preferences path: use _JAVA_OPTIONS

---
 snap/snapcraft.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/snap/snapcraft.yaml b/snap/snapcraft.yaml
index 6873178bf86..cdc75820ea6 100644
--- a/snap/snapcraft.yaml
+++ b/snap/snapcraft.yaml
@@ -12,13 +12,14 @@ apps:
   jabref:
     command: desktop-launch java -jar $SNAP/jar/JabRef-$SNAP_VERSION.jar
     environment:
-      JAVA_OPTS: "-Djava.util.prefs.systemRoot=$SNAP_USER_DATA/.java -Djava.util.prefs.userRoot=$SNAP_USER_DATA/.java/.userPrefs"
+      _JAVA_OPTIONS: "-Djava.util.prefs.systemRoot=$SNAP_USER_DATA/.java/etc/.java -Djava.util.prefs.userRoot=$SNAP_USER_DATA/.java/.userPrefs"
     plugs:
       - desktop
       - desktop-legacy
       - wayland
       - unity7
       - home
+      - opengl
       - network-bind
 
 parts:

From c540ff441afd51b3c6fb8299c291d5d33def1886 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 27 Jan 2019 13:18:50 +0100
Subject: [PATCH 004/184] fix l10n and error in fxml convert rest of the dialog
 add some new methods to preferences service

---
 .../dbproperties/LibraryPropertiesDialog.fxml |  19 +--
 .../LibraryPropertiesDialogView.java          | 129 ++++++++++++++++--
 .../LibraryPropertiesDialogViewModel.java     |  52 ++++++-
 .../jabref/preferences/JabRefPreferences.java |   3 +
 .../preferences/PreferencesService.java       |   7 +
 5 files changed, 182 insertions(+), 28 deletions(-)

diff --git a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml
index e344382c505..c2163dc1dda 100644
--- a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml
+++ b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml
@@ -2,6 +2,7 @@
 
 <?import javafx.geometry.Insets?>
 <?import javafx.scene.control.Button?>
+<?import javafx.scene.control.ButtonType?>
 <?import javafx.scene.control.CheckBox?>
 <?import javafx.scene.control.ComboBox?>
 <?import javafx.scene.control.DialogPane?>
@@ -38,7 +39,7 @@
                   <ComboBox fx:id="encoding" prefWidth="250.0" GridPane.columnIndex="1" GridPane.hgrow="ALWAYS" />
                   <HBox alignment="CENTER" prefHeight="100.0" prefWidth="200.0" GridPane.columnSpan="2147483647" GridPane.rowIndex="1">
                      <children>
-                        <Label alignment="BOTTOM_LEFT" text="Override default file directories" />
+                        <Label alignment="BOTTOM_LEFT" text="%Override default file directories" />
                         <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
                            <opaqueInsets>
                               <Insets left="10.0" right="10.0" top="10.0" />
@@ -57,15 +58,15 @@
                   </HBox>
                   <Label text="General file directory" GridPane.rowIndex="2" />
                   <TextField fx:id="generalFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="2" />
-                  <Button fx:id="browseGeneralFileDir" mnemonicParsing="false" onAction="#browseGeneralFileDirectory" text="Browse" GridPane.columnIndex="2" GridPane.rowIndex="2" />
+                  <Button fx:id="browseGeneralFileDir" mnemonicParsing="false" onAction="#browseGeneralFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="2" />
                   <Label text="User-specific file directory" GridPane.rowIndex="3" />
                   <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
-                  <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
+                  <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
                </children>
             </GridPane>
             <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
                <children>
-                  <Label alignment="BOTTOM_LEFT" text="Save sort order" />
+                  <Label alignment="BOTTOM_LEFT" text="%Save sort order" />
                   <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
                      <opaqueInsets>
                         <Insets left="10.0" right="10.0" top="10.0" />
@@ -84,13 +85,13 @@
               <ToggleGroup fx:id="saveOrderToggleGroup" />
                </fx:define>
                <children>
-                  <RadioButton fx:id="saveInOriginalOrder" mnemonicParsing="false" text="Save entries in their original order" toggleGroup="$saveOrderToggleGroup" />
-                  <RadioButton fx:id="saveInSpecifiedOrder" mnemonicParsing="false" text="Save entries ordered as specified" toggleGroup="$saveOrderToggleGroup" />
+                  <RadioButton fx:id="saveInOriginalOrder" mnemonicParsing="false" text="%Save entries in their original order" toggleGroup="$saveOrderToggleGroup" />
+                  <RadioButton fx:id="saveInSpecifiedOrder" mnemonicParsing="false" text="%Save entries ordered as specified" toggleGroup="$saveOrderToggleGroup" />
                </children>
             </VBox>
             <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
                <children>
-                  <Label alignment="BOTTOM_LEFT" text="Library protection" />
+                  <Label alignment="BOTTOM_LEFT" text="%Library protection" />
                   <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
                      <opaqueInsets>
                         <Insets left="10.0" right="10.0" top="10.0" />
@@ -104,10 +105,10 @@
                   </Separator>
                </children>
             </HBox>
-            <CheckBox fx:id="protect" mnemonicParsing="false" text="Refuse to save the library before external changes have been reviewed" />
+            <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed" />
             <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
                <children>
-                  <Label alignment="BOTTOM_LEFT" text="Save actions" />
+                  <Label alignment="BOTTOM_LEFT" text="%Save actions" />
                   <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
                      <opaqueInsets>
                         <Insets left="10.0" right="10.0" top="10.0" />
diff --git a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java
index d4715b07f99..b91613247dc 100644
--- a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java
+++ b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java
@@ -1,12 +1,14 @@
 package org.jabref.gui.dbproperties;
 
 import java.nio.charset.Charset;
+import java.util.Optional;
 
 import javax.inject.Inject;
 
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
 import javafx.scene.control.Button;
+import javafx.scene.control.ButtonType;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.RadioButton;
@@ -22,6 +24,7 @@
 import org.jabref.logic.cleanup.Cleanups;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.shared.DatabaseLocation;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.metadata.SaveOrderConfig;
 import org.jabref.preferences.PreferencesService;
 
@@ -45,15 +48,20 @@ public class LibraryPropertiesDialogView extends BaseDialog<Void> {
     private LibraryPropertiesDialogViewModel viewModel;
     private final DialogService dialogService;
     @Inject private PreferencesService preferencesService;
+    private FieldFormatterCleanupsPanel fieldFormatterCleanupsPanel;
+    private Object oldSaveOrderConfig;
 
-    public LibraryPropertiesDialogView(DialogService dialogService) {
+    public LibraryPropertiesDialogView(BasePanel panel, DialogService dialogService) {
         this.dialogService = dialogService;
+        this.panel = panel;
         ViewLoader.view(this)
                   .load()
                   .setAsDialogPane(this);
 
         setResultConverter(btn -> {
-
+            if (btn == ButtonType.OK) {
+                storeSettings();
+            }
             return null;
         });
 
@@ -63,7 +71,7 @@ public LibraryPropertiesDialogView(DialogService dialogService) {
 
     @FXML
     private void initialize() {
-        viewModel = new LibraryPropertiesDialogViewModel(dialogService, preferencesService.getWorkingDir());
+        viewModel = new LibraryPropertiesDialogViewModel(panel, dialogService, preferencesService);
 
         generalFileDirectory.textProperty().bindBidirectional(viewModel.generalFileDirectoryPropertyProperty());
         userSpecificFileDirectory.textProperty().bindBidirectional(viewModel.userSpecificFileDirectoryProperty());
@@ -71,12 +79,45 @@ private void initialize() {
         encoding.valueProperty().bind(viewModel.selectedEncodingProperty());
         saveOrderPanel = new SaveOrderConfigDisplay();
         saveOrdervbox.getChildren().add(saveOrderPanel.getJFXPanel());
-        FieldFormatterCleanupsPanel fieldFormatterCleanupsPanel = new FieldFormatterCleanupsPanel(Localization.lang("Enable save actions"),
-                                                                                                  Cleanups.DEFAULT_SAVE_ACTIONS);
+        fieldFormatterCleanupsPanel = new FieldFormatterCleanupsPanel(Localization.lang("Enable save actions"),
+                                                                      Cleanups.DEFAULT_SAVE_ACTIONS);
 
         contentVbox.getChildren().add(fieldFormatterCleanupsPanel);
         saveInOriginalOrder.selectedProperty().bindBidirectional(viewModel.saveInOriginalProperty());
         saveInSpecifiedOrder.selectedProperty().bindBidirectional(viewModel.saveInSpecifiedOrderProperty());
+
+        protect.selectedProperty().bindBidirectional(viewModel.libraryProtectedProperty());
+        saveOrderPanel.getJFXPanel().disableProperty().bind(viewModel.saveInOriginalProperty());
+
+        setValues();
+        updateEnableStatus();
+    }
+
+    private void setValues() {
+
+        viewModel.setValues();
+        Optional<SaveOrderConfig> storedSaveOrderConfig = panel.getBibDatabaseContext().getMetaData().getSaveOrderConfig();
+        boolean selected;
+        if (!storedSaveOrderConfig.isPresent()) {
+            viewModel.saveInOriginalProperty().setValue(true);
+            oldSaveOrderConfig = SaveOrderConfig.getDefaultSaveOrder();
+            selected = false;
+        } else {
+            SaveOrderConfig saveOrderConfig = storedSaveOrderConfig.get();
+            oldSaveOrderConfig = saveOrderConfig;
+            if (saveOrderConfig.saveInOriginalOrder()) {
+                viewModel.saveInOriginalProperty().setValue(true);
+                selected = false;
+            } else {
+                viewModel.saveInSpecifiedOrderProperty().setValue(true);
+                selected = true;
+            }
+            saveOrderPanel.setSaveOrderConfig(saveOrderConfig);
+
+        }
+        saveOrderPanel.setEnabled(selected);
+
+        fieldFormatterCleanupsPanel.setValues(panel.getBibDatabaseContext().getMetaData());
     }
 
     public void updateEnableStatus() {
@@ -89,6 +130,75 @@ public void updateEnableStatus() {
         protect.setDisable(isShared);
     }
 
+    @FXML
+    public void browseGeneralFileDirectory(ActionEvent event) {
+        viewModel.browseGeneralDir();
+    }
+
+    @FXML
+    public void browseUserSpecificFileDirectory(ActionEvent event) {
+        viewModel.browseUserDir();
+    }
+
+    private void storeSettings() {
+        MetaData metaData = panel.getBibDatabaseContext().getMetaData();
+        Charset oldEncoding = metaData.getEncoding()
+                                      .orElse(preferencesService.getDefaultEncoding());
+        Charset newEncoding = viewModel.selectedEncodingProperty().getValue();
+        metaData.setEncoding(newEncoding);
+
+        String text = viewModel.generalFileDirectoryPropertyProperty().getValue().trim();
+        if (text.isEmpty()) {
+            metaData.clearDefaultFileDirectory();
+        } else {
+            metaData.setDefaultFileDirectory(text);
+        }
+        // Repeat for individual file dir - reuse 'text' and 'dir' vars
+        text = viewModel.userSpecificFileDirectoryProperty().getValue();
+        if (text.isEmpty()) {
+            metaData.clearUserFileDirectory(preferencesService.getUser());
+        } else {
+            metaData.setUserFileDirectory(preferencesService.getUser(), text);
+        }
+
+        if (viewModel.libraryProtectedProperty().getValue()) {
+            metaData.markAsProtected();
+        } else {
+            metaData.markAsNotProtected();
+        }
+
+        SaveOrderConfig newSaveOrderConfig = getNewSaveOrderConfig();
+
+        boolean saveOrderConfigChanged = !getNewSaveOrderConfig().equals(oldSaveOrderConfig);
+
+        // See if any of the values have been modified:
+        if (saveOrderConfigChanged) {
+            if (newSaveOrderConfig.equals(SaveOrderConfig.getDefaultSaveOrder())) {
+                metaData.clearSaveOrderConfig();
+            } else {
+                metaData.setSaveOrderConfig(newSaveOrderConfig);
+            }
+        }
+
+        boolean saveActionsChanged = fieldFormatterCleanupsPanel.hasChanged();
+        if (saveActionsChanged) {
+            if (fieldFormatterCleanupsPanel.isDefaultSaveActions()) {
+                metaData.clearSaveActions();
+            } else {
+                fieldFormatterCleanupsPanel.storeSettings(metaData);
+            }
+        }
+
+        boolean changed = saveOrderConfigChanged || !newEncoding.equals(oldEncoding)
+                          || viewModel.generalFileDirChanged() || viewModel.userFileDirChanged()
+                          || viewModel.protectedValueChanged() || saveActionsChanged;
+        // ... if so, mark base changed. Prevent the Undo button from removing
+        // change marking:
+        if (changed) {
+            panel.markNonUndoableBaseChanged();
+        }
+    }
+
     private SaveOrderConfig getNewSaveOrderConfig() {
         SaveOrderConfig saveOrderConfig = null;
         if (saveInOriginalOrder.isSelected()) {
@@ -100,13 +210,4 @@ private SaveOrderConfig getNewSaveOrderConfig() {
         return saveOrderConfig;
     }
 
-    @FXML
-    public void browseGeneralFileDirectory(ActionEvent event) {
-        viewModel.browseGeneralDir();
-    }
-
-    @FXML
-    public void browseUserSpecificFileDirectory(ActionEvent event) {
-        viewModel.browseUserDir();
-    }
 }
diff --git a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java
index cc0c1f78c13..fc857de9d0e 100644
--- a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java
@@ -1,7 +1,7 @@
 package org.jabref.gui.dbproperties;
 
 import java.nio.charset.Charset;
-import java.nio.file.Path;
+import java.util.Optional;
 
 import javafx.beans.property.BooleanProperty;
 import javafx.beans.property.ListProperty;
@@ -13,9 +13,12 @@
 import javafx.beans.property.StringProperty;
 import javafx.collections.FXCollections;
 
+import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.logic.l10n.Encodings;
+import org.jabref.model.metadata.MetaData;
+import org.jabref.preferences.PreferencesService;
 
 public class LibraryPropertiesDialogViewModel {
 
@@ -25,15 +28,25 @@ public class LibraryPropertiesDialogViewModel {
     private final ObjectProperty<Charset> selectedEncodingPropety = new SimpleObjectProperty<>(Encodings.getCharsets().get(0));
     private final BooleanProperty saveInOriginalProperty = new SimpleBooleanProperty();
     private final BooleanProperty saveInSpecifiedOrderProperty = new SimpleBooleanProperty();
+    private final BooleanProperty libraryProtectedProperty = new SimpleBooleanProperty();
 
     private final DialogService dialogService;
     private final DirectoryDialogConfiguration directoryDialogConfiguration;
+    private final MetaData metaData;
+    private final PreferencesService preferencesService;
 
-    public LibraryPropertiesDialogViewModel(DialogService dialogService, Path workingDir) {
+    private String oldUserSpecificFileDir;
+    private String oldGeneralFileDir;
+    private boolean oldLibraryProtected;
+
+    public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogService, PreferencesService preferencesService) {
         this.dialogService = dialogService;
+        this.metaData = panel.getBibDatabaseContext().getMetaData();
+        this.preferencesService = preferencesService;
 
         directoryDialogConfiguration = new DirectoryDialogConfiguration.Builder()
-                                                                                 .withInitialDirectory(workingDir).build();
+                                                                                 .withInitialDirectory(preferencesService.getWorkingDir()).build();
+
     }
 
     public StringProperty generalFileDirectoryPropertyProperty() {
@@ -69,7 +82,36 @@ public BooleanProperty saveInSpecifiedOrderProperty() {
         return this.saveInSpecifiedOrderProperty;
     }
 
-    public void storeSettings() {
-        //TODO
+    public BooleanProperty libraryProtectedProperty() {
+        return this.libraryProtectedProperty;
+    }
+
+    public void setValues() {
+        Optional<Charset> charset = metaData.getEncoding();
+        selectedEncodingPropety.setValue(charset.orElse(preferencesService.getDefaultEncoding()));
+
+        Optional<String> fileD = metaData.getDefaultFileDirectory();
+        fileD.ifPresent(path -> generalFileDirectoryProperty.setValue(path.trim()));
+
+        Optional<String> fileDI = metaData.getUserFileDirectory(preferencesService.getUser());
+        fileDI.ifPresent(userSpecificFileDirectoryProperty::setValue);
+
+        oldUserSpecificFileDir = generalFileDirectoryProperty.getValue();
+        oldGeneralFileDir = userSpecificFileDirectoryProperty.getValue();
+
+        libraryProtectedProperty.setValue(metaData.isProtected());
+        oldLibraryProtected = libraryProtectedProperty.getValue();
+    }
+
+    public boolean generalFileDirChanged() {
+        return !oldGeneralFileDir.equals(generalFileDirectoryProperty.getValue());
+    }
+
+    public boolean userFileDirChanged() {
+        return !oldUserSpecificFileDir.equals(userSpecificFileDirectoryProperty.getValue());
+    }
+
+    public boolean protectedValueChanged() {
+        return !oldLibraryProtected == libraryProtectedProperty.getValue();
     }
 }
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index e7320ee4d95..34fb19c9754 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -932,6 +932,7 @@ public Map<SidePaneType, Integer> getSidePanePreferredPositions() {
         return preferredPositions;
     }
 
+    @Override
     public String getUser() {
         try {
             return get(DEFAULT_OWNER) + '-' + InetAddress.getLocalHost().getHostName();
@@ -1415,10 +1416,12 @@ public String getWrappedUsername() {
         return '[' + get(DEFAULT_OWNER) + ']';
     }
 
+    @Override
     public Charset getDefaultEncoding() {
         return Charset.forName(get(DEFAULT_ENCODING));
     }
 
+    @Override
     public void setDefaultEncoding(Charset encoding) {
         put(DEFAULT_ENCODING, encoding.name());
     }
diff --git a/src/main/java/org/jabref/preferences/PreferencesService.java b/src/main/java/org/jabref/preferences/PreferencesService.java
index 46c208a12f4..bd72de227a8 100644
--- a/src/main/java/org/jabref/preferences/PreferencesService.java
+++ b/src/main/java/org/jabref/preferences/PreferencesService.java
@@ -1,5 +1,6 @@
 package org.jabref.preferences;
 
+import java.nio.charset.Charset;
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Map;
@@ -58,4 +59,10 @@ public interface PreferencesService {
     void setExportWorkingDirectory(String layoutFileDirString);
 
     String getExportWorkingDirectory();
+
+    Charset getDefaultEncoding();
+
+    void setDefaultEncoding(Charset encoding);
+
+    String getUser();
 }

From 095b70b7f052a1a6929a75ba18e8b82fd38e99c8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 28 Jan 2019 08:38:22 +0100
Subject: [PATCH 005/184] Bump checkstyle from 8.16 to 8.17 (#4620)

Bumps [checkstyle](https://github.com/checkstyle/checkstyle) from 8.16 to 8.17.
- [Release notes](https://github.com/checkstyle/checkstyle/releases)
- [Commits](https://github.com/checkstyle/checkstyle/compare/checkstyle-8.16...checkstyle-8.17)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 94a5e380cab..b3f68a91c8c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -181,7 +181,7 @@ dependencies {
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.16'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.17'
 }
 
 jacoco {

From fbf1cc9a406da6018619887b73506a89e1535f14 Mon Sep 17 00:00:00 2001
From: Galileo Sartor <galileo.sartor@gmail.com>
Date: Mon, 28 Jan 2019 18:13:56 +0100
Subject: [PATCH 006/184] snap: disable tests build, add removable media and
 specify architectures (#4619)

* snap: disable tests build, add removable media and specify architectures

* Move to gtk2 fixes the dialogs

* Add snap ignores to .gitignore

* Add source-type: git to enable submodules
---
 .gitignore          |  8 ++++++++
 snap/snapcraft.yaml | 14 ++++++++++----
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index 7c7850841ea..39f4c1f4ac2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,14 @@ status.md
 # Install4J
 install4j6/
 
+# Snap
+parts/
+stage/
+prime/
+*.snap
+jabref_source.tar.bz2
+snap/.snapcraft/
+
 # Gradle
 # generated when `gradlew --gui` is called
 ui/
diff --git a/snap/snapcraft.yaml b/snap/snapcraft.yaml
index cdc75820ea6..b26f84fef0d 100644
--- a/snap/snapcraft.yaml
+++ b/snap/snapcraft.yaml
@@ -1,18 +1,22 @@
 name: jabref
 version: "git"
 version-script: cat build.gradle | grep "^version =" | cut -d'"' -f2
-#icon: snap/gui/icon.png
+#icon: snap/gui/jabref.png
 summary: Bibliography manager
 description: JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.
 
 grade: devel
 confinement: strict
 
+architectures:
+  - build-on: amd64
+  - build-on: i386
+
 apps:
   jabref:
     command: desktop-launch java -jar $SNAP/jar/JabRef-$SNAP_VERSION.jar
     environment:
-      _JAVA_OPTIONS: "-Djava.util.prefs.systemRoot=$SNAP_USER_DATA/.java/etc/.java -Djava.util.prefs.userRoot=$SNAP_USER_DATA/.java/.userPrefs"
+      _JAVA_OPTIONS: "-Duser.home=$SNAP_USER_DATA"
     plugs:
       - desktop
       - desktop-legacy
@@ -21,15 +25,17 @@ apps:
       - home
       - opengl
       - network-bind
+      - removable-media
 
 parts:
   jabref:
     plugin: gradle
     source: .
+    source-type: git
     stage-packages:
       - openjdk-8-jre
       - openjfx
       - x11-utils
-    gradle-options: [snapJar]
+    gradle-options: [snapJar, -xtest]
     gradle-output-dir: 'build/releases'
-    after: [desktop-gtk3]
+    after: [desktop-gtk2]

From e82abdd9d0ab3fcaa27f05594f09d29d2943c9b5 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 28 Jan 2019 18:46:15 +0100
Subject: [PATCH 007/184] Convert db properties to javafx Rename to
 libraryproperties change separator width to make it visible

Remove small font setting on save order config
---
 src/main/java/org/jabref/gui/Base.css         |   2 +-
 src/main/java/org/jabref/gui/JabRefFrame.java |   4 +-
 .../jabref/gui/SaveOrderConfigDisplay.java    |   5 -
 .../gui/actions/DatabasePropertiesAction.java |  21 --
 .../gui/actions/LibraryPropertiesAction.java  |  24 ++
 .../DatabasePropertiesDialog.java             | 330 ------------------
 .../LibraryPropertiesDialog.fxml              |  52 +--
 .../LibraryPropertiesDialogView.java          |   5 +-
 .../LibraryPropertiesDialogViewModel.java     |   2 +-
 9 files changed, 47 insertions(+), 398 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/actions/DatabasePropertiesAction.java
 create mode 100644 src/main/java/org/jabref/gui/actions/LibraryPropertiesAction.java
 delete mode 100644 src/main/java/org/jabref/gui/dbproperties/DatabasePropertiesDialog.java
 rename src/main/java/org/jabref/gui/{dbproperties => libraryproperties}/LibraryPropertiesDialog.fxml (76%)
 rename src/main/java/org/jabref/gui/{dbproperties => libraryproperties}/LibraryPropertiesDialogView.java (97%)
 rename src/main/java/org/jabref/gui/{dbproperties => libraryproperties}/LibraryPropertiesDialogViewModel.java (99%)

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
index ec78513a06b..f5fa9c4ece4 100644
--- a/src/main/java/org/jabref/gui/Base.css
+++ b/src/main/java/org/jabref/gui/Base.css
@@ -818,7 +818,7 @@
 
 .separator:horizontal .line {
     -fx-border-color: -jr-separator;
-    -fx-border-width: 0;
+    -fx-border-width: 0.5;
     -fx-border-insets: 1 0 0 0;
 }
 
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index b1872641c36..59f9f1ccb01 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -60,7 +60,7 @@
 import org.jabref.gui.actions.CopyFilesAction;
 import org.jabref.gui.actions.CustomizeEntryAction;
 import org.jabref.gui.actions.CustomizeKeyBindingAction;
-import org.jabref.gui.actions.DatabasePropertiesAction;
+import org.jabref.gui.actions.LibraryPropertiesAction;
 import org.jabref.gui.actions.EditExternalFileTypesAction;
 import org.jabref.gui.actions.ErrorConsoleAction;
 import org.jabref.gui.actions.LookupIdentifierAction;
@@ -846,7 +846,7 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.LIBRARY_PROPERTIES, new DatabasePropertiesAction(this)),
+                                  factory.createMenuItem(StandardActions.LIBRARY_PROPERTIES, new LibraryPropertiesAction(this, dialogService)),
                 factory.createMenuItem(StandardActions.EDIT_PREAMBLE, new PreambleEditor(this)),
                 factory.createMenuItem(StandardActions.EDIT_STRINGS, new OldDatabaseCommandWrapper(Actions.EDIT_STRINGS, this, Globals.stateManager))
         );
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.java
index 5103fba8d29..3093585f3e8 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.java
@@ -11,7 +11,6 @@
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.Label;
 import javafx.scene.layout.GridPane;
-import javafx.scene.text.Font;
 
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
@@ -49,22 +48,18 @@ private void init() {
         saveSecDesc = new CheckBox(Localization.lang("Descending"));
         saveTerDesc = new CheckBox(Localization.lang("Descending"));
 
-        Font font = new Font(10);
         GridPane builder = new GridPane();
         Label primarySortCriterion = new Label(Localization.lang("Primary sort criterion"));
-        primarySortCriterion.setFont(font);
         builder.add(primarySortCriterion, 1, 1);
         builder.add(savePriSort, 2, 1);
         builder.add(savePriDesc, 3, 1);
 
         Label secondarySortCriterion = new Label(Localization.lang("Secondary sort criterion"));
-        secondarySortCriterion.setFont(font);
         builder.add(secondarySortCriterion, 1, 2);
         builder.add(saveSecSort, 2, 2);
         builder.add(saveSecDesc, 3, 2);
 
         Label tertiarySortCriterion = new Label(Localization.lang("Tertiary sort criterion"));
-        tertiarySortCriterion.setFont(font);
         builder.add(tertiarySortCriterion, 1, 3);
         builder.add(saveTerSort, 2, 3);
         builder.add(saveTerDesc, 3, 3);
diff --git a/src/main/java/org/jabref/gui/actions/DatabasePropertiesAction.java b/src/main/java/org/jabref/gui/actions/DatabasePropertiesAction.java
deleted file mode 100644
index 564b6c5cc2f..00000000000
--- a/src/main/java/org/jabref/gui/actions/DatabasePropertiesAction.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package org.jabref.gui.actions;
-
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.dbproperties.DatabasePropertiesDialog;
-
-public class DatabasePropertiesAction extends SimpleCommand {
-
-    private final JabRefFrame frame;
-
-    public DatabasePropertiesAction(JabRefFrame frame) {
-        this.frame = frame;
-    }
-
-    @Override
-    public void execute() {
-        DatabasePropertiesDialog propertiesDialog = new DatabasePropertiesDialog(frame.getCurrentBasePanel());
-        propertiesDialog.updateEnableStatus();
-        propertiesDialog.setVisible(true);
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/actions/LibraryPropertiesAction.java b/src/main/java/org/jabref/gui/actions/LibraryPropertiesAction.java
new file mode 100644
index 00000000000..1b2299e3f06
--- /dev/null
+++ b/src/main/java/org/jabref/gui/actions/LibraryPropertiesAction.java
@@ -0,0 +1,24 @@
+package org.jabref.gui.actions;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.libraryproperties.LibraryPropertiesDialogView;
+
+public class LibraryPropertiesAction extends SimpleCommand {
+
+    private final JabRefFrame frame;
+    private final DialogService dialogService;
+
+    public LibraryPropertiesAction(JabRefFrame frame, DialogService dialogService) {
+        this.frame = frame;
+        this.dialogService = dialogService;
+    }
+
+    @Override
+    public void execute() {
+        LibraryPropertiesDialogView propertiesDialog = new LibraryPropertiesDialogView(frame.getCurrentBasePanel(), dialogService);
+        propertiesDialog.showAndWait();
+
+    }
+
+}
diff --git a/src/main/java/org/jabref/gui/dbproperties/DatabasePropertiesDialog.java b/src/main/java/org/jabref/gui/dbproperties/DatabasePropertiesDialog.java
deleted file mode 100644
index f1a58b0be7c..00000000000
--- a/src/main/java/org/jabref/gui/dbproperties/DatabasePropertiesDialog.java
+++ /dev/null
@@ -1,330 +0,0 @@
-package org.jabref.gui.dbproperties;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.nio.charset.Charset;
-import java.util.Optional;
-
-import javax.swing.AbstractAction;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.ButtonGroup;
-import javax.swing.DefaultComboBoxModel;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JComponent;
-import javax.swing.JRadioButton;
-import javax.swing.JTextField;
-
-import javafx.embed.swing.JFXPanel;
-import javafx.scene.Parent;
-import javafx.scene.Scene;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.FXDialogService;
-import org.jabref.gui.JabRefDialog;
-import org.jabref.gui.SaveOrderConfigDisplay;
-import org.jabref.gui.cleanup.FieldFormatterCleanupsPanel;
-import org.jabref.gui.customjfx.CustomJFXPanel;
-import org.jabref.gui.help.HelpAction;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.gui.util.DirectoryDialogConfiguration;
-import org.jabref.logic.cleanup.Cleanups;
-import org.jabref.logic.help.HelpFile;
-import org.jabref.logic.l10n.Encodings;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.shared.DatabaseLocation;
-import org.jabref.model.metadata.MetaData;
-import org.jabref.model.metadata.SaveOrderConfig;
-import org.jabref.preferences.JabRefPreferences;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import com.jgoodies.forms.builder.FormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-
-public class DatabasePropertiesDialog extends JabRefDialog {
-
-    private final MetaData metaData;
-    private final BasePanel panel;
-    private final JComboBox<Charset> encoding;
-    private final JButton ok;
-    private final JButton cancel;
-    private final JTextField fileDir = new JTextField(40);
-    private final JTextField fileDirIndv = new JTextField(40);
-    private String oldFileVal = "";
-    private String oldFileIndvVal = "";
-    private SaveOrderConfig oldSaveOrderConfig;
-
-    /* The code for "Save sort order" is copied from ExportSortingPrefsTab and slightly updated to fit storing at metadata */
-    private JRadioButton saveInOriginalOrder;
-
-    private JRadioButton saveInSpecifiedOrder;
-
-    private final JCheckBox protect = new JCheckBox(
-            Localization.lang("Refuse to save the library before external changes have been reviewed."));
-    private boolean oldProtectVal;
-    private SaveOrderConfigDisplay saveOrderPanel;
-
-    private FieldFormatterCleanupsPanel fieldFormatterCleanupsPanel;
-
-    public DatabasePropertiesDialog(BasePanel panel) {
-        super(Localization.lang("Library properties"), true, DatabasePropertiesDialog.class);
-        encoding = new JComboBox<>();
-        encoding.setModel(new DefaultComboBoxModel<>(Encodings.ENCODINGS));
-        ok = new JButton(Localization.lang("OK"));
-        cancel = new JButton(Localization.lang("Cancel"));
-        this.panel = panel;
-        this.metaData = panel.getBibDatabaseContext().getMetaData();
-        init();
-    }
-
-    public void updateEnableStatus() {
-        DatabaseLocation location = panel.getBibDatabaseContext().getLocation();
-        boolean isShared = (location == DatabaseLocation.SHARED);
-        encoding.setEnabled(!isShared); // the encoding of shared database is always UTF-8
-        saveInOriginalOrder.setEnabled(!isShared);
-        saveInSpecifiedOrder.setEnabled(!isShared);
-        saveOrderPanel.setEnabled(!isShared);
-        protect.setEnabled(!isShared);
-    }
-
-    private void init() {
-
-        DirectoryDialogConfiguration directoryDialogConfiguration = new DirectoryDialogConfiguration.Builder()
-                .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)).build();
-        DialogService ds = new FXDialogService();
-
-        JButton browseFile = new JButton(Localization.lang("Browse"));
-        JButton browseFileIndv = new JButton(Localization.lang("Browse"));
-
-        browseFile.addActionListener(e -> DefaultTaskExecutor
-                .runInJavaFXThread(() -> ds.showDirectorySelectionDialog(directoryDialogConfiguration))
-                .ifPresent(f -> fileDir.setText(f.toAbsolutePath().toString())));
-        browseFileIndv.addActionListener(e -> DefaultTaskExecutor
-                .runInJavaFXThread(() -> ds.showDirectorySelectionDialog(directoryDialogConfiguration))
-                .ifPresent(f -> fileDirIndv.setText(f.toAbsolutePath().toString())));
-
-        setupSortOrderConfiguration();
-        FormLayout form = new FormLayout("left:pref, 4dlu, pref:grow, 4dlu, pref:grow, 4dlu, pref",
-                "pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, pref, 2dlu, fill:pref:grow, 180dlu, fill:pref:grow,");
-        FormBuilder builder = FormBuilder.create().layout(form);
-        builder.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        builder.add(Localization.lang("Library encoding")).xy(1, 1);
-        builder.add(encoding).xy(3, 1);
-
-        builder.addSeparator(Localization.lang("Override default file directories")).xyw(1, 3, 5);
-        builder.add(Localization.lang("General file directory")).xy(1, 5);
-        builder.add(fileDir).xy(3, 5);
-        builder.add(browseFile).xy(5, 5);
-        builder.add(Localization.lang("User-specific file directory")).xy(1, 7);
-        builder.add(fileDirIndv).xy(3, 7);
-        builder.add(browseFileIndv).xy(5, 7);
-
-        builder.addSeparator(Localization.lang("Save sort order")).xyw(1, 13, 5);
-        builder.add(saveInOriginalOrder).xyw(1, 15, 5);
-        builder.add(saveInSpecifiedOrder).xyw(1, 17, 5);
-
-        saveOrderPanel = new SaveOrderConfigDisplay();
-        JFXPanel panel = CustomJFXPanel.wrap(new Scene((Parent) saveOrderPanel.getJFXPanel()));
-        builder.add(panel).xyw(1, 21, 5);
-
-        builder.addSeparator(Localization.lang("Library protection")).xyw(1, 23, 5);
-        builder.add(protect).xyw(1, 25, 5);
-
-        fieldFormatterCleanupsPanel = new FieldFormatterCleanupsPanel(Localization.lang("Enable save actions"),
-                Cleanups.DEFAULT_SAVE_ACTIONS);
-        builder.addSeparator(Localization.lang("Save actions")).xyw(1, 27, 5);
-        builder.add(CustomJFXPanel.wrap(new Scene(fieldFormatterCleanupsPanel))).xyw(1, 29, 5);
-
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        bb.addButton(ok);
-        bb.addButton(cancel);
-        bb.addRelatedGap();
-        bb.addButton(new HelpAction(HelpFile.DATABASE_PROPERTIES).getHelpButton());
-        bb.addGlue();
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        getContentPane().add(builder.getPanel(), BorderLayout.CENTER);
-        getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-        pack();
-
-        AbstractAction closeAction = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                dispose();
-            }
-        };
-        ActionMap am = builder.getPanel().getActionMap();
-        InputMap im = builder.getPanel().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", closeAction);
-
-        ok.addActionListener(e -> {
-            if (propertiesChanged()) {
-                storeSettings();
-            }
-            dispose();
-        });
-
-        cancel.addActionListener(e -> dispose());
-    }
-
-    private boolean propertiesChanged() {
-        Charset oldEncoding = panel.getBibDatabaseContext().getMetaData().getEncoding()
-                .orElse(Globals.prefs.getDefaultEncoding());
-        Charset newEncoding = (Charset) encoding.getSelectedItem();
-        boolean saveActionsChanged = fieldFormatterCleanupsPanel.hasChanged();
-        boolean saveOrderConfigChanged = !getNewSaveOrderConfig().equals(oldSaveOrderConfig);
-        boolean changed = saveOrderConfigChanged || !newEncoding.equals(oldEncoding)
-                || !oldFileVal.equals(fileDir.getText()) || !oldFileIndvVal.equals(fileDirIndv.getText())
-                || (oldProtectVal != protect.isSelected()) || saveActionsChanged;
-        return changed;
-    }
-
-    private SaveOrderConfig getNewSaveOrderConfig() {
-        SaveOrderConfig saveOrderConfig = null;
-        if (saveInOriginalOrder.isSelected()) {
-            saveOrderConfig = SaveOrderConfig.getDefaultSaveOrder();
-        } else {
-            saveOrderConfig = saveOrderPanel.getSaveOrderConfig();
-            saveOrderConfig.setSaveInSpecifiedOrder();
-        }
-        return saveOrderConfig;
-    }
-
-    private void setupSortOrderConfiguration() {
-        saveInOriginalOrder = new JRadioButton(Localization.lang("Save entries in their original order"));
-        saveInSpecifiedOrder = new JRadioButton(Localization.lang("Save entries ordered as specified"));
-
-        ButtonGroup bg = new ButtonGroup();
-        bg.add(saveInOriginalOrder);
-        bg.add(saveInSpecifiedOrder);
-        ActionListener listener = e -> {
-            boolean selected = e.getSource() == saveInSpecifiedOrder;
-            saveOrderPanel.setEnabled(selected);
-        };
-
-        saveInOriginalOrder.addActionListener(listener);
-        saveInSpecifiedOrder.addActionListener(listener);
-    }
-
-    @Override
-    public void setVisible(boolean visible) {
-        if (visible) {
-            setValues();
-        }
-        super.setVisible(visible);
-    }
-
-    private void setValues() {
-        Optional<Charset> charset = panel.getBibDatabaseContext().getMetaData().getEncoding();
-        encoding.setSelectedItem(charset.orElse(Globals.prefs.getDefaultEncoding()));
-
-        Optional<SaveOrderConfig> storedSaveOrderConfig = metaData.getSaveOrderConfig();
-        boolean selected;
-        if (!storedSaveOrderConfig.isPresent()) {
-            saveInOriginalOrder.setSelected(true);
-            oldSaveOrderConfig = SaveOrderConfig.getDefaultSaveOrder();
-            selected = false;
-        } else {
-            SaveOrderConfig saveOrderConfig = storedSaveOrderConfig.get();
-            oldSaveOrderConfig = saveOrderConfig;
-            if (saveOrderConfig.saveInOriginalOrder()) {
-                saveInOriginalOrder.setSelected(true);
-                selected = false;
-            } else {
-                saveInSpecifiedOrder.setSelected(true);
-                selected = true;
-            }
-            saveOrderPanel.setSaveOrderConfig(saveOrderConfig);
-        }
-        saveOrderPanel.setEnabled(selected);
-
-        Optional<String> fileD = metaData.getDefaultFileDirectory();
-        if (fileD.isPresent()) {
-            fileDir.setText(fileD.get().trim());
-        } else {
-            fileDir.setText("");
-        }
-
-        String fileDI = metaData.getUserFileDirectory(Globals.prefs.getUser()).orElse(""); // File dir setting
-        fileDirIndv.setText(fileDI);
-        oldFileIndvVal = fileDirIndv.getText();
-
-        protect.setSelected(metaData.isProtected());
-
-        // Store original values to see if they get changed:
-        oldFileVal = fileDir.getText();
-        oldProtectVal = protect.isSelected();
-
-        //set save actions
-        fieldFormatterCleanupsPanel.setValues(metaData);
-    }
-
-    private void storeSettings() {
-        Charset oldEncoding = panel.getBibDatabaseContext().getMetaData().getEncoding()
-                .orElse(Globals.prefs.getDefaultEncoding());
-        Charset newEncoding = (Charset) encoding.getSelectedItem();
-        panel.getBibDatabaseContext().getMetaData().setEncoding(newEncoding);
-
-        String text = fileDir.getText().trim();
-        if (text.isEmpty()) {
-            metaData.clearDefaultFileDirectory();
-        } else {
-            metaData.setDefaultFileDirectory(text);
-        }
-        // Repeat for individual file dir - reuse 'text' and 'dir' vars
-        text = fileDirIndv.getText();
-        if (text.isEmpty()) {
-            metaData.clearUserFileDirectory(Globals.prefs.getUser());
-        } else {
-            metaData.setUserFileDirectory(Globals.prefs.getUser(), text);
-        }
-
-        if (protect.isSelected()) {
-            metaData.markAsProtected();
-        } else {
-            metaData.markAsNotProtected();
-        }
-
-        SaveOrderConfig newSaveOrderConfig = getNewSaveOrderConfig();
-
-        boolean saveOrderConfigChanged = !getNewSaveOrderConfig().equals(oldSaveOrderConfig);
-
-        // See if any of the values have been modified:
-        if (saveOrderConfigChanged) {
-            if (newSaveOrderConfig.equals(SaveOrderConfig.getDefaultSaveOrder())) {
-                metaData.clearSaveOrderConfig();
-            } else {
-                metaData.setSaveOrderConfig(newSaveOrderConfig);
-            }
-        }
-
-        boolean saveActionsChanged = fieldFormatterCleanupsPanel.hasChanged();
-        if (saveActionsChanged) {
-            if (fieldFormatterCleanupsPanel.isDefaultSaveActions()) {
-                metaData.clearSaveActions();
-            } else {
-                fieldFormatterCleanupsPanel.storeSettings(metaData);
-            }
-        }
-
-        boolean changed = saveOrderConfigChanged || !newEncoding.equals(oldEncoding)
-                || !oldFileVal.equals(fileDir.getText()) || !oldFileIndvVal.equals(fileDirIndv.getText())
-                || (oldProtectVal != protect.isSelected()) || saveActionsChanged;
-        // ... if so, mark base changed. Prevent the Undo button from removing
-        // change marking:
-        if (changed) {
-            panel.markNonUndoableBaseChanged();
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
similarity index 76%
rename from src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml
rename to src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
index c2163dc1dda..c78f39dac2e 100644
--- a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialog.fxml
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
@@ -17,12 +17,11 @@
 <?import javafx.scene.layout.RowConstraints?>
 <?import javafx.scene.layout.VBox?>
 
-
-<DialogPane prefHeight="516.0" prefWidth="922.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.dbproperties.LibraryPropertiesDialogView">
+<DialogPane minHeight="-Infinity" prefHeight="784.0" prefWidth="921.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.dbproperties.LibraryPropertiesDialogView">
    <content>
-      <VBox fx:id="contentVbox" prefHeight="200.0" prefWidth="100.0">
+      <VBox fx:id="contentVbox" minHeight="-Infinity" prefHeight="200.0" prefWidth="100.0">
          <children>
-            <GridPane>
+            <GridPane minHeight="-Infinity">
               <columnConstraints>
                 <ColumnConstraints hgrow="SOMETIMES" maxWidth="218.0" minWidth="10.0" prefWidth="200.0" />
                 <ColumnConstraints hgrow="SOMETIMES" maxWidth="797.0" minWidth="10.0" prefWidth="529.0" />
@@ -37,9 +36,15 @@
                <children>
                   <Label text="Library encoding" />
                   <ComboBox fx:id="encoding" prefWidth="250.0" GridPane.columnIndex="1" GridPane.hgrow="ALWAYS" />
-                  <HBox alignment="CENTER" prefHeight="100.0" prefWidth="200.0" GridPane.columnSpan="2147483647" GridPane.rowIndex="1">
+                  <Label text="General file directory" GridPane.rowIndex="2" />
+                  <TextField fx:id="generalFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="2" />
+                  <Button fx:id="browseGeneralFileDir" mnemonicParsing="false" onAction="#browseGeneralFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="2" />
+                  <Label text="User-specific file directory" GridPane.rowIndex="3" />
+                  <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
+                  <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
+                  <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0" GridPane.columnSpan="3" GridPane.rowIndex="1">
                      <children>
-                        <Label alignment="BOTTOM_LEFT" text="%Override default file directories" />
+                        <Label alignment="TOP_LEFT" text="%Override default file directories" />
                         <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
                            <opaqueInsets>
                               <Insets left="10.0" right="10.0" top="10.0" />
@@ -52,37 +57,12 @@
                            </padding>
                         </Separator>
                      </children>
-                     <GridPane.margin>
-                        <Insets />
-                     </GridPane.margin>
                   </HBox>
-                  <Label text="General file directory" GridPane.rowIndex="2" />
-                  <TextField fx:id="generalFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="2" />
-                  <Button fx:id="browseGeneralFileDir" mnemonicParsing="false" onAction="#browseGeneralFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="2" />
-                  <Label text="User-specific file directory" GridPane.rowIndex="3" />
-                  <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
-                  <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
                </children>
             </GridPane>
-            <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
-               <children>
-                  <Label alignment="BOTTOM_LEFT" text="%Save sort order" />
-                  <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
-                     <opaqueInsets>
-                        <Insets left="10.0" right="10.0" top="10.0" />
-                     </opaqueInsets>
-                     <HBox.margin>
-                        <Insets />
-                     </HBox.margin>
-                     <padding>
-                        <Insets left="10.0" />
-                     </padding>
-                  </Separator>
-               </children>
-            </HBox>
-            <VBox fx:id="saveOrdervbox">
-             <fx:define>
-              <ToggleGroup fx:id="saveOrderToggleGroup" />
+            <VBox fx:id="saveOrdervbox" minHeight="-Infinity">
+               <fx:define>
+                 <ToggleGroup fx:id="saveOrderToggleGroup" />
                </fx:define>
                <children>
                   <RadioButton fx:id="saveInOriginalOrder" mnemonicParsing="false" text="%Save entries in their original order" toggleGroup="$saveOrderToggleGroup" />
@@ -91,7 +71,7 @@
             </VBox>
             <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
                <children>
-                  <Label alignment="BOTTOM_LEFT" text="%Library protection" />
+                  <Label alignment="TOP_LEFT" text="%Library protection" />
                   <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
                      <opaqueInsets>
                         <Insets left="10.0" right="10.0" top="10.0" />
@@ -108,7 +88,7 @@
             <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed" />
             <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
                <children>
-                  <Label alignment="BOTTOM_LEFT" text="%Save actions" />
+                  <Label alignment="TOP_LEFT" text="%Save actions" />
                   <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
                      <opaqueInsets>
                         <Insets left="10.0" right="10.0" top="10.0" />
diff --git a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
similarity index 97%
rename from src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java
rename to src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
index b91613247dc..d6a8796466c 100644
--- a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogView.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
@@ -1,4 +1,4 @@
-package org.jabref.gui.dbproperties;
+package org.jabref.gui.libraryproperties;
 
 import java.nio.charset.Charset;
 import java.util.Optional;
@@ -76,7 +76,8 @@ private void initialize() {
         generalFileDirectory.textProperty().bindBidirectional(viewModel.generalFileDirectoryPropertyProperty());
         userSpecificFileDirectory.textProperty().bindBidirectional(viewModel.userSpecificFileDirectoryProperty());
 
-        encoding.valueProperty().bind(viewModel.selectedEncodingProperty());
+        encoding.itemsProperty().bind(viewModel.encodingsProperty());
+        encoding.valueProperty().bindBidirectional(viewModel.selectedEncodingProperty());
         saveOrderPanel = new SaveOrderConfigDisplay();
         saveOrdervbox.getChildren().add(saveOrderPanel.getJFXPanel());
         fieldFormatterCleanupsPanel = new FieldFormatterCleanupsPanel(Localization.lang("Enable save actions"),
diff --git a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
similarity index 99%
rename from src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java
rename to src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
index fc857de9d0e..b51d688aff6 100644
--- a/src/main/java/org/jabref/gui/dbproperties/LibraryPropertiesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
@@ -1,4 +1,4 @@
-package org.jabref.gui.dbproperties;
+package org.jabref.gui.libraryproperties;
 
 import java.nio.charset.Charset;
 import java.util.Optional;

From d246d37ef330230d6b25b6028de54663bb665602 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 28 Jan 2019 19:06:26 +0100
Subject: [PATCH 008/184] fix checkstyle and l10n

---
 src/main/java/org/jabref/gui/JabRefFrame.java             | 2 +-
 .../gui/libraryproperties/LibraryPropertiesDialog.fxml    | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 59f9f1ccb01..82ef76ff085 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -60,9 +60,9 @@
 import org.jabref.gui.actions.CopyFilesAction;
 import org.jabref.gui.actions.CustomizeEntryAction;
 import org.jabref.gui.actions.CustomizeKeyBindingAction;
-import org.jabref.gui.actions.LibraryPropertiesAction;
 import org.jabref.gui.actions.EditExternalFileTypesAction;
 import org.jabref.gui.actions.ErrorConsoleAction;
+import org.jabref.gui.actions.LibraryPropertiesAction;
 import org.jabref.gui.actions.LookupIdentifierAction;
 import org.jabref.gui.actions.ManageCustomExportsAction;
 import org.jabref.gui.actions.ManageCustomImportsAction;
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
index c78f39dac2e..6913c862d78 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
@@ -34,12 +34,12 @@
                   <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
               </rowConstraints>
                <children>
-                  <Label text="Library encoding" />
+                  <Label text="%Library encoding" />
                   <ComboBox fx:id="encoding" prefWidth="250.0" GridPane.columnIndex="1" GridPane.hgrow="ALWAYS" />
-                  <Label text="General file directory" GridPane.rowIndex="2" />
+                  <Label text="%General file directory" GridPane.rowIndex="2" />
                   <TextField fx:id="generalFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="2" />
                   <Button fx:id="browseGeneralFileDir" mnemonicParsing="false" onAction="#browseGeneralFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="2" />
-                  <Label text="User-specific file directory" GridPane.rowIndex="3" />
+                  <Label text="%User-specific file directory" GridPane.rowIndex="3" />
                   <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
                   <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
                   <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0" GridPane.columnSpan="3" GridPane.rowIndex="1">
@@ -85,7 +85,7 @@
                   </Separator>
                </children>
             </HBox>
-            <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed" />
+            <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." />
             <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
                <children>
                   <Label alignment="TOP_LEFT" text="%Save actions" />

From 33b35f7f65ef0fab14fcf866d48ce8daade7adb5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Thu, 31 Jan 2019 08:44:05 +0100
Subject: [PATCH 009/184] Bump wiremock from 2.20.0 to 2.21.0 (#4623)

Bumps [wiremock](https://github.com/tomakehurst/wiremock) from 2.20.0 to 2.21.0.
- [Release notes](https://github.com/tomakehurst/wiremock/releases)
- [Changelog](https://github.com/tomakehurst/wiremock/blob/master/release-settings.gradle)
- [Commits](https://github.com/tomakehurst/wiremock/compare/2.20.0...2.21.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index b3f68a91c8c..9d93378e772 100644
--- a/build.gradle
+++ b/build.gradle
@@ -171,7 +171,7 @@ dependencies {
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.1'
     testCompile 'org.mockito:mockito-core:2.23.4'
-    testCompile 'com.github.tomakehurst:wiremock:2.20.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.21.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'

From 769ebd19e7ed68a511817aa2bc12c2bcdf149446 Mon Sep 17 00:00:00 2001
From: Chelsey Ong <30564248+chelseyong@users.noreply.github.com>
Date: Thu, 31 Jan 2019 16:46:20 +0700
Subject: [PATCH 010/184] Fix preview style configuration (#4613)

* Modify prefsTab to save the selected preview style in preferences

* Fix codacy by changing to equals
---
 src/main/java/org/jabref/gui/PreviewPanel.java           | 9 +++++++--
 .../java/org/jabref/gui/preferences/PreviewPrefsTab.java | 3 +++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/PreviewPanel.java b/src/main/java/org/jabref/gui/PreviewPanel.java
index bffcb4e2bd3..95323116271 100644
--- a/src/main/java/org/jabref/gui/PreviewPanel.java
+++ b/src/main/java/org/jabref/gui/PreviewPanel.java
@@ -62,6 +62,7 @@ public class PreviewPanel extends ScrollPane implements SearchQueryHighlightList
     private final KeyBindingRepository keyBindingRepository;
 
     private String previewStyle;
+    private CitationStyle citationStyle;
     private final String defaultPreviewStyle = "Preview";
     private Optional<BasePanel> basePanel = Optional.empty();
 
@@ -224,13 +225,14 @@ private void updateLayout(PreviewPreferences previewPreferences, boolean init) {
         String style = previewPreferences.getCurrentPreviewStyle();
         if (previewStyle == null) {
             previewStyle = style;
+            CitationStyle.createCitationStyleFromFile(style).ifPresent(cs -> citationStyle = cs);
         }
         if (basePanel.isPresent() && !previewStyle.equals(style)) {
             if (CitationStyle.isCitationStyleFile(style)) {
                 layout = Optional.empty();
                 CitationStyle.createCitationStyleFromFile(style)
-                        .ifPresent(citationStyle -> {
-                            basePanel.get().getCitationStyleCache().setCitationStyle(citationStyle);
+                        .ifPresent(cs -> {
+                            citationStyle = cs;
                             if (!init) {
                                 basePanel.get().output(Localization.lang("Preview style changed to: %0", citationStyle.getTitle()));
                             }
@@ -299,6 +301,9 @@ public void update() {
                                                         .doLayout(entry, databaseContext.getDatabase())));
             setPreviewLabel(sb.toString());
         } else if (basePanel.isPresent() && bibEntry.isPresent()) {
+            if (citationStyle != null && !previewStyle.equals(defaultPreviewStyle)) {
+                basePanel.get().getCitationStyleCache().setCitationStyle(citationStyle);
+            }
             Future<?> citationStyleWorker = BackgroundTask
                                                           .wrap(() -> basePanel.get().getCitationStyleCache().getCitationFor(bibEntry.get()))
                                                           .onRunning(() -> {
diff --git a/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java b/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java
index 071aa23cd0a..76fc314f1b8 100644
--- a/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java
@@ -264,6 +264,9 @@ public void storeSettings() {
                 .withPreviewCycle(styles)
                 .withPreviewStyle(layout.getText().replace("\n", "__NEWLINE__"))
                 .build();
+        if (!chosen.getSelectionModel().isEmpty()) {
+            previewPreferences = previewPreferences.getBuilder().withPreviewCyclePosition(chosen.getSelectionModel().getSelectedIndex()).build();
+        }
         Globals.prefs.storePreviewPreferences(previewPreferences);
 
         // update preview

From 629fcc424f7f7dce419b7c1ab3d8984a84c902e5 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Fri, 1 Feb 2019 16:08:00 +0100
Subject: [PATCH 011/184] Fix NPE and not on FX Thread in PreviewPrefs Tabs
 (#4624)

* Fix NPE and not on FX Thread in PreviewPrefs Tabs


Remove obsolete swing stuff
Create proper javafx binding
Fixes #4621
Fixes #4622

Fix another issue where the Preview stlye is not set correctly

* fix checkstyle

Signed-off-by: Siedlerchr <siedlerkiller@gmail.com>

* fix copying of entry preview

* prevent divide by zero excpetion

* Pass task executor as variable
Use Background Task
add error message
improve binding

* remove empty line
---
 src/main/java/org/jabref/gui/JabRefFrame.java |  27 ++--
 .../java/org/jabref/gui/PreviewPanel.java     |  36 +++--
 .../gui/actions/ShowPreferencesAction.java    |   8 +-
 .../gui/preferences/PreferencesDialog.java    |  53 ++++---
 .../gui/preferences/PreviewPrefsTab.java      | 145 +++++++-----------
 .../preferences/PreviewPreferences.java       |  16 +-
 src/main/resources/l10n/JabRef_en.properties  |   2 +
 7 files changed, 134 insertions(+), 153 deletions(-)

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index b1872641c36..76e14c8e6ce 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -923,24 +923,23 @@ private MenuBar createMenu() {
         );
 
         options.getItems().addAll(
-                factory.createMenuItem(StandardActions.SHOW_PREFS, new ShowPreferencesAction(this)),
+                                  factory.createMenuItem(StandardActions.SHOW_PREFS, new ShowPreferencesAction(this, Globals.TASK_EXECUTOR)),
 
-                new SeparatorMenuItem(),
+                                  new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.SETUP_GENERAL_FIELDS, new SetupGeneralFieldsAction()),
-                factory.createMenuItem(StandardActions.MANAGE_CUSTOM_IMPORTS, new ManageCustomImportsAction()),
-                factory.createMenuItem(StandardActions.MANAGE_CUSTOM_EXPORTS, new ManageCustomExportsAction()),
-                factory.createMenuItem(StandardActions.MANAGE_EXTERNAL_FILETYPES, new EditExternalFileTypesAction()),
-                factory.createMenuItem(StandardActions.MANAGE_JOURNALS, new ManageJournalsAction()),
-                factory.createMenuItem(StandardActions.CUSTOMIZE_KEYBINDING, new CustomizeKeyBindingAction()),
-                factory.createMenuItem(StandardActions.MANAGE_PROTECTED_TERMS, new ManageProtectedTermsAction(this, Globals.protectedTermsLoader)),
+                                  factory.createMenuItem(StandardActions.SETUP_GENERAL_FIELDS, new SetupGeneralFieldsAction()),
+                                  factory.createMenuItem(StandardActions.MANAGE_CUSTOM_IMPORTS, new ManageCustomImportsAction()),
+                                  factory.createMenuItem(StandardActions.MANAGE_CUSTOM_EXPORTS, new ManageCustomExportsAction()),
+                                  factory.createMenuItem(StandardActions.MANAGE_EXTERNAL_FILETYPES, new EditExternalFileTypesAction()),
+                                  factory.createMenuItem(StandardActions.MANAGE_JOURNALS, new ManageJournalsAction()),
+                                  factory.createMenuItem(StandardActions.CUSTOMIZE_KEYBINDING, new CustomizeKeyBindingAction()),
+                                  factory.createMenuItem(StandardActions.MANAGE_PROTECTED_TERMS, new ManageProtectedTermsAction(this, Globals.protectedTermsLoader)),
 
-                new SeparatorMenuItem(),
+                                  new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.MANAGE_CONTENT_SELECTORS, new OldDatabaseCommandWrapper(Actions.MANAGE_SELECTORS, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.CUSTOMIZE_ENTRY_TYPES, new CustomizeEntryAction(this)),
-                factory.createMenuItem(StandardActions.MANAGE_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this))
-        );
+                                  factory.createMenuItem(StandardActions.MANAGE_CONTENT_SELECTORS, new OldDatabaseCommandWrapper(Actions.MANAGE_SELECTORS, this, Globals.stateManager)),
+                                  factory.createMenuItem(StandardActions.CUSTOMIZE_ENTRY_TYPES, new CustomizeEntryAction(this)),
+                                  factory.createMenuItem(StandardActions.MANAGE_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this)));
 
         help.getItems().addAll(
                 factory.createMenuItem(StandardActions.HELP, HelpAction.getMainHelpPageCommand()),
diff --git a/src/main/java/org/jabref/gui/PreviewPanel.java b/src/main/java/org/jabref/gui/PreviewPanel.java
index 95323116271..ff8d6db01bd 100644
--- a/src/main/java/org/jabref/gui/PreviewPanel.java
+++ b/src/main/java/org/jabref/gui/PreviewPanel.java
@@ -94,10 +94,10 @@ public PreviewPanel(BasePanel panel, BibDatabaseContext databaseContext, KeyBind
         this.keyBindingRepository = keyBindingRepository;
 
         fileHandler = new NewDroppedFileHandler(dialogService, databaseContext, externalFileTypes,
-                Globals.prefs.getFilePreferences(),
+                                                Globals.prefs.getFilePreferences(),
                                                 Globals.prefs.getImportFormatPreferences(),
                                                 Globals.prefs.getUpdateFieldPreferences(),
-                Globals.getFileUpdateMonitor());
+                                                Globals.getFileUpdateMonitor());
 
         // Set up scroll pane for preview pane
         setFitToHeight(true);
@@ -231,19 +231,19 @@ private void updateLayout(PreviewPreferences previewPreferences, boolean init) {
             if (CitationStyle.isCitationStyleFile(style)) {
                 layout = Optional.empty();
                 CitationStyle.createCitationStyleFromFile(style)
-                        .ifPresent(cs -> {
-                            citationStyle = cs;
-                            if (!init) {
-                                basePanel.get().output(Localization.lang("Preview style changed to: %0", citationStyle.getTitle()));
-                            }
-                        });
+                             .ifPresent(cs -> {
+                                 citationStyle = cs;
+                                 if (!init) {
+                                     basePanel.get().output(Localization.lang("Preview style changed to: %0", citationStyle.getTitle()));
+                                 }
+                             });
                 previewStyle = style;
-            } else {
-                previewStyle = defaultPreviewStyle;
-                updatePreviewLayout(previewPreferences.getPreviewStyle(), previewPreferences.getLayoutFormatterPreferences());
-                if (!init) {
-                    basePanel.get().output(Localization.lang("Preview style changed to: %0", Localization.lang("Preview")));
-                }
+            }
+        } else {
+            previewStyle = defaultPreviewStyle;
+            updatePreviewLayout(previewPreferences.getPreviewStyle(), previewPreferences.getLayoutFormatterPreferences());
+            if (!init) {
+                basePanel.get().output(Localization.lang("Preview style changed to: %0", Localization.lang("Preview")));
             }
         }
 
@@ -301,7 +301,7 @@ public void update() {
                                                         .doLayout(entry, databaseContext.getDatabase())));
             setPreviewLabel(sb.toString());
         } else if (basePanel.isPresent() && bibEntry.isPresent()) {
-            if (citationStyle != null && !previewStyle.equals(defaultPreviewStyle)) {
+            if ((citationStyle != null) && !previewStyle.equals(defaultPreviewStyle)) {
                 basePanel.get().getCitationStyleCache().setCitationStyle(citationStyle);
             }
             Future<?> citationStyleWorker = BackgroundTask
@@ -368,11 +368,13 @@ public void close() {
     private void copyPreviewToClipBoard() {
         StringBuilder previewStringContent = new StringBuilder();
         Document document = previewView.getEngine().getDocument();
-        NodeList nodeList = document.getElementsByTagName("*");
 
+        NodeList nodeList = document.getElementsByTagName("html");
+
+        //Nodelist does not implement iterable
         for (int i = 0; i < nodeList.getLength(); i++) {
             Element element = (Element) nodeList.item(i);
-            previewStringContent.append(element.getNodeValue()).append("\n");
+            previewStringContent.append(element.getTextContent());
         }
 
         ClipboardContent content = new ClipboardContent();
diff --git a/src/main/java/org/jabref/gui/actions/ShowPreferencesAction.java b/src/main/java/org/jabref/gui/actions/ShowPreferencesAction.java
index 7c13cbcc250..e6c0a29684c 100644
--- a/src/main/java/org/jabref/gui/actions/ShowPreferencesAction.java
+++ b/src/main/java/org/jabref/gui/actions/ShowPreferencesAction.java
@@ -2,17 +2,21 @@
 
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.preferences.PreferencesDialog;
+import org.jabref.gui.util.TaskExecutor;
 
 public class ShowPreferencesAction extends SimpleCommand {
 
     private final JabRefFrame jabRefFrame;
-    public ShowPreferencesAction(JabRefFrame jabRefFrame) {
+    private final TaskExecutor taskExecutor;
+
+    public ShowPreferencesAction(JabRefFrame jabRefFrame, TaskExecutor taskExecutor) {
         this.jabRefFrame = jabRefFrame;
+        this.taskExecutor = taskExecutor;
     }
 
     @Override
     public void execute() {
-        PreferencesDialog preferencesDialog = new PreferencesDialog(jabRefFrame);
+        PreferencesDialog preferencesDialog = new PreferencesDialog(jabRefFrame, taskExecutor);
         preferencesDialog.showAndWait();
     }
 }
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
index a2571e4e5fd..25837b9b62c 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
@@ -25,6 +25,7 @@
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.gui.util.ControlHelper;
 import org.jabref.gui.util.FileDialogConfiguration;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.gui.util.ViewModelListCellFactory;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.exporter.SavePreferences;
@@ -57,7 +58,7 @@ public class PreferencesDialog extends BaseDialog<Void> {
     private final JabRefPreferences prefs;
     private final ObservableList<PrefsTab> preferenceTabs;
 
-    public PreferencesDialog(JabRefFrame parent) {
+    public PreferencesDialog(JabRefFrame parent, TaskExecutor taskExecutor) {
         setTitle(Localization.lang("JabRef preferences"));
         getDialogPane().getScene().getStylesheets().add(this.getClass().getResource("PreferencesDialog.css").toExternalForm());
 
@@ -68,7 +69,7 @@ public PreferencesDialog(JabRefFrame parent) {
             close();
         });
 
-        prefs = JabRefPreferences.getInstance();
+        prefs = Globals.prefs;
         frame = parent;
         dialogService = frame.getDialogService();
 
@@ -77,7 +78,7 @@ public PreferencesDialog(JabRefFrame parent) {
         preferenceTabs.add(new FileTab(dialogService, prefs));
         preferenceTabs.add(new TablePrefsTab(prefs));
         preferenceTabs.add(new TableColumnsTab(prefs, frame));
-        preferenceTabs.add(new PreviewPrefsTab(dialogService, ExternalFileTypes.getInstance()));
+        preferenceTabs.add(new PreviewPrefsTab(dialogService, ExternalFileTypes.getInstance(), taskExecutor));
         preferenceTabs.add(new ExternalTab(frame, this, prefs));
         preferenceTabs.add(new GroupsPrefsTab(prefs));
         preferenceTabs.add(new EntryEditorPrefsTab(prefs));
@@ -111,8 +112,8 @@ private void construct() {
         });
         tabsList.getSelectionModel().selectFirst();
         new ViewModelListCellFactory<PrefsTab>()
-                .withText(PrefsTab::getTabName)
-                .install(tabsList);
+                                                .withText(PrefsTab::getTabName)
+                                                .install(tabsList);
 
         VBox buttonContainer = new VBox();
         buttonContainer.setAlignment(Pos.BOTTOM_LEFT);
@@ -132,21 +133,19 @@ private void construct() {
         resetPreferences.setOnAction(e -> resetPreferences());
         resetPreferences.setMaxWidth(Double.MAX_VALUE);
         buttonContainer.getChildren().addAll(
-                importPreferences,
-                exportPreferences,
-                showPreferences,
-                resetPreferences
-        );
+                                             importPreferences,
+                                             exportPreferences,
+                                             showPreferences,
+                                             resetPreferences);
 
         VBox spacer = new VBox();
         spacer.setPrefHeight(10.0);
         VBox.setVgrow(tabsList, Priority.ALWAYS);
         VBox.setVgrow(spacer, Priority.SOMETIMES);
         vBox.getChildren().addAll(
-                tabsList,
-                spacer,
-                buttonContainer
-        );
+                                  tabsList,
+                                  spacer,
+                                  buttonContainer);
 
         container.setLeft(vBox);
 
@@ -155,16 +154,16 @@ private void construct() {
 
     private void resetPreferences() {
         boolean resetPreferencesConfirmed = dialogService.showConfirmationDialogAndWait(
-                Localization.lang("Reset preferences"),
-                Localization.lang("Are you sure you want to reset all settings to default values?"),
-                Localization.lang("Reset preferences"),
-                Localization.lang("Cancel"));
+                                                                                        Localization.lang("Reset preferences"),
+                                                                                        Localization.lang("Are you sure you want to reset all settings to default values?"),
+                                                                                        Localization.lang("Reset preferences"),
+                                                                                        Localization.lang("Cancel"));
         if (resetPreferencesConfirmed) {
             try {
                 prefs.clear();
 
                 dialogService.showWarningDialogAndWait(Localization.lang("Reset preferences"),
-                        Localization.lang("You must restart JabRef for this to come into effect."));
+                                                       Localization.lang("You must restart JabRef for this to come into effect."));
             } catch (BackingStoreException ex) {
                 LOGGER.error("Error while resetting preferences", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("Reset preferences"), ex);
@@ -175,9 +174,9 @@ private void resetPreferences() {
 
     private void importPreferences() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                .addExtensionFilter(StandardFileType.XML)
-                .withDefaultExtension(StandardFileType.XML)
-                .withInitialDirectory(prefs.setLastPreferencesExportPath()).build();
+                                                                                               .addExtensionFilter(StandardFileType.XML)
+                                                                                               .withDefaultExtension(StandardFileType.XML)
+                                                                                               .withInitialDirectory(prefs.setLastPreferencesExportPath()).build();
 
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> {
             try {
@@ -185,7 +184,7 @@ private void importPreferences() {
                 updateAfterPreferenceChanges();
 
                 dialogService.showWarningDialogAndWait(Localization.lang("Import preferences"),
-                        Localization.lang("You must restart JabRef for this to come into effect."));
+                                                       Localization.lang("You must restart JabRef for this to come into effect."));
             } catch (JabRefException ex) {
                 LOGGER.error("Error while importing preferences", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("Import preferences"), ex);
@@ -230,10 +229,10 @@ public void setValues() {
 
     private void exportPreferences() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                .addExtensionFilter(StandardFileType.XML)
-                .withDefaultExtension(StandardFileType.XML)
-                .withInitialDirectory(prefs.setLastPreferencesExportPath())
-                .build();
+                                                                                               .addExtensionFilter(StandardFileType.XML)
+                                                                                               .withDefaultExtension(StandardFileType.XML)
+                                                                                               .withInitialDirectory(prefs.setLastPreferencesExportPath())
+                                                                                               .build();
 
         dialogService.showFileSaveDialog(fileDialogConfiguration)
                      .ifPresent(exportFile -> {
diff --git a/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java b/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java
index 76fc314f1b8..5ace5352e0a 100644
--- a/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java
@@ -4,11 +4,9 @@
 import java.util.Comparator;
 import java.util.List;
 import java.util.Optional;
-import java.util.concurrent.ExecutionException;
-
-import javax.swing.JPanel;
-import javax.swing.SwingWorker;
 
+import javafx.beans.binding.Bindings;
+import javafx.beans.binding.BooleanBinding;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 import javafx.scene.Node;
@@ -28,7 +26,8 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.PreviewPanel;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.util.DefaultTaskExecutor;
+import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.citationstyle.CitationStyle;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.TestEntry;
@@ -38,12 +37,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class PreviewPrefsTab extends JPanel implements PrefsTab {
+public class PreviewPrefsTab implements PrefsTab {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(PreviewPrefsTab.class);
 
-    private SwingWorker<List<CitationStyle>, Void> discoverCitationStyleWorker;
-
     private final ObservableList<Object> availableModel = FXCollections.observableArrayList();
     private final ObservableList<Object> chosenModel = FXCollections.observableArrayList();
 
@@ -61,25 +58,24 @@ public class PreviewPrefsTab extends JPanel implements PrefsTab {
     private final ScrollPane scrollPane = new ScrollPane(layout);
     private final DialogService dialogService;
     private final ExternalFileTypes externalFileTypes;
+    private final TaskExecutor taskExecutor;
 
-    public PreviewPrefsTab(DialogService dialogService, ExternalFileTypes externalFileTypes) {
+    public PreviewPrefsTab(DialogService dialogService, ExternalFileTypes externalFileTypes, TaskExecutor taskExecutor) {
         this.dialogService = dialogService;
         this.externalFileTypes = externalFileTypes;
+        this.taskExecutor = taskExecutor;
         setupLogic();
         setupGui();
     }
 
     private void setupLogic() {
-        chosen.getSelectionModel().selectedItemProperty().addListener(event -> {
-            if (chosen.getSelectionModel().getSelectedIndices().isEmpty()) {
-                btnLeft.setDisable(true);
-                btnDown.setDisable(true);
-                btnUp.setDisable(true);
-            }
-        });
 
-        available.getSelectionModel().selectedItemProperty().addListener(
-                e -> btnRight.setDisable(available.getSelectionModel().getSelectedIndices().isEmpty()));
+        BooleanBinding nothingSelectedFromChosen = Bindings.isEmpty(chosen.getSelectionModel().getSelectedItems());
+
+        btnLeft.disableProperty().bind(nothingSelectedFromChosen);
+        btnDown.disableProperty().bind(nothingSelectedFromChosen);
+        btnUp.disableProperty().bind(nothingSelectedFromChosen);
+        btnRight.disableProperty().bind(Bindings.isEmpty(available.getSelectionModel().getSelectedItems()));
 
         btnRight.setOnAction(event -> {
             for (Object object : available.getSelectionModel().getSelectedItems()) {
@@ -110,9 +106,9 @@ private void setupLogic() {
 
         btnDown.setOnAction(event -> {
             List<Integer> newSelectedIndices = new ArrayList<>();
-            ObservableList selectedIndices = chosen.getSelectionModel().getSelectedIndices();
+            ObservableList<Integer> selectedIndices = chosen.getSelectionModel().getSelectedIndices();
             for (int i = selectedIndices.size() - 1; i >= 0; i--) {
-                int oldIndex = (int)selectedIndices.get(i);
+                int oldIndex = selectedIndices.get(i);
                 boolean alreadyTaken = newSelectedIndices.contains(oldIndex + 1);
                 int newIndex = ((oldIndex < (chosenModel.size() - 1)) && !alreadyTaken) ? oldIndex + 1 : oldIndex;
                 chosenModel.add(newIndex, chosenModel.remove(oldIndex));
@@ -122,41 +118,33 @@ private void setupLogic() {
         });
 
         btnDefault.setOnAction(event -> layout.setText(Globals.prefs.getPreviewPreferences()
-                .getPreviewStyleDefault()
-                .replace("__NEWLINE__", "\n")));
+                                                                    .getPreviewStyleDefault()
+                                                                    .replace("__NEWLINE__", "\n")));
 
         btnTest.setOnAction(event -> {
             try {
-                DefaultTaskExecutor.runInJavaFXThread(() -> {
-                    PreviewPanel testPane = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), dialogService, externalFileTypes);
-                    if (chosen.getSelectionModel().getSelectedItems().isEmpty()) {
-                        testPane.setFixedLayout(layout.getText());
-                        testPane.setEntry(TestEntry.getTestEntry());
-                    }
-                    else {
-                        int indexStyle = chosen.getSelectionModel().getSelectedIndex();
-                        PreviewPreferences preferences = Globals.prefs.getPreviewPreferences();
-                        preferences = new PreviewPreferences(preferences.getPreviewCycle(),indexStyle,preferences.getPreviewPanelDividerPosition(),preferences.isPreviewPanelEnabled(), preferences.getPreviewStyle(),preferences.getPreviewStyleDefault());
-
-                        testPane = new PreviewPanel(JabRefGUI.getMainFrame().getCurrentBasePanel(), new BibDatabaseContext(), Globals.getKeyPrefs(), preferences, dialogService, externalFileTypes);
-                        testPane.setEntry(TestEntry.getTestEntry());
-                        testPane.updateLayout(preferences);
-                    }
 
-                    DialogPane pane = new DialogPane();
-                    pane.setContent(testPane);
-
-                    dialogService.showCustomDialogAndWait(Localization.lang("Preview"), pane, ButtonType.OK);
+                PreviewPanel testPane = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), dialogService, externalFileTypes);
+                if (chosen.getSelectionModel().getSelectedItems().isEmpty()) {
+                    testPane.setFixedLayout(layout.getText());
+                    testPane.setEntry(TestEntry.getTestEntry());
+                } else {
+                    int indexStyle = chosen.getSelectionModel().getSelectedIndex();
+                    PreviewPreferences preferences = Globals.prefs.getPreviewPreferences();
+                    preferences = new PreviewPreferences(preferences.getPreviewCycle(), indexStyle, preferences.getPreviewPanelDividerPosition(), preferences.isPreviewPanelEnabled(), preferences.getPreviewStyle(), preferences.getPreviewStyleDefault());
+
+                    testPane = new PreviewPanel(JabRefGUI.getMainFrame().getCurrentBasePanel(), new BibDatabaseContext(), Globals.getKeyPrefs(), preferences, dialogService, externalFileTypes);
+                    testPane.setEntry(TestEntry.getTestEntry());
+                    testPane.updateLayout(preferences);
+                }
 
-                });
+                DialogPane pane = new DialogPane();
+                pane.setContent(testPane);
+                dialogService.showCustomDialogAndWait(Localization.lang("Preview"), pane, ButtonType.OK);
 
             } catch (StringIndexOutOfBoundsException exception) {
                 LOGGER.warn("Parsing error.", exception);
-
-              DefaultTaskExecutor.runInJavaFXThread(()->  dialogService.showErrorDialogAndWait(Localization.lang("Parsing error"),
-                        Localization.lang("Parsing error") + ": " + Localization.lang("illegal backslash expression"),
-                        exception));
-
+                dialogService.showErrorDialogAndWait(Localization.lang("Parsing error"), Localization.lang("Parsing error") + ": " + Localization.lang("illegal backslash expression"), exception);
             }
         });
     }
@@ -167,9 +155,9 @@ private void setupGui() {
         btnLeft.setPrefSize(80, 20);
         btnUp.setPrefSize(80, 20);
         btnDown.setPrefSize(80, 20);
-        vBox.getChildren().addAll(new Label(""),  new Label(""), new Label(""), new Label(""), new Label(""),
-                new Label(""), new Label(""), btnRight, btnLeft, new Label(""), new Label(""), new Label(""),
-                btnUp, btnDown);
+        vBox.getChildren().addAll(new Label(""), new Label(""), new Label(""), new Label(""), new Label(""),
+                                  new Label(""), new Label(""), btnRight, btnLeft, new Label(""), new Label(""), new Label(""),
+                                  btnUp, btnDown);
         Label currentPreview = new Label(Localization.lang("Current Preview"));
         currentPreview.getStyleClass().add("sectionHeader");
         gridPane.add(currentPreview, 1, 1);
@@ -182,6 +170,7 @@ private void setupGui() {
         gridPane.add(scrollPane, 1, 9);
     }
 
+    @Override
     public Node getBuilder() {
         return gridPane;
     }
@@ -212,39 +201,17 @@ public void setValues() {
             availableModel.add(Localization.lang("Preview"));
         }
 
-        btnLeft.setDisable(!chosen.getSelectionModel().getSelectedItems().isEmpty());
-        btnRight.setDisable(available.getSelectionModel().getSelectedIndices().isEmpty());
-        btnUp.setDisable(!chosen.getSelectionModel().getSelectedIndices().isEmpty());
-        btnDown.setDisable(!chosen.getSelectionModel().getSelectedIndices().isEmpty());
-
-        if (discoverCitationStyleWorker != null) {
-            discoverCitationStyleWorker.cancel(true);
-        }
-
-        discoverCitationStyleWorker = new SwingWorker<List<CitationStyle>, Void>() {
-            @Override
-            protected List<CitationStyle> doInBackground() throws Exception {
-                return CitationStyle.discoverCitationStyles();
-            }
-
-            @Override
-            public void done() {
-                if (this.isCancelled()) {
-                    return;
-                }
-                try {
-                    get().stream()
-                            .filter(style -> !previewPreferences.getPreviewCycle().contains(style.getFilePath()))
-                            .sorted(Comparator.comparing(CitationStyle::getTitle))
-                            .forEach(availableModel::add);
-
-                    btnRight.setDisable(availableModel.isEmpty());
-                } catch (InterruptedException | ExecutionException e) {
-                    LOGGER.error("something went wrong while adding the discovered CitationStyles to the list ");
-                }
-            }
-        };
-        discoverCitationStyleWorker.execute();
+        BackgroundTask.wrap(() -> CitationStyle.discoverCitationStyles())
+                      .onSuccess(value -> {
+                          value.stream()
+                               .filter(style -> !previewPreferences.getPreviewCycle().contains(style.getFilePath()))
+                               .sorted(Comparator.comparing(CitationStyle::getTitle))
+                               .forEach(availableModel::add);
+                      })
+                      .onFailure(ex -> {
+                          LOGGER.error("something went wrong while adding the discovered CitationStyles to the list ", ex);
+                          dialogService.showErrorDialogAndWait(Localization.lang("Error adding discovered CitationStyles"), ex);
+                      }).executeWith(taskExecutor);
 
         layout.setText(Globals.prefs.getPreviewPreferences().getPreviewStyle().replace("__NEWLINE__", "\n"));
     }
@@ -252,6 +219,10 @@ public void done() {
     @Override
     public void storeSettings() {
         List<String> styles = new ArrayList<>();
+
+        if (chosenModel.isEmpty()) {
+            chosenModel.add(Localization.lang("Preview"));
+        }
         for (Object obj : chosenModel) {
             if (obj instanceof CitationStyle) {
                 styles.add(((CitationStyle) obj).getFilePath());
@@ -260,10 +231,10 @@ public void storeSettings() {
             }
         }
         PreviewPreferences previewPreferences = Globals.prefs.getPreviewPreferences()
-                .getBuilder()
-                .withPreviewCycle(styles)
-                .withPreviewStyle(layout.getText().replace("\n", "__NEWLINE__"))
-                .build();
+                                                             .getBuilder()
+                                                             .withPreviewCycle(styles)
+                                                             .withPreviewStyle(layout.getText().replace("\n", "__NEWLINE__"))
+                                                             .build();
         if (!chosen.getSelectionModel().isEmpty()) {
             previewPreferences = previewPreferences.getBuilder().withPreviewCyclePosition(chosen.getSelectionModel().getSelectedIndex()).build();
         }
diff --git a/src/main/java/org/jabref/preferences/PreviewPreferences.java b/src/main/java/org/jabref/preferences/PreviewPreferences.java
index 835b4fd7da7..c8d879e1a70 100644
--- a/src/main/java/org/jabref/preferences/PreviewPreferences.java
+++ b/src/main/java/org/jabref/preferences/PreviewPreferences.java
@@ -8,7 +8,7 @@
 public class PreviewPreferences {
 
     private final List<String> previewCycle;
-    private int previewCyclePosition;
+    private final int previewCyclePosition;
     private final Number previewPanelDividerPosition;
     private final boolean previewPanelEnabled;
     private final String previewStyle;
@@ -60,6 +60,7 @@ public LayoutFormatterPreferences getLayoutFormatterPreferences() {
     }
 
     public static class Builder {
+
         private List<String> previewCycle;
         private int previeCyclePosition;
         private Number previewPanelDividerPosition;
@@ -67,7 +68,6 @@ public static class Builder {
         private String previewStyle;
         private final String previewStyleDefault;
 
-
         public Builder(PreviewPreferences previewPreferences) {
             this.previewCycle = previewPreferences.getPreviewCycle();
             this.previeCyclePosition = previewPreferences.getPreviewCyclePosition();
@@ -83,11 +83,15 @@ public Builder withPreviewCycle(List<String> previewCycle) {
         }
 
         public Builder withPreviewCyclePosition(int position) {
-            previeCyclePosition = position;
-            while (previeCyclePosition < 0) {
-                previeCyclePosition += previewCycle.size();
+            if (previewCycle.isEmpty()) {
+                previeCyclePosition = 0;
+            } else {
+                previeCyclePosition = position;
+                while (previeCyclePosition < 0) {
+                    previeCyclePosition += previewCycle.size();
+                }
+                previeCyclePosition %= previewCycle.size();
             }
-            previeCyclePosition %= previewCycle.size();
             return this;
         }
 
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 5b5e6925b1e..6e5e0d1a2af 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2216,3 +2216,5 @@ File\ extension\:=File extension\:
 Export\ format\ name\:=Export format name\:
 
 Cleared\ connection\ settings=Cleared connection settings
+
+Error\ adding\ discovered\ CitationStyles=Error adding discovered CitationStyles

From 6fe2ebecc2fcc37f36c433f0af0bd5013ac8a7a3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 4 Feb 2019 13:12:17 +0100
Subject: [PATCH 012/184] Bump mysql-connector-java from 8.0.14 to 8.0.15
 (#4627)

Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.14 to 8.0.15.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.14...8.0.15)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9d93378e772..93cc91533ab 100644
--- a/build.gradle
+++ b/build.gradle
@@ -120,7 +120,7 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.7.2'
     compile 'org.antlr:antlr4-runtime:4.7.2'
 
-    compile 'mysql:mysql-connector-java:8.0.14'
+    compile 'mysql:mysql-connector-java:8.0.15'
 
     compile 'org.postgresql:postgresql:42.2.5'
 

From a0c2e04eae23659d04f5526e7bd9259e8b63ea23 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 4 Feb 2019 13:13:22 +0100
Subject: [PATCH 013/184] Bump mockito-core from 2.23.4 to 2.24.0 (#4626)

Bumps [mockito-core](https://github.com/mockito/mockito) from 2.23.4 to 2.24.0.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v2.23.4...v2.24.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 93cc91533ab..593a8d5ea02 100644
--- a/build.gradle
+++ b/build.gradle
@@ -170,7 +170,7 @@ dependencies {
     testCompile 'org.junit-pioneer:junit-pioneer:0.3.0'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.1'
-    testCompile 'org.mockito:mockito-core:2.23.4'
+    testCompile 'org.mockito:mockito-core:2.24.0'
     testCompile 'com.github.tomakehurst:wiremock:2.21.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'

From 1f792b6bcdcdbf0a2a4fb3602a93a005c1b6489d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 8 Feb 2019 08:51:00 +0100
Subject: [PATCH 014/184] Bump junit-jupiter-engine from 5.3.2 to 5.4.0 (#4635)

Bumps [junit-jupiter-engine](https://github.com/junit-team/junit5) from 5.3.2 to 5.4.0.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/compare/r5.3.2...r5.4.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 593a8d5ea02..aab40c01189 100644
--- a/build.gradle
+++ b/build.gradle
@@ -163,7 +163,7 @@ dependencies {
 
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.3.2'
     testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.2'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.3.2'
+    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.4.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.2'
     testCompile 'org.junit.platform:junit-platform-launcher:1.3.2'
 

From 6b52f5239fdfb3e060165a62e71ab6f3a886b481 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 8 Feb 2019 08:51:20 +0100
Subject: [PATCH 015/184] Bump junit-jupiter-api from 5.3.2 to 5.4.0 (#4639)

Bumps [junit-jupiter-api](https://github.com/junit-team/junit5) from 5.3.2 to 5.4.0.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/compare/r5.3.2...r5.4.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index aab40c01189..9c37bcd6e97 100644
--- a/build.gradle
+++ b/build.gradle
@@ -161,7 +161,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.0'
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.0'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.3.2'
+    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.4.0'
     testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.2'
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.4.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.2'

From 8d26b24f221da225e39c0b09d1721667e29d7c79 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 8 Feb 2019 08:51:54 +0100
Subject: [PATCH 016/184] Bump junit-platform-launcher from 1.3.2 to 1.4.0
 (#4636)

Bumps [junit-platform-launcher](https://github.com/junit-team/junit5) from 1.3.2 to 1.4.0.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/commits)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9c37bcd6e97..9971084fe12 100644
--- a/build.gradle
+++ b/build.gradle
@@ -165,7 +165,7 @@ dependencies {
     testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.2'
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.4.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.2'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.3.2'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
 
     testCompile 'org.junit-pioneer:junit-pioneer:0.3.0'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'

From 6bb14a35bf1eff3401f4bdb109e3e4dd504aab66 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 8 Feb 2019 08:53:42 +0100
Subject: [PATCH 017/184] Bump junit-vintage-engine from 5.3.2 to 5.4.0 (#4637)

Bumps [junit-vintage-engine](https://github.com/junit-team/junit5) from 5.3.2 to 5.4.0.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/compare/r5.3.2...r5.4.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9971084fe12..a667aea6be4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -164,7 +164,7 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.4.0'
     testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.2'
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.4.0'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.2'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.0'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
 
     testCompile 'org.junit-pioneer:junit-pioneer:0.3.0'

From c30896f8e93e5c5819d61dccd3a93588f8ff13de Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 8 Feb 2019 08:54:12 +0100
Subject: [PATCH 018/184] Bump junit-jupiter-params from 5.3.2 to 5.4.0 (#4638)

Bumps [junit-jupiter-params](https://github.com/junit-team/junit5) from 5.3.2 to 5.4.0.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/compare/r5.3.2...r5.4.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index a667aea6be4..827d519782f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -162,7 +162,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.0'
 
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.4.0'
-    testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.2'
+    testCompile 'org.junit.jupiter:junit-jupiter-params:5.4.0'
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.4.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.0'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'

From 891a93ba9ebfa1a820e60093a53eb45e0386e892 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 8 Feb 2019 10:39:13 +0100
Subject: [PATCH 019/184] Use 'junit-jupiter' aggregator module (#4640)

---
 build.gradle | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/build.gradle b/build.gradle
index 827d519782f..9464b267ca7 100644
--- a/build.gradle
+++ b/build.gradle
@@ -161,9 +161,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.0'
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.0'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.4.0'
-    testCompile 'org.junit.jupiter:junit-jupiter-params:5.4.0'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.4.0'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.0'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
 

From 935d625e2dcf58b8d6157567f12bd349accaff1e Mon Sep 17 00:00:00 2001
From: Ronak Lakhotia <ronak.lakhotia999@gmail.com>
Date: Fri, 8 Feb 2019 22:24:21 +0800
Subject: [PATCH 020/184] Add Integrity check for books with edition reported
 as 1

---
 .../java/org/jabref/logic/integrity/EditionChecker.java   | 8 +++++++-
 .../org/jabref/logic/integrity/IntegrityCheckTest.java    | 1 +
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/logic/integrity/EditionChecker.java b/src/main/java/org/jabref/logic/integrity/EditionChecker.java
index 54a1869bfe2..072c7a4a4f1 100644
--- a/src/main/java/org/jabref/logic/integrity/EditionChecker.java
+++ b/src/main/java/org/jabref/logic/integrity/EditionChecker.java
@@ -14,6 +14,7 @@ public class EditionChecker implements ValueChecker {
     private static final Predicate<String> FIRST_LETTER_CAPITALIZED = Pattern.compile("^[A-Z]").asPredicate();
     private static final Predicate<String> ONLY_NUMERALS_OR_LITERALS = Pattern.compile("^([0-9]+|[^0-9].+)$")
             .asPredicate();
+    private static final String FIRST_EDITION = "1";
 
     private final BibDatabaseContext bibDatabaseContextEdition;
 
@@ -44,10 +45,15 @@ public Optional<String> checkValue(String value) {
         }
 
         //BibTeX
-        if (!bibDatabaseContextEdition.isBiblatexMode() && !FIRST_LETTER_CAPITALIZED.test(value.trim())) {
+        if (!bibDatabaseContextEdition.isBiblatexMode() && !FIRST_LETTER_CAPITALIZED.test(value.trim()) &&
+                !value.equals(FIRST_EDITION)) {
             return Optional.of(Localization.lang("should have the first letter capitalized"));
         }
 
+        if (value.equals(FIRST_EDITION)) {
+            return Optional.of(Localization.lang("edition of book reported as just 1"));
+        }
+
         return Optional.empty();
     }
 }
diff --git a/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java b/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java
index 54a1d715e99..8fb2bb73aeb 100644
--- a/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java
+++ b/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java
@@ -86,6 +86,7 @@ void testEditionChecks() {
                 withMode(createContext("edition", "Third, revised and expanded edition"), BibDatabaseMode.BIBLATEX));
         assertCorrect(withMode(createContext("edition", "Edition 2000"), BibDatabaseMode.BIBLATEX));
         assertWrong(withMode(createContext("edition", "2nd"), BibDatabaseMode.BIBLATEX));
+        assertWrong(createContext("edition", "1"));
     }
 
     @Test

From 6da731c6c8da9a75af613144cae058a0303c7cc4 Mon Sep 17 00:00:00 2001
From: Ronak Lakhotia <ronak.lakhotia999@gmail.com>
Date: Fri, 8 Feb 2019 23:00:27 +0800
Subject: [PATCH 021/184] Edit localization file

---
 src/main/resources/l10n/JabRef_en.properties | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 6e5e0d1a2af..f8291d55412 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1986,6 +1986,7 @@ Sumatra\ Reader=Sumatra Reader
 shared=shared
 should\ contain\ an\ integer\ or\ a\ literal=should contain an integer or a literal
 should\ have\ the\ first\ letter\ capitalized=should have the first letter capitalized
+edition\ of\ book\ reported\ as\ just\ 1=edition of book reported as just 1
 Tools=Tools
 What\'s\ new\ in\ this\ version?=What\'s new in this version?
 Want\ to\ help?=Want to help?

From 71e02379a068756a3885aa22161337255683fca3 Mon Sep 17 00:00:00 2001
From: Akash Deep <akash1994deep@users.noreply.github.com>
Date: Sat, 9 Feb 2019 20:06:12 +0530
Subject: [PATCH 022/184] Fix for issue 4641: Remove usage of TempDirectory
 extension from junit-pioneer (#4644)

* Removed the TempDirectory extension from junit-pioneer with the built in
extension of junit 5.4

* Removed unused import
---
 build.gradle                                       |  4 ----
 .../externalfiles/AutoSetFileLinksUtilTest.java    |  6 ++----
 .../gui/fieldeditors/LinkedFileViewModelTest.java  |  6 ++----
 .../ManageJournalAbbreviationsViewModelTest.java   |  6 ++----
 .../gui/util/FileDialogConfigurationTest.java      |  8 +++-----
 .../jabref/logic/cleanup/CleanupWorkerTest.java    | 14 ++++++--------
 .../jabref/logic/cleanup/MoveFilesCleanupTest.java |  6 ++----
 .../jabref/logic/cleanup/RenamePdfCleanupTest.java | 14 ++++++--------
 .../logic/exporter/BibTeXMLExporterTestFiles.java  |  6 ++----
 .../jabref/logic/exporter/CsvExportFormatTest.java | 12 +++++-------
 .../logic/exporter/DocBook5ExporterTest.java       |  6 ++----
 .../org/jabref/logic/exporter/ExporterTest.java    | 10 ++++------
 .../logic/exporter/HtmlExportFormatTest.java       |  6 ++----
 .../logic/exporter/MSBibExportFormatTestFiles.java |  6 ++----
 .../logic/exporter/ModsExportFormatTest.java       |  6 ++----
 .../logic/exporter/ModsExportFormatTestFiles.java  |  6 ++----
 .../logic/exporter/MsBibExportFormatTest.java      |  6 ++----
 .../org/jabref/logic/exporter/XmpExporterTest.java | 12 +++++-------
 .../jabref/logic/integrity/IntegrityCheckTest.java |  6 ++----
 .../protectedterms/ProtectedTermsListTest.java     |  6 ++----
 .../protectedterms/ProtectedTermsLoaderTest.java   | 14 ++++++--------
 .../logic/util/io/CiteKeyBasedFileFinderTest.java  |  6 ++----
 .../org/jabref/logic/util/io/FileUtilTest.java     |  8 +++-----
 .../org/jabref/logic/xmp/XmpUtilWriterTest.java    |  8 +++-----
 24 files changed, 69 insertions(+), 119 deletions(-)

diff --git a/build.gradle b/build.gradle
index 9464b267ca7..fc1c0fec81d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -165,7 +165,6 @@ dependencies {
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.0'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
 
-    testCompile 'org.junit-pioneer:junit-pioneer:0.3.0'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.1'
     testCompile 'org.mockito:mockito-core:2.24.0'
@@ -190,9 +189,6 @@ dependencyUpdates {
     outputFormatter = "json"
 }
 
-//We have to use this as long as junit-pioneer has no official release
-dependencyUpdates.revision = 'integration'
-
 // We have some dependencies which cannot be updated due to various reasons.
 dependencyUpdates.resolutionStrategy = {
     componentSelection { rules ->
diff --git a/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java b/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java
index ae1b46fe557..54be381f4b5 100644
--- a/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java
+++ b/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java
@@ -16,15 +16,13 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
-@ExtendWith(TempDirectory.class)
 public class AutoSetFileLinksUtilTest {
 
     private final FilePreferences fileDirPrefs = mock(FilePreferences.class);
@@ -34,7 +32,7 @@ public class AutoSetFileLinksUtilTest {
     private final BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE);
 
     @BeforeEach
-    public void setUp(@TempDirectory.TempDir Path folder) throws Exception {
+    public void setUp(@TempDir Path folder) throws Exception {
         Path path = folder.resolve("CiteKey.pdf");
         Files.createFile(path);
         entry.setCiteKey("CiteKey");
diff --git a/src/test/java/org/jabref/gui/fieldeditors/LinkedFileViewModelTest.java b/src/test/java/org/jabref/gui/fieldeditors/LinkedFileViewModelTest.java
index a2fcce655cf..7a7893c6d79 100644
--- a/src/test/java/org/jabref/gui/fieldeditors/LinkedFileViewModelTest.java
+++ b/src/test/java/org/jabref/gui/fieldeditors/LinkedFileViewModelTest.java
@@ -17,8 +17,7 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Answers;
 
 import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -31,7 +30,6 @@
 import static org.mockito.Mockito.verifyZeroInteractions;
 import static org.mockito.Mockito.when;
 
-@ExtendWith(TempDirectory.class)
 class LinkedFileViewModelTest {
 
     private Path tempFile;
@@ -43,7 +41,7 @@ class LinkedFileViewModelTest {
     private DialogService dialogService;
 
     @BeforeEach
-    void setUp(@TempDirectory.TempDir Path tempFolder) throws Exception {
+    void setUp(@TempDir Path tempFolder) throws Exception {
         entry = new BibEntry();
         databaseContext = new BibDatabaseContext();
         taskExecutor = mock(TaskExecutor.class);
diff --git a/src/test/java/org/jabref/gui/journals/ManageJournalAbbreviationsViewModelTest.java b/src/test/java/org/jabref/gui/journals/ManageJournalAbbreviationsViewModelTest.java
index 77e7d20cc36..96f00ed4065 100644
--- a/src/test/java/org/jabref/gui/journals/ManageJournalAbbreviationsViewModelTest.java
+++ b/src/test/java/org/jabref/gui/journals/ManageJournalAbbreviationsViewModelTest.java
@@ -23,8 +23,7 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 
 import static org.jabref.logic.util.OS.NEWLINE;
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -37,7 +36,6 @@
 import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
 
-@ExtendWith(TempDirectory.class)
 class ManageJournalAbbreviationsViewModelTest {
 
     private ManageJournalAbbreviationsViewModel viewModel;
@@ -50,7 +48,7 @@ class ManageJournalAbbreviationsViewModelTest {
     private DialogService dialogService;
 
     @BeforeEach
-    void setUpViewModel(@TempDirectory.TempDir Path tempFolder) throws Exception {
+    void setUpViewModel(@TempDir Path tempFolder) throws Exception {
         abbreviationPreferences = mock(JournalAbbreviationPreferences.class);
         PreferencesService preferences = mock(PreferencesService.class);
         when(preferences.getJournalAbbreviationPreferences()).thenReturn(abbreviationPreferences);
diff --git a/src/test/java/org/jabref/gui/util/FileDialogConfigurationTest.java b/src/test/java/org/jabref/gui/util/FileDialogConfigurationTest.java
index 2a19e5593a6..5f608f0ef4a 100644
--- a/src/test/java/org/jabref/gui/util/FileDialogConfigurationTest.java
+++ b/src/test/java/org/jabref/gui/util/FileDialogConfigurationTest.java
@@ -12,16 +12,14 @@
 import org.jabref.logic.util.StandardFileType;
 
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
-@ExtendWith(TempDirectory.class)
 class FileDialogConfigurationTest {
 
     @Test
-    void testWithValidDirectoryString(@TempDirectory.TempDir Path folder) {
+    void testWithValidDirectoryString(@TempDir Path folder) {
         String tempFolder = folder.toAbsolutePath().toString();
 
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
@@ -31,7 +29,7 @@ void testWithValidDirectoryString(@TempDirectory.TempDir Path folder) {
     }
 
     @Test
-    void testWithValidDirectoryPath(@TempDirectory.TempDir Path tempFolder) {
+    void testWithValidDirectoryPath(@TempDir Path tempFolder) {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
                 .withInitialDirectory(tempFolder).build();
 
diff --git a/src/test/java/org/jabref/logic/cleanup/CleanupWorkerTest.java b/src/test/java/org/jabref/logic/cleanup/CleanupWorkerTest.java
index 567dffd1f6a..46431376144 100644
--- a/src/test/java/org/jabref/logic/cleanup/CleanupWorkerTest.java
+++ b/src/test/java/org/jabref/logic/cleanup/CleanupWorkerTest.java
@@ -34,8 +34,7 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Answers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -44,14 +43,13 @@
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
-@ExtendWith(TempDirectory.class)
 class CleanupWorkerTest {
 
     private final CleanupPreset emptyPreset = new CleanupPreset(EnumSet.noneOf(CleanupPreset.CleanupStep.class));
     private CleanupWorker worker;
 
     @BeforeEach
-    void setUp(@TempDirectory.TempDir Path bibFolder) throws IOException {
+    void setUp(@TempDir Path bibFolder) throws IOException {
 
         Path path = bibFolder.resolve("ARandomlyNamedFolder");
         Files.createDirectory(path);
@@ -82,7 +80,7 @@ void cleanupNullEntryThrowsException() {
     }
 
     @Test
-    void cleanupDoesNothingByDefault(@TempDirectory.TempDir Path bibFolder) throws IOException {
+    void cleanupDoesNothingByDefault(@TempDir Path bibFolder) throws IOException {
         BibEntry entry = new BibEntry();
         entry.setCiteKey("Toot");
         entry.setField("pdf", "aPdfFile");
@@ -220,7 +218,7 @@ void cleanupFixFileLinksMovesSingleDescriptionToLink() {
     }
 
     @Test
-    void cleanupMoveFilesMovesFileFromSubfolder(@TempDirectory.TempDir Path bibFolder) throws IOException {
+    void cleanupMoveFilesMovesFileFromSubfolder(@TempDir Path bibFolder) throws IOException {
         CleanupPreset preset = new CleanupPreset(CleanupPreset.CleanupStep.MOVE_PDF);
 
         Path path = bibFolder.resolve("AnotherRandomlyNamedFolder");
@@ -238,7 +236,7 @@ void cleanupMoveFilesMovesFileFromSubfolder(@TempDirectory.TempDir Path bibFolde
     }
 
     @Test
-    void cleanupRelativePathsConvertAbsoluteToRelativePath(@TempDirectory.TempDir Path bibFolder) throws IOException {
+    void cleanupRelativePathsConvertAbsoluteToRelativePath(@TempDir Path bibFolder) throws IOException {
         CleanupPreset preset = new CleanupPreset(CleanupPreset.CleanupStep.MAKE_PATHS_RELATIVE);
 
         Path path = bibFolder.resolve("AnotherRandomlyNamedFile");
@@ -254,7 +252,7 @@ void cleanupRelativePathsConvertAbsoluteToRelativePath(@TempDirectory.TempDir Pa
     }
 
     @Test
-    void cleanupRenamePdfRenamesRelativeFile(@TempDirectory.TempDir Path bibFolder) throws IOException {
+    void cleanupRenamePdfRenamesRelativeFile(@TempDir Path bibFolder) throws IOException {
         CleanupPreset preset = new CleanupPreset(CleanupPreset.CleanupStep.RENAME_PDF);
 
         Path path = bibFolder.resolve("AnotherRandomlyNamedFile.tmp");
diff --git a/src/test/java/org/jabref/logic/cleanup/MoveFilesCleanupTest.java b/src/test/java/org/jabref/logic/cleanup/MoveFilesCleanupTest.java
index 9e9d21bfbd0..bfb0501b11a 100644
--- a/src/test/java/org/jabref/logic/cleanup/MoveFilesCleanupTest.java
+++ b/src/test/java/org/jabref/logic/cleanup/MoveFilesCleanupTest.java
@@ -17,8 +17,7 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -26,7 +25,6 @@
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
-@ExtendWith(TempDirectory.class)
 class MoveFilesCleanupTest {
 
     private Path defaultFileFolder;
@@ -36,7 +34,7 @@ class MoveFilesCleanupTest {
     private FilePreferences filePreferences;
 
     @BeforeEach
-    void setUp(@TempDirectory.TempDir Path bibFolder) throws IOException {
+    void setUp(@TempDir Path bibFolder) throws IOException {
         // The folder where the files should be moved to
         defaultFileFolder = bibFolder.resolve("pdf");
         Files.createDirectory(defaultFileFolder);
diff --git a/src/test/java/org/jabref/logic/cleanup/RenamePdfCleanupTest.java b/src/test/java/org/jabref/logic/cleanup/RenamePdfCleanupTest.java
index eb027f824d0..53449106ff4 100644
--- a/src/test/java/org/jabref/logic/cleanup/RenamePdfCleanupTest.java
+++ b/src/test/java/org/jabref/logic/cleanup/RenamePdfCleanupTest.java
@@ -17,14 +17,12 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
-@ExtendWith(TempDirectory.class)
 class RenamePdfCleanupTest {
 
     private BibEntry entry;
@@ -33,7 +31,7 @@ class RenamePdfCleanupTest {
     private RenamePdfCleanup cleanup;
 
     @BeforeEach
-    void setUp(@TempDirectory.TempDir Path testFolder) {
+    void setUp(@TempDir Path testFolder) {
         Path path = testFolder.resolve("test.bib");
         MetaData metaData = new MetaData();
         BibDatabaseContext context = new BibDatabaseContext(new BibDatabase(), metaData, new Defaults());
@@ -51,7 +49,7 @@ void setUp(@TempDirectory.TempDir Path testFolder) {
      * Test for #466
      */
     @Test
-    void cleanupRenamePdfRenamesFileEvenIfOnlyDifferenceIsCase(@TempDirectory.TempDir Path testFolder) throws IOException {
+    void cleanupRenamePdfRenamesFileEvenIfOnlyDifferenceIsCase(@TempDir Path testFolder) throws IOException {
         Path path = testFolder.resolve("toot.tmp");
         Files.createFile(path);
 
@@ -66,7 +64,7 @@ void cleanupRenamePdfRenamesFileEvenIfOnlyDifferenceIsCase(@TempDirectory.TempDi
     }
 
     @Test
-    void cleanupRenamePdfRenamesWithMultipleFiles(@TempDirectory.TempDir Path testFolder) throws IOException {
+    void cleanupRenamePdfRenamesWithMultipleFiles(@TempDir Path testFolder) throws IOException {
         Path path = testFolder.resolve("Toot.tmp");
         Files.createFile(path);
 
@@ -84,7 +82,7 @@ void cleanupRenamePdfRenamesWithMultipleFiles(@TempDirectory.TempDir Path testFo
     }
 
     @Test
-    void cleanupRenamePdfRenamesFileStartingWithBibtexKey(@TempDirectory.TempDir Path testFolder) throws IOException {
+    void cleanupRenamePdfRenamesFileStartingWithBibtexKey(@TempDir Path testFolder) throws IOException {
         Path path = testFolder.resolve("Toot.tmp");
         Files.createFile(path);
 
@@ -100,7 +98,7 @@ void cleanupRenamePdfRenamesFileStartingWithBibtexKey(@TempDirectory.TempDir Pat
     }
 
     @Test
-    void cleanupRenamePdfRenamesFileInSameFolder(@TempDirectory.TempDir Path testFolder) throws IOException {
+    void cleanupRenamePdfRenamesFileInSameFolder(@TempDir Path testFolder) throws IOException {
         Path path = testFolder.resolve("Toot.pdf");
         Files.createFile(path);
         LinkedFile fileField = new LinkedFile("", "Toot.pdf", "PDF");
diff --git a/src/test/java/org/jabref/logic/exporter/BibTeXMLExporterTestFiles.java b/src/test/java/org/jabref/logic/exporter/BibTeXMLExporterTestFiles.java
index 85051a17351..a1513a6ee9f 100644
--- a/src/test/java/org/jabref/logic/exporter/BibTeXMLExporterTestFiles.java
+++ b/src/test/java/org/jabref/logic/exporter/BibTeXMLExporterTestFiles.java
@@ -18,10 +18,9 @@
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
 import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.api.io.TempDir;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.MethodSource;
-import org.junitpioneer.jupiter.TempDirectory;
 import org.mockito.Answers;
 import org.xmlunit.builder.Input;
 import org.xmlunit.builder.Input.Builder;
@@ -32,7 +31,6 @@
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.mockito.Mockito.mock;
 
-@ExtendWith(TempDirectory.class)
 public class BibTeXMLExporterTestFiles {
 
     private static Path resourceDir;
@@ -52,7 +50,7 @@ public static Stream<String> fileNames() throws IOException, URISyntaxException
     }
 
     @BeforeEach
-    public void setUp(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void setUp(@TempDir Path testFolder) throws Exception {
         databaseContext = new BibDatabaseContext();
         charset = StandardCharsets.UTF_8;
         bibtexmlExportFormat = new BibTeXMLExporter();
diff --git a/src/test/java/org/jabref/logic/exporter/CsvExportFormatTest.java b/src/test/java/org/jabref/logic/exporter/CsvExportFormatTest.java
index a408b035221..1450f3d8295 100644
--- a/src/test/java/org/jabref/logic/exporter/CsvExportFormatTest.java
+++ b/src/test/java/org/jabref/logic/exporter/CsvExportFormatTest.java
@@ -17,14 +17,12 @@
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Answers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.mock;
 
-@ExtendWith(TempDirectory.class)
 public class CsvExportFormatTest {
 
     public BibDatabaseContext databaseContext;
@@ -51,7 +49,7 @@ public void tearDown() {
     }
 
     @Test
-    public void testPerformExportForSingleAuthor(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void testPerformExportForSingleAuthor(@TempDir Path testFolder) throws Exception {
         Path path = testFolder.resolve("ThisIsARandomlyNamedFile");
 
         BibEntry entry = new BibEntry();
@@ -68,7 +66,7 @@ public void testPerformExportForSingleAuthor(@TempDirectory.TempDir Path testFol
     }
 
     @Test
-    public void testPerformExportForMultipleAuthors(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void testPerformExportForMultipleAuthors(@TempDir Path testFolder) throws Exception {
         Path path = testFolder.resolve("ThisIsARandomlyNamedFile");
 
         BibEntry entry = new BibEntry();
@@ -85,7 +83,7 @@ public void testPerformExportForMultipleAuthors(@TempDirectory.TempDir Path test
     }
 
     @Test
-    public void testPerformExportForSingleEditor(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void testPerformExportForSingleEditor(@TempDir Path testFolder) throws Exception {
         Path path = testFolder.resolve("ThisIsARandomlyNamedFile");
         File tmpFile = path.toFile();
         BibEntry entry = new BibEntry();
@@ -102,7 +100,7 @@ public void testPerformExportForSingleEditor(@TempDirectory.TempDir Path testFol
     }
 
     @Test
-    public void testPerformExportForMultipleEditors(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void testPerformExportForMultipleEditors(@TempDir Path testFolder) throws Exception {
         Path path = testFolder.resolve("ThisIsARandomlyNamedFile");
         File tmpFile = path.toFile();
         BibEntry entry = new BibEntry();
diff --git a/src/test/java/org/jabref/logic/exporter/DocBook5ExporterTest.java b/src/test/java/org/jabref/logic/exporter/DocBook5ExporterTest.java
index a97c72ef463..cd0fa728187 100644
--- a/src/test/java/org/jabref/logic/exporter/DocBook5ExporterTest.java
+++ b/src/test/java/org/jabref/logic/exporter/DocBook5ExporterTest.java
@@ -20,8 +20,7 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Answers;
 import org.xmlunit.builder.Input;
 import org.xmlunit.builder.Input.Builder;
@@ -32,7 +31,6 @@
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.mockito.Mockito.mock;
 
-@ExtendWith(TempDirectory.class)
 public class DocBook5ExporterTest {
 
     public BibDatabaseContext databaseContext;
@@ -68,7 +66,7 @@ public void setUp() throws URISyntaxException {
     }
 
     @Test
-    public void testPerformExportForSingleEntry(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void testPerformExportForSingleEntry(@TempDir Path testFolder) throws Exception {
 
         Path path = testFolder.resolve("ThisIsARandomlyNamedFile");
 
diff --git a/src/test/java/org/jabref/logic/exporter/ExporterTest.java b/src/test/java/org/jabref/logic/exporter/ExporterTest.java
index 67c7087f8da..ef33a47b167 100644
--- a/src/test/java/org/jabref/logic/exporter/ExporterTest.java
+++ b/src/test/java/org/jabref/logic/exporter/ExporterTest.java
@@ -16,16 +16,14 @@
 import org.jabref.model.entry.BibEntry;
 
 import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.api.io.TempDir;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.MethodSource;
-import org.junitpioneer.jupiter.TempDirectory;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 import static org.mockito.Mockito.mock;
 
-@ExtendWith(TempDirectory.class)
 public class ExporterTest {
 
     public BibDatabaseContext databaseContext;
@@ -56,7 +54,7 @@ private static Stream<Object[]> exportFormats() {
 
     @ParameterizedTest
     @MethodSource("exportFormats")
-    public void testExportingEmptyDatabaseYieldsEmptyFile(Exporter exportFormat, String name, @TempDirectory.TempDir Path testFolder) throws Exception {
+    public void testExportingEmptyDatabaseYieldsEmptyFile(Exporter exportFormat, String name, @TempDir Path testFolder) throws Exception {
         Path tmpFile = testFolder.resolve("ARandomlyNamedFile");
         Files.createFile(tmpFile);
         exportFormat.export(databaseContext, tmpFile, charset, entries);
@@ -65,7 +63,7 @@ public void testExportingEmptyDatabaseYieldsEmptyFile(Exporter exportFormat, Str
 
     @ParameterizedTest
     @MethodSource("exportFormats")
-    public void testExportingNullDatabaseThrowsNPE(Exporter exportFormat, String name, @TempDirectory.TempDir Path testFolder) {
+    public void testExportingNullDatabaseThrowsNPE(Exporter exportFormat, String name, @TempDir Path testFolder) {
         assertThrows(NullPointerException.class, () -> {
             Path tmpFile = testFolder.resolve("ARandomlyNamedFile");
             Files.createFile(tmpFile);
@@ -75,7 +73,7 @@ public void testExportingNullDatabaseThrowsNPE(Exporter exportFormat, String nam
 
     @ParameterizedTest
     @MethodSource("exportFormats")
-    public void testExportingNullEntriesThrowsNPE(Exporter exportFormat, String name, @TempDirectory.TempDir Path testFolder) {
+    public void testExportingNullEntriesThrowsNPE(Exporter exportFormat, String name, @TempDir Path testFolder) {
         assertThrows(NullPointerException.class, () -> {
             Path tmpFile = testFolder.resolve("ARandomlyNamedFile");
             Files.createFile(tmpFile);
diff --git a/src/test/java/org/jabref/logic/exporter/HtmlExportFormatTest.java b/src/test/java/org/jabref/logic/exporter/HtmlExportFormatTest.java
index 28067d99bde..3fa8628adba 100644
--- a/src/test/java/org/jabref/logic/exporter/HtmlExportFormatTest.java
+++ b/src/test/java/org/jabref/logic/exporter/HtmlExportFormatTest.java
@@ -16,14 +16,12 @@
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Answers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.mock;
 
-@ExtendWith(TempDirectory.class)
 public class HtmlExportFormatTest {
     public BibDatabaseContext databaseContext;
     public Charset charset;
@@ -55,7 +53,7 @@ public void tearDown() {
     }
 
     @Test
-    public void emitWellFormedHtml(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void emitWellFormedHtml(@TempDir Path testFolder) throws Exception {
         Path path = testFolder.resolve("ThisIsARandomlyNamedFile");
         exportFormat.export(databaseContext, path, charset, entries);
         List<String> lines = Files.readAllLines(path);
diff --git a/src/test/java/org/jabref/logic/exporter/MSBibExportFormatTestFiles.java b/src/test/java/org/jabref/logic/exporter/MSBibExportFormatTestFiles.java
index e1de292326a..1a5da06af9b 100644
--- a/src/test/java/org/jabref/logic/exporter/MSBibExportFormatTestFiles.java
+++ b/src/test/java/org/jabref/logic/exporter/MSBibExportFormatTestFiles.java
@@ -18,10 +18,9 @@
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
 import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.api.io.TempDir;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.MethodSource;
-import org.junitpioneer.jupiter.TempDirectory;
 import org.mockito.Answers;
 import org.xmlunit.builder.Input;
 import org.xmlunit.builder.Input.Builder;
@@ -32,7 +31,6 @@
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.mockito.Mockito.mock;
 
-@ExtendWith(TempDirectory.class)
 public class MSBibExportFormatTestFiles {
 
     private static Path resourceDir;
@@ -53,7 +51,7 @@ static Stream<String> fileNames() throws IOException, URISyntaxException {
     }
 
     @BeforeEach
-    void setUp(@TempDirectory.TempDir Path testFolder) throws Exception {
+    void setUp(@TempDir Path testFolder) throws Exception {
         databaseContext = new BibDatabaseContext();
         charset = StandardCharsets.UTF_8;
         msBibExportFormat = new MSBibExporter();
diff --git a/src/test/java/org/jabref/logic/exporter/ModsExportFormatTest.java b/src/test/java/org/jabref/logic/exporter/ModsExportFormatTest.java
index 2d797d4e8de..65ae6465295 100644
--- a/src/test/java/org/jabref/logic/exporter/ModsExportFormatTest.java
+++ b/src/test/java/org/jabref/logic/exporter/ModsExportFormatTest.java
@@ -14,14 +14,12 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Answers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.mock;
 
-@ExtendWith(TempDirectory.class)
 public class ModsExportFormatTest {
 
     public Charset charset;
@@ -38,7 +36,7 @@ public void setUp() throws Exception {
     }
 
     @Test
-    public final void exportForNoEntriesWritesNothing(@TempDirectory.TempDir Path tempFile) throws Exception {
+    public final void exportForNoEntriesWritesNothing(@TempDir Path tempFile) throws Exception {
         Path file = tempFile.resolve("ThisIsARandomlyNamedFile");
         Files.createFile(file);
         modsExportFormat.export(databaseContext, tempFile, charset, Collections.emptyList());
diff --git a/src/test/java/org/jabref/logic/exporter/ModsExportFormatTestFiles.java b/src/test/java/org/jabref/logic/exporter/ModsExportFormatTestFiles.java
index 009c9f461ac..3834d7895d9 100644
--- a/src/test/java/org/jabref/logic/exporter/ModsExportFormatTestFiles.java
+++ b/src/test/java/org/jabref/logic/exporter/ModsExportFormatTestFiles.java
@@ -18,10 +18,9 @@
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
 import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.api.io.TempDir;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.MethodSource;
-import org.junitpioneer.jupiter.TempDirectory;
 import org.mockito.Answers;
 import org.mockito.Mockito;
 import org.xmlunit.builder.Input;
@@ -33,7 +32,6 @@
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.mockito.Mockito.mock;
 
-@ExtendWith(TempDirectory.class)
 public class ModsExportFormatTestFiles {
 
     private static Path resourceDir;
@@ -57,7 +55,7 @@ public static Stream<String> fileNames() throws Exception {
     }
 
     @BeforeEach
-    public void setUp(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void setUp(@TempDir Path testFolder) throws Exception {
         databaseContext = new BibDatabaseContext();
         charset = StandardCharsets.UTF_8;
         modsExportFormat = new ModsExporter();
diff --git a/src/test/java/org/jabref/logic/exporter/MsBibExportFormatTest.java b/src/test/java/org/jabref/logic/exporter/MsBibExportFormatTest.java
index 103d7c4996b..9ddbe119d73 100644
--- a/src/test/java/org/jabref/logic/exporter/MsBibExportFormatTest.java
+++ b/src/test/java/org/jabref/logic/exporter/MsBibExportFormatTest.java
@@ -13,12 +13,10 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
-@ExtendWith(TempDirectory.class)
 public class MsBibExportFormatTest {
 
     public BibDatabaseContext databaseContext;
@@ -33,7 +31,7 @@ public void setUp() throws Exception {
     }
 
     @Test
-    public final void testPerformExportWithNoEntry(@TempDirectory.TempDir Path tempFile) throws IOException, SaveException {
+    public final void testPerformExportWithNoEntry(@TempDir Path tempFile) throws IOException, SaveException {
         Path path = tempFile.resolve("ThisIsARandomlyNamedFile");
         Files.createFile(path);
         List<BibEntry> entries = Collections.emptyList();
diff --git a/src/test/java/org/jabref/logic/exporter/XmpExporterTest.java b/src/test/java/org/jabref/logic/exporter/XmpExporterTest.java
index d06fc91e374..d24b3725624 100644
--- a/src/test/java/org/jabref/logic/exporter/XmpExporterTest.java
+++ b/src/test/java/org/jabref/logic/exporter/XmpExporterTest.java
@@ -18,15 +18,13 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Answers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
-@ExtendWith(TempDirectory.class)
 public class XmpExporterTest {
 
     private Exporter exporter;
@@ -48,7 +46,7 @@ public void setUp() {
     }
 
     @Test
-    public void exportSingleEntry(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void exportSingleEntry(@TempDir Path testFolder) throws Exception {
         Path file = testFolder.resolve("ThisIsARandomlyNamedFile");
         Files.createFile(file);
 
@@ -76,7 +74,7 @@ public void exportSingleEntry(@TempDirectory.TempDir Path testFolder) throws Exc
     }
 
     @Test
-    public void writeMultipleEntriesInASingleFile(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void writeMultipleEntriesInASingleFile(@TempDir Path testFolder) throws Exception {
         Path file = testFolder.resolve("ThisIsARandomlyNamedFile");
         Files.createFile(file);
 
@@ -128,7 +126,7 @@ public void writeMultipleEntriesInASingleFile(@TempDirectory.TempDir Path testFo
     }
 
     @Test
-    public void writeMultipleEntriesInDifferentFiles(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void writeMultipleEntriesInDifferentFiles(@TempDir Path testFolder) throws Exception {
         Path file = testFolder.resolve("split");
         Files.createFile(file);
 
@@ -194,7 +192,7 @@ public void writeMultipleEntriesInDifferentFiles(@TempDirectory.TempDir Path tes
     }
 
     @Test
-    public void exportSingleEntryWithPrivacyFilter(@TempDirectory.TempDir Path testFolder) throws Exception {
+    public void exportSingleEntryWithPrivacyFilter(@TempDir Path testFolder) throws Exception {
         when(xmpPreferences.getXmpPrivacyFilter()).thenReturn(Arrays.asList("author"));
         when(xmpPreferences.isUseXMPPrivacyFilter()).thenReturn(true);
 
diff --git a/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java b/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java
index 54a1d715e99..8884604b67c 100644
--- a/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java
+++ b/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java
@@ -23,8 +23,7 @@
 import org.jabref.model.metadata.MetaData;
 
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Mockito;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -32,7 +31,6 @@
 import static org.mockito.Matchers.any;
 import static org.mockito.Mockito.mock;
 
-@ExtendWith(TempDirectory.class)
 class IntegrityCheckTest {
 
     @Test
@@ -220,7 +218,7 @@ void testFileChecks() {
     }
 
     @Test
-    void fileCheckFindsFilesRelativeToBibFile(@TempDirectory.TempDir Path testFolder) throws IOException {
+    void fileCheckFindsFilesRelativeToBibFile(@TempDir Path testFolder) throws IOException {
         Path bibFile = testFolder.resolve("lit.bib");
         Files.createFile(bibFile);
         Path pdfFile = testFolder.resolve("file.pdf");
diff --git a/src/test/java/org/jabref/logic/protectedterms/ProtectedTermsListTest.java b/src/test/java/org/jabref/logic/protectedterms/ProtectedTermsListTest.java
index c8fbdf7f7e6..54109db5c86 100644
--- a/src/test/java/org/jabref/logic/protectedterms/ProtectedTermsListTest.java
+++ b/src/test/java/org/jabref/logic/protectedterms/ProtectedTermsListTest.java
@@ -8,21 +8,19 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
-@ExtendWith(TempDirectory.class)
 public class ProtectedTermsListTest {
 
     private ProtectedTermsList internalList;
     private ProtectedTermsList externalList;
 
     @BeforeEach
-    public void setUp(@TempDirectory.TempDir Path temporaryFolder) throws IOException {
+    public void setUp(@TempDir Path temporaryFolder) throws IOException {
         Path path = temporaryFolder.resolve("ThisIsARandomlyNamedFile");
         Files.createFile(path);
         String tempFileName = path.toString();
diff --git a/src/test/java/org/jabref/logic/protectedterms/ProtectedTermsLoaderTest.java b/src/test/java/org/jabref/logic/protectedterms/ProtectedTermsLoaderTest.java
index 0cc24dc3b8a..b08c1c3546d 100644
--- a/src/test/java/org/jabref/logic/protectedterms/ProtectedTermsLoaderTest.java
+++ b/src/test/java/org/jabref/logic/protectedterms/ProtectedTermsLoaderTest.java
@@ -14,14 +14,12 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
-@ExtendWith(TempDirectory.class)
 class ProtectedTermsLoaderTest {
 
     private ProtectedTermsLoader loader;
@@ -166,7 +164,7 @@ void testDoNotLoadTheSameInternalListTwice() {
     }
 
     @Test
-    void testAddNewTermListAddsList(@TempDirectory.TempDir Path tempDir) {
+    void testAddNewTermListAddsList(@TempDir Path tempDir) {
 
         ProtectedTermsLoader localLoader = new ProtectedTermsLoader(
                 new ProtectedTermsPreferences(Collections.emptyList(), Collections.emptyList(),
@@ -176,7 +174,7 @@ void testAddNewTermListAddsList(@TempDirectory.TempDir Path tempDir) {
     }
 
     @Test
-    void testAddNewTermListNewListInList(@TempDirectory.TempDir Path tempDir) {
+    void testAddNewTermListNewListInList(@TempDir Path tempDir) {
 
         ProtectedTermsLoader localLoader = new ProtectedTermsLoader(
                 new ProtectedTermsPreferences(Collections.emptyList(), Collections.emptyList(),
@@ -187,7 +185,7 @@ void testAddNewTermListNewListInList(@TempDirectory.TempDir Path tempDir) {
     }
 
     @Test
-    void testRemoveTermList(@TempDirectory.TempDir Path tempDir) {
+    void testRemoveTermList(@TempDir Path tempDir) {
 
         ProtectedTermsLoader localLoader = new ProtectedTermsLoader(
                 new ProtectedTermsPreferences(Collections.emptyList(), Collections.emptyList(),
@@ -197,7 +195,7 @@ void testRemoveTermList(@TempDirectory.TempDir Path tempDir) {
     }
 
     @Test
-    void testRemoveTermListReduceTheCount(@TempDirectory.TempDir Path tempDir) {
+    void testRemoveTermListReduceTheCount(@TempDir Path tempDir) {
 
         ProtectedTermsLoader localLoader = new ProtectedTermsLoader(
                 new ProtectedTermsPreferences(Collections.emptyList(), Collections.emptyList(),
@@ -209,7 +207,7 @@ void testRemoveTermListReduceTheCount(@TempDirectory.TempDir Path tempDir) {
     }
 
     @Test
-    void testAddNewTermListSetsCorrectDescription(@TempDirectory.TempDir Path tempDir) {
+    void testAddNewTermListSetsCorrectDescription(@TempDir Path tempDir) {
 
         ProtectedTermsLoader localLoader = new ProtectedTermsLoader(
                 new ProtectedTermsPreferences(Collections.emptyList(), Collections.emptyList(),
diff --git a/src/test/java/org/jabref/logic/util/io/CiteKeyBasedFileFinderTest.java b/src/test/java/org/jabref/logic/util/io/CiteKeyBasedFileFinderTest.java
index 70c8ea51941..67e5147665e 100644
--- a/src/test/java/org/jabref/logic/util/io/CiteKeyBasedFileFinderTest.java
+++ b/src/test/java/org/jabref/logic/util/io/CiteKeyBasedFileFinderTest.java
@@ -12,12 +12,10 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
-@ExtendWith(TempDirectory.class)
 class CiteKeyBasedFileFinderTest {
 
     private BibEntry entry;
@@ -28,7 +26,7 @@ class CiteKeyBasedFileFinderTest {
     private Path pdfFile;
 
     @BeforeEach
-    void setUp(@TempDirectory.TempDir Path temporaryFolder) throws IOException {
+    void setUp(@TempDir Path temporaryFolder) throws IOException {
         entry = new BibEntry(BibtexEntryTypes.ARTICLE);
         entry.setCiteKey("HipKro03");
 
diff --git a/src/test/java/org/jabref/logic/util/io/FileUtilTest.java b/src/test/java/org/jabref/logic/util/io/FileUtilTest.java
index 4103e8b7d23..386ab268e08 100644
--- a/src/test/java/org/jabref/logic/util/io/FileUtilTest.java
+++ b/src/test/java/org/jabref/logic/util/io/FileUtilTest.java
@@ -18,8 +18,7 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Answers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -29,7 +28,6 @@
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.Mockito.mock;
 
-@ExtendWith(TempDirectory.class)
 class FileUtilTest {
     private final Path nonExistingTestPath = Paths.get("nonExistingTestPath");
     private Path existingTestFile;
@@ -38,7 +36,7 @@ class FileUtilTest {
     private Path rootDir;
 
     @BeforeEach
-    void setUpViewModel(@TempDirectory.TempDir Path temporaryFolder) throws IOException {
+    void setUpViewModel(@TempDir Path temporaryFolder) throws IOException {
         rootDir = temporaryFolder;
         Path subDir = rootDir.resolve("1");
         Files.createDirectory(subDir);
@@ -322,7 +320,7 @@ void testRenameFileWithFromFileExistAndOtherToFileExist() {
     }
 
     @Test
-    void testRenameFileSuccessful(@TempDirectory.TempDir Path otherTemporaryFolder) {
+    void testRenameFileSuccessful(@TempDir Path otherTemporaryFolder) {
         // Be careful. This "otherTemporaryFolder" is the same as the "temporaryFolder"
         // in the @BeforeEach method.
         Path temp = Paths.get(otherTemporaryFolder.resolve("123").toString());
diff --git a/src/test/java/org/jabref/logic/xmp/XmpUtilWriterTest.java b/src/test/java/org/jabref/logic/xmp/XmpUtilWriterTest.java
index f3d57c6bfae..4de6513ca4f 100644
--- a/src/test/java/org/jabref/logic/xmp/XmpUtilWriterTest.java
+++ b/src/test/java/org/jabref/logic/xmp/XmpUtilWriterTest.java
@@ -15,14 +15,12 @@
 import org.apache.pdfbox.pdmodel.PDPage;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junitpioneer.jupiter.TempDirectory;
+import org.junit.jupiter.api.io.TempDir;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
-@ExtendWith(TempDirectory.class)
 class XmpUtilWriterTest {
 
     private static BibEntry olly2018;
@@ -94,7 +92,7 @@ void setUp() {
      * Test for writing a PDF file with a single DublinCore metadata entry.
      */
     @Test
-    void testWriteXmp(@TempDirectory.TempDir Path tempDir) throws IOException, TransformerException {
+    void testWriteXmp(@TempDir Path tempDir) throws IOException, TransformerException {
 
         Path pdfFile = this.createDefaultFile("JabRef_writeSingle.pdf", tempDir);
 
@@ -118,7 +116,7 @@ void testWriteXmp(@TempDirectory.TempDir Path tempDir) throws IOException, Trans
      * Test, which writes multiple metadata entries to a PDF and reads them again to test the size.
      */
     @Test
-    void testWriteMultipleBibEntries(@TempDirectory.TempDir Path tempDir) throws IOException, TransformerException {
+    void testWriteMultipleBibEntries(@TempDir Path tempDir) throws IOException, TransformerException {
 
         Path pdfFile = this.createDefaultFile("JabRef_writeMultiple.pdf", tempDir);
 

From 8e7b1f952ea08f2719f48f8eea7b2a1129865845 Mon Sep 17 00:00:00 2001
From: shubhamatlani <shubhamatlani@gmail.com>
Date: Sun, 10 Feb 2019 03:28:22 +0530
Subject: [PATCH 023/184] Automatically created groups with Field to group by
 as entrytype (#4539) (#4555)

* Filter automatically created groups by entrytype (#4539)

* Address review comments - replace for loop with stream (#4539)

* return value in case of unknown entry type (#4539)
---
 CHANGELOG.md                                          |  1 +
 src/main/java/org/jabref/model/entry/BibEntry.java    | 11 ++++++++++-
 .../org/jabref/model/groups/WordKeywordGroup.java     | 11 +++++++++++
 3 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9c29a663c2b..26e4ebbf307 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -48,6 +48,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
 - We added an option in the preference dialog box that allows user to choose behavior after dragging and dropping files in Entry Editor. [#4356](https://github.com/JabRef/jabref/issues/4356)
 - We added the ability to have an export preference where previously "File"-->"Export"/"Export selected entries" would not save the user's preference[#4495](https://github.com/JabRef/jabref/issues/4495)
+- For automatically created groups, added ability to filter groups by entry type. [#4539](https://github.com/JabRef/jabref/issues/4539)
 - We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added the ability change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)
diff --git a/src/main/java/org/jabref/model/entry/BibEntry.java b/src/main/java/org/jabref/model/entry/BibEntry.java
index bfd5182bd11..4e133b759cf 100644
--- a/src/main/java/org/jabref/model/entry/BibEntry.java
+++ b/src/main/java/org/jabref/model/entry/BibEntry.java
@@ -792,7 +792,7 @@ private void invalidateFieldCache(String fieldName) {
     }
 
     public Optional<String> getLatexFreeField(String name) {
-        if (!hasField(name)) {
+        if (!hasField(name) && !TYPE_HEADER.equals(name)) {
             return Optional.empty();
         } else if (latexFreeFields.containsKey(name)) {
             return Optional.ofNullable(latexFreeFields.get(toLowerCase(name)));
@@ -801,6 +801,15 @@ public Optional<String> getLatexFreeField(String name) {
             Optional<String> citeKey = getCiteKeyOptional();
             latexFreeFields.put(name, citeKey.get());
             return citeKey;
+        } else if (TYPE_HEADER.equals(name)) {
+            Optional<EntryType> entryType = EntryTypes.getType(getType(), BibDatabaseMode.BIBLATEX);
+            if (entryType.isPresent()) {
+                String entryName = entryType.get().getName();
+                latexFreeFields.put(name, entryName);
+                return Optional.of(entryName);
+            } else {
+                return Optional.of(StringUtil.capitalizeFirst(getType()));
+            }
         } else {
             String latexFreeField = LatexToUnicodeAdapter.format(getField(name).get()).intern();
             latexFreeFields.put(name, latexFreeField);
diff --git a/src/main/java/org/jabref/model/groups/WordKeywordGroup.java b/src/main/java/org/jabref/model/groups/WordKeywordGroup.java
index 5353f8e65af..35a5912c332 100644
--- a/src/main/java/org/jabref/model/groups/WordKeywordGroup.java
+++ b/src/main/java/org/jabref/model/groups/WordKeywordGroup.java
@@ -6,10 +6,15 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Objects;
+import java.util.Optional;
 import java.util.Set;
+import java.util.stream.Collectors;
 
+import org.jabref.model.EntryTypes;
 import org.jabref.model.FieldChange;
+import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.EntryType;
 import org.jabref.model.entry.KeywordList;
 import org.jabref.model.strings.StringUtil;
 
@@ -113,6 +118,12 @@ public boolean contains(BibEntry entry) {
 
     private Set<String> getFieldContentAsWords(BibEntry entry) {
         if (onlySplitWordsAtSeparator) {
+            if (BibEntry.TYPE_HEADER.equals(searchField)) {
+                Optional<EntryType> entryType = EntryTypes.getType(entry.getType(), BibDatabaseMode.BIBLATEX);
+                if (entryType.isPresent()) {
+                    return searchWords.stream().filter(sw -> entryType.get().getName().equals(sw)).collect(Collectors.toSet());
+                }
+            }
             return entry.getField(searchField)
                     .map(content -> KeywordList.parse(content, keywordSeparator).toStringList())
                     .orElse(Collections.emptySet());

From b858a2c02ab8c97f817a2ab4c96cd0ff110db6ae Mon Sep 17 00:00:00 2001
From: Ronak Lakhotia <ronak.lakhotia999@gmail.com>
Date: Sun, 10 Feb 2019 20:41:13 +0800
Subject: [PATCH 024/184] Reorder conditional checks

---
 .../org/jabref/logic/integrity/EditionChecker.java    | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/main/java/org/jabref/logic/integrity/EditionChecker.java b/src/main/java/org/jabref/logic/integrity/EditionChecker.java
index 072c7a4a4f1..c382fe7eab1 100644
--- a/src/main/java/org/jabref/logic/integrity/EditionChecker.java
+++ b/src/main/java/org/jabref/logic/integrity/EditionChecker.java
@@ -39,21 +39,20 @@ public Optional<String> checkValue(String value) {
             return Optional.empty();
         }
 
+        if (value.equals(FIRST_EDITION)) {
+            return Optional.of(Localization.lang("edition of book reported as just 1"));
+        }
+
         //biblatex
         if (bibDatabaseContextEdition.isBiblatexMode() && !ONLY_NUMERALS_OR_LITERALS.test(value.trim())) {
             return Optional.of(Localization.lang("should contain an integer or a literal"));
         }
 
         //BibTeX
-        if (!bibDatabaseContextEdition.isBiblatexMode() && !FIRST_LETTER_CAPITALIZED.test(value.trim()) &&
-                !value.equals(FIRST_EDITION)) {
+        if (!bibDatabaseContextEdition.isBiblatexMode() && !FIRST_LETTER_CAPITALIZED.test(value.trim())) {
             return Optional.of(Localization.lang("should have the first letter capitalized"));
         }
 
-        if (value.equals(FIRST_EDITION)) {
-            return Optional.of(Localization.lang("edition of book reported as just 1"));
-        }
-
         return Optional.empty();
     }
 }

From 8520833e684aa9e305dd8745e45696ffd6d984fb Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Sun, 10 Feb 2019 13:47:48 +0100
Subject: [PATCH 025/184] Remove old code for PDF import (#4634)

* Remove old code for PDF import

* Fix tests

* Update Docbook5ExportFormat.xml

* Fix tests

* Fix checkstyle
---
 .../jabref/gui/DuplicateResolverDialog.java   |   4 +-
 .../java/org/jabref/gui/DuplicateSearch.java  |   4 +-
 src/main/java/org/jabref/gui/EntryType.fxml   |  76 +--
 src/main/java/org/jabref/gui/JabRefFrame.java |  26 +-
 .../java/org/jabref/gui/PreviewPanel.java     |  21 +-
 .../java/org/jabref/gui/SidePaneManager.java  |   8 +-
 .../ResolveDuplicateLabelDialog.java          |   2 +-
 .../jabref/gui/copyfiles/CopyFilesTask.java   |   1 -
 .../jabref/gui/entryeditor/EntryEditor.java   |  28 +-
 .../org/jabref/gui/entryeditor/SourceTab.java |   2 +-
 .../exporter/CreateModifyExporterDialog.fxml  |  76 +--
 .../CreateModifyExporterDialogView.java       |   8 +-
 .../CreateModifyExporterDialogViewModel.java  |  13 +-
 .../jabref/gui/exporter/ExportCommand.java    |   4 +-
 .../exporter/ExportCustomizationDialog.fxml   |  39 +-
 .../ExportCustomizationDialogViewModel.java   |   3 +-
 .../gui/exporter/ExportToClipboardAction.java |  12 +-
 .../gui/exporter/ExporterViewModel.java       |   3 -
 .../gui/exporter/SaveDatabaseAction.java      |   4 +-
 .../gui/externalfiles/DroppedFileHandler.java | 568 ------------------
 .../ExternalFilesEntryLinker.java             |  20 +-
 .../gui/externalfiles/FindFullTextAction.java |  10 +-
 .../FindUnlinkedFilesDialog.java              |  96 +--
 .../gui/externalfiles/ImportHandler.java      | 113 ++++
 .../externalfiles/NewDroppedFileHandler.java  | 152 -----
 .../externalfiletype/ExternalFileTypes.java   |   3 +-
 .../EntryFromExternalFileCreator.java         |  36 --
 .../gui/importer/EntryFromFileCreator.java    | 186 ------
 .../importer/EntryFromFileCreatorManager.java | 202 -------
 .../gui/importer/EntryFromPDFCreator.java     |  62 --
 .../gui/importer/ImportInspectionDialog.java  |  11 +-
 .../gui/importer/UnlinkedFilesCrawler.java    |   5 +-
 .../org/jabref/gui/maintable/MainTable.java   |  38 +-
 .../PersistenceVisualStateTable.java          |   2 +-
 .../gui/openoffice/AdvancedCiteDialog.fxml    |  41 +-
 .../openoffice/AdvancedCiteDialogView.java    |   1 -
 .../openoffice/CitationEntryViewModel.java    |   1 -
 .../DetectOpenOfficeInstallation.java         |  10 +-
 .../gui/openoffice/ManageCitationsDialog.fxml |  29 +-
 .../openoffice/ManageCitationsDialogView.java |   4 +-
 .../ManageCitationsDialogViewModel.java       |   8 +-
 .../gui/openoffice/ManualConnectDialog.fxml   |  68 ++-
 .../openoffice/ManualConnectDialogView.java   |   5 +-
 .../ManualConnectDialogViewModel.java         |  10 +-
 .../org/jabref/gui/openoffice/OOBibBase.java  | 444 +++++++-------
 .../gui/openoffice/OpenOfficePanel.java       | 135 ++---
 .../gui/openoffice/StyleSelectDialog.fxml     |  60 +-
 .../gui/openoffice/StyleSelectDialogView.java |  51 +-
 .../StyleSelectDialogViewModel.java           |  15 +-
 .../openoffice/StyleSelectItemViewModel.java  |   1 -
 .../gui/preferences/ImportSettingsTab.java    |  60 --
 .../gui/preferences/PreferencesDialog.java    |  44 +-
 .../gui/preferences/PreviewPrefsTab.java      |   4 +-
 .../gui/preferences/TableColumnsTab.java      |  94 ++-
 .../java/org/jabref/gui/util/BaseDialog.java  |   6 +-
 .../jabref/gui/util/FileFilterConverter.java  |  23 +-
 .../org/jabref/gui/util/ZipFileChooser.java   |   2 +-
 .../comparator/ReadStatusFieldComparator.java |   1 -
 .../logic/exporter/ExporterFactory.java       |   2 +-
 .../logic/exporter/TemplateExporter.java      |  11 +-
 .../ExternalFilesContentImporter.java         |  11 +-
 .../importer/fileformat/BibtexParser.java     |   3 +-
 .../importer/fileformat/MedlineImporter.java  |   2 +-
 .../fileformat/MedlinePlainImporter.java      |   2 +-
 .../fileformat/PdfContentImporter.java        |   3 +
 .../layout/format/CreateDocBook4Authors.java  |   2 -
 .../layout/format/CreateDocBook5Authors.java  |   2 -
 .../layout/format/CreateDocBook5Editors.java  |   2 -
 .../layout/format/DocBookAuthorFormatter.java |  13 +-
 .../jabref/logic/openoffice/OOBibStyle.java   |   3 +-
 .../openoffice/OpenOfficePreferences.java     |   6 +-
 .../org/jabref/logic/util/io/FileUtil.java    |   4 +-
 .../org/jabref/logic/xmp/XmpUtilReader.java   |   7 +-
 .../java/org/jabref/model/entry/BibEntry.java |   4 +-
 .../org/jabref/model/entry/LinkedFile.java    |   8 +
 .../org/jabref/model/util/FileHelper.java     |   2 +-
 .../org/jabref/pdfimport/ImportDialog.java    | 235 --------
 .../org/jabref/pdfimport/PdfFileFilter.java   |  28 -
 .../org/jabref/pdfimport/PdfImporter.java     | 256 --------
 .../jabref/preferences/JabRefPreferences.java |  31 +-
 .../preferences/PreferencesService.java       |   4 +-
 src/main/resources/l10n/JabRef_en.properties  |  45 --
 .../architecture/TestArchitectureTests.java   |   1 -
 .../EntryFromFileCreatorManagerTest.java      |  85 ---
 .../gui/importer/EntryFromPDFCreatorTest.java |  59 --
 .../org/jabref/logic/TypedBibEntryTest.java   |   4 +-
 .../logic/exporter/DocBook5ExporterTest.java  |   6 +-
 .../importer/fileformat/BibtexParserTest.java |   2 +-
 .../fileformat/PdfContentImporterTest.java    |  15 +-
 .../PdfContentImporterTestFiles.java          |   8 +-
 .../org/jabref/logic/layout/LayoutTest.java   |   2 +-
 .../pdf/EntryAnnotationImporterTest.java      |   2 +-
 .../jabref/logic/xmp/XmpUtilReaderTest.java   |  15 +-
 .../jabref/logic/xmp/XmpUtilWriterTest.java   |   8 +-
 .../model/database/BibDatabaseTest.java       |   2 +-
 .../logic/exporter/Docbook5ExportFormat.xml   |   2 +-
 96 files changed, 970 insertions(+), 2882 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/externalfiles/DroppedFileHandler.java
 create mode 100644 src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
 delete mode 100644 src/main/java/org/jabref/gui/externalfiles/NewDroppedFileHandler.java
 delete mode 100644 src/main/java/org/jabref/gui/importer/EntryFromExternalFileCreator.java
 delete mode 100644 src/main/java/org/jabref/gui/importer/EntryFromFileCreator.java
 delete mode 100644 src/main/java/org/jabref/gui/importer/EntryFromFileCreatorManager.java
 delete mode 100644 src/main/java/org/jabref/gui/importer/EntryFromPDFCreator.java
 delete mode 100644 src/main/java/org/jabref/pdfimport/ImportDialog.java
 delete mode 100644 src/main/java/org/jabref/pdfimport/PdfFileFilter.java
 delete mode 100644 src/main/java/org/jabref/pdfimport/PdfImporter.java
 delete mode 100644 src/test/java/org/jabref/gui/importer/EntryFromFileCreatorManagerTest.java
 delete mode 100644 src/test/java/org/jabref/gui/importer/EntryFromPDFCreatorTest.java

diff --git a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
index cb34df3d202..0be0d823c83 100644
--- a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
+++ b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
@@ -68,7 +68,7 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
                 second = new ButtonType(Localization.lang("Remove entry from import"), ButtonData.APPLY);
                 both = new ButtonType(Localization.lang("Keep both"), ButtonData.APPLY);
                 me = new MergeEntries(one, two, Localization.lang("Old entry"),
-                                      Localization.lang("From import"), frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
+                        Localization.lang("From import"), frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
                 break;
             case DUPLICATE_SEARCH_WITH_EXACT:
                 first = new ButtonType(Localization.lang("Keep left"), ButtonData.APPLY);
@@ -84,7 +84,7 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
                 second = new ButtonType(Localization.lang("Do not import entry"), ButtonData.APPLY);
                 both = new ButtonType(Localization.lang("Import and keep old entry"), ButtonData.APPLY);
                 me = new MergeEntries(one, two, Localization.lang("Old entry"),
-                                      Localization.lang("From import"), frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
+                        Localization.lang("From import"), frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
                 break;
         }
         if (removeExactVisible) {
diff --git a/src/main/java/org/jabref/gui/DuplicateSearch.java b/src/main/java/org/jabref/gui/DuplicateSearch.java
index 476b3f70276..9e9921f741a 100644
--- a/src/main/java/org/jabref/gui/DuplicateSearch.java
+++ b/src/main/java/org/jabref/gui/DuplicateSearch.java
@@ -127,7 +127,7 @@ private void askResolveStrategy(DuplicateSearchResult result, BibEntry first, Bi
         DuplicateResolverResult resolverResult = dialog.showAndWait().orElse(DuplicateResolverResult.BREAK);
 
         if ((resolverResult == DuplicateResolverResult.KEEP_LEFT)
-            || (resolverResult == DuplicateResolverResult.AUTOREMOVE_EXACT)) {
+                || (resolverResult == DuplicateResolverResult.AUTOREMOVE_EXACT)) {
             result.remove(second);
             if (resolverResult == DuplicateResolverResult.AUTOREMOVE_EXACT) {
                 autoRemoveExactDuplicates.set(true); // Remember choice
@@ -167,7 +167,7 @@ private void handleDuplicates(DuplicateSearchResult result) {
         }
 
         dialogService.notify(Localization.lang("Duplicates found") + ": " + duplicateCount.get() + ' '
-                             + Localization.lang("pairs processed") + ": " + result.getDuplicateCount());
+                + Localization.lang("pairs processed") + ": " + result.getDuplicateCount());
         compoundEdit.end();
         panel.getUndoManager().addEdit(compoundEdit);
 
diff --git a/src/main/java/org/jabref/gui/EntryType.fxml b/src/main/java/org/jabref/gui/EntryType.fxml
index 7fb864fdf78..0ed5f37b502 100644
--- a/src/main/java/org/jabref/gui/EntryType.fxml
+++ b/src/main/java/org/jabref/gui/EntryType.fxml
@@ -12,41 +12,43 @@
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.RowConstraints?>
 <?import javafx.scene.layout.VBox?>
-
-<DialogPane prefWidth="476.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.EntryTypeView">
-      <buttonTypes>
-        <ButtonType fx:constant="CANCEL" />
-        <ButtonType fx:id="generateButton" buttonData="OK_DONE" text="%Generate" />
-      </buttonTypes>
+<DialogPane xmlns:fx="http://javafx.com/fxml/1" prefWidth="476.0" xmlns="http://javafx.com/javafx/8.0.171"
+            fx:controller="org.jabref.gui.EntryTypeView">
+    <buttonTypes>
+        <ButtonType fx:constant="CANCEL"/>
+        <ButtonType fx:id="generateButton" buttonData="OK_DONE" text="%Generate"/>
+    </buttonTypes>
    <content>
-      <VBox prefHeight="200.0" prefWidth="400.0">
-         <children>
-            <TitledPane fx:id="biblatexTitlePane" animated="false" collapsible="false" text="Biblatex">
-               <content>
-                  <FlowPane fx:id="biblatexPane" prefHeight="200.0" prefWidth="200.0" />
-               </content>
-            </TitledPane>
-            <TitledPane fx:id="bibTexTitlePane" animated="false" collapsible="false" text="BibTeX">
-               <content>
-                  <FlowPane fx:id="bibTexPane" prefHeight="200.0" prefWidth="200.0" />
-               </content>
-            </TitledPane>
-            <TitledPane fx:id="ieeeTranTitlePane" animated="false" collapsible="false" text="IEEETran">
-               <content>
-                  <FlowPane fx:id="ieeetranPane" prefHeight="200.0" prefWidth="200.0" />
-               </content>
-            </TitledPane>
-            <TitledPane fx:id="customTitlePane" animated="false" collapsible="false" text="%Custom">
-               <content>
-                  <FlowPane fx:id="customPane" prefHeight="200.0" prefWidth="200.0" />
-               </content>
-            </TitledPane>
-            <GridPane alignment="CENTER">
+       <VBox prefHeight="200.0" prefWidth="400.0">
+           <children>
+               <TitledPane fx:id="biblatexTitlePane" animated="false" collapsible="false" text="Biblatex">
+                   <content>
+                       <FlowPane fx:id="biblatexPane" prefHeight="200.0" prefWidth="200.0"/>
+                   </content>
+               </TitledPane>
+               <TitledPane fx:id="bibTexTitlePane" animated="false" collapsible="false" text="BibTeX">
+                   <content>
+                       <FlowPane fx:id="bibTexPane" prefHeight="200.0" prefWidth="200.0"/>
+                   </content>
+               </TitledPane>
+               <TitledPane fx:id="ieeeTranTitlePane" animated="false" collapsible="false" text="IEEETran">
+                   <content>
+                       <FlowPane fx:id="ieeetranPane" prefHeight="200.0" prefWidth="200.0"/>
+                   </content>
+               </TitledPane>
+               <TitledPane fx:id="customTitlePane" animated="false" collapsible="false" text="%Custom">
+                   <content>
+                       <FlowPane fx:id="customPane" prefHeight="200.0" prefWidth="200.0"/>
+                   </content>
+               </TitledPane>
+               <GridPane alignment="CENTER">
                <children>
-                  <Label text="%ID type"/>
-                  <ComboBox fx:id="idBasedFetchers" onAction="#focusTextField" prefHeight="30.0" prefWidth="300.0" GridPane.columnIndex="1" />            
-                  <Label text="%ID" GridPane.rowIndex="1" />
-                  <TextField fx:id="idTextField" onAction="#runFetcherWorker" prefHeight="30.0" prefWidth="300.0" GridPane.columnIndex="1" GridPane.rowIndex="1" />
+                   <Label text="%ID type"/>
+                   <ComboBox fx:id="idBasedFetchers" onAction="#focusTextField" prefHeight="30.0" prefWidth="300.0"
+                             GridPane.columnIndex="1"/>
+                   <Label text="%ID" GridPane.rowIndex="1" />
+                   <TextField fx:id="idTextField" onAction="#runFetcherWorker" prefHeight="30.0" prefWidth="300.0"
+                              GridPane.columnIndex="1" GridPane.rowIndex="1"/>
                </children>
                <columnConstraints>
                   <ColumnConstraints hgrow="SOMETIMES" maxWidth="122.0" minWidth="10.0" prefWidth="100.0" />
@@ -56,11 +58,11 @@
                   <Insets bottom="4.0" left="4.0" right="4.0" top="4.0" />
                </opaqueInsets>
                <rowConstraints>
-                  <RowConstraints minHeight="30.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                  <RowConstraints minHeight="30.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                   <RowConstraints minHeight="30.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                   <RowConstraints minHeight="30.0" prefHeight="30.0" vgrow="SOMETIMES"/>
                </rowConstraints>
             </GridPane>
-         </children>
-      </VBox>
+           </children>
+       </VBox>
    </content>
 </DialogPane>
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 76e14c8e6ce..8e4ca768b05 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -923,23 +923,23 @@ private MenuBar createMenu() {
         );
 
         options.getItems().addAll(
-                                  factory.createMenuItem(StandardActions.SHOW_PREFS, new ShowPreferencesAction(this, Globals.TASK_EXECUTOR)),
+                factory.createMenuItem(StandardActions.SHOW_PREFS, new ShowPreferencesAction(this, Globals.TASK_EXECUTOR)),
 
-                                  new SeparatorMenuItem(),
+                new SeparatorMenuItem(),
 
-                                  factory.createMenuItem(StandardActions.SETUP_GENERAL_FIELDS, new SetupGeneralFieldsAction()),
-                                  factory.createMenuItem(StandardActions.MANAGE_CUSTOM_IMPORTS, new ManageCustomImportsAction()),
-                                  factory.createMenuItem(StandardActions.MANAGE_CUSTOM_EXPORTS, new ManageCustomExportsAction()),
-                                  factory.createMenuItem(StandardActions.MANAGE_EXTERNAL_FILETYPES, new EditExternalFileTypesAction()),
-                                  factory.createMenuItem(StandardActions.MANAGE_JOURNALS, new ManageJournalsAction()),
-                                  factory.createMenuItem(StandardActions.CUSTOMIZE_KEYBINDING, new CustomizeKeyBindingAction()),
-                                  factory.createMenuItem(StandardActions.MANAGE_PROTECTED_TERMS, new ManageProtectedTermsAction(this, Globals.protectedTermsLoader)),
+                factory.createMenuItem(StandardActions.SETUP_GENERAL_FIELDS, new SetupGeneralFieldsAction()),
+                factory.createMenuItem(StandardActions.MANAGE_CUSTOM_IMPORTS, new ManageCustomImportsAction()),
+                factory.createMenuItem(StandardActions.MANAGE_CUSTOM_EXPORTS, new ManageCustomExportsAction()),
+                factory.createMenuItem(StandardActions.MANAGE_EXTERNAL_FILETYPES, new EditExternalFileTypesAction()),
+                factory.createMenuItem(StandardActions.MANAGE_JOURNALS, new ManageJournalsAction()),
+                factory.createMenuItem(StandardActions.CUSTOMIZE_KEYBINDING, new CustomizeKeyBindingAction()),
+                factory.createMenuItem(StandardActions.MANAGE_PROTECTED_TERMS, new ManageProtectedTermsAction(this, Globals.protectedTermsLoader)),
 
-                                  new SeparatorMenuItem(),
+                new SeparatorMenuItem(),
 
-                                  factory.createMenuItem(StandardActions.MANAGE_CONTENT_SELECTORS, new OldDatabaseCommandWrapper(Actions.MANAGE_SELECTORS, this, Globals.stateManager)),
-                                  factory.createMenuItem(StandardActions.CUSTOMIZE_ENTRY_TYPES, new CustomizeEntryAction(this)),
-                                  factory.createMenuItem(StandardActions.MANAGE_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this)));
+                factory.createMenuItem(StandardActions.MANAGE_CONTENT_SELECTORS, new OldDatabaseCommandWrapper(Actions.MANAGE_SELECTORS, this, Globals.stateManager)),
+                factory.createMenuItem(StandardActions.CUSTOMIZE_ENTRY_TYPES, new CustomizeEntryAction(this)),
+                factory.createMenuItem(StandardActions.MANAGE_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this)));
 
         help.getItems().addAll(
                 factory.createMenuItem(StandardActions.HELP, HelpAction.getMainHelpPageCommand()),
diff --git a/src/main/java/org/jabref/gui/PreviewPanel.java b/src/main/java/org/jabref/gui/PreviewPanel.java
index ff8d6db01bd..796fafdd016 100644
--- a/src/main/java/org/jabref/gui/PreviewPanel.java
+++ b/src/main/java/org/jabref/gui/PreviewPanel.java
@@ -24,7 +24,7 @@
 import javafx.scene.web.WebView;
 
 import org.jabref.Globals;
-import org.jabref.gui.externalfiles.NewDroppedFileHandler;
+import org.jabref.gui.externalfiles.ExternalFilesEntryLinker;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.keyboard.KeyBinding;
@@ -61,9 +61,9 @@ public class PreviewPanel extends ScrollPane implements SearchQueryHighlightList
     private final DialogService dialogService;
     private final KeyBindingRepository keyBindingRepository;
 
+    private final String defaultPreviewStyle = "Preview";
     private String previewStyle;
     private CitationStyle citationStyle;
-    private final String defaultPreviewStyle = "Preview";
     private Optional<BasePanel> basePanel = Optional.empty();
 
     private boolean fixedLayout;
@@ -80,7 +80,7 @@ public class PreviewPanel extends ScrollPane implements SearchQueryHighlightList
     private final WebView previewView;
     private Optional<Future<?>> citationStyleFuture = Optional.empty();
 
-    private final NewDroppedFileHandler fileHandler;
+    private final ExternalFilesEntryLinker fileLinker;
 
     /**
      * @param panel           (may be null) Only set this if the preview is associated to the main window.
@@ -93,11 +93,7 @@ public PreviewPanel(BasePanel panel, BibDatabaseContext databaseContext, KeyBind
         this.clipBoardManager = Globals.clipboardManager;
         this.keyBindingRepository = keyBindingRepository;
 
-        fileHandler = new NewDroppedFileHandler(dialogService, databaseContext, externalFileTypes,
-                                                Globals.prefs.getFilePreferences(),
-                                                Globals.prefs.getImportFormatPreferences(),
-                                                Globals.prefs.getUpdateFieldPreferences(),
-                                                Globals.getFileUpdateMonitor());
+        fileLinker = new ExternalFilesEntryLinker(externalFileTypes, Globals.prefs.getFilePreferences(), databaseContext);
 
         // Set up scroll pane for preview pane
         setFitToHeight(true);
@@ -135,19 +131,18 @@ public PreviewPanel(BasePanel panel, BibDatabaseContext databaseContext, KeyBind
                 List<Path> files = event.getDragboard().getFiles().stream().map(File::toPath).collect(Collectors.toList());
 
                 if (event.getTransferMode() == TransferMode.MOVE) {
-
                     LOGGER.debug("Mode MOVE"); //shift on win or no modifier
-                    fileHandler.addToEntryRenameAndMoveToFileDir(entry, files);
+                    fileLinker.moveFilesToFileDirAndAddToEntry(entry, files);
                 }
                 if (event.getTransferMode() == TransferMode.LINK) {
                     LOGGER.debug("Node LINK"); //alt on win
-                    fileHandler.addToEntry(entry, files);
-
+                    fileLinker.addFilesToEntry(entry, files);
                 }
                 if (event.getTransferMode() == TransferMode.COPY) {
                     LOGGER.debug("Mode Copy"); //ctrl on win, no modifier on Xubuntu
-                    fileHandler.copyFilesToFileDirAndAddToEntry(entry, files);
+                    fileLinker.copyFilesToFileDirAndAddToEntry(entry, files);
                 }
+                success = true;
             }
 
             event.setDropCompleted(success);
diff --git a/src/main/java/org/jabref/gui/SidePaneManager.java b/src/main/java/org/jabref/gui/SidePaneManager.java
index eef7f01098b..173a11a07c3 100644
--- a/src/main/java/org/jabref/gui/SidePaneManager.java
+++ b/src/main/java/org/jabref/gui/SidePaneManager.java
@@ -31,10 +31,10 @@ public SidePaneManager(JabRefPreferences preferences, JabRefFrame frame) {
 
         OpenOfficePreferences openOfficePreferences = preferences.getOpenOfficePreferences();
         Stream.of(
-                  new FileUpdatePanel(this),
-                  new GroupSidePane(this, preferences, frame.getDialogService()),
-                  new WebSearchPane(this, preferences, frame),
-                  new OpenOfficeSidePanel(this, preferences, frame))
+                new FileUpdatePanel(this),
+                new GroupSidePane(this, preferences, frame.getDialogService()),
+                new WebSearchPane(this, preferences, frame),
+                new OpenOfficeSidePanel(this, preferences, frame))
               .forEach(pane -> components.put(pane.getType(), pane));
 
         if (preferences.getBoolean(JabRefPreferences.GROUP_SIDEPANE_VISIBLE)) {
diff --git a/src/main/java/org/jabref/gui/bibtexkeypattern/ResolveDuplicateLabelDialog.java b/src/main/java/org/jabref/gui/bibtexkeypattern/ResolveDuplicateLabelDialog.java
index 68006125528..f6c6aa5544c 100644
--- a/src/main/java/org/jabref/gui/bibtexkeypattern/ResolveDuplicateLabelDialog.java
+++ b/src/main/java/org/jabref/gui/bibtexkeypattern/ResolveDuplicateLabelDialog.java
@@ -48,7 +48,7 @@ public ResolveDuplicateLabelDialog(BasePanel panel, String key, List<BibEntry> e
         diag = new JDialog((JFrame) null, Localization.lang("Duplicate BibTeX key"), true);
 
         FormBuilder b = FormBuilder.create().layout(new FormLayout(
-                                                                   "left:pref, 4dlu, fill:pref", "p"));
+                "left:pref, 4dlu, fill:pref", "p"));
         b.add(new JLabel(Localization.lang("Duplicate BibTeX key") + ": " + key)).xyw(1, 1, 3);
         b.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
 
diff --git a/src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java b/src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java
index ee562c53401..0938f717905 100644
--- a/src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java
+++ b/src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java
@@ -112,7 +112,6 @@ protected List<CopyFilesResultItemViewModel> call() throws InterruptedException,
                             writeLogMessage(newFile, bw, localizedErrorMessage);
                             addResultToList(newFile, success, localizedErrorMessage);
                         }
-
                     }
 
                 }
diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
index 4289c29d1b2..450da9e98d9 100644
--- a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
+++ b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -31,7 +31,7 @@
 import org.jabref.gui.actions.GenerateBibtexKeySingleAction;
 import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.entryeditor.fileannotationtab.FileAnnotationTab;
-import org.jabref.gui.externalfiles.NewDroppedFileHandler;
+import org.jabref.gui.externalfiles.ExternalFilesEntryLinker;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.help.HelpAction;
 import org.jabref.gui.keyboard.KeyBinding;
@@ -91,7 +91,7 @@ public class EntryEditor extends BorderPane {
 
     private final EntryEditorPreferences preferences;
     private final DialogService dialogService;
-    private final NewDroppedFileHandler fileHandler;
+    private final ExternalFilesEntryLinker fileLinker;
     private final TaskExecutor taskExecutor;
 
     public EntryEditor(BasePanel panel, EntryEditorPreferences preferences, FileUpdateMonitor fileMonitor, DialogService dialogService, ExternalFileTypes externalFileTypes, TaskExecutor taskExecutor) {
@@ -103,11 +103,7 @@ public EntryEditor(BasePanel panel, EntryEditorPreferences preferences, FileUpda
         this.dialogService = dialogService;
         this.taskExecutor = taskExecutor;
 
-        fileHandler = new NewDroppedFileHandler(dialogService, databaseContext, externalFileTypes,
-                Globals.prefs.getFilePreferences(),
-                                                Globals.prefs.getImportFormatPreferences(),
-                                                Globals.prefs.getUpdateFieldPreferences(),
-                Globals.getFileUpdateMonitor());
+        fileLinker = new ExternalFilesEntryLinker(externalFileTypes, Globals.prefs.getFilePreferences(), databaseContext);
 
         ViewLoader.view(this)
                   .root(this)
@@ -151,17 +147,17 @@ public EntryEditor(BasePanel panel, EntryEditorPreferences preferences, FileUpda
                     if (event.getTransferMode() == TransferMode.LINK) //alt on win
                     {
                         LOGGER.debug("Mode LINK");
-                        fileHandler.addToEntry(entry, files);
+                        fileLinker.addFilesToEntry(entry, files);
                     }
                     else if (event.getTransferMode() == TransferMode.COPY) //ctrl on win, no modifier on Xubuntu
                     {
                         LOGGER.debug("Mode COPY");
-                        fileHandler.copyFilesToFileDirAndAddToEntry(entry, files);
+                        fileLinker.copyFilesToFileDirAndAddToEntry(entry, files);
                     }
                     else
                     {
                         LOGGER.debug("Mode MOVE"); //shift on win or no modifier
-                        fileHandler.addToEntryRenameAndMoveToFileDir(entry, files);
+                        fileLinker.moveFilesToFileDirAndAddToEntry(entry, files);
                     }
                 }
 
@@ -170,17 +166,17 @@ else if (event.getTransferMode() == TransferMode.COPY) //ctrl on win, no modifie
                     if (event.getTransferMode() == TransferMode.COPY) //ctrl on win, no modifier on Xubuntu
                     {
                         LOGGER.debug("Mode MOVE");
-                        fileHandler.addToEntryRenameAndMoveToFileDir(entry, files);
+                        fileLinker.moveFilesToFileDirAndAddToEntry(entry, files);
                     }
                     else if (event.getTransferMode() == TransferMode.LINK) //alt on win
                     {
                         LOGGER.debug("Mode LINK");
-                        fileHandler.addToEntry(entry, files);
+                        fileLinker.addFilesToEntry(entry, files);
                     }
                     else
                     {
                         LOGGER.debug("Mode COPY"); //shift on win or no modifier
-                        fileHandler.copyFilesToFileDirAndAddToEntry(entry, files);
+                        fileLinker.copyFilesToFileDirAndAddToEntry(entry, files);
                     }
                 }
 
@@ -189,17 +185,17 @@ else if (event.getTransferMode() == TransferMode.LINK) //alt on win
                     if (event.getTransferMode() == TransferMode.COPY) //ctrl on win, no modifier on Xubuntu
                     {
                         LOGGER.debug("Mode COPY");
-                        fileHandler.copyFilesToFileDirAndAddToEntry(entry, files);
+                        fileLinker.copyFilesToFileDirAndAddToEntry(entry, files);
                     }
                     else if (event.getTransferMode() == TransferMode.LINK) //alt on win
                     {
                         LOGGER.debug("Mode MOVE");
-                        fileHandler.addToEntryRenameAndMoveToFileDir(entry, files);
+                        fileLinker.moveFilesToFileDirAndAddToEntry(entry, files);
                     }
                     else
                     {
                         LOGGER.debug("Mode LINK"); //shift on win or no modifier
-                        fileHandler.addToEntry(entry, files);
+                        fileLinker.addFilesToEntry(entry, files);
                     }
                 }
             }
diff --git a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
index b96fed0bea4..397e3abd921 100644
--- a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
@@ -120,7 +120,7 @@ protected void bindToEntry(BibEntry entry) {
                 } catch (IOException ex) {
                     codeArea.setEditable(false);
                     codeArea.appendText(ex.getMessage() + "\n\n" +
-                                        Localization.lang("Correct the entry, and reopen editor to display/edit source."));
+                            Localization.lang("Correct the entry, and reopen editor to display/edit source."));
                     LOGGER.debug("Incorrect entry", ex);
                 }
             });
diff --git a/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialog.fxml b/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialog.fxml
index 1c63d7e8008..64a4beed541 100644
--- a/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialog.fxml
+++ b/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialog.fxml
@@ -10,43 +10,45 @@
 <?import javafx.scene.layout.ColumnConstraints?>
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.RowConstraints?>
-
-<DialogPane maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" prefHeight="300.0" prefWidth="480.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.exporter.CreateModifyExporterDialogView">
+<DialogPane xmlns:fx="http://javafx.com/fxml/1" maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity"
+            minWidth="-Infinity" prefHeight="300.0" prefWidth="480.0" xmlns="http://javafx.com/javafx/8.0.171"
+            fx:controller="org.jabref.gui.exporter.CreateModifyExporterDialogView">
     <content>
-      <AnchorPane minHeight="0.0" minWidth="0.0" prefHeight="200.0" prefWidth="320.0">
-         <children>
-            <GridPane prefWidth="480.0" scaleShape="false">
-              <columnConstraints>
-                <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
-              </columnConstraints>
-              <rowConstraints>
-                  <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                  <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                  <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                  <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-              </rowConstraints>
-               <children>
-                  <TextField fx:id="name" GridPane.rowIndex="1" />
-                  <Label text="%Main layout file:" GridPane.rowIndex="2" />
-                  <TextField fx:id="fileName" GridPane.rowIndex="3" />
-                  <TextField fx:id="extension" GridPane.rowIndex="6" />
-                  <Label alignment="TOP_LEFT" text="%Export format name:">
-                     <GridPane.margin>
-                        <Insets />
-                     </GridPane.margin>
-                  </Label>
-                  <Label text="%File extension:" GridPane.rowIndex="5" />
-                  <Button fx:id="browseButton" text="%Browse" onAction="#browse" GridPane.rowIndex="4" />
-               </children>
-               <padding>
-                  <Insets bottom="30.0" left="30.0" right="30.0" top="30.0" />
-               </padding>
-            </GridPane>
-         </children></AnchorPane>
+        <AnchorPane minHeight="0.0" minWidth="0.0" prefHeight="200.0" prefWidth="320.0">
+            <children>
+                <GridPane prefWidth="480.0" scaleShape="false">
+                    <columnConstraints>
+                        <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0"/>
+                    </columnConstraints>
+                    <rowConstraints>
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                    </rowConstraints>
+                    <children>
+                        <TextField fx:id="name" GridPane.rowIndex="1"/>
+                        <Label text="%Main layout file:" GridPane.rowIndex="2"/>
+                        <TextField fx:id="fileName" GridPane.rowIndex="3"/>
+                        <TextField fx:id="extension" GridPane.rowIndex="6"/>
+                        <Label alignment="TOP_LEFT" text="%Export format name:">
+                            <GridPane.margin>
+                                <Insets/>
+                            </GridPane.margin>
+                        </Label>
+                        <Label text="%File extension:" GridPane.rowIndex="5"/>
+                        <Button fx:id="browseButton" text="%Browse" onAction="#browse" GridPane.rowIndex="4"/>
+                    </children>
+                    <padding>
+                        <Insets bottom="30.0" left="30.0" right="30.0" top="30.0"/>
+                    </padding>
+                </GridPane>
+            </children>
+        </AnchorPane>
     </content>
-    <ButtonType fx:id="saveExporter" text="%Save exporter" />
-    <ButtonType fx:constant="CANCEL" />
+    <ButtonType fx:id="saveExporter" text="%Save exporter"/>
+    <ButtonType fx:constant="CANCEL"/>
 </DialogPane>
diff --git a/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogView.java b/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogView.java
index c3464567625..4e942a48c14 100644
--- a/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogView.java
+++ b/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogView.java
@@ -18,19 +18,17 @@
 
 public class CreateModifyExporterDialogView extends BaseDialog<ExporterViewModel> {
 
+    @Inject private final JournalAbbreviationLoader loader;
+    private final ExporterViewModel exporter;
     @FXML private Button browseButton;
     @FXML private TextField name;
     @FXML private TextField fileName;
     @FXML private TextField extension;
     @FXML private ButtonType saveExporter;
-
     @Inject private DialogService dialogService;
     @Inject private PreferencesService preferences;
-    @Inject private final JournalAbbreviationLoader loader;
     private CreateModifyExporterDialogViewModel viewModel;
 
-    private final ExporterViewModel exporter;
-
     public CreateModifyExporterDialogView(ExporterViewModel exporter, DialogService dialogService,
                                           PreferencesService preferences, JournalAbbreviationLoader loader) {
         this.setTitle(Localization.lang("Customize Export Formats"));
@@ -64,4 +62,4 @@ private void initialize() {
     private void browse(ActionEvent event) {
         viewModel.browse();
     }
-}
\ No newline at end of file
+}
diff --git a/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogViewModel.java b/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogViewModel.java
index 96331a29842..4fd067f02ae 100644
--- a/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogViewModel.java
@@ -21,12 +21,10 @@
 import org.slf4j.LoggerFactory;
 
 /**
- *
  * This view model can be used both for "add exporter" and "modify exporter" functionalities.
  * It takes an optional exporter which is empty for "add exporter," and takes the selected exporter
  * for "modify exporter."  It returns an optional exporter which empty if an invalid or no exporter is
  * created, and otherwise contains the exporter to be added or that is modified.
- *
  */
 
 public class CreateModifyExporterDialogViewModel extends AbstractViewModel {
@@ -65,7 +63,7 @@ public ExporterViewModel saveExporter() {
 
         // Check that there are no empty strings.
         if (layoutFile.get().isEmpty() || name.get().isEmpty() || extension.get().isEmpty()
-            || !layoutFile.get().endsWith(".layout")) {
+                || !layoutFile.get().endsWith(".layout")) {
 
             LOGGER.info("One of the fields is empty or invalid!");
             return null;
@@ -75,7 +73,7 @@ public ExporterViewModel saveExporter() {
         LayoutFormatterPreferences layoutPreferences = preferences.getLayoutFormatterPreferences(loader);
         SavePreferences savePreferences = preferences.loadForExportFromPreferences();
         TemplateExporter format = new TemplateExporter(name.get(), layoutFile.get(), extension.get(),
-                                                       layoutPreferences, savePreferences);
+                layoutPreferences, savePreferences);
         format.setCustomExport(true);
         return new ExporterViewModel(format);
     }
@@ -86,9 +84,9 @@ public String getExportWorkingDirectory() {
 
     public void browse() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-            .addExtensionFilter(Localization.lang("Custom layout file"), StandardFileType.LAYOUT)
-            .withDefaultExtension(Localization.lang("Custom layout file"), StandardFileType.LAYOUT)
-            .withInitialDirectory(getExportWorkingDirectory()).build();
+                .addExtensionFilter(Localization.lang("Custom layout file"), StandardFileType.LAYOUT)
+                .withDefaultExtension(Localization.lang("Custom layout file"), StandardFileType.LAYOUT)
+                .withInitialDirectory(getExportWorkingDirectory()).build();
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(f -> layoutFile.set(f.toAbsolutePath().toString()));
     }
 
@@ -103,5 +101,4 @@ public StringProperty getLayoutFileName() {
     public StringProperty getExtension() {
         return extension;
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/exporter/ExportCommand.java b/src/main/java/org/jabref/gui/exporter/ExportCommand.java
index 004c7597b5b..36bb095a027 100644
--- a/src/main/java/org/jabref/gui/exporter/ExportCommand.java
+++ b/src/main/java/org/jabref/gui/exporter/ExportCommand.java
@@ -58,8 +58,8 @@ public void execute() {
 
         //Get list of exporters and sort before adding to file dialog
         List<Exporter> exporters = Globals.exportFactory.getExporters().stream()
-                .sorted(Comparator.comparing(Exporter::getName))
-                .collect(Collectors.toList());
+                                                        .sorted(Comparator.comparing(Exporter::getName))
+                                                        .collect(Collectors.toList());
 
         Globals.exportFactory = ExporterFactory.create(customExporters, layoutPreferences, savePreferences, xmpPreferences);
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
diff --git a/src/main/java/org/jabref/gui/exporter/ExportCustomizationDialog.fxml b/src/main/java/org/jabref/gui/exporter/ExportCustomizationDialog.fxml
index d25e272ed38..9a2749a10ca 100644
--- a/src/main/java/org/jabref/gui/exporter/ExportCustomizationDialog.fxml
+++ b/src/main/java/org/jabref/gui/exporter/ExportCustomizationDialog.fxml
@@ -5,25 +5,24 @@
 <?import javafx.scene.control.TableColumn?>
 <?import javafx.scene.control.TableView?>
 <?import javafx.scene.layout.VBox?>
-
-<DialogPane xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1"
+<DialogPane xmlns:fx="http://javafx.com/fxml/1" xmlns="http://javafx.com/javafx/8.0.171"
             fx:controller="org.jabref.gui.exporter.ExportCustomizationDialogView">
-   <content>
-      <VBox prefHeight="200.0" prefWidth="500.0">
-         <children>
-            <TableView fx:id="exporterTable" prefHeight="150.0" prefWidth="500.0">
-              <columns>
-                <TableColumn fx:id="nameColumn" prefWidth="150.0" text="%Export name" />
-                <TableColumn fx:id="layoutColumn" prefWidth="250.0" text="%Main layout file" />
-                <TableColumn fx:id="extensionColumn" prefWidth="100.0" text="%Extension" />
-              </columns>
-            </TableView>
-         </children>
-      </VBox>
-   </content>
-   <ButtonType fx:id="addButton" text="%Add" />
-   <ButtonType fx:id="modifyButton" text="%Modify" />
-   <ButtonType fx:id="removeButton" text="%Remove" />
-   <ButtonType fx:id="closeButton" fx:constant="OK" />
-   <ButtonType fx:constant="CANCEL" />
+    <content>
+        <VBox prefHeight="200.0" prefWidth="500.0">
+            <children>
+                <TableView fx:id="exporterTable" prefHeight="150.0" prefWidth="500.0">
+                    <columns>
+                        <TableColumn fx:id="nameColumn" prefWidth="150.0" text="%Export name"/>
+                        <TableColumn fx:id="layoutColumn" prefWidth="250.0" text="%Main layout file"/>
+                        <TableColumn fx:id="extensionColumn" prefWidth="100.0" text="%Extension"/>
+                    </columns>
+                </TableView>
+            </children>
+        </VBox>
+    </content>
+    <ButtonType fx:id="addButton" text="%Add"/>
+    <ButtonType fx:id="modifyButton" text="%Modify"/>
+    <ButtonType fx:id="removeButton" text="%Remove"/>
+    <ButtonType fx:id="closeButton" fx:constant="OK"/>
+    <ButtonType fx:constant="CANCEL"/>
 </DialogPane>
diff --git a/src/main/java/org/jabref/gui/exporter/ExportCustomizationDialogViewModel.java b/src/main/java/org/jabref/gui/exporter/ExportCustomizationDialogViewModel.java
index 76bbecce5dc..fc3d3f878cd 100644
--- a/src/main/java/org/jabref/gui/exporter/ExportCustomizationDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/exporter/ExportCustomizationDialogViewModel.java
@@ -39,7 +39,7 @@ private void loadExporters() {
 
     public void addExporter() {
         CreateModifyExporterDialogView dialog = new CreateModifyExporterDialogView(null, dialogService, preferences,
-                                                                                   loader);
+                loader);
         Optional<ExporterViewModel> exporter = dialogService.showCustomDialogAndWait(dialog);
         if ((exporter != null) && exporter.isPresent()) {
             exporters.add(exporter.get());
@@ -68,7 +68,6 @@ public void removeExporters() {
     public void saveToPrefs() {
         List<TemplateExporter> exportersLogic = exporters.stream().map(ExporterViewModel::getLogic).collect(Collectors.toList());
         preferences.storeCustomExportFormats(exportersLogic);
-
     }
 
     public ListProperty<ExporterViewModel> selectedExportersProperty() {
diff --git a/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java b/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
index ce48b9bfebe..2148a0146c0 100644
--- a/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
+++ b/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
@@ -63,16 +63,16 @@ public void execute() {
 
         //Find default choice, if any
         Exporter defaultChoice = exporters.stream()
-                .filter(exporter -> exporter.getName().equals(Globals.prefs.get(JabRefPreferences.LAST_USED_EXPORT)))
-                .findAny()
-                .orElse(null);
+                                          .filter(exporter -> exporter.getName().equals(Globals.prefs.get(JabRefPreferences.LAST_USED_EXPORT)))
+                                          .findAny()
+                                          .orElse(null);
 
         Optional<Exporter> selectedExporter = dialogService.showChoiceDialogAndWait(Localization.lang("Export"), Localization.lang("Select export format"),
-                    Localization.lang("Export"), defaultChoice, exporters);
+                Localization.lang("Export"), defaultChoice, exporters);
 
         selectedExporter.ifPresent(exporter -> BackgroundTask.wrap(() -> exportToClipboard(exporter))
-                     .onSuccess(this::setContentToClipboard)
-                     .executeWith(Globals.TASK_EXECUTOR));
+                                                             .onSuccess(this::setContentToClipboard)
+                                                             .executeWith(Globals.TASK_EXECUTOR));
 
     }
 
diff --git a/src/main/java/org/jabref/gui/exporter/ExporterViewModel.java b/src/main/java/org/jabref/gui/exporter/ExporterViewModel.java
index 1b4b838ea69..4bd807881f8 100644
--- a/src/main/java/org/jabref/gui/exporter/ExporterViewModel.java
+++ b/src/main/java/org/jabref/gui/exporter/ExporterViewModel.java
@@ -8,8 +8,6 @@
 /**
  * ExporterViewModel wraps a TemplateExporter from logic and is used in the exporter customization dialog view
  * and ViewModel.
- *
- *
  */
 
 public class ExporterViewModel {
@@ -34,7 +32,6 @@ public TemplateExporter getLogic() {
 
     public StringProperty name() {
         return this.name;
-
     }
 
     public StringProperty layoutFileName() {
diff --git a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
index 3a4fc68ffd2..681cf946275 100644
--- a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
@@ -64,8 +64,8 @@ public SaveDatabaseAction(BasePanel panel, JabRefPreferences prefs) {
     private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding, SavePreferences.DatabaseSaveType saveType) throws SaveException {
         try {
             SavePreferences preferences = prefs.loadForSaveFromPreferences()
-                                                       .withEncoding(encoding)
-                                                       .withSaveType(saveType);
+                                               .withEncoding(encoding)
+                                               .withSaveType(saveType);
 
             AtomicFileWriter fileWriter = new AtomicFileWriter(file, preferences.getEncoding(), preferences.makeBackup());
             BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, preferences);
diff --git a/src/main/java/org/jabref/gui/externalfiles/DroppedFileHandler.java b/src/main/java/org/jabref/gui/externalfiles/DroppedFileHandler.java
deleted file mode 100644
index b4cc4e2e9bf..00000000000
--- a/src/main/java/org/jabref/gui/externalfiles/DroppedFileHandler.java
+++ /dev/null
@@ -1,568 +0,0 @@
-package org.jabref.gui.externalfiles;
-
-import java.awt.BorderLayout;
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.List;
-import java.util.Optional;
-
-import javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBox;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JRadioButton;
-import javax.swing.JTextArea;
-import javax.swing.JTextField;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.filelist.FileListEntry;
-import org.jabref.gui.filelist.FileListTableModel;
-import org.jabref.gui.maintable.MainTable;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.gui.undo.UndoableInsertEntry;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.io.FileUtil;
-import org.jabref.logic.xmp.XmpUtilReader;
-import org.jabref.model.database.BibDatabase;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FieldName;
-import org.jabref.model.entry.IdGenerator;
-import org.jabref.model.util.FileHelper;
-import org.jabref.preferences.JabRefPreferences;
-
-import com.jgoodies.forms.builder.FormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * This class holds the functionality of autolinking to a file that's dropped
- * onto an entry.
- * <p>
- * Options for handling the files are:
- * <p>
- * 1) Link to the file in its current position (disabled if the file is remote)
- * <p>
- * 2) Copy the file to ??? directory, rename after bibtex key, and extension
- * <p>
- * 3) Move the file to ??? directory, rename after bibtex key, and extension
- */
-public class DroppedFileHandler {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(DroppedFileHandler.class);
-
-    private final BasePanel panel;
-
-    private final JRadioButton linkInPlace = new JRadioButton();
-    private final JRadioButton copyRadioButton = new JRadioButton();
-    private final JRadioButton moveRadioButton = new JRadioButton();
-
-    private final JLabel destDirLabel = new JLabel();
-
-    private final JCheckBox renameCheckBox = new JCheckBox();
-
-    private final JTextField renameToTextBox = new JTextField(50);
-
-    private final JPanel optionsPanel = new JPanel();
-    private final DialogService dialogService;
-    private JabRefPreferences preferences;
-
-    public DroppedFileHandler(JabRefFrame frame, BasePanel panel) {
-        this.dialogService = frame.getDialogService();
-        this.preferences = frame.prefs();
-        this.panel = panel;
-
-        ButtonGroup grp = new ButtonGroup();
-        grp.add(linkInPlace);
-        grp.add(copyRadioButton);
-        grp.add(moveRadioButton);
-
-        FormLayout layout = new FormLayout("left:15dlu,pref,pref,pref", "bottom:14pt,pref,pref,pref,pref");
-        layout.setRowGroups(new int[][] {{1, 2, 3, 4, 5}});
-        FormBuilder builder = FormBuilder.create().layout(layout);
-
-        builder.add(linkInPlace).xyw(1, 1, 4);
-        builder.add(destDirLabel).xyw(1, 2, 4);
-        builder.add(copyRadioButton).xyw(2, 3, 3);
-        builder.add(moveRadioButton).xyw(2, 4, 3);
-        builder.add(renameCheckBox).xyw(2, 5, 1);
-        builder.add(renameToTextBox).xyw(4, 5, 1);
-        optionsPanel.add(builder.getPanel());
-    }
-
-    /**
-     * Offer copy/move/linking options for a dragged external file. Perform the
-     * chosen operation, if any.
-     *
-     * @param fileName  The name of the dragged file.
-     * @param fileType  The FileType associated with the file.
-     * @param mainTable The MainTable the file was dragged to.
-     * @param dropRow   The row where the file was dropped.
-     */
-    public void handleDroppedfile(String fileName, ExternalFileType fileType, MainTable mainTable, int dropRow) {
-
-        BibEntry entry = mainTable.getEntryAt(dropRow);
-        handleDroppedfile(fileName, fileType, entry);
-    }
-
-    /**
-     * @param fileName  The name of the dragged file.
-     * @param fileType  The FileType associated with the file.
-     * @param entry     The target entry for the drop.
-     */
-    public void handleDroppedfile(String fileName, ExternalFileType fileType, BibEntry entry) {
-        NamedCompound edits = new NamedCompound(Localization.lang("Drop %0", fileType.getExtension()));
-
-        if (tryXmpImport(fileName, fileType, edits)) {
-            edits.end();
-            panel.getUndoManager().addEdit(edits);
-            return;
-        }
-
-        // Show dialog
-        if (!showLinkMoveCopyRenameDialog(fileName, fileType, entry, panel.getDatabase())) {
-            return;
-        }
-
-        /*
-         * Ok, we're ready to go. See first if we need to do a file copy before
-         * linking:
-         */
-
-        boolean success = true;
-        String destFilename;
-
-        if (linkInPlace.isSelected()) {
-            destFilename = FileUtil.relativize(Paths.get(fileName),
-                    panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()))
-                                   .toString();
-        } else {
-            destFilename = renameCheckBox.isSelected() ? renameToTextBox.getText() : Paths.get(fileName).toString();
-            if (copyRadioButton.isSelected()) {
-                success = doCopy(fileName, destFilename, edits);
-            } else if (moveRadioButton.isSelected()) {
-                success = doMove(fileName, destFilename, edits);
-            }
-        }
-
-        if (success) {
-            doLink(entry, fileType, destFilename, false, edits);
-            panel.markBaseChanged();
-            panel.updateEntryEditorIfShowing();
-        }
-        edits.end();
-        panel.getUndoManager().addEdit(edits);
-
-    }
-
-    // Done by MrDlib
-    public void linkPdfToEntry(String fileName, MainTable entryTable, int dropRow) {
-        BibEntry entry = entryTable.getEntryAt(dropRow);
-        linkPdfToEntry(fileName, entry);
-    }
-
-    public void linkPdfToEntry(String fileName, BibEntry entry) {
-        Optional<ExternalFileType> optFileType = ExternalFileTypes.getInstance().getExternalFileTypeByExt("pdf");
-
-        if (!optFileType.isPresent()) {
-            LOGGER.warn("No file type with extension 'pdf' registered.");
-            return;
-        }
-
-        ExternalFileType fileType = optFileType.get();
-        // Show dialog
-        if (!showLinkMoveCopyRenameDialog(fileName, fileType, entry, panel.getDatabase())) {
-            return;
-        }
-
-        /*
-         * Ok, we're ready to go. See first if we need to do a file copy before
-         * linking:
-         */
-
-        boolean success = true;
-        String destFilename;
-        NamedCompound edits = new NamedCompound(Localization.lang("Drop %0", fileType.getExtension()));
-
-        if (linkInPlace.isSelected()) {
-            destFilename = FileUtil.relativize(Paths.get(fileName),
-                    panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()))
-                                   .toString();
-        } else {
-            destFilename = renameCheckBox.isSelected() ? renameToTextBox.getText() : new File(fileName).getName();
-            if (copyRadioButton.isSelected()) {
-                success = doCopy(fileName, destFilename, edits);
-            } else if (moveRadioButton.isSelected()) {
-                success = doMove(fileName, destFilename, edits);
-            }
-        }
-
-        if (success) {
-            doLink(entry, fileType, destFilename, false, edits);
-            panel.markBaseChanged();
-        }
-        edits.end();
-        panel.getUndoManager().addEdit(edits);
-    }
-
-    // Done by MrDlib
-
-    private boolean tryXmpImport(String fileName, ExternalFileType fileType, NamedCompound edits) {
-
-        if (!"pdf".equals(fileType.getExtension())) {
-            return false;
-        }
-
-        List<BibEntry> xmpEntriesInFile;
-        try {
-            xmpEntriesInFile = XmpUtilReader.readXmp(fileName, Globals.prefs.getXMPPreferences());
-        } catch (IOException e) {
-            LOGGER.warn("Problem reading XMP", e);
-            return false;
-        }
-
-        if ((xmpEntriesInFile == null) || xmpEntriesInFile.isEmpty()) {
-            return false;
-        }
-
-        JLabel confirmationMessage = new JLabel(Localization.lang("The PDF contains one or several BibTeX-records.")
-                + "\n" + Localization.lang("Do you want to import these as new entries into the current library?"));
-        JPanel entriesPanel = new JPanel();
-        entriesPanel.setLayout(new BoxLayout(entriesPanel, BoxLayout.Y_AXIS));
-        xmpEntriesInFile.forEach(entry -> {
-            JTextArea entryArea = new JTextArea(entry.toString());
-            entryArea.setEditable(false);
-            entriesPanel.add(entryArea);
-        });
-
-        JPanel contentPanel = new JPanel(new BorderLayout());
-        contentPanel.add(confirmationMessage, BorderLayout.NORTH);
-        contentPanel.add(entriesPanel, BorderLayout.CENTER);
-
-        int reply = JOptionPane.showConfirmDialog(null, contentPanel,
-                Localization.lang("XMP-metadata found in PDF: %0", fileName), JOptionPane.YES_NO_CANCEL_OPTION,
-                JOptionPane.QUESTION_MESSAGE);
-
-        if (reply == JOptionPane.CANCEL_OPTION) {
-            return true; // The user canceled thus that we are done.
-        }
-        if (reply == JOptionPane.NO_OPTION) {
-            return false;
-        }
-
-        // reply == JOptionPane.YES_OPTION)
-
-        /*
-         * TODO Extract Import functionality from ImportAction then we could
-         * do:
-         *
-         * ImportAction importer = new ImportAction(frame, (mainTable ==
-         * null), new PdfXmpImporter());
-         *
-         * importer.automatedImport(new String[] { fileName });
-         */
-
-        boolean isSingle = xmpEntriesInFile.size() == 1;
-        BibEntry single = isSingle ? xmpEntriesInFile.get(0) : null;
-
-        boolean success = true;
-
-        String destFilename;
-
-        if (linkInPlace.isSelected()) {
-            destFilename = FileUtil.relativize(Paths.get(fileName),
-                    panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()))
-                                   .toString();
-        } else {
-            if (renameCheckBox.isSelected() || (single == null)) {
-                destFilename = fileName;
-            } else {
-                destFilename = single.getCiteKey() + "." + fileType.getExtension();
-            }
-
-            if (copyRadioButton.isSelected()) {
-                success = doCopy(fileName, destFilename, edits);
-            } else if (moveRadioButton.isSelected()) {
-                success = doMove(fileName, destFilename, edits);
-            }
-        }
-        if (success) {
-
-            for (BibEntry aXmpEntriesInFile : xmpEntriesInFile) {
-
-                aXmpEntriesInFile.setId(IdGenerator.next());
-                edits.addEdit(new UndoableInsertEntry(panel.getDatabase(), aXmpEntriesInFile));
-                panel.getDatabase().insertEntry(aXmpEntriesInFile);
-                doLink(aXmpEntriesInFile, fileType, destFilename, true, edits);
-
-            }
-            panel.markBaseChanged();
-            panel.updateEntryEditorIfShowing();
-        }
-        return true;
-    }
-
-    //
-    // @return true if user pushed "OK", false otherwise
-    //
-    private boolean showLinkMoveCopyRenameDialog(String linkFileName, ExternalFileType fileType, BibEntry entry,
-            BibDatabase database) {
-
-        String dialogTitle = Localization.lang("Link to file %0", linkFileName);
-
-        Optional<Path> dir = panel.getBibDatabaseContext()
-                                  .getFirstExistingFileDir(Globals.prefs.getFilePreferences());
-
-        if (!dir.isPresent()) {
-            destDirLabel.setText(Localization.lang("File directory is not set or does not exist!"));
-            copyRadioButton.setEnabled(false);
-            moveRadioButton.setEnabled(false);
-            renameToTextBox.setEnabled(false);
-            renameCheckBox.setEnabled(false);
-            linkInPlace.setSelected(true);
-        } else {
-            destDirLabel.setText(Localization.lang("File directory is '%0':", dir.get().toString()));
-            copyRadioButton.setEnabled(true);
-            moveRadioButton.setEnabled(true);
-            renameToTextBox.setEnabled(true);
-            renameCheckBox.setEnabled(true);
-        }
-
-        ChangeListener cl = arg0 -> {
-            renameCheckBox.setEnabled(!linkInPlace.isSelected());
-            renameToTextBox.setEnabled(!linkInPlace.isSelected());
-        };
-
-        linkInPlace.setText(Localization.lang("Leave file in its current directory"));
-        copyRadioButton.setText(Localization.lang("Copy file to file directory"));
-        moveRadioButton.setText(Localization.lang("Move file to file directory"));
-        renameCheckBox.setText(Localization.lang("Rename file to").concat(": "));
-
-        // Determine which name to suggest:
-        String targetName = FileUtil.createFileNameFromPattern(database, entry,
-                Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN));
-
-        String fileDirPattern = Globals.prefs.get(JabRefPreferences.IMPORT_FILEDIRPATTERN);
-
-        String targetDirName = "";
-        if (!fileDirPattern.isEmpty()) {
-            targetDirName = FileUtil.createDirNameFromPattern(database, entry, fileDirPattern);
-        }
-
-        if (targetDirName.isEmpty()) {
-            renameToTextBox.setText(targetName.concat(".").concat(fileType.getExtension()));
-        } else {
-            renameToTextBox
-                    .setText(targetDirName.concat("/").concat(targetName.concat(".").concat(fileType.getExtension())));
-        }
-        linkInPlace.setSelected(preferences.getBoolean(JabRefPreferences.DROPPEDFILEHANDLER_LEAVE));
-        copyRadioButton.setSelected(preferences.getBoolean(JabRefPreferences.DROPPEDFILEHANDLER_COPY));
-        moveRadioButton.setSelected(preferences.getBoolean(JabRefPreferences.DROPPEDFILEHANDLER_MOVE));
-        renameCheckBox.setSelected(preferences.getBoolean(JabRefPreferences.DROPPEDFILEHANDLER_RENAME));
-
-        linkInPlace.addChangeListener(cl);
-        cl.stateChanged(new ChangeEvent(linkInPlace));
-
-        try {
-            Object[] messages = {Localization.lang("How would you like to link to '%0'?", linkFileName), optionsPanel};
-            int reply = JOptionPane.showConfirmDialog(null, messages, dialogTitle, JOptionPane.OK_CANCEL_OPTION,
-                    JOptionPane.QUESTION_MESSAGE);
-            if (reply == JOptionPane.OK_OPTION) {
-                // store user's choice
-                preferences.putBoolean(JabRefPreferences.DROPPEDFILEHANDLER_LEAVE, linkInPlace.isSelected());
-                preferences.putBoolean(JabRefPreferences.DROPPEDFILEHANDLER_COPY, copyRadioButton.isSelected());
-                preferences.putBoolean(JabRefPreferences.DROPPEDFILEHANDLER_MOVE, moveRadioButton.isSelected());
-                preferences.putBoolean(JabRefPreferences.DROPPEDFILEHANDLER_RENAME, renameCheckBox.isSelected());
-                return true;
-            } else {
-                return false;
-            }
-        } finally {
-            linkInPlace.removeChangeListener(cl);
-        }
-    }
-
-    /**
-     * Make a extension to the file.
-     *
-     * @param entry    The entry to extension from.
-     * @param fileType The FileType associated with the file.
-     * @param filename The path to the file.
-     * @param edits    An NamedCompound action this action is to be added to. If none
-     *                 is given, the edit is added to the panel's undoManager.
-     */
-    private void doLink(BibEntry entry, ExternalFileType fileType, String filename, boolean avoidDuplicate,
-            NamedCompound edits) {
-
-        Optional<String> oldValue = entry.getField(FieldName.FILE);
-        FileListTableModel tm = new FileListTableModel();
-        oldValue.ifPresent(tm::setContent);
-
-        // If avoidDuplicate==true, we should check if this file is already linked:
-        if (avoidDuplicate) {
-            // For comparison, find the absolute filename:
-            List<Path> dirs = panel.getBibDatabaseContext()
-                                   .getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
-            String absFilename;
-            if (new File(filename).isAbsolute() || dirs.isEmpty()) {
-                absFilename = filename;
-            } else {
-                Optional<Path> file = FileHelper.expandFilenameAsPath(filename, dirs);
-                if (file.isPresent()) {
-                    absFilename = file.get().toAbsolutePath().toString();
-                } else {
-                    absFilename = ""; // This shouldn't happen based on the old code, so maybe one should set it something else?
-                }
-            }
-
-            LOGGER.debug("absFilename: " + absFilename);
-
-            for (int i = 0; i < tm.getRowCount(); i++) {
-                FileListEntry flEntry = tm.getEntry(i);
-                // Find the absolute filename for this existing link:
-                String absName = flEntry.toParsedFileField()
-                        .findIn(dirs)
-                        .map(Path::toAbsolutePath)
-                        .map(Path::toString)
-                        .orElse(null);
-
-                LOGGER.debug("absName: " + absName);
-                // If the filenames are equal, we don't need to link, so we simply return:
-                if (absFilename.equals(absName)) {
-                    return;
-                }
-            }
-        }
-
-        tm.addEntry(tm.getRowCount(), new FileListEntry("", filename, fileType));
-        String newValue = tm.getStringRepresentation();
-        UndoableFieldChange edit = new UndoableFieldChange(entry, FieldName.FILE, oldValue.orElse(null), newValue);
-
-        // make sure that the update runs in the Java FX thread to avoid exception in listeners
-        DefaultTaskExecutor.runInJavaFXThread(() -> {
-            entry.setField(FieldName.FILE, newValue);
-        });
-
-        if (edits == null) {
-            panel.getUndoManager().addEdit(edit);
-        } else {
-            edits.addEdit(edit);
-        }
-    }
-
-    /**
-     * Move the given file to the base directory for its file type, and rename
-     * it to the given filename.
-     *
-     * @param fileName     The name of the source file.
-     * @param destFilename The destination filename.
-     * @param edits        TODO we should be able to undo this action
-     * @return true if the operation succeeded.
-     */
-    private boolean doMove(String fileName, String destFilename, NamedCompound edits) {
-        Optional<Path> dir = panel.getBibDatabaseContext()
-                                  .getFirstExistingFileDir(Globals.prefs.getFilePreferences());
-
-        if (dir.isPresent()) {
-            Path destFile = dir.get().resolve(destFilename);
-
-            if (Files.exists(destFile)) {
-                int answer = JOptionPane.showConfirmDialog(null,
-                        Localization.lang("'%0' exists. Overwrite file?", destFile.toString()),
-                        Localization.lang("Overwrite file?"), JOptionPane.YES_NO_OPTION);
-                if (answer == JOptionPane.NO_OPTION) {
-                    return false;
-                }
-            }
-
-            Path fromFile = Paths.get(fileName);
-            try {
-                if (!Files.exists(destFile)) {
-                    Files.createDirectories(destFile);
-                }
-            } catch (IOException e) {
-                LOGGER.error("Problem creating target directories", e);
-            }
-            if (FileUtil.renameFile(fromFile, destFile, true)) {
-                return true;
-            } else {
-                dialogService.showErrorDialogAndWait(
-                        Localization.lang("Move file failed"),
-                        Localization.lang("Could not move file '%0'.", destFile.toString())
-                                + Localization.lang("Please move the file manually and link in place."));
-                return false;
-            }
-        }
-        return false;
-    }
-
-    /**
-     * Copy the given file to the base directory for its file type, and give it
-     * the given name.
-     *
-     * @param fileName The name of the source file.
-     * @param toFile   The destination filename. An existing path-component will be removed.
-     * @param edits    TODO we should be able to undo this!
-     * @return true if the operation succeeded.
-     */
-    private boolean doCopy(String fileName, String toFile, NamedCompound edits) {
-
-        List<String> dirs = panel.getBibDatabaseContext()
-                                 .getFileDirectories(Globals.prefs.getFilePreferences());
-        int found = -1;
-        for (int i = 0; i < dirs.size(); i++) {
-            if (new File(dirs.get(i)).exists()) {
-                found = i;
-                break;
-            }
-        }
-        if (found < 0) {
-            // OOps, we don't know which directory to put it in, or the given
-            // dir doesn't exist....
-            // This should not happen!!
-            LOGGER.warn("Cannot determine destination directory or destination directory does not exist");
-            return false;
-        }
-
-        Path destFile = Paths.get(dirs.get(found)).resolve(toFile);
-        if (destFile.toString().equals(fileName)) {
-            // File is already in the correct position. Don't override!
-            return true;
-        }
-
-        if (Files.exists(destFile)) {
-            int answer = JOptionPane.showConfirmDialog(null,
-                    Localization.lang("'%0' exists. Overwrite file?", destFile.toString()),
-                    Localization.lang("File exists"), JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
-            if (answer == JOptionPane.NO_OPTION) {
-                return false;
-            }
-        }
-        try {
-            //copy does not create directories, therefore we have to create them manually
-            if (!Files.exists(destFile)) {
-                Files.createDirectories(destFile);
-            }
-            FileUtil.copyFile(Paths.get(fileName), destFile, true);
-        } catch (IOException e) {
-            LOGGER.error("Problem copying file", e);
-            return false;
-        }
-        return true;
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/externalfiles/ExternalFilesEntryLinker.java b/src/main/java/org/jabref/gui/externalfiles/ExternalFilesEntryLinker.java
index 98640b3a377..ab2b1e9c819 100644
--- a/src/main/java/org/jabref/gui/externalfiles/ExternalFilesEntryLinker.java
+++ b/src/main/java/org/jabref/gui/externalfiles/ExternalFilesEntryLinker.java
@@ -1,7 +1,6 @@
 package org.jabref.gui.externalfiles;
 
 import java.nio.file.Path;
-import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
 
@@ -51,22 +50,29 @@ public void moveLinkedFilesToFileDir(BibEntry entry) {
         moveFilesCleanup.cleanup(entry);
     }
 
-    public void addFileToEntry(BibEntry entry, Path file) {
-        addFilesToEntry(entry, Arrays.asList(file));
-    }
-
     public void addFilesToEntry(BibEntry entry, List<Path> files) {
         for (Path file : files) {
             FileUtil.getFileExtension(file).ifPresent(ext -> {
-
                 ExternalFileType type = externalFileTypes.getExternalFileTypeByExt(ext)
                                                          .orElse(new UnknownExternalFileType(ext));
                 Path relativePath = FileUtil.relativize(file, bibDatabaseContext.getFileDirectoriesAsPaths(filePreferences));
                 LinkedFile linkedfile = new LinkedFile("", relativePath.toString(), type.getName());
                 entry.addFile(linkedfile);
             });
-
         }
+    }
 
+    public void moveFilesToFileDirAndAddToEntry(BibEntry entry, List<Path> files) {
+        addFilesToEntry(entry, files);
+        moveLinkedFilesToFileDir(entry);
+        renameLinkedFilesToPattern(entry);
+    }
+
+    public void copyFilesToFileDirAndAddToEntry(BibEntry entry, List<Path> files) {
+        for (Path file : files) {
+            copyFileToFileDir(file)
+                    .ifPresent(copiedFile -> addFilesToEntry(entry, files));
+        }
+        renameLinkedFilesToPattern(entry);
     }
 }
diff --git a/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java b/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
index f706e4b692e..3874a503d16 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
@@ -43,8 +43,8 @@ public FindFullTextAction(BasePanel basePanel) {
     @Override
     public void execute() {
         BackgroundTask.wrap(this::findFullTexts)
-                .onSuccess(this::downloadFullTexts)
-                .executeWith(Globals.TASK_EXECUTOR);
+                      .onSuccess(this::downloadFullTexts)
+                      .executeWith(Globals.TASK_EXECUTOR);
     }
 
     private Map<Optional<URL>, BibEntry> findFullTexts() {
@@ -100,8 +100,7 @@ private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
 
                 //Download full text
                 addLinkedFileFromURL(result.get(), entry);
-
-           } else {
+            } else {
                 dialogService.notify(Localization.lang("No full text document found for entry %0.",
                         entry.getCiteKeyOptional().orElse(Localization.lang("undefined"))));
             }
@@ -115,7 +114,8 @@ private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
     /**
      * This method attaches a linked file from a URL (if not already linked) to an entry using the key and value pair
      * from the findFullTexts map
-     * @param url the url "key"
+     *
+     * @param url   the url "key"
      * @param entry the entry "value"
      */
     private void addLinkedFileFromURL(URL url, BibEntry entry) {
diff --git a/src/main/java/org/jabref/gui/externalfiles/FindUnlinkedFilesDialog.java b/src/main/java/org/jabref/gui/externalfiles/FindUnlinkedFilesDialog.java
index 5a8b0e8c5a8..f9e0e8a689c 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FindUnlinkedFilesDialog.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FindUnlinkedFilesDialog.java
@@ -9,9 +9,10 @@
 import java.nio.file.Paths;
 import java.nio.file.StandardOpenOption;
 import java.util.ArrayList;
-import java.util.Collection;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
+import java.util.stream.Collectors;
 
 import javafx.collections.FXCollections;
 import javafx.geometry.Insets;
@@ -19,7 +20,6 @@
 import javafx.scene.control.Button;
 import javafx.scene.control.ButtonBar;
 import javafx.scene.control.ButtonType;
-import javafx.scene.control.CheckBox;
 import javafx.scene.control.CheckBoxTreeItem;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.Label;
@@ -34,24 +34,24 @@
 import javafx.scene.layout.Priority;
 import javafx.scene.layout.StackPane;
 import javafx.scene.layout.VBox;
+import javafx.stage.FileChooser;
 
 import org.jabref.Globals;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.importer.EntryFromFileCreator;
-import org.jabref.gui.importer.EntryFromFileCreatorManager;
 import org.jabref.gui.importer.UnlinkedFilesCrawler;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.FileDialogConfiguration;
+import org.jabref.gui.util.FileFilterConverter;
 import org.jabref.gui.util.ViewModelListCellFactory;
 import org.jabref.gui.util.ViewModelTreeCellFactory;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.EntryTypes;
+import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.EntryType;
 import org.jabref.preferences.JabRefPreferences;
 
 import org.slf4j.Logger;
@@ -65,17 +65,15 @@ public class FindUnlinkedFilesDialog extends BaseDialog<Void> {
     private static final Logger LOGGER = LoggerFactory.getLogger(FindUnlinkedFilesDialog.class);
     private final JabRefFrame frame;
     private final BibDatabaseContext databaseContext;
-    private final EntryFromFileCreatorManager creatorManager;
+    private final ImportHandler importHandler;
     private final JabRefPreferences preferences = Globals.prefs;
     private final DialogService dialogService;
     private Button buttonScan;
     private Button buttonExport;
     private Button buttonApply;
-    private CheckBox checkboxCreateKeywords;
     private TextField textfieldDirectoryPath;
     private TreeView<FileNodeWrapper> tree;
-    private ComboBox<FileFilter> comboBoxFileTypeSelection;
-    private ComboBox<EntryType> comboBoxEntryTypeSelection;
+    private ComboBox<FileChooser.ExtensionFilter> comboBoxFileTypeSelection;
     private VBox panelSearchProgress;
     private BackgroundTask findUnlinkedFilesTask;
 
@@ -86,7 +84,16 @@ public FindUnlinkedFilesDialog(JabRefFrame frame) {
         dialogService = frame.getDialogService();
 
         databaseContext = frame.getCurrentBasePanel().getBibDatabaseContext();
-        creatorManager = new EntryFromFileCreatorManager(ExternalFileTypes.getInstance());
+        importHandler = new ImportHandler(
+                dialogService,
+                databaseContext,
+                ExternalFileTypes.getInstance(),
+                Globals.prefs.getFilePreferences(),
+                Globals.prefs.getImportFormatPreferences(),
+                Globals.prefs.getUpdateFieldPreferences(),
+                Globals.getFileUpdateMonitor(),
+                frame.getUndoManager()
+        );
 
         initialize();
     }
@@ -166,9 +173,6 @@ private void initialize() {
             root.setExpanded(true);
         });
 
-        checkboxCreateKeywords = new CheckBox(Localization.lang("Create directory based keywords"));
-        checkboxCreateKeywords.setTooltip(new Tooltip((Localization.lang("Creates keywords in created entrys with directory pathnames"))));
-
         textfieldDirectoryPath = new TextField();
         Path initialPath = databaseContext.getFirstExistingFileDir(preferences.getFilePreferences())
                                           .orElse(preferences.getWorkingDir());
@@ -177,7 +181,6 @@ private void initialize() {
         Label labelDirectoryDescription = new Label(Localization.lang("Select a directory where the search shall start."));
         Label labelFileTypesDescription = new Label(Localization.lang("Select file type:"));
         Label labelFilesDescription = new Label(Localization.lang("These files are not linked in the active library."));
-        Label labelEntryTypeDescription = new Label(Localization.lang("Entry type to be created:"));
         Label labelSearchingDirectoryInfo = new Label(Localization.lang("Searching file system..."));
 
         tree = new TreeView<>();
@@ -211,29 +214,21 @@ private void initialize() {
                     }
                 })
                 .install(tree);
-        List<FileFilter> fileFilterList = creatorManager.getFileFilterList();
+        List<FileChooser.ExtensionFilter> fileFilterList = Arrays.asList(
+                FileFilterConverter.ANY_FILE,
+                FileFilterConverter.toExtensionFilter(StandardFileType.PDF),
+                FileFilterConverter.toExtensionFilter(StandardFileType.BIBTEX_DB)
+        );
+
         comboBoxFileTypeSelection = new ComboBox<>(FXCollections.observableArrayList(fileFilterList));
         comboBoxFileTypeSelection.getSelectionModel().selectFirst();
-        new ViewModelListCellFactory<FileFilter>()
-                .withText(Object::toString)
-                .withIcon(fileFilter -> {
-                    if (fileFilter instanceof EntryFromFileCreator) {
-                        EntryFromFileCreator creator = (EntryFromFileCreator) fileFilter;
-                        if (creator.getExternalFileType() != null) {
-                            return creator.getExternalFileType().getIcon();
-                        }
-                    }
-                    return null;
-                })
+        new ViewModelListCellFactory<FileChooser.ExtensionFilter>()
+                .withText(fileFilter -> fileFilter.getDescription() + fileFilter.getExtensions().stream().collect(Collectors.joining(", ", " (", ")")))
+                .withIcon(fileFilter -> ExternalFileTypes.getInstance().getExternalFileTypeByExt(fileFilter.getExtensions().get(0))
+                                                         .map(ExternalFileType::getIcon)
+                                                         .orElse(null))
                 .install(comboBoxFileTypeSelection);
 
-        Collection<EntryType> entryTypes = EntryTypes.getAllValues(frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
-        comboBoxEntryTypeSelection = new ComboBox<>(FXCollections.observableArrayList(entryTypes));
-        comboBoxEntryTypeSelection.getSelectionModel().selectFirst();
-        new ViewModelListCellFactory<EntryType>()
-                .withText(EntryType::getName)
-                .install(comboBoxEntryTypeSelection);
-
         panelSearchProgress = new VBox(5, labelSearchingDirectoryInfo, progressBarSearching);
         panelSearchProgress.toFront();
         panelSearchProgress.setVisible(false);
@@ -261,17 +256,10 @@ private void initialize() {
         panelFiles.setCenter(stackPaneTree);
         panelFiles.setBottom(new HBox(5, buttonOptionSelectAll, buttonOptionDeselectAll, buttonOptionExpandAll, buttonOptionCollapseAll, buttonExport));
 
-        VBox panelEntryTypesSelection = new VBox(5);
-        panelEntryTypesSelection.getChildren().setAll(
-                new HBox(15, labelEntryTypeDescription, comboBoxEntryTypeSelection),
-                checkboxCreateKeywords
-        );
-
         VBox container = new VBox(20);
         container.getChildren().addAll(
                 panelDirectory,
-                panelFiles,
-                panelEntryTypesSelection
+                panelFiles
         );
         container.setPrefWidth(600);
         getDialogPane().setContent(container);
@@ -295,7 +283,7 @@ private void expandTree(TreeItem<?> item, boolean expand) {
      */
     private void startSearch() {
         Path directory = getSearchDirectory();
-        FileFilter selectedFileFilter = comboBoxFileTypeSelection.getValue();
+        FileFilter selectedFileFilter = FileFilterConverter.toFileFilter(comboBoxFileTypeSelection.getValue());
 
         findUnlinkedFilesTask = new UnlinkedFilesCrawler(directory, selectedFileFilter, databaseContext)
                 .onRunning(() -> {
@@ -343,27 +331,7 @@ private void startImport() {
             return;
         }
 
-        final EntryType entryType = comboBoxEntryTypeSelection.getValue();
-
-        List<String> errors = creatorManager.addEntriesFromFiles(
-                fileList,
-                databaseContext.getDatabase(),
-                frame.getCurrentBasePanel(),
-                entryType,
-                checkboxCreateKeywords.isSelected());
-
-        if (!errors.isEmpty()) {
-            String message;
-            if (errors.size() == 1) {
-                message = Localization.lang("There was one file that could not be imported.");
-            } else {
-                message = Localization.lang("There were %0 files which could not be imported.",
-                        Integer.toString(errors.size()));
-            }
-            dialogService.showWarningDialogAndWait(
-                    Localization.lang("Warning"),
-                    Localization.lang("The import finished with warnings:") + "\n" + message);
-        }
+        importHandler.importAsNewEntries(fileList);
     }
 
     /**
diff --git a/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java b/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
new file mode 100644
index 00000000000..6d0860f53f0
--- /dev/null
+++ b/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
@@ -0,0 +1,113 @@
+package org.jabref.gui.externalfiles;
+
+import java.nio.file.Path;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.undo.CompoundEdit;
+import javax.swing.undo.UndoManager;
+
+import org.jabref.Globals;
+import org.jabref.gui.DialogService;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.logic.externalfiles.ExternalFilesContentImporter;
+import org.jabref.logic.importer.ImportFormatPreferences;
+import org.jabref.logic.util.UpdateField;
+import org.jabref.logic.util.UpdateFieldPreferences;
+import org.jabref.logic.util.io.FileUtil;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.FieldName;
+import org.jabref.model.metadata.FilePreferences;
+import org.jabref.model.util.FileUpdateMonitor;
+import org.jabref.preferences.JabRefPreferences;
+
+public class ImportHandler {
+
+    private final BibDatabaseContext database;
+    private final UpdateFieldPreferences updateFieldPreferences;
+    private final DialogService dialogService;
+    private final FileUpdateMonitor fileUpdateMonitor;
+    private final ExternalFilesEntryLinker linker;
+    private final ExternalFilesContentImporter contentImporter;
+    private final UndoManager undoManager;
+
+    public ImportHandler(DialogService dialogService,
+                         BibDatabaseContext database,
+                         ExternalFileTypes externalFileTypes,
+                         FilePreferences filePreferences,
+                         ImportFormatPreferences importFormatPreferences,
+                         UpdateFieldPreferences updateFieldPreferences,
+                         FileUpdateMonitor fileupdateMonitor,
+                         UndoManager undoManager) {
+
+        this.dialogService = dialogService;
+        this.database = database;
+        this.updateFieldPreferences = updateFieldPreferences;
+        this.fileUpdateMonitor = fileupdateMonitor;
+
+        this.linker = new ExternalFilesEntryLinker(externalFileTypes, filePreferences, database);
+        this.contentImporter = new ExternalFilesContentImporter(importFormatPreferences);
+        this.undoManager = undoManager;
+    }
+
+    public ExternalFilesEntryLinker getLinker() {
+        return linker;
+    }
+
+    public void importAsNewEntries(List<Path> files) {
+        CompoundEdit ce = new CompoundEdit();
+        for (Path file : files) {
+            List<BibEntry> entriesToAdd;
+            if (FileUtil.getFileExtension(file).filter("pdf"::equals).isPresent()) {
+                List<BibEntry> pdfResult = contentImporter.importPDFContent(file);
+                List<BibEntry> xmpEntriesInFile = contentImporter.importXMPContent(file);
+
+                // First try xmp import, if empty try pdf import, otherwise create empty entry
+                if (!xmpEntriesInFile.isEmpty()) {
+                    if (!pdfResult.isEmpty()) {
+                        //FIXME: Show merge dialog?
+                        entriesToAdd = xmpEntriesInFile;
+                    } else {
+                        entriesToAdd = xmpEntriesInFile;
+                    }
+                } else {
+                    if (!pdfResult.isEmpty()) {
+                        entriesToAdd = pdfResult;
+                    } else {
+                        entriesToAdd = Collections.singletonList(createEmptyEntryWithLink(file));
+                    }
+                }
+            } else {
+                entriesToAdd = Collections.singletonList(createEmptyEntryWithLink(file));
+            }
+
+            insertEntries(entriesToAdd);
+            entriesToAdd.forEach(entry -> ce.addEdit(new UndoableInsertEntry(database.getDatabase(), entry)));
+        }
+        ce.end();
+        undoManager.addEdit(ce);
+    }
+
+    private BibEntry createEmptyEntryWithLink(Path file) {
+        BibEntry entry = new BibEntry();
+        entry.setField(FieldName.TITLE, file.getFileName().toString());
+        linker.addFilesToEntry(entry, Collections.singletonList(file));
+        return entry;
+    }
+
+    public void importEntriesFromBibFiles(Path bibFile) {
+        List<BibEntry> entriesToImport = contentImporter.importFromBibFile(bibFile, fileUpdateMonitor);
+        insertEntries(entriesToImport);
+    }
+
+    private void insertEntries(List<BibEntry> entries) {
+        database.getDatabase().insertEntries(entries);
+
+        if (Globals.prefs.getBoolean(JabRefPreferences.USE_OWNER)) {
+            // Set owner field to default value
+            UpdateField.setAutomaticFields(entries, true, true, updateFieldPreferences);
+        }
+    }
+}
diff --git a/src/main/java/org/jabref/gui/externalfiles/NewDroppedFileHandler.java b/src/main/java/org/jabref/gui/externalfiles/NewDroppedFileHandler.java
deleted file mode 100644
index 77cfd682642..00000000000
--- a/src/main/java/org/jabref/gui/externalfiles/NewDroppedFileHandler.java
+++ /dev/null
@@ -1,152 +0,0 @@
-package org.jabref.gui.externalfiles;
-
-import java.io.IOException;
-import java.nio.file.Path;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Optional;
-
-import javafx.scene.control.ButtonBar.ButtonData;
-import javafx.scene.control.ButtonType;
-import javafx.scene.control.DialogPane;
-import javafx.scene.control.TextArea;
-import javafx.scene.layout.VBox;
-import javafx.scene.text.Text;
-
-import org.jabref.Globals;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.logic.externalfiles.ExternalFilesContentImporter;
-import org.jabref.logic.importer.ImportFormatPreferences;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.UpdateField;
-import org.jabref.logic.util.UpdateFieldPreferences;
-import org.jabref.logic.util.io.FileUtil;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.metadata.FilePreferences;
-import org.jabref.model.util.FileUpdateMonitor;
-import org.jabref.preferences.JabRefPreferences;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class NewDroppedFileHandler {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(NewDroppedFileHandler.class);
-
-    private final BibDatabaseContext bibDatabaseContext;
-    private final UpdateFieldPreferences updateFieldPreferences;
-    private final DialogService dialogService;
-    private final FileUpdateMonitor fileUpdateMonitor;
-    private final ExternalFilesEntryLinker linker;
-    private final ExternalFilesContentImporter contentImporter;
-
-    public NewDroppedFileHandler(DialogService dialogService,
-                                 BibDatabaseContext bibDatabaseContext,
-                                 ExternalFileTypes externalFileTypes,
-                                 FilePreferences filePreferences,
-                                 ImportFormatPreferences importFormatPreferences,
-                                 UpdateFieldPreferences updateFieldPreferences,
-                                 FileUpdateMonitor fileupdateMonitor) {
-
-        this.dialogService = dialogService;
-        this.bibDatabaseContext = bibDatabaseContext;
-        this.updateFieldPreferences = updateFieldPreferences;
-        this.fileUpdateMonitor = fileupdateMonitor;
-
-        this.linker = new ExternalFilesEntryLinker(externalFileTypes, filePreferences, bibDatabaseContext);
-        this.contentImporter = new ExternalFilesContentImporter(importFormatPreferences);
-    }
-
-    public void addNewEntryFromXMPorPDFContent(BibEntry entry, List<Path> files) {
-
-        for (Path file : files) {
-
-            if (FileUtil.getFileExtension(file).filter(ext -> "pdf".equals(ext)).isPresent()) {
-
-                try {
-                    List<BibEntry> pdfResult = contentImporter.importPDFContent(file);
-                    //FIXME: Show merge dialog if working again properly
-                    List<BibEntry> xmpEntriesInFile = contentImporter.importXMPContent(file);
-
-                    //First try xmp import, if empty try pdf import, otherwise show dialog
-                    if (xmpEntriesInFile.isEmpty()) {
-                        if (pdfResult.isEmpty()) {
-                            addToEntryRenameAndMoveToFileDir(entry, files);
-                        } else {
-                            showImportOrLinkFileDialog(pdfResult, file, entry);
-                        }
-                    } else {
-                        showImportOrLinkFileDialog(xmpEntriesInFile, file, entry);
-                    }
-
-                } catch (IOException e) {
-                    LOGGER.warn("Problem reading XMP", e);
-                }
-
-            } else {
-                addToEntryRenameAndMoveToFileDir(entry, files);
-            }
-        }
-    }
-
-    public void importEntriesFromDroppedBibFiles(Path bibFile) {
-
-        List<BibEntry> entriesToImport = contentImporter.importFromBibFile(bibFile, fileUpdateMonitor);
-        bibDatabaseContext.getDatabase().insertEntries(entriesToImport);
-
-        if (Globals.prefs.getBoolean(JabRefPreferences.USE_OWNER)) {
-            // Set owner field to default value
-            UpdateField.setAutomaticFields(entriesToImport, true, true, updateFieldPreferences);
-        }
-    }
-
-    private void showImportOrLinkFileDialog(List<BibEntry> entriesToImport, Path fileName, BibEntry entryToLink) {
-
-        DialogPane pane = new DialogPane();
-
-        VBox vbox = new VBox();
-        Text text = new Text(Localization.lang("The PDF contains one or several BibTeX-records.")
-                             + "\n" + Localization.lang("Do you want to import these as new entries into the current library or do you want to link the file to the entry?"));
-        vbox.getChildren().add(text);
-
-        entriesToImport.forEach(entry -> {
-            TextArea textArea = new TextArea(entry.toString());
-            textArea.setEditable(false);
-            vbox.getChildren().add(textArea);
-        });
-        pane.setContent(vbox);
-
-        ButtonType importButton = new ButtonType("Import into library", ButtonData.OK_DONE);
-        ButtonType linkToEntry = new ButtonType("Link file to entry", ButtonData.OTHER);
-
-        Optional<ButtonType> buttonPressed = dialogService.showCustomDialogAndWait(Localization.lang("XMP-metadata found in PDF: %0", fileName.getFileName().toString()), pane, importButton, linkToEntry, ButtonType.CANCEL);
-
-        if (buttonPressed.equals(Optional.of(importButton))) {
-            bibDatabaseContext.getDatabase().insertEntries(entriesToImport);
-        }
-        if (buttonPressed.equals(Optional.of(linkToEntry))) {
-            addToEntryRenameAndMoveToFileDir(entryToLink, Arrays.asList(fileName));
-        }
-    }
-
-    public void addToEntryRenameAndMoveToFileDir(BibEntry entry, List<Path> files) {
-        linker.addFilesToEntry(entry, files);
-        linker.moveLinkedFilesToFileDir(entry);
-        linker.renameLinkedFilesToPattern(entry);
-    }
-
-    public void copyFilesToFileDirAndAddToEntry(BibEntry entry, List<Path> files) {
-        for (Path file : files) {
-            linker.copyFileToFileDir(file).ifPresent(copiedFile -> {
-                linker.addFilesToEntry(entry, files);
-            });
-        }
-    }
-
-    public void addToEntry(BibEntry entry, List<Path> files) {
-        linker.addFilesToEntry(entry, files);
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypes.java b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypes.java
index 1a2d2fda146..7e7d2836f1b 100644
--- a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypes.java
+++ b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypes.java
@@ -71,7 +71,8 @@ public Optional<ExternalFileType> getExternalFileTypeByName(String name) {
      * @return The ExternalFileType registered, or null if none.
      */
     public Optional<ExternalFileType> getExternalFileTypeByExt(String extension) {
-        return externalFileTypes.stream().filter(type -> type.getExtension().equalsIgnoreCase(extension)).findFirst();
+        String extensionCleaned = extension.replace(".", "").replace("*", "");
+        return externalFileTypes.stream().filter(type -> type.getExtension().equalsIgnoreCase(extensionCleaned)).findFirst();
     }
 
     /**
diff --git a/src/main/java/org/jabref/gui/importer/EntryFromExternalFileCreator.java b/src/main/java/org/jabref/gui/importer/EntryFromExternalFileCreator.java
deleted file mode 100644
index 931dcb2bb00..00000000000
--- a/src/main/java/org/jabref/gui/importer/EntryFromExternalFileCreator.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package org.jabref.gui.importer;
-
-import java.io.File;
-import java.util.Optional;
-
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.model.entry.BibEntry;
-
-/** EntryCreator for any predefined ExternalFileType.
- * This Creator accepts all files with the extension defined in the ExternalFileType.
- */
-public class EntryFromExternalFileCreator extends EntryFromFileCreator {
-
-    public EntryFromExternalFileCreator(ExternalFileType externalFileType) {
-        super(externalFileType);
-    }
-
-    @Override
-    public boolean accept(File f) {
-        return f.getName().endsWith("." + externalFileType.getExtension());
-    }
-
-    @Override
-    protected Optional<BibEntry> createBibtexEntry(File file) {
-        if (!accept(file)) {
-            return Optional.empty();
-        }
-
-        return Optional.of(new BibEntry());
-    }
-
-    @Override
-    public String getFormatName() {
-        return externalFileType.getName();
-    }
-}
diff --git a/src/main/java/org/jabref/gui/importer/EntryFromFileCreator.java b/src/main/java/org/jabref/gui/importer/EntryFromFileCreator.java
deleted file mode 100644
index 80264c77c00..00000000000
--- a/src/main/java/org/jabref/gui/importer/EntryFromFileCreator.java
+++ /dev/null
@@ -1,186 +0,0 @@
-package org.jabref.gui.importer;
-
-import java.io.File;
-import java.io.FileFilter;
-import java.nio.file.Path;
-import java.util.List;
-import java.util.Optional;
-import java.util.StringTokenizer;
-
-import org.jabref.Globals;
-import org.jabref.JabRefGUI;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.filelist.FileListEntry;
-import org.jabref.gui.filelist.FileListTableModel;
-import org.jabref.logic.util.io.FileUtil;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FieldName;
-
-/**
- * The interface EntryFromFileCreator does twice: <br>
- * On the one hand, it defines a set of files, which it can deal with, on the
- * other hand it provides the functionality to create a Bibtex entry out of a
- * file. The interface extends the java.io.FileFilter to inherit a common way of
- * defining file sets.
- */
-public abstract class EntryFromFileCreator implements FileFilter {
-
-    private static final int MIN_PATH_TOKEN_LENGTH = 4;
-
-    protected final ExternalFileType externalFileType;
-
-    /**
-     * Constructor. <br>
-     * Forces subclasses to provide an {@link ExternalFileType} instance, which
-     * they build on.
-     *
-     * @param externalFileType
-     */
-    EntryFromFileCreator(ExternalFileType externalFileType) {
-        this.externalFileType = externalFileType;
-    }
-
-    /**
-     * Splits the path to the file and builds a keywords String in the format
-     * that is used by Jabref.
-     */
-    private static String extractPathesToKeyWordsfield(String absolutePath) {
-        StringBuilder sb = new StringBuilder();
-        StringTokenizer st = new StringTokenizer(absolutePath, String.valueOf(File.separatorChar));
-        while (st.hasMoreTokens()) {
-            String token = st.nextToken();
-            if (!st.hasMoreTokens()) {
-                // ignore last token. The filename ist not wanted as keyword.
-                break;
-            }
-            if (token.length() >= MIN_PATH_TOKEN_LENGTH) {
-                if (sb.length() > 0) {
-                    // TODO: find Jabref constant for delimter
-                    sb.append(',');
-                }
-                sb.append(token);
-            }
-        }
-        return sb.toString();
-    }
-
-    protected abstract Optional<BibEntry> createBibtexEntry(File f);
-
-    /**
-     * <p>
-     * To support platform independence, a creator must define what types of
-     * files it accepts on it's own.
-     * </p>
-     * <p>
-     * Basically, accepting files which end with the file extension that is
-     * described in the nested {@link #externalFileType} would work on windows
-     * systems. This is also the recommended criterion, on which files should be
-     * accepted.
-     * </p>
-     * <p>
-     * However, defining what types of files this creator accepts, is a property
-     * of <i>entry creators</i>, that is left to the user.
-     * </p>
-     */
-    @Override
-    public abstract boolean accept(File f);
-
-    /**
-     * Name of this import format.
-     *
-     * <p>
-     * The name must be unique.
-     * </p>
-     *
-     * @return format name, must be unique and not <code>null</code>
-     */
-    public abstract String getFormatName();
-
-    /**
-     * Create one BibEntry containing information regarding the given File.
-     *
-     * @param f
-     * @param addPathTokensAsKeywords
-     * @return
-     */
-    public Optional<BibEntry> createEntry(File f, boolean addPathTokensAsKeywords) {
-        if ((f == null) || !f.exists()) {
-            return Optional.empty();
-        }
-        Optional<BibEntry> newEntry = createBibtexEntry(f);
-
-        if (!(newEntry.isPresent())) {
-            return newEntry;
-        }
-
-        if (addPathTokensAsKeywords) {
-            appendToField(newEntry.get(), FieldName.KEYWORDS, extractPathesToKeyWordsfield(f.getAbsolutePath()));
-        }
-
-        if (!newEntry.get().hasField(FieldName.TITLE)) {
-            newEntry.get().setField(FieldName.TITLE, f.getName());
-        }
-
-        addFileInfo(newEntry.get(), f);
-        return newEntry;
-    }
-
-    /** Returns the ExternalFileType that is imported here */
-    public ExternalFileType getExternalFileType() {
-        return externalFileType;
-    }
-
-    private void addFileInfo(BibEntry entry, File file) {
-        Optional<ExternalFileType> fileType = ExternalFileTypes.getInstance()
-                .getExternalFileTypeByExt(externalFileType.getFieldName());
-
-        List<Path> possibleFilePaths = JabRefGUI.getMainFrame().getCurrentBasePanel().getBibDatabaseContext()
-                                                .getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
-        Path shortenedFileName = FileUtil.relativize(file.toPath(), possibleFilePaths);
-        FileListEntry fileListEntry = new FileListEntry("", shortenedFileName.toString(), fileType);
-
-        FileListTableModel model = new FileListTableModel();
-        model.addEntry(0, fileListEntry);
-
-        entry.setField(FieldName.FILE, model.getStringRepresentation());
-    }
-
-    protected void appendToField(BibEntry entry, String field, String value) {
-        if ((value == null) || value.isEmpty()) {
-            return;
-        }
-        Optional<String> oVal = entry.getField(field);
-        if (oVal.isPresent()) {
-            // TODO: find Jabref constant for delimter
-            if (!oVal.get().contains(value)) {
-                entry.setField(field, oVal.get() + "," + value);
-            }
-        } else {
-            entry.setField(field, value);
-        }
-    }
-
-    protected void addEntrysToEntry(BibEntry entry, List<BibEntry> entrys) {
-        if (entrys != null) {
-            for (BibEntry e : entrys) {
-                addEntryDataToEntry(entry, e);
-            }
-        }
-    }
-
-    protected void addEntryDataToEntry(BibEntry entry, BibEntry e) {
-        for (String field : e.getFieldNames()) {
-            e.getField(field).ifPresent(fieldContent -> appendToField(entry, field, fieldContent));
-        }
-    }
-
-    @Override
-    public String toString() {
-        if (externalFileType == null) {
-            return "(undefined)";
-        }
-        return externalFileType.getName() + " (." + externalFileType.getExtension() + ")";
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/importer/EntryFromFileCreatorManager.java b/src/main/java/org/jabref/gui/importer/EntryFromFileCreatorManager.java
deleted file mode 100644
index 79b1d93f582..00000000000
--- a/src/main/java/org/jabref/gui/importer/EntryFromFileCreatorManager.java
+++ /dev/null
@@ -1,202 +0,0 @@
-package org.jabref.gui.importer;
-
-import java.io.File;
-import java.io.FileFilter;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Optional;
-
-import javax.swing.undo.CompoundEdit;
-
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.undo.UndoableInsertEntry;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.EntryType;
-import org.jabref.model.entry.IdGenerator;
-
-/**
- * The class EntryFromFileCreatorManager manages entry creators.
- * The manager knows all existing implementations of the interface EntryFromFileCreator.
- * Given a file, the manager can then provide a creator, which is able to create a Bibtex entry for his file.
- * Knowing all implementations of the interface, the manager also knows the set of all files, of which Bibtex entries can be created.
- * The GUI uses this capability for offering the user only such files, of which entries could actually be created.
- *
- */
-public final class EntryFromFileCreatorManager {
-
-    private final List<EntryFromFileCreator> entryCreators;
-
-
-    public EntryFromFileCreatorManager(ExternalFileTypes externalFilesTypes) {
-
-        entryCreators = new ArrayList<>(10);
-        entryCreators.add(new EntryFromPDFCreator(externalFilesTypes));
-
-        // add a creator for each ExternalFileType if there is no specialized
-        // creator existing.
-        Collection<ExternalFileType> fileTypes = externalFilesTypes.getExternalFileTypeSelection();
-
-        for (ExternalFileType exFileType : fileTypes) {
-            if (!hasSpecialisedCreatorForExternalFileType(exFileType)) {
-                entryCreators.add(new EntryFromExternalFileCreator(exFileType));
-            }
-        }
-    }
-
-    private boolean hasSpecialisedCreatorForExternalFileType(
-            ExternalFileType externalFileType) {
-        for (EntryFromFileCreator entryCreator : entryCreators) {
-            if ((entryCreator.getExternalFileType() == null)
-                    || (entryCreator.getExternalFileType().getExtension().isEmpty())) {
-                continue;
-            }
-            if (entryCreator.getExternalFileType().getExtension().equals(
-                    externalFileType.getExtension())) {
-                return true;
-            }
-        }
-        return false;
-    }
-
-    /**
-     * Returns a {@link EntryFromFileCreator} object that is capable of creating a entry for the given file.
-     *
-     * @param file the external file
-     * @return an empty optional if there is no EntryFromFileCreator for this file.
-     */
-    public Optional<EntryFromFileCreator> getEntryCreator(Path file) {
-        if (!Files.exists(file)) {
-            return Optional.empty();
-        }
-        for (EntryFromFileCreator creator : entryCreators) {
-            if (creator.accept(file.toFile())) {
-                return Optional.of(creator);
-            }
-        }
-        return Optional.empty();
-    }
-
-    /**
-     * Tries to add a entry for each file in the List.
-     *
-     * @param files
-     * @param database
-     * @param entryType
-     * @return List of unexpected import event messages including failures.
-     */
-    public List<String> addEntrysFromFiles(List<Path> files,
-                                           BibDatabase database, EntryType entryType,
-                                           boolean generateKeywordsFromPathToFile) {
-        return addEntriesFromFiles(files, database, null, entryType, generateKeywordsFromPathToFile);
-    }
-
-    /**
-     * Tries to add a entry for each file in the List.
-     *
-     * @return Returns a list of unexpected failures while importing
-     */
-    public List<String> addEntriesFromFiles(List<Path> files,
-                                            BibDatabase database, BasePanel panel, EntryType entryType,
-                                            boolean generateKeywordsFromPathToFile) {
-
-        List<String> importGUIMessages = new ArrayList<>();
-        int count = 0;
-        CompoundEdit ce = new CompoundEdit();
-        for (Path f : files) {
-            Optional<EntryFromFileCreator> creator = getEntryCreator(f);
-            if (!creator.isPresent()) {
-                importGUIMessages.add("Problem importing " + f.toAbsolutePath() + ": Unknown filetype.");
-            } else {
-                Optional<BibEntry> entry = creator.get().createEntry(f.toFile(), generateKeywordsFromPathToFile);
-                if (!entry.isPresent()) {
-                    importGUIMessages.add("Problem importing " + f.toAbsolutePath() + ": Entry could not be created.");
-                    continue;
-                }
-                if (entryType != null) {
-                    entry.get().setType(entryType);
-                }
-                if (entry.get().getId() == null) {
-                    entry.get().setId(IdGenerator.next());
-                }
-                /*
-                 * TODO: database.insertEntry(BibEntry) is not sensible. Why
-                 * does 'true' mean "There were duplicates", while 'false' means
-                 * "Everything alright"?
-                 */
-                if (!database.containsEntryWithId(entry.get().getId())) {
-                    // Work around SIDE EFFECT of creator.createEntry. The EntryFromPDFCreator also creates the entry in the table
-                    // Therefore, we only insert the entry if it is not already present
-                    if (database.insertEntry(entry.get())) {
-                        importGUIMessages.add("Problem importing " + f.toAbsolutePath() + ": Insert into BibDatabase failed.");
-                    } else {
-                        count++;
-                        if (panel != null) {
-                            ce.addEdit(new UndoableInsertEntry(database, entry.get()));
-                        }
-                    }
-                }
-            }
-        }
-
-        if ((count > 0) && (panel != null)) {
-            ce.end();
-            panel.getUndoManager().addEdit(ce);
-        }
-        return importGUIMessages;
-
-    }
-
-    /**
-     * Returns a {@link FileFilter} instance which will accept all files, for
-     * which a {@link EntryFromFileCreator} exists, that accepts the files. <br>
-     * <br>
-     * This {@link FileFilter} will be displayed in the GUI as
-     * "All supported files".
-     *
-     * @return A {@link FileFilter} that accepts all files for which creators
-     *         exist.
-     */
-    private FileFilter getFileFilter() {
-        return new FileFilter() {
-
-            /**
-             * Accepts all files, which are accepted by any known creator.
-             */
-            @Override
-            public boolean accept(File file) {
-                for (EntryFromFileCreator creator : entryCreators) {
-                    if (creator.accept(file)) {
-                        return true;
-                    }
-                }
-                return false;
-            }
-
-            @Override
-            public String toString() {
-                return Localization.lang("All external files");
-            }
-        };
-    }
-
-    /**
-     * Returns a list of all {@link FileFilter} instances (i.e.
-     * {@link EntryFromFileCreator}, plus the file filter that comes with the
-     * {@link #getFileFilter()} method.
-     *
-     * @return A List of all known possible file filters.
-     */
-    public List<FileFilter> getFileFilterList() {
-        List<FileFilter> filters = new ArrayList<>();
-        filters.add(getFileFilter());
-        filters.addAll(entryCreators);
-        return filters;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/importer/EntryFromPDFCreator.java b/src/main/java/org/jabref/gui/importer/EntryFromPDFCreator.java
deleted file mode 100644
index 3c50b6823e6..00000000000
--- a/src/main/java/org/jabref/gui/importer/EntryFromPDFCreator.java
+++ /dev/null
@@ -1,62 +0,0 @@
-package org.jabref.gui.importer;
-
-import java.io.File;
-import java.util.Collections;
-import java.util.Locale;
-import java.util.Optional;
-
-import org.jabref.JabRefGUI;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.externalfiletype.StandardExternalFileType;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.pdfimport.PdfImporter;
-import org.jabref.pdfimport.PdfImporter.ImportPdfFilesResult;
-
-/**
- * Uses XMPUtils to get one BibEntry for a PDF-File.
- * Also imports the non-XMP Data (PDDocument-Information) using XMPUtil.getBibtexEntryFromDocumentInformation.
- * If data from more than one entry is read by XMPUtil then this entys are merged into one.
- */
-public class EntryFromPDFCreator extends EntryFromFileCreator {
-
-    public EntryFromPDFCreator(ExternalFileTypes externalFileTypes) {
-        super(EntryFromPDFCreator.getPDFExternalFileType(externalFileTypes));
-    }
-
-    private static ExternalFileType getPDFExternalFileType(ExternalFileTypes externalFileTypes) {
-        return externalFileTypes.getExternalFileTypeByExt("pdf")
-                                .orElse(StandardExternalFileType.PDF);
-    }
-
-    /**
-     * Accepts all Files having as suffix ".PDF" (in ignore case mode).
-     */
-    @Override
-    public boolean accept(File f) {
-        return (f != null) && f.getName().toUpperCase(Locale.ROOT).endsWith(".PDF");
-    }
-
-    @Override
-    protected Optional<BibEntry> createBibtexEntry(File pdfFile) {
-
-        if (!accept(pdfFile)) {
-            return Optional.empty();
-        }
-
-        PdfImporter pi = new PdfImporter(JabRefGUI.getMainFrame(), JabRefGUI.getMainFrame().getCurrentBasePanel(), JabRefGUI.getMainFrame().getCurrentBasePanel().getMainTable(), -1);
-        ImportPdfFilesResult res = pi.importPdfFiles(Collections.singletonList(pdfFile.toString()));
-        if (res.getEntries().size() == 1) {
-            return Optional.of(res.getEntries().get(0));
-        } else {
-            return Optional.empty();
-        }
-
-    }
-
-    @Override
-    public String getFormatName() {
-        return "PDF";
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/importer/ImportInspectionDialog.java b/src/main/java/org/jabref/gui/importer/ImportInspectionDialog.java
index 2ce86d731c4..6906a6e36cc 100644
--- a/src/main/java/org/jabref/gui/importer/ImportInspectionDialog.java
+++ b/src/main/java/org/jabref/gui/importer/ImportInspectionDialog.java
@@ -696,11 +696,11 @@ public void actionPerformed(ActionEvent event) {
                     if (entry.isGroupHit()) {
 
                         boolean continuePressed = DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().showConfirmationDialogWithOptOutAndWait(Localization.lang("Duplicates found"),
-                                                                                                                                                               Localization.lang("There are possible duplicates (marked with an icon) that haven't been resolved. Continue?"),
-                                                                                                                                                               Localization.lang("Continue"),
-                                                                                                                                                               Localization.lang("Cancel"),
-                                                                                                                                                               Localization.lang("Disable this confirmation dialog"),
-                                                                                                                                                               optOut -> Globals.prefs.putBoolean(JabRefPreferences.WARN_ABOUT_DUPLICATES_IN_INSPECTION, !optOut)));
+                                Localization.lang("There are possible duplicates (marked with an icon) that haven't been resolved. Continue?"),
+                                Localization.lang("Continue"),
+                                Localization.lang("Cancel"),
+                                Localization.lang("Disable this confirmation dialog"),
+                                optOut -> Globals.prefs.putBoolean(JabRefPreferences.WARN_ABOUT_DUPLICATES_IN_INSPECTION, !optOut)));
 
                         if (!continuePressed) {
                             return;
@@ -1072,7 +1072,6 @@ public void mousePressed(MouseEvent e) {
                         } finally {
                             entries.getReadWriteLock().writeLock().unlock();
                         }
-
                     } else if (result == DuplicateResolverResult.KEEP_RIGHT) {
                         // Remove the entry from the import inspection dialog.
                         entries.getReadWriteLock().writeLock().lock();
diff --git a/src/main/java/org/jabref/gui/importer/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/importer/UnlinkedFilesCrawler.java
index 77e57a12ab9..492656bb540 100644
--- a/src/main/java/org/jabref/gui/importer/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/importer/UnlinkedFilesCrawler.java
@@ -32,7 +32,7 @@ public UnlinkedFilesCrawler(Path directory, FileFilter fileFilter, BibDatabaseCo
     }
 
     @Override
-    protected CheckBoxTreeItem<FileNodeWrapper> call() throws Exception {
+    protected CheckBoxTreeItem<FileNodeWrapper> call() {
         UnlinkedPDFFileFilter unlinkedPDFFileFilter = new UnlinkedPDFFileFilter(fileFilter, databaseContext);
         return searchDirectory(directory.toFile(), unlinkedPDFFileFilter);
     }
@@ -40,8 +40,7 @@ protected CheckBoxTreeItem<FileNodeWrapper> call() throws Exception {
     /**
      * Searches recursively all files in the specified directory. <br>
      * <br>
-     * All {@link File}s, which match the {@link FileFilter} that comes with the
-     * {@link EntryFromFileCreatorManager}, are taken into the resulting tree. <br>
+     * All files matched by the given {@link UnlinkedPDFFileFilter} are taken into the resulting tree. <br>
      * <br>
      * The result will be a tree structure of nodes of the type
      * {@link CheckBoxTreeItem}. <br>
diff --git a/src/main/java/org/jabref/gui/maintable/MainTable.java b/src/main/java/org/jabref/gui/maintable/MainTable.java
index 156370ec1c3..7ff9de40304 100644
--- a/src/main/java/org/jabref/gui/maintable/MainTable.java
+++ b/src/main/java/org/jabref/gui/maintable/MainTable.java
@@ -30,7 +30,7 @@
 import org.jabref.gui.DragAndDropDataFormats;
 import org.jabref.gui.GUIGlobals;
 import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.externalfiles.NewDroppedFileHandler;
+import org.jabref.gui.externalfiles.ImportHandler;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.keyboard.KeyBindingRepository;
@@ -59,7 +59,7 @@ public class MainTable extends TableView<BibEntryTableViewModel> {
     private final UndoManager undoManager;
 
     private final MainTableDataModel model;
-    private final NewDroppedFileHandler fileHandler;
+    private final ImportHandler importHandler;
     private final CustomLocalDragboard localDragboard = GUIGlobals.localDragboard;
 
     public MainTable(MainTableDataModel model, JabRefFrame frame,
@@ -71,13 +71,13 @@ public MainTable(MainTableDataModel model, JabRefFrame frame,
         this.database = Objects.requireNonNull(database);
         this.undoManager = panel.getUndoManager();
 
-        fileHandler = new NewDroppedFileHandler(frame.getDialogService(), database, externalFileTypes,
-                                                Globals.prefs.getFilePreferences(),
-                                                Globals.prefs.getImportFormatPreferences(),
-                                                Globals.prefs.getUpdateFieldPreferences(),
-                                                Globals.getFileUpdateMonitor()
-
-        );
+        importHandler = new ImportHandler(
+                frame.getDialogService(), database, externalFileTypes,
+                Globals.prefs.getFilePreferences(),
+                Globals.prefs.getImportFormatPreferences(),
+                Globals.prefs.getUpdateFieldPreferences(),
+                Globals.getFileUpdateMonitor(),
+                undoManager);
 
         this.getColumns().addAll(new MainTableColumnFactory(database, preferences.getColumnPreferences(), externalFileTypes, panel.getUndoManager(), frame.getDialogService()).createColumns());
 
@@ -279,42 +279,37 @@ private void handleOnDragDetected(TableRow<BibEntryTableViewModel> row, BibEntry
     }
 
     private void handleOnDragDropped(BibEntryTableViewModel originalItem, DragEvent event) {
-
         boolean success = false;
 
         if (event.getDragboard().hasContent(DataFormat.FILES)) {
-
             List<Path> files = event.getDragboard().getFiles().stream().map(File::toPath).collect(Collectors.toList());
-
             List<Path> bibFiles = files.stream().filter(FileUtil::isBibFile).collect(Collectors.toList());
 
             if (!bibFiles.isEmpty()) {
+                // Import all bibtex entries contained in the dropped bib files
                 for (Path file : bibFiles) {
-                    fileHandler.importEntriesFromDroppedBibFiles(file);
+                    importHandler.importEntriesFromBibFiles(file);
                 }
                 success = true;
-
             }
             if (event.getGestureTarget() instanceof TableRow) {
-
+                // Depending on the pressed modifier, import as new entries or link to drop target
                 BibEntry entry = originalItem.getEntry();
-
                 if ((event.getTransferMode() == TransferMode.MOVE)) {
-
                     LOGGER.debug("Mode MOVE"); //shift on win or no modifier
-                    fileHandler.addNewEntryFromXMPorPDFContent(entry, files);
+                    importHandler.importAsNewEntries(files);
                     success = true;
                 }
 
                 if (event.getTransferMode() == TransferMode.LINK) {
                     LOGGER.debug("LINK"); //alt on win
-                    fileHandler.addToEntryRenameAndMoveToFileDir(entry, files);
+                    importHandler.getLinker().moveFilesToFileDirAndAddToEntry(entry, files);
                     success = true;
-
                 }
+
                 if (event.getTransferMode() == TransferMode.COPY) {
                     LOGGER.debug("Mode Copy"); //ctrl on win
-                    fileHandler.copyFilesToFileDirAndAddToEntry(entry, files);
+                    importHandler.getLinker().copyFilesToFileDirAndAddToEntry(entry, files);
                     success = true;
                 }
             }
@@ -322,7 +317,6 @@ private void handleOnDragDropped(BibEntryTableViewModel originalItem, DragEvent
 
         event.setDropCompleted(success);
         event.consume();
-
     }
 
     public void addSelectionListener(ListChangeListener<? super BibEntryTableViewModel> listener) {
diff --git a/src/main/java/org/jabref/gui/maintable/PersistenceVisualStateTable.java b/src/main/java/org/jabref/gui/maintable/PersistenceVisualStateTable.java
index eb25588f568..8ee6bd949d1 100644
--- a/src/main/java/org/jabref/gui/maintable/PersistenceVisualStateTable.java
+++ b/src/main/java/org/jabref/gui/maintable/PersistenceVisualStateTable.java
@@ -66,7 +66,7 @@ private void updateColumnPreferences() {
         }
 
         if (columnNames.size() == columnsWidths.size() &&
-                columnNames.size() == preferences.getStringList(preferences.COLUMN_NAMES).size()) {
+                columnNames.size() == preferences.getStringList(JabRefPreferences.COLUMN_NAMES).size()) {
             preferences.putStringList(JabRefPreferences.COLUMN_NAMES, columnNames);
             preferences.putStringList(JabRefPreferences.COLUMN_WIDTHS, columnsWidths);
         }
diff --git a/src/main/java/org/jabref/gui/openoffice/AdvancedCiteDialog.fxml b/src/main/java/org/jabref/gui/openoffice/AdvancedCiteDialog.fxml
index 1127c2e08d7..582431c5913 100644
--- a/src/main/java/org/jabref/gui/openoffice/AdvancedCiteDialog.fxml
+++ b/src/main/java/org/jabref/gui/openoffice/AdvancedCiteDialog.fxml
@@ -6,25 +6,26 @@
 <?import javafx.scene.control.RadioButton?>
 <?import javafx.scene.control.TextField?>
 <?import javafx.scene.control.ToggleGroup?>
-<?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.VBox?>
-
-<DialogPane prefHeight="182.0" prefWidth="390.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.openoffice.AdvancedCiteDialogView">
-   <content>
-      <VBox>
-         <fx:define>
-              <ToggleGroup fx:id="citeToggleGroup" />
-         </fx:define>
-         <children>
-            <RadioButton fx:id="inPar" minWidth="-Infinity" mnemonicParsing="false" text="%Cite selected entries between parenthesis" toggleGroup="$citeToggleGroup" />
-            <RadioButton fx:id="inText" minWidth="-Infinity" mnemonicParsing="false" text="%Cite selected entries with in-text citation" toggleGroup="$citeToggleGroup" />
-            <Label minWidth="-Infinity" text="%Extra information (e.g. page number)" />
-            <TextField fx:id="pageInfo" />
-         </children>
-      </VBox>
-   </content>
-  <buttonTypes>
-    <ButtonType fx:constant="CANCEL" />
-    <ButtonType fx:constant="OK" />
-  </buttonTypes>
+<DialogPane xmlns:fx="http://javafx.com/fxml/1" prefHeight="182.0" prefWidth="390.0"
+            xmlns="http://javafx.com/javafx/8.0.171" fx:controller="org.jabref.gui.openoffice.AdvancedCiteDialogView">
+    <content>
+        <VBox>
+            <fx:define>
+                <ToggleGroup fx:id="citeToggleGroup"/>
+            </fx:define>
+            <children>
+                <RadioButton fx:id="inPar" minWidth="-Infinity" mnemonicParsing="false"
+                             text="%Cite selected entries between parenthesis" toggleGroup="$citeToggleGroup"/>
+                <RadioButton fx:id="inText" minWidth="-Infinity" mnemonicParsing="false"
+                             text="%Cite selected entries with in-text citation" toggleGroup="$citeToggleGroup"/>
+                <Label minWidth="-Infinity" text="%Extra information (e.g. page number)"/>
+                <TextField fx:id="pageInfo"/>
+            </children>
+        </VBox>
+    </content>
+    <buttonTypes>
+        <ButtonType fx:constant="CANCEL"/>
+        <ButtonType fx:constant="OK"/>
+    </buttonTypes>
 </DialogPane>
diff --git a/src/main/java/org/jabref/gui/openoffice/AdvancedCiteDialogView.java b/src/main/java/org/jabref/gui/openoffice/AdvancedCiteDialogView.java
index f12e34fcdbe..f11e8ab90ae 100644
--- a/src/main/java/org/jabref/gui/openoffice/AdvancedCiteDialogView.java
+++ b/src/main/java/org/jabref/gui/openoffice/AdvancedCiteDialogView.java
@@ -41,6 +41,5 @@ private void initialize() {
         inPar.selectedProperty().bindBidirectional(viewModel.citeInParProperty());
         inText.selectedProperty().bindBidirectional(viewModel.citeInTextProperty());
         pageInfo.textProperty().bindBidirectional(viewModel.pageInfoProperty());
-
     }
 }
diff --git a/src/main/java/org/jabref/gui/openoffice/CitationEntryViewModel.java b/src/main/java/org/jabref/gui/openoffice/CitationEntryViewModel.java
index 58ac9f04ecd..028990a6bc8 100644
--- a/src/main/java/org/jabref/gui/openoffice/CitationEntryViewModel.java
+++ b/src/main/java/org/jabref/gui/openoffice/CitationEntryViewModel.java
@@ -36,5 +36,4 @@ public StringProperty extraInformationProperty() {
     public void setExtraInfo(String extraInfo) {
         extraInformation.setValue(extraInfo);
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/openoffice/DetectOpenOfficeInstallation.java b/src/main/java/org/jabref/gui/openoffice/DetectOpenOfficeInstallation.java
index 1f4a892f14a..c4e8e47885a 100644
--- a/src/main/java/org/jabref/gui/openoffice/DetectOpenOfficeInstallation.java
+++ b/src/main/java/org/jabref/gui/openoffice/DetectOpenOfficeInstallation.java
@@ -46,10 +46,10 @@ private Optional<Path> selectInstallationPath() {
         final NativeDesktop nativeDesktop = JabRefDesktop.getNativeDesktop();
 
         dialogService.showInformationDialogAndWait(Localization.lang("Could not find OpenOffice/LibreOffice installation"),
-                                                   Localization.lang("Unable to autodetect OpenOffice/LibreOffice installation. Please choose the installation directory manually."));
+                Localization.lang("Unable to autodetect OpenOffice/LibreOffice installation. Please choose the installation directory manually."));
         DirectoryDialogConfiguration dirDialogConfiguration = new DirectoryDialogConfiguration.Builder()
-                                                                                                        .withInitialDirectory(nativeDesktop.getApplicationDirectory())
-                                                                                                        .build();
+                .withInitialDirectory(nativeDesktop.getApplicationDirectory())
+                .build();
         return dialogService.showDirectorySelectionDialog(dirDialogConfiguration);
 
     }
@@ -113,10 +113,10 @@ private Optional<Path> chooseAmongInstallations(List<Path> installDirs) {
         }
 
         String content = Localization.lang("Found more than one OpenOffice/LibreOffice executable.")
-                         + "\n" + Localization.lang("Please choose which one to connect to:");
+                + "\n" + Localization.lang("Please choose which one to connect to:");
 
         Optional<Path> selectedPath = dialogService.showChoiceDialogAndWait(Localization.lang("Choose OpenOffice/LibreOffice executable"),
-                                                                            content, Localization.lang("Use selected instance"), installDirs);
+                content, Localization.lang("Use selected instance"), installDirs);
 
         return selectedPath;
     }
diff --git a/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialog.fxml b/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialog.fxml
index bde42841ce5..b76aabee96e 100644
--- a/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialog.fxml
+++ b/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialog.fxml
@@ -4,18 +4,19 @@
 <?import javafx.scene.control.DialogPane?>
 <?import javafx.scene.control.TableColumn?>
 <?import javafx.scene.control.TableView?>
-
-<DialogPane minHeight="-Infinity" minWidth="-Infinity" prefHeight="470.0" prefWidth="701.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.openoffice.ManageCitationsDialogView">
-	<content>
-		<TableView fx:id="citationsTableView" prefHeight="208.0" prefWidth="662.0">
-			<columns>
-				<TableColumn fx:id="citation" prefWidth="251.0" text="%Citation" />
-				<TableColumn fx:id="extraInfo" prefWidth="425.0" text="%Extra information (e.g. page number)" />
-			</columns>
-		</TableView>
-	</content>
-	<buttonTypes>
-		<ButtonType fx:constant="CANCEL" />
-		<ButtonType fx:constant="OK" />
-	</buttonTypes>
+<DialogPane xmlns:fx="http://javafx.com/fxml/1" minHeight="-Infinity" minWidth="-Infinity" prefHeight="470.0"
+            prefWidth="701.0" xmlns="http://javafx.com/javafx/8.0.171"
+            fx:controller="org.jabref.gui.openoffice.ManageCitationsDialogView">
+    <content>
+        <TableView fx:id="citationsTableView" prefHeight="208.0" prefWidth="662.0">
+            <columns>
+                <TableColumn fx:id="citation" prefWidth="251.0" text="%Citation"/>
+                <TableColumn fx:id="extraInfo" prefWidth="425.0" text="%Extra information (e.g. page number)"/>
+            </columns>
+        </TableView>
+    </content>
+    <buttonTypes>
+        <ButtonType fx:constant="CANCEL"/>
+        <ButtonType fx:constant="OK"/>
+    </buttonTypes>
 </DialogPane>
diff --git a/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialogView.java b/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialogView.java
index 1f50783e89f..a312a4ef375 100644
--- a/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialogView.java
+++ b/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialogView.java
@@ -41,7 +41,6 @@ public class ManageCitationsDialogView extends BaseDialog<Void> {
     public ManageCitationsDialogView(OOBibBase ooBase) {
         this.ooBase = ooBase;
 
-
         ViewLoader.view(this)
                   .load()
                   .setAsDialogPane(this);
@@ -75,14 +74,13 @@ private void initialize() throws NoSuchElementException, WrappedTargetException,
             cell.getRowValue().setExtraInfo(cell.getNewValue());
         });
         extraInfo.setCellFactory(TextFieldTableCell.forTableColumn());
-
     }
 
     private Node getText(String citationContext) {
 
         String inBetween = StringUtil.substringBetween(citationContext, HTML_BOLD_START_TAG, HTML_BOLD_END_TAG);
         String start = citationContext.substring(0, citationContext.indexOf(HTML_BOLD_START_TAG));
-        String end = citationContext.substring(citationContext.lastIndexOf(HTML_BOLD_END_TAG) + HTML_BOLD_END_TAG.length(), citationContext.length());
+        String end = citationContext.substring(citationContext.lastIndexOf(HTML_BOLD_END_TAG) + HTML_BOLD_END_TAG.length());
 
         Text startText = new Text(start);
         Text inBetweenText = new Text(inBetween);
diff --git a/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialogViewModel.java b/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialogViewModel.java
index e928f5ee673..55d532caa62 100644
--- a/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/openoffice/ManageCitationsDialogViewModel.java
@@ -40,13 +40,12 @@ public ManageCitationsDialogViewModel(OOBibBase ooBase, DialogService dialogServ
         for (String name : names) {
 
             CitationEntry entry = new CitationEntry(name,
-                                                    ooBase.getCitationContext(nameAccess, name, 30, 30, true),
-                                                    ooBase.getCustomProperty(name));
+                    ooBase.getCitationContext(nameAccess, name, 30, 30, true),
+                    ooBase.getCustomProperty(name));
 
             CitationEntryViewModel itemViewModelEntry = new CitationEntryViewModel(entry);
             citations.add(itemViewModelEntry);
         }
-
     }
 
     public void storeSettings() {
@@ -59,7 +58,7 @@ public void storeSettings() {
                 }
             }
         } catch (UnknownPropertyException | NotRemoveableException | PropertyExistException | IllegalTypeException |
-                 IllegalArgumentException ex) {
+                IllegalArgumentException ex) {
             LOGGER.warn("Problem modifying citation", ex);
             dialogService.showErrorDialogAndWait(Localization.lang("Problem modifying citation"), ex);
         }
@@ -68,6 +67,5 @@ public void storeSettings() {
     public ListProperty<CitationEntryViewModel> citationsProperty() {
         return citations;
     }
-
 }
 
diff --git a/src/main/java/org/jabref/gui/openoffice/ManualConnectDialog.fxml b/src/main/java/org/jabref/gui/openoffice/ManualConnectDialog.fxml
index 751462763d6..34c8b060fdb 100644
--- a/src/main/java/org/jabref/gui/openoffice/ManualConnectDialog.fxml
+++ b/src/main/java/org/jabref/gui/openoffice/ManualConnectDialog.fxml
@@ -1,5 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+
 <?import javafx.scene.control.Button?>
 <?import javafx.scene.control.ButtonType?>
 <?import javafx.scene.control.DialogPane?>
@@ -8,36 +9,41 @@
 <?import javafx.scene.layout.ColumnConstraints?>
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.RowConstraints?>
-
-
-<DialogPane prefHeight="130.0" prefWidth="317.0" xmlns="http://javafx.com/javafx/8.0.141" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.openoffice.ManualConnectDialogView">
-   <content>
-      <GridPane minWidth="-Infinity" prefHeight="50.0" prefWidth="585.0">
-        <columnConstraints>
-          <ColumnConstraints hgrow="SOMETIMES" maxWidth="255.0" minWidth="10.0" prefWidth="255.0" />
-          <ColumnConstraints hgrow="SOMETIMES" maxWidth="581.0" minWidth="10.0" />
-            <ColumnConstraints hgrow="SOMETIMES" />
-        </columnConstraints>
-        <rowConstraints>
-          <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-          <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-          <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-        </rowConstraints>
-         <children>
-            <Label fx:id="OOPathLabel" minWidth="-Infinity" text="%Path to OpenOffice/LibreOffice directory" managed="${ooPath.visible}" />
-            <TextField fx:id="ooPath" GridPane.columnIndex="1" managed="${ooPath.visible}" />
-            <Button fx:id="browseOOPath" mnemonicParsing="false" onAction="#browseOOPath" text="%Browse" GridPane.columnIndex="2" managed="${ooPath.visible}" />
-            <Button fx:id="browseOOExec" mnemonicParsing="false" onAction="#browseOOExec" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="1" managed="${ooExec.visible}"  />
-            <Button fx:id="browseOOJars" mnemonicParsing="false" onAction="#browseOOJars" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="2"   managed="${ooJars.visible}" />
-            <TextField fx:id="ooExec" GridPane.columnIndex="1" GridPane.rowIndex="1"  managed="${ooExec.visible}"  />
-            <TextField fx:id="ooJars" GridPane.columnIndex="1" GridPane.rowIndex="2"  managed="${ooJars.visible}" />
-            <Label fx:id="ooExecLabel" minWidth="-Infinity" text="%Path to OpenOffice/LibreOffice executable" GridPane.rowIndex="1"  managed="${ooExec.visible}"  />
-            <Label fx:id="ooJarsLabel" minWidth="-Infinity" text="%Path to OpenOffice/LibreOffice library dir" GridPane.rowIndex="2"   managed="${ooJars.visible}" />
-         </children>
-      </GridPane>
-   </content>
-     <buttonTypes>
-        <ButtonType fx:constant="CANCEL" />
+<DialogPane xmlns:fx="http://javafx.com/fxml/1" prefHeight="130.0" prefWidth="317.0"
+            xmlns="http://javafx.com/javafx/8.0.141" fx:controller="org.jabref.gui.openoffice.ManualConnectDialogView">
+    <content>
+        <GridPane minWidth="-Infinity" prefHeight="50.0" prefWidth="585.0">
+            <columnConstraints>
+                <ColumnConstraints hgrow="SOMETIMES" maxWidth="255.0" minWidth="10.0" prefWidth="255.0"/>
+                <ColumnConstraints hgrow="SOMETIMES" maxWidth="581.0" minWidth="10.0"/>
+                <ColumnConstraints hgrow="SOMETIMES"/>
+            </columnConstraints>
+            <rowConstraints>
+                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+            </rowConstraints>
+            <children>
+                <Label fx:id="OOPathLabel" minWidth="-Infinity" text="%Path to OpenOffice/LibreOffice directory"
+                       managed="${ooPath.visible}"/>
+                <TextField fx:id="ooPath" GridPane.columnIndex="1" managed="${ooPath.visible}"/>
+                <Button fx:id="browseOOPath" mnemonicParsing="false" onAction="#browseOOPath" text="%Browse"
+                        GridPane.columnIndex="2" managed="${ooPath.visible}"/>
+                <Button fx:id="browseOOExec" mnemonicParsing="false" onAction="#browseOOExec" text="%Browse"
+                        GridPane.columnIndex="2" GridPane.rowIndex="1" managed="${ooExec.visible}"/>
+                <Button fx:id="browseOOJars" mnemonicParsing="false" onAction="#browseOOJars" text="%Browse"
+                        GridPane.columnIndex="2" GridPane.rowIndex="2" managed="${ooJars.visible}"/>
+                <TextField fx:id="ooExec" GridPane.columnIndex="1" GridPane.rowIndex="1" managed="${ooExec.visible}"/>
+                <TextField fx:id="ooJars" GridPane.columnIndex="1" GridPane.rowIndex="2" managed="${ooJars.visible}"/>
+                <Label fx:id="ooExecLabel" minWidth="-Infinity" text="%Path to OpenOffice/LibreOffice executable"
+                       GridPane.rowIndex="1" managed="${ooExec.visible}"/>
+                <Label fx:id="ooJarsLabel" minWidth="-Infinity" text="%Path to OpenOffice/LibreOffice library dir"
+                       GridPane.rowIndex="2" managed="${ooJars.visible}"/>
+            </children>
+        </GridPane>
+    </content>
+    <buttonTypes>
+        <ButtonType fx:constant="CANCEL"/>
         <ButtonType fx:constant="OK"/>
-      </buttonTypes>
+    </buttonTypes>
 </DialogPane>
diff --git a/src/main/java/org/jabref/gui/openoffice/ManualConnectDialogView.java b/src/main/java/org/jabref/gui/openoffice/ManualConnectDialogView.java
index 5352cf97198..5e7a2e7649a 100644
--- a/src/main/java/org/jabref/gui/openoffice/ManualConnectDialogView.java
+++ b/src/main/java/org/jabref/gui/openoffice/ManualConnectDialogView.java
@@ -19,6 +19,7 @@
 
 public class ManualConnectDialogView extends BaseDialog<Boolean> {
 
+    @Inject private final DialogService dialogService;
     @FXML private Label OOPathLabel;
     @FXML private TextField ooPath;
     @FXML private Button browseOOPath;
@@ -28,10 +29,7 @@ public class ManualConnectDialogView extends BaseDialog<Boolean> {
     @FXML private TextField ooJars;
     @FXML private Label ooExecLabel;
     @FXML private Label ooJarsLabel;
-
     @Inject private PreferencesService preferencesService;
-    @Inject private final DialogService dialogService;
-
     private ManualConnectDialogViewModel viewModel;
 
     public ManualConnectDialogView(DialogService dialogService) {
@@ -86,5 +84,4 @@ private void browseOOExec(ActionEvent event) {
     private void browseOOJars(ActionEvent event) {
         viewModel.browseOOJars();
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/openoffice/ManualConnectDialogViewModel.java b/src/main/java/org/jabref/gui/openoffice/ManualConnectDialogViewModel.java
index c628484296e..9789b717978 100644
--- a/src/main/java/org/jabref/gui/openoffice/ManualConnectDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/openoffice/ManualConnectDialogViewModel.java
@@ -34,11 +34,11 @@ public ManualConnectDialogViewModel(PreferencesService preferencesService, Dialo
         ooJarsProperty().setValue(ooPreferences.getJarsPath());
 
         dirDialogConfiguration = new DirectoryDialogConfiguration.Builder()
-                                                                           .withInitialDirectory(nativeDesktop.getApplicationDirectory())
-                                                                           .build();
+                .withInitialDirectory(nativeDesktop.getApplicationDirectory())
+                .build();
         fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                                                                       .withInitialDirectory(nativeDesktop.getApplicationDirectory())
-                                                                       .build();
+                .withInitialDirectory(nativeDesktop.getApplicationDirectory())
+                .build();
     }
 
     public void browseOOPath() {
@@ -47,7 +47,6 @@ public void browseOOPath() {
 
     public void browseOOExec() {
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(f -> ooExec.setValue(f.toAbsolutePath().toString()));
-
     }
 
     public void browseOOJars() {
@@ -75,5 +74,4 @@ public void save() {
 
         preferencesService.setOpenOfficePreferences(ooPreferences);
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/openoffice/OOBibBase.java b/src/main/java/org/jabref/gui/openoffice/OOBibBase.java
index 560eaf1fe87..39f99b03e9c 100644
--- a/src/main/java/org/jabref/gui/openoffice/OOBibBase.java
+++ b/src/main/java/org/jabref/gui/openoffice/OOBibBase.java
@@ -136,8 +136,8 @@ class OOBibBase {
     private List<String> sortedReferenceMarks;
 
     public OOBibBase(String pathToOO, boolean atEnd) throws IOException, IllegalAccessException,
-                                                     InvocationTargetException, BootstrapException, CreationException, UnknownPropertyException,
-                                                     WrappedTargetException, IndexOutOfBoundsException, NoSuchElementException, NoDocumentException {
+            InvocationTargetException, BootstrapException, CreationException, UnknownPropertyException,
+            WrappedTargetException, IndexOutOfBoundsException, NoSuchElementException, NoDocumentException {
         authorYearTitleList.add(authComp);
         authorYearTitleList.add(yearComp);
         authorYearTitleList.add(titleComp);
@@ -158,13 +158,33 @@ public boolean isConnectedToDocument() {
         return xCurrentComponent != null;
     }
 
+    public static XTextDocument selectComponent(List<XTextDocument> list)
+            throws UnknownPropertyException, WrappedTargetException, IndexOutOfBoundsException {
+        String[] values = new String[list.size()];
+        int ii = 0;
+        for (XTextDocument doc : list) {
+            values[ii] = String.valueOf(OOUtil.getProperty(doc.getCurrentController().getFrame(), "Title"));
+            ii++;
+        }
+        JList<String> sel = new JList<>(values);
+        sel.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+        sel.setSelectedIndex(0);
+        int ans = JOptionPane.showConfirmDialog(null, new JScrollPane(sel), Localization.lang("Select document"),
+                JOptionPane.OK_CANCEL_OPTION);
+        if (ans == JOptionPane.OK_OPTION) {
+            return list.get(sel.getSelectedIndex());
+        } else {
+            return null;
+        }
+    }
+
     public Optional<String> getCurrentDocumentTitle() {
         if (mxDoc == null) {
             return Optional.empty();
         } else {
             try {
                 return Optional
-                               .of(String.valueOf(OOUtil.getProperty(mxDoc.getCurrentController().getFrame(), "Title")));
+                        .of(String.valueOf(OOUtil.getProperty(mxDoc.getCurrentController().getFrame(), "Title")));
             } catch (UnknownPropertyException | WrappedTargetException e) {
                 LOGGER.warn("Could not get document title", e);
                 return Optional.empty();
@@ -173,7 +193,7 @@ public Optional<String> getCurrentDocumentTitle() {
     }
 
     public void selectDocument() throws UnknownPropertyException, WrappedTargetException, IndexOutOfBoundsException,
-        NoSuchElementException, NoDocumentException {
+            NoSuchElementException, NoDocumentException {
         List<XTextDocument> textDocumentList = getTextDocuments();
         XTextDocument selected;
         if (textDocumentList.isEmpty()) {
@@ -211,9 +231,27 @@ public void selectDocument() throws UnknownPropertyException, WrappedTargetExcep
 
     }
 
+    private List<XTextDocument> getTextDocuments() throws NoSuchElementException, WrappedTargetException {
+        List<XTextDocument> result = new ArrayList<>();
+        XEnumerationAccess enumAccess = xDesktop.getComponents();
+        XEnumeration componentEnumeration = enumAccess.createEnumeration();
+
+        // TODO: http://api.openoffice.org/docs/DevelopersGuide/OfficeDev/OfficeDev.xhtml#1_1_3_2_1_2_Frame_Hierarchies
+
+        while (componentEnumeration.hasMoreElements()) {
+            Object nextElement = componentEnumeration.nextElement();
+            XComponent component = UnoRuntime.queryInterface(XComponent.class, nextElement);
+            XTextDocument document = UnoRuntime.queryInterface(XTextDocument.class, component);
+            if (document != null) {
+                result.add(document);
+            }
+        }
+        return result;
+    }
+
     private XDesktop simpleBootstrap(String pathToExecutable)
-        throws IllegalAccessException, InvocationTargetException, BootstrapException,
-        CreationException, IOException {
+            throws IllegalAccessException, InvocationTargetException, BootstrapException,
+            CreationException, IOException {
 
         ClassLoader loader = ClassLoader.getSystemClassLoader();
         if (loader instanceof URLClassLoader) {
@@ -230,7 +268,7 @@ private XDesktop simpleBootstrap(String pathToExecutable)
             }
         } else {
             LOGGER.error("Error occured, URLClassLoader expected but " + loader.getClass()
-                         + " received. Could not continue.");
+                    + " received. Could not continue.");
         }
 
         //Get the office component context:
@@ -252,44 +290,26 @@ private XDesktop simpleBootstrap(String pathToExecutable)
         return resultDesktop;
     }
 
-    private List<XTextDocument> getTextDocuments() throws NoSuchElementException, WrappedTargetException {
-        List<XTextDocument> result = new ArrayList<>();
-        XEnumerationAccess enumAccess = xDesktop.getComponents();
-        XEnumeration componentEnumeration = enumAccess.createEnumeration();
-
-        // TODO: http://api.openoffice.org/docs/DevelopersGuide/OfficeDev/OfficeDev.xhtml#1_1_3_2_1_2_Frame_Hierarchies
-
-        while (componentEnumeration.hasMoreElements()) {
-            Object nextElement = componentEnumeration.nextElement();
-            XComponent component = UnoRuntime.queryInterface(XComponent.class, nextElement);
-            XTextDocument document = UnoRuntime.queryInterface(XTextDocument.class, component);
-            if (document != null) {
-                result.add(document);
-            }
+    public Optional<String> getCustomProperty(String property) throws UnknownPropertyException, WrappedTargetException {
+        if (propertySet.getPropertySetInfo().hasPropertyByName(property)) {
+            return Optional.ofNullable(propertySet.getPropertyValue(property).toString());
         }
-        return result;
+        return Optional.empty();
+    }
+
+    public void updateSortedReferenceMarks() throws WrappedTargetException, NoSuchElementException {
+        sortedReferenceMarks = getSortedReferenceMarks(getReferenceMarks());
     }
 
     public void setCustomProperty(String property, String value) throws UnknownPropertyException,
-        NotRemoveableException, PropertyExistException, IllegalTypeException, IllegalArgumentException {
+            NotRemoveableException, PropertyExistException, IllegalTypeException, IllegalArgumentException {
         if (propertySet.getPropertySetInfo().hasPropertyByName(property)) {
             userProperties.removeProperty(property);
         }
         if (value != null) {
             userProperties.addProperty(property, com.sun.star.beans.PropertyAttribute.REMOVEABLE,
-                                       new Any(Type.STRING, value));
-        }
-    }
-
-    public Optional<String> getCustomProperty(String property) throws UnknownPropertyException, WrappedTargetException {
-        if (propertySet.getPropertySetInfo().hasPropertyByName(property)) {
-            return Optional.ofNullable(propertySet.getPropertyValue(property).toString());
+                    new Any(Type.STRING, value));
         }
-        return Optional.empty();
-    }
-
-    public void updateSortedReferenceMarks() throws WrappedTargetException, NoSuchElementException {
-        sortedReferenceMarks = getSortedReferenceMarks(getReferenceMarks());
     }
 
     /**
@@ -319,10 +339,10 @@ public void updateSortedReferenceMarks() throws WrappedTargetException, NoSuchEl
     public void insertEntry(List<BibEntry> entries, BibDatabase database,
                             List<BibDatabase> allBases, OOBibStyle style,
                             boolean inParenthesis, boolean withText, String pageInfo, boolean sync)
-        throws IllegalArgumentException,
-        UnknownPropertyException, NotRemoveableException, PropertyExistException, IllegalTypeException,
-        UndefinedCharacterFormatException, WrappedTargetException, NoSuchElementException, PropertyVetoException,
-        IOException, CreationException, BibEntryNotFoundException, UndefinedParagraphFormatException {
+            throws IllegalArgumentException,
+            UnknownPropertyException, NotRemoveableException, PropertyExistException, IllegalTypeException,
+            UndefinedCharacterFormatException, WrappedTargetException, NoSuchElementException, PropertyVetoException,
+            IOException, CreationException, BibEntryNotFoundException, UndefinedParagraphFormatException {
 
         try {
 
@@ -337,10 +357,10 @@ public void insertEntry(List<BibEntry> entries, BibDatabase database,
             }
 
             String keyString = String.join(",",
-                                           entries.stream().map(entry -> entry.getCiteKeyOptional().orElse("")).collect(Collectors.toList()));
+                    entries.stream().map(entry -> entry.getCiteKeyOptional().orElse("")).collect(Collectors.toList()));
             // Insert bookmark:
             String bName = getUniqueReferenceMarkName(keyString,
-                                                      withText ? inParenthesis ? OOBibBase.AUTHORYEAR_PAR : OOBibBase.AUTHORYEAR_INTEXT : OOBibBase.INVISIBLE_CIT);
+                    withText ? inParenthesis ? OOBibBase.AUTHORYEAR_PAR : OOBibBase.AUTHORYEAR_INTEXT : OOBibBase.INVISIBLE_CIT);
 
             // If we should store metadata for page info, do that now:
             if (pageInfo != null) {
@@ -355,7 +375,7 @@ public void insertEntry(List<BibEntry> entries, BibDatabase database,
                 try {
                     xCursorProps.setPropertyValue(CHAR_STYLE_NAME, charStyle);
                 } catch (UnknownPropertyException | PropertyVetoException | IllegalArgumentException |
-                         WrappedTargetException ex) {
+                        WrappedTargetException ex) {
                     // Setting the character format failed, so we throw an exception that
                     // will result in an error message for the user. Before that,
                     // delete the space we inserted:
@@ -370,7 +390,7 @@ public void insertEntry(List<BibEntry> entries, BibDatabase database,
                 databaseMap.put(entry, database);
             }
             String citeText = style.isNumberEntries() ? "-" : style.getCitationMarker(entries, databaseMap,
-                                                                                      inParenthesis, null, null);
+                    inParenthesis, null, null);
             insertReferenceMark(bName, citeText, xViewCursor, withText, style);
 
             xViewCursor.collapseToEnd();
@@ -397,6 +417,20 @@ public void insertEntry(List<BibEntry> entries, BibDatabase database,
         }
     }
 
+    public List<String> getJabRefReferenceMarks(XNameAccess nameAccess) {
+        String[] names = nameAccess.getElementNames();
+        // Remove all reference marks that don't look like JabRef citations:
+        List<String> result = new ArrayList<>();
+        if (names != null) {
+            for (String name : names) {
+                if (CITE_PATTERN.matcher(name).find()) {
+                    result.add(name);
+                }
+            }
+        }
+        return result;
+    }
+
     /**
      * Refresh all cite markers in the document.
      * @param databases The databases to get entries from.
@@ -413,9 +447,9 @@ public void insertEntry(List<BibEntry> entries, BibDatabase database,
      * @throws UnknownPropertyException
      */
     public List<String> refreshCiteMarkers(List<BibDatabase> databases, OOBibStyle style)
-        throws WrappedTargetException, IllegalArgumentException, NoSuchElementException,
-        UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException, IOException,
-        CreationException, BibEntryNotFoundException {
+            throws WrappedTargetException, IllegalArgumentException, NoSuchElementException,
+            UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException, IOException,
+            CreationException, BibEntryNotFoundException {
         try {
             return refreshCiteMarkersInternal(databases, style);
         } catch (DisposedException ex) {
@@ -426,24 +460,10 @@ public List<String> refreshCiteMarkers(List<BibDatabase> databases, OOBibStyle s
         }
     }
 
-    public List<String> getJabRefReferenceMarks(XNameAccess nameAccess) {
-        String[] names = nameAccess.getElementNames();
-        // Remove all reference marks that don't look like JabRef citations:
-        List<String> result = new ArrayList<>();
-        if (names != null) {
-            for (String name : names) {
-                if (CITE_PATTERN.matcher(name).find()) {
-                    result.add(name);
-                }
-            }
-        }
-        return result;
-    }
-
     private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOBibStyle style)
-        throws WrappedTargetException, IllegalArgumentException, NoSuchElementException,
-        UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException,
-        CreationException, BibEntryNotFoundException {
+            throws WrappedTargetException, IllegalArgumentException, NoSuchElementException,
+            UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException,
+            CreationException, BibEntryNotFoundException {
 
         List<String> cited = findCitedKeys();
         Map<String, BibDatabase> linkSourceBase = new HashMap<>();
@@ -550,7 +570,7 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
                         citationMarker = style.getNumCitationMarker(num, minGroupingCount, false);
                         for (int j = 0; j < keys.length; j++) {
                             normCitMarker[j] = style.getNumCitationMarker(Collections.singletonList(num.get(j)),
-                                                                          minGroupingCount, false);
+                                    minGroupingCount, false);
                         }
                     } else {
                         // We need to find the number of the cited entry in the bibliography,
@@ -559,7 +579,7 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
 
                         if (num.isEmpty()) {
                             throw new BibEntryNotFoundException(names.get(i), Localization
-                                                                                          .lang("Could not resolve BibTeX entry for citation marker '%0'.", names.get(i)));
+                                    .lang("Could not resolve BibTeX entry for citation marker '%0'.", names.get(i)));
                         } else {
                             citationMarker = style.getNumCitationMarker(num, minGroupingCount, false);
                         }
@@ -585,11 +605,11 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
                     }
 
                     citationMarker = style.getCitationMarker(Arrays.asList(cEntries), entries,
-                                                             type == OOBibBase.AUTHORYEAR_PAR, null, null);
+                            type == OOBibBase.AUTHORYEAR_PAR, null, null);
                     // We need "normalized" (in parenthesis) markers for uniqueness checking purposes:
                     for (int j = 0; j < cEntries.length; j++) {
                         normCitMarker[j] = style.getCitationMarker(Collections.singletonList(cEntries[j]), entries,
-                                                                   true, null, new int[] {-1});
+                                true, null, new int[]{-1});
                     }
                 }
                 citMarkers[i] = citationMarker;
@@ -689,7 +709,7 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
                 }
                 if (needsChange) {
                     citMarkers[j] = style.getCitationMarker(Arrays.asList(cEntries), entries,
-                                                            types[j] == OOBibBase.AUTHORYEAR_PAR, uniquif, firstLimAuthors);
+                            types[j] == OOBibBase.AUTHORYEAR_PAR, uniquif, firstLimAuthors);
                 }
             }
         }
@@ -715,7 +735,7 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
                 try {
                     xCursorProps.setPropertyValue(CHAR_STYLE_NAME, charStyle);
                 } catch (UnknownPropertyException | PropertyVetoException | IllegalArgumentException |
-                         WrappedTargetException ex) {
+                        WrappedTargetException ex) {
                     throw new UndefinedCharacterFormatException(charStyle);
                 }
             }
@@ -745,9 +765,9 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
     }
 
     private List<String> getSortedReferenceMarks(final XNameAccess nameAccess)
-        throws WrappedTargetException, NoSuchElementException {
+            throws WrappedTargetException, NoSuchElementException {
         XTextViewCursorSupplier cursorSupplier = UnoRuntime.queryInterface(XTextViewCursorSupplier.class,
-                                                                           mxDoc.getCurrentController());
+                mxDoc.getCurrentController());
 
         XTextViewCursor viewCursor = cursorSupplier.getViewCursor();
         XTextRange initialPos = viewCursor.getStart();
@@ -780,9 +800,25 @@ private List<String> getSortedReferenceMarks(final XNameAccess nameAccess)
         return result;
     }
 
+    public XNameAccess getReferenceMarks() {
+        XReferenceMarksSupplier supplier = UnoRuntime.queryInterface(XReferenceMarksSupplier.class, xCurrentComponent);
+        return supplier.getReferenceMarks();
+    }
+
+    private String getUniqueReferenceMarkName(String bibtexKey, int type) {
+        XNameAccess xNamedRefMarks = getReferenceMarks();
+        int i = 0;
+        String name = OOBibBase.BIB_CITATION + '_' + type + '_' + bibtexKey;
+        while (xNamedRefMarks.hasByName(name)) {
+            name = OOBibBase.BIB_CITATION + i + '_' + type + '_' + bibtexKey;
+            i++;
+        }
+        return name;
+    }
+
     public void rebuildBibTextSection(List<BibDatabase> databases, OOBibStyle style)
-        throws NoSuchElementException, WrappedTargetException, IllegalArgumentException,
-        CreationException, PropertyVetoException, UnknownPropertyException, UndefinedParagraphFormatException {
+            throws NoSuchElementException, WrappedTargetException, IllegalArgumentException,
+            CreationException, PropertyVetoException, UnknownPropertyException, UndefinedParagraphFormatException {
         List<String> cited = findCitedKeys();
         Map<String, BibDatabase> linkSourceBase = new HashMap<>();
         Map<BibEntry, BibDatabase> entries = findCitedEntries(databases, cited, linkSourceBase); // Although entries are redefined without use, this also updates linkSourceBase
@@ -795,7 +831,7 @@ public void rebuildBibTextSection(List<BibDatabase> databases, OOBibStyle style)
         } else {
             SortedMap<BibEntry, BibDatabase> newMap = new TreeMap<>(entryComparator);
             for (Map.Entry<BibEntry, BibDatabase> bibtexEntryBibtexDatabaseEntry : findCitedEntries(databases, cited,
-                                                                                                    linkSourceBase).entrySet()) {
+                    linkSourceBase).entrySet()) {
                 newMap.put(bibtexEntryBibtexDatabaseEntry.getKey(), bibtexEntryBibtexDatabaseEntry.getValue());
             }
             entries = newMap;
@@ -804,20 +840,23 @@ public void rebuildBibTextSection(List<BibDatabase> databases, OOBibStyle style)
         populateBibTextSection(entries, style);
     }
 
-    public XNameAccess getReferenceMarks() {
-        XReferenceMarksSupplier supplier = UnoRuntime.queryInterface(XReferenceMarksSupplier.class, xCurrentComponent);
-        return supplier.getReferenceMarks();
-    }
+    private List<String> findCitedKeys() throws NoSuchElementException, WrappedTargetException {
+        XNameAccess xNamedMarks = getReferenceMarks();
+        String[] names = xNamedMarks.getElementNames();
+        List<String> keys = new ArrayList<>();
+        for (String name1 : names) {
+            Object bookmark = xNamedMarks.getByName(name1);
+            UnoRuntime.queryInterface(XTextContent.class, bookmark);
 
-    private String getUniqueReferenceMarkName(String bibtexKey, int type) {
-        XNameAccess xNamedRefMarks = getReferenceMarks();
-        int i = 0;
-        String name = OOBibBase.BIB_CITATION + '_' + type + '_' + bibtexKey;
-        while (xNamedRefMarks.hasByName(name)) {
-            name = OOBibBase.BIB_CITATION + i + '_' + type + '_' + bibtexKey;
-            i++;
+            List<String> newKeys = parseRefMarkName(name1);
+            for (String key : newKeys) {
+                if (!keys.contains(key)) {
+                    keys.add(key);
+                }
+            }
         }
-        return name;
+
+        return keys;
     }
 
     private Map<BibEntry, BibDatabase> findCitedEntries(List<BibDatabase> databases, List<String> keys,
@@ -842,55 +881,6 @@ private Map<BibEntry, BibDatabase> findCitedEntries(List<BibDatabase> databases,
         return entries;
     }
 
-    private List<String> findCitedKeys() throws NoSuchElementException, WrappedTargetException {
-        XNameAccess xNamedMarks = getReferenceMarks();
-        String[] names = xNamedMarks.getElementNames();
-        List<String> keys = new ArrayList<>();
-        for (String name1 : names) {
-            Object bookmark = xNamedMarks.getByName(name1);
-            UnoRuntime.queryInterface(XTextContent.class, bookmark);
-
-            List<String> newKeys = parseRefMarkName(name1);
-            for (String key : newKeys) {
-                if (!keys.contains(key)) {
-                    keys.add(key);
-                }
-            }
-        }
-
-        return keys;
-    }
-
-    private Map<BibEntry, BibDatabase> getSortedEntriesFromSortedRefMarks(List<String> names,
-                                                                          Map<String, BibDatabase> linkSourceBase) {
-
-        Map<BibEntry, BibDatabase> newList = new LinkedHashMap<>();
-        for (String name : names) {
-            Matcher citeMatcher = CITE_PATTERN.matcher(name);
-            if (citeMatcher.find()) {
-                String[] keys = citeMatcher.group(2).split(",");
-                for (String key : keys) {
-                    BibDatabase database = linkSourceBase.get(key);
-                    Optional<BibEntry> origEntry = Optional.empty();
-                    if (database != null) {
-                        origEntry = database.getEntryByKey(key);
-                    }
-                    if (origEntry.isPresent()) {
-                        if (!newList.containsKey(origEntry.get())) {
-                            newList.put(origEntry.get(), database);
-                        }
-                    } else {
-                        LOGGER.info("BibTeX key not found: '" + key + "'");
-                        LOGGER.info("Problem with reference mark: '" + name + "'");
-                        newList.put(new UndefinedBibtexEntry(key), null);
-                    }
-                }
-            }
-        }
-
-        return newList;
-    }
-
     private Point findPosition(XTextViewCursor cursor, XTextRange range) {
         cursor.gotoRange(range, false);
         return cursor.getPosition();
@@ -939,9 +929,39 @@ private List<Integer> findCitedEntryIndex(String citRefName, List<String> keys)
         }
     }
 
+    private Map<BibEntry, BibDatabase> getSortedEntriesFromSortedRefMarks(List<String> names,
+                                                                          Map<String, BibDatabase> linkSourceBase) {
+
+        Map<BibEntry, BibDatabase> newList = new LinkedHashMap<>();
+        for (String name : names) {
+            Matcher citeMatcher = CITE_PATTERN.matcher(name);
+            if (citeMatcher.find()) {
+                String[] keys = citeMatcher.group(2).split(",");
+                for (String key : keys) {
+                    BibDatabase database = linkSourceBase.get(key);
+                    Optional<BibEntry> origEntry = Optional.empty();
+                    if (database != null) {
+                        origEntry = database.getEntryByKey(key);
+                    }
+                    if (origEntry.isPresent()) {
+                        if (!newList.containsKey(origEntry.get())) {
+                            newList.put(origEntry.get(), database);
+                        }
+                    } else {
+                        LOGGER.info("BibTeX key not found: '" + key + "'");
+                        LOGGER.info("Problem with reference mark: '" + name + "'");
+                        newList.put(new UndefinedBibtexEntry(key), null);
+                    }
+                }
+            }
+        }
+
+        return newList;
+    }
+
     public String getCitationContext(XNameAccess nameAccess, String refMarkName, int charBefore, int charAfter,
                                      boolean htmlMarkup)
-        throws NoSuchElementException, WrappedTargetException {
+            throws NoSuchElementException, WrappedTargetException {
         Object referenceMark = nameAccess.getByName(refMarkName);
         XTextContent bookmark = UnoRuntime.queryInterface(XTextContent.class, referenceMark);
 
@@ -984,8 +1004,8 @@ public String getCitationContext(XNameAccess nameAccess, String refMarkName, int
 
     private void insertFullReferenceAtCursor(XTextCursor cursor, Map<BibEntry, BibDatabase> entries, OOBibStyle style,
                                              String parFormat)
-        throws UndefinedParagraphFormatException, IllegalArgumentException,
-        UnknownPropertyException, PropertyVetoException, WrappedTargetException {
+            throws UndefinedParagraphFormatException, IllegalArgumentException,
+            UnknownPropertyException, PropertyVetoException, WrappedTargetException {
         Map<BibEntry, BibDatabase> correctEntries;
         // If we don't have numbered entries, we need to sort the entries before adding them:
         if (style.isSortByPosition()) {
@@ -1006,18 +1026,18 @@ private void insertFullReferenceAtCursor(XTextCursor cursor, Map<BibEntry, BibDa
             if (style.isNumberEntries()) {
                 int minGroupingCount = style.getIntCitProperty(OOBibStyle.MINIMUM_GROUPING_COUNT);
                 OOUtil.insertTextAtCurrentLocation(text, cursor,
-                                                   style.getNumCitationMarker(Collections.singletonList(number++), minGroupingCount, true), Collections.emptyList());
+                        style.getNumCitationMarker(Collections.singletonList(number++), minGroupingCount, true), Collections.emptyList());
             }
             Layout layout = style.getReferenceFormat(entry.getKey().getType());
             layout.setPostFormatter(POSTFORMATTER);
             OOUtil.insertFullReferenceAtCurrentLocation(text, cursor, layout, parFormat, entry.getKey(),
-                                                        entry.getValue(), uniquefiers.get(entry.getKey().getCiteKeyOptional().orElse(null)));
+                    entry.getValue(), uniquefiers.get(entry.getKey().getCiteKeyOptional().orElse(null)));
         }
 
     }
 
     private void createBibTextSection2(boolean end)
-        throws IllegalArgumentException, CreationException {
+            throws IllegalArgumentException, CreationException {
 
         XTextCursor mxDocCursor = text.createTextCursor();
         if (end) {
@@ -1028,7 +1048,7 @@ private void createBibTextSection2(boolean end)
         XNamed xChildNamed;
         try {
             xChildNamed = UnoRuntime.queryInterface(XNamed.class,
-                                                    mxDocFactory.createInstance("com.sun.star.text.TextSection"));
+                    mxDocFactory.createInstance("com.sun.star.text.TextSection"));
         } catch (Exception e) {
             throw new CreationException(e.getMessage());
         }
@@ -1041,13 +1061,13 @@ private void createBibTextSection2(boolean end)
     }
 
     private void clearBibTextSectionContent2()
-        throws NoSuchElementException, WrappedTargetException, IllegalArgumentException, CreationException {
+            throws NoSuchElementException, WrappedTargetException, IllegalArgumentException, CreationException {
 
         // Check if the section exists:
         XTextSectionsSupplier supplier = UnoRuntime.queryInterface(XTextSectionsSupplier.class, mxDoc);
         if (supplier.getTextSections().hasByName(OOBibBase.BIB_SECTION_NAME)) {
             XTextSection section = (XTextSection) ((Any) supplier.getTextSections().getByName(OOBibBase.BIB_SECTION_NAME))
-                                                                                                                          .getObject();
+                    .getObject();
             // Clear it:
             XTextCursor cursor = text.createTextCursorByRange(section.getAnchor());
             cursor.gotoRange(section.getAnchor(), false);
@@ -1058,21 +1078,21 @@ private void clearBibTextSectionContent2()
     }
 
     private void populateBibTextSection(Map<BibEntry, BibDatabase> entries, OOBibStyle style)
-        throws NoSuchElementException, WrappedTargetException, PropertyVetoException,
-        UnknownPropertyException, UndefinedParagraphFormatException, IllegalArgumentException, CreationException {
+            throws NoSuchElementException, WrappedTargetException, PropertyVetoException,
+            UnknownPropertyException, UndefinedParagraphFormatException, IllegalArgumentException, CreationException {
         XTextSectionsSupplier supplier = UnoRuntime.queryInterface(XTextSectionsSupplier.class, mxDoc);
         XTextSection section = (XTextSection) ((Any) supplier.getTextSections().getByName(OOBibBase.BIB_SECTION_NAME))
-                                                                                                                      .getObject();
+                .getObject();
         XTextCursor cursor = text.createTextCursorByRange(section.getAnchor());
         OOUtil.insertTextAtCurrentLocation(text, cursor, (String) style.getProperty(OOBibStyle.TITLE),
-                                           (String) style.getProperty(OOBibStyle.REFERENCE_HEADER_PARAGRAPH_FORMAT));
+                (String) style.getProperty(OOBibStyle.REFERENCE_HEADER_PARAGRAPH_FORMAT));
         insertFullReferenceAtCursor(cursor, entries, style,
-                                    (String) style.getProperty(OOBibStyle.REFERENCE_PARAGRAPH_FORMAT));
+                (String) style.getProperty(OOBibStyle.REFERENCE_PARAGRAPH_FORMAT));
         insertBookMark(OOBibBase.BIB_SECTION_END_NAME, cursor);
     }
 
     private XTextContent insertBookMark(String name, XTextCursor position)
-        throws IllegalArgumentException, CreationException {
+            throws IllegalArgumentException, CreationException {
         Object bookmark;
         try {
             bookmark = mxDocFactory.createInstance("com.sun.star.text.Bookmark");
@@ -1093,8 +1113,8 @@ private XTextContent insertBookMark(String name, XTextCursor position)
 
     private void insertReferenceMark(String name, String citationText, XTextCursor position, boolean withText,
                                      OOBibStyle style)
-        throws UnknownPropertyException, WrappedTargetException,
-        PropertyVetoException, IllegalArgumentException, UndefinedCharacterFormatException, CreationException {
+            throws UnknownPropertyException, WrappedTargetException,
+            PropertyVetoException, IllegalArgumentException, UndefinedCharacterFormatException, CreationException {
 
         // Check if there is "page info" stored for this citation. If so, insert it into
         // the citation text before inserting the citation:
@@ -1127,7 +1147,7 @@ private void insertReferenceMark(String name, String citationText, XTextCursor p
                 try {
                     xCursorProps.setPropertyValue(CHAR_STYLE_NAME, charStyle);
                 } catch (UnknownPropertyException | PropertyVetoException | IllegalArgumentException |
-                         WrappedTargetException ex) {
+                        WrappedTargetException ex) {
                     throw new UndefinedCharacterFormatException(charStyle);
                 }
             }
@@ -1154,20 +1174,6 @@ private void insertReferenceMark(String name, String citationText, XTextCursor p
 
     }
 
-    private void italicizeOrBold(XTextCursor position, boolean italicize, int start, int end)
-        throws UnknownPropertyException, PropertyVetoException, IllegalArgumentException, WrappedTargetException {
-        XTextRange range = position.getStart();
-        XTextCursor cursor = position.getText().createTextCursorByRange(range);
-        cursor.goRight((short) start, false);
-        cursor.goRight((short) (end - start), true);
-        XPropertySet xcp = UnoRuntime.queryInterface(XPropertySet.class, cursor);
-        if (italicize) {
-            xcp.setPropertyValue("CharPosture", com.sun.star.awt.FontSlant.ITALIC);
-        } else {
-            xcp.setPropertyValue("CharWeight", com.sun.star.awt.FontWeight.BOLD);
-        }
-    }
-
     private void removeReferenceMark(String name) throws NoSuchElementException, WrappedTargetException {
         XNameAccess xReferenceMarks = getReferenceMarks();
         if (xReferenceMarks.hasByName(name)) {
@@ -1203,10 +1209,24 @@ private XNameAccess getBookmarks() {
         return xNamedBookmarks;
     }
 
+    private void italicizeOrBold(XTextCursor position, boolean italicize, int start, int end)
+            throws UnknownPropertyException, PropertyVetoException, IllegalArgumentException, WrappedTargetException {
+        XTextRange range = position.getStart();
+        XTextCursor cursor = position.getText().createTextCursorByRange(range);
+        cursor.goRight((short) start, false);
+        cursor.goRight((short) (end - start), true);
+        XPropertySet xcp = UnoRuntime.queryInterface(XPropertySet.class, cursor);
+        if (italicize) {
+            xcp.setPropertyValue("CharPosture", com.sun.star.awt.FontSlant.ITALIC);
+        } else {
+            xcp.setPropertyValue("CharWeight", com.sun.star.awt.FontWeight.BOLD);
+        }
+    }
+
     public void combineCiteMarkers(List<BibDatabase> databases, OOBibStyle style)
-        throws IOException, WrappedTargetException, NoSuchElementException, IllegalArgumentException,
-        UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException, CreationException,
-        BibEntryNotFoundException {
+            throws IOException, WrappedTargetException, NoSuchElementException, IllegalArgumentException,
+            UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException, CreationException,
+            BibEntryNotFoundException {
         XNameAccess nameAccess = getReferenceMarks();
         // TODO: doesn't work for citations in footnotes/tables
         List<String> names = getSortedReferenceMarks(nameAccess);
@@ -1243,7 +1263,7 @@ public void combineCiteMarkers(List<BibDatabase> databases, OOBibStyle style)
                     try {
                         xCursorProps.setPropertyValue(CHAR_STYLE_NAME, charStyle);
                     } catch (UnknownPropertyException | PropertyVetoException | IllegalArgumentException |
-                             WrappedTargetException ex) {
+                            WrappedTargetException ex) {
                         // Setting the character format failed, so we throw an exception that
                         // will result in an error message for the user:
                         throw new UndefinedCharacterFormatException(charStyle);
@@ -1282,24 +1302,37 @@ public void combineCiteMarkers(List<BibDatabase> databases, OOBibStyle style)
 
     }
 
-    public static XTextDocument selectComponent(List<XTextDocument> list)
-        throws UnknownPropertyException, WrappedTargetException, IndexOutOfBoundsException {
-        String[] values = new String[list.size()];
-        int ii = 0;
-        for (XTextDocument doc : list) {
-            values[ii] = String.valueOf(OOUtil.getProperty(doc.getCurrentController().getFrame(), "Title"));
-            ii++;
-        }
-        JList<String> sel = new JList<>(values);
-        sel.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        sel.setSelectedIndex(0);
-        int ans = JOptionPane.showConfirmDialog(null, new JScrollPane(sel), Localization.lang("Select document"),
-                                                JOptionPane.OK_CANCEL_OPTION);
-        if (ans == JOptionPane.OK_OPTION) {
-            return list.get(sel.getSelectedIndex());
-        } else {
-            return null;
+    public BibDatabase generateDatabase(List<BibDatabase> databases)
+            throws NoSuchElementException, WrappedTargetException {
+        BibDatabase resultDatabase = new BibDatabase();
+        List<String> cited = findCitedKeys();
+
+        // For each cited key
+        for (String key : cited) {
+            // Loop through the available databases
+            for (BibDatabase loopDatabase : databases) {
+                Optional<BibEntry> entry = loopDatabase.getEntryByKey(key);
+                // If entry found
+                if (entry.isPresent()) {
+                    BibEntry clonedEntry = (BibEntry) entry.get().clone();
+                    // Insert a copy of the entry
+                    resultDatabase.insertEntry(clonedEntry);
+                    // Check if the cloned entry has a crossref field
+                    clonedEntry.getField(FieldName.CROSSREF).ifPresent(crossref -> {
+                        // If the crossref entry is not already in the database
+                        if (!resultDatabase.getEntryByKey(crossref).isPresent()) {
+                            // Add it if it is in the current library
+                            loopDatabase.getEntryByKey(crossref).ifPresent(resultDatabase::insertEntry);
+                        }
+                    });
+
+                    // Be happy with the first found BibEntry and move on to next key
+                    break;
+                }
+            }
         }
+
+        return resultDatabase;
     }
 
     private static class ComparableMark implements Comparable<ComparableMark> {
@@ -1330,7 +1363,7 @@ public boolean equals(Object o) {
             if (o instanceof ComparableMark) {
                 ComparableMark other = (ComparableMark) o;
                 return (this.position.X == other.position.X) && (this.position.Y == other.position.Y)
-                       && Objects.equals(this.name, other.name);
+                        && Objects.equals(this.name, other.name);
             }
             return false;
         }
@@ -1346,37 +1379,4 @@ public int hashCode() {
 
     }
 
-    public BibDatabase generateDatabase(List<BibDatabase> databases)
-        throws NoSuchElementException, WrappedTargetException {
-        BibDatabase resultDatabase = new BibDatabase();
-        List<String> cited = findCitedKeys();
-
-        // For each cited key
-        for (String key : cited) {
-            // Loop through the available databases
-            for (BibDatabase loopDatabase : databases) {
-                Optional<BibEntry> entry = loopDatabase.getEntryByKey(key);
-                // If entry found
-                if (entry.isPresent()) {
-                    BibEntry clonedEntry = (BibEntry) entry.get().clone();
-                    // Insert a copy of the entry
-                    resultDatabase.insertEntry(clonedEntry);
-                    // Check if the cloned entry has a crossref field
-                    clonedEntry.getField(FieldName.CROSSREF).ifPresent(crossref -> {
-                        // If the crossref entry is not already in the database
-                        if (!resultDatabase.getEntryByKey(crossref).isPresent()) {
-                            // Add it if it is in the current library
-                            loopDatabase.getEntryByKey(crossref).ifPresent(resultDatabase::insertEntry);
-                        }
-                    });
-
-                    // Be happy with the first found BibEntry and move on to next key
-                    break;
-                }
-            }
-        }
-
-        return resultDatabase;
-    }
-
 }
diff --git a/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java b/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
index 21b12f02321..9f31cc17a8b 100644
--- a/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
+++ b/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
@@ -94,10 +94,10 @@ public class OpenOfficePanel {
     private OOBibBase ooBase;
     private final JabRefFrame frame;
     private OOBibStyle style;
-    private OpenOfficePreferences ooPrefs;
     private final JabRefPreferences jabRefPreferences;
-    private final StyleLoader loader;
     private final TaskExecutor taskExecutor;
+    private final StyleLoader loader;
+    private OpenOfficePreferences ooPrefs;
 
     public OpenOfficePanel(JabRefFrame frame, JabRefPreferences jabRefPreferences, OpenOfficePreferences ooPrefs, KeyBindingRepository keyBindingRepository) {
         ActionFactory factory = new ActionFactory(keyBindingRepository);
@@ -133,12 +133,29 @@ public OpenOfficePanel(JabRefFrame frame, JabRefPreferences jabRefPreferences, O
         update.setMaxWidth(Double.MAX_VALUE);
 
         loader = new StyleLoader(ooPrefs,
-                                 Globals.prefs.getLayoutFormatterPreferences(Globals.journalAbbreviationLoader),
-                                 Globals.prefs.getDefaultEncoding());
+                Globals.prefs.getLayoutFormatterPreferences(Globals.journalAbbreviationLoader),
+                Globals.prefs.getDefaultEncoding());
 
         initPanel();
     }
 
+    private static void addURL(List<URL> jarList) throws IOException {
+        URLClassLoader sysloader = (URLClassLoader) ClassLoader.getSystemClassLoader();
+        Class<URLClassLoader> sysclass = URLClassLoader.class;
+        try {
+            Method method = sysclass.getDeclaredMethod("addURL", URL.class);
+            method.setAccessible(true);
+            for (URL anU : jarList) {
+                method.invoke(sysloader, anU);
+            }
+        } catch (SecurityException | NoSuchMethodException | IllegalAccessException | IllegalArgumentException |
+                InvocationTargetException e) {
+            LOGGER.error("Could not add URL to system classloader", e);
+            sysloader.close();
+            throw new IOException("Error, could not add URL to system classloader", e);
+        }
+    }
+
     public Node getContent() {
         return vbox;
     }
@@ -154,9 +171,9 @@ private void initPanel() {
             try {
                 ooBase.selectDocument();
                 dialogService.notify(Localization.lang("Connected to document") + ": "
-                                     + ooBase.getCurrentDocumentTitle().orElse(""));
+                        + ooBase.getCurrentDocumentTitle().orElse(""));
             } catch (UnknownPropertyException | WrappedTargetException | IndexOutOfBoundsException |
-                     NoSuchElementException | NoDocumentException ex) {
+                    NoSuchElementException | NoDocumentException ex) {
                 LOGGER.warn("Problem connecting", ex);
                 dialogService.showErrorDialogAndWait(ex);
             }
@@ -209,9 +226,8 @@ private void initPanel() {
                 ooBase.rebuildBibTextSection(databases, style);
                 if (!unresolvedKeys.isEmpty()) {
                     dialogService.showErrorDialogAndWait(Localization.lang("Unable to synchronize bibliography"),
-                                                         Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
-                                                                           unresolvedKeys.get(0)));
-
+                            Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
+                                    unresolvedKeys.get(0)));
                 }
             } catch (UndefinedCharacterFormatException ex) {
                 reportUndefinedCharacterFormat(ex);
@@ -222,19 +238,16 @@ private void initPanel() {
             } catch (IOException ex) {
                 LOGGER.warn("Problem with style file", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("No valid style file defined"),
-                                                     Localization.lang("You must select either a valid style file, or use one of the default styles."));
-
+                        Localization.lang("You must select either a valid style file, or use one of the default styles."));
             } catch (BibEntryNotFoundException ex) {
                 LOGGER.debug("BibEntry not found", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("Unable to synchronize bibliography"), Localization.lang(
-                                                                                                                                "Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
-                                                                                                                                ex.getBibtexKey()));
-
+                        "Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
+                        ex.getBibtexKey()));
             } catch (com.sun.star.lang.IllegalArgumentException | PropertyVetoException | UnknownPropertyException | WrappedTargetException | NoSuchElementException |
-                     CreationException ex) {
+                    CreationException ex) {
                 LOGGER.warn("Could not update bibliography", ex);
             }
-
         });
 
         merge.setMaxWidth(Double.MAX_VALUE);
@@ -245,8 +258,8 @@ private void initPanel() {
             } catch (UndefinedCharacterFormatException ex) {
                 reportUndefinedCharacterFormat(ex);
             } catch (com.sun.star.lang.IllegalArgumentException | UnknownPropertyException | PropertyVetoException |
-                     CreationException | NoSuchElementException | WrappedTargetException | IOException |
-                     BibEntryNotFoundException ex) {
+                    CreationException | NoSuchElementException | WrappedTargetException | IOException |
+                    BibEntryNotFoundException ex) {
                 LOGGER.warn("Problem combining cite markers", ex);
             }
 
@@ -276,7 +289,7 @@ private void initPanel() {
 
         HBox hbox = new HBox();
         hbox.getChildren().addAll(connect, manualConnect, selectDocument, update, help);
-        hbox.getChildren().forEach(btn -> hbox.setHgrow(btn, Priority.ALWAYS));
+        hbox.getChildren().forEach(btn -> HBox.setHgrow(btn, Priority.ALWAYS));
 
         vbox.setFillWidth(true);
         vbox.getChildren().addAll(hbox, setStyleFile, pushEntries, pushEntriesInt, pushEntriesAdvanced, pushEntriesEmpty, merge, manageCitations, exportCitations, settingsB);
@@ -298,8 +311,8 @@ private void exportEntries() {
             if (!unresolvedKeys.isEmpty()) {
 
                 dialogService.showErrorDialogAndWait(Localization.lang("Unable to generate new library"),
-                                                     Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
-                                                                       unresolvedKeys.get(0)));
+                        Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
+                                unresolvedKeys.get(0)));
 
             }
 
@@ -310,12 +323,12 @@ private void exportEntries() {
         } catch (BibEntryNotFoundException ex) {
             LOGGER.debug("BibEntry not found", ex);
             dialogService.showErrorDialogAndWait(Localization.lang("Unable to synchronize bibliography"),
-                                                 Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
-                                                                   ex.getBibtexKey()));
+                    Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
+                            ex.getBibtexKey()));
 
         } catch (com.sun.star.lang.IllegalArgumentException | UnknownPropertyException | PropertyVetoException |
-                 UndefinedCharacterFormatException | NoSuchElementException | WrappedTargetException | IOException |
-                 CreationException e) {
+                UndefinedCharacterFormatException | NoSuchElementException | WrappedTargetException | IOException |
+                CreationException e) {
             LOGGER.warn("Problem generating new database.", e);
         }
 
@@ -398,7 +411,6 @@ protected OOBibBase call() throws Exception {
             merge.setDisable(false);
             manageCitations.setDisable(false);
             exportCitations.setDisable(false);
-
         });
         connectTask.setOnFailed(value -> {
             Throwable ex = connectTask.getException();
@@ -406,17 +418,16 @@ protected OOBibBase call() throws Exception {
                 LOGGER.warn("Could not connect to running OpenOffice/LibreOffice", ex);
 
                 dialogService.showErrorDialogAndWait(Localization.lang("Unable to connect. One possible reason is that JabRef "
-                                                                       + "and OpenOffice/LibreOffice are not both running in either 32 bit mode or 64 bit mode."));
-
+                        + "and OpenOffice/LibreOffice are not both running in either 32 bit mode or 64 bit mode."));
             } else if (ex instanceof IOException) {
                 LOGGER.warn("Could not connect to running OpenOffice/LibreOffice", ex);
 
                 dialogService.showErrorDialogAndWait(Localization.lang("Could not connect to running OpenOffice/LibreOffice."),
-                                                     Localization.lang("Could not connect to running OpenOffice/LibreOffice.")
-                                                                                                                                + "\n"
-                                                                                                                                + Localization.lang("Make sure you have installed OpenOffice/LibreOffice with Java support.") + "\n"
-                                                                                                                                + Localization.lang("If connecting manually, please verify program and library paths.") + "\n" + "\n" + Localization.lang("Error message:"),
-                                                     ex);
+                        Localization.lang("Could not connect to running OpenOffice/LibreOffice.")
+                                + "\n"
+                                + Localization.lang("Make sure you have installed OpenOffice/LibreOffice with Java support.") + "\n"
+                                + Localization.lang("If connecting manually, please verify program and library paths.") + "\n" + "\n" + Localization.lang("Error message:"),
+                        ex);
             } else {
                 dialogService.showErrorDialogAndWait(Localization.lang("Autodetection failed"), Localization.lang("Autodetection failed"), ex);
             }
@@ -442,30 +453,12 @@ private void loadOpenOfficeJars(Path configurationPath) throws IOException {
     }
 
     private OOBibBase createBibBase() throws IOException, InvocationTargetException, IllegalAccessException,
-        WrappedTargetException, BootstrapException, UnknownPropertyException, NoDocumentException,
-        NoSuchElementException, CreationException {
+            WrappedTargetException, BootstrapException, UnknownPropertyException, NoDocumentException,
+            NoSuchElementException, CreationException {
         // Connect
         return new OOBibBase(ooPrefs.getExecutablePath(), true);
     }
 
-    private static void addURL(List<URL> jarList) throws IOException {
-        URLClassLoader sysloader = (URLClassLoader) ClassLoader.getSystemClassLoader();
-        Class<URLClassLoader> sysclass = URLClassLoader.class;
-        try {
-            Method method = sysclass.getDeclaredMethod("addURL", URL.class);
-            method.setAccessible(true);
-            for (URL anU : jarList) {
-                method.invoke(sysloader, anU);
-            }
-        } catch (SecurityException | NoSuchMethodException | IllegalAccessException | IllegalArgumentException |
-                 InvocationTargetException e) {
-            LOGGER.error("Could not add URL to system classloader", e);
-            sysloader.close();
-            throw new IOException("Error, could not add URL to system classloader", e);
-
-        }
-    }
-
     private Optional<Boolean> showManualConnectionDialog() {
         return new ManualConnectDialogView(dialogService).showAndWait();
     }
@@ -504,12 +497,12 @@ private void pushEntries(boolean inParenthesisIn, boolean withText, boolean addP
                         style = loader.getUsedStyle();
                     }
                     ooBase.insertEntry(entries, database, getBaseList(), style, inParenthesis, withText, pageInfo,
-                                       ooPrefs.getSyncWhenCiting());
+                            ooPrefs.getSyncWhenCiting());
                 } catch (FileNotFoundException ex) {
 
                     dialogService.showErrorDialogAndWait(
-                                                         Localization.lang("No valid style file defined"),
-                                                         Localization.lang("You must select either a valid style file, or use one of the default styles."));
+                            Localization.lang("No valid style file defined"),
+                            Localization.lang("You must select either a valid style file, or use one of the default styles."));
 
                     LOGGER.warn("Problem with style file", ex);
                 } catch (ConnectionLostException ex) {
@@ -519,9 +512,9 @@ private void pushEntries(boolean inParenthesisIn, boolean withText, boolean addP
                 } catch (UndefinedParagraphFormatException ex) {
                     reportUndefinedParagraphFormat(ex);
                 } catch (com.sun.star.lang.IllegalArgumentException | UnknownPropertyException | PropertyVetoException |
-                         CreationException | NoSuchElementException | WrappedTargetException | IOException |
-                         BibEntryNotFoundException | IllegalTypeException | PropertyExistException |
-                         NotRemoveableException ex) {
+                        CreationException | NoSuchElementException | WrappedTargetException | IOException |
+                        BibEntryNotFoundException | IllegalTypeException | PropertyExistException |
+                        NotRemoveableException ex) {
                     LOGGER.warn("Could not insert entry", ex);
                 }
             }
@@ -554,9 +547,9 @@ private boolean checkThatEntriesHaveKeys(List<BibEntry> entries) {
 
         // Ask if keys should be generated
         boolean citePressed = dialogService.showConfirmationDialogAndWait(Localization.lang("Cite"),
-                                                                          Localization.lang("Cannot cite entries without BibTeX keys. Generate keys now?"),
-                                                                          Localization.lang("Generate keys"),
-                                                                          Localization.lang("Cancel"));
+                Localization.lang("Cannot cite entries without BibTeX keys. Generate keys now?"),
+                Localization.lang("Generate keys"),
+                Localization.lang("Cancel"));
 
         BasePanel panel = frame.getCurrentBasePanel();
         if (citePressed && (panel != null)) {
@@ -567,8 +560,8 @@ private boolean checkThatEntriesHaveKeys(List<BibEntry> entries) {
                 if (!entry.getCiteKeyOptional().isPresent()) {
                     // Generate key
                     new BibtexKeyGenerator(panel.getBibDatabaseContext(), prefs)
-                                                                                .generateAndSetKey(entry)
-                                                                                .ifPresent(change -> undoCompound.addEdit(new UndoableKeyChange(change)));
+                            .generateAndSetKey(entry)
+                            .ifPresent(change -> undoCompound.addEdit(new UndoableKeyChange(change)));
                 }
             }
             undoCompound.end();
@@ -584,23 +577,23 @@ private boolean checkThatEntriesHaveKeys(List<BibEntry> entries) {
 
     private void showConnectionLostErrorMessage() {
         dialogService.showErrorDialogAndWait(Localization.lang("Connection lost"),
-                                             Localization.lang("Connection to OpenOffice/LibreOffice has been lost. " + "Please make sure OpenOffice/LibreOffice is running, and try to reconnect."));
+                Localization.lang("Connection to OpenOffice/LibreOffice has been lost. " + "Please make sure OpenOffice/LibreOffice is running, and try to reconnect."));
 
     }
 
     private void reportUndefinedParagraphFormat(UndefinedParagraphFormatException ex) {
         dialogService.showErrorDialogAndWait(Localization.lang("Undefined paragraph format"),
-                                             Localization.lang("Your style file specifies the paragraph format '%0', "
-                                                               + "which is undefined in your current OpenOffice/LibreOffice document.",
-                                                               ex.getFormatName()) + "\n" + Localization.lang("The paragraph format is controlled by the property 'ReferenceParagraphFormat' or 'ReferenceHeaderParagraphFormat' in the style file."));
+                Localization.lang("Your style file specifies the paragraph format '%0', "
+                                + "which is undefined in your current OpenOffice/LibreOffice document.",
+                        ex.getFormatName()) + "\n" + Localization.lang("The paragraph format is controlled by the property 'ReferenceParagraphFormat' or 'ReferenceHeaderParagraphFormat' in the style file."));
 
     }
 
     private void reportUndefinedCharacterFormat(UndefinedCharacterFormatException ex) {
         dialogService.showErrorDialogAndWait(Localization.lang("Undefined character format"),
-                                             Localization.lang("Your style file specifies the character format '%0', "
-                                                               + "which is undefined in your current OpenOffice/LibreOffice document.",
-                                                               ex.getFormatName()) + "\n" + Localization.lang("The character format is controlled by the citation property 'CitationCharacterFormat' in the style file.")
+                Localization.lang("Your style file specifies the character format '%0', "
+                                + "which is undefined in your current OpenOffice/LibreOffice document.",
+                        ex.getFormatName()) + "\n" + Localization.lang("The character format is controlled by the citation property 'CitationCharacterFormat' in the style file.")
 
         );
     }
diff --git a/src/main/java/org/jabref/gui/openoffice/StyleSelectDialog.fxml b/src/main/java/org/jabref/gui/openoffice/StyleSelectDialog.fxml
index f994d348787..89d9f67ce04 100644
--- a/src/main/java/org/jabref/gui/openoffice/StyleSelectDialog.fxml
+++ b/src/main/java/org/jabref/gui/openoffice/StyleSelectDialog.fxml
@@ -7,33 +7,35 @@
 <?import javafx.scene.control.TableView?>
 <?import javafx.scene.layout.BorderPane?>
 <?import javafx.scene.layout.VBox?>
-
-<DialogPane minHeight="-Infinity" minWidth="-Infinity" prefHeight="470.0" prefWidth="701.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.openoffice.StyleSelectDialogView">
-   <content>
-      <BorderPane>
-         <top>
-            <TableView fx:id="tvStyles" prefHeight="208.0" prefWidth="662.0" BorderPane.alignment="CENTER">
-              <columns>
-                <TableColumn fx:id="colName" minWidth="100.0" prefWidth="-1.0" text="%Name" />
-                <TableColumn fx:id="colJournals" minWidth="100.0" prefWidth="75.0" text="%Journals" />
-                  <TableColumn fx:id="colFile" minWidth="100.0" prefWidth="-1.0" text="%File" />
-                  <TableColumn fx:id="colDeleteIcon" minWidth="100.0" prefWidth="-1.0" />
-              </columns>
-               <columnResizePolicy>
-                  <TableView fx:constant="CONSTRAINED_RESIZE_POLICY" />
-               </columnResizePolicy>
-            </TableView>
-         </top>
-         <right>
-            <Button fx:id="add" alignment="TOP_RIGHT" mnemonicParsing="false" onAction="#addStyleFile" text="%Add style file" BorderPane.alignment="CENTER" />
-         </right>
-         <bottom>
-            <VBox fx:id="vbox" prefHeight="84.0" prefWidth="665.0" BorderPane.alignment="CENTER" />
-         </bottom>
-      </BorderPane>
-   </content>
-      <buttonTypes>
-        <ButtonType fx:constant="CANCEL" />
-        <ButtonType fx:constant="OK" />
-      </buttonTypes>
+<DialogPane xmlns:fx="http://javafx.com/fxml/1" minHeight="-Infinity" minWidth="-Infinity" prefHeight="470.0"
+            prefWidth="701.0" xmlns="http://javafx.com/javafx/8.0.171"
+            fx:controller="org.jabref.gui.openoffice.StyleSelectDialogView">
+    <content>
+        <BorderPane>
+            <top>
+                <TableView fx:id="tvStyles" prefHeight="208.0" prefWidth="662.0" BorderPane.alignment="CENTER">
+                    <columns>
+                        <TableColumn fx:id="colName" minWidth="100.0" prefWidth="-1.0" text="%Name"/>
+                        <TableColumn fx:id="colJournals" minWidth="100.0" prefWidth="75.0" text="%Journals"/>
+                        <TableColumn fx:id="colFile" minWidth="100.0" prefWidth="-1.0" text="%File"/>
+                        <TableColumn fx:id="colDeleteIcon" minWidth="100.0" prefWidth="-1.0"/>
+                    </columns>
+                    <columnResizePolicy>
+                        <TableView fx:constant="CONSTRAINED_RESIZE_POLICY"/>
+                    </columnResizePolicy>
+                </TableView>
+            </top>
+            <right>
+                <Button fx:id="add" alignment="TOP_RIGHT" mnemonicParsing="false" onAction="#addStyleFile"
+                        text="%Add style file" BorderPane.alignment="CENTER"/>
+            </right>
+            <bottom>
+                <VBox fx:id="vbox" prefHeight="84.0" prefWidth="665.0" BorderPane.alignment="CENTER"/>
+            </bottom>
+        </BorderPane>
+    </content>
+    <buttonTypes>
+        <ButtonType fx:constant="CANCEL"/>
+        <ButtonType fx:constant="OK"/>
+    </buttonTypes>
 </DialogPane>
diff --git a/src/main/java/org/jabref/gui/openoffice/StyleSelectDialogView.java b/src/main/java/org/jabref/gui/openoffice/StyleSelectDialogView.java
index 2a160c15d03..7e5e6a89020 100644
--- a/src/main/java/org/jabref/gui/openoffice/StyleSelectDialogView.java
+++ b/src/main/java/org/jabref/gui/openoffice/StyleSelectDialogView.java
@@ -30,6 +30,9 @@
 
 public class StyleSelectDialogView extends BaseDialog<OOBibStyle> {
 
+    private final MenuItem edit = new MenuItem(Localization.lang("Edit"));
+    private final MenuItem reload = new MenuItem(Localization.lang("Reload"));
+    private final StyleLoader loader;
     @FXML private TableColumn<StyleSelectItemViewModel, String> colName;
     @FXML private TableView<StyleSelectItemViewModel> tvStyles;
     @FXML private TableColumn<StyleSelectItemViewModel, String> colJournals;
@@ -37,14 +40,8 @@ public class StyleSelectDialogView extends BaseDialog<OOBibStyle> {
     @FXML private TableColumn<StyleSelectItemViewModel, Boolean> colDeleteIcon;
     @FXML private Button add;
     @FXML private VBox vbox;
-
     @Inject private PreferencesService preferencesService;
     @Inject private DialogService dialogService;
-
-    private final MenuItem edit = new MenuItem(Localization.lang("Edit"));
-    private final MenuItem reload = new MenuItem(Localization.lang("Reload"));
-    private final StyleLoader loader;
-
     private StyleSelectDialogViewModel viewModel;
     private PreviewPanel previewArticle;
     private PreviewPanel previewBook;
@@ -63,7 +60,6 @@ public StyleSelectDialogView(StyleLoader loader) {
                 return tvStyles.getSelectionModel().getSelectedItem().getStyle();
             }
             return null;
-
         });
         setTitle(Localization.lang("Style selection"));
     }
@@ -87,30 +83,30 @@ private void initialize() {
         colDeleteIcon.setCellValueFactory(cellData -> cellData.getValue().internalStyleProperty());
 
         new ValueTableCellFactory<StyleSelectItemViewModel, Boolean>()
-                                                                      .withGraphic(internalStyle -> {
-                                                                          if (!internalStyle) {
-                                                                              return IconTheme.JabRefIcons.DELETE_ENTRY.getGraphicNode();
-                                                                          }
-                                                                          return null;
-                                                                      })
-                                                                      .withOnMouseClickedEvent(item -> {
-                                                                          return evt -> viewModel.deleteStyle();
-                                                                      })
-                                                                      .withTooltip(item -> {
-                                                                          return Localization.lang("Remove style");
-                                                                      })
-                                                                      .install(colDeleteIcon);
+                .withGraphic(internalStyle -> {
+                    if (!internalStyle) {
+                        return IconTheme.JabRefIcons.DELETE_ENTRY.getGraphicNode();
+                    }
+                    return null;
+                })
+                .withOnMouseClickedEvent(item -> {
+                    return evt -> viewModel.deleteStyle();
+                })
+                .withTooltip(item -> {
+                    return Localization.lang("Remove style");
+                })
+                .install(colDeleteIcon);
 
         edit.setOnAction(e -> viewModel.editStyle());
 
         new ViewModelTableRowFactory<StyleSelectItemViewModel>()
-                                                                .withOnMouseClickedEvent((item, event) -> {
-                                                                    if (event.getClickCount() == 2) {
-                                                                        viewModel.viewStyle(item);
-                                                                    }
-                                                                })
-                                                                .withContextMenu(item -> createContextMenu())
-                                                                .install(tvStyles);
+                .withOnMouseClickedEvent((item, event) -> {
+                    if (event.getClickCount() == 2) {
+                        viewModel.viewStyle(item);
+                    }
+                })
+                .withContextMenu(item -> createContextMenu())
+                .install(tvStyles);
 
         tvStyles.getSelectionModel().selectedItemProperty().addListener((observable, oldvalue, newvalue) -> {
             if (newvalue == null) {
@@ -141,5 +137,4 @@ private ContextMenu createContextMenu() {
     private void addStyleFile() {
         viewModel.addStyleFile();
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/openoffice/StyleSelectDialogViewModel.java b/src/main/java/org/jabref/gui/openoffice/StyleSelectDialogViewModel.java
index 203c495243b..ded9dd93b79 100644
--- a/src/main/java/org/jabref/gui/openoffice/StyleSelectDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/openoffice/StyleSelectDialogViewModel.java
@@ -54,7 +54,6 @@ public StyleSelectDialogViewModel(DialogService dialogService, StyleLoader loade
         } else {
             selectedItem.setValue(styles.get(0));
         }
-
     }
 
     public StyleSelectItemViewModel fromOOBibStyle(OOBibStyle style) {
@@ -67,10 +66,10 @@ public OOBibStyle toOOBibStyle(StyleSelectItemViewModel item) {
 
     public void addStyleFile() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                                                                                               .addExtensionFilter(Localization.lang("Style file"), StandardFileType.JSTYLE)
-                                                                                               .withDefaultExtension(Localization.lang("Style file"), StandardFileType.JSTYLE)
-                                                                                               .withInitialDirectory(preferencesService.getWorkingDir())
-                                                                                               .build();
+                .addExtensionFilter(Localization.lang("Style file"), StandardFileType.JSTYLE)
+                .withDefaultExtension(Localization.lang("Style file"), StandardFileType.JSTYLE)
+                .withInitialDirectory(preferencesService.getWorkingDir())
+                .build();
         Optional<Path> path = dialogService.showFileOpenDialog(fileDialogConfiguration);
         path.map(Path::toAbsolutePath).map(Path::toString).ifPresent(stylePath -> {
             if (loader.addStyleIfValid(stylePath)) {
@@ -80,7 +79,6 @@ public void addStyleFile() {
                 dialogService.showErrorDialogAndWait(Localization.lang("Invalid style selected"), Localization.lang("You must select a valid style file."));
             }
         });
-
     }
 
     public List<StyleSelectItemViewModel> loadStyles() {
@@ -97,7 +95,6 @@ public void deleteStyle() {
         if (loader.removeStyle(style)) {
             styles.remove(selectedItem.get());
         }
-
     }
 
     public void editStyle() {
@@ -106,7 +103,7 @@ public void editStyle() {
         Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByExt("jstyle");
 
         try {
-            JabRefDesktop.openExternalFileAnyFormat(new BibDatabaseContext(), style.getPath().toString(), type);
+            JabRefDesktop.openExternalFileAnyFormat(new BibDatabaseContext(), style.getPath(), type);
         } catch (IOException e) {
             dialogService.showErrorDialogAndWait(e);
         }
@@ -122,7 +119,6 @@ public void viewStyle(StyleSelectItemViewModel item) {
         scrollPane.setContent(styleView);
         pane.setContent(scrollPane);
         dialogService.showCustomDialogAndWait(item.getStyle().getName(), pane, ButtonType.OK);
-
     }
 
     public ObjectProperty<StyleSelectItemViewModel> selectedItemProperty() {
@@ -133,5 +129,4 @@ public void storePrefs() {
         preferences.setCurrentStyle(selectedItem.getValue().getStylePath());
         preferencesService.setOpenOfficePreferences(preferences);
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/openoffice/StyleSelectItemViewModel.java b/src/main/java/org/jabref/gui/openoffice/StyleSelectItemViewModel.java
index 1b4eebf2070..4f5dc9216d9 100644
--- a/src/main/java/org/jabref/gui/openoffice/StyleSelectItemViewModel.java
+++ b/src/main/java/org/jabref/gui/openoffice/StyleSelectItemViewModel.java
@@ -55,5 +55,4 @@ public BooleanProperty internalStyleProperty() {
     public String getStylePath() {
         return style.getPath();
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/preferences/ImportSettingsTab.java b/src/main/java/org/jabref/gui/preferences/ImportSettingsTab.java
index d2dd0896a7e..3067882b2c2 100644
--- a/src/main/java/org/jabref/gui/preferences/ImportSettingsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ImportSettingsTab.java
@@ -4,18 +4,14 @@
 
 import javafx.collections.FXCollections;
 import javafx.scene.Node;
-import javafx.scene.control.CheckBox;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.Label;
-import javafx.scene.control.RadioButton;
 import javafx.scene.control.Separator;
 import javafx.scene.control.TextField;
-import javafx.scene.control.ToggleGroup;
 import javafx.scene.layout.GridPane;
 import javafx.scene.layout.Pane;
 
 import org.jabref.logic.l10n.Localization;
-import org.jabref.pdfimport.ImportDialog;
 import org.jabref.preferences.JabRefPreferences;
 
 public class ImportSettingsTab extends Pane implements PrefsTab {
@@ -23,15 +19,9 @@ public class ImportSettingsTab extends Pane implements PrefsTab {
     public static final String[] DEFAULT_FILENAMEPATTERNS = new String[] {"[bibtexkey]",
             "[bibtexkey] - [title]"};
 
-    public static final int DEFAULT_STYLE = ImportDialog.CONTENT;
     private static final String[] DEFAULT_FILENAMEPATTERNS_DISPLAY = new String[] {"bibtexkey", "bibtexkey - title",};
 
     private final JabRefPreferences prefs;
-    private final RadioButton radioButtonXmp;
-    private final RadioButton radioButtonPDFcontent;
-    private final RadioButton radioButtonNoMeta;
-    private final RadioButton radioButtononlyAttachPDF;
-    private final CheckBox useDefaultPDFImportStyle;
     private final GridPane builder = new GridPane();
     private final TextField fileNamePattern;
     private final ComboBox<String> selectFileNamePattern;
@@ -41,13 +31,6 @@ public class ImportSettingsTab extends Pane implements PrefsTab {
 
     public ImportSettingsTab(JabRefPreferences prefs) {
         this.prefs = Objects.requireNonNull(prefs);
-        radioButtonNoMeta = new RadioButton(Localization.lang("Create blank entry linking the PDF"));
-        radioButtonXmp = new RadioButton(Localization.lang("Create entry based on XMP-metadata"));
-        radioButtonPDFcontent = new RadioButton(Localization.lang("Create entry based on content"));
-        radioButtononlyAttachPDF = new RadioButton(Localization.lang("Only attach PDF"));
-
-        useDefaultPDFImportStyle = new CheckBox(
-                Localization.lang("Always use this PDF import style (and do not ask for each import)"));
 
         fileNamePattern = new TextField();
         fileDirPattern = new TextField();
@@ -61,17 +44,7 @@ public ImportSettingsTab(JabRefPreferences prefs) {
         Label defaultImportStyle = new Label(Localization.lang("Default import style for drag and drop of PDFs"));
         defaultImportStyle.getStyleClass().add("sectionHeader");
         builder.add(defaultImportStyle, 1, 1);
-        final ToggleGroup defaultImportStyleDragDropPdfs = new ToggleGroup();
         builder.add(new Separator(), 2, 1);
-        builder.add(radioButtonNoMeta, 2, 2);
-        builder.add(radioButtonXmp, 2, 3);
-        builder.add(radioButtonPDFcontent, 2, 4);
-        builder.add(radioButtononlyAttachPDF, 2, 5);
-        radioButtonNoMeta.setToggleGroup(defaultImportStyleDragDropPdfs);
-        radioButtonXmp.setToggleGroup(defaultImportStyleDragDropPdfs);
-        radioButtonPDFcontent.setToggleGroup(defaultImportStyleDragDropPdfs);
-        radioButtononlyAttachPDF.setToggleGroup(defaultImportStyleDragDropPdfs);
-        builder.add(useDefaultPDFImportStyle, 2, 6);
         builder.add(new Label(""), 1, 7);
 
         Label defaultPdfFileLinkAction = new Label(Localization.lang("Default PDF file link action"));
@@ -93,45 +66,12 @@ public Node getBuilder() {
 
     @Override
     public void setValues() {
-
-        useDefaultPDFImportStyle.setSelected(prefs.getBoolean(JabRefPreferences.IMPORT_ALWAYSUSE));
-        int style = prefs.getInt(JabRefPreferences.IMPORT_DEFAULT_PDF_IMPORT_STYLE);
-        switch (style) {
-            case ImportDialog.NOMETA:
-                radioButtonNoMeta.setSelected(true);
-                break;
-            case ImportDialog.XMP:
-                radioButtonXmp.setSelected(true);
-                break;
-            case ImportDialog.CONTENT:
-                radioButtonPDFcontent.setSelected(true);
-                break;
-            case ImportDialog.ONLYATTACH:
-                radioButtononlyAttachPDF.setSelected(true);
-                break;
-            default:
-                // fallback
-                radioButtonPDFcontent.setSelected(true);
-                break;
-        }
         fileNamePattern.setText(prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN));
         fileDirPattern.setText(prefs.get(JabRefPreferences.IMPORT_FILEDIRPATTERN));
     }
 
     @Override
     public void storeSettings() {
-        prefs.putBoolean(JabRefPreferences.IMPORT_ALWAYSUSE, useDefaultPDFImportStyle.isSelected());
-        int style = ImportSettingsTab.DEFAULT_STYLE;
-        if (radioButtonNoMeta.isSelected()) {
-            style = ImportDialog.NOMETA;
-        } else if (radioButtonXmp.isSelected()) {
-            style = ImportDialog.XMP;
-        } else if (radioButtonPDFcontent.isSelected()) {
-            style = ImportDialog.CONTENT;
-        } else if (radioButtononlyAttachPDF.isSelected()) {
-            style = ImportDialog.ONLYATTACH;
-        }
-        prefs.putInt(JabRefPreferences.IMPORT_DEFAULT_PDF_IMPORT_STYLE, style);
         prefs.put(JabRefPreferences.IMPORT_FILENAMEPATTERN, fileNamePattern.getText());
         prefs.put(JabRefPreferences.IMPORT_FILEDIRPATTERN, fileDirPattern.getText());
     }
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
index 25837b9b62c..8881f6af654 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
@@ -112,8 +112,8 @@ private void construct() {
         });
         tabsList.getSelectionModel().selectFirst();
         new ViewModelListCellFactory<PrefsTab>()
-                                                .withText(PrefsTab::getTabName)
-                                                .install(tabsList);
+                .withText(PrefsTab::getTabName)
+                .install(tabsList);
 
         VBox buttonContainer = new VBox();
         buttonContainer.setAlignment(Pos.BOTTOM_LEFT);
@@ -133,19 +133,19 @@ private void construct() {
         resetPreferences.setOnAction(e -> resetPreferences());
         resetPreferences.setMaxWidth(Double.MAX_VALUE);
         buttonContainer.getChildren().addAll(
-                                             importPreferences,
-                                             exportPreferences,
-                                             showPreferences,
-                                             resetPreferences);
+                importPreferences,
+                exportPreferences,
+                showPreferences,
+                resetPreferences);
 
         VBox spacer = new VBox();
         spacer.setPrefHeight(10.0);
         VBox.setVgrow(tabsList, Priority.ALWAYS);
         VBox.setVgrow(spacer, Priority.SOMETIMES);
         vBox.getChildren().addAll(
-                                  tabsList,
-                                  spacer,
-                                  buttonContainer);
+                tabsList,
+                spacer,
+                buttonContainer);
 
         container.setLeft(vBox);
 
@@ -154,16 +154,16 @@ private void construct() {
 
     private void resetPreferences() {
         boolean resetPreferencesConfirmed = dialogService.showConfirmationDialogAndWait(
-                                                                                        Localization.lang("Reset preferences"),
-                                                                                        Localization.lang("Are you sure you want to reset all settings to default values?"),
-                                                                                        Localization.lang("Reset preferences"),
-                                                                                        Localization.lang("Cancel"));
+                Localization.lang("Reset preferences"),
+                Localization.lang("Are you sure you want to reset all settings to default values?"),
+                Localization.lang("Reset preferences"),
+                Localization.lang("Cancel"));
         if (resetPreferencesConfirmed) {
             try {
                 prefs.clear();
 
                 dialogService.showWarningDialogAndWait(Localization.lang("Reset preferences"),
-                                                       Localization.lang("You must restart JabRef for this to come into effect."));
+                        Localization.lang("You must restart JabRef for this to come into effect."));
             } catch (BackingStoreException ex) {
                 LOGGER.error("Error while resetting preferences", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("Reset preferences"), ex);
@@ -174,9 +174,9 @@ private void resetPreferences() {
 
     private void importPreferences() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                                                                                               .addExtensionFilter(StandardFileType.XML)
-                                                                                               .withDefaultExtension(StandardFileType.XML)
-                                                                                               .withInitialDirectory(prefs.setLastPreferencesExportPath()).build();
+                .addExtensionFilter(StandardFileType.XML)
+                .withDefaultExtension(StandardFileType.XML)
+                .withInitialDirectory(prefs.setLastPreferencesExportPath()).build();
 
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> {
             try {
@@ -184,7 +184,7 @@ private void importPreferences() {
                 updateAfterPreferenceChanges();
 
                 dialogService.showWarningDialogAndWait(Localization.lang("Import preferences"),
-                                                       Localization.lang("You must restart JabRef for this to come into effect."));
+                        Localization.lang("You must restart JabRef for this to come into effect."));
             } catch (JabRefException ex) {
                 LOGGER.error("Error while importing preferences", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("Import preferences"), ex);
@@ -229,10 +229,10 @@ public void setValues() {
 
     private void exportPreferences() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                                                                                               .addExtensionFilter(StandardFileType.XML)
-                                                                                               .withDefaultExtension(StandardFileType.XML)
-                                                                                               .withInitialDirectory(prefs.setLastPreferencesExportPath())
-                                                                                               .build();
+                .addExtensionFilter(StandardFileType.XML)
+                .withDefaultExtension(StandardFileType.XML)
+                .withInitialDirectory(prefs.setLastPreferencesExportPath())
+                .build();
 
         dialogService.showFileSaveDialog(fileDialogConfiguration)
                      .ifPresent(exportFile -> {
diff --git a/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java b/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java
index 5ace5352e0a..07dedf198b0 100644
--- a/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/PreviewPrefsTab.java
@@ -156,8 +156,8 @@ private void setupGui() {
         btnUp.setPrefSize(80, 20);
         btnDown.setPrefSize(80, 20);
         vBox.getChildren().addAll(new Label(""), new Label(""), new Label(""), new Label(""), new Label(""),
-                                  new Label(""), new Label(""), btnRight, btnLeft, new Label(""), new Label(""), new Label(""),
-                                  btnUp, btnDown);
+                new Label(""), new Label(""), btnRight, btnLeft, new Label(""), new Label(""), new Label(""),
+                btnUp, btnDown);
         Label currentPreview = new Label(Localization.lang("Current Preview"));
         currentPreview.getStyleClass().add("sectionHeader");
         gridPane.add(currentPreview, 1, 1);
diff --git a/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java b/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
index e5d1ff88664..090f22d3020 100644
--- a/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
@@ -97,8 +97,8 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
         this.frame = frame;
 
         /* Populate the data of Entry table columns */
-        List<String> prefColNames = this.prefs.getStringList(this.prefs.COLUMN_NAMES);
-        List<String> prefColWidths = this.prefs.getStringList(this.prefs.COLUMN_WIDTHS);
+        List<String> prefColNames = this.prefs.getStringList(JabRefPreferences.COLUMN_NAMES);
+        List<String> prefColWidths = this.prefs.getStringList(JabRefPreferences.COLUMN_WIDTHS);
         this.data = FXCollections.observableArrayList();
         for (int i = 0; i < prefColNames.size(); i++) {
             this.data.add(new TableRow(prefColNames.get(i), Double.parseDouble(prefColWidths.get(i))));
@@ -119,9 +119,9 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
                     // Since data is an ObservableList, updating it updates the displayed field name.
                     this.data.set(t.getTablePosition().getRow(), new TableRow(t.getNewValue()));
                     // Update the User Preference of COLUMN_NAMES
-                    List<String> tempColumnNames = this.prefs.getStringList(this.prefs.COLUMN_NAMES);
+                    List<String> tempColumnNames = this.prefs.getStringList(JabRefPreferences.COLUMN_NAMES);
                     tempColumnNames.set(t.getTablePosition().getRow(), t.getNewValue());
-                    this.prefs.putStringList(this.prefs.COLUMN_NAMES,tempColumnNames);
+                    this.prefs.putStringList(JabRefPreferences.COLUMN_NAMES, tempColumnNames);
                 });
 
         colSetup.setItems(data);
@@ -368,8 +368,8 @@ public void setValues() {
         /*** end: special fields ***/
 
         data.clear();
-        List<String> prefColNames = this.prefs.getStringList(this.prefs.COLUMN_NAMES);
-        List<String> prefColWidths = this.prefs.getStringList(this.prefs.COLUMN_WIDTHS);
+        List<String> prefColNames = this.prefs.getStringList(JabRefPreferences.COLUMN_NAMES);
+        List<String> prefColWidths = this.prefs.getStringList(JabRefPreferences.COLUMN_WIDTHS);
         for (int i = 0; i < prefColNames.size(); i++) {
             this.data.add(new TableRow(prefColNames.get(i), Double.parseDouble(prefColWidths.get(i))));
         }
@@ -414,48 +414,6 @@ public void setLength(double length) {
         }
     }
 
-    class UpdateOrderAction extends AbstractAction {
-
-        public UpdateOrderAction() {
-            super(Localization.lang("Update to current column order"));
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            BasePanel panel = frame.getCurrentBasePanel();
-            if (panel == null) {
-                return;
-            }
-            // idea: sort elements according to value stored in hash, keep
-            // everything not inside hash/mainTable as it was
-            final HashMap<String, Integer> map = new HashMap<>();
-
-            // first element (#) not inside data
-            /*
-            for (TableColumn<BibEntry, ?> column : panel.getMainTable().getColumns()) {
-                String name = column.getText();
-                if ((name != null) && !name.isEmpty()) {
-                    map.put(name.toLowerCase(Locale.ROOT), i);
-                }
-            }
-            */
-            Collections.sort(data, (o1, o2) -> {
-                Integer n1 = map.get(o1.getName());
-                Integer n2 = map.get(o2.getName());
-                if ((n1 == null) || (n2 == null)) {
-                    return 0;
-                }
-                return n1.compareTo(n2);
-            });
-
-            colSetup.setItems(data);
-            colSetup.refresh();
-            tableChanged = true;
-        }
-    }
-
-
-
     /**
      * Store changes to table preferences. This method is called when
      * the user clicks Ok.
@@ -555,6 +513,46 @@ public void storeSettings() {
 
     }
 
+    class UpdateOrderAction extends AbstractAction {
+
+        public UpdateOrderAction() {
+            super(Localization.lang("Update to current column order"));
+        }
+
+        @Override
+        public void actionPerformed(ActionEvent e) {
+            BasePanel panel = frame.getCurrentBasePanel();
+            if (panel == null) {
+                return;
+            }
+            // idea: sort elements according to value stored in hash, keep
+            // everything not inside hash/mainTable as it was
+            final HashMap<String, Integer> map = new HashMap<>();
+
+            // first element (#) not inside data
+            /*
+            for (TableColumn<BibEntry, ?> column : panel.getMainTable().getColumns()) {
+                String name = column.getText();
+                if ((name != null) && !name.isEmpty()) {
+                    map.put(name.toLowerCase(Locale.ROOT), i);
+                }
+            }
+            */
+            Collections.sort(data, (o1, o2) -> {
+                Integer n1 = map.get(o1.getName());
+                Integer n2 = map.get(o2.getName());
+                if ((n1 == null) || (n2 == null)) {
+                    return 0;
+                }
+                return n1.compareTo(n2);
+            });
+
+            colSetup.setItems(data);
+            colSetup.refresh();
+            tableChanged = true;
+        }
+    }
+
     @Override
     public boolean validateSettings() {
         return true;
diff --git a/src/main/java/org/jabref/gui/util/BaseDialog.java b/src/main/java/org/jabref/gui/util/BaseDialog.java
index a05eb2862ce..6cf9a1faf5b 100644
--- a/src/main/java/org/jabref/gui/util/BaseDialog.java
+++ b/src/main/java/org/jabref/gui/util/BaseDialog.java
@@ -36,9 +36,9 @@ private Optional<Button> getDefaultButton() {
 
     private ButtonType getDefaultButtonType() {
         return getDialogPane().getButtonTypes().stream()
-                .filter(buttonType -> buttonType.getButtonData().isDefaultButton())
-                .findFirst()
-                .orElse(ButtonType.OK);
+                              .filter(buttonType -> buttonType.getButtonData().isDefaultButton())
+                              .findFirst()
+                              .orElse(ButtonType.OK);
     }
 
     private void setDialogIcon(Image image) {
diff --git a/src/main/java/org/jabref/gui/util/FileFilterConverter.java b/src/main/java/org/jabref/gui/util/FileFilterConverter.java
index fdeb734b9c6..c42999e4a9e 100644
--- a/src/main/java/org/jabref/gui/util/FileFilterConverter.java
+++ b/src/main/java/org/jabref/gui/util/FileFilterConverter.java
@@ -1,5 +1,6 @@
 package org.jabref.gui.util;
 
+import java.io.FileFilter;
 import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
@@ -12,6 +13,8 @@
 import org.jabref.logic.importer.Importer;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.FileType;
+import org.jabref.logic.util.io.FileUtil;
+import org.jabref.model.strings.StringUtil;
 
 public class FileFilterConverter {
 
@@ -20,12 +23,12 @@ public class FileFilterConverter {
     private FileFilterConverter() {
     }
 
-    static FileChooser.ExtensionFilter toExtensionFilter(FileType fileType) {
+    public static FileChooser.ExtensionFilter toExtensionFilter(FileType fileType) {
         String description = Localization.lang("%0 file", fileType.toString());
         return new FileChooser.ExtensionFilter(description, fileType.getExtensionsWithDot());
     }
 
-    static FileChooser.ExtensionFilter toExtensionFilter(String description, FileType fileType) {
+    public static FileChooser.ExtensionFilter toExtensionFilter(String description, FileType fileType) {
         return new FileChooser.ExtensionFilter(description, fileType.getExtensionsWithDot());
     }
 
@@ -57,4 +60,20 @@ public static List<FileChooser.ExtensionFilter> exporterToExtensionFilter(Collec
                         .map(exporter -> toExtensionFilter(exporter.getName(), exporter.getFileType()))
                         .collect(Collectors.toList());
     }
+
+    public static FileFilter toFileFilter(FileChooser.ExtensionFilter extensionFilter) {
+        List<String> extensionsCleaned = extensionFilter.getExtensions()
+                                                        .stream()
+                                                        .map(extension -> extension.replace(".", "").replace("*", ""))
+                                                        .filter(StringUtil::isNotBlank)
+                                                        .collect(Collectors.toList());
+        if (extensionsCleaned.isEmpty()) {
+            // Except every file
+            return pathname -> true;
+        } else {
+            return pathname -> FileUtil.getFileExtension(pathname.toPath())
+                                       .map(extensionsCleaned::contains)
+                                       .orElse(false);
+        }
+    }
 }
diff --git a/src/main/java/org/jabref/gui/util/ZipFileChooser.java b/src/main/java/org/jabref/gui/util/ZipFileChooser.java
index 74049324e9d..dd8fd8b63e5 100644
--- a/src/main/java/org/jabref/gui/util/ZipFileChooser.java
+++ b/src/main/java/org/jabref/gui/util/ZipFileChooser.java
@@ -29,7 +29,7 @@ public class ZipFileChooser extends BaseDialog<Path> {
     /**
      * New ZIP file chooser.
      *
-     * @param zipFile                   ZIP-Fle to choose from, must be readable
+     * @param zipFile ZIP-Fle to choose from, must be readable
      */
     public ZipFileChooser(FileSystem zipFile) throws IOException {
         setTitle(Localization.lang("Select file from ZIP-archive"));
diff --git a/src/main/java/org/jabref/gui/util/comparator/ReadStatusFieldComparator.java b/src/main/java/org/jabref/gui/util/comparator/ReadStatusFieldComparator.java
index d4317cd7464..1eeab144dcc 100644
--- a/src/main/java/org/jabref/gui/util/comparator/ReadStatusFieldComparator.java
+++ b/src/main/java/org/jabref/gui/util/comparator/ReadStatusFieldComparator.java
@@ -23,5 +23,4 @@ public int compare(Optional<SpecialFieldValueViewModel> val1, Optional<SpecialFi
             }
         }
     }
-
 }
diff --git a/src/main/java/org/jabref/logic/exporter/ExporterFactory.java b/src/main/java/org/jabref/logic/exporter/ExporterFactory.java
index 52e88dacc73..fbba86a6aa4 100644
--- a/src/main/java/org/jabref/logic/exporter/ExporterFactory.java
+++ b/src/main/java/org/jabref/logic/exporter/ExporterFactory.java
@@ -28,7 +28,7 @@ private ExporterFactory(List<Exporter> exporters) {
     }
 
     public static ExporterFactory create(List<TemplateExporter> customFormats,
-            LayoutFormatterPreferences layoutPreferences, SavePreferences savePreferences, XmpPreferences xmpPreferences) {
+                                         LayoutFormatterPreferences layoutPreferences, SavePreferences savePreferences, XmpPreferences xmpPreferences) {
 
         List<Exporter> exporters = new ArrayList<>();
 
diff --git a/src/main/java/org/jabref/logic/exporter/TemplateExporter.java b/src/main/java/org/jabref/logic/exporter/TemplateExporter.java
index 4694e1b9f7e..ae07443c54c 100644
--- a/src/main/java/org/jabref/logic/exporter/TemplateExporter.java
+++ b/src/main/java/org/jabref/logic/exporter/TemplateExporter.java
@@ -74,12 +74,12 @@ public TemplateExporter(String displayName, String consoleName, String lfFileNam
      * Initialize another export format based on templates stored in dir with
      * layoutFile lfFilename.
      *
-     * @param name to display to the user and to call this format in the console.
-     * @param lfFileName  Name of the main layout file.
-     * @param directory   Directory in which to find the layout file.
-     * @param extension   May or may not contain the . (for instance .txt).
+     * @param name              to display to the user and to call this format in the console.
+     * @param lfFileName        Name of the main layout file.
+     * @param directory         Directory in which to find the layout file.
+     * @param extension         May or may not contain the . (for instance .txt).
      * @param layoutPreferences Preferences for the layout
-     * @param savePreferences Preferences for saving
+     * @param savePreferences   Preferences for saving
      */
     public TemplateExporter(String name, String lfFileName, String extension, LayoutFormatterPreferences layoutPreferences,
                             SavePreferences savePreferences) {
@@ -348,7 +348,6 @@ private void readFormatterFile() {
                         layoutPreferences.putCustomExportNameFormatter(formatterName, contents);
                     }
                 }
-
             } catch (IOException ex) {
                 // TODO: show error message here?
                 LOGGER.warn("Problem opening formatter file.", ex);
diff --git a/src/main/java/org/jabref/logic/externalfiles/ExternalFilesContentImporter.java b/src/main/java/org/jabref/logic/externalfiles/ExternalFilesContentImporter.java
index bdfe5970639..8fbc7252899 100644
--- a/src/main/java/org/jabref/logic/externalfiles/ExternalFilesContentImporter.java
+++ b/src/main/java/org/jabref/logic/externalfiles/ExternalFilesContentImporter.java
@@ -1,6 +1,5 @@
 package org.jabref.logic.externalfiles;
 
-import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.util.List;
@@ -9,27 +8,25 @@
 import org.jabref.logic.importer.OpenDatabase;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.fileformat.PdfContentImporter;
-import org.jabref.logic.xmp.XmpUtilReader;
+import org.jabref.logic.importer.fileformat.PdfXmpImporter;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.util.FileUpdateMonitor;
 
 public class ExternalFilesContentImporter {
 
-    private final PdfContentImporter pdfImporter;
     private final ImportFormatPreferences importFormatPreferences;
 
     public ExternalFilesContentImporter(ImportFormatPreferences importFormatPreferences) {
-        pdfImporter = new PdfContentImporter(importFormatPreferences);
         this.importFormatPreferences = importFormatPreferences;
     }
 
     public List<BibEntry> importPDFContent(Path file) {
-        return pdfImporter.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
+        return new PdfContentImporter(importFormatPreferences).importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
 
     }
 
-    public List<BibEntry> importXMPContent(Path file) throws IOException {
-        return XmpUtilReader.readXmp(file, importFormatPreferences.getXmpPreferences());
+    public List<BibEntry> importXMPContent(Path file) {
+        return new PdfXmpImporter(importFormatPreferences.getXmpPreferences()).importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
 
     }
 
diff --git a/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java b/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
index db4bffee679..8296a534503 100644
--- a/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
+++ b/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
@@ -221,9 +221,8 @@ private void checkEpilog() {
         // This is an incomplete and inaccurate try to verify if something went wrong with previous parsing activity even though there were no warnings so far
         // regex looks for something like 'identifier = blabla ,'
         if (!parserResult.hasWarnings() && Pattern.compile("\\w+\\s*=.*,").matcher(database.getEpilog()).find()) {
-                parserResult.addWarning("following BibTex fragment has not been parsed:\n" + database.getEpilog());
+            parserResult.addWarning("following BibTex fragment has not been parsed:\n" + database.getEpilog());
         }
-
     }
 
     private void parseRemainingContent() {
diff --git a/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java
index 934219824cd..ecb4b609011 100644
--- a/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java
+++ b/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java
@@ -511,7 +511,7 @@ private void addPersonalNames(Map<String, String> fields, PersonalNameSubjectLis
                 for (PersonalNameSubject personalName : personalNameSubject) {
                     String name = personalName.getLastName();
                     if (personalName.getForeName() != null) {
-                        name += ", " + personalName.getForeName().toString();
+                        name += ", " + personalName.getForeName();
                     }
                     personalNames.add(name);
                 }
diff --git a/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java
index 1389c15d40e..bbad11f21c5 100644
--- a/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java
+++ b/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java
@@ -358,7 +358,7 @@ private void addAbstract(Map<String, String> hm, String lab, String value) {
             if (value.contains("Copyright")) {
                 int copyrightIndex = value.lastIndexOf("Copyright");
                 //remove the copyright from the field since the name of the field is copyright
-                String copyrightInfo = value.substring(copyrightIndex, value.length()).replaceAll("Copyright ", "");
+                String copyrightInfo = value.substring(copyrightIndex).replaceAll("Copyright ", "");
                 hm.put("copyright", copyrightInfo);
                 abstractValue = value.substring(0, copyrightIndex);
             } else {
diff --git a/src/main/java/org/jabref/logic/importer/fileformat/PdfContentImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/PdfContentImporter.java
index 73d5f0544fc..c7a9150c093 100644
--- a/src/main/java/org/jabref/logic/importer/fileformat/PdfContentImporter.java
+++ b/src/main/java/org/jabref/logic/importer/fileformat/PdfContentImporter.java
@@ -25,6 +25,7 @@
 import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.EntryType;
 import org.jabref.model.entry.FieldName;
+import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.entry.identifier.DOI;
 
 import com.google.common.base.Strings;
@@ -213,6 +214,7 @@ public ParserResult importDatabase(Path filePath, Charset defaultEncoding) {
                 ParserResult parserResult = new ParserResult(result);
                 Optional<BibEntry> entry = new DoiFetcher(importFormatPreferences).performSearchById(doi.get().getDOI());
                 entry.ifPresent(parserResult.getDatabase()::insertEntry);
+                entry.ifPresent(bibEntry -> bibEntry.addFile(new LinkedFile("", filePath.toAbsolutePath().toString(), "PDF")));
                 return parserResult;
             }
 
@@ -488,6 +490,7 @@ public ParserResult importDatabase(Path filePath, Charset defaultEncoding) {
             return ParserResult.fromErrorMessage(e.getMessage());
         }
 
+        result.forEach(entry -> entry.addFile(new LinkedFile("", filePath.toAbsolutePath().toString(), "PDF")));
         return new ParserResult(result);
     }
 
diff --git a/src/main/java/org/jabref/logic/layout/format/CreateDocBook4Authors.java b/src/main/java/org/jabref/logic/layout/format/CreateDocBook4Authors.java
index 3e04ae04eae..48a3bb622d4 100644
--- a/src/main/java/org/jabref/logic/layout/format/CreateDocBook4Authors.java
+++ b/src/main/java/org/jabref/logic/layout/format/CreateDocBook4Authors.java
@@ -16,7 +16,5 @@ public String format(String fieldText) {
         DocBookAuthorFormatter formatter = new DocBookAuthorFormatter();
         formatter.addBody(sb, al, FieldName.AUTHOR, DocBookVersion.DOCBOOK_4);
         return sb.toString();
-
     }
-
 }
diff --git a/src/main/java/org/jabref/logic/layout/format/CreateDocBook5Authors.java b/src/main/java/org/jabref/logic/layout/format/CreateDocBook5Authors.java
index 53cc52c14d7..1f94b8b2fa2 100644
--- a/src/main/java/org/jabref/logic/layout/format/CreateDocBook5Authors.java
+++ b/src/main/java/org/jabref/logic/layout/format/CreateDocBook5Authors.java
@@ -18,7 +18,5 @@ public String format(String fieldText) {
         DocBookAuthorFormatter authorFormatter = new DocBookAuthorFormatter();
         authorFormatter.addBody(sb, al, FieldName.AUTHOR, DocBookVersion.DOCBOOK_5);
         return sb.toString();
-
     }
-
 }
diff --git a/src/main/java/org/jabref/logic/layout/format/CreateDocBook5Editors.java b/src/main/java/org/jabref/logic/layout/format/CreateDocBook5Editors.java
index 55892a37521..b972695a1b3 100644
--- a/src/main/java/org/jabref/logic/layout/format/CreateDocBook5Editors.java
+++ b/src/main/java/org/jabref/logic/layout/format/CreateDocBook5Editors.java
@@ -17,7 +17,5 @@ public String format(String fieldText) {
         DocBookAuthorFormatter formatter = new DocBookAuthorFormatter();
         formatter.addBody(sb, al, FieldName.EDITOR, DocBookVersion.DOCBOOK_5);
         return sb.toString();
-
     }
-
 }
diff --git a/src/main/java/org/jabref/logic/layout/format/DocBookAuthorFormatter.java b/src/main/java/org/jabref/logic/layout/format/DocBookAuthorFormatter.java
index 8bcf75058d3..3deaf21c625 100644
--- a/src/main/java/org/jabref/logic/layout/format/DocBookAuthorFormatter.java
+++ b/src/main/java/org/jabref/logic/layout/format/DocBookAuthorFormatter.java
@@ -12,9 +12,8 @@ public class DocBookAuthorFormatter {
     private static final XMLChars XML_CHARS = new XMLChars();
 
     /**
-     *
-     * @param sb {@link StringBuilder}
-     * @param al {@link AuthorList}
+     * @param sb      {@link StringBuilder}
+     * @param al      {@link AuthorList}
      * @param tagName Editor or author field/tag
      * @param version @link {@link DocBookVersion}
      */
@@ -26,13 +25,13 @@ public void addBody(StringBuilder sb, AuthorList al, String tagName, DocBookVers
             }
             Author a = al.getAuthor(i);
             a.getFirst().filter(first -> !first.isEmpty()).ifPresent(first -> sb.append("<firstname>")
-                    .append(XML_CHARS.format(first)).append("</firstname>"));
+                                                                                .append(XML_CHARS.format(first)).append("</firstname>"));
             a.getVon().filter(von -> !von.isEmpty()).ifPresent(von -> sb.append("<othername>")
-                    .append(XML_CHARS.format(von)).append("</othername>"));
+                                                                        .append(XML_CHARS.format(von)).append("</othername>"));
             a.getLast().filter(last -> !last.isEmpty()).ifPresent(last -> {
                 sb.append("<surname>").append(XML_CHARS.format(last));
                 a.getJr().filter(jr -> !jr.isEmpty())
-                        .ifPresent(jr -> sb.append(' ').append(XML_CHARS.format(jr)));
+                 .ifPresent(jr -> sb.append(' ').append(XML_CHARS.format(jr)));
                 sb.append("</surname>");
                 if (version == DocBookVersion.DOCBOOK_5) {
                     sb.append("</personname>");
@@ -46,4 +45,4 @@ public void addBody(StringBuilder sb, AuthorList al, String tagName, DocBookVers
             }
         }
     }
-}
\ No newline at end of file
+}
diff --git a/src/main/java/org/jabref/logic/openoffice/OOBibStyle.java b/src/main/java/org/jabref/logic/openoffice/OOBibStyle.java
index 2d71b151207..dcf94806637 100644
--- a/src/main/java/org/jabref/logic/openoffice/OOBibStyle.java
+++ b/src/main/java/org/jabref/logic/openoffice/OOBibStyle.java
@@ -857,6 +857,7 @@ public Object getProperty(String propName) {
 
     /**
      * Indicate if it is an internal style
+     *
      * @return True if an internal style
      */
     public boolean isFromResource() {
@@ -880,7 +881,7 @@ public boolean equals(Object o) {
         if (o instanceof OOBibStyle) {
             OOBibStyle otherStyle = (OOBibStyle) o;
             return Objects.equals(path, otherStyle.path)
-                   && Objects.equals(name, otherStyle.name)
+                    && Objects.equals(name, otherStyle.name)
                     && Objects.equals(citProperties, otherStyle.citProperties)
                     && Objects.equals(properties, otherStyle.properties);
         }
diff --git a/src/main/java/org/jabref/logic/openoffice/OpenOfficePreferences.java b/src/main/java/org/jabref/logic/openoffice/OpenOfficePreferences.java
index f3d6a0b29a0..cf97d1e0551 100644
--- a/src/main/java/org/jabref/logic/openoffice/OpenOfficePreferences.java
+++ b/src/main/java/org/jabref/logic/openoffice/OpenOfficePreferences.java
@@ -33,9 +33,9 @@ public OpenOfficePreferences(
             String jarsPath,
             String executablePath,
             String installationPath,
-                                 boolean useAllDatabases,
-                                 boolean syncWhenCiting,
-                                 boolean showPanel,
+            boolean useAllDatabases,
+            boolean syncWhenCiting,
+            boolean showPanel,
             List<String> externalStyles,
             String currentStyle
     ) {
diff --git a/src/main/java/org/jabref/logic/util/io/FileUtil.java b/src/main/java/org/jabref/logic/util/io/FileUtil.java
index 3f17313bff9..5b6e1f165fc 100644
--- a/src/main/java/org/jabref/logic/util/io/FileUtil.java
+++ b/src/main/java/org/jabref/logic/util/io/FileUtil.java
@@ -42,7 +42,7 @@ private FileUtil() {
     /**
      * Returns the extension of a file name or Optional.empty() if the file does not have one (no "." in name).
      *
-     * @return The extension (without leading dot), trimmed and in lowercase.
+     * @return the extension (without leading dot), trimmed and in lowercase.
      */
     public static Optional<String> getFileExtension(String fileName) {
         int dotPosition = fileName.lastIndexOf('.');
@@ -57,7 +57,7 @@ public static Optional<String> getFileExtension(String fileName) {
     /**
      * Returns the extension of a file or Optional.empty() if the file does not have one (no . in name).
      *
-     * @return The extension, trimmed and in lowercase.
+     * @return the extension (without leading dot), trimmed and in lowercase.
      */
     public static Optional<String> getFileExtension(Path file) {
         return getFileExtension(file.getFileName().toString());
diff --git a/src/main/java/org/jabref/logic/xmp/XmpUtilReader.java b/src/main/java/org/jabref/logic/xmp/XmpUtilReader.java
index 0eb04675789..72eb8941436 100644
--- a/src/main/java/org/jabref/logic/xmp/XmpUtilReader.java
+++ b/src/main/java/org/jabref/logic/xmp/XmpUtilReader.java
@@ -6,12 +6,12 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Optional;
 
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.LinkedFile;
 
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.PDDocumentCatalog;
@@ -96,10 +96,7 @@ public static List<BibEntry> readXmp(Path path, XmpPreferences xmpPreferences)
             }
         }
 
-        // return empty list, if no metadata was found
-        if (result.isEmpty()) {
-            return Collections.emptyList();
-        }
+        result.forEach(entry -> entry.addFile(new LinkedFile("", path.toAbsolutePath().toString(), "PDF")));
         return result;
     }
 
diff --git a/src/main/java/org/jabref/model/entry/BibEntry.java b/src/main/java/org/jabref/model/entry/BibEntry.java
index 4e133b759cf..3f901d9b4cc 100644
--- a/src/main/java/org/jabref/model/entry/BibEntry.java
+++ b/src/main/java/org/jabref/model/entry/BibEntry.java
@@ -100,7 +100,7 @@ private BibEntry(String id, String type) {
      * Constructs a new BibEntry. The internal ID is set to IdGenerator.next()
      */
     public BibEntry(EntryType type) {
-        this(IdGenerator.next(),type.getName());
+        this(IdGenerator.next(), type.getName());
     }
 
     public Optional<FieldChange> setMonth(Month parsedMonth) {
@@ -533,7 +533,7 @@ private boolean atLeastOnePresent(String[] fieldsToCheck, BibDatabase database)
      */
     @Override
     public Object clone() {
-        BibEntry clone = new BibEntry(IdGenerator.next(),type.getValue());
+        BibEntry clone = new BibEntry(IdGenerator.next(), type.getValue());
         clone.fields = FXCollections.observableMap(new ConcurrentHashMap<>(fields));
         return clone;
     }
diff --git a/src/main/java/org/jabref/model/entry/LinkedFile.java b/src/main/java/org/jabref/model/entry/LinkedFile.java
index 63d0dfb2cea..62a71dac417 100644
--- a/src/main/java/org/jabref/model/entry/LinkedFile.java
+++ b/src/main/java/org/jabref/model/entry/LinkedFile.java
@@ -33,6 +33,14 @@ public class LinkedFile implements Serializable {
     private transient StringProperty link = new SimpleStringProperty();
     private transient StringProperty fileType = new SimpleStringProperty();
 
+    public LinkedFile(String description, Path link, String fileType) {
+        this(description, link.toString(), fileType);
+    }
+
+    /**
+     * @deprecated use the other constructor {@link #LinkedFile(String, Path, String)}
+     */
+    @Deprecated
     public LinkedFile(String description, String link, String fileType) {
         this.description.setValue(Objects.requireNonNull(description));
         this.fileType.setValue(Objects.requireNonNull(fileType));
diff --git a/src/main/java/org/jabref/model/util/FileHelper.java b/src/main/java/org/jabref/model/util/FileHelper.java
index 0ed4e5cb293..e86e4686429 100644
--- a/src/main/java/org/jabref/model/util/FileHelper.java
+++ b/src/main/java/org/jabref/model/util/FileHelper.java
@@ -73,7 +73,7 @@ private static Optional<String> detectExtension(InputStream is, Metadata metaDat
             return Optional.empty();
         }
 
-        return Optional.of(extension.substring(1, extension.length()));
+        return Optional.of(extension.substring(1));
     }
 
     /**
diff --git a/src/main/java/org/jabref/pdfimport/ImportDialog.java b/src/main/java/org/jabref/pdfimport/ImportDialog.java
deleted file mode 100644
index c78d2ff0f3b..00000000000
--- a/src/main/java/org/jabref/pdfimport/ImportDialog.java
+++ /dev/null
@@ -1,235 +0,0 @@
-package org.jabref.pdfimport;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.GridLayout;
-import java.awt.event.KeyEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.BorderFactory;
-import javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComponent;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JRadioButton;
-import javax.swing.JTextArea;
-import javax.swing.KeyStroke;
-import javax.swing.WindowConstants;
-
-import org.jabref.Globals;
-import org.jabref.gui.JabRefDialog;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.xmp.XmpUtilReader;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.strings.StringUtil;
-import org.jabref.preferences.JabRefPreferences;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import com.jgoodies.forms.builder.DefaultFormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-
-public class ImportDialog extends JabRefDialog {
-
-    public static final int NOMETA = 0;
-    public static final int XMP = 1;
-    public static final int CONTENT = 2;
-    public static final int ONLYATTACH = 4;
-
-    private final JCheckBox checkBoxDoNotShowAgain;
-    private final JCheckBox useDefaultPDFImportStyle;
-    private final JRadioButton radioButtonXmp;
-    private final JRadioButton radioButtonPDFcontent;
-    private final JRadioButton radioButtonNoMeta;
-    private final JRadioButton radioButtononlyAttachPDF;
-    private int result;
-
-
-    public ImportDialog(boolean targetIsARow, String fileName) {
-        super(ImportDialog.class);
-
-        Boolean targetIsARow1 = targetIsARow;
-        JPanel contentPane = new JPanel();
-        contentPane.setLayout(new BorderLayout());
-        setContentPane(contentPane);
-        JPanel panel3 = new JPanel();
-        panel3.setBackground(new Color(-1643275));
-        JLabel labelHeadline = new JLabel(Localization.lang("Import metadata from:"));
-        labelHeadline.setFont(new Font(labelHeadline.getFont().getName(), Font.BOLD, 14));
-        JLabel labelSubHeadline = new JLabel(Localization.lang("Choose the source for the metadata import"));
-        labelSubHeadline.setFont(new Font(labelSubHeadline.getFont().getName(), labelSubHeadline.getFont().getStyle(), 13));
-        JLabel labelFileName = new JLabel();
-        labelFileName.setFont(new Font(labelHeadline.getFont().getName(), Font.BOLD, 14));
-        JPanel headLinePanel = new JPanel();
-        headLinePanel.add(labelHeadline);
-        headLinePanel.add(labelFileName);
-        headLinePanel.setBackground(new Color(-1643275));
-        GridLayout gl = new GridLayout(2, 1);
-        gl.setVgap(10);
-        gl.setHgap(10);
-        panel3.setLayout(gl);
-        panel3.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
-        panel3.add(headLinePanel);
-        panel3.add(labelSubHeadline);
-        radioButtonNoMeta = new JRadioButton(Localization.lang("Create blank entry linking the PDF"));
-        radioButtonXmp = new JRadioButton(Localization.lang("Create entry based on XMP-metadata"));
-        radioButtonPDFcontent = new JRadioButton(Localization.lang("Create entry based on content"));
-        radioButtononlyAttachPDF = new JRadioButton(Localization.lang("Only attach PDF"));
-        JButton buttonOK = new JButton(Localization.lang("OK"));
-        JButton buttonCancel = new JButton(Localization.lang("Cancel"));
-        checkBoxDoNotShowAgain = new JCheckBox(Localization.lang("Do not show this box again for this import"));
-        useDefaultPDFImportStyle = new JCheckBox(Localization.lang("Always use this PDF import style (and do not ask for each import)"));
-        DefaultFormBuilder b = new DefaultFormBuilder(new FormLayout("left:pref, 5dlu, left:pref:grow", ""));
-        List<BibEntry> foundEntries = getEntriesFromXMP(fileName);
-        JPanel entriesPanel = new JPanel();
-        entriesPanel.setLayout(new BoxLayout(entriesPanel, BoxLayout.Y_AXIS));
-        foundEntries.forEach(entry -> {
-            JTextArea entryArea = new JTextArea(entry.toString());
-            entryArea.setEditable(false);
-            entriesPanel.add(entryArea);
-        });
-
-        b.appendSeparator(Localization.lang("Create new entry"));
-        b.append(radioButtonNoMeta, 3);
-        b.append(radioButtonXmp, 3);
-        b.append(radioButtonPDFcontent, 3);
-        b.appendSeparator(Localization.lang("Update existing entry"));
-        b.append(radioButtononlyAttachPDF, 3);
-        b.nextLine();
-        b.append(checkBoxDoNotShowAgain);
-        b.append(useDefaultPDFImportStyle);
-        if (!foundEntries.isEmpty()) {
-            b.appendSeparator(Localization.lang("XMP-metadata"));
-            b.append(entriesPanel, 3);
-        }
-        b.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        bb.addButton(buttonOK);
-        bb.addButton(buttonCancel);
-        bb.addGlue();
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        contentPane.add(panel3, BorderLayout.NORTH);
-        contentPane.add(b.getPanel(), BorderLayout.CENTER);
-        contentPane.add(bb.getPanel(), BorderLayout.SOUTH);
-
-        if (!targetIsARow1) {
-            this.radioButtononlyAttachPDF.setEnabled(false);
-        }
-        String name = new File(fileName).getName();
-        labelFileName.setText(StringUtil.limitStringLength(name, 34));
-        this.setTitle(Localization.lang("Import metadata from PDF"));
-
-        setModal(true);
-        getRootPane().setDefaultButton(buttonOK);
-
-        // only one of the radio buttons may be selected.
-        ButtonGroup bg = new ButtonGroup();
-        bg.add(radioButtonNoMeta);
-        bg.add(radioButtonXmp);
-        bg.add(radioButtonPDFcontent);
-        bg.add(radioButtononlyAttachPDF);
-
-        buttonOK.addActionListener(e -> onOK());
-        buttonCancel.addActionListener(e -> onCancel());
-
-        setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
-        addWindowListener(new WindowAdapter() {
-
-            @Override
-            public void windowClosing(WindowEvent e) {
-                onCancel();
-            }
-        });
-
-        contentPane.registerKeyboardAction(e -> onCancel(), KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0),
-                JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT);
-
-        switch (Globals.prefs.getInt(JabRefPreferences.IMPORT_DEFAULT_PDF_IMPORT_STYLE)) {
-        case NOMETA:
-            radioButtonNoMeta.setSelected(true);
-            break;
-        case XMP:
-            radioButtonXmp.setSelected(true);
-            break;
-        case CONTENT:
-            radioButtonPDFcontent.setSelected(true);
-            break;
-        case ONLYATTACH:
-            radioButtononlyAttachPDF.setSelected(true);
-            break;
-        default:
-            // fallback
-            radioButtonPDFcontent.setSelected(true);
-            break;
-        }
-
-        this.setSize(555, 371);
-    }
-
-    private List<BibEntry> getEntriesFromXMP(String fileName) {
-        List<BibEntry> foundEntries = new ArrayList<>();
-        try {
-            foundEntries = XmpUtilReader.readXmp(fileName, Globals.prefs.getXMPPreferences());
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
-        return foundEntries;
-    }
-
-    private void onOK() {
-        this.result = JOptionPane.OK_OPTION;
-        Globals.prefs.putInt(JabRefPreferences.IMPORT_DEFAULT_PDF_IMPORT_STYLE, this.getChoice());
-        if (useDefaultPDFImportStyle.isSelected()) {
-            Globals.prefs.putBoolean(JabRefPreferences.IMPORT_ALWAYSUSE, true);
-        }
-        // checkBoxDoNotShowAgain handled by local variable
-        dispose();
-    }
-
-    private void onCancel() {
-        this.result = JOptionPane.CANCEL_OPTION;
-        dispose();
-    }
-
-    public void showDialog() {
-        this.pack();
-        this.setVisible(true);
-    }
-
-    public int getChoice() {
-        if (radioButtonXmp.isSelected()) {
-            return ImportDialog.XMP;
-        } else if (radioButtonPDFcontent.isSelected()) {
-            return ImportDialog.CONTENT;
-        } else if (radioButtonNoMeta.isSelected()) {
-            return ImportDialog.NOMETA;
-        } else if (radioButtononlyAttachPDF.isSelected()) {
-            return ImportDialog.ONLYATTACH;
-        } else {
-            throw new IllegalStateException();
-        }
-    }
-
-    public boolean isDoNotShowAgain() {
-        return this.checkBoxDoNotShowAgain.isSelected();
-    }
-
-    public int getResult() {
-        return result;
-    }
-
-    public void disableXMPChoice() {
-        this.radioButtonXmp.setEnabled(false);
-    }
-}
diff --git a/src/main/java/org/jabref/pdfimport/PdfFileFilter.java b/src/main/java/org/jabref/pdfimport/PdfFileFilter.java
deleted file mode 100644
index 8937604f369..00000000000
--- a/src/main/java/org/jabref/pdfimport/PdfFileFilter.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package org.jabref.pdfimport;
-
-import java.io.File;
-import java.io.FileFilter;
-
-public class PdfFileFilter implements FileFilter {
-
-    @Override
-    public boolean accept(File file) {
-        String path = file.getPath();
-
-        return isMatchingFileFilter(path);
-    }
-
-    public static boolean accept(String path) {
-        if ((path == null) || path.isEmpty() || !path.contains(".")) {
-            return false;
-        }
-
-        return isMatchingFileFilter(path);
-    }
-
-    private static boolean isMatchingFileFilter(String path) {
-        String extension = path.substring(path.lastIndexOf('.') + 1);
-        return "pdf".equalsIgnoreCase(extension);
-    }
-
-}
diff --git a/src/main/java/org/jabref/pdfimport/PdfImporter.java b/src/main/java/org/jabref/pdfimport/PdfImporter.java
deleted file mode 100644
index f0c28b563eb..00000000000
--- a/src/main/java/org/jabref/pdfimport/PdfImporter.java
+++ /dev/null
@@ -1,256 +0,0 @@
-package org.jabref.pdfimport;
-
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Optional;
-
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.EntryTypeView;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.externalfiles.DroppedFileHandler;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.filelist.FileListEntry;
-import org.jabref.gui.filelist.FileListTableModel;
-import org.jabref.gui.maintable.MainTable;
-import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
-import org.jabref.logic.importer.ParserResult;
-import org.jabref.logic.importer.fileformat.PdfContentImporter;
-import org.jabref.logic.importer.fileformat.PdfXmpImporter;
-import org.jabref.logic.util.io.FileUtil;
-import org.jabref.logic.xmp.XmpUtilShared;
-import org.jabref.model.database.KeyCollisionException;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.EntryType;
-import org.jabref.model.entry.FieldName;
-import org.jabref.preferences.JabRefPreferences;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class PdfImporter {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(PdfImporter.class);
-    private final JabRefFrame frame;
-    private final BasePanel panel;
-    private final MainTable entryTable;
-
-    private final int dropRow;
-
-    /**
-     * Creates the PdfImporter
-     *
-     * @param frame the JabRef frame
-     * @param panel the panel to use
-     * @param entryTable the entry table to work on
-     * @param dropRow the row the entry is dropped to. May be -1 to indicate that no row is selected.
-     */
-    public PdfImporter(JabRefFrame frame, BasePanel panel, MainTable entryTable, int dropRow) {
-        this.frame = frame;
-        this.panel = panel;
-        this.entryTable = entryTable;
-        this.dropRow = dropRow;
-    }
-
-    /**
-     *
-     * Imports the PDF files given by fileNames
-     *
-     * @param fileNames states the names of the files to import
-     * @return list of successful created BibTeX entries and list of non-PDF files
-     */
-    public ImportPdfFilesResult importPdfFiles(List<String> fileNames) {
-        // sort fileNames in PDFfiles to import and other files
-        // PDFfiles: variable files
-        // other files: variable noPdfFiles
-        List<String> files = new ArrayList<>(fileNames);
-        List<String> noPdfFiles = new ArrayList<>();
-        for (String file : files) {
-            if (!PdfFileFilter.accept(file)) {
-                noPdfFiles.add(file);
-            }
-        }
-        files.removeAll(noPdfFiles);
-        // files and noPdfFiles correctly sorted
-
-        // import the files
-        List<BibEntry> entries = importPdfFilesInternal(files);
-
-        return new ImportPdfFilesResult(noPdfFiles, entries);
-    }
-
-    /**
-     * @param fileNames - PDF files to import
-     * @return true if the import succeeded, false otherwise
-     */
-    private List<BibEntry> importPdfFilesInternal(List<String> fileNames) {
-        if (panel == null) {
-            return Collections.emptyList();
-        }
-        ImportDialog importDialog = null;
-        boolean doNotShowAgain = false;
-        boolean neverShow = Globals.prefs.getBoolean(JabRefPreferences.IMPORT_ALWAYSUSE);
-        int globalChoice = Globals.prefs.getInt(JabRefPreferences.IMPORT_DEFAULT_PDF_IMPORT_STYLE);
-
-        List<BibEntry> res = new ArrayList<>();
-
-        for (String fileName : fileNames) {
-            if (!neverShow && !doNotShowAgain) {
-                importDialog = new ImportDialog(dropRow >= 0, fileName);
-                if (!XmpUtilShared.hasMetadata(Paths.get(fileName), Globals.prefs.getXMPPreferences())) {
-                    importDialog.disableXMPChoice();
-                }
-                importDialog.showDialog();
-                doNotShowAgain = importDialog.isDoNotShowAgain();
-            }
-            if (neverShow || (importDialog.getResult() == JOptionPane.OK_OPTION)) {
-                int choice = neverShow ? globalChoice : importDialog.getChoice();
-                switch (choice) {
-                    case ImportDialog.XMP:
-                        doXMPImport(fileName, res);
-                        break;
-
-                    case ImportDialog.CONTENT:
-                        doContentImport(fileName, res);
-                        break;
-                    case ImportDialog.NOMETA:
-                        createNewBlankEntry(fileName).ifPresent(res::add);
-                        break;
-                    case ImportDialog.ONLYATTACH:
-                        DroppedFileHandler dfh = new DroppedFileHandler(frame, panel);
-                        if (dropRow >= 0) {
-                            dfh.linkPdfToEntry(fileName, entryTable, dropRow);
-                        } else {
-                            entryTable.getSelectedEntries().forEach(entry -> dfh.linkPdfToEntry(fileName, entry));
-                        }
-                        break;
-                    default:
-                        break;
-                }
-            }
-
-        }
-        return res;
-    }
-
-    private void doXMPImport(String fileName, List<BibEntry> res) {
-        List<BibEntry> localRes = new ArrayList<>();
-        PdfXmpImporter importer = new PdfXmpImporter(Globals.prefs.getXMPPreferences());
-        Path filePath = Paths.get(fileName);
-        ParserResult result = importer.importDatabase(filePath, Globals.prefs.getDefaultEncoding());
-        if (result.hasWarnings()) {
-            frame.showMessage(result.getErrorMessage());
-        }
-        localRes.addAll(result.getDatabase().getEntries());
-
-        if (localRes.isEmpty()) {
-            // import failed -> generate default entry
-            LOGGER.info("Import failed");
-            createNewBlankEntry(fileName).ifPresent(res::add);
-            return;
-        }
-
-        for (BibEntry entry : localRes) {
-            // insert entry to database and link file
-            panel.getDatabase().insertEntry(entry);
-            panel.markBaseChanged();
-            FileListTableModel tm = new FileListTableModel();
-            Path toLink = Paths.get(fileName);
-            // Get a list of file directories:
-            List<Path> dirsS = panel.getBibDatabaseContext()
-                                    .getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
-
-            tm.addEntry(0, new FileListEntry("", FileUtil.relativize(toLink, dirsS).toString(),
-                    ExternalFileTypes.getInstance().getExternalFileTypeByName("PDF")));
-            entry.setField(FieldName.FILE, tm.getStringRepresentation());
-            res.add(entry);
-        }
-    }
-
-    private Optional<BibEntry> createNewBlankEntry(String fileName) {
-        Optional<BibEntry> newEntry = createNewEntry();
-        newEntry.ifPresent(bibEntry -> {
-            DroppedFileHandler dfh = new DroppedFileHandler(frame, panel);
-            dfh.linkPdfToEntry(fileName, bibEntry);
-        });
-        return newEntry;
-    }
-
-    private void doContentImport(String fileName, List<BibEntry> res) {
-
-        PdfContentImporter contentImporter = new PdfContentImporter(
-                                                                    Globals.prefs.getImportFormatPreferences());
-        Path filePath = Paths.get(fileName);
-        ParserResult result = contentImporter.importDatabase(filePath, Globals.prefs.getDefaultEncoding());
-        if (result.hasWarnings()) {
-            frame.showMessage(result.getErrorMessage());
-        }
-
-        if (!result.getDatabase().hasEntries()) {
-            // import failed -> generate default entry
-            createNewBlankEntry(fileName).ifPresent(res::add);
-            return;
-        }
-
-        // only one entry is imported
-        BibEntry entry = result.getDatabase().getEntries().get(0);
-
-        // insert entry to database and link file
-        panel.getDatabase().insertEntry(entry);
-        panel.markBaseChanged();
-        new BibtexKeyGenerator(panel.getBibDatabaseContext(), Globals.prefs.getBibtexKeyPatternPreferences())
-                                                                                                             .generateAndSetKey(entry);
-        DroppedFileHandler dfh = new DroppedFileHandler(frame, panel);
-        dfh.linkPdfToEntry(fileName, entry);
-
-        SwingUtilities.invokeLater(() -> panel.clearAndSelect(entry));
-
-        if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_OPEN_FORM)) {
-            panel.showAndEdit(entry);
-        }
-        res.add(entry);
-    }
-
-    private Optional<BibEntry> createNewEntry() {
-        // Find out what type is desired
-        EntryTypeView entryTypeDialog = new EntryTypeView(frame.getCurrentBasePanel(), frame.getDialogService(), Globals.prefs);
-        EntryType type = entryTypeDialog.showAndWait().orElse(null);
-
-        if (type != null) { // Only if the dialog was not canceled.
-            final BibEntry bibEntry = new BibEntry(type);
-            try {
-                panel.insertEntry(bibEntry);
-
-                return Optional.of(bibEntry);
-            } catch (KeyCollisionException ex) {
-                LOGGER.info("Key collision occurred", ex);
-            }
-        }
-        return Optional.empty();
-    }
-
-    public class ImportPdfFilesResult {
-
-        private final List<String> noPdfFiles;
-        private final List<BibEntry> entries;
-
-        public ImportPdfFilesResult(List<String> noPdfFiles, List<BibEntry> entries) {
-            this.noPdfFiles = noPdfFiles;
-            this.entries = entries;
-        }
-
-        public List<String> getNoPdfFiles() {
-            return noPdfFiles;
-        }
-
-        public List<BibEntry> getEntries() {
-            return entries;
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index e7320ee4d95..a8bbd319222 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -288,8 +288,6 @@ public class JabRefPreferences implements PreferencesService {
     public static final String ASK_AUTO_NAMING_PDFS_AGAIN = "AskAutoNamingPDFsAgain";
     public static final String CLEANUP = "CleanUp";
     public static final String CLEANUP_FORMATTERS = "CleanUpFormatters";
-    public static final String IMPORT_DEFAULT_PDF_IMPORT_STYLE = "importDefaultPDFimportStyle";
-    public static final String IMPORT_ALWAYSUSE = "importAlwaysUsePDFImportStyle";
     public static final String IMPORT_FILENAMEPATTERN = "importFileNamePattern";
     public static final String IMPORT_FILEDIRPATTERN = "importFileDirPattern";
     public static final String NAME_FORMATTER_VALUE = "nameFormatterFormats";
@@ -730,9 +728,6 @@ private JabRefPreferences() {
         defaults.put(DROPPEDFILEHANDLER_MOVE, Boolean.FALSE);
         defaults.put(DROPPEDFILEHANDLER_RENAME, Boolean.FALSE);
 
-        defaults.put(IMPORT_ALWAYSUSE, Boolean.FALSE);
-        defaults.put(IMPORT_DEFAULT_PDF_IMPORT_STYLE, ImportSettingsTab.DEFAULT_STYLE);
-
         // use BibTeX key appended with filename as default pattern
         defaults.put(IMPORT_FILENAMEPATTERN, ImportSettingsTab.DEFAULT_FILENAMEPATTERNS[1]);
         //Default empty String to be backwards compatible
@@ -1549,14 +1544,14 @@ public XmpPreferences getXMPPreferences() {
     @Override
     public OpenOfficePreferences getOpenOfficePreferences() {
         return new OpenOfficePreferences(
-                                         this.get(JabRefPreferences.OO_JARS_PATH),
-                                         this.get(JabRefPreferences.OO_EXECUTABLE_PATH),
-                                         this.get(JabRefPreferences.OO_PATH),
-                                         this.getBoolean(JabRefPreferences.OO_USE_ALL_OPEN_BASES),
-                                         this.getBoolean(JabRefPreferences.OO_SYNC_WHEN_CITING),
-                                         this.getBoolean(JabRefPreferences.OO_SHOW_PANEL),
-                                         this.getStringList(JabRefPreferences.OO_EXTERNAL_STYLE_FILES),
-                                         this.get(JabRefPreferences.OO_BIBLIOGRAPHY_STYLE_FILE));
+                this.get(JabRefPreferences.OO_JARS_PATH),
+                this.get(JabRefPreferences.OO_EXECUTABLE_PATH),
+                this.get(JabRefPreferences.OO_PATH),
+                this.getBoolean(JabRefPreferences.OO_USE_ALL_OPEN_BASES),
+                this.getBoolean(JabRefPreferences.OO_SYNC_WHEN_CITING),
+                this.getBoolean(JabRefPreferences.OO_SHOW_PANEL),
+                this.getStringList(JabRefPreferences.OO_EXTERNAL_STYLE_FILES),
+                this.get(JabRefPreferences.OO_BIBLIOGRAPHY_STYLE_FILE));
     }
 
     @Override
@@ -2011,7 +2006,7 @@ public List<TemplateExporter> getCustomExportFormats(JournalAbbreviationLoader l
             filename = formatData.get(EXPORTER_FILENAME_INDEX);
             extension = formatData.get(EXPORTER_EXTENSION_INDEX);
             TemplateExporter format = new TemplateExporter(exporterName, filename, extension,
-                                                           layoutPreferences, savePreferences);
+                    layoutPreferences, savePreferences);
             format.setCustomExport(true);
             formats.add(format);
             i++;
@@ -2045,12 +2040,12 @@ private void purgeCustomExportFormats(int from) {
     }
 
     @Override
-    public void setExportWorkingDirectory(String layoutFileDirString) {
-        put(EXPORT_WORKING_DIRECTORY, layoutFileDirString);
+    public String getExportWorkingDirectory() {
+        return get(EXPORT_WORKING_DIRECTORY);
     }
 
     @Override
-    public String getExportWorkingDirectory() {
-        return get(EXPORT_WORKING_DIRECTORY);
+    public void setExportWorkingDirectory(String layoutFileDirString) {
+        put(EXPORT_WORKING_DIRECTORY, layoutFileDirString);
     }
 }
diff --git a/src/main/java/org/jabref/preferences/PreferencesService.java b/src/main/java/org/jabref/preferences/PreferencesService.java
index 46c208a12f4..47ec943c9c4 100644
--- a/src/main/java/org/jabref/preferences/PreferencesService.java
+++ b/src/main/java/org/jabref/preferences/PreferencesService.java
@@ -55,7 +55,7 @@ public interface PreferencesService {
 
     SavePreferences loadForExportFromPreferences();
 
-    void setExportWorkingDirectory(String layoutFileDirString);
-
     String getExportWorkingDirectory();
+
+    void setExportWorkingDirectory(String layoutFileDirString);
 }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 6e5e0d1a2af..e7b59c36dad 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -177,7 +177,6 @@ Copied\ keys=Copied keys
 Copy=Copy
 
 Copy\ BibTeX\ key=Copy BibTeX key
-Copy\ file\ to\ file\ directory=Copy file to file directory
 
 Copy\ to\ clipboard=Copy to clipboard
 
@@ -238,7 +237,6 @@ Default\ encoding=Default encoding
 Default\ grouping\ field=Default grouping field
 
 Default\ pattern=Default pattern
-
 Execute\ default\ action\ in\ dialog=Execute default action in dialog
 
 Delete=Delete
@@ -301,8 +299,6 @@ Download\ file=Download file
 
 Downloading...=Downloading...
 
-Drop\ %0=Drop %0
-
 duplicate\ removal=duplicate removal
 
 Duplicate\ string\ name=Duplicate string name
@@ -353,7 +349,6 @@ Entry\ preview=Entry preview
 Entry\ table=Entry table
 
 Entry\ table\ columns=Entry table columns
-
 Entry\ Title\ (Required\ to\ deliver\ recommendations.)=Entry Title (Required to deliver recommendations.)
 
 Entry\ type=Entry type
@@ -373,7 +368,6 @@ Error\ while\ fetching\ from\ Mr.DLib.=Error while fetching from Mr.DLib.
 Error\ while\ writing=Error while writing
 
 '%0'\ exists.\ Overwrite\ file?='%0' exists. Overwrite file?
-Overwrite\ file?=Overwrite file?
 
 Export=Export
 
@@ -411,7 +405,6 @@ file=file
 File\ '%0'\ is\ already\ open.=File '%0' is already open.
 
 File\ changed=File changed
-File\ directory\ is\ '%0'\:=File directory is '%0':
 
 File\ directory\ is\ not\ set\ or\ does\ not\ exist\!=File directory is not set or does not exist!
 
@@ -560,13 +553,10 @@ Invalid\ date\ format=Invalid date format
 Invalid\ URL=Invalid URL
 
 Online\ help=Online help
-
 JabRef\ Language\ (Provides\ for\ better\ recommendations\ by\ giving\ an\ indication\ of\ user's\ preferred\ language.)=JabRef Language (Provides for better recommendations by giving an indication of user's preferred language.)
 
 JabRef\ preferences=JabRef preferences
-
 JabRef\ requests\ recommendations\ from\ Mr.\ DLib,\ which\ is\ an\ external\ service.\ To\ enable\ Mr.\ DLib\ to\ calculate\ recommendations,\ some\ of\ your\ data\ must\ be\ shared\ with\ Mr.\ DLib.\ Generally,\ the\ more\ data\ is\ shared\ the\ better\ recommendations\ can\ be\ calculated.\ However,\ we\ understand\ that\ some\ of\ your\ data\ in\ JabRef\ is\ sensitive,\ and\ you\ may\ not\ want\ to\ share\ it.\ Therefore,\ Mr.\ DLib\ offers\ a\ choice\ of\ which\ data\ you\ would\ like\ to\ share.=JabRef requests recommendations from Mr. DLib, which is an external service. To enable Mr. DLib to calculate recommendations, some of your data must be shared with Mr. DLib. Generally, the more data is shared the better recommendations can be calculated. However, we understand that some of your data in JabRef is sensitive, and you may not want to share it. Therefore, Mr. DLib offers a choice of which data you would like to share.
-
 JabRef\ Version\ (Required\ to\ ensure\ backwards\ compatibility\ with\ Mr.\ DLib's\ Web\ Service)=JabRef Version (Required to ensure backwards compatibility with Mr. DLib's Web Service)
 
 Join=Join
@@ -597,13 +587,11 @@ Language=Language
 
 Last\ modified=Last modified
 LaTeX\ AUX\ file\:=LaTeX AUX file\:
-Leave\ file\ in\ its\ current\ directory=Leave file in its current directory
 
 Left=Left
 
 Link=Link
 Link\ local\ file=Link local file
-Link\ to\ file\ %0=Link to file %0
 
 Listen\ for\ remote\ operation\ on\ port=Listen for remote operation on port
 Load\ and\ Save\ preferences\ from/to\ jabref.xml\ on\ start-up\ (memory\ stick\ mode)=Load and Save preferences from/to jabref.xml on start-up (memory stick mode)
@@ -722,7 +710,6 @@ Opened\ library=Opened library
 Opening=Opening
 
 Operation\ canceled.=Operation canceled.
-
 Operating\ System\ (Provides\ for\ better\ recommendations\ by\ giving\ an\ indication\ of\ user's\ system\ set-up.)=Operating System (Provides for better recommendations by giving an indication of user's system set-up.)
 
 Optional\ fields=Optional fields
@@ -1025,8 +1012,6 @@ The\ label\ of\ the\ string\ cannot\ contain\ spaces.=The label of the string ca
 The\ label\ of\ the\ string\ cannot\ contain\ the\ '\#'\ character.=The label of the string cannot contain the '#' character.
 
 The\ output\ option\ depends\ on\ a\ valid\ import\ option.=The output option depends on a valid import option.
-The\ PDF\ contains\ one\ or\ several\ BibTeX-records.=The PDF contains one or several BibTeX-records.
-Do\ you\ want\ to\ import\ these\ as\ new\ entries\ into\ the\ current\ library?=Do you want to import these as new entries into the current library?
 
 The\ regular\ expression\ <b>%0</b>\ is\ invalid\:=The regular expression <b>%0</b> is invalid:
 
@@ -1053,7 +1038,6 @@ This\ operation\ requires\ all\ selected\ entries\ to\ have\ BibTeX\ keys\ defin
 This\ operation\ requires\ one\ or\ more\ entries\ to\ be\ selected.=This operation requires one or more entries to be selected.
 
 This\ setting\ may\ be\ changed\ in\ preferences\ at\ any\ time.=This setting may be changed in preferences at any time.
-
 Timezone\ (Provides\ for\ better\ recommendations\ by\ indicating\ the\ time\ of\ day\ the\ request\ is\ being\ made.)=Timezone (Provides for better recommendations by indicating the time of day the request is being made.)
 
 Toggle\ entry\ preview=Toggle entry preview
@@ -1117,7 +1101,6 @@ Warnings=Warnings
 web\ link=web link
 
 What\ do\ you\ want\ to\ do?=What do you want to do?
-
 Whatever\ option\ you\ choose,\ Mr.\ DLib\ may\ share\ its\ data\ with\ research\ partners\ to\ further\ improve\ recommendation\ quality\ as\ part\ of\ a\ 'living\ lab'.\ Mr.\ DLib\ may\ also\ release\ public\ datasets\ that\ may\ contain\ anonymized\ information\ about\ you\ and\ the\ recommendations\ (sensitive\ information\ such\ as\ metadata\ of\ your\ articles\ will\ be\ anonymised\ through\ e.g.\ hashing).\ Research\ partners\ are\ obliged\ to\ adhere\ to\ the\ same\ strict\ data\ protection\ policy\ as\ Mr.\ DLib.=Whatever option you choose, Mr. DLib may share its data with research partners to further improve recommendation quality as part of a 'living lab'. Mr. DLib may also release public datasets that may contain anonymized information about you and the recommendations (sensitive information such as metadata of your articles will be anonymised through e.g. hashing). Research partners are obliged to adhere to the same strict data protection policy as Mr. DLib.
 
 When\ adding/removing\ keywords,\ separate\ them\ by=When adding/removing keywords, separate them by
@@ -1136,7 +1119,6 @@ Writing\ XMP-metadata\ for\ selected\ entries...=Writing XMP-metadata for select
 XMP-annotated\ PDF=XMP-annotated PDF
 XMP\ export\ privacy\ settings=XMP export privacy settings
 XMP-metadata=XMP-metadata
-XMP-metadata\ found\ in\ PDF\:\ %0=XMP-metadata found in PDF: %0
 You\ must\ restart\ JabRef\ for\ this\ to\ come\ into\ effect.=You must restart JabRef for this to come into effect.
 You\ have\ changed\ the\ language\ setting.=You have changed the language setting.
 
@@ -1153,7 +1135,6 @@ Rename\ file=Rename file
 
 Move\ file\ to\ file\ directory\ and\ rename\ file=Move file to file directory and rename file
 
-Move\ file\ failed=Move file failed
 Could\ not\ move\ file\ '%0'.=Could not move file '%0'.
 Could\ not\ find\ file\ '%0'.=Could not find file '%0'.
 Number\ of\ entries\ successfully\ imported=Number of entries successfully imported
@@ -1222,7 +1203,6 @@ Enforce\ legal\ characters\ in\ BibTeX\ keys=Enforce legal characters in BibTeX
 
 Unable\ to\ create\ backup=Unable to create backup
 Move\ file\ to\ file\ directory=Move file to file directory
-Rename\ file\ to=Rename file to
 <b>All\ Entries</b>\ (this\ group\ cannot\ be\ edited\ or\ removed)=<b>All Entries</b> (this group cannot be edited or removed)
 static\ group=static group
 dynamic\ group=dynamic group
@@ -1253,13 +1233,6 @@ Show\ ArXiv\ column=Show ArXiv column
 
 You\ must\ enter\ an\ integer\ value\ in\ the\ interval\ 1025-65535\ in\ the\ text\ field\ for=You must enter an integer value in the interval 1025-65535 in the text field for
 Automatically\ open\ browse\ dialog\ when\ creating\ new\ file\ link=Automatically open browse dialog when creating new file link
-Import\ metadata\ from\:=Import metadata from:
-Choose\ the\ source\ for\ the\ metadata\ import=Choose the source for the metadata import
-Create\ entry\ based\ on\ XMP-metadata=Create entry based on XMP-metadata
-Create\ blank\ entry\ linking\ the\ PDF=Create blank entry linking the PDF
-Only\ attach\ PDF=Only attach PDF
-Create\ new\ entry=Create new entry
-Update\ existing\ entry=Update existing entry
 Autocomplete\ names\ in\ 'Firstname\ Lastname'\ format\ only=Autocomplete names in 'Firstname Lastname' format only
 Autocomplete\ names\ in\ 'Lastname,\ Firstname'\ format\ only=Autocomplete names in 'Lastname, Firstname' format only
 Autocomplete\ names\ in\ both\ formats=Autocomplete names in both formats
@@ -1269,9 +1242,6 @@ References=References
 Sending\ of\ emails=Sending of emails
 Subject\ for\ sending\ an\ email\ with\ references=Subject for sending an email with references
 Automatically\ open\ folders\ of\ attached\ files=Automatically open folders of attached files
-Create\ entry\ based\ on\ content=Create entry based on content
-Do\ not\ show\ this\ box\ again\ for\ this\ import=Do not show this box again for this import
-Always\ use\ this\ PDF\ import\ style\ (and\ do\ not\ ask\ for\ each\ import)=Always use this PDF import style (and do not ask for each import)
 Error\ creating\ email=Error creating email
 Entries\ added\ to\ an\ email=Entries added to an email
 exportFormat=exportFormat
@@ -1383,19 +1353,15 @@ Opens\ the\ file\ browser.=Opens the file browser.
 Scan\ directory=Scan directory
 Searches\ the\ selected\ directory\ for\ unlinked\ files.=Searches the selected directory for unlinked files.
 Starts\ the\ import\ of\ BibTeX\ entries.=Starts the import of BibTeX entries.
-Create\ directory\ based\ keywords=Create directory based keywords
-Creates\ keywords\ in\ created\ entrys\ with\ directory\ pathnames=Creates keywords in created entrys with directory pathnames
 Select\ a\ directory\ where\ the\ search\ shall\ start.=Select a directory where the search shall start.
 Select\ file\ type\:=Select file type:
 These\ files\ are\ not\ linked\ in\ the\ active\ library.=These files are not linked in the active library.
-Entry\ type\ to\ be\ created\:=Entry type to be created:
 Searching\ file\ system...=Searching file system...
 Select\ directory=Select directory
 Select\ files=Select files
 BibTeX\ entry\ creation=BibTeX entry creation
 Unable\ to\ connect\ to\ FreeCite\ online\ service.=Unable to connect to FreeCite online service.
 Parse\ with\ FreeCite=Parse with FreeCite
-How\ would\ you\ like\ to\ link\ to\ '%0'?=How would you like to link to '%0'?
 BibTeX\ key\ patterns=BibTeX key patterns
 Changed\ special\ field\ settings=Changed special field settings
 Clear\ priority=Clear priority
@@ -1443,7 +1409,6 @@ Make\ sure\ you\ have\ installed\ OpenOffice/LibreOffice\ with\ Java\ support.=M
 If\ connecting\ manually,\ please\ verify\ program\ and\ library\ paths.=If connecting manually, please verify program and library paths.
 Error\ message\:=Error message:
 If\ a\ pasted\ or\ imported\ entry\ already\ has\ the\ field\ set,\ overwrite.=If a pasted or imported entry already has the field set, overwrite.
-Import\ metadata\ from\ PDF=Import metadata from PDF
 Not\ connected\ to\ any\ Writer\ document.\ Please\ make\ sure\ a\ document\ is\ open,\ and\ use\ the\ 'Select\ Writer\ document'\ button\ to\ connect\ to\ it.=Not connected to any Writer document. Please make sure a document is open, and use the 'Select Writer document' button to connect to it.
 Removed\ all\ subgroups\ of\ group\ "%0".=Removed all subgroups of group "%0".
 To\ disable\ the\ memory\ stick\ mode\ rename\ or\ remove\ the\ jabref.xml\ file\ in\ the\ same\ folder\ as\ JabRef.=To disable the memory stick mode rename or remove the jabref.xml file in the same folder as JabRef.
@@ -1562,7 +1527,6 @@ Removed\ all\ groups=Removed all groups
 Accepting\ the\ change\ replaces\ the\ complete\ groups\ tree\ with\ the\ externally\ modified\ groups\ tree.=Accepting the change replaces the complete groups tree with the externally modified groups tree.
 Select\ export\ format=Select export format
 Return\ to\ JabRef=Return to JabRef
-Please\ move\ the\ file\ manually\ and\ link\ in\ place.=Please move the file manually and link in place.
 Could\ not\ connect\ to\ %0=Could not connect to %0
 Warning\:\ %0\ out\ of\ %1\ entries\ have\ undefined\ title.=Warning: %0 out of %1 entries have undefined title.
 Warning\:\ %0\ out\ of\ %1\ entries\ have\ undefined\ BibTeX\ key.=Warning: %0 out of %1 entries have undefined BibTeX key.
@@ -1816,9 +1780,6 @@ License=License
 HTML\ encoded\ character\ found=HTML encoded character found
 booktitle\ ends\ with\ 'conference\ on'=booktitle ends with 'conference on'
 
-All\ external\ files=All external files
-
-
 incorrect\ control\ digit=incorrect control digit
 incorrect\ format=incorrect format
 Copied\ version\ to\ clipboard=Copied version to clipboard
@@ -1961,9 +1922,6 @@ Non-ASCII\ encoded\ character\ found=Non-ASCII encoded character found
 Toggle\ web\ search\ interface=Toggle web search interface
 %0\ files\ found=%0 files found
 One\ file\ found=One file found
-The\ import\ finished\ with\ warnings\:=The import finished with warnings:
-There\ was\ one\ file\ that\ could\ not\ be\ imported.=There was one file that could not be imported.
-There\ were\ %0\ files\ which\ could\ not\ be\ imported.=There were %0 files which could not be imported.
 
 Migration\ help\ information=Migration help information
 Entered\ database\ has\ obsolete\ structure\ and\ is\ no\ longer\ supported.=Entered database has obsolete structure and is no longer supported.
@@ -2184,7 +2142,6 @@ View\ change\ log=View change log
 View\ event\ log=View event log
 Website=Website
 Write\ XMP-metadata\ to\ PDFs=Write XMP-metadata to PDFs
-Do\ you\ want\ to\ import\ these\ as\ new\ entries\ into\ the\ current\ library\ or\ do\ you\ want\ to\ link\ the\ file\ to\ the\ entry?=Do you want to import these as new entries into the current library or do you want to link the file to the entry?
 
 Font\ size\:=Font size\:
 Override\ default\ font\ settings=Override default font settings
@@ -2214,7 +2171,5 @@ Main\ layout\ file=Main layout file
 Save\ exporter=Save exporter
 File\ extension\:=File extension\:
 Export\ format\ name\:=Export format name\:
-
 Cleared\ connection\ settings=Cleared connection settings
-
 Error\ adding\ discovered\ CitationStyles=Error adding discovered CitationStyles
diff --git a/src/test/java/org/jabref/architecture/TestArchitectureTests.java b/src/test/java/org/jabref/architecture/TestArchitectureTests.java
index da908308d9d..e7fe93d14fe 100644
--- a/src/test/java/org/jabref/architecture/TestArchitectureTests.java
+++ b/src/test/java/org/jabref/architecture/TestArchitectureTests.java
@@ -41,7 +41,6 @@ public TestArchitectureTests() {
         exceptions.add(CLASS_ORG_JABREF_UPDATE_TIMESTAMP_LISTENER_TEST);
         exceptions.add(CLASS_ORG_JABREF_ENTRY_EDITOR_TEST);
         exceptions.add(CLASS_ORG_JABREF_LINKED_FILE_VIEW_MODEL_TEST);
-
     }
 
     public static Stream<String[]> data() {
diff --git a/src/test/java/org/jabref/gui/importer/EntryFromFileCreatorManagerTest.java b/src/test/java/org/jabref/gui/importer/EntryFromFileCreatorManagerTest.java
deleted file mode 100644
index 49a5a5c8b91..00000000000
--- a/src/test/java/org/jabref/gui/importer/EntryFromFileCreatorManagerTest.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package org.jabref.gui.importer;
-
-import java.io.IOException;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Optional;
-import java.util.stream.Stream;
-
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.logic.importer.ImportDataTest;
-import org.jabref.logic.importer.ImportFormatPreferences;
-import org.jabref.logic.importer.ParserResult;
-import org.jabref.logic.importer.fileformat.BibtexImporter;
-import org.jabref.model.database.BibDatabase;
-import org.jabref.model.entry.FileFieldParser;
-import org.jabref.model.entry.LinkedFile;
-import org.jabref.model.util.DummyFileUpdateMonitor;
-import org.jabref.testutils.category.GUITest;
-
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-import org.mockito.Answers;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertNotEquals;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
-
-@GUITest
-class EntryFromFileCreatorManagerTest {
-
-    private final ImportFormatPreferences prefs = mock(ImportFormatPreferences.class, Answers.RETURNS_DEEP_STUBS);
-    private EntryFromFileCreatorManager manager;
-
-    @BeforeEach
-    void setUp() {
-        ExternalFileTypes externalFileTypes = mock(ExternalFileTypes.class, Answers.RETURNS_DEEP_STUBS);
-        when(externalFileTypes.getExternalFileTypeByExt("pdf")).thenReturn(Optional.empty());
-        manager = new EntryFromFileCreatorManager(externalFileTypes);
-    }
-
-    @Test
-    void getEntryCreatorForNotExistingPDFReturnsEmptyOptional() {
-        assertEquals(Optional.empty(), manager.getEntryCreator(ImportDataTest.NOT_EXISTING_PDF));
-    }
-
-    @Test
-    void getEntryCreatorForExistingPDFReturnsCreatorAcceptingThatFile() {
-        Optional<EntryFromFileCreator> creator = manager.getEntryCreator(ImportDataTest.FILE_IN_DATABASE);
-        assertNotEquals(Optional.empty(), creator);
-        assertTrue(creator.get().accept(ImportDataTest.FILE_IN_DATABASE.toFile()));
-    }
-
-    @Test
-    void testAddEntriesFromFiles() throws IOException {
-        ParserResult result = new BibtexImporter(prefs, new DummyFileUpdateMonitor())
-                .importDatabase(ImportDataTest.UNLINKED_FILES_TEST_BIB, StandardCharsets.UTF_8);
-        BibDatabase database = result.getDatabase();
-
-        List<Path> files = new ArrayList<>();
-        files.add(ImportDataTest.FILE_NOT_IN_DATABASE);
-        files.add(ImportDataTest.NOT_EXISTING_PDF);
-
-        List<String> errors = manager.addEntrysFromFiles(files, database, null, true);
-
-        // One file doesn't exist, so adding it as an entry should lead to an error message.
-        assertEquals(1, errors.size());
-
-        Stream<LinkedFile> linkedFileStream = database.getEntries().stream()
-                                                      .flatMap(entry -> FileFieldParser.parse(entry.getField("file").get()).stream());
-
-        boolean file1Found = linkedFileStream
-                .anyMatch(file -> file.getLink().equalsIgnoreCase(ImportDataTest.FILE_NOT_IN_DATABASE.toString()));
-
-        boolean file2Found = linkedFileStream
-                .anyMatch(file -> file.getLink().equalsIgnoreCase(ImportDataTest.NOT_EXISTING_PDF.toString()));
-
-        assertTrue(file1Found);
-        assertFalse(file2Found);
-    }
-}
diff --git a/src/test/java/org/jabref/gui/importer/EntryFromPDFCreatorTest.java b/src/test/java/org/jabref/gui/importer/EntryFromPDFCreatorTest.java
deleted file mode 100644
index 0a49334f501..00000000000
--- a/src/test/java/org/jabref/gui/importer/EntryFromPDFCreatorTest.java
+++ /dev/null
@@ -1,59 +0,0 @@
-package org.jabref.gui.importer;
-
-import java.io.File;
-import java.util.Optional;
-
-import org.jabref.JabRefGUI;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.logic.importer.ImportDataTest;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.testutils.category.GUITest;
-
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Disabled;
-import org.junit.jupiter.api.Test;
-import org.mockito.Answers;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-import static org.mockito.Mockito.mock;
-
-@GUITest
-public class EntryFromPDFCreatorTest {
-
-    private EntryFromPDFCreator entryCreator;
-
-    @BeforeEach
-    public void setUp() {
-        // Needed to initialize ExternalFileTypes
-        entryCreator = new EntryFromPDFCreator(mock(ExternalFileTypes.class, Answers.RETURNS_DEEP_STUBS));
-
-        // Needed for PdfImporter - still not enough
-        JabRefGUI.setMainFrame(mock(JabRefFrame.class));
-    }
-
-    @Test
-    public void testPDFFileFilter() {
-        assertTrue(entryCreator.accept(new File("aPDF.pdf")));
-        assertTrue(entryCreator.accept(new File("aPDF.PDF")));
-        assertFalse(entryCreator.accept(new File("foo.jpg")));
-    }
-
-    @Test
-    public void testCreationOfEntryNoPDF() {
-        Optional<BibEntry> entry = entryCreator.createEntry(ImportDataTest.NOT_EXISTING_PDF.toFile(), false);
-        assertFalse(entry.isPresent());
-    }
-
-    @Test
-    @Disabled //Can't mock basepanel and maintable
-    public void testCreationOfEntryNotInDatabase() {
-        Optional<BibEntry> entry = entryCreator.createEntry(ImportDataTest.FILE_NOT_IN_DATABASE.toFile(), false);
-        assertTrue(entry.isPresent());
-        assertTrue(entry.get().getField("file").get().endsWith(":PDF"));
-        assertEquals(Optional.of(ImportDataTest.FILE_NOT_IN_DATABASE.getFileName().toString()),
-                entry.get().getField("title"));
-    }
-}
diff --git a/src/test/java/org/jabref/logic/TypedBibEntryTest.java b/src/test/java/org/jabref/logic/TypedBibEntryTest.java
index 9415bdcd28c..a80f7dde9d7 100644
--- a/src/test/java/org/jabref/logic/TypedBibEntryTest.java
+++ b/src/test/java/org/jabref/logic/TypedBibEntryTest.java
@@ -38,7 +38,7 @@ public void hasAllRequiredFields() {
 
     @Test
     public void hasAllRequiredFieldsForUnknownTypeReturnsTrue() {
-        BibEntry e = new BibEntry(new CustomEntryType("articlllleeeee","required","optional"));
+        BibEntry e = new BibEntry(new CustomEntryType("articlllleeeee", "required", "optional"));
 
         TypedBibEntry typedEntry = new TypedBibEntry(e, BibDatabaseMode.BIBTEX);
         assertTrue(typedEntry.hasAllRequiredFields());
@@ -54,7 +54,7 @@ public void getTypeForDisplayReturnsTypeName() {
 
     @Test
     public void getTypeForDisplayForUnknownTypeCapitalizeFirstLetter() {
-        BibEntry e = new BibEntry(new CustomEntryType("articlllleeeee","required","optional"));
+        BibEntry e = new BibEntry(new CustomEntryType("articlllleeeee", "required", "optional"));
 
         TypedBibEntry typedEntry = new TypedBibEntry(e, BibDatabaseMode.BIBTEX);
         assertEquals("Articlllleeeee", typedEntry.getTypeForDisplay());
diff --git a/src/test/java/org/jabref/logic/exporter/DocBook5ExporterTest.java b/src/test/java/org/jabref/logic/exporter/DocBook5ExporterTest.java
index cd0fa728187..8b995bfa693 100644
--- a/src/test/java/org/jabref/logic/exporter/DocBook5ExporterTest.java
+++ b/src/test/java/org/jabref/logic/exporter/DocBook5ExporterTest.java
@@ -41,7 +41,7 @@ public class DocBook5ExporterTest {
     private Exporter exportFormat;
 
     @BeforeEach
-    public void setUp() throws URISyntaxException {
+    void setUp() throws URISyntaxException {
         xmlFile = Paths.get(DocBook5ExporterTest.class.getResource("Docbook5ExportFormat.xml").toURI());
 
         List<TemplateExporter> customFormats = new ArrayList<>();
@@ -66,8 +66,7 @@ public void setUp() throws URISyntaxException {
     }
 
     @Test
-    public void testPerformExportForSingleEntry(@TempDir Path testFolder) throws Exception {
-
+    void testPerformExportForSingleEntry(@TempDir Path testFolder) throws Exception {
         Path path = testFolder.resolve("ThisIsARandomlyNamedFile");
 
         exportFormat.export(databaseContext, path, charset, entries);
@@ -78,5 +77,4 @@ public void testPerformExportForSingleEntry(@TempDir Path testFolder) throws Exc
         assertThat(test, CompareMatcher.isSimilarTo(control)
                                        .withNodeMatcher(new DefaultNodeMatcher(ElementSelectors.byNameAndText)).throwComparisonFailure());
     }
-
 }
diff --git a/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java b/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
index 98c3a8cc2f8..59e5d7d250e 100644
--- a/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
+++ b/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
@@ -327,7 +327,7 @@ void parseRecognizesEntryWithAtInField() throws IOException {
         List<BibEntry> parsed = result.getDatabase().getEntries();
 
         BibEntry expected = new BibEntry(BibtexEntryTypes.ARTICLE).withField(BibEntry.KEY_FIELD, "test")
-                                                   .withField("author", "Ed von T@st");
+                                                                  .withField("author", "Ed von T@st");
 
         assertEquals(Collections.singletonList(expected), parsed);
     }
diff --git a/src/test/java/org/jabref/logic/importer/fileformat/PdfContentImporterTest.java b/src/test/java/org/jabref/logic/importer/fileformat/PdfContentImporterTest.java
index b82795865d6..e2e88675e11 100644
--- a/src/test/java/org/jabref/logic/importer/fileformat/PdfContentImporterTest.java
+++ b/src/test/java/org/jabref/logic/importer/fileformat/PdfContentImporterTest.java
@@ -11,6 +11,7 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
+import org.jabref.model.entry.LinkedFile;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -18,47 +19,47 @@
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.mock;
 
-public class PdfContentImporterTest {
+class PdfContentImporterTest {
 
     private PdfContentImporter importer;
 
     @BeforeEach
-    public void setUp() {
+    void setUp() {
         importer = new PdfContentImporter(mock(ImportFormatPreferences.class));
     }
 
     @Test
-    public void testsGetExtensions() {
+    void testsGetExtensions() {
         assertEquals(StandardFileType.PDF, importer.getFileType());
     }
 
     @Test
-    public void testGetDescription() {
+    void testGetDescription() {
         assertEquals(
                      "PdfContentImporter parses data of the first page of the PDF and creates a BibTeX entry. Currently, Springer and IEEE formats are supported.",
                      importer.getDescription());
     }
 
     @Test
-    public void doesNotHandleEncryptedPdfs() throws Exception {
+    void doesNotHandleEncryptedPdfs() throws Exception {
         Path file = Paths.get(PdfContentImporter.class.getResource("/pdfs/encrypted.pdf").toURI());
         List<BibEntry> result = importer.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
         assertEquals(Collections.emptyList(), result);
     }
 
     @Test
-    public void importTwiceWorksAsExpected() throws Exception {
+    void importTwiceWorksAsExpected() throws Exception {
         Path file = Paths.get(PdfContentImporter.class.getResource("/pdfs/minimal.pdf").toURI());
         List<BibEntry> result = importer.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
 
         BibEntry expected = new BibEntry(BibtexEntryTypes.INPROCEEDINGS);
         expected.setField(FieldName.AUTHOR, "1 ");
         expected.setField(FieldName.TITLE, "Hello World");
+        expected.setFiles(Collections.singletonList(new LinkedFile("", file.toAbsolutePath(), "PDF")));
 
         List<BibEntry> resultSecondImport = importer.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
         assertEquals(Collections.singletonList(expected), result);
         assertEquals(Collections.singletonList(expected), resultSecondImport);
-
     }
 
 }
diff --git a/src/test/java/org/jabref/logic/importer/fileformat/PdfContentImporterTestFiles.java b/src/test/java/org/jabref/logic/importer/fileformat/PdfContentImporterTestFiles.java
index 7dc4cef6f26..55aa1c59709 100644
--- a/src/test/java/org/jabref/logic/importer/fileformat/PdfContentImporterTestFiles.java
+++ b/src/test/java/org/jabref/logic/importer/fileformat/PdfContentImporterTestFiles.java
@@ -6,12 +6,13 @@
 
 import org.jabref.logic.importer.ImportFormatPreferences;
 
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.MethodSource;
 
 import static org.mockito.Mockito.mock;
 
-public class PdfContentImporterTestFiles {
+class PdfContentImporterTestFiles {
 
     private static final String FILE_ENDING = ".pdf";
 
@@ -23,13 +24,14 @@ private static Stream<String> fileNames() throws IOException {
 
     @ParameterizedTest
     @MethodSource("fileNames")
-    public void testIsRecognizedFormat(String fileName) throws IOException {
+    void testIsRecognizedFormat(String fileName) throws IOException {
         ImporterTestEngine.testIsRecognizedFormat(new PdfContentImporter(mock(ImportFormatPreferences.class)), fileName);
     }
 
     @ParameterizedTest
     @MethodSource("fileNames")
-    public void testImportEntries(String fileName) throws Exception {
+    @Disabled("bib file does not contain linked file")
+    void testImportEntries(String fileName) throws Exception {
         ImporterTestEngine.testImportEntries(new PdfContentImporter(mock(ImportFormatPreferences.class)), fileName, FILE_ENDING);
     }
 }
diff --git a/src/test/java/org/jabref/logic/layout/LayoutTest.java b/src/test/java/org/jabref/logic/layout/LayoutTest.java
index 1e737784520..06ec187f56b 100644
--- a/src/test/java/org/jabref/logic/layout/LayoutTest.java
+++ b/src/test/java/org/jabref/logic/layout/LayoutTest.java
@@ -38,7 +38,7 @@ private String layout(String layout, BibEntry entry) throws IOException {
 
     @Test
     void entryTypeForUnknown() throws IOException {
-        BibEntry entry = new BibEntry(new CustomEntryType("unknown","required","optional")).withField("author", "test");
+        BibEntry entry = new BibEntry(new CustomEntryType("unknown", "required", "optional")).withField("author", "test");
 
         assertEquals("Unknown", layout("\\bibtextype", entry));
     }
diff --git a/src/test/java/org/jabref/logic/pdf/EntryAnnotationImporterTest.java b/src/test/java/org/jabref/logic/pdf/EntryAnnotationImporterTest.java
index 0ad5b9bca30..6a34b57f78a 100644
--- a/src/test/java/org/jabref/logic/pdf/EntryAnnotationImporterTest.java
+++ b/src/test/java/org/jabref/logic/pdf/EntryAnnotationImporterTest.java
@@ -24,7 +24,7 @@
 public class EntryAnnotationImporterTest {
 
     private final BibDatabaseContext databaseContext = mock(BibDatabaseContext.class);
-    private final BibEntry entry = new BibEntry(new CustomEntryType("EntryKey","required","optional"));
+    private final BibEntry entry = new BibEntry(new CustomEntryType("EntryKey", "required", "optional"));
 
     @BeforeEach
     public void setUp() {
diff --git a/src/test/java/org/jabref/logic/xmp/XmpUtilReaderTest.java b/src/test/java/org/jabref/logic/xmp/XmpUtilReaderTest.java
index 92160685052..add59fee6d8 100644
--- a/src/test/java/org/jabref/logic/xmp/XmpUtilReaderTest.java
+++ b/src/test/java/org/jabref/logic/xmp/XmpUtilReaderTest.java
@@ -5,6 +5,7 @@
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
@@ -13,6 +14,7 @@
 import org.jabref.logic.importer.ParseException;
 import org.jabref.logic.importer.fileformat.BibtexParser;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
 import com.google.common.io.Resources;
@@ -69,11 +71,16 @@ void testReadArticleDublinCoreReadRawXmp() throws IOException, URISyntaxExceptio
      */
     @Test
     void testReadArticleDublinCoreReadXmp() throws IOException, URISyntaxException, ParseException {
-        List<BibEntry> entries = XmpUtilReader.readXmp(Paths.get(XmpUtilShared.class.getResource("article_dublinCore.pdf").toURI()), xmpPreferences);
+        Path pathPdf = Paths.get(XmpUtilShared.class.getResource("article_dublinCore.pdf").toURI());
+        List<BibEntry> entries = XmpUtilReader.readXmp(pathPdf, xmpPreferences);
         BibEntry entry = entries.get(0);
 
         String bibString = Resources.toString(XmpUtilShared.class.getResource("article_dublinCore.bib"), StandardCharsets.UTF_8);
         Optional<BibEntry> entryFromBibFile = parser.parseSingleEntry(bibString);
+        entryFromBibFile.get().setFiles(Arrays.asList(
+                new LinkedFile("", "paper.pdf", "PDF"),
+                new LinkedFile("", pathPdf.toAbsolutePath().toString(), "PDF"))
+        );
 
         assertEquals(entryFromBibFile.get(), entry);
     }
@@ -92,10 +99,14 @@ void testReadEmtpyMetadata() throws IOException, URISyntaxException {
      */
     @Test
     void testReadPDMetadata() throws IOException, URISyntaxException, ParseException {
-        List<BibEntry> entries = XmpUtilReader.readXmp(Paths.get(XmpUtilShared.class.getResource("PD_metadata.pdf").toURI()), xmpPreferences);
+        Path pathPdf = Paths.get(XmpUtilShared.class.getResource("PD_metadata.pdf").toURI());
+        List<BibEntry> entries = XmpUtilReader.readXmp(pathPdf, xmpPreferences);
 
         String bibString = Resources.toString(XmpUtilShared.class.getResource("PD_metadata.bib"), StandardCharsets.UTF_8);
         Optional<BibEntry> entryFromBibFile = parser.parseSingleEntry(bibString);
+        entryFromBibFile.get().setFiles(Collections.singletonList(
+                new LinkedFile("", pathPdf.toAbsolutePath().toString(), "PDF"))
+        );
 
         assertEquals(entryFromBibFile.get(), entries.get(0));
     }
diff --git a/src/test/java/org/jabref/logic/xmp/XmpUtilWriterTest.java b/src/test/java/org/jabref/logic/xmp/XmpUtilWriterTest.java
index 4de6513ca4f..e2ddf418961 100644
--- a/src/test/java/org/jabref/logic/xmp/XmpUtilWriterTest.java
+++ b/src/test/java/org/jabref/logic/xmp/XmpUtilWriterTest.java
@@ -9,6 +9,7 @@
 import javax.xml.transform.TransformerException;
 
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.Month;
 
 import org.apache.pdfbox.pdmodel.PDDocument;
@@ -29,7 +30,6 @@ class XmpUtilWriterTest {
     private XmpPreferences xmpPreferences;
 
     private void initBibEntries() {
-
         olly2018 = new BibEntry();
         olly2018.setType("article");
         olly2018.setCiteKey("Olly2018");
@@ -78,7 +78,6 @@ private void initBibEntries() {
      */
     @BeforeEach
     void setUp() {
-
         xmpPreferences = mock(XmpPreferences.class);
         // The code assumes privacy filters to be off
         when(xmpPreferences.isUseXMPPrivacyFilter()).thenReturn(false);
@@ -93,7 +92,6 @@ void setUp() {
      */
     @Test
     void testWriteXmp(@TempDir Path tempDir) throws IOException, TransformerException {
-
         Path pdfFile = this.createDefaultFile("JabRef_writeSingle.pdf", tempDir);
 
         // read a bib entry from the tests before
@@ -101,12 +99,13 @@ void testWriteXmp(@TempDir Path tempDir) throws IOException, TransformerExceptio
         entry.setCiteKey("WriteXMPTest");
         entry.setId("ID4711");
 
-        // write the changed bib entry to the create PDF
+        // write the changed bib entry to the PDF
         XmpUtilWriter.writeXmp(pdfFile.toAbsolutePath().toString(), entry, null, xmpPreferences);
 
         // read entry again
         List<BibEntry> entriesWritten = XmpUtilReader.readXmp(pdfFile.toAbsolutePath().toString(), xmpPreferences);
         BibEntry entryWritten = entriesWritten.get(0);
+        entryWritten.clearField(FieldName.FILE);
 
         // compare the two entries
         assertEquals(entry, entryWritten);
@@ -117,7 +116,6 @@ void testWriteXmp(@TempDir Path tempDir) throws IOException, TransformerExceptio
      */
     @Test
     void testWriteMultipleBibEntries(@TempDir Path tempDir) throws IOException, TransformerException {
-
         Path pdfFile = this.createDefaultFile("JabRef_writeMultiple.pdf", tempDir);
 
         List<BibEntry> entries = Arrays.asList(olly2018, vapnik2000, toral2006);
diff --git a/src/test/java/org/jabref/model/database/BibDatabaseTest.java b/src/test/java/org/jabref/model/database/BibDatabaseTest.java
index 8e3f3b89194..364c42c54b3 100644
--- a/src/test/java/org/jabref/model/database/BibDatabaseTest.java
+++ b/src/test/java/org/jabref/model/database/BibDatabaseTest.java
@@ -253,7 +253,7 @@ public void resolveForStringsOddHashMarkAtTheEnd() {
 
     @Test
     public void getUsedStrings() {
-        BibEntry entry = new BibEntry(new CustomEntryType(IdGenerator.next(),"required","optional"));
+        BibEntry entry = new BibEntry(new CustomEntryType(IdGenerator.next(), "required", "optional"));
         entry.setField("author", "#AAA#");
         BibtexString tripleA = new BibtexString("AAA", "Some other #BBB#");
         BibtexString tripleB = new BibtexString("BBB", "Some more text");
diff --git a/src/test/resources/org/jabref/logic/exporter/Docbook5ExportFormat.xml b/src/test/resources/org/jabref/logic/exporter/Docbook5ExportFormat.xml
index ddb29f48635..8c03b8f17a4 100644
--- a/src/test/resources/org/jabref/logic/exporter/Docbook5ExportFormat.xml
+++ b/src/test/resources/org/jabref/logic/exporter/Docbook5ExportFormat.xml
@@ -37,4 +37,4 @@
     
 <!--ABSTRACT-->
     
-</biblioentry></bibliography>
\ No newline at end of file
+</biblioentry></bibliography>

From 44d855329cd0adb868f83583ebf7014d032c1a08 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Feb 2019 10:51:37 +0100
Subject: [PATCH 026/184] Bump log4j-core from 2.11.1 to 2.11.2 (#4651)

Bumps log4j-core from 2.11.1 to 2.11.2.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index fc1c0fec81d..df4ece478e0 100644
--- a/build.gradle
+++ b/build.gradle
@@ -150,7 +150,7 @@ dependencies {
     compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.1'
     compile 'org.apache.logging.log4j:log4j-jcl:2.11.1'
     compile 'org.apache.logging.log4j:log4j-api:2.11.1'
-    compile 'org.apache.logging.log4j:log4j-core:2.11.1'
+    compile 'org.apache.logging.log4j:log4j-core:2.11.2'
 
     compile 'de.undercouch:citeproc-java:1.0.1'
 

From d3f571347805a76177d5c6c7981ae2f82a8c7ea7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Feb 2019 10:51:49 +0100
Subject: [PATCH 027/184] Bump log4j-slf4j18-impl from 2.11.1 to 2.11.2 (#4649)

Bumps log4j-slf4j18-impl from 2.11.1 to 2.11.2.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index df4ece478e0..fee558fef6c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -147,7 +147,7 @@ dependencies {
 
     // >1.8.0-beta is required for java 9 compatibility
     compile 'org.slf4j:slf4j-api:1.8.0-beta2'
-    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.1'
+    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.2'
     compile 'org.apache.logging.log4j:log4j-jcl:2.11.1'
     compile 'org.apache.logging.log4j:log4j-api:2.11.1'
     compile 'org.apache.logging.log4j:log4j-core:2.11.2'

From 7c1ca46a4f3dad5902a434890664bc14c5daded4 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Feb 2019 10:52:15 +0100
Subject: [PATCH 028/184] Bump log4j-jul from 2.11.1 to 2.11.2 (#4648)

Bumps log4j-jul from 2.11.1 to 2.11.2.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index fee558fef6c..83a28d34b0e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -166,7 +166,7 @@ dependencies {
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
-    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.1'
+    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
     testCompile 'org.mockito:mockito-core:2.24.0'
     testCompile 'com.github.tomakehurst:wiremock:2.21.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'

From 0c09619bb60c56a23906668eb8022434da4b321c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Feb 2019 10:52:38 +0100
Subject: [PATCH 029/184] Bump assertj-swing-junit from 3.8.0 to 3.9.2 (#4647)

Bumps [assertj-swing-junit](https://github.com/joel-costigliola/assertj-swing) from 3.8.0 to 3.9.2.
- [Release notes](https://github.com/joel-costigliola/assertj-swing/releases)
- [Commits](https://github.com/joel-costigliola/assertj-swing/compare/assertj-swing-parent-pom-3.8.0...assertj-swing-parent-pom-3.9.2)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 83a28d34b0e..db5aec0a196 100644
--- a/build.gradle
+++ b/build.gradle
@@ -169,7 +169,7 @@ dependencies {
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
     testCompile 'org.mockito:mockito-core:2.24.0'
     testCompile 'com.github.tomakehurst:wiremock:2.21.0'
-    testCompile 'org.assertj:assertj-swing-junit:3.8.0'
+    testCompile 'org.assertj:assertj-swing-junit:3.9.2'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'

From a42026775d199e587dc30569a0b478aa69a8cd75 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Feb 2019 10:53:46 +0100
Subject: [PATCH 030/184] Bump log4j-api from 2.11.1 to 2.11.2 (#4650)

Bumps log4j-api from 2.11.1 to 2.11.2.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index db5aec0a196..bfccfe63a0d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -149,7 +149,7 @@ dependencies {
     compile 'org.slf4j:slf4j-api:1.8.0-beta2'
     compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.2'
     compile 'org.apache.logging.log4j:log4j-jcl:2.11.1'
-    compile 'org.apache.logging.log4j:log4j-api:2.11.1'
+    compile 'org.apache.logging.log4j:log4j-api:2.11.2'
     compile 'org.apache.logging.log4j:log4j-core:2.11.2'
 
     compile 'de.undercouch:citeproc-java:1.0.1'

From 3abd4f8165181c31342d26b3df0f397e1cc1d20c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Feb 2019 10:55:15 +0100
Subject: [PATCH 031/184] Bump log4j-jcl from 2.11.1 to 2.11.2 (#4646)

Bumps log4j-jcl from 2.11.1 to 2.11.2.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index bfccfe63a0d..b00e3373951 100644
--- a/build.gradle
+++ b/build.gradle
@@ -148,7 +148,7 @@ dependencies {
     // >1.8.0-beta is required for java 9 compatibility
     compile 'org.slf4j:slf4j-api:1.8.0-beta2'
     compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.2'
-    compile 'org.apache.logging.log4j:log4j-jcl:2.11.1'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.11.2'
     compile 'org.apache.logging.log4j:log4j-api:2.11.2'
     compile 'org.apache.logging.log4j:log4j-core:2.11.2'
 

From 80192eb14d474849d78c58b42bd4180f51221835 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Tue, 12 Feb 2019 10:32:54 +0100
Subject: [PATCH 032/184] Bump bcprov-jdk15on from 1.60 to 1.61 (#4653)

Bumps [bcprov-jdk15on](https://github.com/bcgit/bc-java) from 1.60 to 1.61.
- [Release notes](https://github.com/bcgit/bc-java/releases)
- [Changelog](https://github.com/bcgit/bc-java/blob/master/docs/releasenotes.html)
- [Commits](https://github.com/bcgit/bc-java/commits)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index b00e3373951..1922b2bbb88 100644
--- a/build.gradle
+++ b/build.gradle
@@ -102,7 +102,7 @@ dependencies {
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    compile 'org.bouncycastle:bcprov-jdk15on:1.60'
+    compile 'org.bouncycastle:bcprov-jdk15on:1.61'
 
     compile 'commons-cli:commons-cli:1.4'
 

From 662714d61c2c56b4b59874ca0ec4ca8c4cd2b176 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Wed, 13 Feb 2019 11:20:50 +0100
Subject: [PATCH 033/184] Bump applicationinsights-logging-log4j2 from 2.3.0 to
 2.3.1 (#4657)

Bumps [applicationinsights-logging-log4j2](https://github.com/Microsoft/ApplicationInsights-Java) from 2.3.0 to 2.3.1.
- [Release notes](https://github.com/Microsoft/ApplicationInsights-Java/releases)
- [Changelog](https://github.com/Microsoft/ApplicationInsights-Java/blob/master/CHANGELOG.md)
- [Commits](https://github.com/Microsoft/ApplicationInsights-Java/compare/2.3.0...v2.3.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 1922b2bbb88..2bd70a04933 100644
--- a/build.gradle
+++ b/build.gradle
@@ -159,7 +159,7 @@ dependencies {
     errorproneJavac 'com.google.errorprone:javac:1.8.0-u20'
 
     compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.0'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.4.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.0'

From d95c06b24eab2f39d50180461595c1d26e852bac Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Wed, 13 Feb 2019 11:41:22 +0100
Subject: [PATCH 034/184] Bump applicationinsights-core from 2.3.0 to 2.3.1
 (#4656)

Bumps [applicationinsights-core](https://github.com/Microsoft/ApplicationInsights-Java) from 2.3.0 to 2.3.1.
- [Release notes](https://github.com/Microsoft/ApplicationInsights-Java/releases)
- [Changelog](https://github.com/Microsoft/ApplicationInsights-Java/blob/master/CHANGELOG.md)
- [Commits](https://github.com/Microsoft/ApplicationInsights-Java/compare/2.3.0...v2.3.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 2bd70a04933..1e55cfe71cc 100644
--- a/build.gradle
+++ b/build.gradle
@@ -158,7 +158,7 @@ dependencies {
 
     errorproneJavac 'com.google.errorprone:javac:1.8.0-u20'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.1'
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.4.0'

From e5ede3aef4fa43758172d58bfb078cb77d8ca7e5 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Sun, 17 Feb 2019 23:08:21 +0100
Subject: [PATCH 035/184] Convert Strings Dialog to javafx (#3735)

* Convert String dialog to javafx
TODO: store strings back to db

* add save and cancel buttons

* add method for saving
TODO: validation

* First attempt at validation

* use mvvmfx validation

* Add validation in factory

* remove old comment

* add css but still does not work :(

* convert to new javafx view/controller

* play around with validation
validation icon is now correctly shown, although it needs some css mods
fix toolbar max width

* refactor
TODO: Fix buttons not working

* fix l10n

* fix loading of string dialog

* fix imports

* remove old stuff
TODO: fix validation

* fix Validation
optimize layout a bit
fix l10n

* fix codacy, improve layout

* Refactorings and renamings

* first part for factory

* fix visibilty error

* move validation textfieldtablecell to factory

* fix import order
fix l10n

* fix merge erros in l10n

* remove obsolete key from l10n

* remove unused TextField

* renamings and remove uncessary methods

* extract string adding to bibdatabase
add tests

* fix checkstyle
---
 src/main/java/org/jabref/gui/Base.css         |  18 +
 src/main/java/org/jabref/gui/BasePanel.java   | 107 ++--
 src/main/java/org/jabref/gui/JabRefFrame.java |   8 +-
 .../java/org/jabref/gui/StringDialog.java     | 455 ------------------
 .../gui/collab/StringAddChangeViewModel.java  |   2 +-
 .../gui/collab/StringChangeViewModel.java     |   4 +-
 .../gui/collab/StringNameChangeViewModel.java |   4 +-
 .../collab/StringRemoveChangeViewModel.java   |   2 +-
 .../actions/AppendDatabaseAction.java         |   4 +-
 .../metadata/BibtexStringEditorAction.java    |  20 +
 .../metadata/BibtexStringEditorDialog.fxml    |  38 ++
 .../BibtexStringEditorDialogView.java         | 101 ++++
 .../BibtexStringEditorDialogViewModel.java    |  92 ++++
 .../gui/metadata/BibtexStringViewModel.java   |  90 ++++
 .../gui/{ => metadata}/PreambleEditor.java    |   6 +-
 .../jabref/gui/undo/UndoableInsertString.java |  11 +-
 .../jabref/gui/undo/UndoableRemoveString.java |  14 +-
 .../jabref/gui/undo/UndoableStringChange.java |  23 +-
 .../gui/util/IconValidationDecorator.java     |   6 +-
 ...extFieldTableCellVisualizationFactory.java |  54 +++
 .../jabref/model/database/BibDatabase.java    |  32 +-
 .../org/jabref/model/entry/BibtexString.java  |  15 +-
 src/main/resources/l10n/JabRef_en.properties  |   8 +-
 .../model/database/BibDatabaseTest.java       |  26 +
 24 files changed, 537 insertions(+), 603 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/StringDialog.java
 create mode 100644 src/main/java/org/jabref/gui/metadata/BibtexStringEditorAction.java
 create mode 100644 src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialog.fxml
 create mode 100644 src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogView.java
 create mode 100644 src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogViewModel.java
 create mode 100644 src/main/java/org/jabref/gui/metadata/BibtexStringViewModel.java
 rename src/main/java/org/jabref/gui/{ => metadata}/PreambleEditor.java (92%)
 create mode 100644 src/main/java/org/jabref/gui/util/ViewModelTextFieldTableCellVisualizationFactory.java

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
index ec78513a06b..ab4097899cc 100644
--- a/src/main/java/org/jabref/gui/Base.css
+++ b/src/main/java/org/jabref/gui/Base.css
@@ -975,3 +975,21 @@ We want to have a look that matches our icons in the tool-bar */
 .color-palette-region .button {
     -fx-border-width: 0px;
 }
+
+
+.warning-icon {
+    -fx-fill: -jr-warn;
+}
+
+.error-icon {
+    -fx-text-fill: -jr-error;
+    -fx-fill: -jr-error;
+}
+
+.tooltip-warning {
+    -fx-background-color: -jr-warn;
+}
+
+.tooltip-error {
+    -fx-background-color: -jr-error;
+}
diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index 777c06eaf6f..ef5e2875994 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -150,7 +150,6 @@ public class BasePanel extends StackPane {
     // Used to track whether the base has changed since last save.
     private BibEntry showing;
 
-    private StringDialog stringDialog;
     private SuggestionProviders suggestionProviders;
 
     @SuppressWarnings({"FieldCanBeLocal", "unused"}) private Subscription dividerPositionSubscription;
@@ -308,17 +307,6 @@ private void setupActions() {
 
         actions.put(Actions.SELECT_ALL, mainTable.getSelectionModel()::selectAll);
 
-        // The action for opening the string editor
-        actions.put(Actions.EDIT_STRINGS, () -> {
-            if (stringDialog == null) {
-                StringDialog form = new StringDialog(frame, BasePanel.this, bibDatabaseContext.getDatabase());
-                form.setVisible(true);
-                stringDialog = form;
-            } else {
-                stringDialog.setVisible(true);
-            }
-        });
-
         // The action for auto-generating keys.
         actions.put(Actions.MAKE_KEY, new GenerateBibtexKeyAction(this, frame.getDialogService()));
 
@@ -374,36 +362,36 @@ private void setupActions() {
 
         actions.put(Actions.MERGE_WITH_FETCHED_ENTRY, new MergeWithFetchedEntryAction(this, frame.getDialogService()));
 
-        actions.put(Actions.REPLACE_ALL, ()-> (new ReplaceStringAction(this)).execute());
+        actions.put(Actions.REPLACE_ALL, () -> (new ReplaceStringAction(this)).execute());
 
         actions.put(new SpecialFieldValueViewModel(SpecialField.RELEVANCE.getValues().get(0)).getCommand(),
-                new SpecialFieldViewModel(SpecialField.RELEVANCE, undoManager).getSpecialFieldAction(SpecialField.RELEVANCE.getValues().get(0), frame));
+                    new SpecialFieldViewModel(SpecialField.RELEVANCE, undoManager).getSpecialFieldAction(SpecialField.RELEVANCE.getValues().get(0), frame));
 
         actions.put(new SpecialFieldValueViewModel(SpecialField.QUALITY.getValues().get(0)).getCommand(),
-                new SpecialFieldViewModel(SpecialField.QUALITY, undoManager).getSpecialFieldAction(SpecialField.QUALITY.getValues().get(0), frame));
+                    new SpecialFieldViewModel(SpecialField.QUALITY, undoManager).getSpecialFieldAction(SpecialField.QUALITY.getValues().get(0), frame));
 
         actions.put(new SpecialFieldValueViewModel(SpecialField.PRINTED.getValues().get(0)).getCommand(),
-                new SpecialFieldViewModel(SpecialField.PRINTED, undoManager).getSpecialFieldAction(SpecialField.PRINTED.getValues().get(0), frame));
+                    new SpecialFieldViewModel(SpecialField.PRINTED, undoManager).getSpecialFieldAction(SpecialField.PRINTED.getValues().get(0), frame));
 
         for (SpecialFieldValue prio : SpecialField.PRIORITY.getValues()) {
             actions.put(new SpecialFieldValueViewModel(prio).getCommand(),
-                    new SpecialFieldViewModel(SpecialField.PRIORITY, undoManager).getSpecialFieldAction(prio, this.frame));
+                        new SpecialFieldViewModel(SpecialField.PRIORITY, undoManager).getSpecialFieldAction(prio, this.frame));
         }
         for (SpecialFieldValue rank : SpecialField.RANKING.getValues()) {
             actions.put(new SpecialFieldValueViewModel(rank).getCommand(),
-                    new SpecialFieldViewModel(SpecialField.RANKING, undoManager).getSpecialFieldAction(rank, this.frame));
+                        new SpecialFieldViewModel(SpecialField.RANKING, undoManager).getSpecialFieldAction(rank, this.frame));
         }
         for (SpecialFieldValue status : SpecialField.READ_STATUS.getValues()) {
             actions.put(new SpecialFieldValueViewModel(status).getCommand(),
-                    new SpecialFieldViewModel(SpecialField.READ_STATUS, undoManager).getSpecialFieldAction(status, this.frame));
+                        new SpecialFieldViewModel(SpecialField.READ_STATUS, undoManager).getSpecialFieldAction(status, this.frame));
         }
 
         actions.put(Actions.TOGGLE_PREVIEW, () -> {
             PreviewPreferences previewPreferences = Globals.prefs.getPreviewPreferences();
             boolean enabled = !previewPreferences.isPreviewPanelEnabled();
             PreviewPreferences newPreviewPreferences = previewPreferences.getBuilder()
-                    .withPreviewPanelEnabled(enabled)
-                    .build();
+                                                                         .withPreviewPanelEnabled(enabled)
+                                                                         .build();
             Globals.prefs.storePreviewPreferences(newPreviewPreferences);
             DefaultTaskExecutor.runInJavaFXThread(() -> setPreviewActiveBasePanels(enabled));
         });
@@ -496,9 +484,9 @@ private void copyTitle() {
         if (!selectedBibEntries.isEmpty()) {
             // Collect all non-null titles.
             List<String> titles = selectedBibEntries.stream()
-                    .filter(bibEntry -> bibEntry.getTitle().isPresent())
-                    .map(bibEntry -> bibEntry.getTitle().get())
-                    .collect(Collectors.toList());
+                                                    .filter(bibEntry -> bibEntry.getTitle().isPresent())
+                                                    .map(bibEntry -> bibEntry.getTitle().get())
+                                                    .collect(Collectors.toList());
 
             if (titles.isEmpty()) {
                 output(Localization.lang("None of the selected entries have titles."));
@@ -530,8 +518,8 @@ private void copyCiteKey() {
 
             String sb = String.join(",", keys);
             String citeCommand = Optional.ofNullable(Globals.prefs.get(JabRefPreferences.CITE_COMMAND))
-                    .filter(cite -> cite.contains("\\")) // must contain \
-                    .orElse("\\cite");
+                                         .filter(cite -> cite.contains("\\")) // must contain \
+                                         .orElse("\\cite");
             Globals.clipboardManager.setContent(citeCommand + "{" + sb + '}');
 
             if (keys.size() == bes.size()) {
@@ -575,7 +563,7 @@ private void copyKeyAndTitle() {
             Layout layout;
             try {
                 layout = new LayoutHelper(sr, Globals.prefs.getLayoutFormatterPreferences(Globals.journalAbbreviationLoader))
-                        .getLayoutFromText();
+                                                                                                                             .getLayoutFromText();
             } catch (IOException e) {
                 LOGGER.info("Could not get layout", e);
                 return;
@@ -719,12 +707,12 @@ private void createMainTable() {
 
         // Update entry editor and preview according to selected entries
         mainTable.addSelectionListener(event -> mainTable.getSelectedEntries()
-                .stream()
-                .findFirst()
-                .ifPresent(entry -> {
-                    preview.setEntry(entry);
-                    entryEditor.setEntry(entry);
-                }));
+                                                         .stream()
+                                                         .findFirst()
+                                                         .ifPresent(entry -> {
+                                                             preview.setEntry(entry);
+                                                             entryEditor.setEntry(entry);
+                                                         }));
 
         // TODO: Register these actions globally
         /*
@@ -814,8 +802,8 @@ public void setupMainPanel() {
         // Saves the divider position as soon as it changes
         // We need to keep a reference to the subscription, otherwise the binding gets garbage collected
         dividerPositionSubscription = EasyBind.monadic(Bindings.valueAt(splitPane.getDividers(), 0))
-                .flatMap(SplitPane.Divider::positionProperty)
-                .subscribe((observable, oldValue, newValue) -> saveDividerLocation(newValue));
+                                              .flatMap(SplitPane.Divider::positionProperty)
+                                              .subscribe((observable, oldValue, newValue) -> saveDividerLocation(newValue));
     }
 
     /**
@@ -846,18 +834,6 @@ private void instantiateSearchAutoCompleter() {
         }
     }
 
-    public void assureStringDialogNotEditing() {
-        if (stringDialog != null) {
-            stringDialog.assureNotEditing();
-        }
-    }
-
-    public void updateStringDialog() {
-        if (stringDialog != null) {
-            stringDialog.refreshTable();
-        }
-    }
-
     private void adjustSplitter() {
         if (mode == BasePanelMode.SHOWING_PREVIEW) {
             splitPane.setDividerPositions(Globals.prefs.getPreviewPreferences().getPreviewPanelDividerPosition().doubleValue());
@@ -945,9 +921,9 @@ public void previousPreviewStyle() {
 
     private void cyclePreview(int newPosition) {
         PreviewPreferences previewPreferences = Globals.prefs.getPreviewPreferences()
-                .getBuilder()
-                .withPreviewCyclePosition(newPosition)
-                .build();
+                                                             .getBuilder()
+                                                             .withPreviewCyclePosition(newPosition)
+                                                             .build();
         Globals.prefs.storePreviewPreferences(previewPreferences);
 
         preview.updateLayout(previewPreferences);
@@ -997,7 +973,7 @@ public void entryEditorClosing(EntryEditor editor) {
      */
     public void ensureNotShowingBottomPanel(BibEntry entry) {
         if (((mode == BasePanelMode.SHOWING_EDITOR) && (entryEditor.getEntry() == entry))
-            || ((mode == BasePanelMode.SHOWING_PREVIEW) && (preview.getEntry() == entry))) {
+        || ((mode == BasePanelMode.SHOWING_PREVIEW) && (preview.getEntry() == entry))) {
             closeBottomPane();
         }
     }
@@ -1054,10 +1030,6 @@ public BibDatabase getDatabase() {
         return bibDatabaseContext.getDatabase();
     }
 
-    public void stringsClosing() {
-        stringDialog = null;
-    }
-
     public void changeTypeOfSelectedEntries(String newType) {
         List<BibEntry> bes = mainTable.getSelectedEntries();
         changeType(bes, newType);
@@ -1105,11 +1077,11 @@ public boolean showDeleteConfirmationDialog(int numberOfEntries) {
             }
 
             return dialogService.showConfirmationDialogWithOptOutAndWait(title,
-                    message,
-                    okButton,
-                    cancelButton,
-                    Localization.lang("Disable this confirmation dialog"),
-                    optOut -> Globals.prefs.putBoolean(JabRefPreferences.CONFIRM_DELETE, !optOut));
+                                                                         message,
+                                                                         okButton,
+                                                                         cancelButton,
+                                                                         Localization.lang("Disable this confirmation dialog"),
+                                                                         optOut -> Globals.prefs.putBoolean(JabRefPreferences.CONFIRM_DELETE, !optOut));
         } else {
             return true;
         }
@@ -1125,16 +1097,15 @@ private void saveDividerLocation(Number position) {
 
         if (mode == BasePanelMode.SHOWING_PREVIEW) {
             PreviewPreferences previewPreferences = Globals.prefs.getPreviewPreferences()
-                    .getBuilder()
-                    .withPreviewPanelDividerPosition(position)
-                    .build();
+                                                                 .getBuilder()
+                                                                 .withPreviewPanelDividerPosition(position)
+                                                                 .build();
             Globals.prefs.storePreviewPreferences(previewPreferences);
         } else if (mode == BasePanelMode.SHOWING_EDITOR) {
             preferences.setEntryEditorDividerPosition(position.doubleValue());
         }
     }
 
-
     /**
      * Perform necessary cleanup when this BasePanel is closed.
      */
@@ -1432,8 +1403,8 @@ public void action() {
 
                     Optional<LinkedFile> linkedFile = files.stream()
                                                            .filter(file -> (FieldName.URL.equalsIgnoreCase(file.getFileType())
-                                                                            || FieldName.PS.equalsIgnoreCase(file.getFileType())
-                                                                            || FieldName.PDF.equalsIgnoreCase(file.getFileType())))
+                                                           || FieldName.PS.equalsIgnoreCase(file.getFileType())
+                                                           || FieldName.PDF.equalsIgnoreCase(file.getFileType())))
                                                            .findFirst();
 
                     if (linkedFile.isPresent()) {
@@ -1441,8 +1412,8 @@ public void action() {
                         try {
 
                             JabRefDesktop.openExternalFileAnyFormat(bibDatabaseContext,
-                                    linkedFile.get().getLink(),
-                                    ExternalFileTypes.getInstance().fromLinkedFile(linkedFile.get(), true));
+                                                                    linkedFile.get().getLink(),
+                                                                    ExternalFileTypes.getInstance().fromLinkedFile(linkedFile.get(), true));
 
                             output(Localization.lang("External viewer called") + '.');
                         } catch (IOException e) {
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 8e4ca768b05..b657ee1e1db 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -98,6 +98,8 @@
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.menus.FileHistoryMenu;
 import org.jabref.gui.mergeentries.MergeEntriesAction;
+import org.jabref.gui.metadata.BibtexStringEditorAction;
+import org.jabref.gui.metadata.PreambleEditor;
 import org.jabref.gui.push.PushToApplicationButton;
 import org.jabref.gui.push.PushToApplications;
 import org.jabref.gui.search.GlobalSearchBar;
@@ -848,7 +850,8 @@ private MenuBar createMenu() {
 
                 factory.createMenuItem(StandardActions.LIBRARY_PROPERTIES, new DatabasePropertiesAction(this)),
                 factory.createMenuItem(StandardActions.EDIT_PREAMBLE, new PreambleEditor(this)),
-                factory.createMenuItem(StandardActions.EDIT_STRINGS, new OldDatabaseCommandWrapper(Actions.EDIT_STRINGS, this, Globals.stateManager))
+                factory.createMenuItem(StandardActions.EDIT_STRINGS, new BibtexStringEditorAction(this))
+
         );
 
         Menu lookupIdentifiers = factory.createSubMenu(StandardActions.LOOKUP_DOC_IDENTIFIER);
@@ -857,6 +860,7 @@ private MenuBar createMenu() {
             lookupIdentifiers.getItems().add(factory.createMenuItem(identifierAction.getAction(), identifierAction));
         }
 
+        //@formatter:off
         quality.getItems().addAll(
                 factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(this, dialogService)),
                 factory.createMenuItem(StandardActions.MERGE_ENTRIES, new MergeEntriesAction(this)),
@@ -971,7 +975,7 @@ private MenuBar createMenu() {
                 ),
                 factory.createMenuItem(StandardActions.ABOUT, new AboutAction())
         );
-
+        //@formatter:on
         MenuBar menu = new MenuBar();
         menu.getStyleClass().add("mainMenu");
         menu.getMenus().addAll(
diff --git a/src/main/java/org/jabref/gui/StringDialog.java b/src/main/java/org/jabref/gui/StringDialog.java
deleted file mode 100644
index 1169b1f7dce..00000000000
--- a/src/main/java/org/jabref/gui/StringDialog.java
+++ /dev/null
@@ -1,455 +0,0 @@
-package org.jabref.gui;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.ActionMap;
-import javax.swing.DefaultCellEditor;
-import javax.swing.InputMap;
-import javax.swing.JComponent;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTable;
-import javax.swing.JTextField;
-import javax.swing.JToolBar;
-import javax.swing.LayoutFocusTraversalPolicy;
-import javax.swing.table.AbstractTableModel;
-import javax.swing.table.TableColumnModel;
-import javax.swing.undo.CompoundEdit;
-
-import org.jabref.Globals;
-import org.jabref.gui.actions.Actions;
-import org.jabref.gui.help.HelpAction;
-import org.jabref.gui.icon.IconTheme;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.undo.UndoableInsertString;
-import org.jabref.gui.undo.UndoableRemoveString;
-import org.jabref.gui.undo.UndoableStringChange;
-import org.jabref.gui.util.WindowLocation;
-import org.jabref.logic.bibtex.InvalidFieldValueException;
-import org.jabref.logic.bibtex.LatexFieldFormatter;
-import org.jabref.logic.bibtex.comparator.BibtexStringComparator;
-import org.jabref.logic.help.HelpFile;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
-import org.jabref.model.database.KeyCollisionException;
-import org.jabref.model.entry.BibtexString;
-import org.jabref.preferences.JabRefPreferences;
-
-class StringDialog extends JabRefDialog {
-
-    private static final String STRINGS_TITLE = Localization.lang("Strings for library");
-    // A reference to the entry this object works on.
-    private final BibDatabase base;
-    private final BasePanel panel;
-    private final StringTable table;
-    private final HelpAction helpAction;
-
-    private final SaveDatabaseAction saveAction = new SaveDatabaseAction(this);
-
-    // The action concerned with closing the window.
-    private final CloseAction closeAction = new CloseAction();
-    private List<BibtexString> strings;
-
-
-    public StringDialog(JabRefFrame frame, BasePanel panel, BibDatabase base) {
-        super(StringDialog.class);
-        this.panel = panel;
-        this.base = base;
-
-        sortStrings();
-
-        helpAction = new HelpAction(Localization.lang("Help"), HelpFile.STRING_EDITOR);
-
-        addWindowListener(new WindowAdapter() {
-
-            @Override
-            public void windowClosing(WindowEvent e) {
-                closeAction.actionPerformed(null);
-            }
-        });
-
-        // We replace the default FocusTraversalPolicy with a subclass
-        // that only allows the StringTable to gain keyboard focus.
-        setFocusTraversalPolicy(new LayoutFocusTraversalPolicy() {
-
-            @Override
-            protected boolean accept(Component c) {
-                return super.accept(c) && (c instanceof StringTable);
-            }
-        });
-
-        JPanel pan = new JPanel();
-        GridBagLayout gbl = new GridBagLayout();
-        pan.setLayout(gbl);
-        GridBagConstraints con = new GridBagConstraints();
-        con.fill = GridBagConstraints.BOTH;
-        con.weighty = 1;
-        con.weightx = 1;
-
-        StringTableModel stm = new StringTableModel(this, base);
-        table = new StringTable(stm);
-        if (!base.hasNoStrings()) {
-            table.setRowSelectionInterval(0, 0);
-        }
-
-        gbl.setConstraints(table.getPane(), con);
-        pan.add(table.getPane());
-
-        JToolBar tlb = new OSXCompatibleToolbar();
-        InputMap im = tlb.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        ActionMap am = tlb.getActionMap();
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.STRING_DIALOG_ADD_STRING), "add");
-        NewStringAction newStringAction = new NewStringAction(this);
-        am.put("add", newStringAction);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.STRING_DIALOG_REMOVE_STRING), "remove");
-        RemoveStringAction removeStringAction = new RemoveStringAction(this);
-        am.put("remove", removeStringAction);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.SAVE_DATABASE), "save");
-        am.put("save", saveAction);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", closeAction);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.HELP), "help");
-        am.put("help", helpAction);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.UNDO), "undo");
-        UndoAction undoAction = new UndoAction();
-        am.put("undo", undoAction);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.REDO), "redo");
-        RedoAction redoAction = new RedoAction();
-        am.put("redo", redoAction);
-
-        tlb.add(newStringAction);
-        tlb.add(removeStringAction);
-        tlb.addSeparator();
-        tlb.add(helpAction);
-        Container conPane = getContentPane();
-        conPane.add(tlb, BorderLayout.NORTH);
-        conPane.add(pan, BorderLayout.CENTER);
-
-        setTitle(STRINGS_TITLE + ": "
-                + panel.getBibDatabaseContext().getDatabaseFile().map(File::getName).orElse(GUIGlobals.UNTITLED_TITLE));
-        WindowLocation pw = new WindowLocation(this, JabRefPreferences.STRINGS_POS_X, JabRefPreferences.STRINGS_POS_Y,
-                JabRefPreferences.STRINGS_SIZE_X, JabRefPreferences.STRINGS_SIZE_Y);
-        pw.displayWindowAtStoredLocation();
-    }
-
-    private static boolean isNumber(String name) {
-        // A pure integer number cannot be used as a string label,
-        // since Bibtex will read it as a number.
-        try {
-            Integer.parseInt(name);
-            return true;
-        } catch (NumberFormatException ex) {
-            return false;
-        }
-    }
-
-    private void sortStrings() {
-        // Rebuild our sorted set of strings:
-        strings = new ArrayList<>();
-        for (String s : base.getStringKeySet()) {
-            strings.add(base.getString(s));
-        }
-        Collections.sort(strings, new BibtexStringComparator(false));
-    }
-
-    public void refreshTable() {
-        sortStrings();
-        table.revalidate();
-        table.clearSelection();
-        table.repaint();
-    }
-
-    public void saveDatabase() {
-        panel.runCommand(Actions.SAVE);
-    }
-
-    public void assureNotEditing() {
-        if (table.isEditing()) {
-            int col = table.getEditingColumn();
-            int row = table.getEditingRow();
-            table.getCellEditor(row, col).stopCellEditing();
-        }
-    }
-
-    static class SaveDatabaseAction extends AbstractAction {
-
-        private final StringDialog parent;
-
-
-        public SaveDatabaseAction(StringDialog parent) {
-            super("Save library", IconTheme.JabRefIcons.SAVE.getIcon());
-            putValue(Action.SHORT_DESCRIPTION, Localization.lang("Save library"));
-            this.parent = parent;
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            parent.saveDatabase();
-        }
-    }
-
-    class StringTable extends JTable {
-
-        private final JScrollPane sp = new JScrollPane(this);
-
-
-        public StringTable(StringTableModel stm) {
-            super(stm);
-            setShowVerticalLines(true);
-            setShowHorizontalLines(true);
-            setColumnSelectionAllowed(true);
-            DefaultCellEditor dce = new DefaultCellEditor(new JTextField());
-            dce.setClickCountToStart(2);
-            setDefaultEditor(String.class, dce);
-            TableColumnModel cm = getColumnModel();
-            cm.getColumn(0).setPreferredWidth(800);
-            cm.getColumn(1).setPreferredWidth(2000);
-            getInputMap().put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-            getActionMap().put("close", closeAction);
-            getInputMap().put(Globals.getKeyPrefs().getKey(KeyBinding.HELP), "help");
-            getActionMap().put("help", helpAction);
-        }
-
-        public JComponent getPane() {
-            return sp;
-        }
-
-    }
-
-    class StringTableModel extends AbstractTableModel {
-
-        private final BibDatabase tbase;
-        private final StringDialog parent;
-
-
-        public StringTableModel(StringDialog parent, BibDatabase base) {
-            this.parent = parent;
-            this.tbase = base;
-        }
-
-        @Override
-        public Object getValueAt(int row, int col) {
-            return col == 0 ? strings.get(row).getName() : strings.get(row).getContent();
-        }
-
-        @Override
-        public void setValueAt(Object value, int row, int col) {
-            if (col == 0) {
-                // Change name of string.
-                if (!value.equals(strings.get(row).getName())) {
-                    if (tbase.hasStringLabel((String) value)) {
-                        JOptionPane.showMessageDialog(parent, Localization.lang("A string with that label already exists"),
-                                Localization.lang("Label"), JOptionPane.ERROR_MESSAGE);
-                    } else if (((String) value).contains(" ")) {
-                        JOptionPane.showMessageDialog(parent, Localization.lang("The label of the string cannot contain spaces."),
-                                Localization.lang("Label"), JOptionPane.ERROR_MESSAGE);
-                    } else if (((String) value).contains("#")) {
-                        JOptionPane.showMessageDialog(parent, Localization.lang("The label of the string cannot contain the '#' character."),
-                                Localization.lang("Label"), JOptionPane.ERROR_MESSAGE);
-                    } else if (isNumber((String) value)) {
-                        JOptionPane.showMessageDialog(parent, Localization.lang("The label of the string cannot be a number."),
-                                Localization.lang("Label"), JOptionPane.ERROR_MESSAGE);
-                    } else {
-                        // Store undo information.
-                        BibtexString subject = strings.get(row);
-                        panel.getUndoManager().addEdit(
-                                new UndoableStringChange(panel, subject, true, subject.getName(), (String) value));
-                        subject.setName((String) value);
-                        panel.markBaseChanged();
-                        refreshTable();
-                    }
-                }
-            } else {
-                // Change content of string.
-                BibtexString subject = strings.get(row);
-
-                if (!value.equals(subject.getContent())) {
-                    try {
-                        new LatexFieldFormatter(Globals.prefs.getLatexFieldFormatterPreferences())
-                                .format((String) value, "__dummy");
-                    } catch (InvalidFieldValueException ex) {
-                        return;
-                    }
-                    // Store undo information.
-                    panel.getUndoManager().addEdit(
-                            new UndoableStringChange(panel, subject, false, subject.getContent(), (String) value));
-
-                    subject.setContent((String) value);
-                    panel.markBaseChanged();
-                }
-            }
-        }
-
-        @Override
-        public int getColumnCount() {
-            return 2;
-        }
-
-        @Override
-        public int getRowCount() {
-            return strings.size();
-        }
-
-        @Override
-        public String getColumnName(int col) {
-            return col == 0 ? Localization.lang("Label") :
-                Localization.lang("Content");
-        }
-
-        @Override
-        public boolean isCellEditable(int row, int col) {
-            return true;
-        }
-    }
-
-    class CloseAction extends AbstractAction {
-
-        public CloseAction() {
-            super("Close window");
-            putValue(Action.SHORT_DESCRIPTION, Localization.lang("Close dialog"));
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            panel.stringsClosing();
-            dispose();
-        }
-    }
-
-    class NewStringAction extends AbstractAction {
-
-        private final StringDialog parent;
-
-
-        public NewStringAction(StringDialog parent) {
-            super("New string", IconTheme.JabRefIcons.ADD.getIcon());
-            putValue(Action.SHORT_DESCRIPTION, Localization.lang("New string"));
-            this.parent = parent;
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            String name = JOptionPane.showInputDialog(parent, Localization.lang("Please enter the string's label"));
-            if (name == null) {
-                return;
-            }
-            if (isNumber(name)) {
-                JOptionPane.showMessageDialog(parent, Localization.lang("The label of the string cannot be a number."),
-                        Localization.lang("Label"), JOptionPane.ERROR_MESSAGE);
-                return;
-            }
-            if (name.contains("#")) {
-                JOptionPane.showMessageDialog(parent, Localization.lang("The label of the string cannot contain the '#' character."),
-                        Localization.lang("Label"), JOptionPane.ERROR_MESSAGE);
-                return;
-            }
-            if (name.contains(" ")) {
-                JOptionPane.showMessageDialog(parent, Localization.lang("The label of the string cannot contain spaces."),
-                        Localization.lang("Label"), JOptionPane.ERROR_MESSAGE);
-                return;
-            }
-            try {
-                BibtexString bs = new BibtexString(name, "");
-
-                // Store undo information:
-                panel.getUndoManager().addEdit(new UndoableInsertString(panel, panel.getDatabase(), bs));
-
-                base.addString(bs);
-                refreshTable();
-                panel.markBaseChanged();
-            } catch (KeyCollisionException ex) {
-                JOptionPane.showMessageDialog(parent,
-                        Localization.lang("A string with that label already exists"),
-                        Localization.lang("Label"), JOptionPane.ERROR_MESSAGE);
-            }
-        }
-    }
-
-    class RemoveStringAction extends AbstractAction {
-
-        private final StringDialog parent;
-
-
-        public RemoveStringAction(StringDialog parent) {
-            super("Remove selected strings", IconTheme.JabRefIcons.REMOVE.getIcon());
-            putValue(Action.SHORT_DESCRIPTION, Localization.lang("Remove selected strings"));
-            this.parent = parent;
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            int[] sel = table.getSelectedRows();
-            if (sel.length > 0) {
-
-                // Make sure no cell is being edited, as caused by the
-                // keystroke. This makes the content hang on the screen.
-                assureNotEditing();
-
-                String msg = (sel.length > 1 ? Localization.lang("Really delete the %0 selected entries?",
-                        Integer.toString(sel.length)) : Localization.lang("Really delete the selected entry?"));
-                int answer = JOptionPane.showConfirmDialog(parent, msg, Localization.lang("Delete strings"),
-                        JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
-                if (answer == JOptionPane.YES_OPTION) {
-                    CompoundEdit ce = new CompoundEdit();
-                    for (int i = sel.length - 1; i >= 0; i--) {
-                        // Delete the strings backwards to avoid moving indexes.
-
-                        BibtexString subject = strings.get(sel[i]);
-
-                        // Store undo information:
-                        ce.addEdit(new UndoableRemoveString(panel, base, subject));
-
-                        base.removeString(subject.getId());
-                    }
-                    ce.end();
-                    panel.getUndoManager().addEdit(ce);
-
-                    refreshTable();
-                    if (!base.hasNoStrings()) {
-                        table.setRowSelectionInterval(0, 0);
-                    }
-                }
-            }
-        }
-    }
-
-    class UndoAction extends AbstractAction {
-
-        public UndoAction() {
-            super("Undo", IconTheme.JabRefIcons.UNDO.getIcon());
-            putValue(Action.SHORT_DESCRIPTION, Localization.lang("Undo"));
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            panel.runCommand(Actions.UNDO);
-        }
-    }
-
-    class RedoAction extends AbstractAction {
-
-        public RedoAction() {
-            super("Redo", IconTheme.JabRefIcons.REDO.getIcon());
-            putValue(Action.SHORT_DESCRIPTION, Localization.lang("Redo"));
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            panel.runCommand(Actions.REDO);
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/gui/collab/StringAddChangeViewModel.java b/src/main/java/org/jabref/gui/collab/StringAddChangeViewModel.java
index 20bf1099ef6..dafb80b125f 100644
--- a/src/main/java/org/jabref/gui/collab/StringAddChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/StringAddChangeViewModel.java
@@ -43,7 +43,7 @@ public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound
 
         try {
             panel.getDatabase().addString(string);
-            undoEdit.addEdit(new UndoableInsertString(panel, panel.getDatabase(), string));
+            undoEdit.addEdit(new UndoableInsertString(panel.getDatabase(), string));
         } catch (KeyCollisionException ex) {
             LOGGER.info("Error: could not add string '" + string.getName() + "': " + ex.getMessage(), ex);
         }
diff --git a/src/main/java/org/jabref/gui/collab/StringChangeViewModel.java b/src/main/java/org/jabref/gui/collab/StringChangeViewModel.java
index 19e68f3a0b9..d44ac099658 100644
--- a/src/main/java/org/jabref/gui/collab/StringChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/StringChangeViewModel.java
@@ -59,14 +59,14 @@ public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound
             BibtexString bs = new BibtexString(label, disk);
             try {
                 panel.getDatabase().addString(bs);
-                undoEdit.addEdit(new UndoableInsertString(panel, panel.getDatabase(), bs));
+                undoEdit.addEdit(new UndoableInsertString(panel.getDatabase(), bs));
             } catch (KeyCollisionException ex) {
                 LOGGER.info("Error: could not add string '" + bs.getName() + "': " + ex.getMessage(), ex);
             }
         } else {
             String mem = string.getContent();
             string.setContent(disk);
-            undoEdit.addEdit(new UndoableStringChange(panel, string, false, mem, disk));
+            undoEdit.addEdit(new UndoableStringChange(string, false, mem, disk));
         }
 
         // Update tmp database:
diff --git a/src/main/java/org/jabref/gui/collab/StringNameChangeViewModel.java b/src/main/java/org/jabref/gui/collab/StringNameChangeViewModel.java
index e9bda7c9f40..b9cd5bb80fe 100644
--- a/src/main/java/org/jabref/gui/collab/StringNameChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/StringNameChangeViewModel.java
@@ -50,13 +50,13 @@ public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound
             BibtexString bs = new BibtexString(disk, content);
             try {
                 panel.getDatabase().addString(bs);
-                undoEdit.addEdit(new UndoableInsertString(panel, panel.getDatabase(), bs));
+                undoEdit.addEdit(new UndoableInsertString(panel.getDatabase(), bs));
             } catch (KeyCollisionException ex) {
                 LOGGER.info("Error: could not add string '" + bs.getName() + "': " + ex.getMessage(), ex);
             }
         } else {
             string.setName(disk);
-            undoEdit.addEdit(new UndoableStringChange(panel, string, true, mem, disk));
+            undoEdit.addEdit(new UndoableStringChange(string, true, mem, disk));
         }
 
         // Update tmp database:
diff --git a/src/main/java/org/jabref/gui/collab/StringRemoveChangeViewModel.java b/src/main/java/org/jabref/gui/collab/StringRemoveChangeViewModel.java
index 4501888a240..eaf66d47304 100644
--- a/src/main/java/org/jabref/gui/collab/StringRemoveChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/StringRemoveChangeViewModel.java
@@ -36,7 +36,7 @@ public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound
 
         try {
             panel.getDatabase().removeString(inMem.getId());
-            undoEdit.addEdit(new UndoableRemoveString(panel, panel.getDatabase(), string));
+            undoEdit.addEdit(new UndoableRemoveString(panel.getDatabase(), string));
         } catch (Exception ex) {
             LOGGER.info("Error: could not add string '" + string.getName() + "': " + ex.getMessage(), ex);
         }
diff --git a/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java b/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java
index fbb5d71222e..5231d0edede 100644
--- a/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java
@@ -45,14 +45,12 @@ public class AppendDatabaseAction implements BaseAction {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(AppendDatabaseAction.class);
 
-    private final JabRefFrame frame;
     private final BasePanel panel;
 
     private final List<Path> filesToOpen = new ArrayList<>();
     private final DialogService dialogService;
 
     public AppendDatabaseAction(JabRefFrame frame, BasePanel panel) {
-        this.frame = frame;
         this.panel = panel;
         dialogService = frame.getDialogService();
     }
@@ -87,7 +85,7 @@ private static void mergeFromBibtex(BasePanel panel, ParserResult parserResult,
             for (BibtexString bs : fromDatabase.getStringValues()) {
                 if (!database.hasStringLabel(bs.getName())) {
                     database.addString(bs);
-                    ce.addEdit(new UndoableInsertString(panel, database, bs));
+                    ce.addEdit(new UndoableInsertString(database, bs));
                 }
             }
         }
diff --git a/src/main/java/org/jabref/gui/metadata/BibtexStringEditorAction.java b/src/main/java/org/jabref/gui/metadata/BibtexStringEditorAction.java
new file mode 100644
index 00000000000..7e37e175319
--- /dev/null
+++ b/src/main/java/org/jabref/gui/metadata/BibtexStringEditorAction.java
@@ -0,0 +1,20 @@
+package org.jabref.gui.metadata;
+
+import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.model.database.BibDatabase;
+
+public class BibtexStringEditorAction extends SimpleCommand {
+
+    private final JabRefFrame frame;
+
+    public BibtexStringEditorAction(JabRefFrame jabRefFrame) {
+        this.frame = jabRefFrame;
+    }
+
+    @Override
+    public void execute() {
+        BibDatabase database = frame.getCurrentBasePanel().getDatabase();
+        new BibtexStringEditorDialogView(database).showAndWait();
+    }
+}
diff --git a/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialog.fxml b/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialog.fxml
new file mode 100644
index 00000000000..a9ceca60cd6
--- /dev/null
+++ b/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialog.fxml
@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.ButtonType?>
+<?import javafx.scene.control.DialogPane?>
+<?import javafx.scene.control.TableColumn?>
+<?import javafx.scene.control.TableView?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
+
+<DialogPane minHeight="-Infinity" minWidth="-Infinity" prefHeight="340.0" prefWidth="427.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.metadata.BibtexStringEditorDialogView">
+   <content>
+      <VBox>
+         <children>
+            <TableView fx:id="tblStrings" prefHeight="250.0">
+              <columns>
+                <TableColumn fx:id="colLabel" prefWidth="75.0" text="%Label" />
+                <TableColumn fx:id="colContent" prefWidth="75.0" text="%Content" />
+              </columns>
+               <columnResizePolicy>
+                  <TableView fx:constant="CONSTRAINED_RESIZE_POLICY" />
+               </columnResizePolicy>
+            </TableView>
+            <HBox minWidth="-Infinity" prefHeight="100.0" prefWidth="300.0">
+               <children>
+                <Button fx:id="btnNewString" minWidth="-Infinity" mnemonicParsing="false" onAction="#addString" text="%Add new String" HBox.hgrow="ALWAYS" />
+                  <Button fx:id="btnRemove" mnemonicParsing="false" onAction="#removeString" text="%Remove selected Strings" HBox.hgrow="ALWAYS" />
+                  <Button fx:id="btnHelp" mnemonicParsing="false" onAction="#openHelp" HBox.hgrow="ALWAYS" />
+               </children>
+            </HBox>
+         </children>
+      </VBox>
+   </content>
+   <buttonTypes>
+     <ButtonType fx:constant="CANCEL" />
+     <ButtonType fx:id="saveButton" buttonData="OK_DONE" text="%Save" />
+   </buttonTypes>
+</DialogPane>
diff --git a/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogView.java b/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogView.java
new file mode 100644
index 00000000000..bdb3f169c00
--- /dev/null
+++ b/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogView.java
@@ -0,0 +1,101 @@
+package org.jabref.gui.metadata;
+
+import javafx.event.ActionEvent;
+import javafx.fxml.FXML;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.TableColumn;
+import javafx.scene.control.TableColumn.CellEditEvent;
+import javafx.scene.control.TableView;
+import javafx.scene.control.Tooltip;
+import javafx.util.converter.DefaultStringConverter;
+
+import org.jabref.gui.icon.IconTheme.JabRefIcons;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.IconValidationDecorator;
+import org.jabref.gui.util.ViewModelTextFieldTableCellVisualizationFactory;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.BibDatabase;
+
+import com.airhacks.afterburner.views.ViewLoader;
+import de.saxsys.mvvmfx.utils.validation.visualization.ControlsFxVisualizer;
+
+public class BibtexStringEditorDialogView extends BaseDialog<Void> {
+
+    @FXML private Button btnNewString;
+    @FXML private Button btnRemove;
+    @FXML private Button btnHelp;
+    @FXML private ButtonType saveButton;
+
+    @FXML private TableView<BibtexStringViewModel> tblStrings;
+    @FXML private TableColumn<BibtexStringViewModel, String> colLabel;
+    @FXML private TableColumn<BibtexStringViewModel, String> colContent;
+
+    private final ControlsFxVisualizer visualizer = new ControlsFxVisualizer();
+    private final BibtexStringEditorDialogViewModel viewModel;
+
+    public BibtexStringEditorDialogView(BibDatabase database) {
+        viewModel = new BibtexStringEditorDialogViewModel(database);
+
+        ViewLoader.view(this)
+                  .load()
+                  .setAsDialogPane(this);
+
+        Button btnSave = (Button) this.getDialogPane().lookupButton(saveButton);
+
+        btnSave.disableProperty().bind(viewModel.validProperty().not());
+
+        setResultConverter(btn -> {
+            if (saveButton.equals(btn)) {
+                viewModel.save();
+            }
+            return null;
+        });
+
+        setTitle(Localization.lang("Strings for library"));
+    }
+
+    @FXML
+    private void initialize() {
+        visualizer.setDecoration(new IconValidationDecorator());
+
+        btnHelp.setGraphic(JabRefIcons.HELP.getGraphicNode());
+        btnHelp.setTooltip(new Tooltip(Localization.lang("Open Help page")));
+
+        btnNewString.setTooltip(new Tooltip(Localization.lang("New string")));
+        btnRemove.setTooltip(new Tooltip(Localization.lang("Remove selected strings")));
+
+        colLabel.setCellValueFactory(cellData -> cellData.getValue().labelProperty());
+        new ViewModelTextFieldTableCellVisualizationFactory<BibtexStringViewModel, String>().withValidation(BibtexStringViewModel::labelValidation, visualizer).install(colLabel, new DefaultStringConverter());
+
+        colContent.setCellValueFactory(cellData -> cellData.getValue().contentProperty());
+        new ViewModelTextFieldTableCellVisualizationFactory<BibtexStringViewModel, String>().withValidation(BibtexStringViewModel::labelValidation, visualizer).install(colContent, new DefaultStringConverter());
+
+        colLabel.setOnEditCommit((CellEditEvent<BibtexStringViewModel, String> cell) -> {
+            cell.getRowValue().setLabel(cell.getNewValue());
+        });
+        colContent.setOnEditCommit((CellEditEvent<BibtexStringViewModel, String> cell) -> {
+            cell.getRowValue().setContent(cell.getNewValue());
+        });
+
+        tblStrings.itemsProperty().bindBidirectional(viewModel.allStringsProperty());
+        tblStrings.setEditable(true);
+
+        viewModel.seletedItemProperty().bind(tblStrings.getSelectionModel().selectedItemProperty());
+    }
+
+    @FXML
+    private void addString(ActionEvent event) {
+        viewModel.addNewString();
+    }
+
+    @FXML
+    private void openHelp(ActionEvent event) {
+        viewModel.openHelpPage();
+    }
+
+    @FXML
+    private void removeString(ActionEvent event) {
+        viewModel.removeString();
+    }
+}
diff --git a/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogViewModel.java b/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogViewModel.java
new file mode 100644
index 00000000000..3d4a2789ffa
--- /dev/null
+++ b/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogViewModel.java
@@ -0,0 +1,92 @@
+package org.jabref.gui.metadata;
+
+import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.ListProperty;
+import javafx.beans.property.ObjectProperty;
+import javafx.beans.property.SimpleBooleanProperty;
+import javafx.beans.property.SimpleListProperty;
+import javafx.beans.property.SimpleObjectProperty;
+import javafx.beans.value.ObservableValue;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+
+import org.jabref.gui.AbstractViewModel;
+import org.jabref.gui.help.HelpAction;
+import org.jabref.logic.bibtex.comparator.BibtexStringComparator;
+import org.jabref.logic.help.HelpFile;
+import org.jabref.model.database.BibDatabase;
+import org.jabref.model.entry.BibtexString;
+
+import org.fxmisc.easybind.EasyBind;
+
+public class BibtexStringEditorDialogViewModel extends AbstractViewModel {
+
+    private final ListProperty<BibtexStringViewModel> allStrings = new SimpleListProperty<>(FXCollections.observableArrayList());
+    private final ObjectProperty<BibtexStringViewModel> selectedItemProperty = new SimpleObjectProperty<>();
+    private final BibDatabase bibDatabase;
+    private final BooleanProperty validProperty = new SimpleBooleanProperty();
+
+    public BibtexStringEditorDialogViewModel(BibDatabase bibDatabase) {
+        this.bibDatabase = bibDatabase;
+        addAllStringsFromDB();
+
+        ObservableList<ObservableValue<Boolean>> allValidProperty = EasyBind.map(allStringsProperty(), BibtexStringViewModel::combinedValidationValidProperty);
+
+        validProperty.bind(EasyBind.combine(allValidProperty, stream -> stream.allMatch(valid -> valid)));
+
+    }
+
+    private void addAllStringsFromDB() {
+
+        Set<BibtexStringViewModel> strings = bibDatabase.getStringValues()
+                                                        .stream()
+                                                        .sorted(new BibtexStringComparator(false))
+                                                        .map(this::convertFromBibTexString)
+                                                        .collect(Collectors.toSet());
+        allStrings.addAll(strings);
+    }
+
+    public ListProperty<BibtexStringViewModel> allStringsProperty() {
+        return this.allStrings;
+    }
+
+    public void addNewString() {
+        allStrings.add(new BibtexStringViewModel("", ""));
+    }
+
+    public void removeString() {
+        allStrings.remove(selectedItemProperty.getValue());
+    }
+
+    private BibtexStringViewModel convertFromBibTexString(BibtexString bibtexString) {
+        return new BibtexStringViewModel(bibtexString.getName(), bibtexString.getContent());
+    }
+
+    public ObjectProperty<BibtexStringViewModel> seletedItemProperty() {
+        return this.selectedItemProperty;
+    }
+
+    public void save() {
+        List<BibtexString> stringsToAdd = allStrings.stream().map(this::fromBibtexStringViewModel).collect(Collectors.toList());
+        bibDatabase.addStrings(stringsToAdd);
+    }
+
+    private BibtexString fromBibtexStringViewModel(BibtexStringViewModel viewModel) {
+        String label = viewModel.labelProperty().getValue();
+        String content = viewModel.contentProperty().getValue();
+        return new BibtexString(label, content);
+
+    }
+
+    public BooleanProperty validProperty() {
+        return validProperty;
+    }
+
+    public void openHelpPage() {
+        HelpAction.openHelpPage(HelpFile.STRING_EDITOR);
+    }
+}
diff --git a/src/main/java/org/jabref/gui/metadata/BibtexStringViewModel.java b/src/main/java/org/jabref/gui/metadata/BibtexStringViewModel.java
new file mode 100644
index 00000000000..c8dd02e52a6
--- /dev/null
+++ b/src/main/java/org/jabref/gui/metadata/BibtexStringViewModel.java
@@ -0,0 +1,90 @@
+package org.jabref.gui.metadata;
+
+import java.util.regex.Pattern;
+
+import javafx.beans.property.ReadOnlyBooleanProperty;
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
+
+import org.jabref.logic.l10n.Localization;
+
+import de.saxsys.mvvmfx.utils.validation.CompositeValidator;
+import de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator;
+import de.saxsys.mvvmfx.utils.validation.ValidationMessage;
+import de.saxsys.mvvmfx.utils.validation.ValidationStatus;
+import de.saxsys.mvvmfx.utils.validation.Validator;
+
+public class BibtexStringViewModel {
+
+    private final static Pattern IS_NUMBER = Pattern.compile("-?\\d+(\\.\\d+)?");
+
+    private final StringProperty labelProperty = new SimpleStringProperty();
+    private final StringProperty contentProperty = new SimpleStringProperty();
+
+    private final Validator labelValidator;
+    private final Validator contentValidator;
+    private final CompositeValidator combinedValidator;
+
+    public BibtexStringViewModel(String label, String content) {
+        this.labelProperty.setValue(label);
+        this.contentProperty.setValue(content);
+
+        labelValidator = new FunctionBasedValidator<>(this.labelProperty, BibtexStringViewModel::validateLabel);
+        contentValidator = new FunctionBasedValidator<>(this.contentProperty, BibtexStringViewModel::validateContent);
+        combinedValidator = new CompositeValidator(labelValidator, contentValidator);
+    }
+
+    public ValidationStatus labelValidation() {
+        return labelValidator.getValidationStatus();
+    }
+
+    public ValidationStatus contentValidation() {
+        return contentValidator.getValidationStatus();
+    }
+
+    public ReadOnlyBooleanProperty combinedValidationValidProperty() {
+        return combinedValidator.getValidationStatus().validProperty();
+    }
+
+    public StringProperty labelProperty() {
+        return this.labelProperty;
+    }
+
+    public StringProperty contentProperty() {
+        return this.contentProperty;
+    }
+
+    public void setLabel(String label) {
+        this.labelProperty.setValue(label);
+    }
+
+    public void setContent(String content) {
+        this.contentProperty.setValue(content);
+    }
+
+    private static ValidationMessage validateLabel(String input) {
+        if (input == null) {
+            return ValidationMessage.error("May not be null");
+        } else if (input.trim().isEmpty()) {
+            return ValidationMessage.error(Localization.lang("Please enter the string's label"));
+        } else if (IS_NUMBER.matcher(input).matches()) {
+            return ValidationMessage.error(Localization.lang("The label of the string cannot be a number."));
+        } else if (input.contains("#")) {
+            return ValidationMessage.error(Localization.lang("The label of the string cannot contain the '#' character."));
+        } else if (input.contains(" ")) {
+            return ValidationMessage.error(Localization.lang("The label of the string cannot contain spaces."));
+        } else {
+            return null; // everything is ok
+        }
+    }
+
+    private static ValidationMessage validateContent(String input) {
+        if (input == null) {
+            return ValidationMessage.error(Localization.lang("Must not be empty!"));
+        } else if (input.trim().isEmpty()) {
+            return ValidationMessage.error(Localization.lang("Must not be empty!"));
+        } else {
+            return null; // everything is ok
+        }
+    }
+}
diff --git a/src/main/java/org/jabref/gui/PreambleEditor.java b/src/main/java/org/jabref/gui/metadata/PreambleEditor.java
similarity index 92%
rename from src/main/java/org/jabref/gui/PreambleEditor.java
rename to src/main/java/org/jabref/gui/metadata/PreambleEditor.java
index d28cb2c69c7..757c12aa732 100644
--- a/src/main/java/org/jabref/gui/PreambleEditor.java
+++ b/src/main/java/org/jabref/gui/metadata/PreambleEditor.java
@@ -1,4 +1,4 @@
-package org.jabref.gui;
+package org.jabref.gui.metadata;
 
 import java.util.Optional;
 
@@ -6,12 +6,14 @@
 import javafx.scene.control.DialogPane;
 import javafx.scene.control.TextArea;
 
+import org.jabref.gui.BasePanel;
+import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.undo.UndoablePreambleChange;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabase;
 
-class PreambleEditor extends SimpleCommand {
+public class PreambleEditor extends SimpleCommand {
 
     private final TextArea editor = new TextArea();
 
diff --git a/src/main/java/org/jabref/gui/undo/UndoableInsertString.java b/src/main/java/org/jabref/gui/undo/UndoableInsertString.java
index afaece225d8..6485861abbe 100644
--- a/src/main/java/org/jabref/gui/undo/UndoableInsertString.java
+++ b/src/main/java/org/jabref/gui/undo/UndoableInsertString.java
@@ -1,6 +1,5 @@
 package org.jabref.gui.undo;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.KeyCollisionException;
@@ -15,14 +14,10 @@ public class UndoableInsertString extends AbstractUndoableJabRefEdit {
     private static final Logger LOGGER = LoggerFactory.getLogger(UndoableInsertString.class);
 
     private final BibDatabase base;
-    private final BasePanel panel;
     private final BibtexString string;
 
-
-    public UndoableInsertString(BasePanel panel, BibDatabase base,
-            BibtexString string) {
+    public UndoableInsertString(BibDatabase base, BibtexString string) {
         this.base = base;
-        this.panel = panel;
         this.string = string;
     }
 
@@ -37,7 +32,6 @@ public void undo() {
 
         // Revert the change.
         base.removeString(string.getId());
-        panel.updateStringDialog();
     }
 
     @Override
@@ -50,8 +44,5 @@ public void redo() {
         } catch (KeyCollisionException ex) {
             LOGGER.warn("Problem to redo `insert entry`", ex);
         }
-
-        panel.updateStringDialog();
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/undo/UndoableRemoveString.java b/src/main/java/org/jabref/gui/undo/UndoableRemoveString.java
index 0f82649f521..2c086ed3cf0 100644
--- a/src/main/java/org/jabref/gui/undo/UndoableRemoveString.java
+++ b/src/main/java/org/jabref/gui/undo/UndoableRemoveString.java
@@ -1,6 +1,5 @@
 package org.jabref.gui.undo;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.KeyCollisionException;
@@ -16,13 +15,9 @@ public class UndoableRemoveString extends AbstractUndoableJabRefEdit {
     private final BibDatabase base;
     private final BibtexString string;
 
-    private final BasePanel panel;
-
-    public UndoableRemoveString(BasePanel panel,
-            BibDatabase base, BibtexString string) {
+    public UndoableRemoveString(BibDatabase base, BibtexString string) {
         this.base = base;
         this.string = string;
-        this.panel = panel;
     }
 
     @Override
@@ -33,25 +28,18 @@ public String getPresentationName() {
     @Override
     public void undo() {
         super.undo();
-
         // Revert the change.
         try {
             base.addString(string);
         } catch (KeyCollisionException ex) {
             LOGGER.warn("Problem to undo `remove string`", ex);
         }
-
-        panel.updateStringDialog();
     }
 
     @Override
     public void redo() {
         super.redo();
-
         // Redo the change.
         base.removeString(string.getId());
-
-        panel.updateStringDialog();
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/undo/UndoableStringChange.java b/src/main/java/org/jabref/gui/undo/UndoableStringChange.java
index edcd986833f..9e2c3f0aa49 100644
--- a/src/main/java/org/jabref/gui/undo/UndoableStringChange.java
+++ b/src/main/java/org/jabref/gui/undo/UndoableStringChange.java
@@ -1,6 +1,5 @@
 package org.jabref.gui.undo;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibtexString;
 import org.jabref.model.strings.StringUtil;
@@ -11,24 +10,20 @@ public class UndoableStringChange extends AbstractUndoableJabRefEdit {
     private final String oldValue;
     private final String newValue;
     private final boolean nameChange;
-    private final BasePanel panel;
 
-
-    public UndoableStringChange(BasePanel panel,
-            BibtexString string, boolean nameChange,
-            String oldValue, String newValue) {
+    public UndoableStringChange(BibtexString string, boolean nameChange, String oldValue, String newValue) {
         this.string = string;
         this.oldValue = oldValue;
         this.newValue = newValue;
         this.nameChange = nameChange;
-        this.panel = panel;
     }
 
     @Override
     public String getPresentationName() {
         return (nameChange ? Localization.lang("change string name %0 to %1", StringUtil.boldHTML(oldValue),
-                StringUtil.boldHTML(newValue)) : Localization.lang("change string content %0 to %1",
-                        StringUtil.boldHTML(oldValue), StringUtil.boldHTML(newValue)));
+                                               StringUtil.boldHTML(newValue)) :
+                           Localization.lang("change string content %0 to %1",
+                                             StringUtil.boldHTML(oldValue), StringUtil.boldHTML(newValue)));
     }
 
     @Override
@@ -36,16 +31,11 @@ public void undo() {
         super.undo();
 
         // Revert the change.
-
-        panel.assureStringDialogNotEditing();
-
         if (nameChange) {
             string.setName(oldValue);
         } else {
             string.setContent(oldValue);
         }
-
-        panel.updateStringDialog();
     }
 
     @Override
@@ -53,15 +43,10 @@ public void redo() {
         super.redo();
 
         // Redo the change.
-
-        panel.assureStringDialogNotEditing();
         if (nameChange) {
             string.setName(newValue);
         } else {
             string.setContent(newValue);
         }
-
-        panel.updateStringDialog();
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/util/IconValidationDecorator.java b/src/main/java/org/jabref/gui/util/IconValidationDecorator.java
index 4354f75695b..ada1bf7ab21 100644
--- a/src/main/java/org/jabref/gui/util/IconValidationDecorator.java
+++ b/src/main/java/org/jabref/gui/util/IconValidationDecorator.java
@@ -31,24 +31,28 @@ public IconValidationDecorator(Pos position) {
         this.position = position;
     }
 
+    @Override
     protected Node createErrorNode() {
         return IconTheme.JabRefIcons.ERROR.getGraphicNode();
     }
 
+    @Override
     protected Node createWarningNode() {
         return IconTheme.JabRefIcons.WARNING.getGraphicNode();
     }
 
+    @Override
     public Node createDecorationNode(ValidationMessage message) {
         Node graphic = Severity.ERROR == message.getSeverity() ? createErrorNode() : createWarningNode();
         graphic.getStyleClass().add(Severity.ERROR == message.getSeverity() ? "error-icon" : "warning-icon");
         Label label = new Label();
         label.setGraphic(graphic);
         label.setTooltip(createTooltip(message));
-        label.setAlignment(Pos.CENTER);
+        label.setAlignment(position);
         return label;
     }
 
+    @Override
     protected Tooltip createTooltip(ValidationMessage message) {
         Tooltip tooltip = new Tooltip(message.getText());
         tooltip.getStyleClass().add(Severity.ERROR == message.getSeverity() ? "tooltip-error" : "tooltip-warning");
diff --git a/src/main/java/org/jabref/gui/util/ViewModelTextFieldTableCellVisualizationFactory.java b/src/main/java/org/jabref/gui/util/ViewModelTextFieldTableCellVisualizationFactory.java
new file mode 100644
index 00000000000..fcf93a067b0
--- /dev/null
+++ b/src/main/java/org/jabref/gui/util/ViewModelTextFieldTableCellVisualizationFactory.java
@@ -0,0 +1,54 @@
+package org.jabref.gui.util;
+
+import java.util.function.Function;
+
+import javafx.scene.control.TableCell;
+import javafx.scene.control.TableColumn;
+import javafx.scene.control.cell.TextFieldTableCell;
+import javafx.util.Callback;
+import javafx.util.StringConverter;
+
+import de.saxsys.mvvmfx.utils.validation.ValidationStatus;
+import de.saxsys.mvvmfx.utils.validation.visualization.ControlsFxVisualizer;
+
+public class ViewModelTextFieldTableCellVisualizationFactory<S, T> implements Callback<TableColumn<S, T>, TableCell<S, T>> {
+
+    private ControlsFxVisualizer visualizer;
+    private Function<S, ValidationStatus> validationStatusProperty;
+    private StringConverter<T> stringConverter;
+
+    public ViewModelTextFieldTableCellVisualizationFactory<S, T> withValidation(Function<S, ValidationStatus> validationStatusProperty, ControlsFxVisualizer visualizer) {
+        this.validationStatusProperty = validationStatusProperty;
+        this.visualizer = visualizer;
+        return this;
+    }
+
+    public void install(TableColumn<S, T> column, StringConverter<T> stringConverter) {
+        column.setCellFactory(this);
+        this.stringConverter = stringConverter;
+    }
+
+    @Override
+    public TextFieldTableCell<S, T> call(TableColumn<S, T> param) {
+        return new TextFieldTableCell<S, T>(stringConverter) {
+
+            @Override
+            public void updateItem(T item, boolean empty) {
+                super.updateItem(item, empty);
+
+                if (!empty && (getTableRow() != null)) {
+                    Object rowItem = getTableRow().getItem();
+
+                    if (rowItem != null) {
+                        S vm = (S) rowItem;
+                        if ((visualizer != null) && (validationStatusProperty != null)) {
+                            visualizer.initVisualization(validationStatusProperty.apply(vm), this);
+                        }
+                    }
+                }
+            }
+        };
+
+    }
+
+}
diff --git a/src/main/java/org/jabref/model/database/BibDatabase.java b/src/main/java/org/jabref/model/database/BibDatabase.java
index 40e6abcc0ff..e986136fad2 100644
--- a/src/main/java/org/jabref/model/database/BibDatabase.java
+++ b/src/main/java/org/jabref/model/database/BibDatabase.java
@@ -42,6 +42,7 @@
  * A bibliography database.
  */
 public class BibDatabase {
+
     private static final Logger LOGGER = LoggerFactory.getLogger(BibDatabase.class);
     private static final Pattern RESOLVE_CONTENT_PATTERN = Pattern.compile(".*#[^#]+#.*");
     /**
@@ -131,7 +132,7 @@ public Set<String> getAllVisibleFields() {
             allFields.addAll(e.getFieldNames());
         }
         return allFields.stream().filter(field -> !InternalBibtexFields.isInternalField(field))
-                .collect(Collectors.toSet());
+                        .collect(Collectors.toSet());
     }
 
     /**
@@ -226,7 +227,6 @@ private synchronized void insertEntries(List<BibEntry> newEntries, EntryEventSou
         entries.addAll(newEntries);
     }
 
-
     /**
      * Removes the given entry.
      * The Entry is removed based on the id {@link BibEntry#id}
@@ -287,6 +287,17 @@ public synchronized void addString(BibtexString string) throws KeyCollisionExcep
         bibtexStrings.put(string.getId(), string);
     }
 
+    public void addStrings(Collection<BibtexString> stringsToAdd) {
+        for (BibtexString str : stringsToAdd) {
+            Optional<BibtexString> bibtexString = getStringByName(str.getName());
+            if (bibtexString.isPresent() && !(bibtexString.get().getContent().equals(str.getContent()))) {
+                bibtexString.get().setContent(str.getContent());
+            } else {
+                addString(str);
+            }
+        }
+    }
+
     /**
      * Removes the string with the given id.
      */
@@ -318,15 +329,10 @@ public BibtexString getString(String id) {
     }
 
     /**
-     * Returns the string with the given name.
+     * Returns the string with the given name/label
      */
     public Optional<BibtexString> getStringByName(String name) {
-        for (BibtexString string : getStringValues()) {
-            if (string.getName().equals(name)) {
-                return Optional.of(string);
-            }
-        }
-        return Optional.empty();
+        return getStringValues().stream().filter(string -> string.getName().equals(name)).findFirst();
     }
 
     /**
@@ -356,12 +362,7 @@ public void copyPreamble(BibDatabase database) {
      * Returns true if a string with the given label already exists.
      */
     public synchronized boolean hasStringLabel(String label) {
-        for (BibtexString value : bibtexStrings.values()) {
-            if (value.getName().equals(label)) {
-                return true;
-            }
-        }
-        return false;
+        return bibtexStrings.values().stream().anyMatch(value -> value.getName().equals(label));
     }
 
     /**
@@ -615,5 +616,4 @@ public String generateSharedDatabaseID() {
     public DuplicationChecker getDuplicationChecker() {
         return duplicationChecker;
     }
-
 }
diff --git a/src/main/java/org/jabref/model/entry/BibtexString.java b/src/main/java/org/jabref/model/entry/BibtexString.java
index 52268364cd3..551dc749ad4 100644
--- a/src/main/java/org/jabref/model/entry/BibtexString.java
+++ b/src/main/java/org/jabref/model/entry/BibtexString.java
@@ -7,6 +7,7 @@
  * This class models a BibTex String ("@String")
  */
 public class BibtexString implements Cloneable {
+
     /**
      * Type of a \@String.
      * <p>
@@ -95,6 +96,10 @@ public void setId(String id) {
         hasChanged = true;
     }
 
+    /**
+     * Returns the name/label of the string
+     * @return
+     */
     public String getName() {
         return name;
     }
@@ -176,16 +181,16 @@ public boolean equals(Object o) {
         if (this == o) {
             return true;
         }
-        if (o == null || getClass() != o.getClass()) {
+        if ((o == null) || (getClass() != o.getClass())) {
             return false;
         }
         BibtexString that = (BibtexString) o;
-        return hasChanged == that.hasChanged &&
+        return (Objects.equals(hasChanged,that.hasChanged) &&
                 Objects.equals(name, that.name) &&
                 Objects.equals(content, that.content) &&
-                Objects.equals(id, that.id) &&
-                type == that.type &&
-                Objects.equals(parsedSerialization, that.parsedSerialization);
+                Objects.equals(id, that.id)  &&
+                Objects.equals(type, that.type) &&
+                Objects.equals(parsedSerialization, that.parsedSerialization));
     }
 
     @Override
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index fdeac656d76..634a80d312c 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -253,8 +253,6 @@ Delete\ multiple\ entries=Delete multiple entries
 
 Delete\ rows=Delete rows
 
-Delete\ strings=Delete strings
-
 Deleted=Deleted
 
 Permanently\ delete\ local\ file=Permanently delete local file
@@ -1400,7 +1398,6 @@ Toggle\ print\ status=Toggle print status
 Update\ keywords=Update keywords
 Write\ values\ of\ special\ fields\ as\ separate\ fields\ to\ BibTeX=Write values of special fields as separate fields to BibTeX
 You\ have\ changed\ settings\ for\ special\ fields.=You have changed settings for special fields.
-A\ string\ with\ that\ label\ already\ exists=A string with that label already exists
 Connection\ to\ OpenOffice/LibreOffice\ has\ been\ lost.\ Please\ make\ sure\ OpenOffice/LibreOffice\ is\ running,\ and\ try\ to\ reconnect.=Connection to OpenOffice/LibreOffice has been lost. Please make sure OpenOffice/LibreOffice is running, and try to reconnect.
 JabRef\ will\ send\ at\ least\ one\ request\ per\ entry\ to\ a\ publisher.=JabRef will send at least one request per entry to a publisher.
 Correct\ the\ entry,\ and\ reopen\ editor\ to\ display/edit\ source.=Correct the entry, and reopen editor to display/edit source.
@@ -2174,3 +2171,8 @@ File\ extension\:=File extension\:
 Export\ format\ name\:=Export format name\:
 Cleared\ connection\ settings=Cleared connection settings
 Error\ adding\ discovered\ CitationStyles=Error adding discovered CitationStyles
+
+Add\ new\ String=Add new String
+Remove\ selected\ Strings=Remove selected Strings
+Must\ not\ be\ empty\!=Must not be empty\!
+Open\ Help\ page=Open Help page
\ No newline at end of file
diff --git a/src/test/java/org/jabref/model/database/BibDatabaseTest.java b/src/test/java/org/jabref/model/database/BibDatabaseTest.java
index 364c42c54b3..d5632433ff1 100644
--- a/src/test/java/org/jabref/model/database/BibDatabaseTest.java
+++ b/src/test/java/org/jabref/model/database/BibDatabaseTest.java
@@ -122,6 +122,32 @@ public void hasStringLabelFindsString() {
         assertFalse(database.hasStringLabel("VLSI"));
     }
 
+    @Test
+    public void addStringAsCollection() {
+        BibtexString string = new BibtexString("DSP", "Digital Signal Processing");
+        List<BibtexString> strings = Arrays.asList(string);
+        database.addStrings(strings);
+        assertEquals(Optional.of(string), database.getStringByName("DSP"));
+    }
+
+    @Test
+    public void addStringAsCollectionWithUpdatedContent() {
+        BibtexString string = new BibtexString("DSP", "Digital Signal Processing");
+        List<BibtexString> strings = Arrays.asList(string, new BibtexString("DSP", "ABCD"));
+        database.addStrings(strings);
+        assertEquals(Optional.of(string), database.getStringByName("DSP"));
+    }
+
+    @Test
+    public void addStringAsCollectionWithNewContent() {
+        BibtexString string = new BibtexString("DSP", "Digital Signal Processing");
+        BibtexString vlsi = new BibtexString("VLSI", "Very Large Scale Integration");
+        List<BibtexString> strings = Arrays.asList(string, vlsi);
+        database.addStrings(strings);
+        assertEquals(Optional.of(string), database.getStringByName("DSP"));
+        assertEquals(Optional.of(vlsi), database.getStringByName("VLSI"));
+    }
+
     @Test
     public void addSameStringLabelTwiceThrowsKeyCollisionException() {
         BibtexString string = new BibtexString("DSP", "Digital Signal Processing");

From 06ed9ec5cf221630ef7a1e88f7a3aba99a54c6aa Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 18 Feb 2019 15:56:36 +0100
Subject: [PATCH 036/184] fix package error move setValues method to
 constructor create fxml draft for save order config

---
 .../jabref/gui/SaveOrderConfigDisplay.fxml    | 40 +++++++++++++++++++
 .../gui/SaveOrderConfigDisplayViewModel.java  |  6 +++
 .../LibraryPropertiesDialog.fxml              |  2 +-
 .../LibraryPropertiesDialogView.java          |  1 -
 .../LibraryPropertiesDialogViewModel.java     | 36 ++++++++---------
 5 files changed, 64 insertions(+), 21 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
 create mode 100644 src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
new file mode 100644
index 00000000000..db0e2b2ed37
--- /dev/null
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.CheckBox?>
+<?import javafx.scene.control.ComboBox?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.control.RadioButton?>
+<?import javafx.scene.layout.ColumnConstraints?>
+<?import javafx.scene.layout.GridPane?>
+<?import javafx.scene.layout.RowConstraints?>
+
+
+<GridPane prefHeight="400.0" prefWidth="600.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1">
+  <columnConstraints>
+    <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="100.0" />
+    <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
+      <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
+  </columnConstraints>
+  <rowConstraints>
+    <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
+    <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
+      <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
+      <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
+      <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
+      <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
+  </rowConstraints>s
+   <children>
+      <ComboBox fx:id="savePriSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="3" />
+      <ComboBox fx:id="saveSecSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="4" />
+      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2" />
+      <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="Export in current table sort order" GridPane.columnSpan="3" GridPane.rowIndex="1" />
+      <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="Export entries in their original order" GridPane.columnSpan="3" />
+      <ComboBox fx:id="saveTerSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="5" />
+      <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" />
+      <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" />
+      <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" />
+      <Label text="Primary sort criterion" GridPane.rowIndex="3" />
+      <Label text="Secondary sort criterion" GridPane.rowIndex="4" />
+      <Label text="Tertiary sort criterion" GridPane.rowIndex="5" />
+   </children>
+</GridPane>
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
new file mode 100644
index 00000000000..b1aec9486e8
--- /dev/null
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
@@ -0,0 +1,6 @@
+package org.jabref.gui;
+
+
+public class SaveOrderConfigDisplayViewModel {
+
+}
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
index 6913c862d78..d69795354af 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
@@ -17,7 +17,7 @@
 <?import javafx.scene.layout.RowConstraints?>
 <?import javafx.scene.layout.VBox?>
 
-<DialogPane minHeight="-Infinity" prefHeight="784.0" prefWidth="921.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.dbproperties.LibraryPropertiesDialogView">
+<DialogPane minHeight="-Infinity" prefHeight="784.0" prefWidth="921.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.libraryproperties.LibraryPropertiesDialogView">
    <content>
       <VBox fx:id="contentVbox" minHeight="-Infinity" prefHeight="200.0" prefWidth="100.0">
          <children>
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
index d6a8796466c..e14bf7b6f49 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
@@ -96,7 +96,6 @@ private void initialize() {
 
     private void setValues() {
 
-        viewModel.setValues();
         Optional<SaveOrderConfig> storedSaveOrderConfig = panel.getBibDatabaseContext().getMetaData().getSaveOrderConfig();
         boolean selected;
         if (!storedSaveOrderConfig.isPresent()) {
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
index b51d688aff6..d63dca01b96 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
@@ -35,9 +35,9 @@ public class LibraryPropertiesDialogViewModel {
     private final MetaData metaData;
     private final PreferencesService preferencesService;
 
-    private String oldUserSpecificFileDir;
-    private String oldGeneralFileDir;
-    private boolean oldLibraryProtected;
+    private final String oldUserSpecificFileDir;
+    private final String oldGeneralFileDir;
+    private final boolean oldLibraryProtected;
 
     public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogService, PreferencesService preferencesService) {
         this.dialogService = dialogService;
@@ -47,6 +47,20 @@ public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogSer
         directoryDialogConfiguration = new DirectoryDialogConfiguration.Builder()
                                                                                  .withInitialDirectory(preferencesService.getWorkingDir()).build();
 
+        Optional<Charset> charset = metaData.getEncoding();
+        selectedEncodingPropety.setValue(charset.orElse(preferencesService.getDefaultEncoding()));
+
+        Optional<String> fileD = metaData.getDefaultFileDirectory();
+        fileD.ifPresent(path -> generalFileDirectoryProperty.setValue(path.trim()));
+
+        Optional<String> fileDI = metaData.getUserFileDirectory(preferencesService.getUser());
+        fileDI.ifPresent(userSpecificFileDirectoryProperty::setValue);
+
+        oldUserSpecificFileDir = generalFileDirectoryProperty.getValue();
+        oldGeneralFileDir = userSpecificFileDirectoryProperty.getValue();
+
+        libraryProtectedProperty.setValue(metaData.isProtected());
+        oldLibraryProtected = libraryProtectedProperty.getValue();
     }
 
     public StringProperty generalFileDirectoryPropertyProperty() {
@@ -86,22 +100,6 @@ public BooleanProperty libraryProtectedProperty() {
         return this.libraryProtectedProperty;
     }
 
-    public void setValues() {
-        Optional<Charset> charset = metaData.getEncoding();
-        selectedEncodingPropety.setValue(charset.orElse(preferencesService.getDefaultEncoding()));
-
-        Optional<String> fileD = metaData.getDefaultFileDirectory();
-        fileD.ifPresent(path -> generalFileDirectoryProperty.setValue(path.trim()));
-
-        Optional<String> fileDI = metaData.getUserFileDirectory(preferencesService.getUser());
-        fileDI.ifPresent(userSpecificFileDirectoryProperty::setValue);
-
-        oldUserSpecificFileDir = generalFileDirectoryProperty.getValue();
-        oldGeneralFileDir = userSpecificFileDirectoryProperty.getValue();
-
-        libraryProtectedProperty.setValue(metaData.isProtected());
-        oldLibraryProtected = libraryProtectedProperty.getValue();
-    }
 
     public boolean generalFileDirChanged() {
         return !oldGeneralFileDir.equals(generalFileDirectoryProperty.getValue());

From 3a807eaca83b62a6e25b533f0ff83cdffe0b8e57 Mon Sep 17 00:00:00 2001
From: Jure Slak <jure.slak@gmail.com>
Date: Mon, 18 Feb 2019 17:08:22 +0100
Subject: [PATCH 037/184] Fix issues with double spaces. (#4662)

I noticed that "Applied numerical mathematics" was not abbreviating and found that this is most likely die to a double space present in its name. I also fixed other occurrences.
---
 src/main/resources/journals/journalList.txt | 44 ++++++++++-----------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/src/main/resources/journals/journalList.txt b/src/main/resources/journals/journalList.txt
index c2db98e8d68..389c94551de 100644
--- a/src/main/resources/journals/journalList.txt
+++ b/src/main/resources/journals/journalList.txt
@@ -1384,7 +1384,7 @@ Applied Mechanics Reviews = Appl. Mech. Rev.
 Applied Microbiology = Appl. Microbiol.
 Applied Microbiology and Biotechnology = Appl. Microbiol. Biotechnol.
 Applied Neurophysiology = Appl. Neurophysiol.
-Applied Numerical  Mathematics = Appl. Numer. Math.
+Applied Numerical Mathematics = Appl. Numer. Math.
 Applied Nursing Research = Appl. Nurs. Res.
 Applied Ocean Research = Appl. Ocean Res.
 Applied Optics = Appl. Opt.
@@ -1974,7 +1974,7 @@ Berg- und Huettenmaennische Monatshefte = Berg- Huettenmaenn. Monatsh.
 Bericht uber die Zusammenkunft der Deutschen Ophthalmologischen Gesellschaft = Ber. Zusammenkunft Dtsch. Ophthalmol. Ges.
 Berichte aus der Bonner Universitatsklinik und Poliklinik fur Mund-, Zahn- und Kieferkrankheiten = Ber. Bonn. Univ. Poliklin. Mund. Zahn. Kieferkr.
 Berichte der Bunsen-Gesellschaft = Ber. Bunsen Ges.
-Berichte der Bunsen-Gesellschaft fur Physikalische Chemie = Ber. Bunsen Ges.  Phys. Chem.
+Berichte der Bunsen-Gesellschaft fur Physikalische Chemie = Ber. Bunsen Ges. Phys. Chem.
 Berichte der Deutschen Botanischen Gesellschaft = Ber. Dtsch. Bot. Ges.
 Berichte der Deutschen Chemischen Gesellschaft = Ber. Dtsch. Chem. Ges.
 Berichte der Deutschen Gesellschaft fur Geologische Wissenschaft Reihe A: Geologie und Palaeontologie = Ber. Dtsch. Ges. Geol. Wiss. Reihe A
@@ -2404,7 +2404,7 @@ Bordeaux Medical = Bord. Med.
 Borden's Review of Nutrition Research = Bordens Rev. Nutr. Res.
 Boreal Environment Research = Boreal Environ. Res.
 Bornetandlaegen = Bornetandlaegen
-Botanical Museum Leaflets, Harvard University = Bot. Mus. Leafl.  Harv. Univ.
+Botanical Museum Leaflets, Harvard University = Bot. Mus. Leafl. Harv. Univ.
 Botanical Review = Bot. Rev.
 Boundary-Layer Meteorology = Boundary Layer Meteorol.
 Brachytherapy = Brachytherapy
@@ -3083,7 +3083,7 @@ Chang Gung Medical Journal = Chang Gung Med. J.
 Change = Change
 Changgeng Yi Xue Za Zhi (Chang Gung Medical Journal) = Changgeng Yi Xue Za Zhi
 Changing Times = Changing Times
-Chaos, Solitons & Fractals = Chaos, Solitons  Fractals
+Chaos, Solitons & Fractals = Chaos, Solitons Fractals
 Chart = Chart
 Chem-Bio Informatics Journal = Chem-Bio Inf. J.
 Chembiochem = Chembiochem
@@ -3522,7 +3522,7 @@ Colorado Nurse = Colo. Nurse
 Coloration Technology = Color. Technol.
 Columbia Law Review = Columbia Law Rev.
 Columbus Dental Society Bulletin = Columbus Dent. Soc. Bull.
-Combinatorial Chemistry  -  an Online Journal = Comb. Chem.
+Combinatorial Chemistry - an Online Journal = Comb. Chem.
 Combinatorial Chemistry and High Throughput Screening = Comb. Chem. High Throughput Screening
 Combinatorics, Probability and Computing = Comb. Probab. Comput.
 Combustion and Flame = Combust. Flame
@@ -4617,7 +4617,7 @@ Environmental Conservation = Environ. Conserv.
 Environmental Control in Biology = Environ. Control. Biol.
 Environmental Engineering and Management Journal = Environ. Eng. Manage. J.
 Environmental Engineering and Policy = Environ. Eng. Policy
-Environmental Engineering Research = Environ.  Eng. Res.
+Environmental Engineering Research = Environ. Eng. Res.
 Environmental Engineering Science = Environ. Eng. Sci.
 Environmental Fluid Mechanics = Environ. Fluid Mech.
 Environmental Forensics = Environ. Forensics
@@ -7017,8 +7017,8 @@ Iranian Polymer Journal = Iran. Polym. J.
 Iraqi Dental Journal = Iraqi Dent. J.
 IRB; A Review of Human Subjects Research = IRB.
 IRCS Journal of Medical Science = IRCS J. Med. Sci.
-IRE Transactions on  Industrial Electronics = IRE Trans. Ind. Electron.
-IRE Transactions on  Information Theory = IRE Trans. Inf. Theory
+IRE Transactions on Industrial Electronics = IRE Trans. Ind. Electron.
+IRE Transactions on Information Theory = IRE Trans. Inf. Theory
 IRE Transactions on Aeronautical and Navigational Electronics = IRE Trans. Aeronaut. Navig. Electron.
 IRE Transactions on Aerospace and Navigational Electronics = IRE Trans. Aerosp. Navig. Electron.
 IRE Transactions on Antennas and Propagation = IRE Trans. Anntenas Propag.
@@ -7282,7 +7282,7 @@ Journal fur Landwirtschaft = J. Landwirtschaft
 Journal fur Praktische Chemie = J. Prakt. Chem.
 Journal fur Verbraucherschutz und Lebensmittelsicherheit = J. Verbraucherschutz Lebensmittelsicherh.
 Journal Medical Libanais (Lebanese Medical Journal) = J. Med. Liban.
-Journal of  Circadian Rhythms = J. Circadian Rhythms
+Journal of Circadian Rhythms = J. Circadian Rhythms
 Journal of AAPOS = J. AAPOS
 Journal of Abnormal Child Psychology = J. Abnorm. Child Psychol.
 Journal of Abnormal Psychology = J. Abnorm. Psychol.
@@ -8081,7 +8081,7 @@ Journal of Hospital Dental Practice = J. Hosp. Dent. Pract.
 Journal of Hospital Infection = J. Hosp. Infect.
 Journal of Hospital Marketing = J. Hosp. Mark.
 Journal of Hospital Supply, Processing and Distribution = J. Hosp. Supply. Process. Distrib.
-Journal of Housing and the Built Environment = J. Hous. Built  Environ.
+Journal of Housing and the Built Environment = J. Hous. Built. Environ.
 Journal of Huazhong University of Science and Technology. Medical Sciences = J. Huazhong Univ. Sci. Technolog. Med. Sci.
 Journal of Human Ergology = J. Hum. Ergol. (Tokyo)
 Journal of Human Evolution = J. Hum. Evol.
@@ -9322,7 +9322,7 @@ Journal of Vector Borne Diseases = J. Vector Borne Dis.
 Journal of Vector Ecology = J. Vector Ecol.
 Journal of Vegetation Science = J. Veg. Sci.
 Journal of Venomous Animals and Toxins Including Tropical Diseases = J. Venomous Anim. Toxins Incl. Trop. Dis.
-Journal of Vertebrate Paleontology = J. Vertebr.  Paleontol.
+Journal of Vertebrate Paleontology = J. Vertebr. Paleontol.
 Journal of Vestibular Research = J. Vestib. Res.
 Journal of Veterinary Dentistry = J. Vet. Dent.
 Journal of Veterinary Diagnostic Investigation = J. Vet. Diagn. Invest.
@@ -10543,13 +10543,13 @@ Mutation Research = Mutat. Res.
 Mutation Research Letters = Mutat. Res. Lett.
 Mutation Research, DNA Repair = Mutat. Res. DNA Repair
 Mutation Research, DNA Repair Reports = Mutat. Res. DNA Repair Rep.
-Mutation Research, DNAging: Genetic Instability and Aging = Mutat. Res.  DNAging: Genet. Instab. Aging
+Mutation Research, DNAging: Genetic Instability and Aging = Mutat. Res. DNAging: Genet. Instab. Aging
 Mutation Research, Environmental Mutagenesis and Related Subjects = Mutat. Res. Environ. Mutagen. Relat. Subj.
 Mutation Research, Fundamental and Molecular Mechanisms of Mutagenesis = Mutat. Res. Fundam. Mol. Mech. Mutagen.
 Mutation Research, Genetic Toxicology = Mutat. Res. Genet. Toxicol.
 Mutation Research, Genetic Toxicology and Environmental Mutagenesis = Mutat. Res. Genet. Toxicol. Environ. Mutagen.
 Mutation Research, Genetic Toxicology Testing = Mutat. Res. Genet. Toxicol. Test.
-Mutation Research, Mutation Research Genomics = Mutat. Res.  Mutat. Res. Genomics
+Mutation Research, Mutation Research Genomics = Mutat. Res. Mutat. Res. Genomics
 Mutation Research, Reviews in Genetic Toxicology = Mutat. Res. Rev. Genet. Toxicol.
 Mutation Research, Reviews in Mutation Research = Mutat. Res. Rev. Mutat. Res.
 Mycologia = Mycologia
@@ -10711,7 +10711,7 @@ Naturwissenschaftliche Wochenschrift = Naturwiss. Wochenschr.
 Nauchni Trudove na Nauchno-Izsledovatelskiia Stomatologichen Institut = Nauchni Tr. Nauchnoizsled. Stomatol. Inst. (Sofiia)
 Nauchni Trudove na Visshiia Meditsinski Institut, Sofiia = Nauchni Tr. Vissh. Med. Inst. Sofiia
 Naunyn-Schmiedeberg's Archives of Pharmacology = Naunyn. Schmiedebergs Arch. Pharmacol.
-Naunyn-Schmiedebergs Archiv fur Experimentelle Pathologie und  Pharmacologie = Naunyn-Schmiedeberg's Arch. Exp. Pathol. Pharmacol.
+Naunyn-Schmiedebergs Archiv fur Experimentelle Pathologie und Pharmacologie = Naunyn-Schmiedeberg's Arch. Exp. Pathol. Pharmacol.
 Naunyn-Schmiedebergs Archiv fur Experimentelle Pathologie und Pharmakologie = Naunyn. Schmiedebergs Arch. Exp. Pathol. Pharmakol.
 Naunyn-Schmiedebergs Archiv fur Pharmakologie = Naunyn. Schmiedebergs Arch. Pharmakol.
 Naval Engineers Journal = Nav. Eng. J.
@@ -11519,7 +11519,7 @@ Pakistan Nursing and Health Review = Pak. Nurs. Health Rev.
 Palaeogeography, Palaeoclimatology, Palaeoecology = Palaeogeogr. Palaeoclimatol. Palaeoecol.
 Palaeontologia Electronica = Palaeontol. Electronica
 Palaeontologische Zeitschrift = Palaentolog. Z.
-PalArch's Journal of Vertebrate Palaeontology = PalArch's J.  Vertebr. Palaeontol.
+PalArch's Journal of Vertebrate Palaeontology = PalArch's J. Vertebr. Palaeontol.
 Paleontological Bulletin = Paleontol. Bull.
 Paleontological Journal = Paleontolog. J.
 Paleontological Research = Paleontolog. Res.
@@ -11956,7 +11956,7 @@ PLoS Biology = PLoS Biol.
 PLoS Clinical Trials = PLoS Clin. Trials
 PLoS Computational Biology = PLoS Comput. Biol.
 PLOS Currents: Disasters = PLOS Curr.: Disasters
-PLOS Currents: Evidence on Genomic Tests = PLOS Curr.:  Evidence Genomic Tests
+PLOS Currents: Evidence on Genomic Tests = PLOS Curr.: Evidence Genomic Tests
 PLOS Currents: Huntington Disease = PLOS Curr.: Huntington Dis.
 PLOS Currents: Muscular Dystrophy = PLOS Curr.: Muscular Dystrophy
 PLOS Currents: Outbreaks = PLOS Curr.: Outbreaks
@@ -13202,7 +13202,7 @@ Rhode Island Medicine = R. I. Med.
 Rhodesia Nurse = Rhod. Nurse
 Rhodesian Nurse = Rhod. Nurse
 Rhumatologie = Rhumatologie
-RIAI  Revista Iberoamericana de Automatica e Informatica Industrial = Rev. Iberoam. Autom. Inf. Ind.
+RIAI Revista Iberoamericana de Automatica e Informatica Industrial = Rev. Iberoam. Autom. Inf. Ind.
 RIC Reviews = RIC Rev.
 Rice Science = Rice Sci.
 Ricerca in Clinica e in Laboratorio = Ric. Clin. Lab.
@@ -13483,7 +13483,7 @@ Science = Science
 Science Advances = Sci. Adv.
 Science and Justice = Sci. Justice
 Science and Technology of Advanced Materials = Sci. Technol. Adv. Mater.
-Science and Technology of Archaeological Research = Sci. Technol.  Archaeolog. Res.
+Science and Technology of Archaeological Research = Sci. Technol. Archaeolog. Res.
 Science and Technology of Energetic Materials = Sci. Technol. Energetic Mater.
 Science and Technology of Welding and Joining = Sci. Technol. Weld. Joining
 Science China Materials = Sci. China Mater.
@@ -13945,7 +13945,7 @@ Strength of Materials = Strength Mater.
 Stress = Stress
 Stroke = Stroke
 Struct.--Process., Meas., Phenom. Journal of Vacuum Science & Technology, B: Microelectronics and Nanometer Structures--Processing, Measurement, and Phenomena = J. Vac. Sci. Technol., B: Microelectron. Nanometer
-Structural and Multidisciplinary Optimization = Struct. Multidiscip.  Optim.
+Structural and Multidisciplinary Optimization = Struct. Multidiscip. Optim.
 Structural Chemistry = Struct. Chem.
 Structural Design of Tall and Special Buildings = Struct. Des. Tall Special Build.
 Structural Safety = Struct. Saf.
@@ -14395,7 +14395,7 @@ Transition Metal Chemistry = Transition Met. Chem.
 Translational Materials Research = Transl. Mater. Res.
 Translational Oncology = Trans. Oncol.
 Translational Proteomics = Transl. Proteomics
-Translational Psychiatry = Transl.  Psychiatry
+Translational Psychiatry = Transl. Psychiatry
 Translational Research = Transl. Res.
 Transplant Immunology = Transpl. Immunol.
 Transplant Infectious Disease = Transpl. Infect. Dis.
@@ -14590,7 +14590,7 @@ Vascular Pharmacology = Vascul. Pharmacol.
 Vascular Surgery = Vasc. Surg.
 Vecteur Environnement = Vecteur Environ.
 Vector Borne and Zoonotic Diseases = Vector Borne Zoonotic Dis.
-Vegetable Crops Research Bulletin = Veg. Crops  Res. Bull.
+Vegetable Crops Research Bulletin = Veg. Crops. Res. Bull.
 Vehicle System Dynamics = Veh. Syst. Dyn.
 Vehicular Communications = Veh. Commun.
 Venezuela Odontologica = Venez. Odontol.
@@ -14755,7 +14755,7 @@ Water Quality and Ecosystems Modeling = Water Qual. Ecosyst. Model.
 Water Quality Research Journal of Canada = Water Qual. Res. J. Can.
 Water Quality, Exposure and Health = Water Qual. Exposure Health
 Water Research = Water Res.
-Water Resources  Investigations Report (united States Geological Survey) = Water Resour. Invest. Rep. U.S. Geol. Surv.
+Water Resources Investigations Report (united States Geological Survey) = Water Resour. Invest. Rep. U.S. Geol. Surv.
 Water Resources = Water Resour.
 Water Resources and Economics = Water Resour. Econ.
 Water Resources and Industry = Water Resour. Ind.

From 7e1bf18f9bb02439133d7e9a270ae0cd24d95a8b Mon Sep 17 00:00:00 2001
From: ricantech <michal.rican@gmail.com>
Date: Mon, 18 Feb 2019 22:11:09 +0100
Subject: [PATCH 038/184] Fix for #4628 - cant save new content selectors
 (#4658)

* Design of content selector dialog + initial view commit

* Restyle dialog design + add basic functionalities for field names

* Add logic regarding keywords

* Minor rework of keywords logic + toggling of delete button

* Unify naming convention

* Logic tuneup

* Add english translations

* Add translations + imports

* Convert ObservableList into ListProperty - review changes

* Rework actions on bindings instead of using directly change listener - review changes

* Replace setting of first element with built-in method in selection model

* Use Inject for DialogService
---
 src/main/java/org/jabref/gui/BasePanel.java   |   6 -
 src/main/java/org/jabref/gui/JabRefFrame.java |   3 +-
 .../actions/ManageContentSelectorAction.java  |  29 +
 .../ContentSelectorDialog.fxml                |  67 +++
 .../ContentSelectorDialog.java                | 499 ------------------
 .../ContentSelectorDialogView.java            | 122 +++++
 .../ContentSelectorDialogViewModel.java       | 213 ++++++++
 src/main/resources/l10n/JabRef_en.properties  |  19 +-
 8 files changed, 447 insertions(+), 511 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/actions/ManageContentSelectorAction.java
 create mode 100644 src/main/java/org/jabref/gui/contentselector/ContentSelectorDialog.fxml
 delete mode 100644 src/main/java/org/jabref/gui/contentselector/ContentSelectorDialog.java
 create mode 100644 src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogView.java
 create mode 100644 src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogViewModel.java

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index ef5e2875994..8c99cc4a68a 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -43,7 +43,6 @@
 import org.jabref.gui.bibtexkeypattern.SearchFixDuplicateLabels;
 import org.jabref.gui.collab.DatabaseChangeMonitor;
 import org.jabref.gui.collab.FileUpdatePanel;
-import org.jabref.gui.contentselector.ContentSelectorDialog;
 import org.jabref.gui.desktop.JabRefDesktop;
 import org.jabref.gui.edit.ReplaceStringAction;
 import org.jabref.gui.entryeditor.EntryEditor;
@@ -399,11 +398,6 @@ private void setupActions() {
         actions.put(Actions.NEXT_PREVIEW_STYLE, this::nextPreviewStyle);
         actions.put(Actions.PREVIOUS_PREVIEW_STYLE, this::previousPreviewStyle);
 
-        actions.put(Actions.MANAGE_SELECTORS, () -> {
-            ContentSelectorDialog csd = new ContentSelectorDialog(frame, BasePanel.this, false, null);
-            csd.setVisible(true);
-        });
-
         actions.put(Actions.SEND_AS_EMAIL, new SendAsEMailAction(frame));
 
         actions.put(Actions.WRITE_XMP, new WriteXMPAction(this)::execute);
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index b657ee1e1db..dbbce3f23b3 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -64,6 +64,7 @@
 import org.jabref.gui.actions.EditExternalFileTypesAction;
 import org.jabref.gui.actions.ErrorConsoleAction;
 import org.jabref.gui.actions.LookupIdentifierAction;
+import org.jabref.gui.actions.ManageContentSelectorAction;
 import org.jabref.gui.actions.ManageCustomExportsAction;
 import org.jabref.gui.actions.ManageCustomImportsAction;
 import org.jabref.gui.actions.ManageJournalsAction;
@@ -941,7 +942,7 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.MANAGE_CONTENT_SELECTORS, new OldDatabaseCommandWrapper(Actions.MANAGE_SELECTORS, this, Globals.stateManager)),
+                factory.createMenuItem(StandardActions.MANAGE_CONTENT_SELECTORS, new ManageContentSelectorAction(this)),
                 factory.createMenuItem(StandardActions.CUSTOMIZE_ENTRY_TYPES, new CustomizeEntryAction(this)),
                 factory.createMenuItem(StandardActions.MANAGE_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this)));
 
diff --git a/src/main/java/org/jabref/gui/actions/ManageContentSelectorAction.java b/src/main/java/org/jabref/gui/actions/ManageContentSelectorAction.java
new file mode 100644
index 00000000000..31e2b1e1149
--- /dev/null
+++ b/src/main/java/org/jabref/gui/actions/ManageContentSelectorAction.java
@@ -0,0 +1,29 @@
+package org.jabref.gui.actions;
+
+import org.jabref.gui.BasePanel;
+import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.contentselector.ContentSelectorDialogView;
+import org.jabref.logic.l10n.Localization;
+
+public class ManageContentSelectorAction extends SimpleCommand {
+
+    private final JabRefFrame jabRefFrame;
+
+    public ManageContentSelectorAction(JabRefFrame jabRefFrame) {
+        this.jabRefFrame = jabRefFrame;
+    }
+
+    @Override
+    public void execute() {
+        BasePanel basePanel = jabRefFrame.getCurrentBasePanel();
+        if (noActiveConnectionExists(basePanel)) {
+            jabRefFrame.getDialogService().showErrorDialogAndWait(Localization.lang("Active database connection do not exists!"));
+            return;
+        }
+        new ContentSelectorDialogView(basePanel).showAndWait();
+    }
+
+    private boolean noActiveConnectionExists(BasePanel basePanel) {
+        return basePanel == null || basePanel.getBibDatabaseContext() == null;
+    }
+}
diff --git a/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialog.fxml b/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialog.fxml
new file mode 100644
index 00000000000..94744038b42
--- /dev/null
+++ b/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialog.fxml
@@ -0,0 +1,67 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.geometry.Insets?>
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.ButtonType?>
+<?import javafx.scene.control.DialogPane?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.control.ListView?>
+<?import javafx.scene.control.Separator?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
+
+<DialogPane minHeight="450.0" minWidth="375.0" prefHeight="450.0" prefWidth="407.0" xmlns="http://javafx.com/javafx/8.0.172-ea" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.contentselector.ContentSelectorDialogView">
+    <content>
+        <VBox>
+         <children>
+            <Label prefHeight="27.0" prefWidth="108.0" text="Field names" />
+            <HBox prefHeight="140.0" prefWidth="385.0">
+               <children>
+                  <ListView fx:id="fieldNamesListView" prefHeight="140.0" prefWidth="297.0"/>
+                  <VBox alignment="TOP_CENTER" prefHeight="200.0" prefWidth="100.0">
+                     <children>
+                        <Button fx:id="addFieldNameButton" alignment="CENTER" mnemonicParsing="false" prefHeight="26.0" prefWidth="72.0" text="%Add" onAction="#addNewFieldName">
+                           <VBox.margin>
+                              <Insets top="5.0" />
+                           </VBox.margin>
+                        </Button>
+                        <Button fx:id="removeFieldNameButton" mnemonicParsing="false" text="%Remove" onAction="#removeFieldName">
+                           <VBox.margin>
+                              <Insets top="5.0" />
+                           </VBox.margin>
+                        </Button>
+                     </children>
+                  </VBox>
+               </children>
+            </HBox>
+            <Separator prefWidth="200.0">
+               <VBox.margin>
+                  <Insets top="20.0" />
+               </VBox.margin>
+            </Separator>
+             <Label prefHeight="27.0" prefWidth="108.0" text="Keywords" />
+             <HBox prefHeight="140.0" prefWidth="385.0">
+                 <children>
+                     <ListView fx:id="keywordsListView" prefHeight="140.0" prefWidth="297.0" />
+                     <VBox alignment="TOP_CENTER" prefHeight="200.0" prefWidth="100.0">
+                         <children>
+                             <Button fx:id="addKeywordButton" alignment="CENTER" mnemonicParsing="false" prefHeight="26.0" prefWidth="72.0" text="%Add" onAction="#addNewKeyword">
+                                 <VBox.margin>
+                                     <Insets top="5.0" />
+                                 </VBox.margin>
+                             </Button>
+                             <Button fx:id="removeKeywordButton" mnemonicParsing="false" text="%Remove" onAction="#removeKeyword">
+                                 <VBox.margin>
+                                     <Insets top="5.0" />
+                                 </VBox.margin>
+                             </Button>
+                         </children>
+                     </VBox>
+                 </children>
+             </HBox>
+         </children>
+        </VBox>
+    </content>
+    <ButtonType fx:id="saveButton" buttonData="OK_DONE" text="%Save" />
+    <ButtonType fx:constant="CANCEL" />
+</DialogPane>
diff --git a/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialog.java b/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialog.java
deleted file mode 100644
index a188c1fca8a..00000000000
--- a/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialog.java
+++ /dev/null
@@ -1,499 +0,0 @@
-package org.jabref.gui.contentselector;
-
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.BorderFactory;
-import javax.swing.DefaultListModel;
-import javax.swing.JButton;
-import javax.swing.JList;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTextField;
-
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.JabRefDialog;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.help.HelpAction;
-import org.jabref.gui.keyboard.KeyBinder;
-import org.jabref.logic.help.HelpFile;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.entry.FieldName;
-import org.jabref.model.metadata.ContentSelector;
-import org.jabref.model.metadata.ContentSelectors;
-import org.jabref.model.metadata.MetaData;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class ContentSelectorDialog extends JabRefDialog {
-
-    private static final String WORD_FIRSTLINE_TEXT = Localization.lang("<select word>");
-    private static final String FIELD_FIRST_LINE = Localization.lang("<field name>");
-    private static final Logger LOGGER = LoggerFactory.getLogger(ContentSelectorDialog.class);
-    private final GridBagLayout gbl = new GridBagLayout();
-    private final GridBagConstraints con = new GridBagConstraints();
-    private final JPanel fieldPan = new JPanel();
-    private final JPanel wordPan = new JPanel();
-    private final JPanel buttonPan = new JPanel();
-
-    private final JPanel fieldNamePan = new JPanel();
-    private final JPanel wordEditPan = new JPanel();
-    private final MetaData metaData;
-    private final JabRefFrame frame;
-    private final BasePanel panel;
-    private final JButton newField = new JButton(Localization.lang("New"));
-    private final JButton removeField = new JButton(Localization.lang("Remove"));
-    private final JButton newWord = new JButton(Localization.lang("New"));
-    private final JButton removeWord = new JButton(Localization.lang("Remove"));
-    private final JButton ok = new JButton(Localization.lang("OK"));
-    private final JButton cancel = new JButton();
-    private final JButton apply = new JButton(Localization.lang("Apply"));
-    private final DefaultListModel<String> fieldListModel = new DefaultListModel<>();
-    private final JList<String> fieldList = new JList<>(fieldListModel);
-    private final JTextField fieldNameField = new JTextField("", 20);
-    private final JTextField wordEditField = new JTextField("", 20);
-    private final JScrollPane fPane = new JScrollPane(fieldList);
-    private final Map<String, DefaultListModel<String>> wordListModels = new HashMap<>();
-    private final List<String> removedFields = new ArrayList<>();
-    private DefaultListModel<String> wordListModel = new DefaultListModel<>();
-    private JList<String> wordList = new JList<>(wordListModel);
-    private JScrollPane wPane = new JScrollPane(wordList);
-    private String currentField;
-
-
-    /**
-     *
-     * @param frame the JabRef Frame
-     * @param panel the currently selected BasePanel
-     * @param modal should this dialog be modal?
-     * @param fieldName the field this selector is initialized for. May be null.
-     */
-    public ContentSelectorDialog(JabRefFrame frame, BasePanel panel, boolean modal, String fieldName) {
-        super(Localization.lang("Manage content selectors"), ContentSelectorDialog.class);
-        this.setModal(modal);
-        this.metaData = panel.getBibDatabaseContext().getMetaData();
-        this.frame = frame;
-        this.panel = panel;
-        this.currentField = fieldName;
-
-        initLayout();
-
-        setupFieldSelector();
-        if (currentField != null) {
-            int fieldInd = fieldListModel.indexOf(currentField);
-            if (fieldInd >= 0) {
-                fieldList.setSelectedIndex(fieldInd);
-            }
-        } else {
-            if (!fieldListModel.isEmpty()) {
-                fieldList.setSelectedIndex(0);
-                currentField = fieldList.getSelectedValue();
-            }
-        }
-
-        setupWordSelector();
-        setupActions();
-        KeyBinder.bindCloseDialogKeyToCancelAction(this.rootPane, cancel.getAction());
-
-        pack();
-    }
-
-    private static int findPos(DefaultListModel<String> lm, String item) {
-        for (int i = 0; i < lm.size(); i++) {
-            String s = lm.get(i);
-            if (item.compareToIgnoreCase(s) < 0) { // item precedes s
-                return i;
-            }
-        }
-        return lm.size();
-    }
-
-    private void setupActions() {
-
-        wordList.addListSelectionListener(e -> {
-            wordEditField.setText(wordList.getSelectedValue());
-            wordEditField.selectAll();
-            wordEditField.requestFocus();
-        });
-
-        newWord.addActionListener(e -> newWordAction());
-
-        ActionListener wordEditFieldListener = e -> actOnWordEdit();
-        wordEditField.addActionListener(wordEditFieldListener);
-
-        removeWord.addActionListener(e -> {
-            int index = wordList.getSelectedIndex();
-            if (index == -1) {
-                return;
-            }
-            wordListModel.remove(index);
-            wordEditField.setText("");
-            if (!wordListModel.isEmpty()) {
-                wordList.setSelectedIndex(Math.min(index, wordListModel.size() - 1));
-            }
-        });
-
-        fieldList.addListSelectionListener(e -> {
-            currentField = fieldList.getSelectedValue();
-            fieldNameField.setText("");
-            setupWordSelector();
-        });
-
-        newField.addActionListener(e -> {
-            if (!fieldListModel.get(0).equals(FIELD_FIRST_LINE)) {
-                // only add <field name> once
-                fieldListModel.add(0, FIELD_FIRST_LINE);
-            }
-            fieldList.setSelectedIndex(0);
-            fPane.getVerticalScrollBar().setValue(0);
-            fieldNameField.setEnabled(true);
-            fieldNameField.setText(currentField);
-            fieldNameField.selectAll();
-            fieldNameField.requestFocus();
-        });
-
-        fieldNameField.addActionListener(e -> fieldNameField.transferFocus());
-
-        fieldNameField.addFocusListener(new FieldNameFocusAdapter());
-
-        removeField.addActionListener(e -> {
-            int index = fieldList.getSelectedIndex();
-            if (index == -1) {
-                return;
-            }
-            String fieldName = fieldListModel.get(index);
-            removedFields.add(fieldName);
-            fieldListModel.remove(index);
-            wordListModels.remove(fieldName);
-            fieldNameField.setText("");
-            if (!fieldListModel.isEmpty()) {
-                fieldList.setSelectedIndex(Math.min(index, wordListModel.size() - 1));
-            }
-        });
-
-        ok.addActionListener(e -> {
-            try {
-                applyChanges();
-                dispose();
-            } catch (Exception ex) {
-                LOGGER.info("Could not apply changes in \"Manage content selectors\"", ex);
-                JOptionPane.showMessageDialog(null, Localization.lang("Could not apply changes."));
-            }
-        });
-
-        apply.addActionListener(e -> {
-            // Store if an entry is currently being edited:
-            if (!"".equals(wordEditField.getText())) {
-                wordEditFieldListener.actionPerformed(null);
-            }
-            try {
-                applyChanges();
-            } catch (Exception ex) {
-                LOGGER.info("Could not apply changes in \"Manage content selectors\"", ex);
-                JOptionPane.showMessageDialog(null, Localization.lang("Could not apply changes."));
-            }
-        });
-
-        Action cancelAction = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                dispose();
-            }
-        };
-        cancelAction.putValue(Action.NAME, Localization.lang("Cancel"));
-        cancel.setAction(cancelAction);
-    }
-
-    private void actOnWordEdit() {
-        String old = wordList.getSelectedValue();
-        String newVal = wordEditField.getText();
-        if ("".equals(newVal) || newVal.equals(old)) {
-            return; // Empty string or no change.
-        }
-        int index = wordList.getSelectedIndex();
-        if (wordListModel.contains(newVal)) {
-            // ensure that word already in list is visible
-            index = wordListModel.indexOf(newVal);
-            wordList.ensureIndexIsVisible(index);
-            return;
-        }
-
-        int newIndex = findPos(wordListModel, newVal);
-        if (index >= 0) {
-            // initiate replacement of selected word
-            wordListModel.remove(index);
-            if (newIndex > index) {
-                // newIndex has to be adjusted after removal of previous entry
-                newIndex--;
-            }
-        }
-        wordListModel.add(newIndex, newVal);
-        wordList.ensureIndexIsVisible(newIndex);
-        wordEditField.selectAll();
-    }
-
-    private void newWordAction() {
-        if (wordListModel.isEmpty() || !wordListModel.get(0).equals(WORD_FIRSTLINE_TEXT)) {
-            wordListModel.add(0, WORD_FIRSTLINE_TEXT);
-        }
-        wordList.setSelectedIndex(0);
-        wPane.getVerticalScrollBar().setValue(0);
-    }
-
-    private void applyChanges() {
-        boolean anythingChanged = false; // Watch if we should mark as there is data changed
-
-        // First remove the mappings for fields that have been deleted.
-        // If these were re-added, they will be added below, so it doesn't
-        // cause any harm to remove them here.
-        for (String fieldName : removedFields) {
-            metaData.clearContentSelectors(fieldName);
-            anythingChanged = true;
-        }
-
-        // Cycle through all fields that we have created listmodels for:
-        for (Map.Entry<String, DefaultListModel<String>> entry : wordListModels.entrySet()) {
-            // For each field name, store the values:
-            if ((entry.getKey() == null) || FIELD_FIRST_LINE.equals(entry.getKey())) {
-                continue;
-            }
-            DefaultListModel<String> lm = entry.getValue();
-            int start = 0;
-            // Avoid storing the <new word> marker if it is there:
-            if (!lm.isEmpty()) {
-                while ((start < lm.size()) && lm.get(start).equals(WORD_FIRSTLINE_TEXT)) {
-                    start++;
-                }
-            }
-
-            Set<String> data = new HashSet<>();
-            for (int wrd = start; wrd < lm.size(); wrd++) {
-                String word = lm.get(wrd);
-                data.add(word);
-            }
-
-            // Check if any words have been added
-            if (!data.equals(new HashSet<>(metaData.getContentSelectorValuesForField(entry.getKey())))) {
-                anythingChanged = true;
-            }
-
-            // Check if there are words to be added and previously there were no content selector for the field
-            if (!data.isEmpty() && metaData.getContentSelectorValuesForField(entry.getKey()).isEmpty()) {
-                anythingChanged = true;
-            }
-
-            metaData.addContentSelector(new ContentSelector(entry.getKey(), new ArrayList<>(data)));
-        }
-
-        if (anythingChanged) {
-            // Update all selectors in the current BasePanel.
-            panel.setupMainPanel();
-
-            // Mark the database updated so changes are not lost
-            panel.markNonUndoableBaseChanged();
-        }
-    }
-
-    /**
-     * Set the contents of the field selector list.
-     *
-     */
-    private void setupFieldSelector() {
-        fieldListModel.clear();
-        SortedSet<String> contents = new TreeSet<>();
-        ContentSelectors selectors = metaData.getContentSelectors();
-        for (String s : selectors.getFieldNamesWithSelectors()) {
-            contents.add(s);
-        }
-        if (contents.isEmpty()) {
-            // if nothing was added, put the default fields (as described in the help)
-            fieldListModel.addElement(FieldName.AUTHOR);
-            fieldListModel.addElement(FieldName.JOURNAL);
-            fieldListModel.addElement(FieldName.KEYWORDS);
-            fieldListModel.addElement(FieldName.PUBLISHER);
-        } else {
-            for (String s : contents) {
-                fieldListModel.addElement(s);
-            }
-        }
-
-        if (currentField == null) {
-            // if dialog is created for the whole database,
-            // select the first field to avoid confusions in GUI usage
-            fieldList.setSelectedIndex(0);
-        } else {
-            // a specific field has been chosen at the constructor
-            // select this field
-            int i = fieldListModel.indexOf(currentField);
-            if (i != -1) {
-                // field has been found in list, select it
-                fieldList.setSelectedIndex(i);
-            }
-        }
-    }
-
-    private void setupWordSelector() {
-
-        // Have we already created a listmodel for this field?
-        wordListModel = wordListModels.get(currentField);
-        if (wordListModel == null) {
-            wordListModel = new DefaultListModel<>();
-            wordList.setModel(wordListModel);
-            wordListModels.put(currentField, wordListModel);
-
-            int index = 0;
-            for (String s : metaData.getContentSelectorValuesForField(currentField)) {
-                wordListModel.add(index, s);
-                index++;
-            }
-        } else {
-            wordList.setModel(wordListModel);
-        }
-    }
-
-    private void initLayout() {
-        fieldNameField.setEnabled(false);
-        fieldList.setVisibleRowCount(4);
-        wordList.setVisibleRowCount(10);
-        final String VAL = "Uren luren himmelturen, ja Besseggen.";
-        fieldList.setPrototypeCellValue(VAL);
-        wordList.setPrototypeCellValue(VAL);
-
-        fieldPan.setBorder(
-                BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), Localization.lang("Field name")));
-        wordPan.setBorder(
-                BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(), Localization.lang("Keyword")));
-        fieldPan.setLayout(gbl);
-        wordPan.setLayout(gbl);
-        con.insets = new Insets(2, 2, 2, 2);
-        con.fill = GridBagConstraints.BOTH;
-        con.gridwidth = 2;
-        con.weightx = 1;
-        con.weighty = 1;
-        con.gridx = 0;
-        con.gridy = 0;
-        gbl.setConstraints(fPane, con);
-        fieldPan.add(fPane);
-        gbl.setConstraints(wPane, con);
-        wordPan.add(wPane);
-        con.gridwidth = 1;
-        con.gridx = 2;
-        //con.weightx = 0.7;
-        con.gridheight = 2;
-        gbl.setConstraints(fieldNamePan, con);
-        fieldPan.add(fieldNamePan);
-        gbl.setConstraints(wordEditPan, con);
-        wordPan.add(wordEditPan);
-        con.gridx = 0;
-        con.gridy = 1;
-        con.weightx = 0;
-        con.weighty = 0;
-        con.gridwidth = 1;
-        con.gridheight = 1;
-        con.fill = GridBagConstraints.NONE;
-        con.anchor = GridBagConstraints.WEST;
-        gbl.setConstraints(newField, con);
-        fieldPan.add(newField);
-        gbl.setConstraints(newWord, con);
-        wordPan.add(newWord);
-        con.gridx = 1;
-        //con.anchor = GridBagConstraints.EAST;
-        gbl.setConstraints(removeField, con);
-        fieldPan.add(removeField);
-        gbl.setConstraints(removeWord, con);
-        wordPan.add(removeWord);
-        con.anchor = GridBagConstraints.WEST;
-        con.gridx = 0;
-        con.gridy = 0;
-        gbl.setConstraints(fieldNameField, con);
-        fieldNamePan.add(fieldNameField);
-        gbl.setConstraints(wordEditField, con);
-        wordEditPan.add(wordEditField);
-
-        // Add buttons:
-        ButtonBarBuilder bsb = new ButtonBarBuilder(buttonPan);
-        bsb.addGlue();
-        bsb.addButton(ok);
-        bsb.addButton(apply);
-        bsb.addButton(cancel);
-        bsb.addRelatedGap();
-        bsb.addButton(new HelpAction(HelpFile.CONTENT_SELECTOR).getHelpButton());
-        bsb.addGlue();
-
-        // Add panels to dialog:
-        con.fill = GridBagConstraints.BOTH;
-        getContentPane().setLayout(gbl);
-        con.weightx = 1;
-        con.weighty = 0.5;
-        con.gridwidth = 1;
-        con.gridheight = 1;
-        con.gridx = 0;
-        con.gridy = 0;
-        gbl.setConstraints(fieldPan, con);
-        getContentPane().add(fieldPan);
-        con.gridy = 1;
-        gbl.setConstraints(wordPan, con);
-        getContentPane().add(wordPan);
-        con.weighty = 0;
-        con.gridy = 2;
-        con.insets = new Insets(12, 2, 2, 2);
-        gbl.setConstraints(buttonPan, con);
-        getContentPane().add(buttonPan);
-
-    }
-
-    private class FieldNameFocusAdapter extends FocusAdapter {
-
-        /**
-         * Adds the text value to the list
-         */
-        @Override
-        public void focusLost(FocusEvent e) {
-            String s = fieldNameField.getText();
-            fieldNameField.setText("");
-            fieldNameField.setEnabled(false);
-            if (!FIELD_FIRST_LINE.equals(s) && !"".equals(s)) {
-                // user has typed something
-
-                // remove "<first name>" from list
-                fieldListModel.remove(0);
-
-                int pos;
-                if (fieldListModel.contains(s)) {
-                    // field already exists, scroll to that field (below)
-                    pos = fieldListModel.indexOf(s);
-                } else {
-                    // Add new field.
-                    pos = findPos(fieldListModel, s);
-                    fieldListModel.add(Math.max(0, pos), s);
-                }
-                fieldList.setSelectedIndex(pos);
-                fieldList.ensureIndexIsVisible(pos);
-                currentField = s;
-                setupWordSelector();
-                newWordAction();
-            }
-        }
-
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogView.java b/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogView.java
new file mode 100644
index 00000000000..013cbcb79ad
--- /dev/null
+++ b/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogView.java
@@ -0,0 +1,122 @@
+package org.jabref.gui.contentselector;
+
+import java.util.Optional;
+import java.util.function.Supplier;
+
+import javax.inject.Inject;
+
+import javafx.beans.property.ListProperty;
+import javafx.fxml.FXML;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.ListView;
+import javafx.scene.control.SelectionModel;
+
+import org.jabref.gui.BasePanel;
+import org.jabref.gui.DialogService;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.ControlHelper;
+import org.jabref.logic.l10n.Localization;
+
+import com.airhacks.afterburner.views.ViewLoader;
+import org.fxmisc.easybind.EasyBind;
+
+public class ContentSelectorDialogView extends BaseDialog<Void> {
+
+    @FXML
+    private Button addFieldNameButton;
+    @FXML
+    private Button removeFieldNameButton;
+    @FXML
+    private Button addKeywordButton;
+    @FXML
+    private Button removeKeywordButton;
+    @FXML
+    private ListView<String> fieldNamesListView;
+    @FXML
+    private ListView<String> keywordsListView;
+    @FXML
+    private ButtonType saveButton;
+
+    @Inject
+    private DialogService dialogService;
+    private final BasePanel basePanel;
+    private ContentSelectorDialogViewModel viewModel;
+
+    public ContentSelectorDialogView(BasePanel basePanel) {
+        this.setTitle(Localization.lang("Manage content selectors"));
+        this.getDialogPane().setPrefSize(375, 475);
+
+        this.basePanel = basePanel;
+
+        ViewLoader.view(this)
+                .load()
+                .setAsDialogPane(this);
+
+        ControlHelper.setAction(saveButton, getDialogPane(), event -> saveChangesAndClose());
+    }
+
+    @FXML
+    public void initialize() {
+        viewModel = new ContentSelectorDialogViewModel(basePanel, dialogService);
+
+        initFieldNameComponents();
+        initKeywordsComponents();
+    }
+
+    private void initFieldNameComponents() {
+        initListView(fieldNamesListView, viewModel::getFieldNamesBackingList);
+        viewModel.selectedFieldNameProperty().bind(fieldNamesListView.getSelectionModel().selectedItemProperty());
+        removeFieldNameButton.disableProperty().bind(viewModel.isNoFieldNameSelected());
+        EasyBind.subscribe(viewModel.selectedFieldNameProperty(), viewModel::populateKeywords);
+    }
+
+    private void initKeywordsComponents() {
+        initListView(keywordsListView, viewModel::getKeywordsBackingList);
+        viewModel.selectedKeywordProperty().bind(keywordsListView.getSelectionModel().selectedItemProperty());
+        addKeywordButton.disableProperty().bind(viewModel.isFieldNameListEmpty());
+        removeKeywordButton.disableProperty().bind(viewModel.isNoKeywordSelected());
+    }
+
+    @FXML
+    private void addNewFieldName() {
+        viewModel.showInputFieldNameDialog();
+    }
+
+    @FXML
+    private void removeFieldName() {
+        getSelectedFieldName().ifPresent(viewModel::showRemoveFieldNameConfirmationDialog);
+    }
+
+    @FXML
+    private void addNewKeyword() {
+        getSelectedFieldName().ifPresent(viewModel::showInputKeywordDialog);
+    }
+
+    @FXML
+    private void removeKeyword() {
+        Optional<String> fieldName = getSelectedFieldName();
+        Optional<String> keywordToRemove = getSelectedKeyword();
+        if (fieldName.isPresent() && keywordToRemove.isPresent()) {
+            viewModel.showRemoveKeywordConfirmationDialog(fieldName.get(), keywordToRemove.get());
+        }
+    }
+
+    private void initListView(ListView<String> listViewToInit, Supplier<ListProperty<String>> backingList) {
+        listViewToInit.itemsProperty().bind(backingList.get());
+        listViewToInit.getSelectionModel().selectFirst();
+    }
+
+    private Optional<String> getSelectedFieldName() {
+        return Optional.of(fieldNamesListView.getSelectionModel()).map(SelectionModel::getSelectedItem);
+    }
+
+    private Optional<String> getSelectedKeyword() {
+        return Optional.of(keywordsListView.getSelectionModel()).map(SelectionModel::getSelectedItem);
+    }
+
+    private void saveChangesAndClose() {
+        viewModel.saveChanges();
+        close();
+    }
+}
diff --git a/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogViewModel.java b/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogViewModel.java
new file mode 100644
index 00000000000..4ee85925310
--- /dev/null
+++ b/src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogViewModel.java
@@ -0,0 +1,213 @@
+package org.jabref.gui.contentselector;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import javafx.beans.binding.Bindings;
+import javafx.beans.binding.BooleanBinding;
+import javafx.beans.property.ListProperty;
+import javafx.beans.property.SimpleListProperty;
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
+import javafx.collections.FXCollections;
+
+import org.jabref.gui.AbstractViewModel;
+import org.jabref.gui.BasePanel;
+import org.jabref.gui.DialogService;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.entry.FieldName;
+import org.jabref.model.metadata.ContentSelector;
+import org.jabref.model.metadata.MetaData;
+
+import static com.google.common.collect.ImmutableList.of;
+
+class ContentSelectorDialogViewModel extends AbstractViewModel {
+
+    private static final List<String> DEFAULT_FIELD_NAMES = of(FieldName.AUTHOR, FieldName.JOURNAL, FieldName.KEYWORDS, FieldName.PUBLISHER);
+
+    private final BasePanel basePanel;
+    private final MetaData metaData;
+    private final DialogService dialogService;
+    private final Map<String, List<String>> fieldNameKeywordsMap = new HashMap<>();
+
+    private ListProperty<String> fieldNames = new SimpleListProperty<>(FXCollections.observableArrayList());
+    private ListProperty<String> keywords = new SimpleListProperty<>(FXCollections.observableArrayList());
+    private StringProperty selectedFieldName = new SimpleStringProperty();
+    private StringProperty selectedKeyword = new SimpleStringProperty();
+
+    ContentSelectorDialogViewModel(BasePanel basePanel, DialogService dialogService) {
+        this.basePanel = basePanel;
+        this.metaData = basePanel.getBibDatabaseContext().getMetaData();
+        this.dialogService = dialogService;
+        populateFieldNameKeywordsMapWithExistingValues();
+        populateFieldNamesListWithValues();
+    }
+
+    private void populateFieldNamesListWithValues() {
+        List<String> existingFieldNames = new ArrayList<>(fieldNameKeywordsMap.keySet());
+        Collections.sort(existingFieldNames);
+        fieldNames.addAll(existingFieldNames);
+
+        if (fieldNames.isEmpty()) {
+            DEFAULT_FIELD_NAMES.forEach(this::addFieldNameIfUnique);
+        }
+    }
+
+    private void populateFieldNameKeywordsMapWithExistingValues() {
+        metaData.getContentSelectors().getContentSelectors().forEach(
+                existingContentSelector -> fieldNameKeywordsMap.put(existingContentSelector.getFieldName(), new ArrayList<>(existingContentSelector.getValues()))
+        );
+    }
+
+    ListProperty<String> getFieldNamesBackingList() {
+        return fieldNames;
+    }
+
+    StringProperty selectedFieldNameProperty() {
+        return selectedFieldName;
+    }
+
+    BooleanBinding isFieldNameListEmpty() {
+        return Bindings.isEmpty(fieldNames);
+    }
+
+    BooleanBinding isNoFieldNameSelected() {
+        return Bindings.isEmpty(selectedFieldName);
+    }
+
+    ListProperty<String> getKeywordsBackingList() {
+        return keywords;
+    }
+
+    StringProperty selectedKeywordProperty() {
+        return selectedKeyword;
+    }
+
+    BooleanBinding isNoKeywordSelected() {
+        return Bindings.isEmpty(selectedKeyword);
+    }
+
+    void showInputFieldNameDialog() {
+        dialogService.showInputDialogAndWait(Localization.lang("Add new field name"), Localization.lang("Field name:"))
+                .ifPresent(this::addFieldNameIfUnique);
+    }
+
+    private void addFieldNameIfUnique(String fieldNameToAdd) {
+        boolean exists = fieldNameKeywordsMap.containsKey(fieldNameToAdd);
+        if (exists) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Field name \"%0\" already exists", fieldNameToAdd));
+            return;
+        }
+
+        fieldNameKeywordsMap.put(fieldNameToAdd, new ArrayList<>());
+        fieldNames.add(fieldNameToAdd);
+    }
+
+    void showRemoveFieldNameConfirmationDialog(String fieldNameToRemove) {
+        if (fieldNameToRemove == null) {
+            dialogService.showErrorDialogAndWait(Localization.lang("No field name selected!"));
+            return;
+        }
+
+        boolean deleteConfirmed = dialogService.showConfirmationDialogAndWait(
+                Localization.lang("Remove field name"),
+                Localization.lang("Are you sure you want to remove field name: \"%0\"?", fieldNameToRemove)
+        );
+
+        if (deleteConfirmed) {
+            removeFieldName(fieldNameToRemove);
+        }
+    }
+
+    private void removeFieldName(String fieldNameToRemove) {
+        fieldNameKeywordsMap.remove(fieldNameToRemove);
+        fieldNames.remove(fieldNameToRemove);
+    }
+
+    void populateKeywords(String selectedFieldName) {
+        keywords.clear();
+        if (selectedFieldName != null) {
+            keywords.addAll(fieldNameKeywordsMap.get(selectedFieldName));
+        }
+    }
+
+    void showInputKeywordDialog(String selectedFieldName) {
+        dialogService.showInputDialogAndWait(Localization.lang("Add new keyword"), Localization.lang("Keyword:"))
+                .ifPresent(newKeyword -> addKeywordIfUnique(selectedFieldName, newKeyword));
+    }
+
+    private void addKeywordIfUnique(String fieldName, String keywordToAdd) {
+        boolean exists = fieldNameKeywordsMap.get(fieldName).contains(keywordToAdd);
+        if (exists) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Keyword \"%0\" already exists", keywordToAdd));
+            return;
+        }
+
+        List<String> existingKeywords = fieldNameKeywordsMap.getOrDefault(fieldName, new ArrayList<>());
+        existingKeywords.add(keywordToAdd);
+        fieldNameKeywordsMap.put(fieldName, existingKeywords);
+        keywords.add(keywordToAdd);
+        populateKeywords(fieldName);
+    }
+
+    void showRemoveKeywordConfirmationDialog(String fieldName, String keywordToRemove) {
+        boolean deleteConfirmed = dialogService.showConfirmationDialogAndWait(Localization.lang("Remove keyword"), Localization.lang("Are you sure you want to remove keyword: \"%0\"?", keywordToRemove));
+        if (deleteConfirmed) {
+            removeKeyword(fieldName, keywordToRemove);
+        }
+    }
+
+    private void removeKeyword(String fieldName, String keywordToRemove) {
+        fieldNameKeywordsMap.get(fieldName).remove(keywordToRemove);
+        keywords.remove(keywordToRemove);
+    }
+
+    void saveChanges() {
+        List<String> metaDataFieldNames = metaData.getContentSelectors().getFieldNamesWithSelectors();
+        fieldNameKeywordsMap.forEach((fieldName, keywords) -> updateMetaDataContentSelector(metaDataFieldNames, fieldName, keywords));
+
+        List<String> fieldNamesToRemove = filterFieldNamesToRemove();
+        fieldNamesToRemove.forEach(metaData::clearContentSelectors);
+
+        basePanel.setupMainPanel();
+        basePanel.markNonUndoableBaseChanged();
+    }
+
+    private List<String> filterFieldNamesToRemove() {
+        Set<String> newlyAddedKeywords = fieldNameKeywordsMap.keySet();
+        return metaData.getContentSelectors().getFieldNamesWithSelectors().stream()
+                .filter(fieldName -> !newlyAddedKeywords.contains(fieldName))
+                .collect(Collectors.toList());
+    }
+
+    private void updateMetaDataContentSelector(List<String> existingFieldNames, String fieldName, List<String> keywords) {
+        boolean fieldNameDoNotExists = !existingFieldNames.contains(fieldName);
+        if (fieldNameDoNotExists) {
+            metaData.addContentSelector(new ContentSelector(fieldName, keywords));
+        }
+
+        if (keywordsHaveChanged(fieldName, keywords)) {
+            metaData.clearContentSelectors(fieldName);
+            metaData.addContentSelector(new ContentSelector(fieldName, keywords));
+        }
+    }
+
+    private boolean keywordsHaveChanged(String fieldName, List<String> keywords) {
+        HashSet<String> keywordsSet = asHashSet(keywords);
+        List<String> existingKeywords = metaData.getContentSelectorValuesForField(fieldName);
+        if (!keywordsSet.equals(asHashSet(existingKeywords))) {
+            return true;
+        }
+        return !keywordsSet.isEmpty() && existingKeywords.isEmpty();
+    }
+
+    private HashSet<String> asHashSet(List<String> listToConvert) {
+        return new HashSet<>(listToConvert);
+    }
+}
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 634a80d312c..9275461a40a 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -12,9 +12,6 @@
 
 %0\ matches\ the\ term\ <b>%1</b>=%0 matches the term <b>%1</b>
 
-<field\ name>=<field name>
-
-<select\ word>=<select word>
 Abbreviate\ journal\ names\ of\ the\ selected\ entries\ (ISO\ abbreviation)=Abbreviate journal names of the selected entries (ISO abbreviation)
 Abbreviate\ journal\ names\ of\ the\ selected\ entries\ (MEDLINE\ abbreviation)=Abbreviate journal names of the selected entries (MEDLINE abbreviation)
 
@@ -1470,7 +1467,6 @@ Move\ to\ group=Move to group
 
 Clear\ read\ status=Clear read status
 Convert\ to\ biblatex\ format\ (for\ example,\ move\ the\ value\ of\ the\ 'journal'\ field\ to\ 'journaltitle')=Convert to biblatex format (for example, move the value of the 'journal' field to 'journaltitle')
-Could\ not\ apply\ changes.=Could not apply changes.
 Deprecated\ fields=Deprecated fields
 No\ read\ status\ information=No read status information
 Printed=Printed
@@ -2175,4 +2171,17 @@ Error\ adding\ discovered\ CitationStyles=Error adding discovered CitationStyles
 Add\ new\ String=Add new String
 Remove\ selected\ Strings=Remove selected Strings
 Must\ not\ be\ empty\!=Must not be empty\!
-Open\ Help\ page=Open Help page
\ No newline at end of file
+Open\ Help\ page=Open Help page
+
+Active\ database\ connection\ do\ not\ exists\!=Active database connection do not exists!
+Add\ new\ field\ name=Add new field name
+Field\ name\:=Field name:
+Field\ name\ \"%0\"\ already\ exists=Field name "%0" already exists
+No\ field\ name\ selected\!=No field name selected!
+Remove\ field\ name=Remove field name
+Are\ you\ sure\ you\ want\ to\ remove\ field\ name\:\ \"%0\"?=Are you sure you want to remove field name: "%0"?
+Add\ new\ keyword=Add new keyword
+Keyword\:=Keyword:
+Keyword\ \"%0\"\ already\ exists=Keyword "%0" already exists
+Remove\ keyword=Remove keyword
+Are\ you\ sure\ you\ want\ to\ remove\ keyword\:\ \"%0\"?=Are you sure you want to remove keyword: "%0"?

From 623718aa9a08a969bf965ccfeb3cb83f77c2f006 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Tue, 19 Feb 2019 08:33:11 +0100
Subject: [PATCH 039/184] Bump mockito-core from 2.24.0 to 2.24.5 (#4663)

Bumps [mockito-core](https://github.com/mockito/mockito) from 2.24.0 to 2.24.5.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v2.24.0...v2.24.5)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 1e55cfe71cc..9a7e49aafea 100644
--- a/build.gradle
+++ b/build.gradle
@@ -167,7 +167,7 @@ dependencies {
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
-    testCompile 'org.mockito:mockito-core:2.24.0'
+    testCompile 'org.mockito:mockito-core:2.24.5'
     testCompile 'com.github.tomakehurst:wiremock:2.21.0'
     testCompile 'org.assertj:assertj-swing-junit:3.9.2'
     testCompile 'org.reflections:reflections:0.9.11'

From 49e3600f094beef6508f5ec8b2f5057d5820fcf4 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Tue, 19 Feb 2019 16:40:39 +0100
Subject: [PATCH 040/184] add new fxml

---
 .../jabref/gui/SaveOrderConfigDisplay.fxml    | 25 ++++++++++--------
 .../gui/SaveOrderConfigDisplayController.java | 26 +++++++++++++++++++
 .../gui/SaveOrderConfigDisplayViewModel.java  |  1 +
 3 files changed, 41 insertions(+), 11 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/SaveOrderConfigDisplayController.java

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
index db0e2b2ed37..78ce75cfc6e 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
@@ -4,11 +4,11 @@
 <?import javafx.scene.control.ComboBox?>
 <?import javafx.scene.control.Label?>
 <?import javafx.scene.control.RadioButton?>
+<?import javafx.scene.control.ToggleGroup?>
 <?import javafx.scene.layout.ColumnConstraints?>
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.RowConstraints?>
 
-
 <GridPane prefHeight="400.0" prefWidth="600.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1">
   <columnConstraints>
     <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="100.0" />
@@ -22,19 +22,22 @@
       <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
       <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
       <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
-  </rowConstraints>s
+  </rowConstraints>
+     <fx:define>
+       <ToggleGroup fx:id="saveOrderToggleGroup" />
+     </fx:define>
    <children>
       <ComboBox fx:id="savePriSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="3" />
       <ComboBox fx:id="saveSecSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="4" />
-      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2" />
-      <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="Export in current table sort order" GridPane.columnSpan="3" GridPane.rowIndex="1" />
-      <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="Export entries in their original order" GridPane.columnSpan="3" />
       <ComboBox fx:id="saveTerSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="5" />
-      <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" />
-      <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" />
-      <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" />
-      <Label text="Primary sort criterion" GridPane.rowIndex="3" />
-      <Label text="Secondary sort criterion" GridPane.rowIndex="4" />
-      <Label text="Tertiary sort criterion" GridPane.rowIndex="5" />
+      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2" />
+      <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" GridPane.columnSpan="3" GridPane.rowIndex="1" />
+      <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" GridPane.columnSpan="3"/>
+      <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" enabled="${exportInSpecifiedOrder.selected}"/>
+      <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="4 "enabled="${exportInSpecifiedOrder.selected}" />
+      <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" enabled="${exportInSpecifiedOrder.selected}" />
+      <Label text="Primary sort criterion" GridPane.rowIndex="3" enabled="${exportInSpecifiedOrder.selected}" />
+      <Label text="Secondary sort criterion" GridPane.rowIndex="4" enabled="${exportInSpecifiedOrder.selected}" />
+      <Label text="Tertiary sort criterion" GridPane.rowIndex="5" enabled="${exportInSpecifiedOrder.selected}"/>
    </children>
 </GridPane>
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayController.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayController.java
new file mode 100644
index 00000000000..03d209dc3e0
--- /dev/null
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayController.java
@@ -0,0 +1,26 @@
+package org.jabref.gui;
+
+import javafx.fxml.FXML;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.ComboBox;
+import javafx.scene.control.RadioButton;
+import javafx.scene.control.ToggleGroup;
+
+public class SaveOrderConfigDisplayController {
+
+    @FXML private ToggleGroup saveOrderToggleGroup;
+    @FXML private ComboBox<String> savePriSort;
+    @FXML private ComboBox<String> saveSecSort;
+    @FXML private ComboBox<String> saveTerSort;
+    @FXML private RadioButton exportInSpecifiedOrder;
+    @FXML private RadioButton exportInTableOrder;
+    @FXML private RadioButton exportInOriginalOrder;
+    @FXML private CheckBox savePriDesc;
+    @FXML private CheckBox saveSecDesc;
+    @FXML private CheckBox saveTerDesc;
+
+    public void init() {
+
+    }
+
+}
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
index b1aec9486e8..35fdabbc674 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
@@ -3,4 +3,5 @@
 
 public class SaveOrderConfigDisplayViewModel {
 
+
 }

From 22e9bf811337aa47374d49238be2551ffe87a66e Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Tue, 19 Feb 2019 16:41:30 +0100
Subject: [PATCH 041/184] fix copy base bug in Strings Dialog validation

---
 .../org/jabref/gui/metadata/BibtexStringEditorDialogView.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogView.java b/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogView.java
index bdb3f169c00..a5afc2c8215 100644
--- a/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogView.java
+++ b/src/main/java/org/jabref/gui/metadata/BibtexStringEditorDialogView.java
@@ -69,7 +69,7 @@ private void initialize() {
         new ViewModelTextFieldTableCellVisualizationFactory<BibtexStringViewModel, String>().withValidation(BibtexStringViewModel::labelValidation, visualizer).install(colLabel, new DefaultStringConverter());
 
         colContent.setCellValueFactory(cellData -> cellData.getValue().contentProperty());
-        new ViewModelTextFieldTableCellVisualizationFactory<BibtexStringViewModel, String>().withValidation(BibtexStringViewModel::labelValidation, visualizer).install(colContent, new DefaultStringConverter());
+        new ViewModelTextFieldTableCellVisualizationFactory<BibtexStringViewModel, String>().withValidation(BibtexStringViewModel::contentValidation, visualizer).install(colContent, new DefaultStringConverter());
 
         colLabel.setOnEditCommit((CellEditEvent<BibtexStringViewModel, String> cell) -> {
             cell.getRowValue().setLabel(cell.getNewValue());

From 3589dc3cb066c729da3b124fb34dae73f5a86a70 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Wed, 20 Feb 2019 09:22:32 +0100
Subject: [PATCH 042/184] Bump slf4j-api from 1.8.0-beta2 to 1.8.0-beta4
 (#4675)

Bumps [slf4j-api](https://github.com/qos-ch/slf4j) from 1.8.0-beta2 to 1.8.0-beta4.
- [Release notes](https://github.com/qos-ch/slf4j/releases)
- [Commits](https://github.com/qos-ch/slf4j/commits/v_1.8.0-beta4)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9a7e49aafea..26d139a3c12 100644
--- a/build.gradle
+++ b/build.gradle
@@ -146,7 +146,7 @@ dependencies {
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     // >1.8.0-beta is required for java 9 compatibility
-    compile 'org.slf4j:slf4j-api:1.8.0-beta2'
+    compile 'org.slf4j:slf4j-api:1.8.0-beta4'
     compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.2'
     compile 'org.apache.logging.log4j:log4j-jcl:2.11.2'
     compile 'org.apache.logging.log4j:log4j-api:2.11.2'

From 5657fed6eefe24c2f018315689779057f460efde Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Thu, 21 Feb 2019 19:17:36 +0100
Subject: [PATCH 043/184] Create properties in view Model for SaveOrderConfig
 Use Expressions in fxml code for enabling/disabling

---
 .../jabref/gui/SaveOrderConfigDisplay.fxml    |  12 +-
 .../gui/SaveOrderConfigDisplayController.java |  26 ----
 .../gui/SaveOrderConfigDisplayView.java       |  56 ++++++++
 .../gui/SaveOrderConfigDisplayViewModel.java  | 129 ++++++++++++++++++
 4 files changed, 191 insertions(+), 32 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/SaveOrderConfigDisplayController.java
 create mode 100644 src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
index 78ce75cfc6e..ed8a74897cd 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
@@ -33,11 +33,11 @@
       <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2" />
       <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" GridPane.columnSpan="3" GridPane.rowIndex="1" />
       <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" GridPane.columnSpan="3"/>
-      <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" enabled="${exportInSpecifiedOrder.selected}"/>
-      <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="4 "enabled="${exportInSpecifiedOrder.selected}" />
-      <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" enabled="${exportInSpecifiedOrder.selected}" />
-      <Label text="Primary sort criterion" GridPane.rowIndex="3" enabled="${exportInSpecifiedOrder.selected}" />
-      <Label text="Secondary sort criterion" GridPane.rowIndex="4" enabled="${exportInSpecifiedOrder.selected}" />
-      <Label text="Tertiary sort criterion" GridPane.rowIndex="5" enabled="${exportInSpecifiedOrder.selected}"/>
+      <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" disabled="${!exportInSpecifiedOrder.selected}"/>
+      <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" disabled="${!exportInSpecifiedOrder.selected}" />
+      <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" disabled="${!exportInSpecifiedOrder.selected}" />
+      <Label text="Primary sort criterion" GridPane.rowIndex="3" disabled="${!exportInSpecifiedOrder.selected}" />
+      <Label text="Secondary sort criterion" GridPane.rowIndex="4" disabled="${!exportInSpecifiedOrder.selected}" />
+      <Label text="Tertiary sort criterion" GridPane.rowIndex="5" disabled="${!exportInSpecifiedOrder.selected}"/>
    </children>
 </GridPane>
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayController.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayController.java
deleted file mode 100644
index 03d209dc3e0..00000000000
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayController.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package org.jabref.gui;
-
-import javafx.fxml.FXML;
-import javafx.scene.control.CheckBox;
-import javafx.scene.control.ComboBox;
-import javafx.scene.control.RadioButton;
-import javafx.scene.control.ToggleGroup;
-
-public class SaveOrderConfigDisplayController {
-
-    @FXML private ToggleGroup saveOrderToggleGroup;
-    @FXML private ComboBox<String> savePriSort;
-    @FXML private ComboBox<String> saveSecSort;
-    @FXML private ComboBox<String> saveTerSort;
-    @FXML private RadioButton exportInSpecifiedOrder;
-    @FXML private RadioButton exportInTableOrder;
-    @FXML private RadioButton exportInOriginalOrder;
-    @FXML private CheckBox savePriDesc;
-    @FXML private CheckBox saveSecDesc;
-    @FXML private CheckBox saveTerDesc;
-
-    public void init() {
-
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
new file mode 100644
index 00000000000..e0a389d8c56
--- /dev/null
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
@@ -0,0 +1,56 @@
+package org.jabref.gui;
+
+import javafx.fxml.FXML;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.ComboBox;
+import javafx.scene.control.RadioButton;
+import javafx.scene.control.ToggleGroup;
+
+import org.jabref.model.metadata.MetaData;
+
+public class SaveOrderConfigDisplayView {
+
+    @FXML private ToggleGroup saveOrderToggleGroup;
+    @FXML private ComboBox<String> savePriSort;
+    @FXML private ComboBox<String> saveSecSort;
+    @FXML private ComboBox<String> saveTerSort;
+    @FXML private RadioButton exportInSpecifiedOrder;
+    @FXML private RadioButton exportInTableOrder;
+    @FXML private RadioButton exportInOriginalOrder;
+    @FXML private CheckBox savePriDesc;
+    @FXML private CheckBox saveSecDesc;
+    @FXML private CheckBox saveTerDesc;
+    private SaveOrderConfigDisplayViewModel viewModel;
+    private final MetaData metadata;
+
+    public SaveOrderConfigDisplayView(MetaData metadata) {
+        this.metadata = metadata;
+    }
+
+    @FXML
+    private void initialize() {
+
+        viewModel = new SaveOrderConfigDisplayViewModel(metadata);
+
+        exportInSpecifiedOrder.selectedProperty().bindBidirectional(viewModel.saveInSpecifiedOrderProperty());
+        exportInTableOrder.selectedProperty().bindBidirectional(viewModel.saveInTableOrderProperty());
+        exportInOriginalOrder.selectedProperty().bindBidirectional(viewModel.saveInOriginalProperty());
+
+        savePriSort.itemsProperty().bindBidirectional(viewModel.priSortFieldsProperty());
+        saveSecSort.itemsProperty().bindBidirectional(viewModel.secSortFieldsProperty());
+        saveTerSort.itemsProperty().bindBidirectional(viewModel.terSortFieldsProperty());
+
+        savePriSort.valueProperty().bindBidirectional(viewModel.savePriSortSelectedValueProperty());
+        saveSecSort.valueProperty().bindBidirectional(viewModel.saveSecSortSelectedValueProperty());
+        saveTerSort.valueProperty().bindBidirectional(viewModel.saveTerSortSelectedValueProperty());
+
+        savePriDesc.selectedProperty().bindBidirectional(viewModel.savePriDescPropertySelected());
+        saveSecDesc.selectedProperty().bindBidirectional(viewModel.saveSecDescPropertySelected());
+        saveTerDesc.selectedProperty().bindBidirectional(viewModel.saveTerDescPropertySelected());
+
+    }
+
+    public void storeConfig() {
+        viewModel.storeConfig();
+    }
+}
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
index 35fdabbc674..8ef3135afd3 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
@@ -1,7 +1,136 @@
 package org.jabref.gui;
 
+import java.util.Collections;
+import java.util.List;
+import java.util.Locale;
+import java.util.Objects;
+import java.util.Optional;
+
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.ListProperty;
+import javafx.beans.property.SimpleBooleanProperty;
+import javafx.beans.property.SimpleListProperty;
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
+import javafx.collections.FXCollections;
+
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.InternalBibtexFields;
+import org.jabref.model.metadata.MetaData;
+import org.jabref.model.metadata.SaveOrderConfig;
+import org.jabref.model.metadata.SaveOrderConfig.SortCriterion;
 
 public class SaveOrderConfigDisplayViewModel {
 
+    private final ListProperty<String> priSortFieldsProperty = new SimpleListProperty<>(FXCollections.observableArrayList());
+    private final ListProperty<String> secSortFieldsProperty = new SimpleListProperty<>(FXCollections.observableArrayList());
+    private final ListProperty<String> terSortFieldsProperty = new SimpleListProperty<>(FXCollections.observableArrayList());
+
+    private final BooleanProperty savePriDescPropertySelected = new SimpleBooleanProperty();
+    private final BooleanProperty saveSecDescPropertySelected = new SimpleBooleanProperty();
+    private final BooleanProperty saveTerDescPropertySelected = new SimpleBooleanProperty();
+
+    private final StringProperty savePriSortSelectedValueProperty = new SimpleStringProperty("");
+    private final StringProperty saveSecSortSelectedValueProperty = new SimpleStringProperty("");
+    private final StringProperty saveTerSortSelectedValueProperty = new SimpleStringProperty("");
+
+    private final BooleanProperty saveInOriginalProperty = new SimpleBooleanProperty();
+    private final BooleanProperty saveInTableOrderProperty = new SimpleBooleanProperty();
+    private final BooleanProperty saveInSpecifiedOrderProperty = new SimpleBooleanProperty();
+
+    private final MetaData metadata;
+
+    public SaveOrderConfigDisplayViewModel(MetaData metaData) {
+        this.metadata = metaData;
+
+        Optional<SaveOrderConfig> storedSaveOrderConfig = metaData.getSaveOrderConfig();
+
+        List<String> fieldNames = InternalBibtexFields.getAllPublicFieldNames();
+        fieldNames.add(BibEntry.KEY_FIELD);
+        Collections.sort(fieldNames);
+
+        priSortFieldsProperty.addAll(fieldNames);
+        secSortFieldsProperty.addAll(fieldNames);
+        terSortFieldsProperty.addAll(fieldNames);
+    }
+
+    public ListProperty<String> priSortFieldsProperty() {
+        return priSortFieldsProperty;
+    }
+
+    public ListProperty<String> secSortFieldsProperty() {
+        return secSortFieldsProperty;
+    }
+
+    public ListProperty<String> terSortFieldsProperty() {
+        return terSortFieldsProperty;
+    }
+
+    public SaveOrderConfig getSaveOrderConfig() {
+        SaveOrderConfig saveOrderConfig = new SaveOrderConfig();
+        SortCriterion primary = new SortCriterion(getSelectedItemAsLowerCaseTrim(savePriSortSelectedValueProperty), savePriDescPropertySelected.getValue());
+        saveOrderConfig.getSortCriteria().add(primary);
+        SortCriterion secondary = new SortCriterion(getSelectedItemAsLowerCaseTrim(saveSecSortSelectedValueProperty), saveSecDescPropertySelected.getValue());
+        saveOrderConfig.getSortCriteria().add(secondary);
+        SortCriterion tertiary = new SortCriterion(getSelectedItemAsLowerCaseTrim(saveTerSortSelectedValueProperty), saveTerDescPropertySelected.getValue());
+        saveOrderConfig.getSortCriteria().add(tertiary);
+
+        return saveOrderConfig;
+    }
+
+    public void setSaveOrderConfig(SaveOrderConfig saveOrderConfig) {
+        Objects.requireNonNull(saveOrderConfig);
+
+        savePriSortSelectedValueProperty.setValue(saveOrderConfig.getSortCriteria().get(0).field);
+        savePriDescPropertySelected.setValue(saveOrderConfig.getSortCriteria().get(0).descending);
+        saveSecSortSelectedValueProperty.setValue(saveOrderConfig.getSortCriteria().get(1).field);
+        saveSecDescPropertySelected.setValue(saveOrderConfig.getSortCriteria().get(1).descending);
+        saveTerSortSelectedValueProperty.setValue(saveOrderConfig.getSortCriteria().get(2).field);
+        saveTerDescPropertySelected.setValue(saveOrderConfig.getSortCriteria().get(2).descending);
+    }
+
+    private String getSelectedItemAsLowerCaseTrim(StringProperty string) {
+        return string.getValue().toLowerCase(Locale.ROOT).trim();
+    }
+
+    public BooleanProperty savePriDescPropertySelected() {
+        return savePriDescPropertySelected;
+    }
+
+    public BooleanProperty saveSecDescPropertySelected() {
+        return saveSecDescPropertySelected;
+    }
+
+    public BooleanProperty saveTerDescPropertySelected() {
+        return saveTerDescPropertySelected;
+    }
+
+    public StringProperty savePriSortSelectedValueProperty() {
+        return savePriSortSelectedValueProperty;
+    }
+
+    public StringProperty saveSecSortSelectedValueProperty() {
+        return saveSecSortSelectedValueProperty;
+    }
+
+    public StringProperty saveTerSortSelectedValueProperty() {
+        return saveTerSortSelectedValueProperty;
+    }
+
+    public void storeConfig() {
+        metadata.setSaveOrderConfig(this.getSaveOrderConfig());
+    }
+
+    public BooleanProperty saveInOriginalProperty() {
+        return saveInOriginalProperty;
+    }
+
+    public BooleanProperty saveInTableOrderProperty() {
+        return saveInTableOrderProperty;
+    }
+
+    public BooleanProperty saveInSpecifiedOrderProperty() {
+        return this.saveInSpecifiedOrderProperty;
+    }
 
 }

From 2415c3cefe474996042ef109f769b1f3b3ad17d9 Mon Sep 17 00:00:00 2001
From: LeonhardWolz <leonhard.wo@gmx.de>
Date: Thu, 21 Feb 2019 22:24:22 +0100
Subject: [PATCH 044/184] fixes #4610. Changed the way the GroupDialog
 description is displayed.  (#4660)

* Changed the way the GroupDialog description is displayed. It now uses a TextFlow Node to display the stylised text. The string with html tags is parsed and the sections of text within html tags are put in stylised Text Nodes. Rearranged the GroupDialog window, since the window grew larger then the display size. GroupDialog window is no longer resizable. fixes #4610

* Added a check to see if a database is currently open when attempting to create a new group. If no database is open we show a warning to the user. Added a german translation.

* Changed wording of an error message. Databases are nor referred to as libraries.
---
 .../jabref/gui/groups/GroupDescriptions.java  |   6 +-
 .../org/jabref/gui/groups/GroupDialog.java    | 103 +++++++++++++-----
 .../jabref/gui/groups/GroupTreeViewModel.java |  12 +-
 src/main/resources/l10n/JabRef_de.properties  |   4 +
 src/main/resources/l10n/JabRef_en.properties  |   4 +
 5 files changed, 96 insertions(+), 33 deletions(-)

diff --git a/src/main/java/org/jabref/gui/groups/GroupDescriptions.java b/src/main/java/org/jabref/gui/groups/GroupDescriptions.java
index 07fd780be6b..6548c0cb1a8 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDescriptions.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDescriptions.java
@@ -14,9 +14,9 @@ private GroupDescriptions() {
     public static String getDescriptionForPreview(String field, String expr, boolean caseSensitive, boolean regExp) {
         String header = regExp ? Localization.lang(
                 "This group contains entries whose <b>%0</b> field contains the regular expression <b>%1</b>",
-                field, StringUtil.quoteForHTML(expr)) : Localization.lang(
+                field, expr) : Localization.lang(
                         "This group contains entries whose <b>%0</b> field contains the keyword <b>%1</b>",
-                        field, StringUtil.quoteForHTML(expr));
+                        field, expr);
         String caseSensitiveText = caseSensitive ? Localization.lang("case sensitive") : Localization
                 .lang("case insensitive");
         String footer = regExp ? Localization
@@ -30,7 +30,7 @@ public static String getDescriptionForPreview(String field, String expr, boolean
                                 + "then using the context menu. "
                                 + "This process removes the term <b>%1</b> from "
                                 + "each entry's <b>%0</b> field.",
-                        field, StringUtil.quoteForHTML(expr));
+                        field, expr);
         return String.format("%s (%s). %s", header, caseSensitiveText, footer);
     }
 
diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
index 3d334919446..dc7d4ebd615 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDialog.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -2,6 +2,7 @@
 
 import java.io.IOException;
 import java.nio.file.Paths;
+import java.util.ArrayList;
 import java.util.Optional;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
@@ -9,6 +10,7 @@
 import javafx.beans.value.ChangeListener;
 import javafx.beans.value.ObservableValue;
 import javafx.geometry.Insets;
+import javafx.geometry.Orientation;
 import javafx.scene.Node;
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.CheckBox;
@@ -16,6 +18,7 @@
 import javafx.scene.control.RadioButton;
 import javafx.scene.control.ScrollPane;
 import javafx.scene.control.ScrollPane.ScrollBarPolicy;
+import javafx.scene.control.Separator;
 import javafx.scene.control.TextField;
 import javafx.scene.control.Toggle;
 import javafx.scene.control.ToggleGroup;
@@ -26,7 +29,6 @@
 import javafx.scene.text.FontPosture;
 import javafx.scene.text.Text;
 import javafx.scene.text.TextFlow;
-import javafx.scene.web.WebView;
 
 import org.jabref.Globals;
 import org.jabref.JabRefGUI;
@@ -104,7 +106,7 @@ class GroupDialog extends BaseDialog<AbstractGroup> {
     private final TextField texGroupFilePath = new TextField();
 
     // for all types
-    private final WebView descriptionWebView = new WebView();
+    private final TextFlow descriptionTextFlow = new TextFlow();
     private final StackPane optionsPanel = new StackPane();
 
 
@@ -120,7 +122,10 @@ public GroupDialog(JabRefFrame jabrefFrame, AbstractGroup editedGroup) {
 
         explicitRadioButton.setSelected(true);
 
-        descriptionWebView.setPrefWidth(585);
+        descriptionTextFlow.setMinWidth(585);
+        descriptionTextFlow.setPrefWidth(585);
+        descriptionTextFlow.setMinHeight(180);
+        descriptionTextFlow.setPrefHeight(180);
 
         // set default values (overwritten if editedGroup != null)
         keywordGroupSearchField.setText(jabrefFrame.prefs().get(JabRefPreferences.GROUPS_DEFAULT_FIELD));
@@ -196,26 +201,31 @@ public GroupDialog(JabRefFrame jabrefFrame, AbstractGroup editedGroup) {
         selectPanel.setPadding(new Insets(0, 0, 0, 10));
 
         // Description panel
-        ScrollPane descriptionPane = new ScrollPane(descriptionWebView);
+        ScrollPane descriptionPane = new ScrollPane(descriptionTextFlow);
         descriptionPane.setHbarPolicy(ScrollBarPolicy.AS_NEEDED);
         descriptionPane.setVbarPolicy(ScrollBarPolicy.AS_NEEDED);
 
         // create layout
-        VBox mainPanel = new VBox(15);
+        HBox mainPanel = new HBox(15);
         getDialogPane().setContent(mainPanel);
         mainPanel.setPadding(new Insets(5, 15, 5, 15));
         mainPanel.getChildren().setAll(
-                generalPanel,
                 new VBox(5,
-                        new Label(Localization.lang("Type")),
-                        selectPanel
-                ),
-                new VBox(
-                        new Label(Localization.lang("Options")),
-                        optionsPanel
+                        generalPanel,
+                        new VBox(5,
+                                new Label(Localization.lang("Type")),
+                                selectPanel
+                        )
                 ),
-                new Label(Localization.lang("Description")),
-                descriptionPane
+                new Separator(Orientation.VERTICAL),
+                new VBox(5,
+                        new VBox(
+                                new Label(Localization.lang("Options")),
+                                optionsPanel
+                        ),
+                        new Label(Localization.lang("Description")),
+                        descriptionPane
+                )
         );
 
         updateComponents();
@@ -393,6 +403,9 @@ groupName, getContext(),
                 texGroupFilePath.setText(group.getFilePath().toString());
             }
         }
+
+        setResizable(false);
+        getDialogPane().getScene().getWindow().sizeToScene();
     }
 
     public GroupDialog() {
@@ -517,7 +530,7 @@ private void updateComponents() {
         boolean okEnabled = !nameField.getText().trim().isEmpty();
         if (!okEnabled) {
             setDescription(Localization.lang("Please enter a name for the group."));
-            //TODO: okButton.setDisable(true);
+            getDialogPane().lookupButton(ButtonType.OK).setDisable(true);
             return;
         }
         String s1;
@@ -532,18 +545,18 @@ private void updateComponents() {
                     try {
                         Pattern.compile(s2);
                         setDescription(GroupDescriptions.getDescriptionForPreview(s1, s2, keywordGroupCaseSensitive.isSelected(),
-                                                                                  keywordGroupRegExp.isSelected()));
+                                keywordGroupRegExp.isSelected()));
                     } catch (PatternSyntaxException e) {
                         okEnabled = false;
                         setDescription(formatRegExException(s2, e));
                     }
                 } else {
                     setDescription(GroupDescriptions.getDescriptionForPreview(s1, s2, keywordGroupCaseSensitive.isSelected(),
-                                                                              keywordGroupRegExp.isSelected()));
+                            keywordGroupRegExp.isSelected()));
                 }
             } else {
                 setDescription(Localization.lang(
-                                                 "Please enter the field to search (e.g. <b>keywords</b>) and the keyword to search it for (e.g. <b>electrical</b>)."));
+                        "Please enter the field to search (e.g. <b>keywords</b>) and the keyword to search it for (e.g. <b>electrical</b>)."));
             }
             setNameFontItalic(true);
         } else if (searchRadioButton.isSelected()) {
@@ -551,8 +564,8 @@ private void updateComponents() {
             okEnabled = okEnabled & !s1.isEmpty();
             if (okEnabled) {
                 setDescription(fromTextFlowToHTMLString(SearchDescribers.getSearchDescriberFor(
-                                                                                               new SearchQuery(s1, isCaseSensitive(), isRegex()))
-                                                                        .getDescription()));
+                        new SearchQuery(s1, isCaseSensitive(), isRegex()))
+                        .getDescription()));
 
                 if (isRegex()) {
                     try {
@@ -564,17 +577,17 @@ private void updateComponents() {
                 }
             } else {
                 setDescription(Localization
-                                           .lang("Please enter a search term. For example, to search all fields for <b>Smith</b>, enter:<p>"
-                                                 + "<tt>smith</tt><p>"
-                                                 + "To search the field <b>Author</b> for <b>Smith</b> and the field <b>Title</b> for <b>electrical</b>, enter:<p>"
-                                                 + "<tt>author=smith and title=electrical</tt>"));
+                        .lang("Please enter a search term. For example, to search all fields for <b>Smith</b>, enter:<p>"
+                                + "<tt>smith</tt><p>"
+                                + "To search the field <b>Author</b> for <b>Smith</b> and the field <b>Title</b> for <b>electrical</b>, enter:<p>"
+                                + "<tt>author=smith and title=electrical</tt>"));
             }
             setNameFontItalic(true);
         } else if (explicitRadioButton.isSelected()) {
             setDescription(GroupDescriptions.getDescriptionForPreview());
             setNameFontItalic(false);
         }
-        //TODO: okButton.setDisable(!okEnabled);
+        getDialogPane().lookupButton(ButtonType.OK).setDisable(!okEnabled);
     }
 
     private String fromTextFlowToHTMLString(TextFlow textFlow) {
@@ -596,7 +609,45 @@ private boolean isCaseSensitive() {
     }
 
     private void setDescription(String description) {
-        descriptionWebView.getEngine().loadContent("<html>" + description + "</html>");
+        descriptionTextFlow.getChildren().setAll(createFormattedDescription(description));
+    }
+
+    private ArrayList<Node> createFormattedDescription(String descriptionHTML) {
+        ArrayList<Node> nodes = new ArrayList<>();
+
+        descriptionHTML = descriptionHTML.replaceAll("<p>|<br>", "\n");
+
+        String[] boldSplit = descriptionHTML.split("(?=<b>)|(?<=</b>)|(?=<i>)|(?<=</i>)|(?=<tt>)|(?<=</tt>)|(?=<kbd>)|(?<=</kbd>)");
+
+        for (String bs : boldSplit) {
+
+            if (bs.matches("<b>[^<>]*</b>")) {
+
+                bs = bs.replaceAll("<b>|</b>", "");
+                Text textElement = new Text(bs);
+                textElement.setStyle("-fx-font-weight: bold");
+                nodes.add(textElement);
+
+            } else if (bs.matches("<i>[^<>]*</i>")) {
+
+                bs = bs.replaceAll("<i>|</i>", "");
+                Text textElement = new Text(bs);
+                textElement.setStyle("-fx-font-style: italic");
+                nodes.add(textElement);
+
+            } else if (bs.matches("<tt>[^<>]*</tt>|<kbd>[^<>]*</kbd>")) {
+
+                bs = bs.replaceAll("<tt>|</tt>|<kbd>|</kbd>", "");
+                Text textElement = new Text(bs);
+                textElement.setStyle("-fx-font-family: 'Courier New', Courier, monospace");
+                nodes.add(textElement);
+
+            } else {
+                nodes.add(new Text(bs));
+            }
+        }
+
+        return nodes;
     }
 
     /**
diff --git a/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java b/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java
index ab1cb4449e6..de4c279e59c 100644
--- a/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java
+++ b/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java
@@ -106,7 +106,11 @@ private void onSelectedGroupChanged(ObservableList<GroupNodeViewModel> newValue)
      * Opens "New Group Dialog" and add the resulting group to the root
      */
     public void addNewGroupToRoot() {
-        addNewSubgroup(rootGroup.get());
+        if (currentDatabase.isPresent()) {
+            addNewSubgroup(rootGroup.get());
+        } else {
+            dialogService.showWarningDialogAndWait(Localization.lang("Cannot create group"), Localization.lang("Cannot create group. Please create a library first."));
+        }
     }
 
     /**
@@ -124,8 +128,8 @@ private void onActiveDatabaseChanged(Optional<BibDatabaseContext> newDatabase) {
             rootGroup.setValue(newRoot);
             this.selectedGroups.setAll(
                     stateManager.getSelectedGroup(newDatabase.get()).stream()
-                                .map(selectedGroup -> new GroupNodeViewModel(newDatabase.get(), stateManager, taskExecutor, selectedGroup, localDragboard))
-                                .collect(Collectors.toList()));
+                            .map(selectedGroup -> new GroupNodeViewModel(newDatabase.get(), stateManager, taskExecutor, selectedGroup, localDragboard))
+                            .collect(Collectors.toList()));
         } else {
             rootGroup.setValue(GroupNodeViewModel.getAllEntriesGroup(new BibDatabaseContext(), stateManager, taskExecutor, localDragboard));
         }
@@ -228,7 +232,7 @@ public void removeGroupKeepSubgroups(GroupNodeViewModel group) {
             //panel.getUndoManager().addEdit(undo);
             GroupTreeNode groupNode = group.getGroupNode();
             groupNode.getParent()
-                     .ifPresent(parent -> groupNode.moveAllChildrenTo(parent, parent.getIndexOfChild(groupNode).get()));
+                    .ifPresent(parent -> groupNode.moveAllChildrenTo(parent, parent.getIndexOfChild(groupNode).get()));
             groupNode.removeFromParent();
 
             dialogService.notify(Localization.lang("Removed group \"%0\".", group.getDisplayName()));
diff --git a/src/main/resources/l10n/JabRef_de.properties b/src/main/resources/l10n/JabRef_de.properties
index af35ed23e3e..775e06a9ae7 100644
--- a/src/main/resources/l10n/JabRef_de.properties
+++ b/src/main/resources/l10n/JabRef_de.properties
@@ -127,6 +127,10 @@ Cancel=Abbrechen
 
 Cannot\ add\ entries\ to\ group\ without\ generating\ keys.\ Generate\ keys\ now?=Einträge können einer Gruppe nicht hinzugefügt werden, ohne Keys zu generieren. Sollen die Keys jetzt generiert werden?
 
+Cannot\ create\ group=Gruppe kann nicht erstellt werden
+
+Cannot\ create\ group.\ Please\ create\ a\ library\ first.=Gruppe kann nicht erstellt werden. Erstellen sie zuerst eine Bibliothek.
+
 Cannot\ merge\ this\ change=Kann diese Änderung nicht einfügen
 
 case\ insensitive=Groß-/Kleinschreibung wird nicht unterschieden
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 9275461a40a..352b53bbb83 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -114,6 +114,10 @@ Cancel=Cancel
 
 Cannot\ add\ entries\ to\ group\ without\ generating\ keys.\ Generate\ keys\ now?=Cannot add entries to group without generating keys. Generate keys now?
 
+Cannot\ create\ group=Cannot create group
+
+Cannot\ create\ group.\ Please\ create\ a\ library\ first.=Cannot create group. Please create a library first.
+
 Cannot\ merge\ this\ change=Cannot merge this change
 
 case\ insensitive=case insensitive

From 4deb5814ed6347372e51e5413fc3924dc3b6db3b Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Sat, 23 Feb 2019 17:49:36 +0100
Subject: [PATCH 045/184] Remove resolve duplicate keys dialog (#4696)

---
 CHANGELOG.md                                  |   1 +
 src/main/java/org/jabref/gui/BasePanel.java   |   3 -
 src/main/java/org/jabref/gui/JabRefFrame.java |   1 -
 .../java/org/jabref/gui/actions/Actions.java  |   1 -
 .../ResolveDuplicateLabelDialog.java          | 138 ------------------
 .../SearchFixDuplicateLabels.java             | 108 --------------
 .../actions/HandleDuplicateWarnings.java      |  31 ----
 .../importer/actions/OpenDatabaseAction.java  |   5 +-
 src/main/resources/l10n/JabRef_en.properties  |   4 -
 9 files changed, 3 insertions(+), 289 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/bibtexkeypattern/ResolveDuplicateLabelDialog.java
 delete mode 100644 src/main/java/org/jabref/gui/bibtexkeypattern/SearchFixDuplicateLabels.java
 delete mode 100644 src/main/java/org/jabref/gui/importer/actions/HandleDuplicateWarnings.java

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 26e4ebbf307..560b2236e0a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -103,6 +103,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.
 - The number column was removed.
 - We removed the coloring of cells in the maintable according to whether the field is optional/required.
+- We removed the feature to find and resolve duplicate BibTeX keys (as this use case is already covered by the integrity check).
 - We removed a few commands from the right-click menu that are not needed often and thus don't need to be placed that prominently:
   - Print entry preview: available through entry preview
   - All commands related to marking: marking is not yet reimplemented
diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index 8c99cc4a68a..330b0e76eec 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -40,7 +40,6 @@
 import org.jabref.gui.autocompleter.AutoCompleteUpdater;
 import org.jabref.gui.autocompleter.PersonNameSuggestionProvider;
 import org.jabref.gui.autocompleter.SuggestionProviders;
-import org.jabref.gui.bibtexkeypattern.SearchFixDuplicateLabels;
 import org.jabref.gui.collab.DatabaseChangeMonitor;
 import org.jabref.gui.collab.FileUpdatePanel;
 import org.jabref.gui.desktop.JabRefDesktop;
@@ -406,8 +405,6 @@ private void setupActions() {
         actions.put(Actions.ABBREVIATE_MEDLINE, new AbbreviateAction(this, false));
         actions.put(Actions.UNABBREVIATE, new UnabbreviateAction(this));
 
-        actions.put(Actions.RESOLVE_DUPLICATE_KEYS, new SearchFixDuplicateLabels(this));
-
         actions.put(Actions.ADD_TO_GROUP, new GroupAddRemoveDialog(this, true, false));
         actions.put(Actions.REMOVE_FROM_GROUP, new GroupAddRemoveDialog(this, false, false));
         actions.put(Actions.MOVE_TO_GROUP, new GroupAddRemoveDialog(this, true, true));
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index dbbce3f23b3..8346fe58e7f 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -868,7 +868,6 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.RESOLVE_DUPLICATE_KEYS, new OldDatabaseCommandWrapper(Actions.RESOLVE_DUPLICATE_KEYS, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.CHECK_INTEGRITY, new IntegrityCheckAction(this)),
                 factory.createMenuItem(StandardActions.CLEANUP_ENTRIES, new OldDatabaseCommandWrapper(Actions.CLEANUP, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, Globals.stateManager)),
diff --git a/src/main/java/org/jabref/gui/actions/Actions.java b/src/main/java/org/jabref/gui/actions/Actions.java
index 4a72f33a45f..c3776047608 100644
--- a/src/main/java/org/jabref/gui/actions/Actions.java
+++ b/src/main/java/org/jabref/gui/actions/Actions.java
@@ -45,7 +45,6 @@ public enum Actions {
     REDO,
     REMOVE_FROM_GROUP,
     REPLACE_ALL,
-    RESOLVE_DUPLICATE_KEYS,
     SAVE,
     SAVE_AS,
     SAVE_SELECTED_AS_PLAIN,
diff --git a/src/main/java/org/jabref/gui/bibtexkeypattern/ResolveDuplicateLabelDialog.java b/src/main/java/org/jabref/gui/bibtexkeypattern/ResolveDuplicateLabelDialog.java
deleted file mode 100644
index f6c6aa5544c..00000000000
--- a/src/main/java/org/jabref/gui/bibtexkeypattern/ResolveDuplicateLabelDialog.java
+++ /dev/null
@@ -1,138 +0,0 @@
-package org.jabref.gui.bibtexkeypattern;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.AbstractAction;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-
-import javafx.embed.swing.JFXPanel;
-import javafx.scene.Scene;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.FXDialogService;
-import org.jabref.gui.PreviewPanel;
-import org.jabref.gui.customjfx.CustomJFXPanel;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.entry.BibEntry;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import com.jgoodies.forms.builder.FormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-
-/**
- * Dialog box for resolving duplicate bibte keys
- */
-class ResolveDuplicateLabelDialog {
-
-    private final JDialog diag;
-    private final List<JCheckBox> cbs = new ArrayList<>();
-    private boolean okPressed;
-    private boolean cancelPressed;
-
-    public ResolveDuplicateLabelDialog(BasePanel panel, String key, List<BibEntry> entries) {
-        diag = new JDialog((JFrame) null, Localization.lang("Duplicate BibTeX key"), true);
-
-        FormBuilder b = FormBuilder.create().layout(new FormLayout(
-                "left:pref, 4dlu, fill:pref", "p"));
-        b.add(new JLabel(Localization.lang("Duplicate BibTeX key") + ": " + key)).xyw(1, 1, 3);
-        b.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        boolean first = true;
-        int row = 3;
-        for (BibEntry entry : entries) {
-            JCheckBox cb = new JCheckBox(Localization.lang("Generate BibTeX key"), !first);
-            b.appendRows("1dlu, p");
-            b.add(cb).xy(1, row);
-            PreviewPanel previewPanel = new PreviewPanel(null, panel.getBibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
-            previewPanel.setEntry(entry);
-            JFXPanel container = CustomJFXPanel.wrap(new Scene(previewPanel));
-            container.setPreferredSize(new Dimension(800, 90));
-            b.add(container).xy(3, row);
-            row += 2;
-            cbs.add(cb);
-            first = false;
-        }
-
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        JButton ok = new JButton(Localization.lang("OK"));
-        bb.addButton(ok);
-        JButton ignore = new JButton(Localization.lang("Ignore"));
-        bb.addButton(ignore);
-        JButton cancel = new JButton(Localization.lang("Cancel"));
-        bb.addButton(cancel);
-        bb.addGlue();
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        diag.getContentPane().add(b.getPanel(), BorderLayout.CENTER);
-        diag.getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-
-        diag.pack();
-
-        ok.addActionListener(e -> {
-            okPressed = true;
-            diag.dispose();
-        });
-
-        ignore.addActionListener(e -> diag.dispose());
-
-        AbstractAction closeAction = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                cancelPressed = true;
-                diag.dispose();
-            }
-        };
-
-        cancel.addActionListener(closeAction);
-
-        ActionMap am = b.getPanel().getActionMap();
-        InputMap im = b.getPanel().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", closeAction);
-    }
-
-    /**
-     * After the dialog has been closed, this query answers whether the dialog was okPressed
-     * (by cancel button or by closing the dialog directly).
-     * @return true if it was okPressed, false if Ok was pressed.
-     */
-    public boolean isOkPressed() {
-        return okPressed;
-    }
-
-    /**
-     * Get the list of checkboxes where the user has selected which entries to generate
-     * new keys for.
-     * @return the list of checkboxes
-     */
-    public List<JCheckBox> getCheckBoxes() {
-        return cbs;
-    }
-
-    public void show() {
-        okPressed = false;
-        diag.setLocationRelativeTo(diag.getParent());
-        diag.setVisible(true);
-    }
-
-    public boolean isCancelPressed() {
-        return cancelPressed;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/bibtexkeypattern/SearchFixDuplicateLabels.java b/src/main/java/org/jabref/gui/bibtexkeypattern/SearchFixDuplicateLabels.java
deleted file mode 100644
index 297d42a64c5..00000000000
--- a/src/main/java/org/jabref/gui/bibtexkeypattern/SearchFixDuplicateLabels.java
+++ /dev/null
@@ -1,108 +0,0 @@
-package org.jabref.gui.bibtexkeypattern;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
-
-import javax.swing.JCheckBox;
-import javax.swing.SwingUtilities;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.actions.BaseAction;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableKeyChange;
-import org.jabref.gui.util.BackgroundTask;
-import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.FieldChange;
-import org.jabref.model.database.BibDatabase;
-import org.jabref.model.entry.BibEntry;
-
-/**
- * Function for resolving duplicate BibTeX keys.
- */
-public class SearchFixDuplicateLabels implements BaseAction {
-
-    private final BasePanel panel;
-
-    public SearchFixDuplicateLabels(BasePanel panel) {
-        this.panel = panel;
-    }
-
-    @Override
-    public void action() throws Exception {
-        panel.output(Localization.lang("Resolving duplicate BibTeX keys..."));
-        BackgroundTask.wrap(this::findDuplicates)
-                      .onSuccess(dupes -> SwingUtilities.invokeLater(() -> resolveDuplicates(dupes)))
-                      .executeWith(Globals.TASK_EXECUTOR);
-    }
-
-    private void resolveDuplicates(Map<String, List<BibEntry>> dupes) {
-        List<BibEntry> toGenerateFor = new ArrayList<>();
-        for (Map.Entry<String, List<BibEntry>> dupeEntry : dupes.entrySet()) {
-            ResolveDuplicateLabelDialog rdld = new ResolveDuplicateLabelDialog(panel, dupeEntry.getKey(), dupeEntry.getValue());
-            rdld.show();
-            if (rdld.isOkPressed()) {
-                List<JCheckBox> cbs = rdld.getCheckBoxes();
-                for (int i = 0; i < cbs.size(); i++) {
-                    if (cbs.get(i).isSelected()) {
-                        // The checkbox for entry i has been selected, so we should generate a new key for it:
-                        toGenerateFor.add(dupeEntry.getValue().get(i));
-                    }
-                }
-            } else if (rdld.isCancelPressed()) {
-                break;
-            }
-        }
-
-        // Do the actual generation:
-        if (!toGenerateFor.isEmpty()) {
-            NamedCompound ce = new NamedCompound(Localization.lang("Resolve duplicate BibTeX keys"));
-            BibtexKeyGenerator keyGenerator = new BibtexKeyGenerator(panel.getBibDatabaseContext(), Globals.prefs.getBibtexKeyPatternPreferences());
-            for (BibEntry entry : toGenerateFor) {
-                Optional<FieldChange> change = keyGenerator.generateAndSetKey(entry);
-                change.ifPresent(fieldChange -> ce.addEdit(new UndoableKeyChange(fieldChange)));
-            }
-            ce.end();
-            panel.getUndoManager().addEdit(ce);
-            panel.markBaseChanged();
-        }
-        panel.output(Localization.lang("Finished resolving duplicate BibTeX keys. %0 entries modified.",
-                String.valueOf(toGenerateFor.size())));
-    }
-
-    private Map<String, List<BibEntry>> findDuplicates() {
-        // Find all multiple occurrences of BibTeX keys.
-        Map<String, List<BibEntry>> dupes = new HashMap<>();
-
-        Map<String, BibEntry> foundKeys = new HashMap<>();
-        BibDatabase db = panel.getDatabase();
-        for (BibEntry entry : db.getEntries()) {
-            entry.getCiteKeyOptional().filter(key -> !key.isEmpty()).ifPresent(key -> {
-                // See whether this entry's key is already known:
-                if (foundKeys.containsKey(key)) {
-                    // Already known, so we have found a dupe. See if it was already found as a dupe:
-                    if (dupes.containsKey(key)) {
-                        // Already in the dupe map. Add this entry as well:
-                        dupes.get(key).add(entry);
-                    } else {
-                        // Construct a list of entries for this key:
-                        List<BibEntry> al = new ArrayList<>();
-                        // Add both the first one we found, and the one we found just now:
-                        al.add(foundKeys.get(key));
-                        al.add(entry);
-                        // Add the list to the dupe map:
-                        dupes.put(key, al);
-                    }
-                } else {
-                    // Not already known. Add key and entry to map:
-                    foundKeys.put(key, entry);
-                }
-            });
-        }
-        return dupes;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/importer/actions/HandleDuplicateWarnings.java b/src/main/java/org/jabref/gui/importer/actions/HandleDuplicateWarnings.java
deleted file mode 100644
index fb79d60ac8b..00000000000
--- a/src/main/java/org/jabref/gui/importer/actions/HandleDuplicateWarnings.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package org.jabref.gui.importer.actions;
-
-import javax.swing.JOptionPane;
-
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.actions.Actions;
-import org.jabref.logic.importer.ParserResult;
-import org.jabref.logic.l10n.Localization;
-
-/**
- * GUIPostOpenAction that checks whether there are warnings about duplicate BibTeX keys, and
- * if so, offers to start the duplicate resolving process.
- */
-public class HandleDuplicateWarnings implements GUIPostOpenAction {
-
-    @Override
-    public boolean isActionNecessary(ParserResult pr) {
-        return pr.hasDuplicateKeys();
-    }
-
-    @Override
-    public void performAction(BasePanel panel, ParserResult pr) {
-        int answer = JOptionPane.showConfirmDialog(null,
-                "<html><p>" + Localization.lang("This library contains one or more duplicated BibTeX keys.")
-                        + "</p><p>" + Localization.lang("Do you want to resolve duplicate keys now?"),
-                Localization.lang("Duplicate BibTeX key"), JOptionPane.YES_NO_OPTION);
-        if (answer == JOptionPane.YES_OPTION) {
-            panel.runCommand(Actions.RESOLVE_DUPLICATE_KEYS);
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java b/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
index 0fdba4fd411..9a87333b386 100644
--- a/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
@@ -57,9 +57,8 @@ public class OpenDatabaseAction extends SimpleCommand {
             new FileLinksUpgradeWarning(),
 
             // Check for new custom entry types loaded from the BIB file:
-            new CheckForNewEntryTypesAction(),
-            // Warning about and handling duplicate BibTeX keys:
-            new HandleDuplicateWarnings());
+            new CheckForNewEntryTypesAction()
+    );
 
     private final JabRefFrame frame;
 
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 352b53bbb83..8d1927343d2 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1212,10 +1212,6 @@ search\ expression=search expression
 
 Optional\ fields\ 2=Optional fields 2
 Waiting\ for\ save\ operation\ to\ finish=Waiting for save operation to finish
-Resolving\ duplicate\ BibTeX\ keys...=Resolving duplicate BibTeX keys...
-Finished\ resolving\ duplicate\ BibTeX\ keys.\ %0\ entries\ modified.=Finished resolving duplicate BibTeX keys. %0 entries modified.
-This\ library\ contains\ one\ or\ more\ duplicated\ BibTeX\ keys.=This library contains one or more duplicated BibTeX keys.
-Do\ you\ want\ to\ resolve\ duplicate\ keys\ now?=Do you want to resolve duplicate keys now?
 
 Find\ and\ remove\ duplicate\ BibTeX\ keys=Find and remove duplicate BibTeX keys
 Expected\ syntax\ for\ --fetch\='<name\ of\ fetcher>\:<query>'=Expected syntax for --fetch='<name of fetcher>:<query>'

From 395609de29a9b46f0d40fda3e0559b2698e21480 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Sun, 24 Feb 2019 18:37:08 +0100
Subject: [PATCH 046/184] Catch NumberFormatException in BibTeXML exporter
 (#4698)

---
 .../logic/exporter/BibTeXMLExporter.java      | 30 +++++++++++--------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/src/main/java/org/jabref/logic/exporter/BibTeXMLExporter.java b/src/main/java/org/jabref/logic/exporter/BibTeXMLExporter.java
index 01a74e9f855..363a67bca42 100644
--- a/src/main/java/org/jabref/logic/exporter/BibTeXMLExporter.java
+++ b/src/main/java/org/jabref/logic/exporter/BibTeXMLExporter.java
@@ -141,7 +141,7 @@ private void createMarshallerAndWriteToFile(File file, Path resultFile) throws S
     }
 
     /**
-     * Contains same logic as the {@link parse()} method, but inbook needs a special treatment, because
+     * Contains same logic as the {@link #parse(Object, BibEntry, Entry)} method, but inbook needs a special treatment, because
      * the contents of inbook are stored in a List of JAXBElements. So we first need to create
      * a JAXBElement for every field and then add it to the content list.
      */
@@ -192,33 +192,37 @@ private void parseInbook(Inbook inbook, BibEntry bibEntry, Entry entry) {
      */
     private <T> void parse(T entryType, BibEntry bibEntry, Entry entry) {
         List<Method> declaredSetMethods = getListOfSetMethods(entryType);
-        Map<String, String> fieldMap = bibEntry.getFieldMap();
-        for (Map.Entry<String, String> entryField : fieldMap.entrySet()) {
-            String value = entryField.getValue();
+        for (Map.Entry<String, String> entryField : bibEntry.getFieldMap().entrySet()) {
             String key = entryField.getKey();
+            String value = entryField.getValue();
             for (Method method : declaredSetMethods) {
                 String methodNameWithoutSet = method.getName().replace("set", "").toLowerCase(ENGLISH);
-                try {
+                if (!methodNameWithoutSet.equals(key)) {
+                    continue;
+                }
 
-                    if ("year".equals(key) && key.equals(methodNameWithoutSet)) {
+                try {
+                    if ("year".equals(key)) {
                         try {
-
-                            XMLGregorianCalendar calendar = DatatypeFactory.newInstance()
-                                    .newXMLGregorianCalendar(value);
+                            XMLGregorianCalendar calendar = DatatypeFactory.newInstance().newXMLGregorianCalendar(value);
                             method.invoke(entryType, calendar);
                         } catch (DatatypeConfigurationException e) {
                             LOGGER.error("A configuration error occured");
                         }
                         break;
-                    } else if ("number".equals(key) && key.equals(methodNameWithoutSet)) {
-                        method.invoke(entryType, new BigInteger(value));
+                    } else if ("number".equals(key)) {
+                        try {
+                            method.invoke(entryType, new BigInteger(value));
+                        } catch (NumberFormatException exception) {
+                            LOGGER.warn("The value %s of the 'number' field is not an integer and thus is ignored for the export", value);
+                        }
                         break;
-                    } else if (key.equals(methodNameWithoutSet)) {
+                    } else {
                         method.invoke(entryType, value);
                         break;
                     }
                 } catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
-                    LOGGER.error("Could not invoke method", e);
+                    LOGGER.error("Could not invoke method " + method.getName(), e);
                 }
             }
 

From 159c48aa27c699bd49798057db2c1aac9752b15e Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 24 Feb 2019 20:17:54 +0100
Subject: [PATCH 047/184] create empty dialog pane for preferences dialog to
 make root components work

move old save order config to the new class
add toggle group

TODO: Find out why initialize is not called
---
 .../jabref/gui/SaveOrderConfigDisplay.fxml    | 10 ++--
 .../gui/SaveOrderConfigDisplayView.java       | 31 ++++++++--
 .../gui/SaveOrderConfigDisplayViewModel.java  | 39 +++++++++----
 .../preferences/ExportSortingPrefsTab.java    | 43 ++------------
 .../gui/preferences/PreferencesDialog.fxml    |  6 ++
 .../gui/preferences/PreferencesDialog.java    | 57 ++++++++++++-------
 .../model/metadata/SaveOrderConfig.java       | 14 +++--
 .../jabref/preferences/JabRefPreferences.java |  2 +
 .../preferences/PreferencesService.java       |  5 ++
 9 files changed, 119 insertions(+), 88 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/preferences/PreferencesDialog.fxml

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
index ed8a74897cd..f05d16e55ef 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
@@ -9,7 +9,7 @@
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.RowConstraints?>
 
-<GridPane prefHeight="400.0" prefWidth="600.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1">
+<fx:root type="javafx.scene.layout.GridPane" prefHeight="400.0" prefWidth="600.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1">
   <columnConstraints>
     <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="100.0" />
     <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
@@ -30,9 +30,9 @@
       <ComboBox fx:id="savePriSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="3" />
       <ComboBox fx:id="saveSecSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="4" />
       <ComboBox fx:id="saveTerSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="5" />
-      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2" />
-      <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" GridPane.columnSpan="3" GridPane.rowIndex="1" />
-      <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" GridPane.columnSpan="3"/>
+      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2" toggleGroup="$saveOrderToggleGroup"/>
+      <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" GridPane.columnSpan="3" GridPane.rowIndex="1" toggleGroup="$saveOrderToggleGroup"/>
+      <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" GridPane.columnSpan="3" toggleGroup="$saveOrderToggleGroup"/>
       <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" disabled="${!exportInSpecifiedOrder.selected}"/>
       <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" disabled="${!exportInSpecifiedOrder.selected}" />
       <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" disabled="${!exportInSpecifiedOrder.selected}" />
@@ -40,4 +40,4 @@
       <Label text="Secondary sort criterion" GridPane.rowIndex="4" disabled="${!exportInSpecifiedOrder.selected}" />
       <Label text="Tertiary sort criterion" GridPane.rowIndex="5" disabled="${!exportInSpecifiedOrder.selected}"/>
    </children>
-</GridPane>
+</fx:root>
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
index e0a389d8c56..769a468f314 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
@@ -1,14 +1,23 @@
 package org.jabref.gui;
 
+import javax.inject.Inject;
+
 import javafx.fxml.FXML;
+import javafx.scene.Node;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.RadioButton;
 import javafx.scene.control.ToggleGroup;
+import javafx.scene.layout.GridPane;
+
+import org.jabref.model.metadata.SaveOrderConfig;
+import org.jabref.preferences.PreferencesService;
 
-import org.jabref.model.metadata.MetaData;
+import com.airhacks.afterburner.views.ViewLoader;
 
-public class SaveOrderConfigDisplayView {
+public class SaveOrderConfigDisplayView extends GridPane {
+
+    private final SaveOrderConfig config;
 
     @FXML private ToggleGroup saveOrderToggleGroup;
     @FXML private ComboBox<String> savePriSort;
@@ -20,17 +29,23 @@ public class SaveOrderConfigDisplayView {
     @FXML private CheckBox savePriDesc;
     @FXML private CheckBox saveSecDesc;
     @FXML private CheckBox saveTerDesc;
+    @Inject private PreferencesService preferencesService;
+
     private SaveOrderConfigDisplayViewModel viewModel;
-    private final MetaData metadata;
 
-    public SaveOrderConfigDisplayView(MetaData metadata) {
-        this.metadata = metadata;
+    public SaveOrderConfigDisplayView(SaveOrderConfig config) {
+        this.config = config;
+
+        ViewLoader.view(this)
+                  .root(this)
+                  .controller(this)
+                  .load();
     }
 
     @FXML
     private void initialize() {
 
-        viewModel = new SaveOrderConfigDisplayViewModel(metadata);
+        viewModel = new SaveOrderConfigDisplayViewModel(config, preferencesService);
 
         exportInSpecifiedOrder.selectedProperty().bindBidirectional(viewModel.saveInSpecifiedOrderProperty());
         exportInTableOrder.selectedProperty().bindBidirectional(viewModel.saveInTableOrderProperty());
@@ -53,4 +68,8 @@ private void initialize() {
     public void storeConfig() {
         viewModel.storeConfig();
     }
+
+    public Node getJFXPanel() {
+        return this;
+    }
 }
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
index 8ef3135afd3..1d251e78ba6 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
@@ -4,7 +4,6 @@
 import java.util.List;
 import java.util.Locale;
 import java.util.Objects;
-import java.util.Optional;
 
 import javafx.beans.property.BooleanProperty;
 import javafx.beans.property.ListProperty;
@@ -16,9 +15,9 @@
 
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.InternalBibtexFields;
-import org.jabref.model.metadata.MetaData;
 import org.jabref.model.metadata.SaveOrderConfig;
 import org.jabref.model.metadata.SaveOrderConfig.SortCriterion;
+import org.jabref.preferences.PreferencesService;
 
 public class SaveOrderConfigDisplayViewModel {
 
@@ -38,13 +37,14 @@ public class SaveOrderConfigDisplayViewModel {
     private final BooleanProperty saveInTableOrderProperty = new SimpleBooleanProperty();
     private final BooleanProperty saveInSpecifiedOrderProperty = new SimpleBooleanProperty();
 
-    private final MetaData metadata;
+    private final SaveOrderConfig config;
+    private final PreferencesService prefs;
 
-    public SaveOrderConfigDisplayViewModel(MetaData metaData) {
-        this.metadata = metaData;
-
-        Optional<SaveOrderConfig> storedSaveOrderConfig = metaData.getSaveOrderConfig();
+    public SaveOrderConfigDisplayViewModel(SaveOrderConfig config, PreferencesService prefs) {
+        this.config = config;
+        this.prefs = prefs;
 
+        SaveOrderConfig storedSaveOrderConfig = config;
         List<String> fieldNames = InternalBibtexFields.getAllPublicFieldNames();
         fieldNames.add(BibEntry.KEY_FIELD);
         Collections.sort(fieldNames);
@@ -52,6 +52,16 @@ public SaveOrderConfigDisplayViewModel(MetaData metaData) {
         priSortFieldsProperty.addAll(fieldNames);
         secSortFieldsProperty.addAll(fieldNames);
         terSortFieldsProperty.addAll(fieldNames);
+
+        if (config.saveInOriginalOrder()) {
+            saveInOriginalProperty.setValue(true);
+        } else if (config.saveInSpecifiedOrder()) {
+            saveInSpecifiedOrderProperty.setValue(true);
+        } else {
+            saveInTableOrderProperty.setValue(true);
+        }
+        setSaveOrderConfig(config);
+
     }
 
     public ListProperty<String> priSortFieldsProperty() {
@@ -67,13 +77,12 @@ public ListProperty<String> terSortFieldsProperty() {
     }
 
     public SaveOrderConfig getSaveOrderConfig() {
-        SaveOrderConfig saveOrderConfig = new SaveOrderConfig();
+
         SortCriterion primary = new SortCriterion(getSelectedItemAsLowerCaseTrim(savePriSortSelectedValueProperty), savePriDescPropertySelected.getValue());
-        saveOrderConfig.getSortCriteria().add(primary);
         SortCriterion secondary = new SortCriterion(getSelectedItemAsLowerCaseTrim(saveSecSortSelectedValueProperty), saveSecDescPropertySelected.getValue());
-        saveOrderConfig.getSortCriteria().add(secondary);
         SortCriterion tertiary = new SortCriterion(getSelectedItemAsLowerCaseTrim(saveTerSortSelectedValueProperty), saveTerDescPropertySelected.getValue());
-        saveOrderConfig.getSortCriteria().add(tertiary);
+
+        SaveOrderConfig saveOrderConfig = new SaveOrderConfig(saveInOriginalProperty.getValue(), primary, secondary, tertiary);
 
         return saveOrderConfig;
     }
@@ -87,6 +96,12 @@ public void setSaveOrderConfig(SaveOrderConfig saveOrderConfig) {
         saveSecDescPropertySelected.setValue(saveOrderConfig.getSortCriteria().get(1).descending);
         saveTerSortSelectedValueProperty.setValue(saveOrderConfig.getSortCriteria().get(2).field);
         saveTerDescPropertySelected.setValue(saveOrderConfig.getSortCriteria().get(2).descending);
+
+        if (saveInOriginalProperty.getValue()) {
+            saveOrderConfig.setSaveInOriginalOrder();
+        } else {
+            saveOrderConfig.setSaveInSpecifiedOrder();
+        }
     }
 
     private String getSelectedItemAsLowerCaseTrim(StringProperty string) {
@@ -118,7 +133,7 @@ public StringProperty saveTerSortSelectedValueProperty() {
     }
 
     public void storeConfig() {
-        metadata.setSaveOrderConfig(this.getSaveOrderConfig());
+        prefs.storeExportSaveOrder(this.getSaveOrderConfig());
     }
 
     public BooleanProperty saveInOriginalProperty() {
diff --git a/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java b/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
index c567619ee61..f67fda34e81 100644
--- a/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
@@ -1,17 +1,14 @@
 package org.jabref.gui.preferences;
 
-import javafx.event.ActionEvent;
-import javafx.event.EventHandler;
 import javafx.scene.Node;
 import javafx.scene.control.Label;
 import javafx.scene.control.RadioButton;
-import javafx.scene.control.Separator;
 import javafx.scene.control.ToggleGroup;
 import javafx.scene.layout.GridPane;
 import javafx.scene.layout.Pane;
 import javafx.scene.shape.Line;
 
-import org.jabref.gui.SaveOrderConfigDisplay;
+import org.jabref.gui.SaveOrderConfigDisplayView;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.preferences.JabRefPreferences;
 
@@ -25,7 +22,7 @@ class ExportSortingPrefsTab extends Pane implements PrefsTab {
     private final RadioButton exportInOriginalOrder;
     private final RadioButton exportInTableOrder;
     private final RadioButton exportInSpecifiedOrder;
-    private final SaveOrderConfigDisplay exportOrderPanel;
+    private final SaveOrderConfigDisplayView exportOrderPanel;
     private final GridPane builder = new GridPane();
 
     public ExportSortingPrefsTab(JabRefPreferences prefs) {
@@ -41,28 +38,11 @@ public ExportSortingPrefsTab(JabRefPreferences prefs) {
         exportInTableOrder.setToggleGroup(group);
         exportInSpecifiedOrder.setToggleGroup(group);
 
-        exportOrderPanel = new SaveOrderConfigDisplay();
-
-        EventHandler<ActionEvent> listener = (event) -> {
-            boolean selected = event.getSource() == exportInSpecifiedOrder;
-            exportOrderPanel.setEnabled(selected);
-        };
-
-        exportInOriginalOrder.setOnAction(listener);
-        exportInTableOrder.setOnAction(listener);
-        exportInSpecifiedOrder.setOnAction(listener);
+        exportOrderPanel = new SaveOrderConfigDisplayView(prefs.loadExportSaveOrder());
 
         Label exportSortOrder = new Label(Localization.lang("Export sort order"));
         exportSortOrder.getStyleClass().add("sectionHeader");
         // create GUI
-        builder.add(exportSortOrder, 1, 1);
-        builder.add(new Separator(), 2, 1);
-        builder.add(exportInOriginalOrder, 1, 2);
-        builder.add(new Line(), 2, 3);
-        builder.add(exportInTableOrder, 1, 4);
-        builder.add(new Line(), 2, 5);
-        builder.add(exportInSpecifiedOrder, 1, 6);
-        builder.add(new Line(), 2, 7);
 
         builder.add(exportOrderPanel.getJFXPanel(), 1, 8);
         builder.add(new Line(), 2, 9);
@@ -76,25 +56,12 @@ public Node getBuilder() {
 
     @Override
     public void setValues() {
-        if (prefs.getBoolean(JabRefPreferences.EXPORT_IN_ORIGINAL_ORDER)) {
-            exportInOriginalOrder.setSelected(true);
-        } else if (prefs.getBoolean(JabRefPreferences.EXPORT_IN_SPECIFIED_ORDER)) {
-            exportInSpecifiedOrder.setSelected(true);
-        } else {
-            exportInTableOrder.setSelected(true);
-        }
-
-        boolean selected = prefs.getBoolean(JabRefPreferences.EXPORT_IN_SPECIFIED_ORDER);
-        exportOrderPanel.setEnabled(selected);
-        exportOrderPanel.setSaveOrderConfig(prefs.loadExportSaveOrder());
+
     }
 
     @Override
     public void storeSettings() {
-        prefs.putBoolean(JabRefPreferences.EXPORT_IN_ORIGINAL_ORDER, exportInOriginalOrder.isSelected());
-        prefs.putBoolean(JabRefPreferences.EXPORT_IN_SPECIFIED_ORDER, exportInSpecifiedOrder.isSelected());
-
-        prefs.storeExportSaveOrder(exportOrderPanel.getSaveOrderConfig());
+        exportOrderPanel.storeConfig();
     }
 
     @Override
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.fxml b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.fxml
new file mode 100644
index 00000000000..2e41e88e6c2
--- /dev/null
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.fxml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.DialogPane?>
+
+
+<DialogPane prefHeight="514.0" prefWidth="818.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.preferences.PreferencesDialog" />
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
index 8881f6af654..1727658b210 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
@@ -5,6 +5,7 @@
 
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
+import javafx.fxml.FXML;
 import javafx.geometry.Pos;
 import javafx.scene.control.Button;
 import javafx.scene.control.ButtonBar.ButtonData;
@@ -37,6 +38,7 @@
 import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.JabRefPreferencesFilter;
 
+import com.airhacks.afterburner.views.ViewLoader;
 import org.fxmisc.easybind.EasyBind;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -62,6 +64,10 @@ public PreferencesDialog(JabRefFrame parent, TaskExecutor taskExecutor) {
         setTitle(Localization.lang("JabRef preferences"));
         getDialogPane().getScene().getStylesheets().add(this.getClass().getResource("PreferencesDialog.css").toExternalForm());
 
+        ViewLoader.view(this)
+                  .load()
+                  .setAsDialogPane(this);
+
         ButtonType save = new ButtonType(Localization.lang("Save"), ButtonData.OK_DONE);
         getDialogPane().getButtonTypes().addAll(save, ButtonType.CANCEL);
         ControlHelper.setAction(save, getDialogPane(), event -> {
@@ -93,9 +99,15 @@ public PreferencesDialog(JabRefFrame parent, TaskExecutor taskExecutor) {
 
         container = new BorderPane();
         getDialogPane().setContent(container);
+
         construct();
     }
 
+    @FXML
+    private void initalize() {
+
+    }
+
     private void construct() {
         VBox vBox = new VBox();
         vBox.setPrefWidth(160);
@@ -112,8 +124,8 @@ private void construct() {
         });
         tabsList.getSelectionModel().selectFirst();
         new ViewModelListCellFactory<PrefsTab>()
-                .withText(PrefsTab::getTabName)
-                .install(tabsList);
+                                                .withText(PrefsTab::getTabName)
+                                                .install(tabsList);
 
         VBox buttonContainer = new VBox();
         buttonContainer.setAlignment(Pos.BOTTOM_LEFT);
@@ -133,37 +145,38 @@ private void construct() {
         resetPreferences.setOnAction(e -> resetPreferences());
         resetPreferences.setMaxWidth(Double.MAX_VALUE);
         buttonContainer.getChildren().addAll(
-                importPreferences,
-                exportPreferences,
-                showPreferences,
-                resetPreferences);
+                                             importPreferences,
+                                             exportPreferences,
+                                             showPreferences,
+                                             resetPreferences);
 
         VBox spacer = new VBox();
         spacer.setPrefHeight(10.0);
         VBox.setVgrow(tabsList, Priority.ALWAYS);
         VBox.setVgrow(spacer, Priority.SOMETIMES);
         vBox.getChildren().addAll(
-                tabsList,
-                spacer,
-                buttonContainer);
+                                  tabsList,
+                                  spacer,
+                                  buttonContainer);
 
         container.setLeft(vBox);
 
         setValues();
+
     }
 
     private void resetPreferences() {
         boolean resetPreferencesConfirmed = dialogService.showConfirmationDialogAndWait(
-                Localization.lang("Reset preferences"),
-                Localization.lang("Are you sure you want to reset all settings to default values?"),
-                Localization.lang("Reset preferences"),
-                Localization.lang("Cancel"));
+                                                                                        Localization.lang("Reset preferences"),
+                                                                                        Localization.lang("Are you sure you want to reset all settings to default values?"),
+                                                                                        Localization.lang("Reset preferences"),
+                                                                                        Localization.lang("Cancel"));
         if (resetPreferencesConfirmed) {
             try {
                 prefs.clear();
 
                 dialogService.showWarningDialogAndWait(Localization.lang("Reset preferences"),
-                        Localization.lang("You must restart JabRef for this to come into effect."));
+                                                       Localization.lang("You must restart JabRef for this to come into effect."));
             } catch (BackingStoreException ex) {
                 LOGGER.error("Error while resetting preferences", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("Reset preferences"), ex);
@@ -174,9 +187,9 @@ private void resetPreferences() {
 
     private void importPreferences() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                .addExtensionFilter(StandardFileType.XML)
-                .withDefaultExtension(StandardFileType.XML)
-                .withInitialDirectory(prefs.setLastPreferencesExportPath()).build();
+                                                                                               .addExtensionFilter(StandardFileType.XML)
+                                                                                               .withDefaultExtension(StandardFileType.XML)
+                                                                                               .withInitialDirectory(prefs.setLastPreferencesExportPath()).build();
 
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> {
             try {
@@ -184,7 +197,7 @@ private void importPreferences() {
                 updateAfterPreferenceChanges();
 
                 dialogService.showWarningDialogAndWait(Localization.lang("Import preferences"),
-                        Localization.lang("You must restart JabRef for this to come into effect."));
+                                                       Localization.lang("You must restart JabRef for this to come into effect."));
             } catch (JabRefException ex) {
                 LOGGER.error("Error while importing preferences", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("Import preferences"), ex);
@@ -229,10 +242,10 @@ public void setValues() {
 
     private void exportPreferences() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                .addExtensionFilter(StandardFileType.XML)
-                .withDefaultExtension(StandardFileType.XML)
-                .withInitialDirectory(prefs.setLastPreferencesExportPath())
-                .build();
+                                                                                               .addExtensionFilter(StandardFileType.XML)
+                                                                                               .withDefaultExtension(StandardFileType.XML)
+                                                                                               .withInitialDirectory(prefs.setLastPreferencesExportPath())
+                                                                                               .build();
 
         dialogService.showFileSaveDialog(fileDialogConfiguration)
                      .ifPresent(exportFile -> {
diff --git a/src/main/java/org/jabref/model/metadata/SaveOrderConfig.java b/src/main/java/org/jabref/model/metadata/SaveOrderConfig.java
index 63b43eb4d45..59fbfaa2d42 100644
--- a/src/main/java/org/jabref/model/metadata/SaveOrderConfig.java
+++ b/src/main/java/org/jabref/model/metadata/SaveOrderConfig.java
@@ -61,6 +61,10 @@ public boolean saveInOriginalOrder() {
         return saveInOriginalOrder;
     }
 
+    public boolean saveInSpecifiedOrder() {
+        return !saveInOriginalOrder;
+    }
+
     public LinkedList<SortCriterion> getSortCriteria() {
         return sortCriteria;
     }
@@ -85,8 +89,8 @@ public int hashCode() {
     @Override
     public String toString() {
         return "SaveOrderConfig{" + "saveInOriginalOrder=" + saveInOriginalOrder +
-                ", sortCriteria=" + sortCriteria +
-                '}';
+               ", sortCriteria=" + sortCriteria +
+               '}';
     }
 
     public void setSaveInOriginalOrder() {
@@ -139,8 +143,8 @@ public SortCriterion() {
         @Override
         public String toString() {
             return "SortCriterion{" + "field='" + field + '\'' +
-                    ", descending=" + descending +
-                    '}';
+                   ", descending=" + descending +
+                   '}';
         }
 
         @Override
@@ -153,7 +157,7 @@ public boolean equals(Object o) {
             }
             SortCriterion that = (SortCriterion) o;
             return Objects.equals(descending, that.descending) &&
-                    Objects.equals(field, that.field);
+                   Objects.equals(field, that.field);
         }
 
         @Override
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index b1235fabb37..3fa8e4f50b5 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -1706,6 +1706,7 @@ public void setRemotePreferences(RemotePreferences remotePreferences) {
         putBoolean(USE_REMOTE_SERVER, remotePreferences.useRemoteServer());
     }
 
+    @Override
     public void storeExportSaveOrder(SaveOrderConfig config) {
         putBoolean(EXPORT_PRIMARY_SORT_DESCENDING, config.getSortCriteria().get(0).descending);
         putBoolean(EXPORT_SECONDARY_SORT_DESCENDING, config.getSortCriteria().get(1).descending);
@@ -1728,6 +1729,7 @@ private SaveOrderConfig loadTableSaveOrder() {
         return config;
     }
 
+    @Override
     public SaveOrderConfig loadExportSaveOrder() {
         return new SaveOrderConfig(true,
                 new SaveOrderConfig.SortCriterion(get(EXPORT_PRIMARY_SORT_FIELD), getBoolean(EXPORT_PRIMARY_SORT_DESCENDING)),
diff --git a/src/main/java/org/jabref/preferences/PreferencesService.java b/src/main/java/org/jabref/preferences/PreferencesService.java
index 9f835c1b12c..e75f51f05f5 100644
--- a/src/main/java/org/jabref/preferences/PreferencesService.java
+++ b/src/main/java/org/jabref/preferences/PreferencesService.java
@@ -13,6 +13,7 @@
 import org.jabref.logic.layout.LayoutFormatterPreferences;
 import org.jabref.logic.openoffice.OpenOfficePreferences;
 import org.jabref.model.metadata.FilePreferences;
+import org.jabref.model.metadata.SaveOrderConfig;
 
 public interface PreferencesService {
 
@@ -65,4 +66,8 @@ public interface PreferencesService {
     String getUser();
 
     void setExportWorkingDirectory(String layoutFileDirString);
+
+    SaveOrderConfig loadExportSaveOrder();
+
+    void storeExportSaveOrder(SaveOrderConfig config);
 }

From e2ee5f424dc2bb1440504a028c8be735b82c334b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 25 Feb 2019 08:35:21 +0100
Subject: [PATCH 048/184] Bump checkstyle from 8.17 to 8.18 (#4700)

Bumps [checkstyle](https://github.com/checkstyle/checkstyle) from 8.17 to 8.18.
- [Release notes](https://github.com/checkstyle/checkstyle/releases)
- [Commits](https://github.com/checkstyle/checkstyle/compare/checkstyle-8.17...checkstyle-8.18)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 26d139a3c12..d8a23f7ccf2 100644
--- a/build.gradle
+++ b/build.gradle
@@ -178,7 +178,7 @@ dependencies {
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.17'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.18'
 }
 
 jacoco {

From 20d6c05efa2fcbbeb19ec8acc2cf55e9bc73048a Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 25 Feb 2019 12:02:51 +0100
Subject: [PATCH 049/184] fix checkstyle

---
 .../gui/libraryproperties/LibraryPropertiesDialogViewModel.java | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
index d63dca01b96..2a5d538389c 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
@@ -85,7 +85,6 @@ public void browseGeneralDir() {
 
     public void browseUserDir() {
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> userSpecificFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
-
     }
 
     public BooleanProperty saveInOriginalProperty() {
@@ -100,7 +99,6 @@ public BooleanProperty libraryProtectedProperty() {
         return this.libraryProtectedProperty;
     }
 
-
     public boolean generalFileDirChanged() {
         return !oldGeneralFileDir.equals(generalFileDirectoryProperty.getValue());
     }

From 3cf609cd7f90f0ad8a011c02392a8633d2a8fcab Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Wed, 27 Feb 2019 08:27:19 +0100
Subject: [PATCH 050/184] Improve parser warnings (#4702)

Based on http://discourse.jabref.org/t/warnings-by-jabref-start/1532, in which a user (rightfully) complained that the error message is not very helpful.
---
 .../jabref/logic/importer/fileformat/BibtexParser.java | 10 +++++-----
 src/main/resources/l10n/JabRef_en.properties           |  7 +++----
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java b/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
index 8296a534503..b9f8e6b2513 100644
--- a/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
+++ b/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
@@ -703,21 +703,21 @@ private String fixKey() throws IOException {
                     }
 
                     // Finished, now reverse newKey and remove whitespaces:
-                    parserResult.addWarning(
-                            Localization.lang("Line %0: Found corrupted BibTeX key.", String.valueOf(line)));
                     key = newKey.reverse();
+                    parserResult.addWarning(
+                            Localization.lang("Line %0: Found corrupted BibTeX key %1.", String.valueOf(line), key.toString()));
                 }
             }
             break;
 
         case ',':
-            parserResult.addWarning(Localization.lang("Line %0: Found corrupted BibTeX key (contains whitespaces).",
-                    String.valueOf(line)));
+            parserResult.addWarning(
+                    Localization.lang("Line %0: Found corrupted BibTeX key %1 (contains whitespaces).", String.valueOf(line), key.toString()));
             break;
 
         case '\n':
             parserResult.addWarning(
-                    Localization.lang("Line %0: Found corrupted BibTeX key (comma missing).", String.valueOf(line)));
+                    Localization.lang("Line %0: Found corrupted BibTeX key %1 (comma missing).", String.valueOf(line), key.toString()));
             break;
 
         default:
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 8d1927343d2..e38d7c151da 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1160,10 +1160,9 @@ Use\ IEEE\ LaTeX\ abbreviations=Use IEEE LaTeX abbreviations
 
 When\ opening\ file\ link,\ search\ for\ matching\ file\ if\ no\ link\ is\ defined=When opening file link, search for matching file if no link is defined
 Settings\ for\ %0=Settings for %0
-
-Line\ %0\:\ Found\ corrupted\ BibTeX\ key.=Line %0: Found corrupted BibTeX key.
-Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ (contains\ whitespaces).=Line %0: Found corrupted BibTeX key (contains whitespaces).
-Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ (comma\ missing).=Line %0: Found corrupted BibTeX key (comma missing).
+Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ %1.=Line %0: Found corrupted BibTeX key %1.
+Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ %1\ (contains\ whitespaces).=Line %0: Found corrupted BibTeX key %1 (contains whitespaces).
+Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ %1\ (comma\ missing).=Line %0: Found corrupted BibTeX key %1 (comma missing).
 No\ full\ text\ document\ found=No full text document found
 Update\ to\ current\ column\ order=Update to current column order
 Download\ from\ URL=Download from URL

From 8db78c289922292cf0c8310c9dc99a772f1b66b4 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Wed, 27 Feb 2019 15:44:17 +0100
Subject: [PATCH 051/184] add missing controller and fix disable property

---
 src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
index f05d16e55ef..0bd01d6e05c 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
@@ -9,7 +9,7 @@
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.RowConstraints?>
 
-<fx:root type="javafx.scene.layout.GridPane" prefHeight="400.0" prefWidth="600.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1">
+<fx:root type="javafx.scene.layout.GridPane" prefHeight="400.0" prefWidth="600.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.SaveOrderConfigDisplayView">
   <columnConstraints>
     <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="100.0" />
     <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
@@ -33,9 +33,9 @@
       <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2" toggleGroup="$saveOrderToggleGroup"/>
       <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" GridPane.columnSpan="3" GridPane.rowIndex="1" toggleGroup="$saveOrderToggleGroup"/>
       <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" GridPane.columnSpan="3" toggleGroup="$saveOrderToggleGroup"/>
-      <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" disabled="${!exportInSpecifiedOrder.selected}"/>
-      <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" disabled="${!exportInSpecifiedOrder.selected}" />
-      <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" disabled="${!exportInSpecifiedOrder.selected}" />
+      <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" disable="${!exportInSpecifiedOrder.selected}"/>
+      <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" disable="${!exportInSpecifiedOrder.selected}" />
+      <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" disable="${!exportInSpecifiedOrder.selected}" />
       <Label text="Primary sort criterion" GridPane.rowIndex="3" disabled="${!exportInSpecifiedOrder.selected}" />
       <Label text="Secondary sort criterion" GridPane.rowIndex="4" disabled="${!exportInSpecifiedOrder.selected}" />
       <Label text="Tertiary sort criterion" GridPane.rowIndex="5" disabled="${!exportInSpecifiedOrder.selected}"/>

From 42e42ffc2e2fc17e1489edf9841b3cafb421ed83 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Mar 2019 08:10:23 +0100
Subject: [PATCH 052/184] Bump xmpbox from 2.0.13 to 2.0.14 (#4704)

Bumps xmpbox from 2.0.13 to 2.0.14.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index d8a23f7ccf2..b0f8743b4f3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -97,7 +97,7 @@ dependencies {
 
     compile 'org.apache.pdfbox:pdfbox:2.0.13'
     compile 'org.apache.pdfbox:fontbox:2.0.13'
-    compile 'org.apache.pdfbox:xmpbox:2.0.13'
+    compile 'org.apache.pdfbox:xmpbox:2.0.14'
 
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'
 

From ae49277f41aadddc166de1d8c4c1de39bce0da4f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Mar 2019 08:11:28 +0100
Subject: [PATCH 053/184] Bump pdfbox from 2.0.13 to 2.0.14 (#4706)

Bumps pdfbox from 2.0.13 to 2.0.14.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index b0f8743b4f3..8b7d8f6b140 100644
--- a/build.gradle
+++ b/build.gradle
@@ -95,7 +95,7 @@ dependencies {
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.13'
+    compile 'org.apache.pdfbox:pdfbox:2.0.14'
     compile 'org.apache.pdfbox:fontbox:2.0.13'
     compile 'org.apache.pdfbox:xmpbox:2.0.14'
 

From b041d98feb235745d74bc07634c41e783e5b509e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Mar 2019 08:40:07 +0100
Subject: [PATCH 054/184] Bump fontbox from 2.0.13 to 2.0.14 (#4705)

Bumps fontbox from 2.0.13 to 2.0.14.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 8b7d8f6b140..a5c470c8f20 100644
--- a/build.gradle
+++ b/build.gradle
@@ -96,7 +96,7 @@ dependencies {
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
     compile 'org.apache.pdfbox:pdfbox:2.0.14'
-    compile 'org.apache.pdfbox:fontbox:2.0.13'
+    compile 'org.apache.pdfbox:fontbox:2.0.14'
     compile 'org.apache.pdfbox:xmpbox:2.0.14'
 
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'

From 760a6c29ed207fbd41ef96cc3f0ee2eff80ad795 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Fri, 1 Mar 2019 15:33:22 +0100
Subject: [PATCH 055/184] remove old save order config display replace library
 properties save order config by custom component refactor

---
 .../jabref/gui/SaveOrderConfigDisplay.java    | 108 ------------------
 .../gui/SaveOrderConfigDisplayView.java       |   6 +-
 .../gui/SaveOrderConfigDisplayViewModel.java  |   4 +-
 .../LibraryPropertiesDialog.fxml              |  13 +--
 .../LibraryPropertiesDialogView.java          |  87 ++++----------
 .../LibraryPropertiesDialogViewModel.java     |  28 +++--
 .../preferences/ExportSortingPrefsTab.java    |   3 -
 7 files changed, 45 insertions(+), 204 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/SaveOrderConfigDisplay.java

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.java
deleted file mode 100644
index 3093585f3e8..00000000000
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.java
+++ /dev/null
@@ -1,108 +0,0 @@
-package org.jabref.gui;
-
-import java.util.Collections;
-import java.util.List;
-import java.util.Locale;
-import java.util.Objects;
-
-import javafx.collections.FXCollections;
-import javafx.scene.Node;
-import javafx.scene.control.CheckBox;
-import javafx.scene.control.ComboBox;
-import javafx.scene.control.Label;
-import javafx.scene.layout.GridPane;
-
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.InternalBibtexFields;
-import org.jabref.model.metadata.SaveOrderConfig;
-import org.jabref.model.metadata.SaveOrderConfig.SortCriterion;
-
-public class SaveOrderConfigDisplay {
-
-    private GridPane panel;
-    private ComboBox<String> savePriSort;
-    private ComboBox<String> saveSecSort;
-    private ComboBox<String> saveTerSort;
-    private CheckBox savePriDesc;
-    private CheckBox saveSecDesc;
-    private CheckBox saveTerDesc;
-
-
-    public SaveOrderConfigDisplay() {
-        init();
-    }
-
-    private void init() {
-        List<String> fieldNames = InternalBibtexFields.getAllPublicFieldNames();
-        fieldNames.add(BibEntry.KEY_FIELD);
-        Collections.sort(fieldNames);
-        savePriSort = new ComboBox<>(FXCollections.observableArrayList(fieldNames));
-        savePriSort.setEditable(true);
-        saveSecSort = new ComboBox<>(FXCollections.observableArrayList(fieldNames));
-        saveSecSort.setEditable(true);
-        saveTerSort = new ComboBox<>(FXCollections.observableArrayList(fieldNames));
-        saveTerSort.setEditable(true);
-
-        savePriDesc = new CheckBox(Localization.lang("Descending"));
-        saveSecDesc = new CheckBox(Localization.lang("Descending"));
-        saveTerDesc = new CheckBox(Localization.lang("Descending"));
-
-        GridPane builder = new GridPane();
-        Label primarySortCriterion = new Label(Localization.lang("Primary sort criterion"));
-        builder.add(primarySortCriterion, 1, 1);
-        builder.add(savePriSort, 2, 1);
-        builder.add(savePriDesc, 3, 1);
-
-        Label secondarySortCriterion = new Label(Localization.lang("Secondary sort criterion"));
-        builder.add(secondarySortCriterion, 1, 2);
-        builder.add(saveSecSort, 2, 2);
-        builder.add(saveSecDesc, 3, 2);
-
-        Label tertiarySortCriterion = new Label(Localization.lang("Tertiary sort criterion"));
-        builder.add(tertiarySortCriterion, 1, 3);
-        builder.add(saveTerSort, 2, 3);
-        builder.add(saveTerDesc, 3, 3);
-        panel = builder;
-    }
-
-    public Node getJFXPanel() {
-        return panel;
-    }
-
-    public void setEnabled(boolean enabled) {
-        savePriSort.setDisable(!enabled);
-        savePriDesc.setDisable(!enabled);
-        saveSecSort.setDisable(!enabled);
-        saveSecDesc.setDisable(!enabled);
-        saveTerSort.setDisable(!enabled);
-        saveTerDesc.setDisable(!enabled);
-    }
-
-    public SaveOrderConfig getSaveOrderConfig() {
-        SaveOrderConfig saveOrderConfig = new SaveOrderConfig();
-        SortCriterion primary = new SortCriterion(getSelectedItemAsLowerCaseTrim(savePriSort), savePriDesc.isSelected());
-        saveOrderConfig.getSortCriteria().add(primary);
-        SortCriterion secondary = new SortCriterion(getSelectedItemAsLowerCaseTrim(saveSecSort), saveSecDesc.isSelected());
-        saveOrderConfig.getSortCriteria().add(secondary);
-        SortCriterion tertiary = new SortCriterion(getSelectedItemAsLowerCaseTrim(saveTerSort), saveTerDesc.isSelected());
-        saveOrderConfig.getSortCriteria().add(tertiary);
-
-        return saveOrderConfig;
-    }
-
-    public void setSaveOrderConfig(SaveOrderConfig saveOrderConfig) {
-        Objects.requireNonNull(saveOrderConfig);
-
-        savePriSort.setValue(saveOrderConfig.getSortCriteria().get(0).field);
-        savePriDesc.setSelected(saveOrderConfig.getSortCriteria().get(0).descending);
-        saveSecSort.setValue(saveOrderConfig.getSortCriteria().get(1).field);
-        saveSecDesc.setSelected(saveOrderConfig.getSortCriteria().get(1).descending);
-        saveTerSort.setValue(saveOrderConfig.getSortCriteria().get(2).field);
-        saveTerDesc.setSelected(saveOrderConfig.getSortCriteria().get(2).descending);
-    }
-
-    private String getSelectedItemAsLowerCaseTrim(ComboBox<String> sortBox) {
-        return sortBox.getValue().toLowerCase(Locale.ROOT).trim();
-    }
-}
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
index 769a468f314..2f0e36ca318 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
@@ -66,7 +66,11 @@ private void initialize() {
     }
 
     public void storeConfig() {
-        viewModel.storeConfig();
+        viewModel.storeConfigInPrefs();
+    }
+
+    public SaveOrderConfig getSaveOrderConfig() {
+        return viewModel.getSaveOrderConfig();
     }
 
     public Node getJFXPanel() {
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
index 1d251e78ba6..08e9db6df75 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
@@ -44,7 +44,6 @@ public SaveOrderConfigDisplayViewModel(SaveOrderConfig config, PreferencesServic
         this.config = config;
         this.prefs = prefs;
 
-        SaveOrderConfig storedSaveOrderConfig = config;
         List<String> fieldNames = InternalBibtexFields.getAllPublicFieldNames();
         fieldNames.add(BibEntry.KEY_FIELD);
         Collections.sort(fieldNames);
@@ -132,7 +131,7 @@ public StringProperty saveTerSortSelectedValueProperty() {
         return saveTerSortSelectedValueProperty;
     }
 
-    public void storeConfig() {
+    public void storeConfigInPrefs() {
         prefs.storeExportSaveOrder(this.getSaveOrderConfig());
     }
 
@@ -147,5 +146,4 @@ public BooleanProperty saveInTableOrderProperty() {
     public BooleanProperty saveInSpecifiedOrderProperty() {
         return this.saveInSpecifiedOrderProperty;
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
index d69795354af..f4db88618a9 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
@@ -7,10 +7,8 @@
 <?import javafx.scene.control.ComboBox?>
 <?import javafx.scene.control.DialogPane?>
 <?import javafx.scene.control.Label?>
-<?import javafx.scene.control.RadioButton?>
 <?import javafx.scene.control.Separator?>
 <?import javafx.scene.control.TextField?>
-<?import javafx.scene.control.ToggleGroup?>
 <?import javafx.scene.layout.ColumnConstraints?>
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.HBox?>
@@ -19,7 +17,7 @@
 
 <DialogPane minHeight="-Infinity" prefHeight="784.0" prefWidth="921.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.libraryproperties.LibraryPropertiesDialogView">
    <content>
-      <VBox fx:id="contentVbox" minHeight="-Infinity" prefHeight="200.0" prefWidth="100.0">
+      <VBox fx:id="contentVbox" prefHeight="200.0" prefWidth="100.0">
          <children>
             <GridPane minHeight="-Infinity">
               <columnConstraints>
@@ -60,15 +58,6 @@
                   </HBox>
                </children>
             </GridPane>
-            <VBox fx:id="saveOrdervbox" minHeight="-Infinity">
-               <fx:define>
-                 <ToggleGroup fx:id="saveOrderToggleGroup" />
-               </fx:define>
-               <children>
-                  <RadioButton fx:id="saveInOriginalOrder" mnemonicParsing="false" text="%Save entries in their original order" toggleGroup="$saveOrderToggleGroup" />
-                  <RadioButton fx:id="saveInSpecifiedOrder" mnemonicParsing="false" text="%Save entries ordered as specified" toggleGroup="$saveOrderToggleGroup" />
-               </children>
-            </VBox>
             <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
                <children>
                   <Label alignment="TOP_LEFT" text="%Library protection" />
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
index e14bf7b6f49..55dd64e57c6 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
@@ -11,19 +11,16 @@
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.ComboBox;
-import javafx.scene.control.RadioButton;
 import javafx.scene.control.TextField;
-import javafx.scene.control.ToggleGroup;
 import javafx.scene.layout.VBox;
 
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
-import org.jabref.gui.SaveOrderConfigDisplay;
+import org.jabref.gui.SaveOrderConfigDisplayView;
 import org.jabref.gui.cleanup.FieldFormatterCleanupsPanel;
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.logic.cleanup.Cleanups;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.shared.DatabaseLocation;
 import org.jabref.model.metadata.MetaData;
 import org.jabref.model.metadata.SaveOrderConfig;
 import org.jabref.preferences.PreferencesService;
@@ -38,18 +35,15 @@ public class LibraryPropertiesDialogView extends BaseDialog<Void> {
     @FXML private Button browseGeneralFileDir;
     @FXML private TextField userSpecificFileDirectory;
     @FXML private Button browseUserSpefiicFileDir;
-    @FXML private VBox saveOrdervbox;
-    @FXML private ToggleGroup saveOrderToggleGroup;
-    @FXML private RadioButton saveInOriginalOrder;
-    @FXML private RadioButton saveInSpecifiedOrder;
     @FXML private CheckBox protect;
-    private SaveOrderConfigDisplay saveOrderPanel;
+    @Inject private PreferencesService preferencesService;
+
     private BasePanel panel;
     private LibraryPropertiesDialogViewModel viewModel;
     private final DialogService dialogService;
-    @Inject private PreferencesService preferencesService;
     private FieldFormatterCleanupsPanel fieldFormatterCleanupsPanel;
-    private Object oldSaveOrderConfig;
+    private SaveOrderConfigDisplayView saveOrderConfigDisplayView;
+    private SaveOrderConfig oldSaveOrderConfig;
 
     public LibraryPropertiesDialogView(BasePanel panel, DialogService dialogService) {
         this.dialogService = dialogService;
@@ -78,58 +72,31 @@ private void initialize() {
 
         encoding.itemsProperty().bind(viewModel.encodingsProperty());
         encoding.valueProperty().bindBidirectional(viewModel.selectedEncodingProperty());
-        saveOrderPanel = new SaveOrderConfigDisplay();
-        saveOrdervbox.getChildren().add(saveOrderPanel.getJFXPanel());
+        encoding.disableProperty().bind(viewModel.encodingDisableProperty());
+        protect.disableProperty().bind(viewModel.protectDisableProperty());
+
+        Optional<SaveOrderConfig> storedSaveOrderConfig = panel.getBibDatabaseContext().getMetaData().getSaveOrderConfig();
+        if (storedSaveOrderConfig.isPresent()) {
+            saveOrderConfigDisplayView = new SaveOrderConfigDisplayView(storedSaveOrderConfig.get());
+            oldSaveOrderConfig = storedSaveOrderConfig.get();
+        } else {
+            oldSaveOrderConfig = preferencesService.loadExportSaveOrder();
+            saveOrderConfigDisplayView = new SaveOrderConfigDisplayView(preferencesService.loadExportSaveOrder());
+        }
+
         fieldFormatterCleanupsPanel = new FieldFormatterCleanupsPanel(Localization.lang("Enable save actions"),
                                                                       Cleanups.DEFAULT_SAVE_ACTIONS);
-
-        contentVbox.getChildren().add(fieldFormatterCleanupsPanel);
-        saveInOriginalOrder.selectedProperty().bindBidirectional(viewModel.saveInOriginalProperty());
-        saveInSpecifiedOrder.selectedProperty().bindBidirectional(viewModel.saveInSpecifiedOrderProperty());
+        contentVbox.getChildren().addAll(saveOrderConfigDisplayView, fieldFormatterCleanupsPanel);
 
         protect.selectedProperty().bindBidirectional(viewModel.libraryProtectedProperty());
-        saveOrderPanel.getJFXPanel().disableProperty().bind(viewModel.saveInOriginalProperty());
 
         setValues();
-        updateEnableStatus();
     }
 
     private void setValues() {
-
-        Optional<SaveOrderConfig> storedSaveOrderConfig = panel.getBibDatabaseContext().getMetaData().getSaveOrderConfig();
-        boolean selected;
-        if (!storedSaveOrderConfig.isPresent()) {
-            viewModel.saveInOriginalProperty().setValue(true);
-            oldSaveOrderConfig = SaveOrderConfig.getDefaultSaveOrder();
-            selected = false;
-        } else {
-            SaveOrderConfig saveOrderConfig = storedSaveOrderConfig.get();
-            oldSaveOrderConfig = saveOrderConfig;
-            if (saveOrderConfig.saveInOriginalOrder()) {
-                viewModel.saveInOriginalProperty().setValue(true);
-                selected = false;
-            } else {
-                viewModel.saveInSpecifiedOrderProperty().setValue(true);
-                selected = true;
-            }
-            saveOrderPanel.setSaveOrderConfig(saveOrderConfig);
-
-        }
-        saveOrderPanel.setEnabled(selected);
-
         fieldFormatterCleanupsPanel.setValues(panel.getBibDatabaseContext().getMetaData());
     }
 
-    public void updateEnableStatus() {
-        DatabaseLocation location = panel.getBibDatabaseContext().getLocation();
-        boolean isShared = (location == DatabaseLocation.SHARED);
-        encoding.setDisable(isShared); // the encoding of shared database is always UTF-8
-        saveInOriginalOrder.setDisable(isShared);
-        saveInSpecifiedOrder.setDisable(isShared);
-        saveOrderPanel.setEnabled(!isShared);
-        protect.setDisable(isShared);
-    }
-
     @FXML
     public void browseGeneralFileDirectory(ActionEvent event) {
         viewModel.browseGeneralDir();
@@ -167,9 +134,9 @@ private void storeSettings() {
             metaData.markAsNotProtected();
         }
 
-        SaveOrderConfig newSaveOrderConfig = getNewSaveOrderConfig();
+        SaveOrderConfig newSaveOrderConfig = saveOrderConfigDisplayView.getSaveOrderConfig();
 
-        boolean saveOrderConfigChanged = !getNewSaveOrderConfig().equals(oldSaveOrderConfig);
+        boolean saveOrderConfigChanged = !newSaveOrderConfig.equals(oldSaveOrderConfig);
 
         // See if any of the values have been modified:
         if (saveOrderConfigChanged) {
@@ -188,8 +155,9 @@ private void storeSettings() {
                 fieldFormatterCleanupsPanel.storeSettings(metaData);
             }
         }
+        boolean encodingChanged = !newEncoding.equals(oldEncoding);
 
-        boolean changed = saveOrderConfigChanged || !newEncoding.equals(oldEncoding)
+        boolean changed = saveOrderConfigChanged || encodingChanged
                           || viewModel.generalFileDirChanged() || viewModel.userFileDirChanged()
                           || viewModel.protectedValueChanged() || saveActionsChanged;
         // ... if so, mark base changed. Prevent the Undo button from removing
@@ -199,15 +167,4 @@ private void storeSettings() {
         }
     }
 
-    private SaveOrderConfig getNewSaveOrderConfig() {
-        SaveOrderConfig saveOrderConfig = null;
-        if (saveInOriginalOrder.isSelected()) {
-            saveOrderConfig = SaveOrderConfig.getDefaultSaveOrder();
-        } else {
-            saveOrderConfig = saveOrderPanel.getSaveOrderConfig();
-            saveOrderConfig.setSaveInSpecifiedOrder();
-        }
-        return saveOrderConfig;
-    }
-
 }
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
index 2a5d538389c..03aa19a1714 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
@@ -17,6 +17,7 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.logic.l10n.Encodings;
+import org.jabref.model.database.shared.DatabaseLocation;
 import org.jabref.model.metadata.MetaData;
 import org.jabref.preferences.PreferencesService;
 
@@ -26,14 +27,13 @@ public class LibraryPropertiesDialogViewModel {
     private final StringProperty userSpecificFileDirectoryProperty = new SimpleStringProperty("");
     private final ListProperty<Charset> encodingsProperty = new SimpleListProperty<>(FXCollections.observableArrayList(Encodings.getCharsets()));
     private final ObjectProperty<Charset> selectedEncodingPropety = new SimpleObjectProperty<>(Encodings.getCharsets().get(0));
-    private final BooleanProperty saveInOriginalProperty = new SimpleBooleanProperty();
-    private final BooleanProperty saveInSpecifiedOrderProperty = new SimpleBooleanProperty();
     private final BooleanProperty libraryProtectedProperty = new SimpleBooleanProperty();
+    private final BooleanProperty encodingDisableProperty = new SimpleBooleanProperty();
+    private final BooleanProperty protectDisableProperty = new SimpleBooleanProperty();
 
     private final DialogService dialogService;
     private final DirectoryDialogConfiguration directoryDialogConfiguration;
     private final MetaData metaData;
-    private final PreferencesService preferencesService;
 
     private final String oldUserSpecificFileDir;
     private final String oldGeneralFileDir;
@@ -42,7 +42,11 @@ public class LibraryPropertiesDialogViewModel {
     public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogService, PreferencesService preferencesService) {
         this.dialogService = dialogService;
         this.metaData = panel.getBibDatabaseContext().getMetaData();
-        this.preferencesService = preferencesService;
+
+        DatabaseLocation location = panel.getBibDatabaseContext().getLocation();
+        boolean isShared = (location == DatabaseLocation.SHARED);
+        encodingDisableProperty.setValue(isShared); // the encoding of shared database is always UTF-8
+        protectDisableProperty.setValue(isShared);
 
         directoryDialogConfiguration = new DirectoryDialogConfiguration.Builder()
                                                                                  .withInitialDirectory(preferencesService.getWorkingDir()).build();
@@ -87,14 +91,6 @@ public void browseUserDir() {
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> userSpecificFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
     }
 
-    public BooleanProperty saveInOriginalProperty() {
-        return this.saveInOriginalProperty;
-    }
-
-    public BooleanProperty saveInSpecifiedOrderProperty() {
-        return this.saveInSpecifiedOrderProperty;
-    }
-
     public BooleanProperty libraryProtectedProperty() {
         return this.libraryProtectedProperty;
     }
@@ -110,4 +106,12 @@ public boolean userFileDirChanged() {
     public boolean protectedValueChanged() {
         return !oldLibraryProtected == libraryProtectedProperty.getValue();
     }
+
+    public BooleanProperty encodingDisableProperty() {
+        return encodingDisableProperty;
+    }
+
+    public BooleanProperty protectDisableProperty() {
+        return protectDisableProperty;
+    }
 }
diff --git a/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java b/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
index f67fda34e81..0b466334ea0 100644
--- a/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
@@ -17,8 +17,6 @@
  */
 class ExportSortingPrefsTab extends Pane implements PrefsTab {
 
-    private final JabRefPreferences prefs;
-
     private final RadioButton exportInOriginalOrder;
     private final RadioButton exportInTableOrder;
     private final RadioButton exportInSpecifiedOrder;
@@ -26,7 +24,6 @@ class ExportSortingPrefsTab extends Pane implements PrefsTab {
     private final GridPane builder = new GridPane();
 
     public ExportSortingPrefsTab(JabRefPreferences prefs) {
-        this.prefs = prefs;
         // EXPORT SORT ORDER
         // create Components
         exportInOriginalOrder = new RadioButton(Localization.lang("Export entries in their original order"));

From bf4a55c6ff4289cd8888ce4112b3c931823c7720 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 1 Mar 2019 15:44:45 +0100
Subject: [PATCH 056/184] Disable rank column by default (#4708)

Closes https://github.com/JabRef/jabref/issues/4585.
---
 src/main/java/org/jabref/preferences/JabRefPreferences.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index a8bbd319222..c3070474954 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -650,7 +650,7 @@ private JabRefPreferences() {
         defaults.put(SPECIALFIELDSENABLED, Boolean.TRUE);
         defaults.put(SHOWCOLUMN_PRIORITY, Boolean.FALSE);
         defaults.put(SHOWCOLUMN_QUALITY, Boolean.FALSE);
-        defaults.put(SHOWCOLUMN_RANKING, Boolean.TRUE);
+        defaults.put(SHOWCOLUMN_RANKING, Boolean.FALSE);
         defaults.put(SHOWCOLUMN_RELEVANCE, Boolean.FALSE);
         defaults.put(SHOWCOLUMN_PRINTED, Boolean.FALSE);
         defaults.put(SHOWCOLUMN_READ, Boolean.FALSE);

From 28d3f56e022d7d0cc55590bdeba7e23682280d4b Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Fri, 1 Mar 2019 17:38:25 +0100
Subject: [PATCH 057/184] some layout stuff add css section header remove some
 old stuff

---
 src/main/java/org/jabref/gui/Base.css         |  2 +-
 .../jabref/gui/SaveOrderConfigDisplay.fxml    | 12 ++--
 .../LibraryPropertiesDialog.css               |  4 ++
 .../LibraryPropertiesDialog.fxml              | 65 +++----------------
 .../LibraryPropertiesDialogView.java          |  6 +-
 .../preferences/ExportSortingPrefsTab.java    | 22 -------
 6 files changed, 26 insertions(+), 85 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.css

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
index 831b549f943..ab4097899cc 100644
--- a/src/main/java/org/jabref/gui/Base.css
+++ b/src/main/java/org/jabref/gui/Base.css
@@ -818,7 +818,7 @@
 
 .separator:horizontal .line {
     -fx-border-color: -jr-separator;
-    -fx-border-width: 0.5;
+    -fx-border-width: 0;
     -fx-border-insets: 1 0 0 0;
 }
 
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
index 0bd01d6e05c..b54c0564a5e 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
@@ -33,11 +33,11 @@
       <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2" toggleGroup="$saveOrderToggleGroup"/>
       <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" GridPane.columnSpan="3" GridPane.rowIndex="1" toggleGroup="$saveOrderToggleGroup"/>
       <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" GridPane.columnSpan="3" toggleGroup="$saveOrderToggleGroup"/>
-      <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" disable="${!exportInSpecifiedOrder.selected}"/>
-      <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" disable="${!exportInSpecifiedOrder.selected}" />
-      <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" disable="${!exportInSpecifiedOrder.selected}" />
-      <Label text="Primary sort criterion" GridPane.rowIndex="3" disabled="${!exportInSpecifiedOrder.selected}" />
-      <Label text="Secondary sort criterion" GridPane.rowIndex="4" disabled="${!exportInSpecifiedOrder.selected}" />
-      <Label text="Tertiary sort criterion" GridPane.rowIndex="5" disabled="${!exportInSpecifiedOrder.selected}"/>
+      <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" disable="${!exportInSpecifiedOrder.selected}"/>
+      <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" disable="${!exportInSpecifiedOrder.selected}" />
+      <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" disable="${!exportInSpecifiedOrder.selected}" />
+      <Label text="%Primary sort criterion" GridPane.rowIndex="3" disabled="${!exportInSpecifiedOrder.selected}" />
+      <Label text="%Secondary sort criterion" GridPane.rowIndex="4" disabled="${!exportInSpecifiedOrder.selected}" />
+      <Label text="%Tertiary sort criterion" GridPane.rowIndex="5" disabled="${!exportInSpecifiedOrder.selected}"/>
    </children>
 </fx:root>
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.css b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.css
new file mode 100644
index 00000000000..6377d4e01ba
--- /dev/null
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.css
@@ -0,0 +1,4 @@
+.sectionHeader {
+    -fx-font-size: 1.5em;
+    -fx-padding: 1em 0em 1em 0em;
+}
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
index f4db88618a9..980e13f0560 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
@@ -1,23 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<?import javafx.geometry.Insets?>
 <?import javafx.scene.control.Button?>
 <?import javafx.scene.control.ButtonType?>
 <?import javafx.scene.control.CheckBox?>
 <?import javafx.scene.control.ComboBox?>
 <?import javafx.scene.control.DialogPane?>
 <?import javafx.scene.control.Label?>
-<?import javafx.scene.control.Separator?>
 <?import javafx.scene.control.TextField?>
 <?import javafx.scene.layout.ColumnConstraints?>
 <?import javafx.scene.layout.GridPane?>
-<?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.RowConstraints?>
 <?import javafx.scene.layout.VBox?>
 
 <DialogPane minHeight="-Infinity" prefHeight="784.0" prefWidth="921.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.libraryproperties.LibraryPropertiesDialogView">
    <content>
-      <VBox fx:id="contentVbox" prefHeight="200.0" prefWidth="100.0">
+      <VBox fx:id="contentVbox" minHeight="-Infinity" prefHeight="200.0" prefWidth="100.0">
          <children>
             <GridPane minHeight="-Infinity">
               <columnConstraints>
@@ -27,9 +24,12 @@
               </columnConstraints>
               <rowConstraints>
                 <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="SOMETIMES" />
+                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="ALWAYS" />
                   <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                  <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="ALWAYS" />
+                  <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                  <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="SOMETIMES" />
               </rowConstraints>
                <children>
                   <Label text="%Library encoding" />
@@ -40,57 +40,12 @@
                   <Label text="%User-specific file directory" GridPane.rowIndex="3" />
                   <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
                   <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
-                  <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0" GridPane.columnSpan="3" GridPane.rowIndex="1">
-                     <children>
-                        <Label alignment="TOP_LEFT" text="%Override default file directories" />
-                        <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
-                           <opaqueInsets>
-                              <Insets left="10.0" right="10.0" top="10.0" />
-                           </opaqueInsets>
-                           <HBox.margin>
-                              <Insets />
-                           </HBox.margin>
-                           <padding>
-                              <Insets left="10.0" />
-                           </padding>
-                        </Separator>
-                     </children>
-                  </HBox>
+                  <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Override default file directories" GridPane.columnSpan="3" GridPane.rowIndex="1" />
+                  <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Library protection" GridPane.columnSpan="3" GridPane.rowIndex="4" />
+                  <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." GridPane.columnSpan="3" GridPane.rowIndex="5" />
+                  <Label styleClass="sectionHeader" text="%Export sort order" GridPane.rowIndex="6" />
                </children>
             </GridPane>
-            <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
-               <children>
-                  <Label alignment="TOP_LEFT" text="%Library protection" />
-                  <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
-                     <opaqueInsets>
-                        <Insets left="10.0" right="10.0" top="10.0" />
-                     </opaqueInsets>
-                     <HBox.margin>
-                        <Insets />
-                     </HBox.margin>
-                     <padding>
-                        <Insets left="10.0" />
-                     </padding>
-                  </Separator>
-               </children>
-            </HBox>
-            <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." />
-            <HBox alignment="CENTER" prefHeight="50.0" prefWidth="200.0">
-               <children>
-                  <Label alignment="TOP_LEFT" text="%Save actions" />
-                  <Separator halignment="LEFT" valignment="BOTTOM" HBox.hgrow="ALWAYS">
-                     <opaqueInsets>
-                        <Insets left="10.0" right="10.0" top="10.0" />
-                     </opaqueInsets>
-                     <HBox.margin>
-                        <Insets />
-                     </HBox.margin>
-                     <padding>
-                        <Insets left="10.0" />
-                     </padding>
-                  </Separator>
-               </children>
-            </HBox>
          </children>
       </VBox>
    </content>
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
index 55dd64e57c6..9f241d4409d 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
@@ -11,6 +11,7 @@
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.ComboBox;
+import javafx.scene.control.Label;
 import javafx.scene.control.TextField;
 import javafx.scene.layout.VBox;
 
@@ -86,7 +87,10 @@ private void initialize() {
 
         fieldFormatterCleanupsPanel = new FieldFormatterCleanupsPanel(Localization.lang("Enable save actions"),
                                                                       Cleanups.DEFAULT_SAVE_ACTIONS);
-        contentVbox.getChildren().addAll(saveOrderConfigDisplayView, fieldFormatterCleanupsPanel);
+        Label saveActions = new Label(Localization.lang("Save actions"));
+        saveActions.getStyleClass().add("sectionHeader");
+
+        contentVbox.getChildren().addAll(saveOrderConfigDisplayView, saveActions, fieldFormatterCleanupsPanel);
 
         protect.selectedProperty().bindBidirectional(viewModel.libraryProtectedProperty());
 
diff --git a/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java b/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
index 0b466334ea0..d6482f567ce 100644
--- a/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
@@ -1,9 +1,6 @@
 package org.jabref.gui.preferences;
 
 import javafx.scene.Node;
-import javafx.scene.control.Label;
-import javafx.scene.control.RadioButton;
-import javafx.scene.control.ToggleGroup;
 import javafx.scene.layout.GridPane;
 import javafx.scene.layout.Pane;
 import javafx.scene.shape.Line;
@@ -17,33 +14,14 @@
  */
 class ExportSortingPrefsTab extends Pane implements PrefsTab {
 
-    private final RadioButton exportInOriginalOrder;
-    private final RadioButton exportInTableOrder;
-    private final RadioButton exportInSpecifiedOrder;
     private final SaveOrderConfigDisplayView exportOrderPanel;
     private final GridPane builder = new GridPane();
 
     public ExportSortingPrefsTab(JabRefPreferences prefs) {
-        // EXPORT SORT ORDER
-        // create Components
-        exportInOriginalOrder = new RadioButton(Localization.lang("Export entries in their original order"));
-        exportInTableOrder = new RadioButton(Localization.lang("Export in current table sort order"));
-        exportInSpecifiedOrder = new RadioButton(Localization.lang("Export entries ordered as specified"));
-
-        final ToggleGroup group = new ToggleGroup();
-        exportInOriginalOrder.setToggleGroup(group);
-        exportInTableOrder.setToggleGroup(group);
-        exportInSpecifiedOrder.setToggleGroup(group);
-
         exportOrderPanel = new SaveOrderConfigDisplayView(prefs.loadExportSaveOrder());
 
-        Label exportSortOrder = new Label(Localization.lang("Export sort order"));
-        exportSortOrder.getStyleClass().add("sectionHeader");
-        // create GUI
-
         builder.add(exportOrderPanel.getJFXPanel(), 1, 8);
         builder.add(new Line(), 2, 9);
-
     }
 
     @Override

From 1a05b8fb3d110b27b9c87e10fb99948ba7f9bc52 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Fri, 1 Mar 2019 17:49:55 +0100
Subject: [PATCH 058/184] reduce sizes still no effect

---
 .../jabref/gui/SaveOrderConfigDisplay.fxml    | 35 ++++++++++---------
 1 file changed, 19 insertions(+), 16 deletions(-)

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
index b54c0564a5e..13832fb7b0d 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
@@ -9,19 +9,19 @@
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.RowConstraints?>
 
-<fx:root type="javafx.scene.layout.GridPane" prefHeight="400.0" prefWidth="600.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.SaveOrderConfigDisplayView">
+<fx:root prefHeight="200.0" prefWidth="600.0" type="javafx.scene.layout.GridPane" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.SaveOrderConfigDisplayView">
   <columnConstraints>
     <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="100.0" />
     <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
       <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
   </columnConstraints>
   <rowConstraints>
-    <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
-    <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
-      <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
-      <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
-      <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
-      <RowConstraints minHeight="-Infinity" prefHeight="30.0" />
+    <RowConstraints prefHeight="30.0" />
+    <RowConstraints prefHeight="30.0" />
+      <RowConstraints prefHeight="30.0" />
+      <RowConstraints prefHeight="30.0" />
+      <RowConstraints prefHeight="30.0" />
+      <RowConstraints prefHeight="30.0" />
   </rowConstraints>
      <fx:define>
        <ToggleGroup fx:id="saveOrderToggleGroup" />
@@ -30,14 +30,17 @@
       <ComboBox fx:id="savePriSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="3" />
       <ComboBox fx:id="saveSecSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="4" />
       <ComboBox fx:id="saveTerSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="5" />
-      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2" toggleGroup="$saveOrderToggleGroup"/>
-      <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" GridPane.columnSpan="3" GridPane.rowIndex="1" toggleGroup="$saveOrderToggleGroup"/>
-      <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" GridPane.columnSpan="3" toggleGroup="$saveOrderToggleGroup"/>
-      <CheckBox fx:id="savePriDesc" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" disable="${!exportInSpecifiedOrder.selected}"/>
-      <CheckBox fx:id="saveSecDesc" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" disable="${!exportInSpecifiedOrder.selected}" />
-      <CheckBox fx:id="saveTerDesc" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" disable="${!exportInSpecifiedOrder.selected}" />
-      <Label text="%Primary sort criterion" GridPane.rowIndex="3" disabled="${!exportInSpecifiedOrder.selected}" />
-      <Label text="%Secondary sort criterion" GridPane.rowIndex="4" disabled="${!exportInSpecifiedOrder.selected}" />
-      <Label text="%Tertiary sort criterion" GridPane.rowIndex="5" disabled="${!exportInSpecifiedOrder.selected}"/>
+      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2">
+         <toggleGroup>
+            <ToggleGroup fx:id="saveOrderToggleGroup" />
+         </toggleGroup></RadioButton>
+      <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" GridPane.rowIndex="1" />
+      <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" />
+      <CheckBox fx:id="savePriDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" />
+      <CheckBox fx:id="saveSecDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" />
+      <CheckBox fx:id="saveTerDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" />
+      <Label disabled="${!exportInSpecifiedOrder.selected}" text="%Primary sort criterion" GridPane.rowIndex="3" />
+      <Label disabled="${!exportInSpecifiedOrder.selected}" text="%Secondary sort criterion" GridPane.rowIndex="4" />
+      <Label disabled="${!exportInSpecifiedOrder.selected}" text="%Tertiary sort criterion" GridPane.rowIndex="5" />
    </children>
 </fx:root>

From 0cf3c87dafa232d47727cf2d8c747034339277dd Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Fri, 1 Mar 2019 18:08:00 +0100
Subject: [PATCH 059/184] add method for changing the radio button texts to
 save fix l10n

---
 .../java/org/jabref/gui/SaveOrderConfigDisplayView.java    | 7 +++++++
 .../gui/libraryproperties/LibraryPropertiesDialogView.java | 1 +
 src/main/resources/l10n/JabRef_en.properties               | 2 +-
 3 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
index 2f0e36ca318..3f7e253f231 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
@@ -10,6 +10,7 @@
 import javafx.scene.control.ToggleGroup;
 import javafx.scene.layout.GridPane;
 
+import org.jabref.logic.l10n.Localization;
 import org.jabref.model.metadata.SaveOrderConfig;
 import org.jabref.preferences.PreferencesService;
 
@@ -65,6 +66,12 @@ private void initialize() {
 
     }
 
+    public void changeExportDescriptionToSave() {
+        exportInOriginalOrder.setText(Localization.lang("Save entries in their original order"));
+        exportInSpecifiedOrder.setText(Localization.lang("Save entries ordered as specified"));
+        exportInTableOrder.setText(Localization.lang("Save in current table sort order"));
+    }
+
     public void storeConfig() {
         viewModel.storeConfigInPrefs();
     }
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
index 9f241d4409d..9cbeaf2a637 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
@@ -85,6 +85,7 @@ private void initialize() {
             saveOrderConfigDisplayView = new SaveOrderConfigDisplayView(preferencesService.loadExportSaveOrder());
         }
 
+        saveOrderConfigDisplayView.changeExportDescriptionToSave();
         fieldFormatterCleanupsPanel = new FieldFormatterCleanupsPanel(Localization.lang("Enable save actions"),
                                                                       Cleanups.DEFAULT_SAVE_ACTIONS);
         Label saveActions = new Label(Localization.lang("Save actions"));
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index e38d7c151da..1aa6a98b4f0 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1456,8 +1456,8 @@ Export\ sort\ order=Export sort order
 Export\ sorting=Export sorting
 Newline\ separator=Newline separator
 
+Save\ in\ current\ table\ sort\ order=Save in current table sort order
 Save\ entries\ ordered\ as\ specified=Save entries ordered as specified
-Save\ sort\ order=Save sort order
 Show\ extra\ columns=Show extra columns
 Parsing\ error=Parsing error
 illegal\ backslash\ expression=illegal backslash expression

From 9e9450fa8ab4fbb5a7e3f17d7ea5f2f6cb0be02a Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sat, 2 Mar 2019 17:31:55 +0100
Subject: [PATCH 060/184] move radio button toggle group back as property
 remove unused variables

---
 src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml     | 5 +----
 .../java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java | 4 ----
 .../libraryproperties/LibraryPropertiesDialogViewModel.java  | 3 +--
 .../java/org/jabref/gui/preferences/PreferencesDialog.java   | 2 +-
 4 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
index 13832fb7b0d..b3b286c7f92 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
@@ -30,10 +30,7 @@
       <ComboBox fx:id="savePriSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="3" />
       <ComboBox fx:id="saveSecSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="4" />
       <ComboBox fx:id="saveTerSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="5" />
-      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" GridPane.columnSpan="3" GridPane.rowIndex="2">
-         <toggleGroup>
-            <ToggleGroup fx:id="saveOrderToggleGroup" />
-         </toggleGroup></RadioButton>
+      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" GridPane.rowIndex="2">
       <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" GridPane.rowIndex="1" />
       <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" />
       <CheckBox fx:id="savePriDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" />
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
index 08e9db6df75..36ec54a7fcd 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
@@ -37,11 +37,9 @@ public class SaveOrderConfigDisplayViewModel {
     private final BooleanProperty saveInTableOrderProperty = new SimpleBooleanProperty();
     private final BooleanProperty saveInSpecifiedOrderProperty = new SimpleBooleanProperty();
 
-    private final SaveOrderConfig config;
     private final PreferencesService prefs;
 
     public SaveOrderConfigDisplayViewModel(SaveOrderConfig config, PreferencesService prefs) {
-        this.config = config;
         this.prefs = prefs;
 
         List<String> fieldNames = InternalBibtexFields.getAllPublicFieldNames();
@@ -60,7 +58,6 @@ public SaveOrderConfigDisplayViewModel(SaveOrderConfig config, PreferencesServic
             saveInTableOrderProperty.setValue(true);
         }
         setSaveOrderConfig(config);
-
     }
 
     public ListProperty<String> priSortFieldsProperty() {
@@ -76,7 +73,6 @@ public ListProperty<String> terSortFieldsProperty() {
     }
 
     public SaveOrderConfig getSaveOrderConfig() {
-
         SortCriterion primary = new SortCriterion(getSelectedItemAsLowerCaseTrim(savePriSortSelectedValueProperty), savePriDescPropertySelected.getValue());
         SortCriterion secondary = new SortCriterion(getSelectedItemAsLowerCaseTrim(saveSecSortSelectedValueProperty), saveSecDescPropertySelected.getValue());
         SortCriterion tertiary = new SortCriterion(getSelectedItemAsLowerCaseTrim(saveTerSortSelectedValueProperty), saveTerDescPropertySelected.getValue());
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
index 03aa19a1714..05f3982d7e0 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
@@ -33,7 +33,6 @@ public class LibraryPropertiesDialogViewModel {
 
     private final DialogService dialogService;
     private final DirectoryDialogConfiguration directoryDialogConfiguration;
-    private final MetaData metaData;
 
     private final String oldUserSpecificFileDir;
     private final String oldGeneralFileDir;
@@ -41,7 +40,7 @@ public class LibraryPropertiesDialogViewModel {
 
     public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogService, PreferencesService preferencesService) {
         this.dialogService = dialogService;
-        this.metaData = panel.getBibDatabaseContext().getMetaData();
+        MetaData metaData = panel.getBibDatabaseContext().getMetaData();
 
         DatabaseLocation location = panel.getBibDatabaseContext().getLocation();
         boolean isShared = (location == DatabaseLocation.SHARED);
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
index 1727658b210..e966cd2eb66 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
@@ -105,7 +105,7 @@ public PreferencesDialog(JabRefFrame parent, TaskExecutor taskExecutor) {
 
     @FXML
     private void initalize() {
-
+        //FIXME: Model whole dialog as fxml
     }
 
     private void construct() {

From 028cbc189d5b13cbeb932245fad497761e6e355c Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 3 Mar 2019 12:28:25 +0100
Subject: [PATCH 061/184] store values for sort order radio box

---
 .../org/jabref/gui/SaveOrderConfigDisplay.fxml   |  2 +-
 .../gui/SaveOrderConfigDisplayViewModel.java     | 16 ++++++----------
 .../jabref/preferences/JabRefPreferences.java    |  4 +++-
 3 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
index b3b286c7f92..6fab26dcfd1 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
@@ -30,7 +30,7 @@
       <ComboBox fx:id="savePriSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="3" />
       <ComboBox fx:id="saveSecSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="4" />
       <ComboBox fx:id="saveTerSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="5" />
-      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" GridPane.rowIndex="2">
+      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" GridPane.rowIndex="2"/>
       <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" GridPane.rowIndex="1" />
       <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" />
       <CheckBox fx:id="savePriDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" />
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
index 36ec54a7fcd..a653a10e319 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
@@ -50,13 +50,6 @@ public SaveOrderConfigDisplayViewModel(SaveOrderConfig config, PreferencesServic
         secSortFieldsProperty.addAll(fieldNames);
         terSortFieldsProperty.addAll(fieldNames);
 
-        if (config.saveInOriginalOrder()) {
-            saveInOriginalProperty.setValue(true);
-        } else if (config.saveInSpecifiedOrder()) {
-            saveInSpecifiedOrderProperty.setValue(true);
-        } else {
-            saveInTableOrderProperty.setValue(true);
-        }
         setSaveOrderConfig(config);
     }
 
@@ -92,11 +85,14 @@ public void setSaveOrderConfig(SaveOrderConfig saveOrderConfig) {
         saveTerSortSelectedValueProperty.setValue(saveOrderConfig.getSortCriteria().get(2).field);
         saveTerDescPropertySelected.setValue(saveOrderConfig.getSortCriteria().get(2).descending);
 
-        if (saveInOriginalProperty.getValue()) {
-            saveOrderConfig.setSaveInOriginalOrder();
+        if (saveOrderConfig.saveInOriginalOrder()) {
+            saveInOriginalProperty.setValue(true);
+        } else if (saveOrderConfig.saveInSpecifiedOrder()) {
+            saveInSpecifiedOrderProperty.setValue(true);
         } else {
-            saveOrderConfig.setSaveInSpecifiedOrder();
+            saveInTableOrderProperty.setValue(true);
         }
+
     }
 
     private String getSelectedItemAsLowerCaseTrim(StringProperty string) {
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index 3fa8e4f50b5..83fb0c7ac6c 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -1711,6 +1711,8 @@ public void storeExportSaveOrder(SaveOrderConfig config) {
         putBoolean(EXPORT_PRIMARY_SORT_DESCENDING, config.getSortCriteria().get(0).descending);
         putBoolean(EXPORT_SECONDARY_SORT_DESCENDING, config.getSortCriteria().get(1).descending);
         putBoolean(EXPORT_TERTIARY_SORT_DESCENDING, config.getSortCriteria().get(2).descending);
+        putBoolean(EXPORT_IN_ORIGINAL_ORDER, config.saveInOriginalOrder());
+        putBoolean(EXPORT_IN_SPECIFIED_ORDER, config.saveInSpecifiedOrder());
 
         put(EXPORT_PRIMARY_SORT_FIELD, config.getSortCriteria().get(0).field);
         put(EXPORT_SECONDARY_SORT_FIELD, config.getSortCriteria().get(1).field);
@@ -1731,7 +1733,7 @@ private SaveOrderConfig loadTableSaveOrder() {
 
     @Override
     public SaveOrderConfig loadExportSaveOrder() {
-        return new SaveOrderConfig(true,
+        return new SaveOrderConfig(getBoolean(EXPORT_IN_ORIGINAL_ORDER),
                 new SaveOrderConfig.SortCriterion(get(EXPORT_PRIMARY_SORT_FIELD), getBoolean(EXPORT_PRIMARY_SORT_DESCENDING)),
                 new SaveOrderConfig.SortCriterion(get(EXPORT_SECONDARY_SORT_FIELD), getBoolean(EXPORT_SECONDARY_SORT_DESCENDING)),
                 new SaveOrderConfig.SortCriterion(get(EXPORT_TERTIARY_SORT_FIELD), getBoolean(EXPORT_TERTIARY_SORT_DESCENDING))

From 0313b4e77f94ebeaa2b3cf2e078c6f43c24d2872 Mon Sep 17 00:00:00 2001
From: Chelsey Ong <chelseyong@gmail.com>
Date: Sun, 3 Mar 2019 18:37:51 +0700
Subject: [PATCH 062/184] Clean key in BracketedPattern after author value is
 retrieved

---
 .../logic/bibtexkeypattern/BibtexKeyGenerator.java |  2 +-
 .../logic/bibtexkeypattern/BracketedPattern.java   | 14 +++++++++-----
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
index ff61a9035da..ffea572e61e 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
@@ -123,7 +123,7 @@ public String generateKey(BibEntry entry) {
                     List<String> parts = parseFieldMarker(typeListEntry);
                     Character delimiter = bibtexKeyPatternPreferences.getKeywordDelimiter();
                     String pattern = "[" + parts.get(0) + "]";
-                    String label = expandBrackets(pattern, delimiter, entry, database);
+                    String label = expandBrackets(pattern, delimiter, entry, database, bibtexKeyPatternPreferences.isEnforceLegalKey());
                     // apply modifier if present
                     if (parts.size() > 1) {
                         label = applyModifiers(label, parts, 1);
diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
index f88e98b3842..7c8114613e7 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
@@ -92,6 +92,10 @@ public String expand(BibEntry bibentry, Character keywordDelimiter, BibDatabase
         return expandBrackets(this.pattern, keywordDelimiter, bibentry, database);
     }
 
+    public static String expandBrackets(String pattern, Character keywordDelimiter, BibEntry entry, BibDatabase database) {
+        return expandBrackets(pattern, keywordDelimiter, entry, database, false);
+    }
+
     /**
      * Expands a pattern
      *
@@ -101,7 +105,7 @@ public String expand(BibEntry bibentry, Character keywordDelimiter, BibDatabase
      * @param database The database for field resolving. May be null.
      * @return The expanded pattern. Not null.
      */
-    public static String expandBrackets(String pattern, Character keywordDelimiter, BibEntry entry, BibDatabase database) {
+    public static String expandBrackets(String pattern, Character keywordDelimiter, BibEntry entry, BibDatabase database, boolean isEnforceLegalKey) {
         Objects.requireNonNull(pattern);
         Objects.requireNonNull(entry);
         StringBuilder sb = new StringBuilder();
@@ -122,10 +126,10 @@ public static String expandBrackets(String pattern, Character keywordDelimiter,
                     // check whether there is a modifier on the end such as
                     // ":lower":
                     if (fieldParts.size() <= 1) {
-                        sb.append(getFieldValue(entry, token, keywordDelimiter, database));
+                        sb.append(getFieldValue(entry, token, keywordDelimiter, database, isEnforceLegalKey));
                     } else {
                         // apply modifiers:
-                        String fieldValue = getFieldValue(entry, fieldParts.get(0), keywordDelimiter, database);
+                        String fieldValue = getFieldValue(entry, fieldParts.get(0), keywordDelimiter, database, isEnforceLegalKey);
                         sb.append(applyModifiers(fieldValue, fieldParts, 1));
                     }
                     // Fetch and discard the closing ']'
@@ -156,7 +160,7 @@ public static String expandBrackets(String pattern, Character keywordDelimiter,
      *
      * @return String containing the evaluation result. Empty string if the pattern cannot be resolved.
      */
-    public static String getFieldValue(BibEntry entry, String value, Character keywordDelimiter, BibDatabase database) {
+    public static String getFieldValue(BibEntry entry, String value, Character keywordDelimiter, BibDatabase database, boolean isEnforceLegalKey) {
 
         String val = value;
         try {
@@ -187,7 +191,7 @@ public static String getFieldValue(BibEntry entry, String value, Character keywo
                         }
                     }
                 }
-
+                authString = BibtexKeyGenerator.cleanKey(authString, isEnforceLegalKey);
                 // Gather all author-related checks, so we don't
                 // have to check all the time.
                 if ("auth".equals(val)) {

From 094a0395e610f52091d730754076b2c2e86fcae3 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Sun, 3 Mar 2019 12:47:55 +0100
Subject: [PATCH 063/184] Improve error mesage on save, add current field
 content (#4710)

* Improve error mesage on save, add current field content

* fix spaces around plus sign

* fix formatting
---
 .../logic/bibtex/LatexFieldFormatter.java     | 30 +++++++++----------
 1 file changed, 14 insertions(+), 16 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bibtex/LatexFieldFormatter.java b/src/main/java/org/jabref/logic/bibtex/LatexFieldFormatter.java
index 64346eb96cb..b69a6480a71 100644
--- a/src/main/java/org/jabref/logic/bibtex/LatexFieldFormatter.java
+++ b/src/main/java/org/jabref/logic/bibtex/LatexFieldFormatter.java
@@ -23,7 +23,6 @@ public class LatexFieldFormatter {
     private final FieldContentParser parser;
     private StringBuilder stringBuilder;
 
-
     public LatexFieldFormatter(LatexFieldFormatterPreferences prefs) {
         this(true, prefs);
     }
@@ -48,26 +47,26 @@ private static void checkBraces(String text) throws InvalidFieldValueException {
             char item = text.charAt(i);
 
             boolean charBeforeIsEscape = false;
-            if (i > 0 && text.charAt(i - 1) == '\\') {
+            if ((i > 0) && (text.charAt(i - 1) == '\\')) {
                 charBeforeIsEscape = true;
             }
 
-            if (!charBeforeIsEscape && item == '{') {
+            if (!charBeforeIsEscape && (item == '{')) {
                 left++;
-            } else if (!charBeforeIsEscape && item == '}') {
+            } else if (!charBeforeIsEscape && (item == '}')) {
                 right++;
             }
         }
 
         // Then we throw an exception if the error criteria are met.
         if (!(right == 0) && (left == 0)) {
-            throw new InvalidFieldValueException("Unescaped '}' character without opening bracket ends string prematurely.");
+            throw new InvalidFieldValueException("Unescaped '}' character without opening bracket ends string prematurely. Field value: " + text);
         }
         if (!(right == 0) && (right < left)) {
-            throw new InvalidFieldValueException("Unescaped '}' character without opening bracket ends string prematurely.");
+            throw new InvalidFieldValueException("Unescaped '}' character without opening bracket ends string prematurely. Field value: " + text);
         }
         if (left != right) {
-            throw new InvalidFieldValueException("Braces don't match.");
+            throw new InvalidFieldValueException("Braces don't match. Field value: " + text);
         }
     }
 
@@ -146,9 +145,9 @@ private String formatAndResolveStrings(String content, String fieldName) throws
                         pos1 = content.length(); // just write out the rest of the text, and throw no exception
                     } else {
                         throw new InvalidFieldValueException(
-                                "The # character is not allowed in BibTeX strings unless escaped as in '\\#'.\n"
-                                        + "In JabRef, use pairs of # characters to indicate a string.\n"
-                                        + "Note that the entry causing the problem has been selected.");
+                                                             "The # character is not allowed in BibTeX strings unless escaped as in '\\#'.\n"
+                                                             + "In JabRef, use pairs of # characters to indicate a string.\n"
+                                                             + "Note that the entry causing the problem has been selected. Field value: " + content);
                     }
                 }
             }
@@ -161,7 +160,7 @@ private String formatAndResolveStrings(String content, String fieldName) throws
                 // an occurrence of ## will simply be ignored. Should it instead
                 // cause an error message?
                 writeStringLabel(content, pos1 + 1, pos2, pos1 == pivot,
-                        (pos2 + 1) == content.length());
+                                 (pos2 + 1) == content.length());
             }
 
             if (pos2 > -1) {
@@ -187,7 +186,7 @@ private boolean shouldResolveStrings(String fieldName) {
         } else {
             // Default operation - we only resolve strings for standard fields:
             resolveStrings = InternalBibtexFields.isStandardField(fieldName)
-                    || BIBTEX_STRING.equals(fieldName);
+                             || BIBTEX_STRING.equals(fieldName);
         }
         return resolveStrings;
     }
@@ -195,8 +194,7 @@ private boolean shouldResolveStrings(String fieldName) {
     private String formatWithoutResolvingStrings(String content, String fieldName) throws InvalidFieldValueException {
         checkBraces(content);
 
-        stringBuilder = new StringBuilder(
-                String.valueOf(FIELD_START));
+        stringBuilder = new StringBuilder(String.valueOf(FIELD_START));
 
         stringBuilder.append(parser.format(content, fieldName));
 
@@ -258,7 +256,7 @@ private void writeText(String text, int startPos, int endPos) {
             // We add a backslash before any ampersand characters, with one exception: if
             // we are inside an \\url{...} command, we should write it as it is. Maybe.
             if ((c == '&') && !escape && !(inCommand && "url".equals(commandName.toString()))
-                    && (nestedEnvironments == 0)) {
+                && (nestedEnvironments == 0)) {
                 stringBuilder.append("\\&");
             } else {
                 stringBuilder.append(c);
@@ -271,7 +269,7 @@ private void writeText(String text, int startPos, int endPos) {
     private void writeStringLabel(String text, int startPos, int endPos,
                                   boolean first, boolean last) {
         putIn((first ? "" : " # ") + text.substring(startPos, endPos)
-                + (last ? "" : " # "));
+              + (last ? "" : " # "));
     }
 
     private void putIn(String s) {

From 7d8de04a6af8f8e556c7735376bed94ae63fb304 Mon Sep 17 00:00:00 2001
From: Chelsey Ong <chelseyong@gmail.com>
Date: Sun, 3 Mar 2019 22:44:48 +0700
Subject: [PATCH 064/184] Shift cleaning of authString to authN only

---
 .../org/jabref/logic/bibtexkeypattern/BracketedPattern.java    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
index 7c8114613e7..12d9a1d93bb 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
@@ -191,7 +191,7 @@ public static String getFieldValue(BibEntry entry, String value, Character keywo
                         }
                     }
                 }
-                authString = BibtexKeyGenerator.cleanKey(authString, isEnforceLegalKey);
+
                 // Gather all author-related checks, so we don't
                 // have to check all the time.
                 if ("auth".equals(val)) {
@@ -231,6 +231,7 @@ else if ("authorLast".equals(val)) {
                     // authN. First N chars of the first author's last
                     // name.
 
+                    authString = BibtexKeyGenerator.cleanKey(authString, isEnforceLegalKey);
                     String fa = firstAuthor(authString);
                     int num = Integer.parseInt(val.substring(4));
                     if (num > fa.length()) {

From 038a4bf440f9b42ae9e1f8d6a916d46cccd9fd83 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 4 Mar 2019 08:27:28 +0100
Subject: [PATCH 065/184] Bump richtextfx from 0.9.2 to 0.9.3 (#4718)

Bumps [richtextfx](https://github.com/FXMisc/RichTextFX) from 0.9.2 to 0.9.3.
- [Release notes](https://github.com/FXMisc/RichTextFX/releases)
- [Changelog](https://github.com/FXMisc/RichTextFX/blob/master/CHANGELOG.md)
- [Commits](https://github.com/FXMisc/RichTextFX/compare/v0.9.2...v0.9.3)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index a5c470c8f20..ea5d8e813b2 100644
--- a/build.gradle
+++ b/build.gradle
@@ -134,7 +134,7 @@ dependencies {
     compile 'de.saxsys:mvvmfx:1.7.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
-    compile 'org.fxmisc.richtext:richtextfx:0.9.2'
+    compile 'org.fxmisc.richtext:richtextfx:0.9.3'
     compile 'com.sibvisions.external.jvxfx:dndtabpane:0.1'
     compile 'javax.inject:javax.inject:1'
     compile 'com.jfoenix:jfoenix:8.0.8'

From e189016db93c15583e0c83d90966ee3b34c20c08 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Mon, 4 Mar 2019 20:22:44 +0100
Subject: [PATCH 066/184] Temporarily remove "Customize entry types" (#4716)

* Temporarily remove "Customize entry types"

* Add reference to issue
---
 src/main/java/org/jabref/gui/JabRefFrame.java |  4 +-
 .../CustomizeEntryAction.java                 | 10 ++-
 .../EntryTypeCustomizationDialog.java         | 61 +++----------------
 3 files changed, 13 insertions(+), 62 deletions(-)
 rename src/main/java/org/jabref/gui/{actions => customentrytypes}/CustomizeEntryAction.java (54%)

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 8346fe58e7f..f89fa8fc21d 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -58,7 +58,6 @@
 import org.jabref.gui.actions.BibtexKeyPatternAction;
 import org.jabref.gui.actions.ConnectToSharedDatabaseCommand;
 import org.jabref.gui.actions.CopyFilesAction;
-import org.jabref.gui.actions.CustomizeEntryAction;
 import org.jabref.gui.actions.CustomizeKeyBindingAction;
 import org.jabref.gui.actions.DatabasePropertiesAction;
 import org.jabref.gui.actions.EditExternalFileTypesAction;
@@ -942,7 +941,8 @@ private MenuBar createMenu() {
                 new SeparatorMenuItem(),
 
                 factory.createMenuItem(StandardActions.MANAGE_CONTENT_SELECTORS, new ManageContentSelectorAction(this)),
-                factory.createMenuItem(StandardActions.CUSTOMIZE_ENTRY_TYPES, new CustomizeEntryAction(this)),
+                // TODO: Reenable customize entry types feature (https://github.com/JabRef/jabref/issues/4719)
+                //factory.createMenuItem(StandardActions.CUSTOMIZE_ENTRY_TYPES, new CustomizeEntryAction(this)),
                 factory.createMenuItem(StandardActions.MANAGE_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this)));
 
         help.getItems().addAll(
diff --git a/src/main/java/org/jabref/gui/actions/CustomizeEntryAction.java b/src/main/java/org/jabref/gui/customentrytypes/CustomizeEntryAction.java
similarity index 54%
rename from src/main/java/org/jabref/gui/actions/CustomizeEntryAction.java
rename to src/main/java/org/jabref/gui/customentrytypes/CustomizeEntryAction.java
index b8ea7ee567b..3fb6a635a53 100644
--- a/src/main/java/org/jabref/gui/actions/CustomizeEntryAction.java
+++ b/src/main/java/org/jabref/gui/customentrytypes/CustomizeEntryAction.java
@@ -1,9 +1,7 @@
-package org.jabref.gui.actions;
-
-import javax.swing.JDialog;
+package org.jabref.gui.customentrytypes;
 
 import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.customentrytypes.EntryTypeCustomizationDialog;
+import org.jabref.gui.actions.SimpleCommand;
 
 public class CustomizeEntryAction extends SimpleCommand {
 
@@ -15,7 +13,7 @@ public CustomizeEntryAction(JabRefFrame frame) {
 
     @Override
     public void execute() {
-        JDialog dialog = new EntryTypeCustomizationDialog(frame);
-        dialog.setVisible(true);
+        EntryTypeCustomizationDialog dialog = new EntryTypeCustomizationDialog();
+        dialog.showAndWait();
     }
 }
diff --git a/src/main/java/org/jabref/gui/customentrytypes/EntryTypeCustomizationDialog.java b/src/main/java/org/jabref/gui/customentrytypes/EntryTypeCustomizationDialog.java
index 0361f3013a1..cf0439125d1 100644
--- a/src/main/java/org/jabref/gui/customentrytypes/EntryTypeCustomizationDialog.java
+++ b/src/main/java/org/jabref/gui/customentrytypes/EntryTypeCustomizationDialog.java
@@ -1,56 +1,11 @@
 package org.jabref.gui.customentrytypes;
 
-import java.awt.BorderLayout;
-import java.awt.Container;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.GridLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Locale;
-import java.util.Map;
-import java.util.Optional;
-import java.util.Set;
-import java.util.stream.Collectors;
-
-import javax.swing.AbstractAction;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JList;
-import javax.swing.JPanel;
-import javax.swing.ListSelectionModel;
-import javax.swing.event.ListDataEvent;
-import javax.swing.event.ListDataListener;
-import javax.swing.event.ListSelectionEvent;
-import javax.swing.event.ListSelectionListener;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.JabRefDialog;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.EntryTypes;
-import org.jabref.model.database.BibDatabaseMode;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.CustomEntryType;
-import org.jabref.model.entry.EntryType;
-import org.jabref.model.entry.InternalBibtexFields;
-import org.jabref.model.strings.StringUtil;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-
-public class EntryTypeCustomizationDialog extends JabRefDialog implements ListSelectionListener {
+import org.jabref.gui.util.BaseDialog;
 
+public class EntryTypeCustomizationDialog extends BaseDialog<Void> {
+
+    // TODO: Re-implement customize entry types feature (https://github.com/JabRef/jabref/issues/4719)
+    /*
     protected GridBagLayout gbl = new GridBagLayout();
     protected GridBagConstraints con = new GridBagConstraints();
     protected JButton delete;
@@ -70,9 +25,6 @@ public class EntryTypeCustomizationDialog extends JabRefDialog implements ListSe
     private boolean biblatexMode;
     private BibDatabaseMode bibDatabaseMode;
 
-    /**
-     * Creates a new instance of EntryTypeCustomizationDialog
-     */
     public EntryTypeCustomizationDialog(JabRefFrame frame) {
         super(Localization.lang("Customize entry types"), false, EntryTypeCustomizationDialog.class);
 
@@ -419,6 +371,7 @@ private void record() {
             changed.add(lastSelected);
             typeComp.enable(lastSelected, true);
         }
-
     }
+
+    */
 }

From 1a198f716213aaf5e3fd7d92c4eb89b485994f6d Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Mon, 4 Mar 2019 21:13:47 +0100
Subject: [PATCH 067/184] Convert "Protected terms" dialog to JavaFX (#4715)

* Convert "Protected terms" dialog to JavaFX

* Improve code according to feedback
---
 .../java/org/jabref/gui/DefaultInjector.java  |   3 +
 src/main/java/org/jabref/gui/JabRefFrame.java |   4 +-
 .../actions/ManageProtectedTermsAction.java   |  23 -
 .../contextmenu/ProtectedTermsMenu.java       |  20 -
 .../ManageProtectedTermsAction.java           |  12 +
 .../ManageProtectedTermsDialog.fxml           |  36 ++
 .../ManageProtectedTermsDialog.java           | 128 +++++
 .../ManageProtectedTermsViewModel.java        |  99 ++++
 .../NewProtectedTermsFileDialog.java          | 127 ++---
 .../protectedterms/ProtectedTermsDialog.java  | 489 ------------------
 .../org/jabref/gui/util/BindingsHelper.java   |  12 +-
 .../org/jabref/model/util/OptionalUtil.java   |   8 +
 .../jabref/preferences/JabRefPreferences.java |  10 +-
 .../preferences/PreferencesService.java       |   3 +
 src/main/resources/l10n/JabRef_en.properties  |   3 -
 15 files changed, 335 insertions(+), 642 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/actions/ManageProtectedTermsAction.java
 create mode 100644 src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsAction.java
 create mode 100644 src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsDialog.fxml
 create mode 100644 src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsDialog.java
 create mode 100644 src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsViewModel.java
 delete mode 100644 src/main/java/org/jabref/gui/protectedterms/ProtectedTermsDialog.java

diff --git a/src/main/java/org/jabref/gui/DefaultInjector.java b/src/main/java/org/jabref/gui/DefaultInjector.java
index e94e6fe8697..4f18a03b9e6 100644
--- a/src/main/java/org/jabref/gui/DefaultInjector.java
+++ b/src/main/java/org/jabref/gui/DefaultInjector.java
@@ -6,6 +6,7 @@
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
+import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.PreferencesService;
 
@@ -38,6 +39,8 @@ private static Object createDependency(Class<?> clazz) {
             return Globals.stateManager;
         } else if (clazz == FileUpdateMonitor.class) {
             return Globals.getFileUpdateMonitor();
+        } else if (clazz == ProtectedTermsLoader.class) {
+            return Globals.protectedTermsLoader;
         } else if (clazz == ClipBoardManager.class) {
             return Globals.clipboardManager;
         } else {
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index f89fa8fc21d..760709e1504 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -68,7 +68,6 @@
 import org.jabref.gui.actions.ManageCustomImportsAction;
 import org.jabref.gui.actions.ManageJournalsAction;
 import org.jabref.gui.actions.ManageKeywordsAction;
-import org.jabref.gui.actions.ManageProtectedTermsAction;
 import org.jabref.gui.actions.NewDatabaseAction;
 import org.jabref.gui.actions.NewEntryAction;
 import org.jabref.gui.actions.NewEntryFromPlainTextAction;
@@ -100,6 +99,7 @@
 import org.jabref.gui.mergeentries.MergeEntriesAction;
 import org.jabref.gui.metadata.BibtexStringEditorAction;
 import org.jabref.gui.metadata.PreambleEditor;
+import org.jabref.gui.protectedterms.ManageProtectedTermsAction;
 import org.jabref.gui.push.PushToApplicationButton;
 import org.jabref.gui.push.PushToApplications;
 import org.jabref.gui.search.GlobalSearchBar;
@@ -936,7 +936,7 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.MANAGE_EXTERNAL_FILETYPES, new EditExternalFileTypesAction()),
                 factory.createMenuItem(StandardActions.MANAGE_JOURNALS, new ManageJournalsAction()),
                 factory.createMenuItem(StandardActions.CUSTOMIZE_KEYBINDING, new CustomizeKeyBindingAction()),
-                factory.createMenuItem(StandardActions.MANAGE_PROTECTED_TERMS, new ManageProtectedTermsAction(this, Globals.protectedTermsLoader)),
+                factory.createMenuItem(StandardActions.MANAGE_PROTECTED_TERMS, new ManageProtectedTermsAction()),
 
                 new SeparatorMenuItem(),
 
diff --git a/src/main/java/org/jabref/gui/actions/ManageProtectedTermsAction.java b/src/main/java/org/jabref/gui/actions/ManageProtectedTermsAction.java
deleted file mode 100644
index c4f05f955cf..00000000000
--- a/src/main/java/org/jabref/gui/actions/ManageProtectedTermsAction.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.jabref.gui.actions;
-
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.protectedterms.ProtectedTermsDialog;
-import org.jabref.logic.protectedterms.ProtectedTermsLoader;
-
-public class ManageProtectedTermsAction extends SimpleCommand {
-
-    private final JabRefFrame jabRefFrame;
-    private final ProtectedTermsLoader termsLoader;
-
-    public ManageProtectedTermsAction(JabRefFrame jabRefFrame, ProtectedTermsLoader termsLoader) {
-        this.jabRefFrame = jabRefFrame;
-        this.termsLoader = termsLoader;
-    }
-    @Override
-    public void execute() {
-        ProtectedTermsDialog protectTermsDialog = new ProtectedTermsDialog(jabRefFrame);
-        protectTermsDialog.setVisible(true);
-
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/fieldeditors/contextmenu/ProtectedTermsMenu.java b/src/main/java/org/jabref/gui/fieldeditors/contextmenu/ProtectedTermsMenu.java
index 4af7fec8023..85bd758232d 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/contextmenu/ProtectedTermsMenu.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/contextmenu/ProtectedTermsMenu.java
@@ -3,16 +3,12 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
-import javax.swing.SwingUtilities;
-
 import javafx.scene.control.Menu;
 import javafx.scene.control.MenuItem;
 import javafx.scene.control.SeparatorMenuItem;
 import javafx.scene.control.TextInputControl;
 
 import org.jabref.Globals;
-import org.jabref.JabRefGUI;
-import org.jabref.gui.protectedterms.NewProtectedTermsFileDialog;
 import org.jabref.logic.formatter.casechanger.ProtectTermsFormatter;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.protectedterms.ProtectedTermsList;
@@ -65,21 +61,5 @@ private void updateFiles() {
             externalFiles.getItems().add(fileItem);
         }
         externalFiles.getItems().add(new SeparatorMenuItem());
-        MenuItem addToNewFileItem = new MenuItem(Localization.lang("New") + "...");
-        addToNewFileItem.setOnAction(event -> {
-            NewProtectedTermsFileDialog dialog = new NewProtectedTermsFileDialog(JabRefGUI.getMainFrame().getDialogService(),
-                    loader);
-
-            SwingUtilities.invokeLater(() -> {
-                dialog.setVisible(true);
-
-                if (dialog.isOKPressed()) {
-                    // Update preferences with new list
-                    Globals.prefs.setProtectedTermsPreferences(loader);
-                    this.updateFiles();
-                }
-            });
-        });
-        externalFiles.getItems().add(addToNewFileItem);
     }
 }
diff --git a/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsAction.java b/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsAction.java
new file mode 100644
index 00000000000..34f4ff3f116
--- /dev/null
+++ b/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsAction.java
@@ -0,0 +1,12 @@
+package org.jabref.gui.protectedterms;
+
+import org.jabref.gui.actions.SimpleCommand;
+
+public class ManageProtectedTermsAction extends SimpleCommand {
+
+    @Override
+    public void execute() {
+        ManageProtectedTermsDialog protectTermsDialog = new ManageProtectedTermsDialog();
+        protectTermsDialog.showAndWait();
+    }
+}
diff --git a/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsDialog.fxml b/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsDialog.fxml
new file mode 100644
index 00000000000..0b23bc0ccaf
--- /dev/null
+++ b/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsDialog.fxml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.ButtonType?>
+<?import javafx.scene.control.DialogPane?>
+<?import javafx.scene.control.TableColumn?>
+<?import javafx.scene.control.TableView?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
+<DialogPane xmlns:fx="http://javafx.com/fxml"
+            xmlns="http://javafx.com/javafx"
+            fx:controller="org.jabref.gui.protectedterms.ManageProtectedTermsDialog"
+            prefHeight="400.0" prefWidth="600.0">
+    <content>
+        <VBox spacing="10">
+            <TableView fx:id="filesTable" editable="true" VBox.vgrow="ALWAYS">
+                <columns>
+                    <TableColumn fx:id="filesTableEnabledColumn" text="%Enabled" minWidth="80" maxWidth="80"/>
+                    <TableColumn fx:id="filesTableDescriptionColumn" text="%Description"/>
+                    <TableColumn fx:id="filesTableFileColumn" text="%File"/>
+                    <TableColumn fx:id="filesTableEditColumn" maxWidth="40" minWidth="40.0"/>
+                    <TableColumn fx:id="filesTableDeleteColumn" maxWidth="40" minWidth="40.0"/>
+                </columns>
+                <columnResizePolicy>
+                    <TableView fx:constant="CONSTRAINED_RESIZE_POLICY"/>
+                </columnResizePolicy>
+            </TableView>
+            <HBox>
+                <Button text="%Add protected terms file" onAction="#addFile"/>
+                <Button text="%New protected terms file" onAction="#createNewFile"/>
+            </HBox>
+        </VBox>
+    </content>
+    <ButtonType fx:constant="CANCEL"/>
+    <ButtonType fx:constant="APPLY"/>
+</DialogPane>
diff --git a/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsDialog.java b/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsDialog.java
new file mode 100644
index 00000000000..474304d2383
--- /dev/null
+++ b/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsDialog.java
@@ -0,0 +1,128 @@
+package org.jabref.gui.protectedterms;
+
+import javax.inject.Inject;
+
+import javafx.fxml.FXML;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.ContextMenu;
+import javafx.scene.control.MenuItem;
+import javafx.scene.control.TableColumn;
+import javafx.scene.control.TableView;
+import javafx.scene.control.cell.CheckBoxTableCell;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.icon.IconTheme;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.BindingsHelper;
+import org.jabref.gui.util.ValueTableCellFactory;
+import org.jabref.gui.util.ViewModelTableRowFactory;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.protectedterms.ProtectedTermsList;
+import org.jabref.logic.protectedterms.ProtectedTermsLoader;
+import org.jabref.preferences.PreferencesService;
+
+import com.airhacks.afterburner.views.ViewLoader;
+
+/**
+ * Dialog for managing term list files.
+ */
+public class ManageProtectedTermsDialog extends BaseDialog<Void> {
+
+    @FXML private TableView<ProtectedTermsList> filesTable;
+    @FXML private TableColumn<ProtectedTermsList, Boolean> filesTableEnabledColumn;
+    @FXML private TableColumn<ProtectedTermsList, String> filesTableDescriptionColumn;
+    @FXML private TableColumn<ProtectedTermsList, String> filesTableFileColumn;
+    @FXML private TableColumn<ProtectedTermsList, Boolean> filesTableEditColumn;
+    @FXML private TableColumn<ProtectedTermsList, Boolean> filesTableDeleteColumn;
+
+    @Inject private ProtectedTermsLoader termsLoader;
+    @Inject private DialogService dialogService;
+    @Inject private PreferencesService preferences;
+    private ManageProtectedTermsViewModel viewModel;
+
+    public ManageProtectedTermsDialog() {
+        this.setTitle(Localization.lang("Manage protected terms files"));
+
+        ViewLoader.view(this)
+                  .load()
+                  .setAsDialogPane(this);
+
+        setResultConverter(button -> {
+            if (button == ButtonType.APPLY) {
+                viewModel.save();
+            }
+            return null;
+        });
+    }
+
+    @FXML
+    public void initialize() {
+        viewModel = new ManageProtectedTermsViewModel(termsLoader, dialogService, preferences);
+
+        filesTable.setItems(viewModel.getTermsFiles());
+        new ViewModelTableRowFactory<ProtectedTermsList>()
+                .withContextMenu(this::createContextMenu)
+                .install(filesTable);
+        filesTableEnabledColumn.setCellValueFactory(data -> BindingsHelper.constantOf(data.getValue().isEnabled()));
+        filesTableEnabledColumn.setCellFactory(CheckBoxTableCell.forTableColumn(filesTableEnabledColumn));
+        filesTableDescriptionColumn.setCellValueFactory(data -> BindingsHelper.constantOf(data.getValue().getDescription()));
+        filesTableFileColumn.setCellValueFactory(data -> {
+            ProtectedTermsList list = data.getValue();
+            if (list.isInternalList()) {
+                return BindingsHelper.constantOf(Localization.lang("Internal list"));
+            } else {
+                return BindingsHelper.constantOf(data.getValue().getLocation());
+            }
+        });
+        filesTableEditColumn.setCellValueFactory(data -> BindingsHelper.constantOf(true));
+        filesTableDeleteColumn.setCellValueFactory(data -> BindingsHelper.constantOf(true));
+
+        new ValueTableCellFactory<ProtectedTermsList, Boolean>()
+                .withGraphic(none -> IconTheme.JabRefIcons.EDIT.getGraphicNode())
+                .withOnMouseClickedEvent((file, none) -> event -> viewModel.edit(file))
+                .install(filesTableEditColumn);
+        new ValueTableCellFactory<ProtectedTermsList, Boolean>()
+                .withGraphic(none -> IconTheme.JabRefIcons.REMOVE.getGraphicNode())
+                .withTooltip(none -> Localization.lang("Remove protected terms file"))
+                .withOnMouseClickedEvent((file, none) -> event -> viewModel.removeFile(file))
+                .install(filesTableDeleteColumn);
+    }
+
+    private ContextMenu createContextMenu(ProtectedTermsList file) {
+        MenuItem edit = new MenuItem(Localization.lang("Edit"));
+        edit.setOnAction(event -> viewModel.edit(file));
+        MenuItem show = new MenuItem(Localization.lang("View"));
+        show.setOnAction(event -> viewModel.displayContent(file));
+        MenuItem remove = new MenuItem(Localization.lang("Remove"));
+        remove.setOnAction(event -> viewModel.removeFile(file));
+        MenuItem reload = new MenuItem(Localization.lang("Reload"));
+        reload.setOnAction(event -> viewModel.reloadFile(file));
+
+        // Enable/disable context menu items
+        if (file.isInternalList()) {
+            edit.setDisable(true);
+            show.setDisable(false);
+            remove.setDisable(true);
+            reload.setDisable(true);
+        } else {
+            edit.setDisable(false);
+            show.setDisable(false);
+            remove.setDisable(false);
+            reload.setDisable(false);
+        }
+
+        final ContextMenu contextMenu = new ContextMenu();
+        contextMenu.getItems().addAll(edit, show, remove, reload);
+        return contextMenu;
+    }
+
+    @FXML
+    private void addFile() {
+        viewModel.addFile();
+    }
+
+    @FXML
+    private void createNewFile() {
+        viewModel.createNewFile();
+    }
+}
diff --git a/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsViewModel.java b/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsViewModel.java
new file mode 100644
index 00000000000..3fca8b6e63b
--- /dev/null
+++ b/src/main/java/org/jabref/gui/protectedterms/ManageProtectedTermsViewModel.java
@@ -0,0 +1,99 @@
+package org.jabref.gui.protectedterms;
+
+import java.io.IOException;
+import java.util.Optional;
+
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.desktop.JabRefDesktop;
+import org.jabref.gui.externalfiletype.ExternalFileType;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.util.FileDialogConfiguration;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.protectedterms.ProtectedTermsList;
+import org.jabref.logic.protectedterms.ProtectedTermsLoader;
+import org.jabref.logic.util.StandardFileType;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.util.OptionalUtil;
+import org.jabref.preferences.PreferencesService;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class ManageProtectedTermsViewModel {
+    private static final Logger LOGGER = LoggerFactory.getLogger(ManageProtectedTermsViewModel.class);
+
+    private final ProtectedTermsLoader termsLoader;
+    private final ObservableList<ProtectedTermsList> termsFiles;
+    private final PreferencesService preferences;
+    private final DialogService dialogService;
+
+    public ManageProtectedTermsViewModel(ProtectedTermsLoader termsLoader, DialogService dialogService, PreferencesService preferences) {
+        this.termsLoader = termsLoader;
+        this.dialogService = dialogService;
+        this.termsFiles = FXCollections.observableArrayList(termsLoader.getProtectedTermsLists());
+        this.preferences = preferences;
+    }
+
+    public ObservableList<ProtectedTermsList> getTermsFiles() {
+        return termsFiles;
+    }
+
+    public void save() {
+        preferences.setProtectedTermsPreferences(termsLoader);
+    }
+
+    public void addFile() {
+        FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
+                .addExtensionFilter(Localization.lang("Protected terms file"), StandardFileType.TERMS)
+                .withDefaultExtension(Localization.lang("Protected terms file"), StandardFileType.TERMS)
+                .withInitialDirectory(preferences.getWorkingDir())
+                .build();
+
+        dialogService.showFileOpenDialog(fileDialogConfiguration)
+                     .ifPresent(file -> termsLoader.addProtectedTermsListFromFile(file.toAbsolutePath().toString(), true));
+    }
+
+    public void removeFile(ProtectedTermsList list) {
+        if (!list.isInternalList() && dialogService.showConfirmationDialogAndWait(Localization.lang("Remove protected terms file"),
+                Localization.lang("Are you sure you want to remove the protected terms file?"),
+                Localization.lang("Remove protected terms file"),
+                Localization.lang("Cancel"))) {
+            if (!termsLoader.removeProtectedTermsList(list)) {
+                LOGGER.info("Problem removing protected terms file");
+            }
+        }
+    }
+
+    public void createNewFile() {
+        NewProtectedTermsFileDialog newDialog = new NewProtectedTermsFileDialog(termsLoader, dialogService);
+        newDialog.showAndWait();
+    }
+
+    public void edit(ProtectedTermsList file) {
+        Optional<ExternalFileType> termsFileType = OptionalUtil.orElse(
+                ExternalFileTypes.getInstance().getExternalFileTypeByExt("terms"),
+                ExternalFileTypes.getInstance().getExternalFileTypeByExt("txt")
+        );
+
+        String fileName = file.getLocation();
+        try {
+            JabRefDesktop.openExternalFileAnyFormat(new BibDatabaseContext(), fileName, termsFileType);
+        } catch (IOException e) {
+            LOGGER.warn("Problem open protected terms file editor", e);
+        }
+    }
+
+    public void displayContent(ProtectedTermsList list) {
+        dialogService.showInformationDialogAndWait(
+                list.getDescription() + " - " + list.getLocation(),
+                list.getTermListing()
+        );
+    }
+
+    public void reloadFile(ProtectedTermsList file) {
+        termsLoader.reloadProtectedTermsList(file);
+    }
+}
diff --git a/src/main/java/org/jabref/gui/protectedterms/NewProtectedTermsFileDialog.java b/src/main/java/org/jabref/gui/protectedterms/NewProtectedTermsFileDialog.java
index b0bd76d7276..d97e6ccc9fb 100644
--- a/src/main/java/org/jabref/gui/protectedterms/NewProtectedTermsFileDialog.java
+++ b/src/main/java/org/jabref/gui/protectedterms/NewProtectedTermsFileDialog.java
@@ -1,61 +1,30 @@
 package org.jabref.gui.protectedterms;
 
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.nio.file.Path;
-import java.util.Optional;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.BorderFactory;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JTextField;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.Label;
+import javafx.scene.control.TextField;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.VBox;
 
 import org.jabref.Globals;
 import org.jabref.gui.DialogService;
-import org.jabref.gui.JabRefDialog;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.util.DefaultTaskExecutor;
+import org.jabref.gui.util.BaseDialog;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.preferences.JabRefPreferences;
 
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import com.jgoodies.forms.builder.FormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-
-public class NewProtectedTermsFileDialog extends JabRefDialog {
+public class NewProtectedTermsFileDialog extends BaseDialog<Void> {
 
-    private final JTextField newFile = new JTextField();
-    private final JTextField newDescription = new JTextField();
-    private final JCheckBox enabled = new JCheckBox(Localization.lang("Enabled"));
-    private boolean addOKPressed;
-    private final ProtectedTermsLoader loader;
+    private final TextField newFile = new TextField();
     private final DialogService dialogService;
 
-    public NewProtectedTermsFileDialog(JDialog parent, ProtectedTermsLoader loader, DialogService dialogService) {
-        super(parent, Localization.lang("New protected terms file"), true, NewProtectedTermsFileDialog.class);
-        this.loader = loader;
-        this.dialogService = dialogService;
-
-        setupDialog();
-        setLocationRelativeTo(parent);
-    }
-
-    public NewProtectedTermsFileDialog(DialogService dialogService, ProtectedTermsLoader loader) {
-        super(Localization.lang("New protected terms file"), true, NewProtectedTermsFileDialog.class);
-        this.loader = loader;
+    public NewProtectedTermsFileDialog(ProtectedTermsLoader termsLoader, DialogService dialogService) {
         this.dialogService = dialogService;
-        setupDialog();
-    }
 
-    private void setupDialog() {
-        JButton browse = new JButton(Localization.lang("Browse"));
+        this.setTitle(Localization.lang("New protected terms file"));
 
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
                 .addExtensionFilter(Localization.lang("Protected terms file"), StandardFileType.TERMS)
@@ -63,61 +32,29 @@ private void setupDialog() {
                 .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY))
                 .build();
 
-        browse.addActionListener(e -> {
-            Optional<Path> file = DefaultTaskExecutor
-                    .runInJavaFXThread(() -> dialogService.showFileSaveDialog(fileDialogConfiguration));
-            file.ifPresent(f -> newFile.setText(f.toAbsolutePath().toString()));
-        });
-
-        // Build content panel
-        FormBuilder builder = FormBuilder.create();
-        builder.layout(new FormLayout("left:pref, 4dlu, fill:100dlu:grow, 4dlu, pref", "p, 4dlu, p, 4dlu, p"));
-        builder.add(Localization.lang("Description")).xy(1, 1);
-        builder.add(newDescription).xyw(3, 1, 3);
-        builder.add(Localization.lang("File")).xy(1, 3);
-        builder.add(newFile).xy(3, 3);
-        builder.add(browse).xy(5, 3);
-        builder.add(enabled).xyw(1, 5, 5);
-        enabled.setSelected(true);
-        builder.padding("10dlu, 10dlu, 10dlu, 10dlu");
-        getContentPane().add(builder.build(), BorderLayout.CENTER);
-
-        // Buttons
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        JButton addOKButton = new JButton(Localization.lang("OK"));
-        JButton addCancelButton = new JButton(Localization.lang("Cancel"));
-        bb.addGlue();
-        bb.addButton(addOKButton);
-        bb.addButton(addCancelButton);
-        bb.addGlue();
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-        getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-        addOKButton.addActionListener(e -> {
-            addOKPressed = true;
-            loader.addNewProtectedTermsList(newDescription.getText(), newFile.getText(),
-                    enabled.isSelected());
-            dispose();
+        Button browse = new Button(Localization.lang("Browse"));
+        browse.setOnAction(event -> {
+            this.dialogService.showFileSaveDialog(fileDialogConfiguration)
+                              .ifPresent(file -> newFile.setText(file.toAbsolutePath().toString()));
         });
 
-        Action cancelAction = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                addOKPressed = false;
-                dispose();
+        TextField newDescription = new TextField();
+        VBox container = new VBox(10,
+                new VBox(5, new Label(Localization.lang("Description")), newDescription),
+                new VBox(5, new Label(Localization.lang("File")), new HBox(10, newFile, browse))
+        );
+        getDialogPane().setContent(container);
+
+        getDialogPane().getButtonTypes().setAll(
+                ButtonType.OK,
+                ButtonType.CANCEL
+        );
+
+        setResultConverter(button -> {
+            if (button == ButtonType.OK) {
+                termsLoader.addNewProtectedTermsList(newDescription.getText(), newFile.getText(), true);
             }
-        };
-        addCancelButton.addActionListener(cancelAction);
-
-        // Key bindings:
-        bb.getPanel().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
-          .put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        bb.getPanel().getActionMap().put("close", cancelAction);
-        pack();
-    }
-
-    public boolean isOKPressed() {
-        return addOKPressed;
+            return null;
+        });
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/protectedterms/ProtectedTermsDialog.java b/src/main/java/org/jabref/gui/protectedterms/ProtectedTermsDialog.java
deleted file mode 100644
index cef0db50b0d..00000000000
--- a/src/main/java/org/jabref/gui/protectedterms/ProtectedTermsDialog.java
+++ /dev/null
@@ -1,489 +0,0 @@
-package org.jabref.gui.protectedterms;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.io.IOException;
-import java.nio.file.Path;
-import java.util.Objects;
-import java.util.Optional;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JFrame;
-import javax.swing.JMenuItem;
-import javax.swing.JPopupMenu;
-import javax.swing.JScrollPane;
-import javax.swing.JTable;
-import javax.swing.JTextArea;
-import javax.swing.JTextField;
-import javax.swing.KeyStroke;
-import javax.swing.ListSelectionModel;
-import javax.swing.event.ListSelectionEvent;
-import javax.swing.event.ListSelectionListener;
-import javax.swing.table.DefaultTableModel;
-import javax.swing.table.TableColumnModel;
-
-import org.jabref.Globals;
-import org.jabref.gui.JabRefDialog;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.desktop.JabRefDesktop;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.icon.IconTheme;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.gui.util.FileDialogConfiguration;
-import org.jabref.gui.util.WindowLocation;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.protectedterms.ProtectedTermsList;
-import org.jabref.logic.protectedterms.ProtectedTermsLoader;
-import org.jabref.logic.util.StandardFileType;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.preferences.JabRefPreferences;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import com.jgoodies.forms.builder.FormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * This class produces a dialog box for managing term list files.
- */
-public class ProtectedTermsDialog {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(ProtectedTermsDialog.class);
-
-    private final JabRefFrame frame;
-    private JDialog diag;
-    private JTable table;
-    private DefaultTableModel tableModel;
-    private final JPopupMenu popup = new JPopupMenu();
-    private final JMenuItem edit = new JMenuItem(Localization.lang("Edit"));
-    private final JMenuItem show = new JMenuItem(Localization.lang("View"));
-    private final JMenuItem remove = new JMenuItem(Localization.lang("Remove"));
-    private final JMenuItem reload = new JMenuItem(Localization.lang("Reload"));
-    private final JMenuItem enabled = new JCheckBoxMenuItem(Localization.lang("Enabled"));
-    private final JButton loadButton = new JButton(IconTheme.JabRefIcons.OPEN.getIcon());
-    private final JButton removeButton = new JButton(IconTheme.JabRefIcons.DELETE_ENTRY.getIcon());
-    private final JButton newButton = new JButton(IconTheme.JabRefIcons.NEW.getIcon());
-    private ActionListener removeAction;
-
-    private final JButton ok = new JButton(Localization.lang("OK"));
-    private final JButton cancel = new JButton(Localization.lang("Cancel"));
-
-    private boolean okPressed;
-    private final ProtectedTermsLoader loader;
-
-    public ProtectedTermsDialog(JabRefFrame frame) {
-
-        this.frame = Objects.requireNonNull(frame);
-        this.loader = Globals.protectedTermsLoader;
-        init();
-
-    }
-
-    private void init() {
-        setupPopupMenu();
-
-        loadButton.addActionListener(actionEvent -> {
-            AddFileDialog addDialog = new AddFileDialog();
-            addDialog.setVisible(true);
-            addDialog.getFileName().ifPresent(fileName -> loader.addProtectedTermsListFromFile(fileName, true));
-            tableModel.fireTableDataChanged();
-        });
-        loadButton.setToolTipText(Localization.lang("Add protected terms file"));
-
-        removeButton.addActionListener(removeAction);
-        removeButton.setToolTipText(Localization.lang("Remove protected terms file"));
-
-        newButton.addActionListener(actionEvent -> {
-            NewProtectedTermsFileDialog newDialog = new NewProtectedTermsFileDialog(diag, loader, frame.getDialogService());
-            newDialog.setVisible(true);
-            tableModel.fireTableDataChanged();
-        });
-        newButton.setToolTipText(Localization.lang("New protected terms file"));
-
-        setupTable();
-
-        // Build dialog
-        diag = new JDialog((JFrame) null, Localization.lang("Manage protected terms files"), true);
-
-        FormBuilder builder = FormBuilder.create();
-        builder.layout(new FormLayout("fill:pref:grow, 4dlu, left:pref, 4dlu, left:pref, 4dlu, left:pref",
-                "100dlu:grow, 4dlu, pref"));
-        builder.add(new JScrollPane(table)).xyw(1, 1, 7);
-        builder.add(newButton).xy(3, 3);
-        builder.add(loadButton).xy(5, 3);
-        builder.add(removeButton).xy(7, 3);
-        builder.padding("5dlu, 5dlu, 5dlu, 5dlu");
-
-        diag.add(builder.getPanel(), BorderLayout.CENTER);
-
-        AbstractAction okListener = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent event) {
-                // Write changes to preferences
-                storePreferences();
-                diag.dispose();
-            }
-        };
-        ok.addActionListener(okListener);
-
-        Action cancelListener = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent event) {
-                // Restore from preferences
-                loader.update(Globals.prefs.getProtectedTermsPreferences());
-                diag.dispose();
-            }
-        };
-        cancel.addActionListener(cancelListener);
-
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        bb.addButton(ok);
-        bb.addButton(cancel);
-        bb.addGlue();
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-        diag.add(bb.getPanel(), BorderLayout.SOUTH);
-
-        ActionMap am = bb.getPanel().getActionMap();
-        InputMap im = bb.getPanel().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", cancelListener);
-        im.put(KeyStroke.getKeyStroke("ENTER"), "enterOk");
-        am.put("enterOk", okListener);
-
-        diag.pack();
-
-        WindowLocation pw = new WindowLocation(diag, JabRefPreferences.TERMS_POS_X, JabRefPreferences.TERMS_POS_Y,
-                JabRefPreferences.TERMS_SIZE_X, JabRefPreferences.TERMS_SIZE_Y);
-        pw.displayWindowAtStoredLocation();
-    }
-
-    private void setupTable() {
-        tableModel = new TermTableModel();
-        table = new JTable(tableModel);
-        TableColumnModel cm = table.getColumnModel();
-        cm.getColumn(0).setMinWidth((cm.getColumn(0).getPreferredWidth() * 11) / 10);
-        cm.getColumn(0).setMaxWidth((cm.getColumn(0).getPreferredWidth() * 11) / 10);
-        cm.getColumn(1).setPreferredWidth(100);
-        cm.getColumn(2).setPreferredWidth(100);
-
-        table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        table.addMouseListener(new MouseAdapter() {
-
-            @Override
-            public void mousePressed(MouseEvent mouseEvent) {
-                if (mouseEvent.isPopupTrigger()) {
-                    tablePopup(mouseEvent);
-                }
-            }
-
-            @Override
-            public void mouseReleased(MouseEvent mouseEvent) {
-                if (mouseEvent.isPopupTrigger()) {
-                    tablePopup(mouseEvent);
-                }
-            }
-
-            @Override
-            public void mouseClicked(MouseEvent mouseEvent) {
-                if (mouseEvent.getClickCount() == 2) {
-                    getSelectedTermsList().ifPresent(list -> list.setEnabled(!list.isEnabled()));
-                    tableModel.fireTableDataChanged();
-                }
-            }
-        });
-
-        table.getSelectionModel().addListSelectionListener(new EntrySelectionListener());
-    }
-
-    private void setupPopupMenu() {
-        popup.add(edit);
-        popup.add(show);
-        popup.add(remove);
-        popup.add(reload);
-        popup.addSeparator();
-        popup.add(enabled);
-
-        // Add action listener to "Edit" menu item, which is supposed to open the term file in an external editor:
-        edit.addActionListener(actionEvent -> getSelectedTermsList().ifPresent(term -> {
-            Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByExt("terms");
-            String fileName = term.getLocation();
-            try {
-                if (type.isPresent()) {
-                    JabRefDesktop.openExternalFileAnyFormat(new BibDatabaseContext(), fileName, type);
-                } else {
-                    // Fall back to ".txt"
-                    Optional<ExternalFileType> txtType = ExternalFileTypes.getInstance()
-                            .getExternalFileTypeByExt("txt");
-                    JabRefDesktop.openExternalFileAnyFormat(new BibDatabaseContext(), fileName, type);
-
-                }
-            } catch (IOException e) {
-                LOGGER.warn("Problem open protected terms file editor", e);
-            }
-        }));
-
-        // Add action listener to "Show" menu item, which is supposed to open the term file in a dialog:
-        show.addActionListener(actionEvent -> getSelectedTermsList().ifPresent(this::displayTerms));
-
-        // Create action listener for removing a term file, also used for the remove button
-        removeAction = actionEvent -> getSelectedTermsList().ifPresent(list -> {
-
-            if (!list.isInternalList() && frame.getDialogService().showConfirmationDialogAndWait(Localization.lang("Remove protected terms file"),
-                    Localization.lang("Are you sure you want to remove the protected terms file?"),
-                    Localization.lang("Remove protected terms file"),
-                    Localization.lang("Cancel"))) {
-                if (!loader.removeProtectedTermsList(list)) {
-                    LOGGER.info("Problem removing protected terms file");
-                }
-                tableModel.fireTableDataChanged();
-            }
-        });
-        // Add it to the remove menu item
-        remove.addActionListener(removeAction);
-
-        // Add action listener to the "Reload" menu item, which is supposed to reload an external term file
-        reload.addActionListener(actionEvent -> {
-            getSelectedTermsList().ifPresent(loader::reloadProtectedTermsList);
-        });
-
-        enabled.addActionListener(actionEvent -> getSelectedTermsList().ifPresent(list -> {
-            list.setEnabled(enabled.isSelected());
-        }));
-
-    }
-
-    public void setVisible(boolean visible) {
-        okPressed = false;
-        diag.setVisible(visible);
-    }
-
-    /**
-     * Get the currently selected term list.
-     * @return the selected term list, or empty if no term list is selected.
-     */
-    private Optional<ProtectedTermsList> getSelectedTermsList() {
-        if (table.getSelectedRow() != -1) {
-            return Optional.of(loader.getProtectedTermsLists().get(table.getSelectedRow()));
-        }
-        return Optional.empty();
-    }
-
-    class TermTableModel extends DefaultTableModel {
-
-        @Override
-        public int getColumnCount() {
-            return 3;
-        }
-
-        @Override
-        public int getRowCount() {
-            return loader.getProtectedTermsLists().size();
-        }
-
-        @Override
-        public String getColumnName(int i) {
-            switch (i) {
-                case 0:
-                    return Localization.lang("Enabled");
-                case 1:
-                    return Localization.lang("Description");
-                case 2:
-                    return Localization.lang("File");
-                default:
-                    return "";
-            }
-        }
-
-        @Override
-        public Object getValueAt(int row, int column) {
-            switch (column) {
-                case 0:
-                    return loader.getProtectedTermsLists().get(row).isEnabled();
-                case 1:
-                    return loader.getProtectedTermsLists().get(row).getDescription();
-                case 2:
-                    ProtectedTermsList list = loader.getProtectedTermsLists().get(row);
-                    return list.isInternalList() ? Localization.lang("Internal list") + " - " + list.getLocation() : list
-                            .getLocation();
-                default:
-                    return "";
-            }
-        }
-
-        @Override
-        public boolean isCellEditable(int row, int column) {
-            return column == 0;
-        }
-
-        @Override
-        public Class<?> getColumnClass(int column) {
-            switch (column) {
-                case 0:
-                    return Boolean.class;
-                case 1:
-                    return String.class;
-                case 2:
-                    return String.class;
-                default:
-                    return String.class;
-            }
-        }
-
-        @Override
-        public void setValueAt(Object cell, int row, int column) {
-            if (column == 0) {
-                ProtectedTermsList list = loader.getProtectedTermsLists().get(row);
-                list.setEnabled(!list.isEnabled());
-                this.fireTableCellUpdated(row, column);
-            }
-        }
-
-    }
-
-    public boolean isOkPressed() {
-        return okPressed;
-    }
-
-    private void tablePopup(MouseEvent e) {
-        popup.show(e.getComponent(), e.getX(), e.getY());
-    }
-
-    private void displayTerms(ProtectedTermsList list) {
-        // Make a dialog box to display the contents:
-        final JDialog dd = new JDialog(diag, list.getDescription() + " - " + list.getLocation(), true);
-
-        JTextArea ta = new JTextArea(list.getTermListing());
-        ta.setEditable(false);
-        JScrollPane sp = new JScrollPane(ta);
-        sp.setPreferredSize(new Dimension(700, 500));
-        dd.getContentPane().add(sp, BorderLayout.CENTER);
-        JButton okButton = new JButton(Localization.lang("OK"));
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        bb.addButton(okButton);
-        bb.addGlue();
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-        dd.getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-        okButton.addActionListener(actionEvent -> dd.dispose());
-        dd.pack();
-        dd.setLocationRelativeTo(diag);
-        dd.setVisible(true);
-    }
-
-    /**
-     * The listener for the table monitoring the current selection.
-     */
-    private class EntrySelectionListener implements ListSelectionListener {
-
-        @Override
-        public void valueChanged(ListSelectionEvent listEvent) {
-            getSelectedTermsList().ifPresent(list -> {
-                // Enable/disable popup menu items and buttons
-                if (list.isInternalList()) {
-                    remove.setEnabled(false);
-                    edit.setEnabled(false);
-                    reload.setEnabled(false);
-                    removeButton.setEnabled(false);
-                } else {
-                    remove.setEnabled(true);
-                    edit.setEnabled(true);
-                    reload.setEnabled(true);
-                    removeButton.setEnabled(true);
-                }
-                enabled.setSelected(list.isEnabled());
-            });
-        }
-    }
-
-    private class AddFileDialog extends JabRefDialog {
-
-        private final JTextField newFile = new JTextField();
-        private boolean addOKPressed;
-
-        public AddFileDialog() {
-            super(diag, Localization.lang("Add protected terms file"), true, AddFileDialog.class);
-
-            JButton browse = new JButton(Localization.lang("Browse"));
-            FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                    .addExtensionFilter(Localization.lang("Protected terms file"), StandardFileType.TERMS)
-                    .withDefaultExtension(Localization.lang("Protected terms file"), StandardFileType.TERMS)
-                    .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)).build();
-
-            browse.addActionListener(e -> {
-                Optional<Path> file = DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().showFileOpenDialog(fileDialogConfiguration));
-                file.ifPresent(f -> newFile.setText(f.toAbsolutePath().toString()));
-            });
-
-            // Build content panel
-            FormBuilder builder = FormBuilder.create();
-            builder.layout(new FormLayout("left:pref, 4dlu, fill:100dlu:grow, 4dlu, pref", "p"));
-            builder.add(Localization.lang("File")).xy(1, 1);
-            builder.add(newFile).xy(3, 1);
-            builder.add(browse).xy(5, 1);
-            builder.padding("10dlu, 10dlu, 10dlu, 10dlu");
-            getContentPane().add(builder.build(), BorderLayout.CENTER);
-
-            // Buttons
-            ButtonBarBuilder bb = new ButtonBarBuilder();
-            JButton addOKButton = new JButton(Localization.lang("OK"));
-            JButton addCancelButton = new JButton(Localization.lang("Cancel"));
-            bb.addGlue();
-            bb.addButton(addOKButton);
-            bb.addButton(addCancelButton);
-            bb.addGlue();
-            bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-            getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-            addOKButton.addActionListener(e -> {
-                addOKPressed = true;
-                dispose();
-            });
-
-            Action cancelAction = new AbstractAction() {
-
-                @Override
-                public void actionPerformed(ActionEvent e) {
-                    addOKPressed = false;
-                    dispose();
-                }
-            };
-            addCancelButton.addActionListener(cancelAction);
-
-            // Key bindings:
-            bb.getPanel().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
-              .put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-            bb.getPanel().getActionMap().put("close", cancelAction);
-            pack();
-            setLocationRelativeTo(diag);
-        }
-
-        public Optional<String> getFileName() {
-            if (addOKPressed && (newFile.getText() != null) && !newFile.getText().isEmpty()) {
-                return Optional.of(newFile.getText());
-            }
-            return Optional.empty();
-        }
-
-    }
-
-    private void storePreferences() {
-        Globals.prefs.setProtectedTermsPreferences(loader);
-    }
-}
diff --git a/src/main/java/org/jabref/gui/util/BindingsHelper.java b/src/main/java/org/jabref/gui/util/BindingsHelper.java
index 162fb210065..af0fafd441b 100644
--- a/src/main/java/org/jabref/gui/util/BindingsHelper.java
+++ b/src/main/java/org/jabref/gui/util/BindingsHelper.java
@@ -8,6 +8,7 @@
 
 import javafx.beans.binding.Bindings;
 import javafx.beans.binding.BooleanBinding;
+import javafx.beans.binding.ObjectBinding;
 import javafx.beans.binding.StringBinding;
 import javafx.beans.property.ListProperty;
 import javafx.beans.property.Property;
@@ -148,7 +149,16 @@ public static <A, V, B> void bindContentBidirectional(ObservableMap<A, V> proper
                 updateB);
     }
 
-    public static ObservableValue<? extends Boolean> constantOf(boolean value) {
+    public static <T> ObservableValue<T> constantOf(T value) {
+        return new ObjectBinding<T>() {
+            @Override
+            protected T computeValue() {
+                return value;
+            }
+        };
+    }
+
+    public static ObservableValue<Boolean> constantOf(boolean value) {
         return new BooleanBinding() {
             @Override
             protected boolean computeValue() {
diff --git a/src/main/java/org/jabref/model/util/OptionalUtil.java b/src/main/java/org/jabref/model/util/OptionalUtil.java
index 525477f415e..6d127c4e5ce 100644
--- a/src/main/java/org/jabref/model/util/OptionalUtil.java
+++ b/src/main/java/org/jabref/model/util/OptionalUtil.java
@@ -59,4 +59,12 @@ public static <T, S, R> Optional<R> combine(Optional<T> valueOne, Optional<S> va
             return Optional.empty();
         }
     }
+
+    public static <T> Optional<T> orElse(Optional<T> valueOne, Optional<T> valueTwo) {
+        if (valueOne.isPresent()) {
+            return valueOne;
+        } else {
+            return valueTwo;
+        }
+    }
 }
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index c3070474954..39ef552b6f0 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -183,10 +183,6 @@ public class JabRefPreferences implements PreferencesService {
     public static final String PREAMBLE_SIZE_X = "preambleSizeX";
     public static final String PREAMBLE_POS_Y = "preamblePosY";
     public static final String PREAMBLE_POS_X = "preamblePosX";
-    public static final String TERMS_SIZE_Y = "termsSizeY";
-    public static final String TERMS_SIZE_X = "termsSizeX";
-    public static final String TERMS_POS_Y = "termsPosY";
-    public static final String TERMS_POS_X = "termsPosX";
     public static final String SEARCH_DIALOG_HEIGHT = "searchDialogHeight";
     public static final String SEARCH_DIALOG_WIDTH = "searchDialogWidth";
     public static final String IMPORT_INSPECTION_DIALOG_HEIGHT = "importInspectionDialogHeight";
@@ -563,10 +559,6 @@ private JabRefPreferences() {
         defaults.put(PREAMBLE_POS_Y, 0);
         defaults.put(PREAMBLE_SIZE_X, 600);
         defaults.put(PREAMBLE_SIZE_Y, 400);
-        defaults.put(TERMS_POS_X, 0);
-        defaults.put(TERMS_POS_Y, 0);
-        defaults.put(TERMS_SIZE_X, 500);
-        defaults.put(TERMS_SIZE_Y, 500);
         defaults.put(DEFAULT_SHOW_SOURCE, Boolean.FALSE);
 
         defaults.put(DEFAULT_AUTO_SORT, Boolean.FALSE);
@@ -1631,6 +1623,7 @@ public ProtectedTermsPreferences getProtectedTermsPreferences() {
                                              getStringList(PROTECTED_TERMS_DISABLED_EXTERNAL));
     }
 
+    @Override
     public void setProtectedTermsPreferences(ProtectedTermsLoader loader) {
         List<String> enabledExternalList = new ArrayList<>();
         List<String> disabledExternalList = new ArrayList<>();
@@ -1657,7 +1650,6 @@ public void setProtectedTermsPreferences(ProtectedTermsLoader loader) {
         putStringList(PROTECTED_TERMS_DISABLED_EXTERNAL, disabledExternalList);
         putStringList(PROTECTED_TERMS_ENABLED_INTERNAL, enabledInternalList);
         putStringList(PROTECTED_TERMS_DISABLED_INTERNAL, disabledInternalList);
-
     }
 
     @Override
diff --git a/src/main/java/org/jabref/preferences/PreferencesService.java b/src/main/java/org/jabref/preferences/PreferencesService.java
index 47ec943c9c4..24a33ba283c 100644
--- a/src/main/java/org/jabref/preferences/PreferencesService.java
+++ b/src/main/java/org/jabref/preferences/PreferencesService.java
@@ -11,10 +11,13 @@
 import org.jabref.logic.journals.JournalAbbreviationPreferences;
 import org.jabref.logic.layout.LayoutFormatterPreferences;
 import org.jabref.logic.openoffice.OpenOfficePreferences;
+import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.model.metadata.FilePreferences;
 
 public interface PreferencesService {
 
+    void setProtectedTermsPreferences(ProtectedTermsLoader loader);
+
     JournalAbbreviationPreferences getJournalAbbreviationPreferences();
 
     void storeKeyBindingRepository(KeyBindingRepository keyBindingRepository);
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index e38d7c151da..b5233752d16 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -637,9 +637,6 @@ Name\ formatter=Name formatter
 Natbib\ style=Natbib style
 
 nested\ AUX\ files=nested AUX files
-
-New=New
-
 new=new
 
 New\ BibTeX\ sublibrary=New BibTeX sublibrary

From d11f6f0a6f74079f03f45651a12708888a7d2dfb Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Mon, 4 Mar 2019 21:30:42 +0100
Subject: [PATCH 068/184] Convert Manage keywords dialog to JavaFX (#4701)

* Convert Manage keywords dialog to JavaFX

* Improve code
---
 src/main/java/org/jabref/gui/JabRefFrame.java |   2 +-
 .../gui/actions/ManageKeywordsAction.java     | 356 ------------------
 .../jabref/gui/edit/ManageKeywordsAction.java |  34 ++
 .../jabref/gui/edit/ManageKeywordsDialog.fxml |  42 +++
 .../jabref/gui/edit/ManageKeywordsDialog.java |  83 ++++
 .../gui/edit/ManageKeywordsDisplayType.java   |   6 +
 .../gui/edit/ManageKeywordsViewModel.java     | 139 +++++++
 .../org/jabref/model/entry/KeywordList.java   |   4 +
 .../jabref/preferences/JabRefPreferences.java |   4 +-
 .../preferences/PreferencesService.java       |   4 +
 src/main/resources/l10n/JabRef_en.properties  |   4 -
 11 files changed, 316 insertions(+), 362 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/actions/ManageKeywordsAction.java
 create mode 100644 src/main/java/org/jabref/gui/edit/ManageKeywordsAction.java
 create mode 100644 src/main/java/org/jabref/gui/edit/ManageKeywordsDialog.fxml
 create mode 100644 src/main/java/org/jabref/gui/edit/ManageKeywordsDialog.java
 create mode 100644 src/main/java/org/jabref/gui/edit/ManageKeywordsDisplayType.java
 create mode 100644 src/main/java/org/jabref/gui/edit/ManageKeywordsViewModel.java

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 760709e1504..dc1077e570e 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -67,7 +67,6 @@
 import org.jabref.gui.actions.ManageCustomExportsAction;
 import org.jabref.gui.actions.ManageCustomImportsAction;
 import org.jabref.gui.actions.ManageJournalsAction;
-import org.jabref.gui.actions.ManageKeywordsAction;
 import org.jabref.gui.actions.NewDatabaseAction;
 import org.jabref.gui.actions.NewEntryAction;
 import org.jabref.gui.actions.NewEntryFromPlainTextAction;
@@ -81,6 +80,7 @@
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.dialogs.AutosaveUIManager;
+import org.jabref.gui.edit.ManageKeywordsAction;
 import org.jabref.gui.edit.MassSetFieldsAction;
 import org.jabref.gui.exporter.ExportCommand;
 import org.jabref.gui.exporter.ExportToClipboardAction;
diff --git a/src/main/java/org/jabref/gui/actions/ManageKeywordsAction.java b/src/main/java/org/jabref/gui/actions/ManageKeywordsAction.java
deleted file mode 100644
index 0af7a02f91c..00000000000
--- a/src/main/java/org/jabref/gui/actions/ManageKeywordsAction.java
+++ /dev/null
@@ -1,356 +0,0 @@
-package org.jabref.gui.actions;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Objects;
-import java.util.Optional;
-import java.util.stream.Collectors;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.ButtonGroup;
-import javax.swing.DefaultListModel;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JFrame;
-import javax.swing.JList;
-import javax.swing.JRadioButton;
-import javax.swing.JScrollPane;
-import javax.swing.JTextField;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.specialfields.SpecialFieldsUtils;
-import org.jabref.model.FieldChange;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.Keyword;
-import org.jabref.model.entry.KeywordList;
-import org.jabref.model.strings.StringUtil;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import com.jgoodies.forms.builder.FormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-
-/**
- * An Action for launching keyword managing dialog
- *
- */
-public class ManageKeywordsAction extends SimpleCommand {
-
-    private final JabRefFrame frame;
-    private final KeywordList sortedKeywordsOfAllEntriesBeforeUpdateByUser = new KeywordList();
-    private JDialog diag;
-    private DefaultListModel<Keyword> keywordListModel;
-    private JRadioButton intersectKeywords;
-    private JRadioButton mergeKeywords;
-    private boolean canceled;
-
-
-    public ManageKeywordsAction(JabRefFrame frame) {
-        this.frame = frame;
-    }
-
-    private void createDialog() {
-        if (diag != null) {
-            return;
-        }
-        // keyword to add
-        JTextField keyword = new JTextField();
-
-        keywordListModel = new DefaultListModel<>();
-        JList<Keyword> keywordList = new JList<>(keywordListModel);
-        keywordList.setVisibleRowCount(8);
-        JScrollPane kPane = new JScrollPane(keywordList);
-
-        diag = new JDialog((JFrame) null, Localization.lang("Manage keywords"), true);
-
-        JButton ok = new JButton(Localization.lang("OK"));
-        JButton cancel = new JButton(Localization.lang("Cancel"));
-        JButton add = new JButton(Localization.lang("Add"));
-        JButton remove = new JButton(Localization.lang("Remove"));
-        JButton replace = new JButton(Localization.lang("Replace"));
-        JButton join = new JButton(Localization.lang("Join"));
-
-        join.setToolTipText(Localization.lang("Joins selected keywords and deletes selected keywords."));
-
-        keywordList.setVisibleRowCount(10);
-
-        intersectKeywords = new JRadioButton(Localization.lang("Display keywords appearing in ALL entries"));
-        mergeKeywords = new JRadioButton(Localization.lang("Display keywords appearing in ANY entry"));
-        ButtonGroup group = new ButtonGroup();
-        group.add(intersectKeywords);
-        group.add(mergeKeywords);
-        ActionListener stateChanged = e -> fillKeyWordList();
-        intersectKeywords.addActionListener(stateChanged);
-        mergeKeywords.addActionListener(stateChanged);
-        intersectKeywords.setSelected(true);
-
-        FormBuilder builder = FormBuilder.create().layout(new FormLayout("fill:200dlu:grow, pref, fill:pref",
-                "pref, 2dlu, pref, 1dlu, pref, 2dlu, fill:100dlu:grow, 4dlu, pref, 4dlu, pref, "));
-
-        builder.addSeparator(Localization.lang("Keywords of selected entries")).xyw(1, 1, 3);
-        builder.add(intersectKeywords).xyw(1, 3, 3);
-        builder.add(mergeKeywords).xyw(1, 5, 3);
-        builder.add(kPane).xywh(1, 7, 1, 3);
-        builder.add(join).xy(2,9);
-        builder.add(replace).xy(3, 9);
-        builder.add(keyword).xy(1, 11);
-        builder.add(add).xy(2, 11);
-        builder.add(remove).xy(3, 11);
-
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        bb.addButton(ok);
-        bb.addButton(cancel);
-        bb.addGlue();
-        builder.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        ok.addActionListener(e -> {
-            canceled = false;
-            diag.dispose();
-        });
-
-        Action cancelAction = new AbstractAction() {
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                canceled = true;
-                diag.dispose();
-            }
-        };
-        cancel.addActionListener(cancelAction);
-
-        final ActionListener addActionListener = arg0 -> addButtonActionListener(keyword);
-
-        add.addActionListener(addActionListener);
-
-        final ActionListener removeActionListener = arg0 -> {
-            // keywordList.getSelectedIndices(); does not work, therefore we operate on the values
-            List<Keyword> values = keywordList.getSelectedValuesList();
-
-            for (Keyword val : values) {
-                keywordListModel.removeElement(val);
-            }
-        };
-
-        remove.addActionListener(removeActionListener);
-
-        final ActionListener joinActionListener = arg0 -> {
-            List<Keyword> values = keywordList.getSelectedValuesList();
-            String joinedKeyword = values.stream().map(currentKeyword -> currentKeyword.get()).collect(Collectors.joining(" "));
-            this.addKeywordToKeywordListModel(joinedKeyword);
-
-            for (Keyword val : values) {
-                this.keywordListModel.removeElement(val);
-            }
-        };
-
-        join.addActionListener(joinActionListener);
-
-        final ActionListener replaceActionListener = arg0 -> {
-            List<Keyword> values = keywordList.getSelectedValuesList();
-
-            for (Keyword val : values) {
-                keywordListModel.removeElement(val);
-            }
-            addButtonActionListener(keyword);
-        };
-
-        replace.addActionListener(replaceActionListener);
-
-        //enable a user to press Delete to delete a keyword
-        keywordList.addKeyListener(new KeyAdapter() {
-
-            @Override
-            public void keyPressed(KeyEvent arg0) {
-                if (arg0.getKeyCode() == KeyEvent.VK_DELETE) {
-                    removeActionListener.actionPerformed(null);
-                }
-            }
-        });
-
-        //enable a user to press Enter to add a keyword
-        keyword.addKeyListener(new KeyAdapter() {
-
-            @Override
-            public void keyPressed(KeyEvent e) {
-                if (e.getKeyCode() == KeyEvent.VK_ENTER) {
-                    addActionListener.actionPerformed(null);
-                }
-            }
-        });
-
-        // Key bindings:
-        ActionMap am = builder.getPanel().getActionMap();
-        InputMap im = builder.getPanel().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", cancelAction);
-
-        diag.getContentPane().add(builder.getPanel(), BorderLayout.CENTER);
-        diag.getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-    }
-
-    private void addButtonActionListener(JTextField keywordTextField) {
-        if (StringUtil.isBlank(keywordTextField.getText())) {
-            return; // nothing to add
-        }
-        addKeywordToKeywordListModel(keywordTextField.getText());
-        keywordTextField.setText(null);
-        keywordTextField.requestFocusInWindow();
-
-    }
-
-    /**
-     * Adds given keyword to the keyword list model
-     */
-    private void addKeywordToKeywordListModel(String keyword) {
-        String keywordToAdd = Objects.requireNonNull(keyword).trim();
-        Keyword newKeyword = new Keyword(keywordToAdd);
-        if (keywordListModel.isEmpty()) {
-            keywordListModel.addElement(newKeyword);
-        } else {
-            int idx = 0;
-            Keyword element = keywordListModel.getElementAt(idx);
-            while ((idx < keywordListModel.size()) && (element.compareTo(newKeyword) < 0)) {
-                idx++;
-            }
-            if (idx == keywordListModel.size()) {
-                // list is empty or word is greater than last word in list
-                keywordListModel.addElement(newKeyword);
-            } else if (element.compareTo(newKeyword) == 0) {
-                // nothing to do, word already in table
-            } else {
-                keywordListModel.add(idx, newKeyword);
-            }
-        }
-    }
-
-    @Override
-    public void execute() {
-        BasePanel bp = frame.getCurrentBasePanel();
-        if (bp == null) {
-            return;
-        }
-        if (bp.getSelectedEntries().isEmpty()) {
-            bp.output(Localization.lang("Select at least one entry to manage keywords."));
-            return;
-        }
-
-        // Lazy creation of the dialog:
-        createDialog();
-
-        canceled = true;
-
-        fillKeyWordList();
-
-        diag.pack();
-        diag.setVisible(true);
-        if (canceled) {
-            return;
-        }
-
-        KeywordList keywordsToAdd = new KeywordList();
-        KeywordList userSelectedKeywords = new KeywordList();
-        // build keywordsToAdd and userSelectedKeywords in parallel
-        for (Enumeration<Keyword> keywords = keywordListModel.elements(); keywords.hasMoreElements();) {
-            Keyword keyword = keywords.nextElement();
-            userSelectedKeywords.add(keyword);
-            if (!sortedKeywordsOfAllEntriesBeforeUpdateByUser.contains(keyword)) {
-                keywordsToAdd.add(keyword);
-            }
-        }
-
-        KeywordList keywordsToRemove = new KeywordList();
-        for (Keyword kword : sortedKeywordsOfAllEntriesBeforeUpdateByUser) {
-            if (!userSelectedKeywords.contains(kword)) {
-                keywordsToRemove.add(kword);
-            }
-        }
-
-        if (keywordsToAdd.isEmpty() && keywordsToRemove.isEmpty()) {
-            // nothing to be done if nothing is new and nothing is obsolete
-            return;
-        }
-
-        if (Globals.prefs.isKeywordSyncEnabled() && !keywordsToAdd.isEmpty()) {
-            SpecialFieldsUtils.synchronizeSpecialFields(keywordsToAdd, keywordsToRemove);
-        }
-
-        NamedCompound ce = updateKeywords(bp.getSelectedEntries(), keywordsToAdd, keywordsToRemove);
-        bp.getUndoManager().addEdit(ce);
-        bp.markBaseChanged();
-    }
-
-    private NamedCompound updateKeywords(List<BibEntry> entries, KeywordList keywordsToAdd,
-                                         KeywordList keywordsToRemove) {
-        NamedCompound ce = new NamedCompound(Localization.lang("Update keywords"));
-        for (BibEntry entry : entries) {
-            KeywordList keywords = entry.getKeywords(Globals.prefs.getKeywordDelimiter());
-
-            // update keywords
-            keywords.removeAll(keywordsToRemove);
-            keywords.addAll(keywordsToAdd);
-
-            // put keywords back
-            Optional<FieldChange> change = entry.putKeywords(keywords, Globals.prefs.getKeywordDelimiter());
-            if (change.isPresent()) {
-                ce.addEdit(new UndoableFieldChange(change.get()));
-            }
-
-            if (Globals.prefs.isKeywordSyncEnabled()) {
-                SpecialFieldsUtils.syncSpecialFieldsFromKeywords(entry, Globals.prefs.getKeywordDelimiter());
-            }
-        }
-        ce.end();
-        return ce;
-    }
-
-    private void fillKeyWordList() {
-        BasePanel bp = frame.getCurrentBasePanel();
-        List<BibEntry> entries = bp.getSelectedEntries();
-
-        // fill dialog with values
-        keywordListModel.clear();
-        sortedKeywordsOfAllEntriesBeforeUpdateByUser.clear();
-
-        if (mergeKeywords.isSelected()) {
-            for (BibEntry entry : entries) {
-                KeywordList separatedKeywords = entry.getKeywords(Globals.prefs.getKeywordDelimiter());
-                sortedKeywordsOfAllEntriesBeforeUpdateByUser.addAll(separatedKeywords);
-            }
-        } else {
-            assert intersectKeywords.isSelected();
-
-            // all keywords from first entry have to be added
-            BibEntry firstEntry = entries.get(0);
-            KeywordList separatedKeywords = firstEntry.getKeywords(Globals.prefs.getKeywordDelimiter());
-            sortedKeywordsOfAllEntriesBeforeUpdateByUser.addAll(separatedKeywords);
-
-            // for the remaining entries, intersection has to be used
-            // this approach ensures that one empty keyword list leads to an empty set of common keywords
-            for (int i = 1; i < entries.size(); i++) {
-                BibEntry entry = entries.get(i);
-                separatedKeywords = entry.getKeywords(Globals.prefs.getKeywordDelimiter());
-                sortedKeywordsOfAllEntriesBeforeUpdateByUser.retainAll(separatedKeywords);
-            }
-        }
-        for (Keyword keyword : sortedKeywordsOfAllEntriesBeforeUpdateByUser) {
-            keywordListModel.addElement(keyword);
-        }
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/edit/ManageKeywordsAction.java b/src/main/java/org/jabref/gui/edit/ManageKeywordsAction.java
new file mode 100644
index 00000000000..333e206cd02
--- /dev/null
+++ b/src/main/java/org/jabref/gui/edit/ManageKeywordsAction.java
@@ -0,0 +1,34 @@
+package org.jabref.gui.edit;
+
+import org.jabref.gui.BasePanel;
+import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.logic.l10n.Localization;
+
+/**
+ * An Action for launching keyword managing dialog
+ *
+ */
+public class ManageKeywordsAction extends SimpleCommand {
+
+    private final JabRefFrame frame;
+
+    public ManageKeywordsAction(JabRefFrame frame) {
+        this.frame = frame;
+    }
+
+    @Override
+    public void execute() {
+        BasePanel basePanel = frame.getCurrentBasePanel();
+        if (basePanel == null) {
+            return;
+        }
+        if (basePanel.getSelectedEntries().isEmpty()) {
+            basePanel.output(Localization.lang("Select at least one entry to manage keywords."));
+            return;
+        }
+
+        ManageKeywordsDialog dialog = new ManageKeywordsDialog(basePanel.getSelectedEntries());
+        dialog.showAndWait();
+    }
+}
diff --git a/src/main/java/org/jabref/gui/edit/ManageKeywordsDialog.fxml b/src/main/java/org/jabref/gui/edit/ManageKeywordsDialog.fxml
new file mode 100644
index 00000000000..609c6655bb9
--- /dev/null
+++ b/src/main/java/org/jabref/gui/edit/ManageKeywordsDialog.fxml
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.ButtonType?>
+<?import javafx.scene.control.DialogPane?>
+<?import javafx.scene.control.RadioButton?>
+<?import javafx.scene.control.TableColumn?>
+<?import javafx.scene.control.TableView?>
+<?import javafx.scene.control.ToggleGroup?>
+<?import javafx.scene.layout.VBox?>
+<?import org.jabref.gui.edit.ManageKeywordsDisplayType?>
+<DialogPane xmlns:fx="http://javafx.com/fxml/1" prefHeight="400.0" prefWidth="600.0"
+            xmlns="http://javafx.com/javafx/8.0.172-ea" fx:controller="org.jabref.gui.edit.ManageKeywordsDialog">
+    <fx:define>
+        <ToggleGroup fx:id="displayType"/>
+    </fx:define>
+    <content>
+        <VBox>
+            <TableView fx:id="keywordsTable" editable="true" VBox.vgrow="ALWAYS">
+                <columns>
+                    <TableColumn fx:id="keywordsTableMainColumn" text="%Keywords of selected entries"/>
+                    <TableColumn fx:id="keywordsTableEditColumn" maxWidth="40" minWidth="40.0" prefWidth="40.0"/>
+                    <TableColumn fx:id="keywordsTableDeleteColumn" maxWidth="40" minWidth="40.0" prefWidth="40.0"/>
+                </columns>
+                <columnResizePolicy>
+                    <TableView fx:constant="CONSTRAINED_RESIZE_POLICY"/>
+                </columnResizePolicy>
+            </TableView>
+            <RadioButton text="%Display keywords appearing in ALL entries" toggleGroup="$displayType" selected="true">
+                <userData>
+                    <ManageKeywordsDisplayType fx:constant="CONTAINED_IN_ALL_ENTRIES"/>
+                </userData>
+            </RadioButton>
+            <RadioButton text="%Display keywords appearing in ANY entry" toggleGroup="$displayType">
+                <userData>
+                    <ManageKeywordsDisplayType fx:constant="CONTAINED_IN_ANY_ENTRY"/>
+                </userData>
+            </RadioButton>
+        </VBox>
+    </content>
+    <ButtonType fx:constant="CANCEL"/>
+    <ButtonType fx:constant="APPLY"/>
+</DialogPane>
diff --git a/src/main/java/org/jabref/gui/edit/ManageKeywordsDialog.java b/src/main/java/org/jabref/gui/edit/ManageKeywordsDialog.java
new file mode 100644
index 00000000000..2b1201fd24e
--- /dev/null
+++ b/src/main/java/org/jabref/gui/edit/ManageKeywordsDialog.java
@@ -0,0 +1,83 @@
+package org.jabref.gui.edit;
+
+import java.util.List;
+
+import javax.inject.Inject;
+
+import javafx.fxml.FXML;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.TableColumn;
+import javafx.scene.control.TableView;
+import javafx.scene.control.ToggleGroup;
+import javafx.scene.control.cell.TextFieldTableCell;
+
+import org.jabref.gui.icon.IconTheme;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.BindingsHelper;
+import org.jabref.gui.util.ValueTableCellFactory;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.preferences.PreferencesService;
+
+import com.airhacks.afterburner.views.ViewLoader;
+import org.fxmisc.easybind.EasyBind;
+
+public class ManageKeywordsDialog extends BaseDialog<Void> {
+    private final List<BibEntry> entries;
+    @FXML private TableColumn<String, String> keywordsTableMainColumn;
+    @FXML private TableColumn<String, Boolean> keywordsTableEditColumn;
+    @FXML private TableColumn<String, Boolean> keywordsTableDeleteColumn;
+    @FXML private TableView<String> keywordsTable;
+    @FXML private ToggleGroup displayType;
+    @Inject private PreferencesService preferences;
+    private ManageKeywordsViewModel viewModel;
+
+    public ManageKeywordsDialog(List<BibEntry> entries) {
+        this.entries = entries;
+        this.setTitle(Localization.lang("Manage keywords"));
+
+        ViewLoader.view(this)
+                  .load()
+                  .setAsDialogPane(this);
+
+        setResultConverter(button -> {
+            if (button == ButtonType.APPLY) {
+                viewModel.saveChanges();
+            }
+            return null;
+        });
+    }
+
+    @FXML
+    public void initialize() {
+        viewModel = new ManageKeywordsViewModel(preferences, entries);
+
+        viewModel.displayTypeProperty().bind(
+                EasyBind.map(displayType.selectedToggleProperty(), toggle -> {
+                    if (toggle != null) {
+                        return (ManageKeywordsDisplayType) toggle.getUserData();
+                    } else {
+                        return ManageKeywordsDisplayType.CONTAINED_IN_ALL_ENTRIES;
+                    }
+                })
+        );
+
+        keywordsTable.setItems(viewModel.getKeywords());
+        keywordsTableMainColumn.setCellValueFactory(data -> BindingsHelper.constantOf(data.getValue()));
+        keywordsTableMainColumn.setOnEditCommit(event -> {
+            // Poor mans reverse databinding (necessary because we use a constant value above)
+            viewModel.getKeywords().set(event.getTablePosition().getRow(), event.getNewValue());
+        });
+        keywordsTableMainColumn.setCellFactory(TextFieldTableCell.forTableColumn());
+        keywordsTableEditColumn.setCellValueFactory(data -> BindingsHelper.constantOf(true));
+        keywordsTableDeleteColumn.setCellValueFactory(data -> BindingsHelper.constantOf(true));
+        new ValueTableCellFactory<String, Boolean>()
+                .withGraphic(none -> IconTheme.JabRefIcons.EDIT.getGraphicNode())
+                .withOnMouseClickedEvent(none -> event -> keywordsTable.edit(keywordsTable.getFocusModel().getFocusedIndex(), keywordsTableMainColumn))
+                .install(keywordsTableEditColumn);
+        new ValueTableCellFactory<String, Boolean>()
+                .withGraphic(none -> IconTheme.JabRefIcons.REMOVE.getGraphicNode())
+                .withOnMouseClickedEvent((keyword, none) -> event -> viewModel.removeKeyword(keyword))
+                .install(keywordsTableDeleteColumn);
+    }
+}
diff --git a/src/main/java/org/jabref/gui/edit/ManageKeywordsDisplayType.java b/src/main/java/org/jabref/gui/edit/ManageKeywordsDisplayType.java
new file mode 100644
index 00000000000..0af51af0734
--- /dev/null
+++ b/src/main/java/org/jabref/gui/edit/ManageKeywordsDisplayType.java
@@ -0,0 +1,6 @@
+package org.jabref.gui.edit;
+
+public enum ManageKeywordsDisplayType {
+    CONTAINED_IN_ALL_ENTRIES,
+    CONTAINED_IN_ANY_ENTRY,
+}
diff --git a/src/main/java/org/jabref/gui/edit/ManageKeywordsViewModel.java b/src/main/java/org/jabref/gui/edit/ManageKeywordsViewModel.java
new file mode 100644
index 00000000000..c071e652033
--- /dev/null
+++ b/src/main/java/org/jabref/gui/edit/ManageKeywordsViewModel.java
@@ -0,0 +1,139 @@
+package org.jabref.gui.edit;
+
+import java.util.List;
+import java.util.Optional;
+
+import javafx.beans.property.ObjectProperty;
+import javafx.beans.property.SimpleObjectProperty;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.gui.undo.UndoableFieldChange;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.specialfields.SpecialFieldsUtils;
+import org.jabref.model.FieldChange;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.Keyword;
+import org.jabref.model.entry.KeywordList;
+import org.jabref.preferences.PreferencesService;
+
+import org.fxmisc.easybind.EasyBind;
+
+public class ManageKeywordsViewModel {
+
+    private final List<BibEntry> entries;
+    private final KeywordList sortedKeywordsOfAllEntriesBeforeUpdateByUser = new KeywordList();
+    private final PreferencesService preferences;
+    private final ObjectProperty<ManageKeywordsDisplayType> displayType = new SimpleObjectProperty<>(ManageKeywordsDisplayType.CONTAINED_IN_ALL_ENTRIES);
+    private final ObservableList<String> keywords;
+
+    public ManageKeywordsViewModel(PreferencesService preferences, List<BibEntry> entries) {
+        this.preferences = preferences;
+        this.entries = entries;
+        this.keywords = FXCollections.observableArrayList();
+
+        EasyBind.subscribe(displayType, this::fillKeywordsList);
+    }
+
+    public ManageKeywordsDisplayType getDisplayType() {
+        return displayType.get();
+    }
+
+    public ObjectProperty<ManageKeywordsDisplayType> displayTypeProperty() {
+        return displayType;
+    }
+
+    private void fillKeywordsList(ManageKeywordsDisplayType type) {
+        keywords.clear();
+        sortedKeywordsOfAllEntriesBeforeUpdateByUser.clear();
+
+        if (type == ManageKeywordsDisplayType.CONTAINED_IN_ALL_ENTRIES) {
+            for (BibEntry entry : entries) {
+                KeywordList separatedKeywords = entry.getKeywords(preferences.getKeywordDelimiter());
+                sortedKeywordsOfAllEntriesBeforeUpdateByUser.addAll(separatedKeywords);
+            }
+        } else if (type == ManageKeywordsDisplayType.CONTAINED_IN_ANY_ENTRY) {
+
+            // all keywords from first entry have to be added
+            BibEntry firstEntry = entries.get(0);
+            KeywordList separatedKeywords = firstEntry.getKeywords(preferences.getKeywordDelimiter());
+            sortedKeywordsOfAllEntriesBeforeUpdateByUser.addAll(separatedKeywords);
+
+            // for the remaining entries, intersection has to be used
+            // this approach ensures that one empty keyword list leads to an empty set of common keywords
+            for (BibEntry entry : entries) {
+                separatedKeywords = entry.getKeywords(preferences.getKeywordDelimiter());
+                sortedKeywordsOfAllEntriesBeforeUpdateByUser.retainAll(separatedKeywords);
+            }
+        } else {
+            throw new IllegalStateException("DisplayType " + type + " not handled");
+        }
+        for (Keyword keyword : sortedKeywordsOfAllEntriesBeforeUpdateByUser) {
+            keywords.add(keyword.get());
+        }
+    }
+
+    public ObservableList<String> getKeywords() {
+        return keywords;
+    }
+
+    public void removeKeyword(String keyword) {
+        keywords.remove(keyword);
+    }
+
+    public void saveChanges() {
+        KeywordList keywordsToAdd = new KeywordList();
+        KeywordList userSelectedKeywords = new KeywordList();
+        // build keywordsToAdd and userSelectedKeywords in parallel
+        for (String keyword : keywords) {
+            userSelectedKeywords.add(keyword);
+            if (!sortedKeywordsOfAllEntriesBeforeUpdateByUser.contains(keyword)) {
+                keywordsToAdd.add(keyword);
+            }
+        }
+
+        KeywordList keywordsToRemove = new KeywordList();
+        for (Keyword kword : sortedKeywordsOfAllEntriesBeforeUpdateByUser) {
+            if (!userSelectedKeywords.contains(kword)) {
+                keywordsToRemove.add(kword);
+            }
+        }
+
+        if (keywordsToAdd.isEmpty() && keywordsToRemove.isEmpty()) {
+            // nothing to be done if nothing is new and nothing is obsolete
+            return;
+        }
+
+        if (preferences.isKeywordSyncEnabled() && !keywordsToAdd.isEmpty()) {
+            SpecialFieldsUtils.synchronizeSpecialFields(keywordsToAdd, keywordsToRemove);
+        }
+
+        NamedCompound ce = updateKeywords(entries, keywordsToAdd, keywordsToRemove);
+        //TODO: bp.getUndoManager().addEdit(ce);
+    }
+
+    private NamedCompound updateKeywords(List<BibEntry> entries, KeywordList keywordsToAdd,
+                                         KeywordList keywordsToRemove) {
+        NamedCompound ce = new NamedCompound(Localization.lang("Update keywords"));
+        for (BibEntry entry : entries) {
+            KeywordList keywords = entry.getKeywords(preferences.getKeywordDelimiter());
+
+            // update keywords
+            keywords.removeAll(keywordsToRemove);
+            keywords.addAll(keywordsToAdd);
+
+            // put keywords back
+            Optional<FieldChange> change = entry.putKeywords(keywords, preferences.getKeywordDelimiter());
+            if (change.isPresent()) {
+                ce.addEdit(new UndoableFieldChange(change.get()));
+            }
+
+            if (preferences.isKeywordSyncEnabled()) {
+                SpecialFieldsUtils.syncSpecialFieldsFromKeywords(entry, preferences.getKeywordDelimiter());
+            }
+        }
+        ce.end();
+        return ce;
+    }
+}
diff --git a/src/main/java/org/jabref/model/entry/KeywordList.java b/src/main/java/org/jabref/model/entry/KeywordList.java
index 2e13ce4c63f..aad112c7e87 100644
--- a/src/main/java/org/jabref/model/entry/KeywordList.java
+++ b/src/main/java/org/jabref/model/entry/KeywordList.java
@@ -137,6 +137,10 @@ public boolean contains(Keyword o) {
         return keywordChains.contains(o);
     }
 
+    public boolean contains(String keywordString) {
+        return contains(new Keyword(keywordString));
+    }
+
     public boolean remove(Keyword o) {
         return keywordChains.remove(o);
     }
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index 39ef552b6f0..a5aaf265c09 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -1447,9 +1447,10 @@ public FieldContentParserPreferences getFieldContentParserPreferences() {
         return new FieldContentParserPreferences(getStringList(NON_WRAPPABLE_FIELDS));
     }
 
+    @Override
     public boolean isKeywordSyncEnabled() {
         return getBoolean(JabRefPreferences.SPECIALFIELDSENABLED)
-               && getBoolean(JabRefPreferences.AUTOSYNCSPECIALFIELDSTOKEYWORDS);
+                && getBoolean(JabRefPreferences.AUTOSYNCSPECIALFIELDSTOKEYWORDS);
     }
 
     public ImportFormatPreferences getImportFormatPreferences() {
@@ -1725,6 +1726,7 @@ public SaveOrderConfig loadExportSaveOrder() {
         );
     }
 
+    @Override
     public Character getKeywordDelimiter() {
         return get(KEYWORD_SEPARATOR).charAt(0);
     }
diff --git a/src/main/java/org/jabref/preferences/PreferencesService.java b/src/main/java/org/jabref/preferences/PreferencesService.java
index 24a33ba283c..21550d547cb 100644
--- a/src/main/java/org/jabref/preferences/PreferencesService.java
+++ b/src/main/java/org/jabref/preferences/PreferencesService.java
@@ -20,6 +20,8 @@ public interface PreferencesService {
 
     JournalAbbreviationPreferences getJournalAbbreviationPreferences();
 
+    Character getKeywordDelimiter();
+
     void storeKeyBindingRepository(KeyBindingRepository keyBindingRepository);
 
     KeyBindingRepository getKeyBindingRepository();
@@ -56,6 +58,8 @@ public interface PreferencesService {
 
     LayoutFormatterPreferences getLayoutFormatterPreferences(JournalAbbreviationLoader loader);
 
+    boolean isKeywordSyncEnabled();
+
     SavePreferences loadForExportFromPreferences();
 
     String getExportWorkingDirectory();
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index b5233752d16..84a2215b2e2 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -558,10 +558,6 @@ JabRef\ preferences=JabRef preferences
 JabRef\ requests\ recommendations\ from\ Mr.\ DLib,\ which\ is\ an\ external\ service.\ To\ enable\ Mr.\ DLib\ to\ calculate\ recommendations,\ some\ of\ your\ data\ must\ be\ shared\ with\ Mr.\ DLib.\ Generally,\ the\ more\ data\ is\ shared\ the\ better\ recommendations\ can\ be\ calculated.\ However,\ we\ understand\ that\ some\ of\ your\ data\ in\ JabRef\ is\ sensitive,\ and\ you\ may\ not\ want\ to\ share\ it.\ Therefore,\ Mr.\ DLib\ offers\ a\ choice\ of\ which\ data\ you\ would\ like\ to\ share.=JabRef requests recommendations from Mr. DLib, which is an external service. To enable Mr. DLib to calculate recommendations, some of your data must be shared with Mr. DLib. Generally, the more data is shared the better recommendations can be calculated. However, we understand that some of your data in JabRef is sensitive, and you may not want to share it. Therefore, Mr. DLib offers a choice of which data you would like to share.
 JabRef\ Version\ (Required\ to\ ensure\ backwards\ compatibility\ with\ Mr.\ DLib's\ Web\ Service)=JabRef Version (Required to ensure backwards compatibility with Mr. DLib's Web Service)
 
-Join=Join
-
-Joins\ selected\ keywords\ and\ deletes\ selected\ keywords.=Joins selected keywords and deletes selected keywords.
-
 Journal\ abbreviations=Journal abbreviations
 
 Keep=Keep

From fb9f3ecf79a8a908129432100846679650b88a66 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20M=C3=A9ndez?= <hello@davidemdot.com>
Date: Tue, 5 Mar 2019 09:20:52 +0100
Subject: [PATCH 069/184] Group and reorder the Main Menu (tabs & icons)
 (#4707)

* Group and reorder the Main Menu (tabs & icons)

* Remove 'ISO' and 'MEDLINE' localizations

* Fix possible typo: 'PDV_VIEWER' to 'PDF_VIEWER'

* Put 'Rank' back on the menu

* Fix synchronization checks-panels & reorder entry preview items

* Fix code line

* Rename 'Replace string' to 'Find and replace'

* Move 'New sublibrary based on AUX file' to 'Tools'
---
 CHANGELOG.md                                  |   1 +
 src/main/java/org/jabref/gui/Base.css         |   4 +-
 src/main/java/org/jabref/gui/JabRefFrame.java | 124 ++++++++----------
 .../org/jabref/gui/actions/ActionFactory.java |   9 ++
 .../jabref/gui/actions/StandardActions.java   |  51 +++----
 .../java/org/jabref/gui/icon/IconTheme.java   |   8 +-
 src/main/resources/l10n/JabRef_en.properties  |  24 ++--
 7 files changed, 115 insertions(+), 106 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 560b2236e0a..646ffbe4bd9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -52,6 +52,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added the ability change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)
+- We grouped and reordered the Main Menu (File, Edit, Library, Quality, Tools, and View tabs & icons). [#4666](https://github.com/JabRef/jabref/issues/4666) [#4667](https://github.com/JabRef/jabref/issues/4667) [#4668](https://github.com/JabRef/jabref/issues/4668) [#4669](https://github.com/JabRef/jabref/issues/4669) [#4670](https://github.com/JabRef/jabref/issues/4670) [#4671](https://github.com/JabRef/jabref/issues/4671) [#4672](https://github.com/JabRef/jabref/issues/4672) [#4673](https://github.com/JabRef/jabref/issues/4673)
 
 
 
diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
index ab4097899cc..e9c36458ba8 100644
--- a/src/main/java/org/jabref/gui/Base.css
+++ b/src/main/java/org/jabref/gui/Base.css
@@ -818,8 +818,8 @@
 
 .separator:horizontal .line {
     -fx-border-color: -jr-separator;
-    -fx-border-width: 0;
-    -fx-border-insets: 1 0 0 0;
+    -fx-border-width: 0.3;
+    -fx-border-insets: 1 15 0 20;
 }
 
 .separator:vertical .line {
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index dc1077e570e..2e41bbc7e64 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -125,7 +125,6 @@
 import org.jabref.model.database.shared.DatabaseLocation;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BiblatexEntryTypes;
-import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.specialfields.SpecialField;
 import org.jabref.preferences.JabRefPreferences;
@@ -734,35 +733,35 @@ private MenuBar createMenu() {
         Menu help = new Menu(Localization.lang("Help"));
 
         file.getItems().addAll(
-                factory.createMenuItem(StandardActions.NEW_LIBRARY_BIBTEX, new NewDatabaseAction(this, BibDatabaseMode.BIBTEX)),
-                factory.createMenuItem(StandardActions.NEW_LIBRARY_BIBLATEX, new NewDatabaseAction(this, BibDatabaseMode.BIBLATEX)),
+                factory.createSubMenu(StandardActions.NEW_LIBRARY,
+                        factory.createMenuItem(StandardActions.NEW_LIBRARY_BIBTEX, new NewDatabaseAction(this, BibDatabaseMode.BIBTEX)),
+                        factory.createMenuItem(StandardActions.NEW_LIBRARY_BIBLATEX, new NewDatabaseAction(this, BibDatabaseMode.BIBLATEX))),
+
                 factory.createMenuItem(StandardActions.OPEN_LIBRARY, getOpenDatabaseAction()),
+                fileHistory,
                 factory.createMenuItem(StandardActions.SAVE_LIBRARY, new OldDatabaseCommandWrapper(Actions.SAVE, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.SAVE_LIBRARY_AS, new OldDatabaseCommandWrapper(Actions.SAVE_AS, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.SAVE_ALL, new SaveAllAction(this)),
 
-                factory.createSubMenu(StandardActions.IMPORT_EXPORT,
+                new SeparatorMenuItem(),
+
+                factory.createSubMenu(StandardActions.IMPORT,
                         factory.createMenuItem(StandardActions.MERGE_DATABASE, new OldDatabaseCommandWrapper(Actions.MERGE_DATABASE, this, Globals.stateManager)), // TODO: merge with import
                         factory.createMenuItem(StandardActions.IMPORT_INTO_CURRENT_LIBRARY, new ImportCommand(this, false)),
-                        factory.createMenuItem(StandardActions.IMPORT_INTO_NEW_LIBRARY, new ImportCommand(this, true)),
+                        factory.createMenuItem(StandardActions.IMPORT_INTO_NEW_LIBRARY, new ImportCommand(this, true))),
+
+                factory.createSubMenu(StandardActions.EXPORT,
                         factory.createMenuItem(StandardActions.EXPORT_ALL, new ExportCommand(this, false, Globals.prefs)),
                         factory.createMenuItem(StandardActions.EXPORT_SELECTED, new ExportCommand(this, true, Globals.prefs)),
                         factory.createMenuItem(StandardActions.SAVE_SELECTED_AS_PLAIN_BIBTEX, new OldDatabaseCommandWrapper(Actions.SAVE_SELECTED_AS_PLAIN, this, Globals.stateManager))),
 
-                new SeparatorMenuItem(),
-
                 factory.createMenuItem(StandardActions.CONNECT_TO_SHARED_DB, new ConnectToSharedDatabaseCommand(this)),
                 factory.createMenuItem(StandardActions.PULL_CHANGES_FROM_SHARED_DB, new OldDatabaseCommandWrapper(Actions.PULL_CHANGES_FROM_SHARED_DATABASE, this, Globals.stateManager)),
 
                 new SeparatorMenuItem(),
 
-                fileHistory,
-
-                new SeparatorMenuItem(),
-
                 factory.createMenuItem(StandardActions.CLOSE_LIBRARY, new CloseDatabaseAction()),
                 factory.createMenuItem(StandardActions.QUIT, new CloseAction())
-
         );
 
         edit.getItems().addAll(
@@ -787,10 +786,7 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.SEND_AS_EMAIL, new OldDatabaseCommandWrapper(Actions.SEND_AS_EMAIL, this, Globals.stateManager)),
-
-                new SeparatorMenuItem()
-
+                factory.createMenuItem(StandardActions.MANAGE_KEYWORDS, new ManageKeywordsAction(this))
         );
 
         if (Globals.prefs.getBoolean(JabRefPreferences.SPECIALFIELDSENABLED)) {
@@ -830,28 +826,17 @@ private MenuBar createMenu() {
             }
         }
 
-        edit.getItems().addAll(
-                factory.createMenuItem(StandardActions.MANAGE_KEYWORDS, new ManageKeywordsAction(this)),
-                factory.createMenuItem(StandardActions.REPLACE_ALL, new OldDatabaseCommandWrapper(Actions.REPLACE_ALL, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.MASS_SET_FIELDS, new MassSetFieldsAction(this))
-
-        );
-
         library.getItems().addAll(
-                factory.createMenuItem(StandardActions.NEW_ARTICLE, new NewEntryAction(this, BibtexEntryTypes.ARTICLE, dialogService, Globals.prefs)),
                 factory.createMenuItem(StandardActions.NEW_ENTRY, new NewEntryAction(this, dialogService, Globals.prefs)),
                 factory.createMenuItem(StandardActions.NEW_ENTRY_FROM_PLAINTEX, new NewEntryFromPlainTextAction(this, Globals.prefs.getUpdateFieldPreferences(), dialogService, Globals.prefs)),
-
-                new SeparatorMenuItem(),
-
                 factory.createMenuItem(StandardActions.DELETE_ENTRY, new OldDatabaseCommandWrapper(Actions.DELETE, this, Globals.stateManager)),
 
                 new SeparatorMenuItem(),
 
                 factory.createMenuItem(StandardActions.LIBRARY_PROPERTIES, new DatabasePropertiesAction(this)),
                 factory.createMenuItem(StandardActions.EDIT_PREAMBLE, new PreambleEditor(this)),
-                factory.createMenuItem(StandardActions.EDIT_STRINGS, new BibtexStringEditorAction(this))
-
+                factory.createMenuItem(StandardActions.EDIT_STRINGS, new BibtexStringEditorAction(this)),
+                factory.createMenuItem(StandardActions.MASS_SET_FIELDS, new MassSetFieldsAction(this))
         );
 
         Menu lookupIdentifiers = factory.createSubMenu(StandardActions.LOOKUP_DOC_IDENTIFIER);
@@ -864,67 +849,66 @@ private MenuBar createMenu() {
         quality.getItems().addAll(
                 factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(this, dialogService)),
                 factory.createMenuItem(StandardActions.MERGE_ENTRIES, new MergeEntriesAction(this)),
-
-                new SeparatorMenuItem(),
-
                 factory.createMenuItem(StandardActions.CHECK_INTEGRITY, new IntegrityCheckAction(this)),
                 factory.createMenuItem(StandardActions.CLEANUP_ENTRIES, new OldDatabaseCommandWrapper(Actions.CLEANUP, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, Globals.stateManager)),
-
-                new SeparatorMenuItem(),
-
-                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction()),
-                factory.createMenuItem(StandardActions.FIND_UNLINKED_FILES, new FindUnlinkedFilesAction(this)),
-                lookupIdentifiers,
-                factory.createMenuItem(StandardActions.DOWNLOAD_FULL_TEXT, new OldDatabaseCommandWrapper(Actions.DOWNLOAD_FULL_TEXT, this, Globals.stateManager))
-        );
-
-        SidePaneComponent webSearch = sidePaneManager.getComponent(SidePaneType.WEB_SEARCH);
-        SidePaneComponent groups = sidePaneManager.getComponent(SidePaneType.GROUPS);
-        SidePaneComponent openOffice = sidePaneManager.getComponent(SidePaneType.OPEN_OFFICE);
-
-        view.getItems().addAll(
-                factory.createMenuItem(webSearch.getToggleAction(), webSearch.getToggleCommand()),
-                factory.createMenuItem(groups.getToggleAction(), groups.getToggleCommand()),
-                factory.createMenuItem(StandardActions.TOGGLE_PREVIEW, new OldDatabaseCommandWrapper(Actions.TOGGLE_PREVIEW, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.EDIT_ENTRY, new OldDatabaseCommandWrapper(Actions.EDIT, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.SHOW_PDV_VIEWER, new ShowDocumentViewerAction()),
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.SELECT_ALL, new OldDatabaseCommandWrapper(Actions.SELECT_ALL, this, Globals.stateManager)),
-
-                new SeparatorMenuItem(),
-
-                factory.createMenuItem(StandardActions.NEXT_PREVIEW_STYLE, new OldDatabaseCommandWrapper(Actions.NEXT_PREVIEW_STYLE, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.PREVIOUS_PREVIEW_STYLE, new OldDatabaseCommandWrapper(Actions.PREVIOUS_PREVIEW_STYLE, this, Globals.stateManager))
+                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction())
         );
 
         PushToApplicationButton pushToExternal = new PushToApplicationButton(this, pushApplications.getApplications());
         tools.getItems().addAll(
                 factory.createMenuItem(StandardActions.NEW_SUB_LIBRARY_FROM_AUX, new NewSubLibraryAction(this)),
+                factory.createMenuItem(StandardActions.FIND_UNLINKED_FILES, new FindUnlinkedFilesAction(this)),
                 factory.createMenuItem(StandardActions.WRITE_XMP, new OldDatabaseCommandWrapper(Actions.WRITE_XMP, this, Globals.stateManager)),
+                factory.createMenuItem(StandardActions.COPY_LINKED_FILES, new CopyFilesAction(this)),
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(openOffice.getToggleAction(), openOffice.getToggleCommand()),
-                factory.createMenuItem(pushToExternal.getMenuAction(), pushToExternal),
+                lookupIdentifiers,
+                factory.createMenuItem(StandardActions.DOWNLOAD_FULL_TEXT, new OldDatabaseCommandWrapper(Actions.DOWNLOAD_FULL_TEXT, this, Globals.stateManager)),
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.OPEN_FOLDER, new OldDatabaseCommandWrapper(Actions.OPEN_FOLDER, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.OPEN_FILE, new OldDatabaseCommandWrapper(Actions.OPEN_EXTERNAL_FILE, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.OPEN_URL, new OldDatabaseCommandWrapper(Actions.OPEN_URL, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.OPEN_CONSOLE, new OldDatabaseCommandWrapper(Actions.OPEN_CONSOLE, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.COPY_LINKED_FILES, new CopyFilesAction(this)),
+                factory.createMenuItem(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, Globals.stateManager)),
+                factory.createMenuItem(StandardActions.REPLACE_ALL, new OldDatabaseCommandWrapper(Actions.REPLACE_ALL, this, Globals.stateManager)),
+                factory.createMenuItem(StandardActions.SEND_AS_EMAIL, new OldDatabaseCommandWrapper(Actions.SEND_AS_EMAIL, this, Globals.stateManager)),
+                factory.createMenuItem(pushToExternal.getMenuAction(), pushToExternal),
 
-                new SeparatorMenuItem(),
+                factory.createSubMenu(StandardActions.ABBREVIATE,
+                        factory.createMenuItem(StandardActions.ABBREVIATE_ISO, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_ISO, this, Globals.stateManager)),
+                        factory.createMenuItem(StandardActions.ABBREVIATE_MEDLINE, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_MEDLINE, this, Globals.stateManager))),
 
-                factory.createMenuItem(StandardActions.ABBREVIATE_ISO, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_ISO, this, Globals.stateManager)),
-                factory.createMenuItem(StandardActions.ABBREVIATE_MEDLINE, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_MEDLINE, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.UNABBREVIATE, new OldDatabaseCommandWrapper(Actions.UNABBREVIATE, this, Globals.stateManager))
         );
 
+        SidePaneComponent webSearch = sidePaneManager.getComponent(SidePaneType.WEB_SEARCH);
+        SidePaneComponent groups = sidePaneManager.getComponent(SidePaneType.GROUPS);
+        SidePaneComponent openOffice = sidePaneManager.getComponent(SidePaneType.OPEN_OFFICE);
+
+        view.getItems().add(new SeparatorMenuItem());
+        view.setOnShowing(event -> {
+            view.getItems().clear();
+            view.getItems().addAll(
+                    factory.createCheckMenuItem(webSearch.getToggleAction(), webSearch.getToggleCommand(), sidePaneManager.isComponentVisible(SidePaneType.WEB_SEARCH)),
+                    factory.createCheckMenuItem(groups.getToggleAction(), groups.getToggleCommand(), sidePaneManager.isComponentVisible(SidePaneType.GROUPS)),
+                    factory.createCheckMenuItem(openOffice.getToggleAction(), openOffice.getToggleCommand(), sidePaneManager.isComponentVisible(SidePaneType.OPEN_OFFICE)),
+
+                    new SeparatorMenuItem(),
+
+                    factory.createCheckMenuItem(StandardActions.TOGGLE_PREVIEW, new OldDatabaseCommandWrapper(Actions.TOGGLE_PREVIEW, this, Globals.stateManager), Globals.prefs.getPreviewPreferences().isPreviewPanelEnabled()),
+                    factory.createMenuItem(StandardActions.NEXT_PREVIEW_STYLE, new OldDatabaseCommandWrapper(Actions.NEXT_PREVIEW_STYLE, this, Globals.stateManager)),
+                    factory.createMenuItem(StandardActions.PREVIOUS_PREVIEW_STYLE, new OldDatabaseCommandWrapper(Actions.PREVIOUS_PREVIEW_STYLE, this, Globals.stateManager)),
+
+                    new SeparatorMenuItem(),
+
+                    factory.createMenuItem(StandardActions.SHOW_PDF_VIEWER, new ShowDocumentViewerAction()),
+                    factory.createMenuItem(StandardActions.EDIT_ENTRY, new OldDatabaseCommandWrapper(Actions.EDIT, this, Globals.stateManager)),
+                    factory.createMenuItem(StandardActions.OPEN_CONSOLE, new OldDatabaseCommandWrapper(Actions.OPEN_CONSOLE, this, Globals.stateManager))
+            );
+        });
+
         options.getItems().addAll(
                 factory.createMenuItem(StandardActions.SHOW_PREFS, new ShowPreferencesAction(this, Globals.TASK_EXECUTOR)),
 
@@ -943,7 +927,8 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.MANAGE_CONTENT_SELECTORS, new ManageContentSelectorAction(this)),
                 // TODO: Reenable customize entry types feature (https://github.com/JabRef/jabref/issues/4719)
                 //factory.createMenuItem(StandardActions.CUSTOMIZE_ENTRY_TYPES, new CustomizeEntryAction(this)),
-                factory.createMenuItem(StandardActions.MANAGE_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this)));
+                factory.createMenuItem(StandardActions.MANAGE_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this))
+        );
 
         help.getItems().addAll(
                 factory.createMenuItem(StandardActions.HELP, HelpAction.getMainHelpPageCommand()),
@@ -975,6 +960,7 @@ private MenuBar createMenu() {
                 ),
                 factory.createMenuItem(StandardActions.ABOUT, new AboutAction())
         );
+
         //@formatter:on
         MenuBar menu = new MenuBar();
         menu.getStyleClass().add("mainMenu");
diff --git a/src/main/java/org/jabref/gui/actions/ActionFactory.java b/src/main/java/org/jabref/gui/actions/ActionFactory.java
index 51c77f1f8d2..69c5531db65 100644
--- a/src/main/java/org/jabref/gui/actions/ActionFactory.java
+++ b/src/main/java/org/jabref/gui/actions/ActionFactory.java
@@ -5,6 +5,7 @@
 import javafx.scene.Node;
 import javafx.scene.control.Button;
 import javafx.scene.control.ButtonBase;
+import javafx.scene.control.CheckMenuItem;
 import javafx.scene.control.Menu;
 import javafx.scene.control.MenuItem;
 
@@ -43,6 +44,14 @@ public MenuItem createMenuItem(Action action, Command command) {
         return menuItem;
     }
 
+    public CheckMenuItem createCheckMenuItem(Action action, Command command, boolean selected) {
+        CheckMenuItem checkMenuItem = ActionUtils.createCheckMenuItem(new JabRefAction(action, command, keyBindingRepository));
+        checkMenuItem.setSelected(selected);
+        setGraphic(checkMenuItem, action);
+
+        return checkMenuItem;
+    }
+
     public Menu createMenu(Action action) {
         Menu menu = ActionUtils.createMenu(new JabRefAction(action, keyBindingRepository));
 
diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
index 69321ed5766..b3b10e3aeaa 100644
--- a/src/main/java/org/jabref/gui/actions/StandardActions.java
+++ b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -60,10 +60,12 @@ public enum StandardActions implements Action {
     SKIMMED(Localization.lang("Set read status to skimmed"), IconTheme.JabRefIcons.READ_STATUS_SKIMMED),
     RELEVANCE(Localization.lang("Relevance"), IconTheme.JabRefIcons.RELEVANCE),
     RELEVANT(Localization.lang("Toggle relevance"), IconTheme.JabRefIcons.RELEVANCE),
-    NEW_LIBRARY_BIBTEX(Localization.lang("New %0 library", BibDatabaseMode.BIBTEX.getFormattedName()), IconTheme.JabRefIcons.NEW),
-    NEW_LIBRARY_BIBLATEX(Localization.lang("New %0 library", BibDatabaseMode.BIBLATEX.getFormattedName()), IconTheme.JabRefIcons.NEW),
+    NEW_LIBRARY(Localization.lang("New library"), IconTheme.JabRefIcons.NEW),
+    NEW_LIBRARY_BIBTEX(Localization.lang("New %0 library", BibDatabaseMode.BIBTEX.getFormattedName())),
+    NEW_LIBRARY_BIBLATEX(Localization.lang("New %0 library", BibDatabaseMode.BIBLATEX.getFormattedName())),
     OPEN_LIBRARY(Localization.lang("Open library"), IconTheme.JabRefIcons.OPEN, KeyBinding.OPEN_DATABASE),
-    IMPORT_EXPORT(Localization.lang("Import & Export"), IconTheme.JabRefIcons.IMPORT_EXPORT),
+    IMPORT(Localization.lang("Import"), IconTheme.JabRefIcons.IMPORT),
+    EXPORT(Localization.lang("Export"), IconTheme.JabRefIcons.EXPORT),
     MERGE_DATABASE(Localization.lang("Append library"), Localization.lang("Append contents from a BibTeX library into the currently viewed library")),
     SAVE_LIBRARY(Localization.lang("Save library"), IconTheme.JabRefIcons.SAVE, KeyBinding.SAVE_DATABASE),
     SAVE_LIBRARY_AS(Localization.lang("Save library as..."), KeyBinding.SAVE_DATABASE_AS),
@@ -71,19 +73,19 @@ public enum StandardActions implements Action {
     SAVE_ALL(Localization.lang("Save all"), Localization.lang("Save all open libraries"), IconTheme.JabRefIcons.SAVE_ALL, KeyBinding.SAVE_ALL),
     IMPORT_INTO_NEW_LIBRARY(Localization.lang("Import into new library"), KeyBinding.IMPORT_INTO_NEW_DATABASE),
     IMPORT_INTO_CURRENT_LIBRARY(Localization.lang("Import into current library"), KeyBinding.IMPORT_INTO_CURRENT_DATABASE),
-    EXPORT_ALL(Localization.lang("Export")),
+    EXPORT_ALL(Localization.lang("Export all entries")),
     EXPORT_SELECTED(Localization.lang("Export selected entries")),
-    CONNECT_TO_SHARED_DB(Localization.lang("Connect to shared database")),
-    PULL_CHANGES_FROM_SHARED_DB(Localization.lang("Pull changes from shared database"), IconTheme.JabRefIcons.PULL, KeyBinding.PULL_CHANGES_FROM_SHARED_DATABASE),
+    CONNECT_TO_SHARED_DB(Localization.lang("Connect to shared database"), IconTheme.JabRefIcons.CONNECT_DB),
+    PULL_CHANGES_FROM_SHARED_DB(Localization.lang("Pull changes from shared database"), KeyBinding.PULL_CHANGES_FROM_SHARED_DATABASE),
     CLOSE_LIBRARY(Localization.lang("Close library"), Localization.lang("Close the current library"), IconTheme.JabRefIcons.CLOSE, KeyBinding.CLOSE_DATABASE),
     QUIT(Localization.lang("Quit"), Localization.lang("Quit JabRef"), IconTheme.JabRefIcons.CLOSE_JABREF, KeyBinding.QUIT_JABREF),
     UNDO(Localization.lang("Undo"), IconTheme.JabRefIcons.UNDO, KeyBinding.UNDO),
     REDO(Localization.lang("Redo"), IconTheme.JabRefIcons.REDO, KeyBinding.REDO),
-    REPLACE_ALL(Localization.lang("Replace string"), KeyBinding.REPLACE_STRING),
+    REPLACE_ALL(Localization.lang("Find and replace"), KeyBinding.REPLACE_STRING),
     MANAGE_KEYWORDS(Localization.lang("Manage keywords")),
-    MASS_SET_FIELDS(Localization.lang("Set/clear/append/rename fields")),
-    TOGGLE_GROUPS(Localization.lang("Toggle groups interface"), IconTheme.JabRefIcons.TOGGLE_GROUPS, KeyBinding.TOGGLE_GROUPS_INTERFACE),
-    TOOGLE_OO(Localization.lang("OpenOffice/LibreOffice connection"), IconTheme.JabRefIcons.FILE_OPENOFFICE, KeyBinding.OPEN_OPEN_OFFICE_LIBRE_OFFICE_CONNECTION),
+    MASS_SET_FIELDS(Localization.lang("Manage field names & content")),
+    TOGGLE_GROUPS(Localization.lang("Groups interface"), IconTheme.JabRefIcons.TOGGLE_GROUPS, KeyBinding.TOGGLE_GROUPS_INTERFACE),
+    TOOGLE_OO(Localization.lang("OpenOffice/LibreOffice"), IconTheme.JabRefIcons.FILE_OPENOFFICE, KeyBinding.OPEN_OPEN_OFFICE_LIBRE_OFFICE_CONNECTION),
     TOGGLE_WEB_SEARCH(Localization.lang("Web search"), Localization.lang("Toggle web search interface"), IconTheme.JabRefIcons.WWW, KeyBinding.WEB_SEARCH),
 
     NEW_SUB_LIBRARY_FROM_AUX(Localization.lang("New sublibrary based on AUX file") + "...", Localization.lang("New BibTeX sublibrary") + Localization.lang("This feature generates a new library based on which entries are needed in an existing LaTeX document."), IconTheme.JabRefIcons.NEW),
@@ -92,8 +94,9 @@ public enum StandardActions implements Action {
     OPEN_FILE(Localization.lang("Open file"), Localization.lang("Open file"), IconTheme.JabRefIcons.FILE, KeyBinding.OPEN_FILE),
     OPEN_CONSOLE(Localization.lang("Open terminal here"), Localization.lang("Open terminal here"), IconTheme.JabRefIcons.CONSOLE, KeyBinding.OPEN_CONSOLE),
     COPY_LINKED_FILES(Localization.lang("Copy linked files to folder...")),
-    ABBREVIATE_ISO(Localization.lang("Abbreviate journal names (ISO)"), Localization.lang("Abbreviate journal names of the selected entries (ISO abbreviation)"), KeyBinding.ABBREVIATE),
-    ABBREVIATE_MEDLINE(Localization.lang("Abbreviate journal names (MEDLINE)"), Localization.lang("Abbreviate journal names of the selected entries (MEDLINE abbreviation)")),
+    ABBREVIATE(Localization.lang("Abbreviate journal names")),
+    ABBREVIATE_ISO("ISO", Localization.lang("Abbreviate journal names of the selected entries (ISO abbreviation)"), KeyBinding.ABBREVIATE),
+    ABBREVIATE_MEDLINE("MEDLINE", Localization.lang("Abbreviate journal names of the selected entries (MEDLINE abbreviation)")),
     UNABBREVIATE(Localization.lang("Unabbreviate journal names"), Localization.lang("Unabbreviate journal names of the selected entries"), KeyBinding.UNABBREVIATE),
 
     MANAGE_CUSTOM_EXPORTS(Localization.lang("Manage custom exports")),
@@ -109,11 +112,11 @@ public enum StandardActions implements Action {
     MANAGE_CONTENT_SELECTORS(Localization.lang("Manage content selectors"), IconTheme.JabRefIcons.PREFERENCES),
     MANAGE_CITE_KEY_PATTERNS(Localization.lang("BibTeX key patterns")),
 
-    TOGGLE_PREVIEW(Localization.lang("Toggle entry preview"), IconTheme.JabRefIcons.TOGGLE_ENTRY_PREVIEW, KeyBinding.TOGGLE_ENTRY_PREVIEW),
-    EDIT_ENTRY(Localization.lang("Edit entry"), IconTheme.JabRefIcons.EDIT_ENTRY, KeyBinding.EDIT_ENTRY),
-    SHOW_PDV_VIEWER(Localization.lang("Show document viewer"), IconTheme.JabRefIcons.PDF_FILE),
-    NEXT_PREVIEW_STYLE(Localization.lang("Next preview layout"), KeyBinding.NEXT_PREVIEW_LAYOUT),
-    PREVIOUS_PREVIEW_STYLE(Localization.lang("Previous preview layout"), KeyBinding.PREVIOUS_PREVIEW_LAYOUT),
+    EDIT_ENTRY(Localization.lang("Open entry editor"), IconTheme.JabRefIcons.EDIT_ENTRY, KeyBinding.EDIT_ENTRY),
+    SHOW_PDF_VIEWER(Localization.lang("Open document viewer"), IconTheme.JabRefIcons.PDF_FILE),
+    TOGGLE_PREVIEW(Localization.lang("Entry preview"), IconTheme.JabRefIcons.TOGGLE_ENTRY_PREVIEW, KeyBinding.TOGGLE_ENTRY_PREVIEW),
+    NEXT_PREVIEW_STYLE(Localization.lang("Next citation style"), KeyBinding.NEXT_PREVIEW_LAYOUT),
+    PREVIOUS_PREVIEW_STYLE(Localization.lang("Previous citation style"), KeyBinding.PREVIOUS_PREVIEW_LAYOUT),
     SELECT_ALL(Localization.lang("Select all"), KeyBinding.SELECT_ALL),
 
     NEW_ENTRY(Localization.lang("New entry"), IconTheme.JabRefIcons.ADD_ENTRY, KeyBinding.NEW_ENTRY),
@@ -121,21 +124,21 @@ public enum StandardActions implements Action {
     NEW_ENTRY_FROM_PLAINTEX(Localization.lang("New entry from plain text"), KeyBinding.NEW_FROM_PLAIN_TEXT),
     LIBRARY_PROPERTIES(Localization.lang("Library properties")),
     EDIT_PREAMBLE(Localization.lang("Edit preamble")),
-    EDIT_STRINGS(Localization.lang("Edit strings"), IconTheme.JabRefIcons.EDIT_STRINGS, KeyBinding.EDIT_STRINGS),
+    EDIT_STRINGS(Localization.lang("Edit string constants"), IconTheme.JabRefIcons.EDIT_STRINGS, KeyBinding.EDIT_STRINGS),
 
     FIND_DUPLICATES(Localization.lang("Find duplicates"), IconTheme.JabRefIcons.FIND_DUPLICATES),
     MERGE_ENTRIES(Localization.lang("Merge entries"), IconTheme.JabRefIcons.MERGE_ENTRIES),
     RESOLVE_DUPLICATE_KEYS(Localization.lang("Resolve duplicate BibTeX keys"), Localization.lang("Find and remove duplicate BibTeX keys"), KeyBinding.RESOLVE_DUPLICATE_BIBTEX_KEYS),
     CHECK_INTEGRITY(Localization.lang("Check integrity"), KeyBinding.CHECK_INTEGRITY),
-    FIND_UNLINKED_FILES(Localization.lang("Find unlinked files"), Localization.lang("Searches for unlinked PDF files on the file system"), KeyBinding.FIND_UNLINKED_FILES),
+    FIND_UNLINKED_FILES(Localization.lang("Search for unlinked local files"), IconTheme.JabRefIcons.SEARCH, KeyBinding.FIND_UNLINKED_FILES),
     AUTO_LINK_FILES(Localization.lang("Automatically set file links"), IconTheme.JabRefIcons.AUTO_FILE_LINK, KeyBinding.AUTOMATICALLY_LINK_FILES),
-    LOOKUP_DOC_IDENTIFIER(Localization.lang("Look up document identifier")),
-    LOOKUP_FULLTEXT(Localization.lang("Look up full text documents"), KeyBinding.DOWNLOAD_FULL_TEXT),
+    LOOKUP_DOC_IDENTIFIER(Localization.lang("Search document identifier online")),
+    LOOKUP_FULLTEXT(Localization.lang("Search full text documents online"), IconTheme.JabRefIcons.FILE_SEARCH, KeyBinding.DOWNLOAD_FULL_TEXT),
     GENERATE_CITE_KEY(Localization.lang("Generate BibTeX key"), IconTheme.JabRefIcons.MAKE_KEY, KeyBinding.AUTOGENERATE_BIBTEX_KEYS),
-    GENERATE_CITE_KEYS(Localization.lang("Autogenerate BibTeX keys"), IconTheme.JabRefIcons.MAKE_KEY, KeyBinding.AUTOGENERATE_BIBTEX_KEYS),
-    DOWNLOAD_FULL_TEXT(Localization.lang("Look up full text documents"), KeyBinding.DOWNLOAD_FULL_TEXT),
+    GENERATE_CITE_KEYS(Localization.lang("Generate BibTeX keys"), IconTheme.JabRefIcons.MAKE_KEY, KeyBinding.AUTOGENERATE_BIBTEX_KEYS),
+    DOWNLOAD_FULL_TEXT(Localization.lang("Search full text documents online"), IconTheme.JabRefIcons.FILE_SEARCH, KeyBinding.DOWNLOAD_FULL_TEXT),
     CLEANUP_ENTRIES(Localization.lang("Cleanup entries"), IconTheme.JabRefIcons.CLEANUP_ENTRIES, KeyBinding.CLEANUP),
-    SET_FILE_LINKS(Localization.lang("Automatically set file links"), IconTheme.JabRefIcons.AUTO_FILE_LINK, KeyBinding.AUTOMATICALLY_LINK_FILES),
+    SET_FILE_LINKS(Localization.lang("Automatically set file links"), KeyBinding.AUTOMATICALLY_LINK_FILES),
 
     HELP(Localization.lang("Online help"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
     WEB_MENU(Localization.lang("JabRef resources")),
diff --git a/src/main/java/org/jabref/gui/icon/IconTheme.java b/src/main/java/org/jabref/gui/icon/IconTheme.java
index 5c0510f862a..49cfe8ba53a 100644
--- a/src/main/java/org/jabref/gui/icon/IconTheme.java
+++ b/src/main/java/org/jabref/gui/icon/IconTheme.java
@@ -205,6 +205,7 @@ public enum JabRefIcons implements JabRefIcon {
         REFRESH(MaterialDesignIcon.REFRESH),
         DELETE_ENTRY(MaterialDesignIcon.DELETE),
         SEARCH(MaterialDesignIcon.MAGNIFY),
+        FILE_SEARCH(MaterialDesignIcon.FILE_FIND),
         ADVANCED_SEARCH(Color.CYAN, MaterialDesignIcon.MAGNIFY),
         PREFERENCES(MaterialDesignIcon.SETTINGS),
         HELP(MaterialDesignIcon.HELP_CIRCLE),
@@ -238,7 +239,7 @@ public enum JabRefIcons implements JabRefIcon {
         AUTO_FILE_LINK(MaterialDesignIcon.FILE_FIND) /*css: file-find */,
         QUALITY_ASSURED(MaterialDesignIcon.CERTIFICATE), /*css: certificate */
         QUALITY(MaterialDesignIcon.CERTIFICATE),/*css: certificate */
-        OPEN(MaterialDesignIcon.FOLDER) /*css: folder */,
+        OPEN(MaterialDesignIcon.FOLDER_OUTLINE) /*css: folder-outline */,
         ADD_ROW(MaterialDesignIcon.SERVER_PLUS) /* css: server-plus*/,
         REMOVE_ROW(MaterialDesignIcon.SERVER_MINUS) /*css: server-minus */,
         PICTURE(MaterialDesignIcon.FILE_IMAGE) /*css: file-image */,
@@ -276,7 +277,7 @@ public enum JabRefIcons implements JabRefIcon {
         APPLICATION_WINEDT(JabRefMaterialDesignIcon.WINEDT),
         KEY_BINDINGS(MaterialDesignIcon.KEYBOARD), /*css: keyboard */
         FIND_DUPLICATES(MaterialDesignIcon.CODE_EQUAL), /*css: code-equal */
-        PULL(MaterialDesignIcon.SOURCE_PULL), /*source-pull*/
+        CONNECT_DB(MaterialDesignIcon.CLOUD_UPLOAD), /*cloud-upload*/
         SUCCESS(MaterialDesignIcon.CHECK_CIRCLE),
         WARNING(MaterialDesignIcon.ALERT),
         ERROR(MaterialDesignIcon.ALERT_CIRCLE),
@@ -293,7 +294,8 @@ public enum JabRefIcons implements JabRefIcon {
         DEFAULT_GROUP_ICON_COLORED(MaterialDesignIcon.PLAY),
         DEFAULT_GROUP_ICON(MaterialDesignIcon.LABEL_OUTLINE),
         ALL_ENTRIES_GROUP_ICON(DefaultGroupsFactory.ALL_ENTRIES_GROUP_DEFAULT_ICON),
-        IMPORT_EXPORT(MaterialDesignIcon.SWAP_VERTICAL),
+        IMPORT(MaterialDesignIcon.CALL_RECEIVED),
+        EXPORT(MaterialDesignIcon.CALL_MADE),
         PREVIOUS_LEFT(MaterialDesignIcon.CHEVRON_LEFT),
         PREVIOUS_UP(MaterialDesignIcon.CHEVRON_UP),
         NEXT_RIGHT(MaterialDesignIcon.CHEVRON_RIGHT),
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 84a2215b2e2..8c0d5cedea9 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1160,7 +1160,6 @@ No\ full\ text\ document\ found=No full text document found
 Update\ to\ current\ column\ order=Update to current column order
 Download\ from\ URL=Download from URL
 Rename\ field=Rename field
-Set/clear/append/rename\ fields=Set/clear/append/rename fields
 Append\ field=Append field
 Append\ to\ fields=Append to fields
 Rename\ field\ to=Rename field to
@@ -1293,7 +1292,6 @@ No\ valid\ style\ file\ defined=No valid style file defined
 Choose\ pattern=Choose pattern
 Use\ the\ BIB\ file\ location\ as\ primary\ file\ directory=Use the BIB file location as primary file directory
 Could\ not\ run\ the\ gnuclient/emacsclient\ program.\ Make\ sure\ you\ have\ the\ emacsclient/gnuclient\ program\ installed\ and\ available\ in\ the\ PATH.=Could not run the gnuclient/emacsclient program. Make sure you have the emacsclient/gnuclient program installed and available in the PATH.
-OpenOffice/LibreOffice\ connection=OpenOffice/LibreOffice connection
 You\ must\ select\ either\ a\ valid\ style\ file,\ or\ use\ one\ of\ the\ default\ styles.=You must select either a valid style file, or use one of the default styles.
 
 This\ is\ a\ simple\ copy\ and\ paste\ dialog.\ First\ load\ or\ paste\ some\ text\ into\ the\ text\ input\ area.<br>After\ that,\ you\ can\ mark\ text\ and\ assign\ it\ to\ a\ BibTeX\ field.=This is a simple copy and paste dialog. First load or paste some text into the text input area.<br>After that, you can mark text and assign it to a BibTeX field.
@@ -1443,7 +1441,6 @@ Rebind\ C-a,\ too=Rebind C-a, too
 Rebind\ C-f,\ too=Rebind C-f, too
 
 Open\ folder=Open folder
-Searches\ for\ unlinked\ PDF\ files\ on\ the\ file\ system=Searches for unlinked PDF files on the file system
 Export\ entries\ ordered\ as\ specified=Export entries ordered as specified
 Export\ sort\ order=Export sort order
 Export\ sorting=Export sorting
@@ -2003,7 +2000,6 @@ Next\ page=Next page
 Document\ viewer=Document viewer
 Live=Live
 Locked=Locked
-Show\ document\ viewer=Show document viewer
 Show\ the\ document\ of\ the\ currently\ selected\ entry.=Show the document of the currently selected entry.
 Show\ this\ document\ until\ unlocked.=Show this document until unlocked.
 Set\ current\ user\ name\ as\ owner.=Set current user name as owner.
@@ -2060,8 +2056,6 @@ No\ linked\ files\ found\ for\ export.=No linked files found for export.
 No\ full\ text\ document\ found\ for\ entry\ %0.=No full text document found for entry %0.
 
 Delete\ Entry=Delete Entry
-Import\ &\ Export=Import & Export
-Look\ up\ document\ identifier=Look up document identifier
 Next\ library=Next library
 Previous\ library=Previous library
 add\ group=add group
@@ -2101,8 +2095,6 @@ Toggle\ intersection=Toggle intersection
 Toggle\ union=Toggle union
 Jump\ to\ entry=Jump to entry
 The\ group\ name\ contains\ the\ keyword\ separator\ "%0"\ and\ thus\ probably\ does\ not\ work\ as\ expected.=The group name contains the keyword separator "%0" and thus probably does not work as expected.
-Abbreviate\ journal\ names\ (ISO)=Abbreviate journal names (ISO)
-Abbreviate\ journal\ names\ (MEDLINE)=Abbreviate journal names (MEDLINE)
 Blog=Blog
 Check\ integrity=Check integrity
 Cleanup\ URL\ link=Cleanup URL link
@@ -2177,3 +2169,19 @@ Keyword\:=Keyword:
 Keyword\ \"%0\"\ already\ exists=Keyword "%0" already exists
 Remove\ keyword=Remove keyword
 Are\ you\ sure\ you\ want\ to\ remove\ keyword\:\ \"%0\"?=Are you sure you want to remove keyword: "%0"?
+
+Edit\ string\ constants=Edit string constants
+Export\ all\ entries=Export all entries
+Generate\ BibTeX\ keys=Generate BibTeX keys
+Groups\ interface=Groups interface
+Manage\ field\ names\ &\ content=Manage field names & content
+New\ library=New library
+Next\ citation\ style=Next citation style
+OpenOffice/LibreOffice=OpenOffice/LibreOffice
+Open\ document\ viewer=Open document viewer
+Open\ entry\ editor=Open entry editor
+Previous\ citation\ style=Previous citation style
+Search\ document\ identifier\ online=Search document identifier online
+Search\ for\ unlinked\ local\ files=Search for unlinked local files
+Search\ full\ text\ documents\ online=Search full text documents online
+Find\ and\ replace=Find and replace
\ No newline at end of file

From bdf7aa6b7ecc4c51592d30042919dabfa96fca28 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 5 Mar 2019 12:55:36 +0100
Subject: [PATCH 070/184] Fix #4703: Newline format couldn't be changed (#4720)

Fixes #4703.
---
 src/main/java/org/jabref/gui/preferences/FileTab.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/preferences/FileTab.java b/src/main/java/org/jabref/gui/preferences/FileTab.java
index 55e599e67ae..3bbc387f130 100644
--- a/src/main/java/org/jabref/gui/preferences/FileTab.java
+++ b/src/main/java/org/jabref/gui/preferences/FileTab.java
@@ -211,7 +211,7 @@ public void storeSettings() {
         }
 
         String newline;
-        switch (newlineSeparator.getPromptText()) {
+        switch (newlineSeparator.getValue()) {
             case "CR":
                 newline = "\r";
                 break;

From b231bb02ab85a4e1a061257baf948bc497353496 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Tue, 5 Mar 2019 19:20:48 +0100
Subject: [PATCH 071/184] remove unused swing stuff convert help  buttons

---
 src/main/java/org/jabref/gui/WrapLayout.java  | 175 ------------
 .../BibtexKeyPatternPanel.java                |  15 +-
 .../java/org/jabref/gui/help/HelpAction.java  |  19 --
 .../journals/JournalAbbreviationsUtil.java    |  34 ---
 .../jabref/gui/preferences/AdvancedTab.java   |  10 +-
 .../jabref/gui/preferences/ExternalTab.java   |  22 +-
 .../logic/citationstyle/CSLAdapter.java       |   8 +-
 .../migrations/FileLinksUpgradeWarning.java   | 256 ------------------
 8 files changed, 28 insertions(+), 511 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/WrapLayout.java
 delete mode 100644 src/main/java/org/jabref/gui/journals/JournalAbbreviationsUtil.java
 delete mode 100644 src/main/java/org/jabref/migrations/FileLinksUpgradeWarning.java

diff --git a/src/main/java/org/jabref/gui/WrapLayout.java b/src/main/java/org/jabref/gui/WrapLayout.java
deleted file mode 100644
index 999c7abd3f0..00000000000
--- a/src/main/java/org/jabref/gui/WrapLayout.java
+++ /dev/null
@@ -1,175 +0,0 @@
-package org.jabref.gui;
-
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.FlowLayout;
-import java.awt.Insets;
-
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
-/**
- *  FlowLayout subclass that fully supports wrapping of components.
- */
-public class WrapLayout extends FlowLayout {
-    /**
-     * Constructs a new <code>WrapLayout</code> with a left
-     * alignment and a default 5-unit horizontal and vertical gap.
-     */
-    public WrapLayout() {
-        super();
-    }
-
-    /**
-     * Constructs a new <code>FlowLayout</code> with the specified
-     * alignment and a default 5-unit horizontal and vertical gap.
-     * The value of the alignment argument must be one of
-     * <code>WrapLayout</code>, <code>WrapLayout</code>,
-     * or <code>WrapLayout</code>.
-     * @param align the alignment value
-     */
-    public WrapLayout(int align) {
-        super(align);
-    }
-
-    /**
-     * Creates a new flow layout manager with the indicated alignment
-     * and the indicated horizontal and vertical gaps.
-     * <p>
-     * The value of the alignment argument must be one of
-     * <code>WrapLayout</code>, <code>WrapLayout</code>,
-     * or <code>WrapLayout</code>.
-     * @param align the alignment value
-     * @param hgap the horizontal gap between components
-     * @param vgap the vertical gap between components
-     */
-    public WrapLayout(int align, int hgap, int vgap) {
-        super(align, hgap, vgap);
-    }
-
-    /**
-     * Returns the preferred dimensions for this layout given the
-     * <i>visible</i> components in the specified target container.
-     * @param target the component which needs to be laid out
-     * @return the preferred dimensions to lay out the
-     * subcomponents of the specified container
-     */
-    @Override
-    public Dimension preferredLayoutSize(Container target) {
-        return layoutSize(target, true);
-    }
-
-    /**
-     * Returns the minimum dimensions needed to layout the <i>visible</i>
-     * components contained in the specified target container.
-     * @param target the component which needs to be laid out
-     * @return the minimum dimensions to lay out the
-     * subcomponents of the specified container
-     */
-    @Override
-    public Dimension minimumLayoutSize(Container target) {
-        Dimension minimum = layoutSize(target, false);
-        minimum.width -= (getHgap() + 1);
-        return minimum;
-    }
-
-    /**
-     * Returns the minimum or preferred dimension needed to layout the target
-     * container.
-     *
-     * @param target target to get layout size for
-     * @param preferred should preferred size be calculated
-     * @return the dimension to layout the target container
-     */
-    private Dimension layoutSize(Container target, boolean preferred) {
-        synchronized (target.getTreeLock()) {
-            //  Each row must fit with the width allocated to the container.
-            //  When the container width = 0, the preferred width of the container
-            //  has not yet been calculated so lets ask for the maximum.
-
-            int targetWidth = target.getSize().width;
-
-            if (targetWidth == 0) {
-                targetWidth = Integer.MAX_VALUE;
-            }
-
-            int hgap = getHgap();
-            int vgap = getVgap();
-            Insets insets = target.getInsets();
-            int horizontalInsetsAndGap = insets.left + insets.right + (hgap * 2);
-            int maxWidth = targetWidth - horizontalInsetsAndGap;
-
-            //  Fit components into the allowed width
-
-            Dimension dim = new Dimension(0, 0);
-            int rowWidth = 0;
-            int rowHeight = 0;
-
-            int nmembers = target.getComponentCount();
-
-            for (int i = 0; i < nmembers; i++) {
-                Component m = target.getComponent(i);
-
-                if (m.isVisible()) {
-                    Dimension d = preferred ? m.getPreferredSize() : m.getMinimumSize();
-
-                    if (d != null) {
-                        //  Can't add the component to current row. Start a new row.
-
-                        if ((rowWidth + d.width) > maxWidth) {
-                            addRow(dim, rowWidth, rowHeight);
-                            rowWidth = 0;
-                            rowHeight = 0;
-                        }
-
-                        //  Add a horizontal gap for all components after the first
-
-                        if (rowWidth != 0) {
-                            rowWidth += hgap;
-                        }
-
-                        rowWidth += d.width;
-                        rowHeight = Math.max(rowHeight, d.height);
-                    }
-                }
-            }
-
-            addRow(dim, rowWidth, rowHeight);
-
-            dim.width += horizontalInsetsAndGap;
-            dim.height += insets.top + insets.bottom + (vgap * 2);
-
-            //	When using a scroll pane or the DecoratedLookAndFeel we need to
-            //  make sure the preferred size is less than the size of the
-            //  target container so shrinking the container size works
-            //  correctly. Removing the horizontal gap is an easy way to do this.
-
-            Container scrollPane = SwingUtilities.getAncestorOfClass(JScrollPane.class, target);
-
-            if (scrollPane != null) {
-                dim.width -= (hgap + 1);
-            }
-
-            return dim;
-        }
-    }
-
-    /*
-     *  A new row has been completed. Use the dimensions of this row
-     *  to update the preferred size for the container.
-     *
-     *  @param dim update the width and height when appropriate
-     *  @param rowWidth the width of the row to add
-     *  @param rowHeight the height of the row to add
-     */
-    private void addRow(Dimension dim, int rowWidth, int rowHeight) {
-        dim.width = Math.max(dim.width, rowWidth);
-
-        if (dim.height > 0) {
-            dim.height += getVgap();
-        }
-
-        dim.height += rowHeight;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java b/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
index 994452e5efa..a5a8b27c55b 100644
--- a/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
+++ b/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
@@ -15,6 +15,8 @@
 
 import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
+import org.jabref.gui.actions.ActionFactory;
+import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.help.HelpAction;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.l10n.Localization;
@@ -34,7 +36,6 @@ public class BibtexKeyPatternPanel extends Pane {
 
     // default pattern
     protected final TextField defaultPat = new TextField();
-    private final HelpAction help;
 
     private final int COLUMNS = 2;
 
@@ -45,7 +46,6 @@ public class BibtexKeyPatternPanel extends Pane {
 
     public BibtexKeyPatternPanel(BasePanel panel) {
         this.panel = panel;
-        help = new HelpAction(Localization.lang("Help on key patterns"), HelpFile.BIBTEX_KEY_PATTERN);
         gridPane.setHgap(10);
         gridPane.setVgap(5);
         buildGUI();
@@ -93,7 +93,7 @@ private void buildGUI() {
 
             textFields.put(type.getName().toLowerCase(Locale.ROOT), textField);
 
-            if (columnIndex == COLUMNS - 1) {
+            if (columnIndex == (COLUMNS - 1)) {
                 columnIndex = 0;
                 rowIndex++;
             } else {
@@ -103,9 +103,10 @@ private void buildGUI() {
 
         rowIndex++;
 
-        Button help1 = new Button("?");
-        help1.setOnAction(e -> new HelpAction(Localization.lang("Help on key patterns"), HelpFile.BIBTEX_KEY_PATTERN).getHelpButton().doClick());
-        gridPane.add(help1, 1, rowIndex);
+
+        ActionFactory factory = new ActionFactory(Globals.prefs.getKeyBindingRepository());
+        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on key patterns"), HelpFile.BIBTEX_KEY_PATTERN).getCommand());
+        gridPane.add(help, 1, rowIndex);
 
         Button btnDefaultAll1 = new Button(Localization.lang("Reset all"));
         btnDefaultAll1.setOnAction(e -> {
@@ -162,7 +163,7 @@ public void setValues(AbstractBibtexKeyPattern keyPattern) {
             setValue(entry.getValue(), entry.getKey(), keyPattern);
         }
 
-        if (keyPattern.getDefaultValue() == null || keyPattern.getDefaultValue().isEmpty()) {
+        if ((keyPattern.getDefaultValue() == null) || keyPattern.getDefaultValue().isEmpty()) {
             defaultPat.setText("");
         } else {
             defaultPat.setText(keyPattern.getDefaultValue().get(0));
diff --git a/src/main/java/org/jabref/gui/help/HelpAction.java b/src/main/java/org/jabref/gui/help/HelpAction.java
index ab7ae84e027..e8d410de343 100644
--- a/src/main/java/org/jabref/gui/help/HelpAction.java
+++ b/src/main/java/org/jabref/gui/help/HelpAction.java
@@ -1,11 +1,7 @@
 package org.jabref.gui.help;
 
-import java.awt.Color;
-import java.awt.Cursor;
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
 import java.util.HashSet;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -14,7 +10,6 @@
 import javax.swing.Action;
 import javax.swing.Icon;
 import javax.swing.JButton;
-import javax.swing.JLabel;
 import javax.swing.KeyStroke;
 
 import org.jabref.Globals;
@@ -91,20 +86,6 @@ public void setHelpFile(HelpFile urlPart) {
         this.helpPage = urlPart;
     }
 
-    public JLabel getHelpLabel(String labelText) {
-        JLabel helpLabel = new JLabel("<html><u>" + labelText + "</u></html>");
-        helpLabel.setForeground(Color.BLUE);
-        helpLabel.setCursor(new Cursor(Cursor.HAND_CURSOR));
-        helpLabel.addMouseListener(new MouseAdapter() {
-
-            @Override
-            public void mouseClicked(MouseEvent e) {
-                openHelpPage(helpPage);
-            }
-        });
-        return helpLabel;
-    }
-
     @Override
     public void actionPerformed(ActionEvent e) {
         openHelpPage(helpPage);
diff --git a/src/main/java/org/jabref/gui/journals/JournalAbbreviationsUtil.java b/src/main/java/org/jabref/gui/journals/JournalAbbreviationsUtil.java
deleted file mode 100644
index 86a284cd78f..00000000000
--- a/src/main/java/org/jabref/gui/journals/JournalAbbreviationsUtil.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package org.jabref.gui.journals;
-
-import java.util.Collection;
-
-import javax.swing.table.DefaultTableModel;
-import javax.swing.table.TableModel;
-
-import org.jabref.logic.journals.Abbreviation;
-import org.jabref.logic.l10n.Localization;
-
-public class JournalAbbreviationsUtil {
-
-    private JournalAbbreviationsUtil() {
-    }
-
-    public static TableModel getTableModel(Collection<Abbreviation> abbreviations) {
-        Object[][] cells = new Object[abbreviations.size()][2];
-        int row = 0;
-        for (Abbreviation abbreviation : abbreviations) {
-            cells[row][0] = abbreviation.getName();
-            cells[row][1] = abbreviation.getIsoAbbreviation();
-            row++;
-        }
-
-        return new DefaultTableModel(cells, new Object[] {Localization.lang("Full name"),
-                Localization.lang("Abbreviation")}) {
-
-            @Override
-            public boolean isCellEditable(int row1, int column) {
-                return false;
-            }
-        };
-    }
-}
diff --git a/src/main/java/org/jabref/gui/preferences/AdvancedTab.java b/src/main/java/org/jabref/gui/preferences/AdvancedTab.java
index 3fcd0516ce5..4a8dbf0a075 100644
--- a/src/main/java/org/jabref/gui/preferences/AdvancedTab.java
+++ b/src/main/java/org/jabref/gui/preferences/AdvancedTab.java
@@ -15,6 +15,8 @@
 
 import org.jabref.Globals;
 import org.jabref.gui.DialogService;
+import org.jabref.gui.actions.ActionFactory;
+import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.help.HelpAction;
 import org.jabref.gui.remote.JabRefMessageHandler;
 import org.jabref.gui.util.DefaultTaskExecutor;
@@ -76,9 +78,11 @@ public AdvancedTab(DialogService dialogService, JabRefPreferences prefs) {
         HBox p = new HBox();
         p.getChildren().add(useRemoteServer);
         p.getChildren().add(remoteServerPort);
-        Button helpButton = new Button("?");
-        helpButton.setOnAction(event -> new HelpAction(HelpFile.REMOTE).getHelpButton().doClick());
-        p.getChildren().add(helpButton);
+
+        ActionFactory factory = new ActionFactory(preferences.getKeyBindingRepository());
+        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.REMOTE).getCommand());
+        help.setMaxWidth(Double.MAX_VALUE);
+        p.getChildren().add(help);
 
         builder.add(p, 2, 9);
         builder.add(new Label(""), 1, 10);
diff --git a/src/main/java/org/jabref/gui/preferences/ExternalTab.java b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
index 782a14fa11d..3b819033f9d 100644
--- a/src/main/java/org/jabref/gui/preferences/ExternalTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
@@ -1,13 +1,8 @@
 package org.jabref.gui.preferences;
 
-import java.awt.BorderLayout;
-
 import javax.swing.JFileChooser;
-import javax.swing.JPanel;
 
-import javafx.embed.swing.JFXPanel;
 import javafx.scene.Node;
-import javafx.scene.Scene;
 import javafx.scene.control.Button;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.Label;
@@ -15,10 +10,10 @@
 import javafx.scene.control.TextField;
 import javafx.scene.control.ToggleGroup;
 import javafx.scene.layout.GridPane;
+import javafx.scene.layout.Pane;
 
 import org.jabref.Globals;
 import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.customjfx.CustomJFXPanel;
 import org.jabref.gui.externalfiletype.ExternalFileTypeEditor;
 import org.jabref.gui.push.PushToApplication;
 import org.jabref.gui.push.PushToApplicationSettings;
@@ -28,7 +23,7 @@
 import org.jabref.logic.util.OS;
 import org.jabref.preferences.JabRefPreferences;
 
-class ExternalTab extends JPanel implements PrefsTab {
+class ExternalTab extends Pane implements PrefsTab {
 
     private final JabRefPreferences prefs;
     private final TextField emailSubject;
@@ -135,11 +130,11 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
         builder.add(openPdf,  1, 12);
 
         builder.add(pdfOptionPanel, 1, 13);
-        JFXPanel panel = CustomJFXPanel.wrap(new Scene(builder));
-        setLayout(new BorderLayout());
-        add(panel, BorderLayout.CENTER);
+
+        FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder().
     }
 
+    @Override
     public Node getBuilder() {
         return builder;
     }
@@ -149,10 +144,10 @@ private void addSettingsButton(final PushToApplication application, GridPane pan
         Button button = new Button(Localization.lang("Settings for %0", application.getApplicationName()));
         button.setPrefSize(150, 20);
         button.setOnAction(e -> PushToApplicationSettingsDialog.showSettingsDialog(null, settings, index));
-        if (index % 2 == 0) {
-            panel.add(button, 1, index / 2 + 1);
+        if ((index % 2) == 0) {
+            panel.add(button, 1, (index / 2) + 1);
         } else {
-            panel.add(button, 2, index / 2 + 1);
+            panel.add(button, 2, (index / 2) + 1);
         }
     }
 
@@ -213,6 +208,7 @@ private void updateExecuteConsoleButtonAndFieldEnabledState() {
     }
 
     private void showConsoleChooser() {
+
         JFileChooser consoleChooser = new JFileChooser();
         int answer = consoleChooser.showOpenDialog(ExternalTab.this);
         if (answer == JFileChooser.APPROVE_OPTION) {
diff --git a/src/main/java/org/jabref/logic/citationstyle/CSLAdapter.java b/src/main/java/org/jabref/logic/citationstyle/CSLAdapter.java
index cda929568d2..0de338a1f0f 100644
--- a/src/main/java/org/jabref/logic/citationstyle/CSLAdapter.java
+++ b/src/main/java/org/jabref/logic/citationstyle/CSLAdapter.java
@@ -31,9 +31,9 @@
  * same style. Changing the output format is cheap.
  * @implNote The main function {@link #makeBibliography} will enforce
  * synchronized calling. The main CSL engine under the hood is not thread-safe. Since this class is usually called from
- * a SwingWorker, the only other option would be to create several CSL instances which is wasting a lot of resources and very slow.
+ * a BackgroundTakk, the only other option would be to create several CSL instances which is wasting a lot of resources and very slow.
  * In the current scheme, {@link #makeBibliography} can be called as usual
- * SwingWorker task and to the best of my knowledge, concurrent calls will pile up and processed sequentially.
+ * background task and to the best of my knowledge, concurrent calls will pile up and processed sequentially.
  */
 public class CSLAdapter {
 
@@ -63,7 +63,7 @@ public synchronized List<String> makeBibliography(List<BibEntry> bibEntries, Str
      * @throws IOException An error occurred in the underlying JavaScript framework
      */
     private void initialize(String newStyle, CitationStyleOutputFormat newFormat) throws IOException {
-        if (cslInstance == null || !Objects.equals(newStyle, style)) {
+        if ((cslInstance == null) || !Objects.equals(newStyle, style)) {
             // lang and forceLang are set to the default values of other CSL constructors
             cslInstance = new CSL(dataProvider, new JabRefLocaleProvider(), newStyle, "en-US", false);
             style = newStyle;
@@ -81,7 +81,7 @@ private void initialize(String newStyle, CitationStyleOutputFormat newFormat) th
      */
     private static class JabRefItemDataProvider implements ItemDataProvider {
 
-        private ArrayList<BibEntry> data = new ArrayList<>();
+        private final ArrayList<BibEntry> data = new ArrayList<>();
 
         /**
          * Converts the {@link BibEntry} into {@link CSLItemData}.
diff --git a/src/main/java/org/jabref/migrations/FileLinksUpgradeWarning.java b/src/main/java/org/jabref/migrations/FileLinksUpgradeWarning.java
deleted file mode 100644
index eed9497457e..00000000000
--- a/src/main/java/org/jabref/migrations/FileLinksUpgradeWarning.java
+++ /dev/null
@@ -1,256 +0,0 @@
-package org.jabref.migrations;
-
-import java.util.List;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.FXDialogService;
-import org.jabref.gui.importer.actions.GUIPostOpenAction;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.gui.util.FileDialogConfiguration;
-import org.jabref.logic.cleanup.UpgradePdfPsToFileCleanup;
-import org.jabref.logic.importer.ParserResult;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.FieldChange;
-import org.jabref.model.database.BibDatabase;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FieldName;
-import org.jabref.model.metadata.FilePreferences;
-import org.jabref.preferences.JabRefPreferences;
-
-import com.jgoodies.forms.builder.FormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-
-/**
- * This class defines the warning that can be offered when opening a pre-2.3
- * JabRef file into a later version. This warning mentions the new external file
- * link system in this version of JabRef, and offers to:
- *
- * * upgrade old-style PDF/PS links into the "file" field
- * * modify General fields to show "file" instead of "pdf" / "ps"
- * * modify table column settings to show "file" instead of "pdf" / "ps"
- */
-public class FileLinksUpgradeWarning implements GUIPostOpenAction {
-
-    private static final String[] FIELDS_TO_LOOK_FOR = new String[]{FieldName.PDF, FieldName.PS};
-
-    private boolean offerChangeSettings;
-
-    private boolean offerChangeDatabase;
-
-    private boolean offerSetFileDir;
-
-    /**
-     * Collect file links from the given set of fields, and add them to the list contained in the field
-     * GUIGlobals.FILE_FIELD.
-     *
-     * @param database The database to modify.
-     * @return A CompoundEdit specifying the undo operation for the whole operation.
-     */
-    private static NamedCompound upgradePdfPsToFile(BibDatabase database) {
-        NamedCompound ce = new NamedCompound(Localization.lang("Move external links to 'file' field"));
-
-        UpgradePdfPsToFileCleanup cleanupJob = new UpgradePdfPsToFileCleanup();
-        for (BibEntry entry : database.getEntries()) {
-            List<FieldChange> changes = cleanupJob.cleanup(entry);
-
-            for (FieldChange change : changes) {
-                ce.addEdit(new UndoableFieldChange(change));
-            }
-        }
-
-        ce.end();
-        return ce;
-    }
-
-    /**
-     * This method should be performed if the major/minor versions recorded in the ParserResult
-     * are less than or equal to 2.2.
-     *
-     * @return true if the file was written by a jabref version <=2.2
-     */
-    @Override
-    public boolean isActionNecessary(ParserResult pr) {
-        // Find out which actions should be offered:
-        // Only offer to change Preferences if file column is not already visible:
-        offerChangeSettings = !Globals.prefs.getBoolean(JabRefPreferences.FILE_COLUMN) || !showsFileInGenFields();
-        // Only offer to upgrade links if the pdf/ps fields are used:
-        offerChangeDatabase = linksFound(pr.getDatabase(), FileLinksUpgradeWarning.FIELDS_TO_LOOK_FOR);
-        // If the "file" directory is not set, offer to migrate pdf/ps dir:
-        offerSetFileDir = !Globals.prefs.hasKey(FieldName.FILE + FilePreferences.DIR_SUFFIX)
-                && (Globals.prefs.hasKey(FieldName.PDF + FilePreferences.DIR_SUFFIX)
-                || Globals.prefs.hasKey(FieldName.PS + FilePreferences.DIR_SUFFIX));
-
-        // First check if this warning is disabled:
-        return Globals.prefs.getBoolean(JabRefPreferences.SHOW_FILE_LINKS_UPGRADE_WARNING)
-                && isThereSomethingToBeDone();
-    }
-
-    /*
-     * This method presents a dialog box explaining and offering to make the
-     * changes. If the user confirms, the changes are performed.
-     */
-    @Override
-    public void performAction(BasePanel panel, ParserResult parserResult) {
-
-        if (!isThereSomethingToBeDone()) {
-            return; // Nothing to do, just return.
-        }
-
-        JCheckBox changeSettings = new JCheckBox(
-                Localization.lang("Change table column and General fields settings to use the new feature"),
-                offerChangeSettings);
-        JCheckBox changeDatabase = new JCheckBox(
-                Localization.lang("Upgrade old external file links to use the new feature"),
-                offerChangeDatabase);
-        JCheckBox setFileDir = new JCheckBox(Localization.lang("Set main external file directory") + ":",
-                offerSetFileDir);
-        JTextField fileDir = new JTextField(30);
-        JCheckBox doNotShowDialog = new JCheckBox(Localization.lang("Do not show these options in the future"),
-                false);
-
-        JPanel message = new JPanel();
-        FormBuilder formBuilder = FormBuilder.create().layout(new FormLayout("left:pref", "p"));
-        // Keep the formatting of these lines. Otherwise, strings have to be translated again.
-        // See updated JabRef_en.properties modifications by python syncLang.py -s -u
-        int row = 1;
-        formBuilder.add(new JLabel("<html>" + Localization.lang("This library uses outdated file links.") + "<br><br>"
-                + Localization
-                .lang("JabRef no longer supports 'ps' or 'pdf' fields.<br>File links are now stored in the 'file' field and files are stored in an external file directory.<br>To make use of this feature, JabRef needs to upgrade file links.<br><br>")
-                + "<p>"
-                + Localization.lang("Do you want JabRef to do the following operations?") + "</html>")).xy(1, row);
-
-        if (offerChangeSettings) {
-            formBuilder.appendRows("2dlu, p");
-            row += 2;
-            formBuilder.add(changeSettings).xy(1, row);
-        }
-        if (offerChangeDatabase) {
-            formBuilder.appendRows("2dlu, p");
-            row += 2;
-            formBuilder.add(changeDatabase).xy(1, row);
-        }
-        if (offerSetFileDir) {
-            if (Globals.prefs.hasKey(FieldName.PDF + FilePreferences.DIR_SUFFIX)) {
-                fileDir.setText(Globals.prefs.get(FieldName.PDF + FilePreferences.DIR_SUFFIX));
-            } else {
-                fileDir.setText(Globals.prefs.get(FieldName.PS + FilePreferences.DIR_SUFFIX));
-            }
-            JPanel builderPanel = new JPanel();
-            builderPanel.add(setFileDir);
-            builderPanel.add(fileDir);
-            JButton browse = new JButton(Localization.lang("Browse"));
-
-            FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                    .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)).build();
-            DialogService ds = new FXDialogService();
-
-            browse.addActionListener(
-                    e -> DefaultTaskExecutor.runInJavaFXThread(() -> ds.showFileOpenDialog(fileDialogConfiguration)
-                            .ifPresent(f -> fileDir.setText(f.toAbsolutePath().toString()))));
-            builderPanel.add(browse);
-            formBuilder.appendRows("2dlu, p");
-            row += 2;
-            formBuilder.add(builderPanel).xy(1, row);
-        }
-        formBuilder.appendRows("6dlu, p");
-        formBuilder.add(doNotShowDialog).xy(1, row + 2);
-
-        message.add(formBuilder.build());
-
-        int answer = JOptionPane.showConfirmDialog(null,
-                message, Localization.lang("Upgrade file"), JOptionPane.YES_NO_OPTION);
-        if (doNotShowDialog.isSelected()) {
-            Globals.prefs.putBoolean(JabRefPreferences.SHOW_FILE_LINKS_UPGRADE_WARNING, false);
-        }
-
-        if (answer == JOptionPane.YES_OPTION) {
-            makeChanges(panel, parserResult, changeSettings.isSelected(), changeDatabase.isSelected(),
-                    setFileDir.isSelected() ? fileDir.getText() : null);
-        }
-    }
-
-    private boolean isThereSomethingToBeDone() {
-        return offerChangeSettings || offerChangeDatabase || offerSetFileDir;
-    }
-
-    /**
-     * Check the database to find out whether any of a set of fields are used
-     * for any of the entries.
-     *
-     * @param database The BIB database.
-     * @param fields   The set of fields to look for.
-     * @return true if at least one of the given fields is set in at least one entry,
-     * false otherwise.
-     */
-    private boolean linksFound(BibDatabase database, String[] fields) {
-        for (BibEntry entry : database.getEntries()) {
-            for (String field : fields) {
-                if (entry.hasField(field)) {
-                    return true;
-                }
-            }
-        }
-        return false;
-    }
-
-    /**
-     * This method performs the actual changes.
-     *
-     * @param fileDir The path to the file directory to set, or null if it should not be set.
-     */
-    private void makeChanges(BasePanel panel, ParserResult pr, boolean upgradePrefs,
-                             boolean upgradeDatabase, String fileDir) {
-
-        if (upgradeDatabase) {
-            // Update file links links in the database:
-            NamedCompound ce = upgradePdfPsToFile(pr.getDatabase());
-            panel.getUndoManager().addEdit(ce);
-            panel.markBaseChanged();
-        }
-
-        if (fileDir != null) {
-            Globals.prefs.put(FieldName.FILE + FilePreferences.DIR_SUFFIX, fileDir);
-        }
-
-        if (upgradePrefs) {
-            // Exchange table columns:
-            Globals.prefs.putBoolean(JabRefPreferences.FILE_COLUMN, Boolean.TRUE);
-
-            // Modify General fields if necessary:
-            // If we don't find the file field, insert it at the bottom of the first tab:
-            if (!showsFileInGenFields()) {
-                String gfs = Globals.prefs.get(JabRefPreferences.CUSTOM_TAB_FIELDS + "0");
-                StringBuilder sb = new StringBuilder(gfs);
-                if (!gfs.isEmpty()) {
-                    sb.append(';');
-                }
-                sb.append(FieldName.FILE);
-                Globals.prefs.put(JabRefPreferences.CUSTOM_TAB_FIELDS + "0", sb.toString());
-                Globals.prefs.updateEntryEditorTabList();
-            }
-            panel.frame().setupAllTables();
-        }
-    }
-
-    private boolean showsFileInGenFields() {
-        for (List<String> fields : Globals.prefs.getEntryEditorTabList().values()) {
-            for (String field : fields) {
-                if (field.equals(FieldName.FILE)) {
-                    return true;
-                }
-            }
-        }
-        return false;
-    }
-}

From 187cc0fcb47c905f520d59f8e876e4a9ebecb424 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Tue, 5 Mar 2019 19:31:16 +0100
Subject: [PATCH 072/184] convert file chooser in preferences

---
 .../jabref/gui/preferences/ExternalTab.java   | 54 ++++++++-----------
 1 file changed, 22 insertions(+), 32 deletions(-)

diff --git a/src/main/java/org/jabref/gui/preferences/ExternalTab.java b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
index 3b819033f9d..8d3b1bf17e9 100644
--- a/src/main/java/org/jabref/gui/preferences/ExternalTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
@@ -1,7 +1,5 @@
 package org.jabref.gui.preferences;
 
-import javax.swing.JFileChooser;
-
 import javafx.scene.Node;
 import javafx.scene.control.Button;
 import javafx.scene.control.CheckBox;
@@ -13,12 +11,14 @@
 import javafx.scene.layout.Pane;
 
 import org.jabref.Globals;
+import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.externalfiletype.ExternalFileTypeEditor;
 import org.jabref.gui.push.PushToApplication;
 import org.jabref.gui.push.PushToApplicationSettings;
 import org.jabref.gui.push.PushToApplicationSettingsDialog;
 import org.jabref.gui.push.PushToApplications;
+import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.OS;
 import org.jabref.preferences.JabRefPreferences;
@@ -40,12 +40,15 @@ class ExternalTab extends Pane implements PrefsTab {
     private final TextField adobeAcrobatReaderPath;
     private final TextField sumatraReaderPath;
     private final GridPane builder = new GridPane();
+    private final DialogService dialogService;
+    private final FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder().build();
 
     public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPreferences prefs) {
         this.prefs = prefs;
+        dialogService = frame.getDialogService();
         Button editFileTypes = new Button(Localization.lang("Manage external file types"));
         citeCommand = new TextField();
-        editFileTypes.setOnAction(e->ExternalFileTypeEditor.getAction());
+        editFileTypes.setOnAction(e -> ExternalFileTypeEditor.getAction());
         defaultConsole = new RadioButton(Localization.lang("Use default terminal emulator"));
         executeConsole = new RadioButton(Localization.lang("Execute command") + ":");
         consoleCommand = new TextField();
@@ -68,25 +71,25 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
         final ToggleGroup consoleGroup = new ToggleGroup();
         defaultConsole.setToggleGroup(consoleGroup);
         executeConsole.setToggleGroup(consoleGroup);
-        consoleOptionPanel.add(defaultConsole,  1, 1);
-        consoleOptionPanel.add(executeConsole,  1, 2);
-        consoleOptionPanel.add(consoleCommand,  2, 2);
-        consoleOptionPanel.add(browseButton,  3, 2);
-        consoleOptionPanel.add(commandDescription,  2, 3);
+        consoleOptionPanel.add(defaultConsole, 1, 1);
+        consoleOptionPanel.add(executeConsole, 1, 2);
+        consoleOptionPanel.add(consoleCommand, 2, 2);
+        consoleOptionPanel.add(browseButton, 3, 2);
+        consoleOptionPanel.add(commandDescription, 2, 3);
 
         GridPane pdfOptionPanel = new GridPane();
         final ToggleGroup pdfReaderGroup = new ToggleGroup();
-        pdfOptionPanel.add(adobeAcrobatReader,  1, 1);
-        pdfOptionPanel.add(adobeAcrobatReaderPath,  2, 1);
+        pdfOptionPanel.add(adobeAcrobatReader, 1, 1);
+        pdfOptionPanel.add(adobeAcrobatReaderPath, 2, 1);
         adobeAcrobatReader.setToggleGroup(pdfReaderGroup);
-        pdfOptionPanel.add(browseAdobeAcrobatReader,  3, 1);
+        pdfOptionPanel.add(browseAdobeAcrobatReader, 3, 1);
 
         if (OS.WINDOWS) {
             browseSumatraReader.setOnAction(e -> showSumatraChooser());
-            pdfOptionPanel.add(sumatraReader,  1, 2);
+            pdfOptionPanel.add(sumatraReader, 1, 2);
             sumatraReader.setToggleGroup(pdfReaderGroup);
-            pdfOptionPanel.add(sumatraReaderPath,  2, 2);
-            pdfOptionPanel.add(browseSumatraReader,  3, 2);
+            pdfOptionPanel.add(sumatraReaderPath, 2, 2);
+            pdfOptionPanel.add(browseSumatraReader, 3, 2);
         }
 
         Label sendingOfEmails = new Label(Localization.lang("Sending of emails"));
@@ -127,11 +130,10 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
 
         Label openPdf = new Label(Localization.lang("Open PDF"));
         openPdf.getStyleClass().add("sectionHeader");
-        builder.add(openPdf,  1, 12);
+        builder.add(openPdf, 1, 12);
 
         builder.add(pdfOptionPanel, 1, 13);
 
-        FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder().
     }
 
     @Override
@@ -208,28 +210,16 @@ private void updateExecuteConsoleButtonAndFieldEnabledState() {
     }
 
     private void showConsoleChooser() {
-
-        JFileChooser consoleChooser = new JFileChooser();
-        int answer = consoleChooser.showOpenDialog(ExternalTab.this);
-        if (answer == JFileChooser.APPROVE_OPTION) {
-            consoleCommand.setText(consoleChooser.getSelectedFile().getAbsolutePath());
-        }
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> consoleCommand.setText(file.toAbsolutePath().toString()));
     }
 
     private void showAdobeChooser() {
-        JFileChooser adobeChooser = new JFileChooser();
-        int answer = adobeChooser.showOpenDialog(ExternalTab.this);
-        if (answer == JFileChooser.APPROVE_OPTION) {
-            adobeAcrobatReaderPath.setText(adobeChooser.getSelectedFile().getAbsolutePath());
-        }
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> adobeAcrobatReaderPath.setText(file.toAbsolutePath().toString()));
+
     }
 
     private void showSumatraChooser() {
-        JFileChooser adobeChooser = new JFileChooser();
-        int answer = adobeChooser.showOpenDialog(ExternalTab.this);
-        if (answer == JFileChooser.APPROVE_OPTION) {
-            sumatraReaderPath.setText(adobeChooser.getSelectedFile().getAbsolutePath());
-        }
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> sumatraReaderPath.setText(file.toAbsolutePath().toString()));
     }
 
     private void readerSelected() {

From d6f0b5854adbadf695ab50dbfa4dbe832982585e Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Tue, 5 Mar 2019 19:35:27 +0100
Subject: [PATCH 073/184] cleanup

---
 src/main/java/org/jabref/gui/preferences/ExternalTab.java | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/preferences/ExternalTab.java b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
index 8d3b1bf17e9..0f96816e55e 100644
--- a/src/main/java/org/jabref/gui/preferences/ExternalTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
@@ -8,7 +8,6 @@
 import javafx.scene.control.TextField;
 import javafx.scene.control.ToggleGroup;
 import javafx.scene.layout.GridPane;
-import javafx.scene.layout.Pane;
 
 import org.jabref.Globals;
 import org.jabref.gui.DialogService;
@@ -23,7 +22,7 @@
 import org.jabref.logic.util.OS;
 import org.jabref.preferences.JabRefPreferences;
 
-class ExternalTab extends Pane implements PrefsTab {
+class ExternalTab implements PrefsTab {
 
     private final JabRefPreferences prefs;
     private final TextField emailSubject;

From 0a155b9364554aad6ea1d7e21f53832c567ed04d Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Tue, 5 Mar 2019 19:36:40 +0100
Subject: [PATCH 074/184] fix build

---
 .../org/jabref/gui/importer/actions/OpenDatabaseAction.java   | 4 ----
 src/main/java/org/jabref/gui/preferences/ExternalTab.java     | 1 -
 2 files changed, 5 deletions(-)

diff --git a/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java b/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
index 9a87333b386..67bd022cbc0 100644
--- a/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
@@ -35,7 +35,6 @@
 import org.jabref.logic.shared.exception.InvalidDBMSConnectionPropertiesException;
 import org.jabref.logic.shared.exception.NotASharedDatabaseException;
 import org.jabref.logic.util.StandardFileType;
-import org.jabref.migrations.FileLinksUpgradeWarning;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.shared.DatabaseNotSupportedException;
 import org.jabref.preferences.JabRefPreferences;
@@ -53,9 +52,6 @@ public class OpenDatabaseAction extends SimpleCommand {
             // Migrations:
             // Warning for migrating the Review into the Comment field
             new MergeReviewIntoCommentAction(),
-            // External file handling system in version 2.3:
-            new FileLinksUpgradeWarning(),
-
             // Check for new custom entry types loaded from the BIB file:
             new CheckForNewEntryTypesAction()
     );
diff --git a/src/main/java/org/jabref/gui/preferences/ExternalTab.java b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
index 0f96816e55e..0328eaf4e1b 100644
--- a/src/main/java/org/jabref/gui/preferences/ExternalTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
@@ -214,7 +214,6 @@ private void showConsoleChooser() {
 
     private void showAdobeChooser() {
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> adobeAcrobatReaderPath.setText(file.toAbsolutePath().toString()));
-
     }
 
     private void showSumatraChooser() {

From 731b9d2ea588e9e03c0fac385da8120b523344f4 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Tue, 5 Mar 2019 20:49:18 +0100
Subject: [PATCH 075/184] remove obsolete localization strings fix checkstyle

---
 .../bibtexkeypattern/BibtexKeyPatternPanel.java   |  5 +----
 src/main/resources/l10n/JabRef_en.properties      | 15 ---------------
 2 files changed, 1 insertion(+), 19 deletions(-)

diff --git a/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java b/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
index a5a8b27c55b..e3796c623ee 100644
--- a/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
+++ b/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
@@ -103,7 +103,6 @@ private void buildGUI() {
 
         rowIndex++;
 
-
         ActionFactory factory = new ActionFactory(Globals.prefs.getKeyBindingRepository());
         Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on key patterns"), HelpFile.BIBTEX_KEY_PATTERN).getCommand());
         gridPane.add(help, 1, rowIndex);
@@ -119,7 +118,6 @@ private void buildGUI() {
         gridPane.add(btnDefaultAll1, 2, rowIndex);
     }
 
-
     /**
      * fill the given LabelPattern by values generated from the text fields
      */
@@ -141,8 +139,7 @@ private void fillPatternUsingPanelData(AbstractBibtexKeyPattern keypatterns) {
 
     protected GlobalBibtexKeyPattern getKeyPatternAsGlobalBibtexKeyPattern() {
         GlobalBibtexKeyPattern res = GlobalBibtexKeyPattern.fromPattern(
-                JabRefPreferences.getInstance().get(JabRefPreferences.DEFAULT_BIBTEX_KEY_PATTERN)
-        );
+                                                                        JabRefPreferences.getInstance().get(JabRefPreferences.DEFAULT_BIBTEX_KEY_PATTERN));
         fillPatternUsingPanelData(res);
         return res;
     }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 8c0d5cedea9..b7f8e0dd5ea 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -137,8 +137,6 @@ Change\ of\ Grouping\ Method=Change of Grouping Method
 
 change\ preamble=change preamble
 
-Change\ table\ column\ and\ General\ fields\ settings\ to\ use\ the\ new\ feature=Change table column and General fields settings to use the new feature
-
 Changed\ language\ settings=Changed language settings
 
 Changed\ preamble=Changed preamble
@@ -283,13 +281,10 @@ Do\ not\ import\ entry=Do not import entry
 Do\ not\ open\ any\ files\ at\ startup=Do not open any files at startup
 
 Do\ not\ overwrite\ existing\ keys=Do not overwrite existing keys
-Do\ not\ show\ these\ options\ in\ the\ future=Do not show these options in the future
 
 Do\ not\ wrap\ the\ following\ fields\ when\ saving=Do not wrap the following fields when saving
 Do\ not\ write\ the\ following\ fields\ to\ XMP\ Metadata\:=Do not write the following fields to XMP Metadata:
 
-Do\ you\ want\ JabRef\ to\ do\ the\ following\ operations?=Do you want JabRef to do the following operations?
-
 Donate\ to\ JabRef=Donate to JabRef
 
 Down=Down
@@ -439,8 +434,6 @@ Formatter\ name=Formatter name
 
 found\ in\ AUX\ file=found in AUX file
 
-Full\ name=Full name
-
 Further\ information\ about\ Mr\ DLib.\ for\ JabRef\ users.=Further information about Mr DLib. for JabRef users.
 
 General=General
@@ -619,8 +612,6 @@ Modify=Modify
 
 Move\ down=Move down
 
-Move\ external\ links\ to\ 'file'\ field=Move external links to 'file' field
-
 move\ group=move group
 
 Move\ up=Move up
@@ -918,8 +909,6 @@ Set\ fields=Set fields
 
 Set\ General\ Fields=Set General Fields
 
-Set\ main\ external\ file\ directory=Set main external file directory
-
 Settings=Settings
 
 Shortcut=Shortcut
@@ -1062,8 +1051,6 @@ untitled=untitled
 Up=Up
 
 Upgrade\ external\ PDF/PS\ links\ to\ use\ the\ '%0'\ field.=Upgrade external PDF/PS links to use the '%0' field.
-Upgrade\ file=Upgrade file
-Upgrade\ old\ external\ file\ links\ to\ use\ the\ new\ feature=Upgrade old external file links to use the new feature
 
 usage=usage
 Use\ autocompletion\ for\ the\ following\ fields=Use autocompletion for the following fields
@@ -1553,8 +1540,6 @@ This\ search\ contains\ entries\ in\ which\ any\ field\ contains\ the\ term\ <b>
 This\ search\ contains\ entries\ in\ which=This search contains entries in which
 
 Unable\ to\ autodetect\ OpenOffice/LibreOffice\ installation.\ Please\ choose\ the\ installation\ directory\ manually.=Unable to autodetect OpenOffice/LibreOffice installation. Please choose the installation directory manually.
-JabRef\ no\ longer\ supports\ 'ps'\ or\ 'pdf'\ fields.<br>File\ links\ are\ now\ stored\ in\ the\ 'file'\ field\ and\ files\ are\ stored\ in\ an\ external\ file\ directory.<br>To\ make\ use\ of\ this\ feature,\ JabRef\ needs\ to\ upgrade\ file\ links.<br><br>=JabRef no longer supports 'ps' or 'pdf' fields.<br>File links are now stored in the 'file' field and files are stored in an external file directory.<br>To make use of this feature, JabRef needs to upgrade file links.<br><br>
-This\ library\ uses\ outdated\ file\ links.=This library uses outdated file links.
 
 Close\ library=Close library
 Decrease\ table\ font\ size=Decrease table font size

From ddd12aec466eee9b9eb3434948d4b2459298eae6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Wed, 6 Mar 2019 08:54:34 +0100
Subject: [PATCH 076/184] Bump mockito-core from 2.24.5 to 2.25.0 (#4723)

Bumps [mockito-core](https://github.com/mockito/mockito) from 2.24.5 to 2.25.0.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v2.24.5...v2.25.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index ea5d8e813b2..d08efe7b1a2 100644
--- a/build.gradle
+++ b/build.gradle
@@ -167,7 +167,7 @@ dependencies {
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
-    testCompile 'org.mockito:mockito-core:2.24.5'
+    testCompile 'org.mockito:mockito-core:2.25.0'
     testCompile 'com.github.tomakehurst:wiremock:2.21.0'
     testCompile 'org.assertj:assertj-swing-junit:3.9.2'
     testCompile 'org.reflections:reflections:0.9.11'

From a73a676cf778fe5076f9d06b90aa8379e7b52c79 Mon Sep 17 00:00:00 2001
From: Yash  Kothari <yashkothari199767@gmail.com>
Date: Wed, 6 Mar 2019 18:19:18 +0530
Subject: [PATCH 077/184] Adding "von" part to Author's last name when
 exporting to MS Office 2007 (#4725)

* Adding "von" part from Author's last name when exporting to MS Office
2007

Fixes #4655

* Adding "von" to Author's last name when exporting to MS Office 2007

Fixes #4655
---
 src/main/java/org/jabref/logic/msbib/MsBibAuthor.java     | 2 +-
 src/test/java/org/jabref/logic/msbib/MsBibAuthorTest.java | 7 +++++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/logic/msbib/MsBibAuthor.java b/src/main/java/org/jabref/logic/msbib/MsBibAuthor.java
index caad384ec22..8da1d4e49ca 100644
--- a/src/main/java/org/jabref/logic/msbib/MsBibAuthor.java
+++ b/src/main/java/org/jabref/logic/msbib/MsBibAuthor.java
@@ -48,7 +48,7 @@ public String getMiddleName() {
     }
 
     public String getLastName() {
-        return author.getLast().orElse(null);
+        return author.getLastOnly();
     }
 
     public String getFirstLast() {
diff --git a/src/test/java/org/jabref/logic/msbib/MsBibAuthorTest.java b/src/test/java/org/jabref/logic/msbib/MsBibAuthorTest.java
index cbb37c47408..8736b6542e1 100644
--- a/src/test/java/org/jabref/logic/msbib/MsBibAuthorTest.java
+++ b/src/test/java/org/jabref/logic/msbib/MsBibAuthorTest.java
@@ -44,4 +44,11 @@ public void testGetLastName() {
         MsBibAuthor msBibAuthor = new MsBibAuthor(author);
         assertEquals("Bach", msBibAuthor.getLastName());
     }
+
+    @Test
+    public void testGetVonAndLastName() {
+        Author author = new Author("John", null, "von", "Neumann", null);
+        MsBibAuthor msBibAuthor = new MsBibAuthor(author);
+        assertEquals("von Neumann", msBibAuthor.getLastName());
+    }
 }

From 8deb0623f02508e3716da35ed6818fff047e802f Mon Sep 17 00:00:00 2001
From: matthiasgeiger <matthias.geiger@uni-bamberg.de>
Date: Tue, 5 Mar 2019 20:23:29 +0100
Subject: [PATCH 078/184] Adding additional modifiers to be used in bibtex key
 generator

---
 CHANGELOG.md                                  |  2 +-
 .../jabref/logic/formatter/Formatters.java    |  6 +++
 .../BibtexKeyGeneratorTest.java               | 54 +++++++++++++++++++
 3 files changed, 61 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 646ffbe4bd9..be3982fb06c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -53,7 +53,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added the ability change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)
 - We grouped and reordered the Main Menu (File, Edit, Library, Quality, Tools, and View tabs & icons). [#4666](https://github.com/JabRef/jabref/issues/4666) [#4667](https://github.com/JabRef/jabref/issues/4667) [#4668](https://github.com/JabRef/jabref/issues/4668) [#4669](https://github.com/JabRef/jabref/issues/4669) [#4670](https://github.com/JabRef/jabref/issues/4670) [#4671](https://github.com/JabRef/jabref/issues/4671) [#4672](https://github.com/JabRef/jabref/issues/4672) [#4673](https://github.com/JabRef/jabref/issues/4673)
-
+- We added additional modifiers (capitalize, titlecase and sentencecase) to the Bibtex key generator. [#1506](https://github.com/JabRef/jabref/issues/1506)
 
 
 
diff --git a/src/main/java/org/jabref/logic/formatter/Formatters.java b/src/main/java/org/jabref/logic/formatter/Formatters.java
index 4e1d25f968f..9e867ac23ed 100644
--- a/src/main/java/org/jabref/logic/formatter/Formatters.java
+++ b/src/main/java/org/jabref/logic/formatter/Formatters.java
@@ -87,6 +87,12 @@ public static Optional<Formatter> getFormatterForModifier(String modifier) {
                 return Optional.of(new LowerCaseFormatter());
             case "upper":
                 return Optional.of(new UpperCaseFormatter());
+            case "capitalize":
+                return Optional.of(new CapitalizeFormatter());
+            case "titlecase":
+                return Optional.of(new TitleCaseFormatter());
+            case "sentencecase":
+                return Optional.of(new SentenceCaseFormatter());
         }
 
         if (modifier.startsWith(RegexFormatter.KEY)) {
diff --git a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
index 4ed5b5bb728..f09b091fb7e 100644
--- a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
+++ b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
@@ -1007,4 +1007,58 @@ public void generateKeyWithTwoModifiers() throws Exception {
         entry.setField("title", "The Interesting Title");
         assertEquals("theinterestingtitle", BibtexKeyGenerator.generateKey(entry, "title:lower:(_)"));
     }
+
+    @Test
+    public void generateKeyWithTitleCapitalizeModifier() throws Exception {
+        BibEntry entry = new BibEntry();
+        entry.setField("title", "the InTeresting title longer than THREE words");
+        assertEquals("TheInterestingTitleLongerThanThreeWords", BibtexKeyGenerator.generateKey(entry, "title:capitalize"));
+    }
+
+    @Test
+    public void generateKeyWithShortTitleCapitalizeModifier() throws Exception {
+        BibEntry entry = new BibEntry();
+        entry.setField("title", "the InTeresting title longer than THREE words");
+        assertEquals("InterestingTitleLonger", BibtexKeyGenerator.generateKey(entry, "shorttitle:capitalize"));
+    }
+
+    @Test
+    public void generateKeyWithTitleTitleCaseModifier() throws Exception {
+        BibEntry entry = new BibEntry();
+        entry.setField("title", "A title WITH some of The key words");
+        assertEquals("ATitlewithSomeoftheKeyWords", BibtexKeyGenerator.generateKey(entry, "title:titlecase"));
+    }
+
+    @Test
+    public void generateKeyWithShortTitleTitleCaseModifier() throws Exception {
+        BibEntry entry = new BibEntry();
+        entry.setField("title", "the InTeresting title longer than THREE words");
+        assertEquals("InterestingTitleLonger", BibtexKeyGenerator.generateKey(entry, "shorttitle:titlecase"));
+    }
+
+    @Test
+    public void generateKeyWithTitleSentenceCaseModifier() throws Exception {
+        BibEntry entry = new BibEntry();
+        entry.setField("title", "A title WITH some of The key words");
+        assertEquals("Atitlewithsomeofthekeywords", BibtexKeyGenerator.generateKey(entry, "title:sentencecase"));
+    }
+
+    @Test
+    public void generateKeyWithAuthUpperYearShortTitleCapitalizeModifier() throws Exception {
+        BibEntry entry = new BibEntry();
+        entry.setField("author", AUTHOR_STRING_FIRSTNAME_FULL_LASTNAME_FULL_COUNT_1);
+        entry.setField("year", "2019");
+        entry.setField("title", "the InTeresting title longer than THREE words");
+        assertEquals("NEWTON2019InterestingTitleLonger", BibtexKeyGenerator.generateKey(entry, "[auth:upper][year][shorttitle:capitalize]"));
+    }
+
+    @Test
+    public void generateKeyWithYearAuthUpperTitleSentenceCaseModifier() throws Exception {
+        BibEntry entry = new BibEntry();
+        entry.setField("author", AUTHOR_STRING_FIRSTNAME_FULL_LASTNAME_FULL_COUNT_3);
+        entry.setField("year", "2019");
+        entry.setField("title", "the InTeresting title longer than THREE words");
+        assertEquals("NewtonMaxwellEtAl_2019_TheInterestingTitleLongerThanThreeWords", BibtexKeyGenerator.generateKey(entry, "[authors2]_[year]_[title:capitalize]"));
+    }
+
 }

From a1858cb9efbaa7a721be465d042aca5f225a3bab Mon Sep 17 00:00:00 2001
From: kaiquekk <kaique.komata@gmail.com>
Date: Mon, 4 Mar 2019 13:05:42 -0300
Subject: [PATCH 079/184] Change toolbar icons and add separators

Changed some toolbar icons and grouped them visually with vertical
separators.

Signed-off-by: kaiquekk <kaique.komata@gmail.com>
---
 src/main/java/org/jabref/gui/Base.css            |  2 +-
 src/main/java/org/jabref/gui/JabRefFrame.java    | 11 ++++++-----
 src/main/java/org/jabref/gui/icon/IconTheme.java |  4 ++--
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
index e9c36458ba8..14c7861eb45 100644
--- a/src/main/java/org/jabref/gui/Base.css
+++ b/src/main/java/org/jabref/gui/Base.css
@@ -825,7 +825,7 @@
 .separator:vertical .line {
     -fx-border-color: -jr-separator;
     -fx-border-width: 1;
-    -fx-border-insets: 0 0 0 1;
+    -fx-border-insets: 5 15 5 15;
 }
 
 .mainToolbar {
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 2e41bbc7e64..804903672cd 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -25,6 +25,7 @@
 import javafx.beans.value.ChangeListener;
 import javafx.beans.value.ObservableValue;
 import javafx.collections.ListChangeListener;
+import javafx.geometry.Orientation;
 import javafx.scene.Node;
 import javafx.scene.control.Alert;
 import javafx.scene.control.Button;
@@ -33,6 +34,7 @@
 import javafx.scene.control.Menu;
 import javafx.scene.control.MenuBar;
 import javafx.scene.control.ProgressBar;
+import javafx.scene.control.Separator;
 import javafx.scene.control.SeparatorMenuItem;
 import javafx.scene.control.SplitPane;
 import javafx.scene.control.Tab;
@@ -617,21 +619,20 @@ private Node createToolbar() {
         leftSide.setMinWidth(100);
         leftSide.prefWidthProperty().bind(sidePane.widthProperty());
         leftSide.maxWidthProperty().bind(sidePane.widthProperty());
-
         PushToApplicationButton pushToExternal = new PushToApplicationButton(this, pushApplications.getApplications());
         HBox rightSide = new HBox(
                 factory.createIconButton(StandardActions.NEW_ARTICLE, new NewEntryAction(this, BiblatexEntryTypes.ARTICLE, dialogService, Globals.prefs)),
                 factory.createIconButton(StandardActions.DELETE_ENTRY, new OldDatabaseCommandWrapper(Actions.DELETE, this, Globals.stateManager)),
-
+                new Separator(Orientation.VERTICAL),
                 factory.createIconButton(StandardActions.UNDO, new OldDatabaseCommandWrapper(Actions.UNDO, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.REDO, new OldDatabaseCommandWrapper(Actions.REDO, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.CUT, new OldDatabaseCommandWrapper(Actions.CUT, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.COPY, new OldDatabaseCommandWrapper(Actions.COPY, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.PASTE, new OldDatabaseCommandWrapper(Actions.PASTE, this, Globals.stateManager)),
-
-                factory.createIconButton(StandardActions.CLEANUP_ENTRIES, new OldDatabaseCommandWrapper(Actions.CLEANUP, this, Globals.stateManager)),
+                new Separator(Orientation.VERTICAL),
                 factory.createIconButton(pushToExternal.getMenuAction(), pushToExternal),
-
+                factory.createIconButton(StandardActions.CLEANUP_ENTRIES, new OldDatabaseCommandWrapper(Actions.CLEANUP, this, Globals.stateManager)),
+                new Separator(Orientation.VERTICAL),
                 factory.createIconButton(StandardActions.FORK_ME, new OpenBrowserAction("https://github.com/JabRef/jabref")),
                 factory.createIconButton(StandardActions.OPEN_FACEBOOK, new OpenBrowserAction("https://www.facebook.com/JabRef/")),
                 factory.createIconButton(StandardActions.OPEN_TWITTER, new OpenBrowserAction("https://twitter.com/jabref_org"))
diff --git a/src/main/java/org/jabref/gui/icon/IconTheme.java b/src/main/java/org/jabref/gui/icon/IconTheme.java
index 49cfe8ba53a..55341a664d0 100644
--- a/src/main/java/org/jabref/gui/icon/IconTheme.java
+++ b/src/main/java/org/jabref/gui/icon/IconTheme.java
@@ -197,7 +197,7 @@ public enum JabRefIcons implements JabRefIcon {
         CLOSE(MaterialDesignIcon.CLOSE_CIRCLE),
         PASTE(JabRefMaterialDesignIcon.PASTE),
         CUT(MaterialDesignIcon.CONTENT_CUT),
-        COPY(JabRefMaterialDesignIcon.COPY),
+        COPY(MaterialDesignIcon.CONTENT_COPY),
         COMMENT(MaterialDesignIcon.COMMENT),
         REDO(MaterialDesignIcon.REDO),
         UNDO(MaterialDesignIcon.UNDO),
@@ -239,7 +239,7 @@ public enum JabRefIcons implements JabRefIcon {
         AUTO_FILE_LINK(MaterialDesignIcon.FILE_FIND) /*css: file-find */,
         QUALITY_ASSURED(MaterialDesignIcon.CERTIFICATE), /*css: certificate */
         QUALITY(MaterialDesignIcon.CERTIFICATE),/*css: certificate */
-        OPEN(MaterialDesignIcon.FOLDER_OUTLINE) /*css: folder-outline */,
+        OPEN(MaterialDesignIcon.FOLDER_OUTLINE) /*css: folder */,
         ADD_ROW(MaterialDesignIcon.SERVER_PLUS) /* css: server-plus*/,
         REMOVE_ROW(MaterialDesignIcon.SERVER_MINUS) /*css: server-minus */,
         PICTURE(MaterialDesignIcon.FILE_IMAGE) /*css: file-image */,

From d157b9d7e1cf7b14c91893976ddc6d79c7a1b706 Mon Sep 17 00:00:00 2001
From: yurickyh <yurickyussuke@hotmail.com>
Date: Mon, 4 Mar 2019 13:48:21 -0300
Subject: [PATCH 080/184] Adding GENERATE_CITE_KEYS button to toolbar.

Signed-off-by: yurickyh <yurickyussuke@hotmail.com>
---
 src/main/java/org/jabref/gui/JabRefFrame.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 804903672cd..ad3f0747106 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -631,6 +631,7 @@ private Node createToolbar() {
                 factory.createIconButton(StandardActions.PASTE, new OldDatabaseCommandWrapper(Actions.PASTE, this, Globals.stateManager)),
                 new Separator(Orientation.VERTICAL),
                 factory.createIconButton(pushToExternal.getMenuAction(), pushToExternal),
+                factory.createIconButton(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.CLEANUP_ENTRIES, new OldDatabaseCommandWrapper(Actions.CLEANUP, this, Globals.stateManager)),
                 new Separator(Orientation.VERTICAL),
                 factory.createIconButton(StandardActions.FORK_ME, new OpenBrowserAction("https://github.com/JabRef/jabref")),

From 5025d0b38a3b76593fe46b5912cf4610c742e946 Mon Sep 17 00:00:00 2001
From: kaiquekk <kaique.komata@gmail.com>
Date: Wed, 6 Mar 2019 16:41:50 -0300
Subject: [PATCH 081/184] Add changes to CHANGELOG and fix New Library icons

Signed-off-by: kaiquekk <kaique.komata@gmail.com>
---
 CHANGELOG.md                                              | 2 +-
 src/main/java/org/jabref/gui/actions/StandardActions.java | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index be3982fb06c..a262139b69b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -54,7 +54,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)
 - We grouped and reordered the Main Menu (File, Edit, Library, Quality, Tools, and View tabs & icons). [#4666](https://github.com/JabRef/jabref/issues/4666) [#4667](https://github.com/JabRef/jabref/issues/4667) [#4668](https://github.com/JabRef/jabref/issues/4668) [#4669](https://github.com/JabRef/jabref/issues/4669) [#4670](https://github.com/JabRef/jabref/issues/4670) [#4671](https://github.com/JabRef/jabref/issues/4671) [#4672](https://github.com/JabRef/jabref/issues/4672) [#4673](https://github.com/JabRef/jabref/issues/4673)
 - We added additional modifiers (capitalize, titlecase and sentencecase) to the Bibtex key generator. [#1506](https://github.com/JabRef/jabref/issues/1506)
-
+- We grouped the toolbar icons and changed the Open Library and Copy icons. [#4584](https://github.com/JabRef/jabref/issues/4584) 
 
 
 ### Fixed
diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
index b3b10e3aeaa..15e662dec5e 100644
--- a/src/main/java/org/jabref/gui/actions/StandardActions.java
+++ b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -61,8 +61,8 @@ public enum StandardActions implements Action {
     RELEVANCE(Localization.lang("Relevance"), IconTheme.JabRefIcons.RELEVANCE),
     RELEVANT(Localization.lang("Toggle relevance"), IconTheme.JabRefIcons.RELEVANCE),
     NEW_LIBRARY(Localization.lang("New library"), IconTheme.JabRefIcons.NEW),
-    NEW_LIBRARY_BIBTEX(Localization.lang("New %0 library", BibDatabaseMode.BIBTEX.getFormattedName())),
-    NEW_LIBRARY_BIBLATEX(Localization.lang("New %0 library", BibDatabaseMode.BIBLATEX.getFormattedName())),
+    NEW_LIBRARY_BIBTEX(Localization.lang("New %0 library", BibDatabaseMode.BIBTEX.getFormattedName()), IconTheme.JabRefIcons.NEW),
+    NEW_LIBRARY_BIBLATEX(Localization.lang("New %0 library", BibDatabaseMode.BIBLATEX.getFormattedName()), IconTheme.JabRefIcons.NEW),
     OPEN_LIBRARY(Localization.lang("Open library"), IconTheme.JabRefIcons.OPEN, KeyBinding.OPEN_DATABASE),
     IMPORT(Localization.lang("Import"), IconTheme.JabRefIcons.IMPORT),
     EXPORT(Localization.lang("Export"), IconTheme.JabRefIcons.EXPORT),

From 2f7aa7a6305a1dd760e08d35f8954ffcb1a9faa0 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Thu, 7 Mar 2019 09:04:37 +0100
Subject: [PATCH 082/184] Convert "wait for save" dialog to JavaFX (#4697)

---
 src/main/java/org/jabref/gui/JabRefFrame.java | 13 +--
 .../jabref/gui/WaitForSaveFinishedDialog.java | 43 ++++++++++
 .../org/jabref/gui/WaitForSaveOperation.java  | 82 -------------------
 3 files changed, 45 insertions(+), 93 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/WaitForSaveFinishedDialog.java
 delete mode 100644 src/main/java/org/jabref/gui/WaitForSaveOperation.java

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 2e41bbc7e64..81290cfaab2 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -500,17 +500,8 @@ public boolean quit() {
             context.getDatabaseFile().map(File::getAbsolutePath).ifPresent(filenames::add);
         }
 
-        // Wait for save operations to finish
-        for (int i = 0; i < tabbedPane.getTabs().size(); i++) {
-            if (getBasePanelAt(i).isSaving()) {
-                // There is a database still being saved, so we need to wait.
-                WaitForSaveOperation w = new WaitForSaveOperation(this);
-                w.show(); // This method won't return until canceled or the save operation is done.
-                if (w.canceled()) {
-                    return false; // The user clicked cancel.
-                }
-            }
-        }
+        WaitForSaveFinishedDialog waitForSaveFinishedDialog = new WaitForSaveFinishedDialog(dialogService);
+        waitForSaveFinishedDialog.showAndWait(getBasePanelList());
 
         // Good bye!
         tearDownJabRef(filenames);
diff --git a/src/main/java/org/jabref/gui/WaitForSaveFinishedDialog.java b/src/main/java/org/jabref/gui/WaitForSaveFinishedDialog.java
new file mode 100644
index 00000000000..f8758ab8e1e
--- /dev/null
+++ b/src/main/java/org/jabref/gui/WaitForSaveFinishedDialog.java
@@ -0,0 +1,43 @@
+package org.jabref.gui;
+
+import java.util.List;
+
+import javafx.concurrent.Task;
+
+import org.jabref.logic.l10n.Localization;
+
+/**
+ * Dialog shown when closing of application needs to wait for a save operation to finish.
+ */
+public class WaitForSaveFinishedDialog {
+
+    private final DialogService dialogService;
+
+    public WaitForSaveFinishedDialog(DialogService dialogService) {
+        this.dialogService = dialogService;
+    }
+
+    public void showAndWait(List<BasePanel> basePanels) {
+        if (basePanels.stream().anyMatch(BasePanel::isSaving)) {
+            Task<Void> waitForSaveFinished = new Task<Void>() {
+                @Override
+                protected Void call() throws Exception {
+                    while (basePanels.stream().anyMatch(BasePanel::isSaving)) {
+                        if (isCancelled()) {
+                            return null;
+                        } else {
+                            Thread.sleep(100);
+                        }
+                    }
+                    return null;
+                }
+            };
+
+            dialogService.showProgressDialogAndWait(
+                    Localization.lang("Please wait..."),
+                    Localization.lang("Waiting for save operation to finish") + "...",
+                    waitForSaveFinished
+            );
+        }
+    }
+}
diff --git a/src/main/java/org/jabref/gui/WaitForSaveOperation.java b/src/main/java/org/jabref/gui/WaitForSaveOperation.java
deleted file mode 100644
index 86b2e0a2f8b..00000000000
--- a/src/main/java/org/jabref/gui/WaitForSaveOperation.java
+++ /dev/null
@@ -1,82 +0,0 @@
-package org.jabref.gui;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.BorderFactory;
-import javax.swing.JButton;
-import javax.swing.JDialog;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JProgressBar;
-import javax.swing.Timer;
-
-import org.jabref.logic.l10n.Localization;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-
-/**
- * Dialog shown when closing of application needs to wait for a save operation to finish.
- */
-public class WaitForSaveOperation implements ActionListener {
-
-    private final JabRefFrame frame;
-    private final JDialog diag;
-    private final Timer t = new Timer(500, this);
-    private boolean canceled;
-
-
-    public WaitForSaveOperation(JabRefFrame frame) {
-        this.frame = frame;
-
-        JButton cancel = new JButton(Localization.lang("Cancel"));
-        JProgressBar prog = new JProgressBar(0);
-        prog.setIndeterminate(true);
-        prog.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-        diag = new JDialog((JFrame) null, Localization.lang("Please wait..."), true);
-
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        bb.addButton(cancel);
-        bb.addGlue();
-        cancel.addActionListener(e -> {
-            canceled = true;
-            t.stop();
-            diag.dispose();
-        });
-
-        JLabel message = new JLabel(Localization.lang("Waiting for save operation to finish") + "...");
-        message.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        diag.getContentPane().add(message, BorderLayout.NORTH);
-        diag.getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-        diag.getContentPane().add(prog, BorderLayout.CENTER);
-        diag.pack();
-    }
-
-    public void show() {
-        t.start();
-        diag.setVisible(true);
-
-    }
-
-    public boolean canceled() {
-        return canceled;
-    }
-
-    @Override
-    public void actionPerformed(ActionEvent actionEvent) {
-        boolean anySaving = false;
-        for (BasePanel basePanel : frame.getBasePanelList()) {
-            if (basePanel.isSaving()) {
-                anySaving = true;
-                break;
-            }
-        }
-        if (!anySaving) {
-            t.stop();
-            diag.dispose();
-        }
-    }
-}

From fa73ea0246d75077a4fe20b73c4bfaa077645d00 Mon Sep 17 00:00:00 2001
From: Chelsey Ong <chelseyong@gmail.com>
Date: Fri, 8 Mar 2019 09:37:08 +0700
Subject: [PATCH 083/184] Extract authN method

---
 .../bibtexkeypattern/BracketedPattern.java    | 22 +++++++++++--------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
index 12d9a1d93bb..36e11757552 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
@@ -228,16 +228,8 @@ else if ("authorLast".equals(val)) {
                     return authNofMth(authString, Integer.parseInt(nums[0]),
                             Integer.parseInt(nums[1]));
                 } else if (val.matches("auth\\d+")) {
-                    // authN. First N chars of the first author's last
-                    // name.
-
-                    authString = BibtexKeyGenerator.cleanKey(authString, isEnforceLegalKey);
-                    String fa = firstAuthor(authString);
                     int num = Integer.parseInt(val.substring(4));
-                    if (num > fa.length()) {
-                        num = fa.length();
-                    }
-                    return fa.substring(0, num);
+                    return authN(authString, num, isEnforceLegalKey);
                 } else if (val.matches("authors\\d+")) {
                     return nAuthors(authString, Integer.parseInt(val.substring(7)));
                 } else {
@@ -845,6 +837,18 @@ public static String authNofMth(String authorField, int n, int m) {
         }
     }
 
+    /**
+     * First N chars of the first author's last name.
+     */
+    public static String authN(String authString, int num, boolean isEnforceLegalKey) {
+        authString = BibtexKeyGenerator.cleanKey(authString, isEnforceLegalKey);
+        String fa = firstAuthor(authString);
+        if (num > fa.length()) {
+            num = fa.length();
+        }
+        return fa.substring(0, num);
+    }
+
     /**
      * authshort format:
      * added by Kolja Brix, kbx@users.sourceforge.net

From f71ed752b2f6822ddc7317b4ff395594841fe4da Mon Sep 17 00:00:00 2001
From: Ronak Lakhotia <ronak.lakhotia999@gmail.com>
Date: Fri, 8 Mar 2019 18:07:35 +0800
Subject: [PATCH 084/184] Add key bindings (#4732)

---
 src/main/java/org/jabref/gui/actions/StandardActions.java | 4 ++--
 src/main/java/org/jabref/gui/keyboard/KeyBinding.java     | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
index b3b10e3aeaa..302bc7359bd 100644
--- a/src/main/java/org/jabref/gui/actions/StandardActions.java
+++ b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -65,7 +65,7 @@ public enum StandardActions implements Action {
     NEW_LIBRARY_BIBLATEX(Localization.lang("New %0 library", BibDatabaseMode.BIBLATEX.getFormattedName())),
     OPEN_LIBRARY(Localization.lang("Open library"), IconTheme.JabRefIcons.OPEN, KeyBinding.OPEN_DATABASE),
     IMPORT(Localization.lang("Import"), IconTheme.JabRefIcons.IMPORT),
-    EXPORT(Localization.lang("Export"), IconTheme.JabRefIcons.EXPORT),
+    EXPORT(Localization.lang("Export"), IconTheme.JabRefIcons.EXPORT, KeyBinding.EXPORT),
     MERGE_DATABASE(Localization.lang("Append library"), Localization.lang("Append contents from a BibTeX library into the currently viewed library")),
     SAVE_LIBRARY(Localization.lang("Save library"), IconTheme.JabRefIcons.SAVE, KeyBinding.SAVE_DATABASE),
     SAVE_LIBRARY_AS(Localization.lang("Save library as..."), KeyBinding.SAVE_DATABASE_AS),
@@ -74,7 +74,7 @@ public enum StandardActions implements Action {
     IMPORT_INTO_NEW_LIBRARY(Localization.lang("Import into new library"), KeyBinding.IMPORT_INTO_NEW_DATABASE),
     IMPORT_INTO_CURRENT_LIBRARY(Localization.lang("Import into current library"), KeyBinding.IMPORT_INTO_CURRENT_DATABASE),
     EXPORT_ALL(Localization.lang("Export all entries")),
-    EXPORT_SELECTED(Localization.lang("Export selected entries")),
+    EXPORT_SELECTED(Localization.lang("Export selected entries"), KeyBinding.EXPORT_SELECTED),
     CONNECT_TO_SHARED_DB(Localization.lang("Connect to shared database"), IconTheme.JabRefIcons.CONNECT_DB),
     PULL_CHANGES_FROM_SHARED_DB(Localization.lang("Pull changes from shared database"), KeyBinding.PULL_CHANGES_FROM_SHARED_DATABASE),
     CLOSE_LIBRARY(Localization.lang("Close library"), Localization.lang("Close the current library"), IconTheme.JabRefIcons.CLOSE, KeyBinding.CLOSE_DATABASE),
diff --git a/src/main/java/org/jabref/gui/keyboard/KeyBinding.java b/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
index b73fbc6b0c3..b1b2cbbb4b5 100644
--- a/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
+++ b/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
@@ -28,6 +28,8 @@ public enum KeyBinding {
     DEFAULT_DIALOG_ACTION("Execute default action in dialog", Localization.lang("Execute default action in dialog"), "ctrl+ENTER", KeyBindingCategory.VIEW),
     DOWNLOAD_FULL_TEXT("Look up full text documents", Localization.lang("Look up full text documents"), "alt+F7", KeyBindingCategory.QUALITY),
     EDIT_ENTRY("Edit entry", Localization.lang("Edit entry"), "ctrl+E", KeyBindingCategory.BIBTEX),
+    EXPORT("Export", Localization.lang("Export"), "ctrl+alt+e", KeyBindingCategory.FILE),
+    EXPORT_SELECTED("Export Selected", Localization.lang("Export selected entries"), "ctrl+shift+e", KeyBindingCategory.FILE),
     EDIT_STRINGS("Edit strings", Localization.lang("Edit strings"), "ctrl+T", KeyBindingCategory.BIBTEX),
     ENTRY_EDITOR_NEXT_ENTRY("Entry editor, next entry", Localization.lang("Entry editor, next entry"), "alt+DOWN", KeyBindingCategory.VIEW),
     ENTRY_EDITOR_NEXT_PANEL("Entry editor, next panel", Localization.lang("Entry editor, next panel"), "ctrl+TAB", KeyBindingCategory.VIEW),

From 4d1738d34dba565a7ab14eeb499995afebca9be7 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Fri, 8 Mar 2019 11:09:40 +0100
Subject: [PATCH 085/184] Fix default import format pattern (#4731)

Remove Display Array
Add migration
Fixe #4724
---
 .../jabref/gui/preferences/ImportSettingsTab.java    | 12 +++++-------
 .../org/jabref/migrations/PreferencesMigrations.java |  8 +++++++-
 .../jabref/migrations/PreferencesMigrationsTest.java |  2 +-
 3 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/main/java/org/jabref/gui/preferences/ImportSettingsTab.java b/src/main/java/org/jabref/gui/preferences/ImportSettingsTab.java
index 3067882b2c2..80873eab063 100644
--- a/src/main/java/org/jabref/gui/preferences/ImportSettingsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ImportSettingsTab.java
@@ -9,24 +9,20 @@
 import javafx.scene.control.Separator;
 import javafx.scene.control.TextField;
 import javafx.scene.layout.GridPane;
-import javafx.scene.layout.Pane;
 
 import org.jabref.logic.l10n.Localization;
 import org.jabref.preferences.JabRefPreferences;
 
-public class ImportSettingsTab extends Pane implements PrefsTab {
+public class ImportSettingsTab implements PrefsTab {
 
     public static final String[] DEFAULT_FILENAMEPATTERNS = new String[] {"[bibtexkey]",
-            "[bibtexkey] - [title]"};
-
-    private static final String[] DEFAULT_FILENAMEPATTERNS_DISPLAY = new String[] {"bibtexkey", "bibtexkey - title",};
+                                                                          "[bibtexkey] - [title]"};
 
     private final JabRefPreferences prefs;
     private final GridPane builder = new GridPane();
     private final TextField fileNamePattern;
     private final ComboBox<String> selectFileNamePattern;
 
-
     private final TextField fileDirPattern;
 
     public ImportSettingsTab(JabRefPreferences prefs) {
@@ -35,8 +31,9 @@ public ImportSettingsTab(JabRefPreferences prefs) {
         fileNamePattern = new TextField();
         fileDirPattern = new TextField();
         selectFileNamePattern = new ComboBox<>();
-        selectFileNamePattern.getItems().addAll(FXCollections.observableArrayList(DEFAULT_FILENAMEPATTERNS_DISPLAY));
+        selectFileNamePattern.getItems().addAll(FXCollections.observableArrayList(DEFAULT_FILENAMEPATTERNS));
         selectFileNamePattern.setValue(Localization.lang("Choose pattern"));
+
         selectFileNamePattern.setOnAction(e -> {
             fileNamePattern.setText(selectFileNamePattern.getValue());
         });
@@ -60,6 +57,7 @@ public ImportSettingsTab(JabRefPreferences prefs) {
         builder.add(fileDirPattern, 2, 10);
     }
 
+    @Override
     public Node getBuilder() {
         return builder;
     }
diff --git a/src/main/java/org/jabref/migrations/PreferencesMigrations.java b/src/main/java/org/jabref/migrations/PreferencesMigrations.java
index f0923915177..70a4357ef3b 100644
--- a/src/main/java/org/jabref/migrations/PreferencesMigrations.java
+++ b/src/main/java/org/jabref/migrations/PreferencesMigrations.java
@@ -237,10 +237,16 @@ static void upgradeImportFileAndDirePatterns(JabRefPreferences prefs, Preference
             String[] oldStylePatterns = new String[] {"\\bibtexkey",
                                                       "\\bibtexkey\\begin{title} - \\format[RemoveBrackets]{\\title}\\end{title}"};
             String[] newStylePatterns = new String[] {"[bibtexkey]",
-                                                      "[bibtexkey] - [fulltitle]"};
+                                                      "[bibtexkey] - [title]"};
+
+            String[] oldDisplayStylePattern = new String[] {"bibtexkey", "bibtexkey - title",};
+
             for (int i = 0; i < oldStylePatterns.length; i++) {
                 migrateFileImportPattern(oldStylePatterns[i], newStylePatterns[i], prefs, mainPrefsNode);
             }
+            for (int i = 0; i < oldDisplayStylePattern.length; i++) {
+                migrateFileImportPattern(oldDisplayStylePattern[i], newStylePatterns[i], prefs, mainPrefsNode);
+            }
         }
         // Directory preferences are not yet migrated, since it is not quote clear how to parse and reinterpret
         // the user defined old-style patterns, and the default pattern is "".
diff --git a/src/test/java/org/jabref/migrations/PreferencesMigrationsTest.java b/src/test/java/org/jabref/migrations/PreferencesMigrationsTest.java
index c646bab55bb..6a2ee9bc5e8 100644
--- a/src/test/java/org/jabref/migrations/PreferencesMigrationsTest.java
+++ b/src/test/java/org/jabref/migrations/PreferencesMigrationsTest.java
@@ -20,7 +20,7 @@ class PreferencesMigrationsTest {
     private final String[] oldStylePatterns = new String[]{"\\bibtexkey",
             "\\bibtexkey\\begin{title} - \\format[RemoveBrackets]{\\title}\\end{title}"};
     private final String[] newStylePatterns = new String[]{"[bibtexkey]",
-            "[bibtexkey] - [fulltitle]"};
+                                                            "[bibtexkey] - [title]"};
 
     @BeforeEach
     void setUp() {

From 7650a9f2c597711363f85d96f789df5556762fb9 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Fri, 8 Mar 2019 14:10:31 +0100
Subject: [PATCH 086/184] Fix entry preview copy exception (#4721)

* Fix entry preview copy exception


Fixes #4714

* add new method

* renamings
---
 src/main/java/org/jabref/gui/BasePanel.java   |   9 +-
 .../CitationStyleToClipboardWorker.java       | 141 +++++++++---------
 2 files changed, 76 insertions(+), 74 deletions(-)

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index 330b0e76eec..812335db076 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -418,7 +418,8 @@ private void setupActions() {
      * @param outputFormat the desired {@link CitationStyleOutputFormat}
      */
     private void copyCitationToClipboard(CitationStyleOutputFormat outputFormat) {
-        new CitationStyleToClipboardWorker(this, outputFormat).execute();
+        CitationStyleToClipboardWorker worker = new CitationStyleToClipboardWorker(this, outputFormat, dialogService, Globals.clipboardManager, Globals.prefs.getPreviewPreferences());
+        worker.copyCitationStyleToClipboard(Globals.TASK_EXECUTOR);
     }
 
     /**
@@ -964,7 +965,7 @@ public void entryEditorClosing(EntryEditor editor) {
      */
     public void ensureNotShowingBottomPanel(BibEntry entry) {
         if (((mode == BasePanelMode.SHOWING_EDITOR) && (entryEditor.getEntry() == entry))
-        || ((mode == BasePanelMode.SHOWING_PREVIEW) && (preview.getEntry() == entry))) {
+            || ((mode == BasePanelMode.SHOWING_PREVIEW) && (preview.getEntry() == entry))) {
             closeBottomPane();
         }
     }
@@ -1394,8 +1395,8 @@ public void action() {
 
                     Optional<LinkedFile> linkedFile = files.stream()
                                                            .filter(file -> (FieldName.URL.equalsIgnoreCase(file.getFileType())
-                                                           || FieldName.PS.equalsIgnoreCase(file.getFileType())
-                                                           || FieldName.PDF.equalsIgnoreCase(file.getFileType())))
+                                                                            || FieldName.PS.equalsIgnoreCase(file.getFileType())
+                                                                            || FieldName.PDF.equalsIgnoreCase(file.getFileType())))
                                                            .findFirst();
 
                     if (linkedFile.isPresent()) {
diff --git a/src/main/java/org/jabref/gui/worker/CitationStyleToClipboardWorker.java b/src/main/java/org/jabref/gui/worker/CitationStyleToClipboardWorker.java
index 73fe46be70d..6308ce55d7a 100644
--- a/src/main/java/org/jabref/gui/worker/CitationStyleToClipboardWorker.java
+++ b/src/main/java/org/jabref/gui/worker/CitationStyleToClipboardWorker.java
@@ -1,17 +1,18 @@
 package org.jabref.gui.worker;
 
+import java.io.IOException;
 import java.io.StringReader;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.concurrent.ExecutionException;
-
-import javax.swing.SwingWorker;
 
 import javafx.scene.input.ClipboardContent;
 
 import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.ClipBoardManager;
+import org.jabref.gui.DialogService;
+import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.citationstyle.CitationStyle;
 import org.jabref.logic.citationstyle.CitationStyleGenerator;
 import org.jabref.logic.citationstyle.CitationStyleOutputFormat;
@@ -30,7 +31,7 @@
  * Copies the selected entries and formats them with the selected citation style (or preview), then it is copied to the clipboard.
  * This worker cannot be reused.
  */
-public class CitationStyleToClipboardWorker extends SwingWorker<List<String>, Void> {
+public class CitationStyleToClipboardWorker {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(CitationStyleToClipboardWorker.class);
 
@@ -39,29 +40,36 @@ public class CitationStyleToClipboardWorker extends SwingWorker<List<String>, Vo
     private final String style;
     private final String previewStyle;
     private final CitationStyleOutputFormat outputFormat;
+    private final DialogService dialogService;
+    private final ClipBoardManager clipBoardManager;
 
-
-    public CitationStyleToClipboardWorker(BasePanel basePanel, CitationStyleOutputFormat outputFormat) {
+    public CitationStyleToClipboardWorker(BasePanel basePanel, CitationStyleOutputFormat outputFormat, DialogService dialogService, ClipBoardManager clipBoardManager, PreviewPreferences previewPreferences) {
         this.basePanel = basePanel;
         this.selectedEntries = basePanel.getSelectedEntries();
-        PreviewPreferences previewPreferences = Globals.prefs.getPreviewPreferences();
         this.style = previewPreferences.getPreviewCycle().get(previewPreferences.getPreviewCyclePosition());
-        this.previewStyle = Globals.prefs.getPreviewPreferences().getPreviewStyle();
+        this.previewStyle = previewPreferences.getPreviewStyle();
         this.outputFormat = outputFormat;
+        this.clipBoardManager = clipBoardManager;
+        this.dialogService = dialogService;
+    }
 
-        basePanel.frame().setStatus(Localization.lang("Copying..."));
+    public void copyCitationStyleToClipboard(TaskExecutor taskExecutor) {
+        dialogService.notify(Localization.lang("Copying..."));
+        BackgroundTask.wrap(this::generateCitations)
+                      .onFailure(ex -> LOGGER.error("Error while copying citations to the clipboard", ex))
+                      .onSuccess(this::setClipBoardContent)
+                      .executeWith(taskExecutor);
     }
 
-    @Override
-    protected List<String> doInBackground() throws Exception {
+    private List<String> generateCitations() throws IOException {
         // This worker stored the style as filename. The CSLAdapter and the CitationStyleCache store the source of the
         // style. Therefore, we extract the style source from the file.
         String styleSource = null;
         if (CitationStyle.isCitationStyleFile(style)) {
             styleSource = CitationStyle.createCitationStyleFromFile(style)
-                    .filter(citationStyleFromFile -> !citationStyleFromFile.getSource().isEmpty())
-                    .map(CitationStyle::getSource)
-                    .orElse(null);
+                                       .filter(citationStyleFromFile -> !citationStyleFromFile.getSource().isEmpty())
+                                       .map(CitationStyle::getSource)
+                                       .orElse(null);
         }
         if (styleSource != null) {
             return CitationStyleGenerator.generateCitations(selectedEntries, styleSource, outputFormat);
@@ -100,8 +108,8 @@ protected static ClipboardContent processText(List<String> citations) {
      */
     protected static ClipboardContent processRtf(List<String> citations) {
         String result = "{\\rtf" + OS.NEWLINE +
-                String.join(CitationStyleOutputFormat.RTF.getLineSeparator(), citations) +
-                "}";
+                        String.join(CitationStyleOutputFormat.RTF.getLineSeparator(), citations) +
+                        "}";
         ClipboardContent content = new ClipboardContent();
         content.putRtf(result);
         return content;
@@ -112,21 +120,21 @@ protected static ClipboardContent processRtf(List<String> citations) {
      */
     protected static ClipboardContent processXslFo(List<String> citations) {
         String result = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" + OS.NEWLINE +
-                "<fo:root xmlns:fo=\"http://www.w3.org/1999/XSL/Format\">" + OS.NEWLINE +
-                "   <fo:layout-master-set>" + OS.NEWLINE +
-                "      <fo:simple-page-master master-name=\"citations\">" + OS.NEWLINE +
-                "         <fo:region-body/>" + OS.NEWLINE +
-                "      </fo:simple-page-master>" + OS.NEWLINE +
-                "   </fo:layout-master-set>" + OS.NEWLINE +
-                "   <fo:page-sequence master-reference=\"citations\">" + OS.NEWLINE +
-                "      <fo:flow flow-name=\"xsl-region-body\">" + OS.NEWLINE + OS.NEWLINE;
+                        "<fo:root xmlns:fo=\"http://www.w3.org/1999/XSL/Format\">" + OS.NEWLINE +
+                        "   <fo:layout-master-set>" + OS.NEWLINE +
+                        "      <fo:simple-page-master master-name=\"citations\">" + OS.NEWLINE +
+                        "         <fo:region-body/>" + OS.NEWLINE +
+                        "      </fo:simple-page-master>" + OS.NEWLINE +
+                        "   </fo:layout-master-set>" + OS.NEWLINE +
+                        "   <fo:page-sequence master-reference=\"citations\">" + OS.NEWLINE +
+                        "      <fo:flow flow-name=\"xsl-region-body\">" + OS.NEWLINE + OS.NEWLINE;
 
         result += String.join(CitationStyleOutputFormat.XSL_FO.getLineSeparator(), citations);
 
         result += OS.NEWLINE +
-                "      </fo:flow>" + OS.NEWLINE +
-                "   </fo:page-sequence>" + OS.NEWLINE +
-                "</fo:root>" + OS.NEWLINE;
+                  "      </fo:flow>" + OS.NEWLINE +
+                  "   </fo:page-sequence>" + OS.NEWLINE +
+                  "</fo:root>" + OS.NEWLINE;
 
         ClipboardContent content = new ClipboardContent();
         content.put(ClipBoardManager.XML, result);
@@ -138,59 +146,52 @@ protected static ClipboardContent processXslFo(List<String> citations) {
      */
     protected static ClipboardContent processHtml(List<String> citations) {
         String result = "<!DOCTYPE html>" + OS.NEWLINE +
-                "<html>" + OS.NEWLINE +
-                "   <head>" + OS.NEWLINE +
-                "      <meta charset=\"utf-8\">" + OS.NEWLINE +
-                "   </head>" + OS.NEWLINE +
-                "   <body>" + OS.NEWLINE + OS.NEWLINE;
+                        "<html>" + OS.NEWLINE +
+                        "   <head>" + OS.NEWLINE +
+                        "      <meta charset=\"utf-8\">" + OS.NEWLINE +
+                        "   </head>" + OS.NEWLINE +
+                        "   <body>" + OS.NEWLINE + OS.NEWLINE;
 
         result += String.join(CitationStyleOutputFormat.HTML.getLineSeparator(), citations);
-
         result += OS.NEWLINE +
-                "   </body>" + OS.NEWLINE +
-                "</html>" + OS.NEWLINE;
+                  "   </body>" + OS.NEWLINE +
+                  "</html>" + OS.NEWLINE;
 
         ClipboardContent content = new ClipboardContent();
         content.putHtml(result);
         return content;
     }
 
-    @Override
-    public void done() {
-        try {
-            List<String> citations = get();
-
-            // if it's not a citation style take care of the preview
-            if (!CitationStyle.isCitationStyleFile(style)) {
-                Globals.clipboardManager.setHtmlContent(processPreview(citations));
-            } else {
-                // if it's generated by a citation style take care of each output format
-                ClipboardContent content;
-                switch (outputFormat) {
-                    case HTML:
-                        content = processHtml(citations);
-                        break;
-                    case RTF:
-                        content = processRtf(citations);
-                        break;
-                    case XSL_FO:
-                        content = processXslFo(citations);
-                        break;
-                    case ASCII_DOC:
-                    case TEXT:
-                        content = processText(citations);
-                        break;
-                    default:
-                        LOGGER.warn("unknown output format: '" + outputFormat + "', processing it via the default.");
-                        content = processText(citations);
-                        break;
-                }
-                Globals.clipboardManager.setContent(content);
+    private void setClipBoardContent(List<String> citations) {
+        // if it's not a citation style take care of the preview
+        if (!CitationStyle.isCitationStyleFile(style)) {
+            clipBoardManager.setHtmlContent(processPreview(citations));
+        } else {
+            // if it's generated by a citation style take care of each output format
+            ClipboardContent content;
+            switch (outputFormat) {
+                case HTML:
+                    content = processHtml(citations);
+                    break;
+                case RTF:
+                    content = processRtf(citations);
+                    break;
+                case XSL_FO:
+                    content = processXslFo(citations);
+                    break;
+                case ASCII_DOC:
+                case TEXT:
+                    content = processText(citations);
+                    break;
+                default:
+                    LOGGER.warn("unknown output format: '" + outputFormat + "', processing it via the default.");
+                    content = processText(citations);
+                    break;
             }
-
-            basePanel.frame().setStatus(Localization.lang("Copied %0 citations.", String.valueOf(selectedEntries.size())));
-        } catch (InterruptedException | ExecutionException e) {
-            LOGGER.error("Error while copying citations to the clipboard", e);
+            clipBoardManager.setContent(content);
         }
+
+        dialogService.notify(Localization.lang("Copied %0 citations.", String.valueOf(selectedEntries.size())));
     }
+
 }

From f1de7bddeb3e643e8114f61dda789b8a04324d00 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 8 Mar 2019 15:26:12 +0100
Subject: [PATCH 087/184] Remove add/move/remove from group dialog (#4695)

* Remove add/move/remove from group dialog

* Update CHANGELOG.md
---
 CHANGELOG.md                                  |   1 +
 src/main/java/org/jabref/gui/BasePanel.java   |   5 -
 .../java/org/jabref/gui/actions/Actions.java  |   3 -
 .../jabref/gui/actions/StandardActions.java   |   3 -
 .../gui/groups/GroupAddRemoveDialog.java      | 227 ------------------
 .../jabref/gui/maintable/RightClickMenu.java  |  29 ---
 src/main/resources/l10n/JabRef_en.properties  |   4 -
 7 files changed, 1 insertion(+), 271 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/groups/GroupAddRemoveDialog.java

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a262139b69b..eecbaff3814 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -111,6 +111,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
   - Set/clear/append/rename fields: available through Edit menu
   - Manage keywords: available through Edit menu
   - Copy linked files to folder: available through File menu
+  - Add/move/remove from group: removed completely (functionality still available through group interface)
 - We removed the option to change the column widths in the preferences dialog. [#4546](https://github.com/JabRef/jabref/issues/4546)
 
 
diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index 812335db076..89d54058434 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -52,7 +52,6 @@
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.filelist.FileListEntry;
 import org.jabref.gui.filelist.FileListTableModel;
-import org.jabref.gui.groups.GroupAddRemoveDialog;
 import org.jabref.gui.icon.JabRefIcon;
 import org.jabref.gui.importer.actions.AppendDatabaseAction;
 import org.jabref.gui.journals.AbbreviateAction;
@@ -405,10 +404,6 @@ private void setupActions() {
         actions.put(Actions.ABBREVIATE_MEDLINE, new AbbreviateAction(this, false));
         actions.put(Actions.UNABBREVIATE, new UnabbreviateAction(this));
 
-        actions.put(Actions.ADD_TO_GROUP, new GroupAddRemoveDialog(this, true, false));
-        actions.put(Actions.REMOVE_FROM_GROUP, new GroupAddRemoveDialog(this, false, false));
-        actions.put(Actions.MOVE_TO_GROUP, new GroupAddRemoveDialog(this, true, true));
-
         actions.put(Actions.DOWNLOAD_FULL_TEXT, new FindFullTextAction(this)::execute);
     }
 
diff --git a/src/main/java/org/jabref/gui/actions/Actions.java b/src/main/java/org/jabref/gui/actions/Actions.java
index c3776047608..f115eda059c 100644
--- a/src/main/java/org/jabref/gui/actions/Actions.java
+++ b/src/main/java/org/jabref/gui/actions/Actions.java
@@ -8,7 +8,6 @@ public enum Actions {
     ABBREVIATE_ISO,
     ABBREVIATE_MEDLINE,
     ADD_FILE_LINK,
-    ADD_TO_GROUP,
     CLEANUP,
     COPY,
     COPY_CITATION_ASCII_DOC,
@@ -34,7 +33,6 @@ public enum Actions {
     MERGE_ENTRIES,
     MERGE_WITH_FETCHED_ENTRY,
     NEXT_PREVIEW_STYLE,
-    MOVE_TO_GROUP,
     OPEN_CONSOLE,
     OPEN_EXTERNAL_FILE,
     OPEN_FOLDER,
@@ -43,7 +41,6 @@ public enum Actions {
     PREVIOUS_PREVIEW_STYLE,
     PULL_CHANGES_FROM_SHARED_DATABASE,
     REDO,
-    REMOVE_FROM_GROUP,
     REPLACE_ALL,
     SAVE,
     SAVE_AS,
diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
index f6e843de78d..6e7493f32d7 100644
--- a/src/main/java/org/jabref/gui/actions/StandardActions.java
+++ b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -35,9 +35,6 @@ public enum StandardActions implements Action {
     OPEN_URL(Localization.lang("Open URL or DOI"), IconTheme.JabRefIcons.WWW, KeyBinding.OPEN_URL_OR_DOI),
     MERGE_WITH_FETCHED_ENTRY(Localization.lang("Get BibTeX data from %0", "DOI/ISBN/...")),
     ATTACH_FILE(Localization.lang("Attach file"), IconTheme.JabRefIcons.ATTACH_FILE),
-    ADD_TO_GROUP(Localization.lang("Add to group")),
-    REMOVE_FROM_GROUP(Localization.lang("Remove from group")),
-    MOVE_TO_GROUP(Localization.lang("Move to group")),
     PRIORITY(Localization.lang("Priority"), IconTheme.JabRefIcons.PRIORITY),
     CLEAR_PRIORITY(Localization.lang("Clear priority")),
     PRIORITY_HIGH(Localization.lang("Set priority to high"), IconTheme.JabRefIcons.PRIORITY_HIGH),
diff --git a/src/main/java/org/jabref/gui/groups/GroupAddRemoveDialog.java b/src/main/java/org/jabref/gui/groups/GroupAddRemoveDialog.java
deleted file mode 100644
index 870af219e7b..00000000000
--- a/src/main/java/org/jabref/gui/groups/GroupAddRemoveDialog.java
+++ /dev/null
@@ -1,227 +0,0 @@
-package org.jabref.gui.groups;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.event.ActionEvent;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Optional;
-
-import javax.swing.AbstractAction;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JFrame;
-import javax.swing.JScrollPane;
-import javax.swing.JTree;
-import javax.swing.SwingUtilities;
-import javax.swing.tree.DefaultTreeModel;
-import javax.swing.tree.TreeNode;
-import javax.swing.tree.TreePath;
-import javax.swing.tree.TreeSelectionModel;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.actions.BaseAction;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.groups.GroupTreeNode;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-
-public class GroupAddRemoveDialog implements BaseAction {
-
-    private final BasePanel panel;
-    private final boolean add;
-    private final boolean move;
-    private List<BibEntry> selection;
-    private JTree tree;
-
-    public GroupAddRemoveDialog(BasePanel panel, boolean add, boolean move) {
-        this.panel = panel;
-        this.add = add;
-        this.move = move;
-    }
-
-    @Override
-    public void action() throws Exception {
-        Optional<GroupTreeNode> groups = panel.getBibDatabaseContext().getMetaData().getGroups();
-        if (!groups.isPresent()) {
-            return;
-        }
-
-        selection = panel.getSelectedEntries();
-
-        final JDialog diag = new JDialog((JFrame) null,
-                                         (add ? (move ? Localization.lang("Move to group") : Localization.lang("Add to group")) : Localization
-                                                                                                                                              .lang("Remove from group")),
-                                         true);
-        JButton ok = new JButton(Localization.lang("OK"));
-        JButton cancel = new JButton(Localization.lang("Cancel"));
-        tree = new JTree(new GroupTreeNodeViewModel(groups.get()));
-        tree.setCellRenderer(new AddRemoveGroupTreeCellRenderer());
-        tree.setVisibleRowCount(22);
-
-        //        tree.setPreferredSize(new Dimension(200, tree.getPreferredSize().height));
-        //      The scrollbar appears when the preferred size of a component is greater than the size of the viewport. If one hard coded the preferred size, it will never change according to the expansion/collapse. Thus the scrollbar cannot appear accordingly.
-        //tree.setSelectionModel(new VetoableTreeSelectionModel());
-        tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
-        tree.addTreeSelectionListener(e -> {
-            GroupTreeNodeViewModel node = (GroupTreeNodeViewModel) e.getNewLeadSelectionPath().getLastPathComponent();
-            ok.setEnabled(checkGroupEnable(node));
-        });
-
-        //STA add expand and collapse all buttons
-        JButton jbExpandAll = new JButton("Expand All");
-
-        jbExpandAll.addActionListener(e -> expandAll(tree, true));
-
-        JButton jbCollapseAll = new JButton("Collapse All");
-        jbCollapseAll.addActionListener(e -> expandAll(tree, false));
-        //END add expand and collapse all buttons
-
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        bb.addButton(ok);
-        bb.addButton(cancel);
-
-        bb.addButton(jbExpandAll);
-        bb.addButton(jbCollapseAll);
-
-        bb.addGlue();
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        ok.addActionListener(actionEvent -> {
-            if (doAddOrRemove()) {
-                diag.dispose();
-                tree.repaint();
-            }
-        });
-        cancel.addActionListener(actionEvent -> diag.dispose());
-        ok.setEnabled(false);
-
-        JScrollPane sp = new JScrollPane(tree);
-
-        // Key bindings:
-        ActionMap am = sp.getActionMap();
-        InputMap im = sp.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                diag.dispose();
-            }
-        });
-
-        diag.getContentPane().add(sp, BorderLayout.CENTER);
-
-        diag.getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-        diag.pack();
-        diag.setVisible(true);
-
-    }
-
-    // If "expand" is true, all nodes in the tree area expanded
-    // otherwise all nodes in the tree are collapsed:
-    private void expandAll(final JTree subtree, final boolean expand) {
-        SwingUtilities.invokeLater(() -> {
-            TreeNode root = ((TreeNode) subtree.getModel().getRoot());
-            // walk through the tree, beginning at the root:
-            expandAll(subtree, new TreePath(((DefaultTreeModel) subtree.getModel()).getPathToRoot(root)), expand);
-            tree.requestFocusInWindow();
-        });
-    }
-
-    private void expandAll(final JTree subtree, final TreePath parent, final boolean expand) {
-        // walk through the children:
-        TreeNode node = (TreeNode) parent.getLastPathComponent();
-        int numChildren = node.getChildCount();
-        if (numChildren > 0) {
-            for (int i = 0; i < numChildren; i++) {
-                TreeNode child = node.getChildAt(i);
-                TreePath path = parent.pathByAddingChild(child);
-                expandAll(subtree, path, expand);
-            }
-        }
-        // "expand" / "collapse" occurs from bottom to top:
-        if (expand) {
-            tree.expandPath(parent);
-        } else {
-            if (node.getParent() != null) {
-                tree.collapsePath(parent);
-            }
-        }
-    }
-
-    private boolean doAddOrRemove() {
-        TreePath path = tree.getSelectionPath();
-        if (path == null) {
-            return false;
-        } else {
-            GroupTreeNodeViewModel node = (GroupTreeNodeViewModel) path.getLastPathComponent();
-            if (checkGroupEnable(node)) {
-
-                //we need to copy the contents of the observable list here, because when removeFromEntries is called,
-                //probably the focus changes to the first entry in the all entries group and thus getSelectedEntries() no longer contains our entry we want to move
-                List<BibEntry> entries = new ArrayList<>(Globals.stateManager.getSelectedEntries());
-
-                if (move) {
-                    recuriveRemoveFromNode((GroupTreeNodeViewModel) tree.getModel().getRoot(), entries);
-                }
-
-                if (add) {
-                    node.addEntriesToGroup(entries);
-                } else {
-                    node.removeEntriesFromGroup(entries);
-                }
-
-                return true;
-            } else {
-                return false;
-            }
-        }
-    }
-
-    private void recuriveRemoveFromNode(GroupTreeNodeViewModel node, List<BibEntry> entries) {
-        node.removeEntriesFromGroup(entries);
-        for (GroupTreeNodeViewModel child : node.getChildren()) {
-            recuriveRemoveFromNode(child, entries);
-        }
-    }
-
-    /**
-     * Check if we can perform the action for this group. Determines whether
-     * the group should be shown in an enabled state, and if selecting it should
-     * leave the Ok button enabled.
-     * @param node The group to check
-     * @return true if this dialog's action can be performed on the group
-     */
-    private boolean checkGroupEnable(GroupTreeNodeViewModel node) {
-        return (add ? node.canAddEntries(selection) : node.canRemoveEntries(selection));
-    }
-
-    class AddRemoveGroupTreeCellRenderer extends GroupTreeCellRenderer {
-
-        @Override
-        public Component getTreeCellRendererComponent(JTree tree, Object value, boolean selected, boolean expanded,
-                                                      boolean leaf, int row, boolean hasFocus) {
-            Component c = super.getTreeCellRendererComponent(tree, value, selected, expanded, leaf, row, hasFocus);
-
-            GroupTreeNodeViewModel node = (GroupTreeNodeViewModel) value;
-            if (checkGroupEnable(node)) {
-                c.setForeground(Color.black);
-            } else {
-                c.setForeground(Color.gray);
-            }
-
-            return c;
-        }
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/maintable/RightClickMenu.java b/src/main/java/org/jabref/gui/maintable/RightClickMenu.java
index f0bd9d61775..3070a50a2b7 100644
--- a/src/main/java/org/jabref/gui/maintable/RightClickMenu.java
+++ b/src/main/java/org/jabref/gui/maintable/RightClickMenu.java
@@ -21,7 +21,6 @@
 import org.jabref.gui.mergeentries.FetchAndMergeEntry;
 import org.jabref.gui.specialfields.SpecialFieldMenuItemFactory;
 import org.jabref.logic.citationstyle.CitationStyle;
-import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.specialfields.SpecialField;
@@ -85,33 +84,9 @@ public static ContextMenu create(BibEntryTableViewModel entry, KeyBindingReposit
         contextMenu.getItems().add(factory.createMenuItem(StandardActions.ATTACH_FILE, new AttachFileAction(panel, dialogService)));
         contextMenu.getItems().add(factory.createMenuItem(StandardActions.MERGE_ENTRIES, mergeEntries(panel)));
 
-        contextMenu.getItems().add(new SeparatorMenuItem());
-
-        contextMenu.getItems().add(factory.createMenuItem(StandardActions.ADD_TO_GROUP, addToGroup(panel)));
-        contextMenu.getItems().add(factory.createMenuItem(StandardActions.REMOVE_FROM_GROUP, removeFromGroup(panel)));
-        contextMenu.getItems().add(factory.createMenuItem(StandardActions.MOVE_TO_GROUP, moveToGroup(panel)));
-
         return contextMenu;
     }
 
-    private static OldCommandWrapper moveToGroup(BasePanel panel) {
-        OldCommandWrapper command = new OldCommandWrapper(Actions.MOVE_TO_GROUP, panel);
-        command.setExecutable(areGroupsPresent(panel.getBibDatabaseContext()));
-        return command;
-    }
-
-    private static OldCommandWrapper removeFromGroup(BasePanel panel) {
-        OldCommandWrapper command = new OldCommandWrapper(Actions.REMOVE_FROM_GROUP, panel);
-        command.setExecutable(areGroupsPresent(panel.getBibDatabaseContext()));
-        return command;
-    }
-
-    private static OldCommandWrapper addToGroup(BasePanel panel) {
-        OldCommandWrapper command = new OldCommandWrapper(Actions.ADD_TO_GROUP, panel);
-        command.setExecutable(areGroupsPresent(panel.getBibDatabaseContext()));
-        return command;
-    }
-
     private static OldCommandWrapper mergeEntries(BasePanel panel) {
         OldCommandWrapper command = new OldCommandWrapper(Actions.MERGE_ENTRIES, panel);
         command.setExecutable(panel.getMainTable().getSelectedEntries().size() == 2);
@@ -169,10 +144,6 @@ private static Menu createCopySubMenu(BasePanel panel, ActionFactory factory, Di
         return copySpecialMenu;
     }
 
-    private static boolean areGroupsPresent(BibDatabaseContext database) {
-        return database.getMetaData().getGroups().isPresent();
-    }
-
     private static boolean isFieldSetForSelectedEntry(String field, BasePanel panel) {
         return isAnyFieldSetForSelectedEntry(Collections.singletonList(field), panel);
     }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index b7f8e0dd5ea..54ccec1845d 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -801,8 +801,6 @@ Remove\ selected\ entries\ from\ this\ group=Remove selected entries from this g
 
 Remove\ entry\ type=Remove entry type
 
-Remove\ from\ group=Remove from group
-
 Remove\ group=Remove group
 
 Remove\ group,\ keep\ subgroups=Remove group, keep subgroups
@@ -1439,8 +1437,6 @@ Show\ extra\ columns=Show extra columns
 Parsing\ error=Parsing error
 illegal\ backslash\ expression=illegal backslash expression
 
-Move\ to\ group=Move to group
-
 Clear\ read\ status=Clear read status
 Convert\ to\ biblatex\ format\ (for\ example,\ move\ the\ value\ of\ the\ 'journal'\ field\ to\ 'journaltitle')=Convert to biblatex format (for example, move the value of the 'journal' field to 'journaltitle')
 Deprecated\ fields=Deprecated fields

From 917ddef60315c44b79852942a7368b39a98a9213 Mon Sep 17 00:00:00 2001
From: CaptainDaVinci <yashkothari199767@gmail.com>
Date: Fri, 8 Mar 2019 19:59:39 +0530
Subject: [PATCH 088/184] Adding support for input methods

Fixes #4474
---
 .../org/jabref/gui/entryeditor/SourceTab.java | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
index 397e3abd921..89f97ffbf2e 100644
--- a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
@@ -11,7 +11,9 @@
 import javafx.beans.property.ObjectProperty;
 import javafx.beans.property.SimpleObjectProperty;
 import javafx.collections.ListChangeListener;
+import javafx.geometry.Point2D;
 import javafx.scene.control.Tooltip;
+import javafx.scene.input.InputMethodRequests;
 
 import org.jabref.gui.DialogService;
 import org.jabref.gui.icon.IconTheme;
@@ -77,9 +79,42 @@ private static String getSourceString(BibEntry entry, BibDatabaseMode type, Late
         return stringWriter.getBuffer().toString();
     }
 
+    /* Work around for different input methods.
+     * https://github.com/FXMisc/RichTextFX/issues/146
+     */
+    private class InputMethodRequestsObject implements InputMethodRequests {
+
+        @Override
+        public String getSelectedText() {
+            return "";
+        }
+
+        @Override
+        public int getLocationOffset(int x, int y) {
+            return 0;
+        }
+
+        @Override
+        public void cancelLatestCommittedText() {
+            return;
+        }
+
+        @Override
+        public Point2D getTextLocation(int offset) {
+            return new Point2D(0, 0);
+        }
+    }
+
     private CodeArea createSourceEditor() {
         CodeArea codeArea = new CodeArea();
         codeArea.setWrapText(true);
+        codeArea.setInputMethodRequests(new InputMethodRequestsObject());
+        codeArea.setOnInputMethodTextChanged(event -> {
+            String committed = event.getCommitted();
+            if (!committed.isEmpty()) {
+                codeArea.insertText(codeArea.getCaretPosition(), committed);
+            }
+        });
         return codeArea;
     }
 

From c16f733b8f4cc3a06760e3f3ad3b4d07c08879c4 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 8 Mar 2019 15:31:42 +0100
Subject: [PATCH 089/184] Convert "Manage external file types" dialog to JavaFX
 (#4711)

* Convert "Manage external file types" dialog to JavaFX

* Fix language file
---
 .../actions/EditExternalFileTypesAction.java  |   6 +-
 .../CustomizeExternalFileTypesDialog.fxml     |  39 +++
 .../CustomizeExternalFileTypesDialog.java     |  86 +++++
 .../CustomizeExternalFileTypesViewModel.java  |  59 ++++
 .../ExternalFileTypeEditor.java               | 321 ------------------
 .../ExternalFileTypeEntryEditor.java          |  10 -
 .../jabref/gui/preferences/ExternalTab.java   |   4 +-
 src/main/resources/l10n/JabRef_en.properties  |   4 +-
 8 files changed, 191 insertions(+), 338 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesDialog.fxml
 create mode 100644 src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesDialog.java
 create mode 100644 src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesViewModel.java
 delete mode 100644 src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEditor.java

diff --git a/src/main/java/org/jabref/gui/actions/EditExternalFileTypesAction.java b/src/main/java/org/jabref/gui/actions/EditExternalFileTypesAction.java
index 82bbc9123ce..c5ea26bb8cb 100644
--- a/src/main/java/org/jabref/gui/actions/EditExternalFileTypesAction.java
+++ b/src/main/java/org/jabref/gui/actions/EditExternalFileTypesAction.java
@@ -1,12 +1,12 @@
 package org.jabref.gui.actions;
 
-import org.jabref.gui.externalfiletype.ExternalFileTypeEditor;
+import org.jabref.gui.externalfiletype.CustomizeExternalFileTypesDialog;
 
 public class EditExternalFileTypesAction extends SimpleCommand {
 
     @Override
     public void execute() {
-        ExternalFileTypeEditor editor = new ExternalFileTypeEditor();
-        editor.show();
+        CustomizeExternalFileTypesDialog editor = new CustomizeExternalFileTypesDialog();
+        editor.showAndWait();
     }
 }
diff --git a/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesDialog.fxml b/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesDialog.fxml
new file mode 100644
index 00000000000..6489e52a788
--- /dev/null
+++ b/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesDialog.fxml
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.ButtonType?>
+<?import javafx.scene.control.DialogPane?>
+<?import javafx.scene.control.TableColumn?>
+<?import javafx.scene.control.TableView?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
+<DialogPane xmlns:fx="http://javafx.com/fxml"
+            xmlns="http://javafx.com/javafx"
+            fx:controller="org.jabref.gui.externalfiletype.CustomizeExternalFileTypesDialog"
+            prefHeight="500.0" prefWidth="750.0">
+    <content>
+        <VBox spacing="10">
+            <TableView fx:id="fileTypesTable" VBox.vgrow="ALWAYS">
+                <columns>
+                    <TableColumn fx:id="fileTypesTableIconColumn" minWidth="40.0" maxWidth="40.0"/>
+                    <TableColumn fx:id="fileTypesTableNameColumn" text="%Name"/>
+                    <TableColumn fx:id="fileTypesTableExtensionColumn" text="%Extension" prefWidth="120"/>
+                    <TableColumn fx:id="fileTypesTableTypeColumn" text="%MIME type" prefWidth="150"/>
+                    <TableColumn fx:id="fileTypesTableApplicationColumn" text="%Application" prefWidth="100"/>
+                    <TableColumn fx:id="fileTypesTableEditColumn" minWidth="40.0" maxWidth="40.0"/>
+                    <TableColumn fx:id="fileTypesTableDeleteColumn" minWidth="40.0" maxWidth="40.0"/>
+                </columns>
+                <columnResizePolicy>
+                    <TableView fx:constant="CONSTRAINED_RESIZE_POLICY"/>
+                </columnResizePolicy>
+            </TableView>
+            <HBox>
+                <Button text="%Add new file type" onAction="#addNewType"/>
+                <HBox HBox.hgrow="ALWAYS"/>
+                <Button text="%Reset to default" onAction="#resetToDefault" styleClass="text-button"/>
+            </HBox>
+        </VBox>
+    </content>
+    <ButtonType fx:constant="OK"/>
+    <ButtonType fx:constant="CANCEL"/>
+</DialogPane>
diff --git a/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesDialog.java b/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesDialog.java
new file mode 100644
index 00000000000..e7a2d1492ef
--- /dev/null
+++ b/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesDialog.java
@@ -0,0 +1,86 @@
+package org.jabref.gui.externalfiletype;
+
+import javafx.fxml.FXML;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.TableColumn;
+import javafx.scene.control.TableView;
+
+import org.jabref.gui.icon.IconTheme;
+import org.jabref.gui.icon.JabRefIcon;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.BindingsHelper;
+import org.jabref.gui.util.ValueTableCellFactory;
+import org.jabref.logic.l10n.Localization;
+
+import com.airhacks.afterburner.views.ViewLoader;
+
+/**
+ * Editor for external file types.
+ */
+public class CustomizeExternalFileTypesDialog extends BaseDialog<Void> {
+
+    @FXML private TableColumn<ExternalFileType, JabRefIcon> fileTypesTableIconColumn;
+    @FXML private TableColumn<ExternalFileType, String> fileTypesTableNameColumn;
+    @FXML private TableColumn<ExternalFileType, String> fileTypesTableExtensionColumn;
+    @FXML private TableColumn<ExternalFileType, String> fileTypesTableTypeColumn;
+    @FXML private TableColumn<ExternalFileType, String> fileTypesTableApplicationColumn;
+    @FXML private TableColumn<ExternalFileType, Boolean> fileTypesTableEditColumn;
+    @FXML private TableColumn<ExternalFileType, Boolean> fileTypesTableDeleteColumn;
+    @FXML private TableView<ExternalFileType> fileTypesTable;
+
+    private CustomizeExternalFileTypesViewModel viewModel;
+
+    public CustomizeExternalFileTypesDialog() {
+        this.setTitle(Localization.lang("Manage external file types"));
+
+        ViewLoader.view(this)
+                  .load()
+                  .setAsDialogPane(this);
+
+        this.setResultConverter(button -> {
+            if (button == ButtonType.OK) {
+                viewModel.storeSettings();
+            }
+            return null;
+        });
+    }
+
+    @FXML
+    public void initialize() {
+        viewModel = new CustomizeExternalFileTypesViewModel();
+
+        fileTypesTable.setItems(viewModel.getFileTypes());
+
+        fileTypesTableIconColumn.setCellValueFactory(data -> BindingsHelper.constantOf(data.getValue().getIcon()));
+        fileTypesTableNameColumn.setCellValueFactory(data -> BindingsHelper.constantOf(data.getValue().getName()));
+        fileTypesTableExtensionColumn.setCellValueFactory(data -> BindingsHelper.constantOf(data.getValue().getExtension()));
+        fileTypesTableTypeColumn.setCellValueFactory(data -> BindingsHelper.constantOf(data.getValue().getMimeType()));
+        fileTypesTableApplicationColumn.setCellValueFactory(data -> BindingsHelper.constantOf(data.getValue().getOpenWithApplication()));
+        fileTypesTableEditColumn.setCellValueFactory(data -> BindingsHelper.constantOf(true));
+        fileTypesTableDeleteColumn.setCellValueFactory(data -> BindingsHelper.constantOf(true));
+
+        new ValueTableCellFactory<ExternalFileType, JabRefIcon>()
+                .withGraphic(JabRefIcon::getGraphicNode)
+                .install(fileTypesTableIconColumn);
+        new ValueTableCellFactory<ExternalFileType, Boolean>()
+                .withGraphic(none -> IconTheme.JabRefIcons.EDIT.getGraphicNode())
+                .withOnMouseClickedEvent((type, none) -> event -> viewModel.edit(type))
+                .install(fileTypesTableEditColumn);
+        new ValueTableCellFactory<ExternalFileType, Boolean>()
+                .withGraphic(none -> IconTheme.JabRefIcons.REMOVE.getGraphicNode())
+                .withOnMouseClickedEvent((type, none) -> event -> viewModel.remove(type))
+                .install(fileTypesTableDeleteColumn);
+    }
+
+    @FXML
+    private void addNewType() {
+        viewModel.addNewType();
+        fileTypesTable.getSelectionModel().selectLast();
+        fileTypesTable.scrollTo(viewModel.getFileTypes().size() - 1);
+    }
+
+    @FXML
+    private void resetToDefault() {
+        viewModel.resetToDefaults();
+    }
+}
diff --git a/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesViewModel.java b/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesViewModel.java
new file mode 100644
index 00000000000..5d8c68e9fa4
--- /dev/null
+++ b/src/main/java/org/jabref/gui/externalfiletype/CustomizeExternalFileTypesViewModel.java
@@ -0,0 +1,59 @@
+package org.jabref.gui.externalfiletype;
+
+import java.util.Comparator;
+import java.util.List;
+import java.util.Set;
+
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+
+import org.jabref.gui.icon.IconTheme;
+
+public class CustomizeExternalFileTypesViewModel {
+    private ObservableList<ExternalFileType> fileTypes;
+
+    public CustomizeExternalFileTypesViewModel() {
+        Set<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
+        fileTypes = FXCollections.observableArrayList(types);
+        fileTypes.sort(Comparator.comparing(ExternalFileType::getName));
+    }
+
+    /**
+     * Stores the list of external entry types in the preferences.
+     */
+    public void storeSettings() {
+        ExternalFileTypes.getInstance().setExternalFileTypes(fileTypes);
+    }
+
+    public void resetToDefaults() {
+        List<ExternalFileType> list = ExternalFileTypes.getDefaultExternalFileTypes();
+        fileTypes.setAll(list);
+        fileTypes.sort(Comparator.comparing(ExternalFileType::getName));
+    }
+
+    public void addNewType() {
+        CustomExternalFileType type = new CustomExternalFileType("", "", "", "", "new", IconTheme.JabRefIcons.FILE);
+        fileTypes.add(type);
+        edit(type);
+    }
+
+    public ObservableList<ExternalFileType> getFileTypes() {
+        return fileTypes;
+    }
+
+    public void edit(ExternalFileType type) {
+        CustomExternalFileType typeForEdit;
+        if (type instanceof CustomExternalFileType) {
+            typeForEdit = (CustomExternalFileType) type;
+        } else {
+            typeForEdit = new CustomExternalFileType(type);
+        }
+
+        ExternalFileTypeEntryEditor entryEditor = new ExternalFileTypeEntryEditor(typeForEdit);
+        entryEditor.setVisible(true);
+    }
+
+    public void remove(ExternalFileType type) {
+        fileTypes.remove(type);
+    }
+}
diff --git a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEditor.java b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEditor.java
deleted file mode 100644
index ce1192c5d47..00000000000
--- a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEditor.java
+++ /dev/null
@@ -1,321 +0,0 @@
-package org.jabref.gui.externalfiletype;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.BorderFactory;
-import javax.swing.ImageIcon;
-import javax.swing.JButton;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTable;
-import javax.swing.table.AbstractTableModel;
-import javax.swing.table.TableCellRenderer;
-
-import javafx.scene.control.ButtonType;
-import javafx.stage.Modality;
-
-import org.jabref.gui.actions.MnemonicAwareAction;
-import org.jabref.gui.icon.IconTheme;
-import org.jabref.gui.icon.JabRefIcon;
-import org.jabref.gui.util.BaseDialog;
-import org.jabref.gui.util.ControlHelper;
-import org.jabref.logic.l10n.Localization;
-
-import com.jgoodies.forms.builder.ButtonStackBuilder;
-
-/**
- * Editor for external file types.
- */
-public class ExternalFileTypeEditor extends BaseDialog<Void> {
-
-    private List<ExternalFileType> fileTypes;
-    private JTable table;
-    private ExternalFileTypeEntryEditor entryEditor;
-    private FileTypeTableModel tableModel;
-    private final JButton add = new JButton(IconTheme.JabRefIcons.ADD_NOBOX.getIcon());
-    private final JButton remove = new JButton(IconTheme.JabRefIcons.REMOVE_NOBOX.getIcon());
-    private final JButton edit = new JButton(IconTheme.JabRefIcons.EDIT.getIcon());
-    private final JButton toDefaults = new JButton(Localization.lang("Default"));
-    private final EditListener editListener = new EditListener();
-
-    public ExternalFileTypeEditor() {
-        this.setTitle(Localization.lang("Manage external file types"));
-        this.initModality(Modality.APPLICATION_MODAL);
-        this.getDialogPane().setPrefSize(600, 500);
-
-        init();
-    }
-
-    /**
-     * Update the editor to show the current settings in Preferences.
-     */
-    private void setValues() {
-        fileTypes.clear();
-        Collection<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
-        fileTypes.addAll(types);
-        fileTypes.sort(Comparator.comparing(ExternalFileType::getName));
-    }
-
-    /**
-     * Store the list of external entry types to Preferences.
-     */
-    private void storeSettings() {
-        ExternalFileTypes.getInstance().setExternalFileTypes(fileTypes);
-    }
-
-    /**
-     * Get an AbstractAction for opening the external file types editor.
-     *
-     * @return An Action for opening the editor.
-     */
-    public static AbstractAction getAction() {
-        return new EditExternalFileTypesAction();
-    }
-
-    private void init() {
-
-        this.getDialogPane().getButtonTypes().setAll(
-                ButtonType.CANCEL,
-                ButtonType.OK
-        );
-
-        this.setResultConverter(button -> {
-            if (button == ButtonType.OK) {
-                storeSettings();
-            }
-            return null;
-        });
-
-        // The toDefaults resets the entire list to its default values.
-        toDefaults.addActionListener(e -> {
-            /*int reply = JOptionPane.showConfirmDialog(ExternalFileTypeEditor.this,
-                    Globals.lang("All custom file types will be lost. Proceed?"),
-                    Globals.lang("Reset file type definitions"), JOptionPane.YES_NO_OPTION,
-                    JOptionPane.QUESTION_MESSAGE);*/
-            //if (reply == JOptionPane.YES_OPTION) {
-            List<ExternalFileType> list = ExternalFileTypes.getDefaultExternalFileTypes();
-            fileTypes.clear();
-            fileTypes.addAll(list);
-            fileTypes.sort(Comparator.comparing(ExternalFileType::getName));
-            //Globals.prefs.resetExternalFileTypesToDefault();
-            //setValues();
-            tableModel.fireTableDataChanged();
-            //}
-        });
-
-        add.addActionListener(e -> {
-            // Generate a new file type:
-            CustomExternalFileType type = new CustomExternalFileType("", "", "", "", "new",
-                    IconTheme.JabRefIcons.FILE);
-            // Show the file type editor:
-            getEditor(type).setVisible(true);
-            if (entryEditor.okPressed()) {
-                // Ok was pressed. Add the new file type and update the table:
-                fileTypes.add(type);
-                tableModel.fireTableDataChanged();
-            }
-        });
-
-        remove.addActionListener(e -> {
-            int[] rows = table.getSelectedRows();
-            if (rows.length == 0) {
-                return;
-            }
-            for (int i = rows.length - 1; i >= 0; i--) {
-                fileTypes.remove(rows[i]);
-            }
-            tableModel.fireTableDataChanged();
-            if (!fileTypes.isEmpty()) {
-                int row = Math.min(rows[0], fileTypes.size() - 1);
-                table.setRowSelectionInterval(row, row);
-            }
-        });
-
-        edit.addActionListener(editListener);
-        fileTypes = new ArrayList<>();
-        setValues();
-
-        tableModel = new FileTypeTableModel();
-        table = new JTable(tableModel);
-        table.setDefaultRenderer(ImageIcon.class, new IconRenderer());
-        table.addMouseListener(new TableClickListener());
-
-        table.getColumnModel().getColumn(0).setMaxWidth(24);
-        table.getColumnModel().getColumn(0).setMinWidth(24);
-        table.getColumnModel().getColumn(1).setMinWidth(170);
-        table.getColumnModel().getColumn(2).setMinWidth(60);
-        table.getColumnModel().getColumn(3).setMinWidth(100);
-        table.getColumnModel().getColumn(0).setResizable(false);
-
-        JScrollPane sp = new JScrollPane(table);
-
-        JPanel upper = new JPanel();
-        upper.setLayout(new BorderLayout());
-        upper.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-        upper.add(sp, BorderLayout.CENTER);
-        ControlHelper.setSwingContent(getDialogPane(), upper);
-
-        ButtonStackBuilder bs = new ButtonStackBuilder();
-        bs.addButton(add);
-        bs.addButton(remove);
-        bs.addButton(edit);
-        bs.addRelatedGap();
-        bs.addButton(toDefaults);
-        upper.add(bs.getPanel(), BorderLayout.EAST);
-    }
-
-    private ExternalFileTypeEntryEditor getEditor(ExternalFileType type) {
-        CustomExternalFileType typeForEdit;
-        if (type instanceof CustomExternalFileType) {
-            typeForEdit = (CustomExternalFileType) type;
-        } else {
-            typeForEdit = new CustomExternalFileType(type);
-        }
-
-        if (entryEditor == null) {
-            entryEditor = new ExternalFileTypeEntryEditor(typeForEdit);
-        } else {
-            entryEditor.setEntry(typeForEdit);
-        }
-        return entryEditor;
-    }
-
-    class EditListener implements ActionListener {
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            int[] rows = table.getSelectedRows();
-            if (rows.length != 1) {
-                return;
-            }
-            getEditor(fileTypes.get(rows[0])).setVisible(true);
-            if (entryEditor.okPressed()) {
-                tableModel.fireTableDataChanged();
-            }
-        }
-    }
-
-    static class IconRenderer implements TableCellRenderer {
-
-        private final JLabel lab = new JLabel();
-
-        @Override
-        public Component getTableCellRendererComponent(JTable tab, Object value, boolean isSelected, boolean hasFocus,
-                int row, int column) {
-            lab.setText(null);
-            lab.setIcon(((JabRefIcon) value).getIcon());
-            return lab;
-        }
-    }
-
-    private class FileTypeTableModel extends AbstractTableModel {
-
-        @Override
-        public int getColumnCount() {
-            return 5;
-        }
-
-        @Override
-        public int getRowCount() {
-            return fileTypes.size();
-        }
-
-        @Override
-        public String getColumnName(int column) {
-            switch (column) {
-            case 0:
-                return " ";
-            case 1:
-                return Localization.lang("Name");
-            case 2:
-                return Localization.lang("Extension");
-            case 3:
-                return Localization.lang("MIME type");
-            default: // Five columns
-                return Localization.lang("Application");
-            }
-        }
-
-        @Override
-        public Class<?> getColumnClass(int columnIndex) {
-            if (columnIndex == 0) {
-                return ImageIcon.class;
-            } else {
-                return String.class;
-            }
-        }
-
-        @Override
-        public Object getValueAt(int rowIndex, int columnIndex) {
-            ExternalFileType type = fileTypes.get(rowIndex);
-            switch (columnIndex) {
-            case 0:
-                return type.getIcon();
-            case 1:
-                return type.getName();
-            case 2:
-                return type.getExtension();
-            case 3:
-                return type.getMimeType();
-            default:
-                return type.getOpenWithApplication();
-            }
-        }
-    }
-
-    class TableClickListener extends MouseAdapter {
-
-        private void handleClick(MouseEvent e) {
-            if (e.getClickCount() == 2) {
-                editListener.actionPerformed(null);
-            }
-        }
-
-        @Override
-        public void mouseClicked(MouseEvent e) {
-            handleClick(e);
-        }
-
-        @Override
-        public void mousePressed(MouseEvent e) {
-            handleClick(e);
-        }
-
-        @Override
-        public void mouseReleased(MouseEvent e) {
-            handleClick(e);
-        }
-    }
-
-    public static class EditExternalFileTypesAction extends MnemonicAwareAction {
-
-        private ExternalFileTypeEditor editor;
-
-        public EditExternalFileTypesAction() {
-            super();
-            putValue(Action.NAME, Localization.lang("Manage external file types"));
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            if (editor == null) {
-                editor = new ExternalFileTypeEditor();
-            }
-            editor.setValues();
-            editor.show();
-        }
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java
index a28fcb73d65..e620e69e84b 100644
--- a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java
+++ b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java
@@ -178,16 +178,6 @@ public void changedUpdate(DocumentEvent documentEvent) {
         setValues(entry);
     }
 
-    public void setEntry(CustomExternalFileType entry) {
-        this.entry = entry;
-        if (entry.getName().isEmpty()) {
-            diag.setTitle(newFileTitle);
-        } else {
-            diag.setTitle(editFileTitle);
-        }
-        setValues(entry);
-    }
-
     public void setVisible(boolean visible) {
         if (visible) {
             okPressed = false;
diff --git a/src/main/java/org/jabref/gui/preferences/ExternalTab.java b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
index 0328eaf4e1b..e872abeadb4 100644
--- a/src/main/java/org/jabref/gui/preferences/ExternalTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
@@ -12,7 +12,7 @@
 import org.jabref.Globals;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.externalfiletype.ExternalFileTypeEditor;
+import org.jabref.gui.actions.EditExternalFileTypesAction;
 import org.jabref.gui.push.PushToApplication;
 import org.jabref.gui.push.PushToApplicationSettings;
 import org.jabref.gui.push.PushToApplicationSettingsDialog;
@@ -47,7 +47,7 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
         dialogService = frame.getDialogService();
         Button editFileTypes = new Button(Localization.lang("Manage external file types"));
         citeCommand = new TextField();
-        editFileTypes.setOnAction(e -> ExternalFileTypeEditor.getAction());
+        editFileTypes.setOnAction(e -> new EditExternalFileTypesAction().execute());
         defaultConsole = new RadioButton(Localization.lang("Use default terminal emulator"));
         executeConsole = new RadioButton(Localization.lang("Execute command") + ":");
         consoleCommand = new TextField();
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 54ccec1845d..b8bfd4a718d 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2150,7 +2150,7 @@ Keyword\:=Keyword:
 Keyword\ \"%0\"\ already\ exists=Keyword "%0" already exists
 Remove\ keyword=Remove keyword
 Are\ you\ sure\ you\ want\ to\ remove\ keyword\:\ \"%0\"?=Are you sure you want to remove keyword: "%0"?
-
+Reset\ to\ default=Reset to default
 Edit\ string\ constants=Edit string constants
 Export\ all\ entries=Export all entries
 Generate\ BibTeX\ keys=Generate BibTeX keys
@@ -2165,4 +2165,4 @@ Previous\ citation\ style=Previous citation style
 Search\ document\ identifier\ online=Search document identifier online
 Search\ for\ unlinked\ local\ files=Search for unlinked local files
 Search\ full\ text\ documents\ online=Search full text documents online
-Find\ and\ replace=Find and replace
\ No newline at end of file
+Find\ and\ replace=Find and replace

From 5ce22f2e0d2e7a567dddc91846a5d036dbdd858b Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Fri, 8 Mar 2019 15:44:44 +0100
Subject: [PATCH 090/184] move css rule to base.css add comemnt fix indencation

---
 src/main/java/org/jabref/gui/Base.css                       | 5 +++++
 src/main/java/org/jabref/gui/JabRefFrame.java               | 6 +++---
 .../gui/libraryproperties/LibraryPropertiesDialog.css       | 4 ----
 .../gui/libraryproperties/LibraryPropertiesDialogView.java  | 2 +-
 .../java/org/jabref/gui/preferences/PreferencesDialog.css   | 5 -----
 5 files changed, 9 insertions(+), 13 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.css

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
index 14c7861eb45..f2d02b9cc95 100644
--- a/src/main/java/org/jabref/gui/Base.css
+++ b/src/main/java/org/jabref/gui/Base.css
@@ -993,3 +993,8 @@ We want to have a look that matches our icons in the tool-bar */
 .tooltip-error {
     -fx-background-color: -jr-error;
 }
+
+.sectionHeader {
+    -fx-font-size: 1.5em;
+    -fx-padding: 1em 0em 1em 0em;
+}
\ No newline at end of file
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 1946c40461e..c09d09561f9 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -818,7 +818,7 @@ private MenuBar createMenu() {
                 edit.getItems().add(new SeparatorMenuItem());
             }
         }
-
+        //@formatter:off
         library.getItems().addAll(
                 factory.createMenuItem(StandardActions.NEW_ENTRY, new NewEntryAction(this, dialogService, Globals.prefs)),
                 factory.createMenuItem(StandardActions.NEW_ENTRY_FROM_PLAINTEX, new NewEntryFromPlainTextAction(this, Globals.prefs.getUpdateFieldPreferences(), dialogService, Globals.prefs)),
@@ -826,7 +826,7 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                                  factory.createMenuItem(StandardActions.LIBRARY_PROPERTIES, new LibraryPropertiesAction(this, dialogService)),
+                factory.createMenuItem(StandardActions.LIBRARY_PROPERTIES, new LibraryPropertiesAction(this, dialogService)),
                 factory.createMenuItem(StandardActions.EDIT_PREAMBLE, new PreambleEditor(this)),
                 factory.createMenuItem(StandardActions.EDIT_STRINGS, new BibtexStringEditorAction(this)),
                 factory.createMenuItem(StandardActions.MASS_SET_FIELDS, new MassSetFieldsAction(this))
@@ -838,7 +838,7 @@ private MenuBar createMenu() {
             lookupIdentifiers.getItems().add(factory.createMenuItem(identifierAction.getAction(), identifierAction));
         }
 
-        //@formatter:off
+
         quality.getItems().addAll(
                 factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(this, dialogService)),
                 factory.createMenuItem(StandardActions.MERGE_ENTRIES, new MergeEntriesAction(this)),
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.css b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.css
deleted file mode 100644
index 6377d4e01ba..00000000000
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.css
+++ /dev/null
@@ -1,4 +0,0 @@
-.sectionHeader {
-    -fx-font-size: 1.5em;
-    -fx-padding: 1em 0em 1em 0em;
-}
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
index 9cbeaf2a637..8ed238faf8a 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
@@ -113,6 +113,7 @@ public void browseUserSpecificFileDirectory(ActionEvent event) {
     }
 
     private void storeSettings() {
+        //FIXME: Move to viewModel until fieldFormatterCleanupsPanel is property implemented
         MetaData metaData = panel.getBibDatabaseContext().getMetaData();
         Charset oldEncoding = metaData.getEncoding()
                                       .orElse(preferencesService.getDefaultEncoding());
@@ -171,5 +172,4 @@ private void storeSettings() {
             panel.markNonUndoableBaseChanged();
         }
     }
-
 }
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css
index 2b2d8c34859..f79bfba706e 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css
@@ -12,8 +12,3 @@
 .preferencePaneContainer {
     -fx-padding: 0em 1em 0em 3em;
 }
-
-.sectionHeader {
-    -fx-font-size: 1.5em;
-    -fx-padding: 1em 0em 1em 0em;
-}

From eb522bbcc066ca232c377ab6e4948de7c2ed7666 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 8 Mar 2019 15:45:46 +0100
Subject: [PATCH 091/184] Remove old swing-based tests

---
 build.gradle                                  |   1 -
 .../org/jabref/gui/AWTExceptionHandler.java   |  24 ---
 .../java/org/jabref/gui/AbstractUITest.java   | 105 ----------
 src/test/java/org/jabref/gui/DialogTest.java  |  51 -----
 src/test/java/org/jabref/gui/DialogTest2.java |  43 ----
 .../java/org/jabref/gui/EntryTableTest.java   |  65 ------
 .../org/jabref/gui/IdFetcherDialogTest.java   | 121 -----------
 .../gui/ParameterizedDialogNewEntryTest.java  | 191 ------------------
 .../jabref/gui/ParameterizedDialogTest.java   | 133 ------------
 .../gui/ParameterizedMenuNewEntryTest.java    |  64 ------
 .../jabref/gui/entryeditor/SourceTabTest.java |   2 +
 .../mergeentries/DiffHighlightingTest.java    |   3 +
 ...sAndRegexBasedSearchRuleDescriberTest.java |   2 +
 .../GrammarBasedSearchRuleDescriberTest.java  |   2 +
 .../jabref/gui/search/SearchResultsTest.java  |  96 ---------
 15 files changed, 9 insertions(+), 894 deletions(-)
 delete mode 100644 src/test/java/org/jabref/gui/AWTExceptionHandler.java
 delete mode 100644 src/test/java/org/jabref/gui/AbstractUITest.java
 delete mode 100644 src/test/java/org/jabref/gui/DialogTest.java
 delete mode 100644 src/test/java/org/jabref/gui/DialogTest2.java
 delete mode 100644 src/test/java/org/jabref/gui/EntryTableTest.java
 delete mode 100644 src/test/java/org/jabref/gui/IdFetcherDialogTest.java
 delete mode 100644 src/test/java/org/jabref/gui/ParameterizedDialogNewEntryTest.java
 delete mode 100644 src/test/java/org/jabref/gui/ParameterizedDialogTest.java
 delete mode 100644 src/test/java/org/jabref/gui/ParameterizedMenuNewEntryTest.java
 delete mode 100644 src/test/java/org/jabref/gui/search/SearchResultsTest.java

diff --git a/build.gradle b/build.gradle
index d08efe7b1a2..a3a9a3f66ab 100644
--- a/build.gradle
+++ b/build.gradle
@@ -169,7 +169,6 @@ dependencies {
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
     testCompile 'org.mockito:mockito-core:2.25.0'
     testCompile 'com.github.tomakehurst:wiremock:2.21.0'
-    testCompile 'org.assertj:assertj-swing-junit:3.9.2'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
diff --git a/src/test/java/org/jabref/gui/AWTExceptionHandler.java b/src/test/java/org/jabref/gui/AWTExceptionHandler.java
deleted file mode 100644
index 74586f4d709..00000000000
--- a/src/test/java/org/jabref/gui/AWTExceptionHandler.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package org.jabref.gui;
-
-import java.util.List;
-import java.util.concurrent.CopyOnWriteArrayList;
-
-import javax.swing.SwingUtilities;
-
-/**
- * Can catch any exceptions occurring on the EDT thread for assertion.
- */
-public class AWTExceptionHandler {
-
-    private final List<Throwable> list = new CopyOnWriteArrayList<>();
-
-    public void installExceptionDetectionInEDT() {
-        SwingUtilities.invokeLater(() -> Thread.currentThread().setUncaughtExceptionHandler((t, e) -> list.add(e)));
-    }
-
-    public void assertNoExceptions() {
-        if (!list.isEmpty()) {
-            throw new AssertionError("Uncaught exception in EDT", list.get(0));
-        }
-    }
-}
diff --git a/src/test/java/org/jabref/gui/AbstractUITest.java b/src/test/java/org/jabref/gui/AbstractUITest.java
deleted file mode 100644
index dfc33236d98..00000000000
--- a/src/test/java/org/jabref/gui/AbstractUITest.java
+++ /dev/null
@@ -1,105 +0,0 @@
-package org.jabref.gui;
-
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.net.URL;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-
-import org.jabref.JabRefMain;
-
-import org.assertj.swing.fixture.AbstractWindowFixture;
-import org.assertj.swing.fixture.FrameFixture;
-import org.assertj.swing.fixture.JFileChooserFixture;
-import org.assertj.swing.fixture.JTableFixture;
-import org.assertj.swing.image.ScreenshotTaker;
-import org.assertj.swing.junit.testcase.AssertJSwingJUnitTestCase;
-import org.assertj.swing.timing.Pause;
-import org.junit.jupiter.api.Tag;
-
-import static org.assertj.swing.launcher.ApplicationLauncher.application;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
-@Tag("GUITest")
-public abstract class AbstractUITest extends AssertJSwingJUnitTestCase {
-
-    protected final static int SPEED_NORMAL = 50;
-
-    protected AWTExceptionHandler awtExceptionHandler;
-    protected FrameFixture mainFrame;
-
-    @Override
-    protected void onSetUp() {
-        awtExceptionHandler = new AWTExceptionHandler();
-        awtExceptionHandler.installExceptionDetectionInEDT();
-        application(JabRefMain.class).start();
-
-        robot().waitForIdle();
-
-        robot().settings().timeoutToFindSubMenu(1_000);
-        robot().settings().delayBetweenEvents(SPEED_NORMAL);
-
-        //mainFrame = findFrame(null).withTimeout(10_000).using(robot());
-        robot().waitForIdle();
-    }
-
-    /**
-     * Returns the absolute Path of the given relative Path The backlashes are replaced with forwardslashes b/c assertJ
-     * can't type the former one on windows
-     *
-     * @param relativePath the relative path to the resource database
-     */
-    protected String getAbsolutePath(String relativePath) throws URISyntaxException {
-        final URL resource = this.getClass().getClassLoader().getResource(relativePath);
-        return Paths.get(resource.toURI()).toAbsolutePath().toString().replace("\\", "/");
-    }
-
-    /**
-     * opens a database and gives JabRef a second to open it before proceeding
-     */
-    protected void importBibIntoNewDatabase(String path) {
-        mainFrame.menuItemWithPath("File", "Import into new library").click();
-        JFileChooserFixture openFileDialog = mainFrame.fileChooser();
-        robot().settings().delayBetweenEvents(1);
-        openFileDialog.fileNameTextBox().enterText(path);
-        openFileDialog.approve();
-        Pause.pause(1_000);
-    }
-
-    protected void exitJabRef() {
-        mainFrame.menuItemWithPath("File", "Quit").click();
-        awtExceptionHandler.assertNoExceptions();
-    }
-
-    protected void newDatabase() {
-        mainFrame.menuItemWithPath("File", "New BibTeX database").click();
-    }
-
-    protected void closeDatabase() {
-        mainFrame.menuItemWithPath("File", "Close library").click();
-    }
-
-    protected void takeScreenshot(AbstractWindowFixture<?, ?, ?> dialog, String filename) throws IOException {
-        ScreenshotTaker screenshotTaker = new ScreenshotTaker();
-        Path folder = Paths.get("build", "screenshots");
-        // Create build/srceenshots folder if not present
-        if (!Files.exists(folder)) {
-            Files.createDirectory(folder);
-        }
-        Path file = folder.resolve(filename + ".png").toAbsolutePath();
-        // Delete already present file
-        if (Files.exists(file)) {
-            Files.delete(file);
-        }
-        screenshotTaker.saveComponentAsPng(dialog.target(), file.toString());
-    }
-
-    protected void assertColumnValue(JTableFixture table, int rowIndex, int columnIndex, String selectionValue) {
-        String[][] tableContent;
-        tableContent = table.contents();
-
-        String value = tableContent[rowIndex][columnIndex];
-        assertEquals(value, selectionValue);
-    }
-}
diff --git a/src/test/java/org/jabref/gui/DialogTest.java b/src/test/java/org/jabref/gui/DialogTest.java
deleted file mode 100644
index e97eb1a56dc..00000000000
--- a/src/test/java/org/jabref/gui/DialogTest.java
+++ /dev/null
@@ -1,51 +0,0 @@
-package org.jabref.gui;
-
-import javax.swing.JButton;
-import javax.swing.JDialog;
-
-import org.assertj.swing.core.GenericTypeMatcher;
-import org.assertj.swing.dependency.jsr305.Nonnull;
-import org.junit.jupiter.api.Tag;
-import org.junit.jupiter.api.Test;
-
-import static org.assertj.swing.finder.WindowFinder.findDialog;
-
-/**
- * This test has been split to work, the other part can be found at DialogTest2
- */
-@Tag("GUITest")
-public class DialogTest extends AbstractUITest {
-
-    @Test
-    public void testCancelStyleSelectDialog() {
-        mainFrame.menuItemWithPath("Tools", "OpenOffice/LibreOffice connection").click();
-
-        GenericTypeMatcher<JButton> buttonMatcher = new GenericTypeMatcher<JButton>(JButton.class) {
-
-            @Override
-            protected boolean isMatching(@Nonnull JButton jButton) {
-                return "Select style".equals(jButton.getText());
-            }
-        };
-
-        mainFrame.button(buttonMatcher).click();
-
-        GenericTypeMatcher<JDialog> styleDialogMatcher = new GenericTypeMatcher<JDialog>(JDialog.class) {
-
-            @Override
-            protected boolean isMatching(JDialog dialog) {
-                return "Select style".equals(dialog.getTitle()); // Only a single SidePane
-            }
-        };
-
-        GenericTypeMatcher<JButton> buttonMatcher2 = new GenericTypeMatcher<JButton>(JButton.class) {
-
-            @Override
-            protected boolean isMatching(@Nonnull JButton jButton) {
-                return "Cancel".equals(jButton.getText());
-            }
-        };
-        findDialog(styleDialogMatcher).withTimeout(10_000).using(robot()).button(buttonMatcher2).click();
-        exitJabRef();
-    }
-}
diff --git a/src/test/java/org/jabref/gui/DialogTest2.java b/src/test/java/org/jabref/gui/DialogTest2.java
deleted file mode 100644
index 652532dd9bb..00000000000
--- a/src/test/java/org/jabref/gui/DialogTest2.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package org.jabref.gui;
-
-import javax.swing.JButton;
-import javax.swing.JDialog;
-
-import org.assertj.swing.core.GenericTypeMatcher;
-import org.assertj.swing.dependency.jsr305.Nonnull;
-import org.junit.jupiter.api.Tag;
-import org.junit.jupiter.api.Test;
-
-import static org.assertj.swing.finder.WindowFinder.findDialog;
-
-/**
- * Split of DialogTest, since the test cases were only running separately
- */
-@Tag("GUITest")
-public class DialogTest2 extends AbstractUITest {
-    @Test
-    public void testCloseStyleSelectDialog() {
-        mainFrame.menuItemWithPath("Tools", "OpenOffice/LibreOffice connection").click();
-
-        GenericTypeMatcher<JButton> buttonMatcher = new GenericTypeMatcher<JButton>(JButton.class) {
-
-            @Override
-            protected boolean isMatching(@Nonnull JButton jButton) {
-                return "Select style".equals(jButton.getText());
-            }
-        };
-
-        mainFrame.button(buttonMatcher).click();
-
-        GenericTypeMatcher<JDialog> styleDialogMatcher = new GenericTypeMatcher<JDialog>(JDialog.class) {
-
-            @Override
-            protected boolean isMatching(JDialog dialog) {
-                return "Select style".equals(dialog.getTitle()); // Only a single SidePane
-            }
-        };
-
-        findDialog(styleDialogMatcher).withTimeout(10_000).using(robot()).close();
-        exitJabRef();
-    }
-}
diff --git a/src/test/java/org/jabref/gui/EntryTableTest.java b/src/test/java/org/jabref/gui/EntryTableTest.java
deleted file mode 100644
index d5f4fbfa861..00000000000
--- a/src/test/java/org/jabref/gui/EntryTableTest.java
+++ /dev/null
@@ -1,65 +0,0 @@
-package org.jabref.gui;
-
-import java.awt.event.KeyEvent;
-import java.util.regex.Pattern;
-
-import org.assertj.swing.fixture.JTableCellFixture;
-import org.assertj.swing.fixture.JTableFixture;
-import org.junit.jupiter.api.Tag;
-import org.junit.jupiter.api.Test;
-
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-
-/**
- * Specific Use-Case: I import a database. Then I doubleclick on the first entry in the table to open the entry editor.
- * Then I click on the first entry again, and scroll through all of the lists entries, without having to click on the
- * table again.
- */
-@Tag("GUITest")
-public class EntryTableTest extends AbstractUITest {
-
-    private final static int SCROLL_ACTION_EXECUTION = 5;
-    private final static String TEST_FILE_NAME = "testbib/testjabref.bib";
-    private final static int DOWN = KeyEvent.VK_DOWN;
-    private final static int UP = KeyEvent.VK_UP;
-    private final static int TITLE_COLUMN_INDEX = 5;
-
-    @Test
-    public void scrollThroughEntryList() throws Exception {
-        String path = getAbsolutePath(TEST_FILE_NAME);
-
-        importBibIntoNewDatabase(path);
-
-        JTableFixture entryTable = mainFrame.table();
-
-        //use a pattern from the first row to select it since it seems to be the best way to get the cell object
-        Pattern pattern = Pattern.compile("256.*");
-        JTableCellFixture firstCell = entryTable.cell(pattern);
-
-        entryTable.selectRows(0).doubleClick();
-        //delay has to be shortened so that double click is recognized
-        robot().settings().delayBetweenEvents(0);
-        firstCell.doubleClick();
-        robot().settings().delayBetweenEvents(SPEED_NORMAL);
-
-        firstCell.click();
-        //is the first table entry selected?
-        assertColumnValue(entryTable, 0, TITLE_COLUMN_INDEX, entryTable.selectionValue());
-
-        //go throught the table and check if the entry with the correct index is selected
-        for (int i = 0; i < SCROLL_ACTION_EXECUTION; i++) {
-            robot().pressAndReleaseKey(DOWN);
-            assertNotNull(entryTable.selectionValue());
-            assertColumnValue(entryTable, i + 1, TITLE_COLUMN_INDEX, entryTable.selectionValue());
-        }
-        //do the same going up again
-        for (int i = SCROLL_ACTION_EXECUTION; i > 0; i--) {
-            robot().pressAndReleaseKey(UP);
-            assertNotNull(entryTable.selectionValue());
-            assertColumnValue(entryTable, i - 1, TITLE_COLUMN_INDEX, entryTable.selectionValue());
-        }
-
-        closeDatabase();
-        exitJabRef();
-    }
-}
diff --git a/src/test/java/org/jabref/gui/IdFetcherDialogTest.java b/src/test/java/org/jabref/gui/IdFetcherDialogTest.java
deleted file mode 100644
index 65a1330b25a..00000000000
--- a/src/test/java/org/jabref/gui/IdFetcherDialogTest.java
+++ /dev/null
@@ -1,121 +0,0 @@
-package org.jabref.gui;
-
-import java.util.stream.Stream;
-
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JDialog;
-import javax.swing.text.JTextComponent;
-
-import org.assertj.swing.core.GenericTypeMatcher;
-import org.assertj.swing.dependency.jsr305.Nonnull;
-import org.assertj.swing.fixture.JTableFixture;
-import org.assertj.swing.timing.Condition;
-import org.junit.jupiter.api.Tag;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.MethodSource;
-
-import static org.assertj.swing.finder.WindowFinder.findDialog;
-import static org.assertj.swing.timing.Pause.pause;
-
-@Tag("GUITest")
-public class IdFetcherDialogTest extends AbstractUITest {
-
-    @ParameterizedTest
-    @MethodSource("instancesToTest")
-    public void insertEmptySearchID(String databaseMode, String fetcherType, String fetchID) {
-        mainFrame.menuItemWithPath("File", "New " + databaseMode + " database").click();
-        JTableFixture entryTable = mainFrame.table();
-
-        entryTable.requireRowCount(0);
-        mainFrame.menuItemWithPath("BibTeX", "New entry...").click();
-
-        GenericTypeMatcher<JDialog> matcher = new GenericTypeMatcher<JDialog>(JDialog.class) {
-            @Override
-            protected boolean isMatching(JDialog dialog) {
-                return "Select entry type".equals(dialog.getTitle());
-            }
-        };
-
-        findDialog(matcher).withTimeout(10_000).using(robot()).button(new GenericTypeMatcher<JButton>(JButton.class) {
-
-            @Override
-            protected boolean isMatching(@Nonnull JButton jButton) {
-                return "Generate".equals(jButton.getText());
-            }
-        }).click();
-
-        GenericTypeMatcher<JDialog> matcherEmptyDialog = new GenericTypeMatcher<JDialog>(JDialog.class) {
-            @Override
-            protected boolean isMatching(JDialog dialog) {
-                return "Empty search ID".equals(dialog.getTitle());
-            }
-        };
-
-        findDialog(matcherEmptyDialog).withTimeout(10_000).using(robot()).button(new GenericTypeMatcher<JButton>(JButton.class) {
-
-            @Override
-            protected boolean isMatching(@Nonnull JButton jButton) {
-                return "OK".equals(jButton.getText());
-            }
-        }).click();
-
-        entryTable.requireRowCount(0);
-    }
-
-    @ParameterizedTest
-    @MethodSource("instancesToTest")
-    public void testFetcherDialog(String databaseMode, String fetcherType, String fetchID) {
-        mainFrame.menuItemWithPath("File", "New " + databaseMode + " database").click();
-        JTableFixture entryTable = mainFrame.table();
-
-        entryTable.requireRowCount(0);
-        mainFrame.menuItemWithPath("BibTeX", "New entry...").click();
-
-        GenericTypeMatcher<JDialog> matcher = new GenericTypeMatcher<JDialog>(JDialog.class) {
-            @Override
-            protected boolean isMatching(JDialog dialog) {
-                return "Select entry type".equals(dialog.getTitle());
-            }
-        };
-
-        findDialog(matcher).withTimeout(10_000).using(robot()).comboBox(new GenericTypeMatcher<JComboBox>(JComboBox.class) {
-            @Override
-            protected boolean isMatching(@Nonnull JComboBox component) {
-                return true;
-            }
-        }).selectItem(fetcherType);
-
-        findDialog(matcher).withTimeout(10_000).using(robot()).textBox(new GenericTypeMatcher<JTextComponent>(JTextComponent.class) {
-            @Override
-            protected boolean isMatching(@Nonnull JTextComponent component) {
-                return true;
-            }
-        }).enterText(fetchID);
-
-        findDialog(matcher).withTimeout(10_000).using(robot()).button(new GenericTypeMatcher<JButton>(JButton.class) {
-            @Override
-            protected boolean isMatching(@Nonnull JButton jButton) {
-                return "Generate".equals(jButton.getText());
-            }
-        }).click();
-
-        pause(new Condition("entrySize") {
-            @Override
-            public boolean test() {
-                return entryTable.rowCount() == 1;
-            }
-        }, 10_000);
-
-        entryTable.requireRowCount(1);
-    }
-
-    public static Stream<Object[]> instancesToTest() {
-        return Stream.of(
-                new Object[]{"BibTeX", "DOI", "10.1002/9781118257517"},
-                new Object[]{"biblatex", "DOI", "10.1002/9781118257517"},
-                new Object[]{"BibTeX", "ISBN", "9780321356680"},
-                new Object[]{"biblatex", "ISBN", "9780321356680"}
-        );
-    }
-}
diff --git a/src/test/java/org/jabref/gui/ParameterizedDialogNewEntryTest.java b/src/test/java/org/jabref/gui/ParameterizedDialogNewEntryTest.java
deleted file mode 100644
index 2cfd70baa8a..00000000000
--- a/src/test/java/org/jabref/gui/ParameterizedDialogNewEntryTest.java
+++ /dev/null
@@ -1,191 +0,0 @@
-package org.jabref.gui;
-
-import java.util.Locale;
-import java.util.stream.Stream;
-
-import javax.swing.JButton;
-import javax.swing.JDialog;
-
-import org.assertj.swing.core.GenericTypeMatcher;
-import org.assertj.swing.dependency.jsr305.Nonnull;
-import org.assertj.swing.fixture.JTableFixture;
-import org.junit.jupiter.api.Tag;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.MethodSource;
-
-import static org.assertj.swing.finder.WindowFinder.findDialog;
-
-@Tag("GUITest")
-public class ParameterizedDialogNewEntryTest extends AbstractUITest {
-
-    @ParameterizedTest
-    @MethodSource("instancesToTest")
-    public void addEntryOfGivenType(String databaseMode, String entryType) {
-        mainFrame.menuItemWithPath("File", "New " + databaseMode + " database").click();
-        JTableFixture entryTable = mainFrame.table();
-
-        entryTable.requireRowCount(0);
-        mainFrame.menuItemWithPath("BibTeX", "New entry...").click();
-
-        selectEntryType(entryType);
-
-        entryTable.requireRowCount(1);
-    }
-
-    private void selectEntryType(String entryType) {
-        GenericTypeMatcher<JDialog> matcher = new GenericTypeMatcher<JDialog>(JDialog.class) {
-
-            @Override
-            protected boolean isMatching(JDialog dialog) {
-                return "Select entry type".equals(dialog.getTitle());
-            }
-        };
-
-        findDialog(matcher).withTimeout(10_000).using(robot()).button(new GenericTypeMatcher<JButton>(JButton.class) {
-
-            @Override
-            protected boolean isMatching(@Nonnull JButton jButton) {
-                return entryType.equals(jButton.getText());
-            }
-        }).click();
-    }
-
-    @ParameterizedTest
-    @MethodSource("instancesToTest")
-    public void addEntryPlainTextOfGivenType(String databaseMode, String entryType) {
-        mainFrame.menuItemWithPath("File", "New " + databaseMode + " database").click();
-        JTableFixture entryTable = mainFrame.table();
-
-        entryTable.requireRowCount(0);
-        mainFrame.menuItemWithPath("BibTeX", "New entry from plain text...").click();
-
-        selectEntryType(entryType);
-
-        GenericTypeMatcher<JDialog> matcher2 = plainTextMatcher(entryType);
-
-        findDialog(matcher2).withTimeout(10_000).using(robot()).button(new GenericTypeMatcher<JButton>(JButton.class) {
-
-            @Override
-            protected boolean isMatching(@Nonnull JButton jButton) {
-                return "Accept".equals(jButton.getText());
-            }
-        }).click();
-
-        entryTable.requireRowCount(1);
-    }
-
-    @ParameterizedTest
-    @MethodSource("instancesToTest")
-    public void closeAddingEntryPlainTextOfGivenType(String databaseMode, String entryType) {
-        mainFrame.menuItemWithPath("File", "New " + databaseMode + " database").click();
-        JTableFixture entryTable = mainFrame.table();
-
-        entryTable.requireRowCount(0);
-        mainFrame.menuItemWithPath("BibTeX", "New entry from plain text...").click();
-
-        selectEntryType(entryType);
-
-        GenericTypeMatcher<JDialog> matcher2 = plainTextMatcher(entryType);
-
-        findDialog(matcher2).withTimeout(10_000).using(robot()).close();
-        entryTable.requireRowCount(0);
-    }
-
-    @ParameterizedTest
-    @MethodSource("instancesToTest")
-    public void cancelAddingEntryPlainTextOfGivenType(String databaseMode, String entryType) {
-        mainFrame.menuItemWithPath("File", "New " + databaseMode + " database").click();
-        JTableFixture entryTable = mainFrame.table();
-
-        entryTable.requireRowCount(0);
-        mainFrame.menuItemWithPath("BibTeX", "New entry from plain text...").click();
-
-        selectEntryType(entryType);
-
-        GenericTypeMatcher<JDialog> matcher2 = plainTextMatcher(entryType);
-
-        findDialog(matcher2).withTimeout(10_000).using(robot()).button(new GenericTypeMatcher<JButton>(JButton.class) {
-
-            @Override
-            protected boolean isMatching(@Nonnull JButton jButton) {
-                return "Cancel".equals(jButton.getText());
-            }
-        }).click();
-
-        entryTable.requireRowCount(0);
-    }
-
-    private GenericTypeMatcher<JDialog> plainTextMatcher(String entryType) {
-        GenericTypeMatcher<JDialog> matcher2 = new GenericTypeMatcher<JDialog>(JDialog.class) {
-
-            @Override
-            protected boolean isMatching(JDialog dialog) {
-                return ("Plain text import for " + entryType.toLowerCase(Locale.ENGLISH)).equals(dialog.getTitle());
-            }
-        };
-        return matcher2;
-    }
-
-    public static Stream<Object[]> instancesToTest() {
-        // Create entry from menu
-        // Structure:
-        // {"BibTeX"/"biblatex", "type"}
-        // @formatter:off
-        return Stream.of(
-                new Object[]{"BibTeX", "Article"},
-/*                new Object[]{"BibTeX", "InBook"},
-                new Object[]{"BibTeX", "Book"},
-                new Object[]{"BibTeX", "Booklet"},
-                new Object[]{"BibTeX", "InCollection"},
-                new Object[]{"BibTeX", "Conference"},
-                new Object[]{"BibTeX", "InProceedings"},
-                new Object[]{"BibTeX", "Proceedings"},
-                new Object[]{"BibTeX", "Manual"},
-                new Object[]{"BibTeX", "MastersThesis"},
-                new Object[]{"BibTeX", "PhdThesis"},
-                new Object[]{"BibTeX", "TechReport"},
-                new Object[]{"BibTeX", "Unpublished"},
-                new Object[]{"BibTeX", "Misc"},
-                new Object[]{"BibTeX", "Electronic"},
-                new Object[]{"BibTeX", "IEEEtranBSTCTL"},
-                new Object[]{"BibTeX", "Periodical"},
-                new Object[]{"BibTeX", "Patent"},
-                new Object[]{"BibTeX", "Standard"},
-                new Object[]{"biblatex", "Article"},
-                new Object[]{"biblatex", "Book"},
-                new Object[]{"biblatex", "BookInBook"},
-                new Object[]{"biblatex", "Booklet"},
-                new Object[]{"biblatex", "Collection"},
-                new Object[]{"biblatex", "Conference"},
-                new Object[]{"biblatex", "Electronic"},
-                new Object[]{"biblatex", "IEEEtranBSTCTL"},
-                new Object[]{"biblatex", "InBook"},
-                new Object[]{"biblatex", "InCollection"},
-                new Object[]{"biblatex", "InProceedings"},
-                new Object[]{"biblatex", "InReference"},
-                new Object[]{"biblatex", "Manual"},
-                new Object[]{"biblatex", "MastersThesis"},
-                new Object[]{"biblatex", "Misc"},
-                new Object[]{"biblatex", "MvBook"},
-                new Object[]{"biblatex", "MvCollection"},
-                new Object[]{"biblatex", "MvProceedings"},
-                new Object[]{"biblatex", "MvReference"},
-                new Object[]{"biblatex", "Online"},
-                new Object[]{"biblatex", "Patent"},
-                new Object[]{"biblatex", "Periodical"},
-                new Object[]{"biblatex", "PhdThesis"},
-                new Object[]{"biblatex", "Proceedings"},
-                new Object[]{"biblatex", "Reference"},
-                new Object[]{"biblatex", "Report"},
-                new Object[]{"biblatex", "Set"},
-                new Object[]{"biblatex", "SuppBook"},
-                new Object[]{"biblatex", "SuppCollection"},
-                new Object[]{"biblatex", "SuppPeriodical"},
-                new Object[]{"biblatex", "TechReport"},
-                new Object[]{"biblatex", "Thesis"},
-                new Object[]{"biblatex", "Unpublished"},*/
-                new Object[]{"biblatex", "WWW"}
-        );
-        // @formatter:on
-    }
-}
diff --git a/src/test/java/org/jabref/gui/ParameterizedDialogTest.java b/src/test/java/org/jabref/gui/ParameterizedDialogTest.java
deleted file mode 100644
index de3d6dcfc43..00000000000
--- a/src/test/java/org/jabref/gui/ParameterizedDialogTest.java
+++ /dev/null
@@ -1,133 +0,0 @@
-package org.jabref.gui;
-
-import java.util.stream.Stream;
-
-import javax.swing.JButton;
-import javax.swing.JDialog;
-
-import org.assertj.swing.core.GenericTypeMatcher;
-import org.assertj.swing.dependency.jsr305.Nonnull;
-import org.junit.jupiter.api.Tag;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.MethodSource;
-
-import static org.assertj.swing.finder.WindowFinder.findDialog;
-
-@Tag("GUITest")
-public class ParameterizedDialogTest extends AbstractUITest {
-
-    @ParameterizedTest
-    @MethodSource("instancesToTest")
-    public void openAndExitDialog(boolean createDatabase, String[] menuPath, String dialogTitle, String buttonName,
-                                  boolean closeButton) {
-        if (createDatabase) {
-            newDatabase();
-        }
-        mainFrame.menuItemWithPath(menuPath).click();
-        GenericTypeMatcher<JDialog> matcher = new GenericTypeMatcher<JDialog>(JDialog.class) {
-
-            @Override
-            protected boolean isMatching(JDialog dialog) {
-                return dialogTitle.equals(dialog.getTitle());
-            }
-        };
-
-        if (closeButton) {
-            findDialog(matcher).withTimeout(10_000).using(robot()).close();
-        } else {
-            findDialog(matcher).withTimeout(10_000).using(robot())
-                               .button(new GenericTypeMatcher<JButton>(JButton.class) {
-
-                                   @Override
-                                   protected boolean isMatching(@Nonnull JButton jButton) {
-                                       return buttonName.equals(jButton.getText());
-                                   }
-                               }).click();
-        }
-        if (createDatabase) {
-            closeDatabase();
-        }
-        exitJabRef();
-    }
-
-    public static Stream<Object[]> instancesToTest() {
-        // Opening and closing (in different ways) the dialogs accessible from the menus without doing anything else
-        // Structure:
-        // {create new database, {"Menu", "Submenu", "Sub-sub-menu"}, "Dialog title", "Button name", use close button}
-        // @formatter:off
-        return Stream.of(
-                new Object[]{false, new String[]{"File", "Open library"}, "Open", "Cancel", false},
-                new Object[]{false, new String[]{"File", "Open library"}, "Open", "Close button", true},
-                new Object[]{true, new String[]{"File", "Append library"}, "Append library", "Cancel", false},
-                new Object[]{true, new String[]{"File", "Append library"}, "Append library", "Close button", true},
-                new Object[]{true, new String[]{"File", "Save library"}, "Save", "Cancel", false},
-                new Object[]{true, new String[]{"File", "Save library"}, "Save", "Close button", true},
-                new Object[]{true, new String[]{"File", "Save library as..."}, "Save", "Cancel", false},
-                new Object[]{true, new String[]{"File", "Save library as..."}, "Save", "Close button", true},
-                new Object[]{true, new String[]{"File", "Save all"}, "Save", "Cancel", false},
-                new Object[]{true, new String[]{"File", "Save all"}, "Save", "Close button", true},
-                new Object[]{false, new String[]{"File", "Import into new library"}, "Open", "Cancel", false},
-                new Object[]{false, new String[]{"File", "Import into new library"}, "Open", "Close button", true},
-                new Object[]{true, new String[]{"File", "Import into current library"}, "Open", "Cancel", false},
-                new Object[]{true, new String[]{"File", "Import into current library"}, "Open", "Close button", true},
-                new Object[]{true, new String[]{"File", "Export"}, "Save", "Cancel", false},
-                new Object[]{true, new String[]{"File", "Export"}, "Save", "Close button", true},
-                new Object[]{true, new String[]{"File", "Open shared database"}, "Open shared database", "Cancel", false},
-                new Object[]{true, new String[]{"File", "Library properties"}, "Library properties", "Cancel", false},
-                new Object[]{true, new String[]{"File", "Library properties"}, "Library properties", "OK", false},
-                new Object[]{true, new String[]{"File", "Library properties"}, "Library properties", "Close button", true},
-                new Object[]{true, new String[]{"Edit", "Set/clear/rename fields..."}, "Set/clear/rename fields", "Cancel", false},
-                //new Object[]{true, new String[]{"Edit", "Set/clear/rename fields..."}, "Set/clear/rename fields", "OK", false},
-                new Object[]{true, new String[]{"Edit", "Set/clear/rename fields..."}, "Set/clear/rename fields", "Close button", true},
-                new Object[]{true, new String[]{"Search", "Replace string..."}, "Replace string", "Cancel", false},
-                new Object[]{true, new String[]{"Search", "Replace string..."}, "Replace string", "Close button", true},
-                new Object[]{true, new String[]{"Groups", "Add to group..."}, "Add to group", "Cancel", false},
-                new Object[]{true, new String[]{"Groups", "Add to group..."}, "Add to group", "Close button", true},
-                new Object[]{true, new String[]{"Groups", "Remove from group..."}, "Remove from group", "Cancel", false},
-                new Object[]{true, new String[]{"Groups", "Remove from group..."}, "Remove from group", "Close button", true},
-                new Object[]{true, new String[]{"Groups", "Move to group..."}, "Move to group", "Cancel", false},
-                new Object[]{true, new String[]{"Groups", "Move to group..."}, "Move to group", "Close button", true},
-                new Object[]{true, new String[]{"BibTeX", "New entry..."}, "Select entry type", "Cancel", false},
-                new Object[]{true, new String[]{"BibTeX", "New entry..."}, "Select entry type", "Close button", true},
-                new Object[]{true, new String[]{"BibTeX", "Edit preamble"}, "Edit preamble", "Close button", true},
-                new Object[]{true, new String[]{"BibTeX", "Edit strings"}, "Strings for library: untitled", "Close button", true},
-                new Object[]{true, new String[]{"BibTeX", "Customize entry types"}, "Customize entry types", "Cancel", false},
-                new Object[]{true, new String[]{"BibTeX", "Customize entry types"}, "Customize entry types", "OK", false},
-                new Object[]{true, new String[]{"BibTeX", "Customize entry types"}, "Customize entry types", "Close button", true},
-                new Object[]{true, new String[]{"Quality", "Synchronize file links..."}, "Synchronize file links", "Cancel", false},
-                new Object[]{true, new String[]{"Quality", "Synchronize file links..."}, "Synchronize file links", "Close button", true},
-                new Object[]{true, new String[]{"Quality", "Find unlinked files..."}, "Find unlinked files", "Close", false},
-                new Object[]{true, new String[]{"Quality", "Find unlinked files..."}, "Find unlinked files", "Close button", true},
-                new Object[]{true, new String[]{"Tools", "New sublibrary based on AUX file..."}, "AUX file import", "Cancel", false},
-                new Object[]{true, new String[]{"Tools", "New sublibrary based on AUX file..."}, "AUX file import", "Close button", true},
-                new Object[]{false, new String[]{"Options", "Preferences"}, "JabRef preferences", "Cancel", false},
-                new Object[]{false, new String[]{"Options", "Preferences"}, "JabRef preferences", "OK", false},
-                new Object[]{false, new String[]{"Options", "Preferences"}, "JabRef preferences", "Close button", true},
-                new Object[]{false, new String[]{"Options", "Set up general fields"}, "Set general fields", "Cancel", false},
-                new Object[]{false, new String[]{"Options", "Set up general fields"}, "Set general fields", "OK", false},
-                new Object[]{false, new String[]{"Options", "Set up general fields"}, "Set general fields", "Close button", true},
-                new Object[]{false, new String[]{"Options", "Manage custom exports"}, "Manage custom exports", "Close", false},
-                new Object[]{false, new String[]{"Options", "Manage custom exports"}, "Manage custom exports", "Close button", true},
-                new Object[]{false, new String[]{"Options", "Manage custom imports"}, "Manage custom imports", "Close", false},
-                new Object[]{false, new String[]{"Options", "Manage custom imports"}, "Manage custom imports", "Close button", true},
-                new Object[]{false, new String[]{"Options", "Manage external file types"}, "Manage external file types", "Cancel", false},
-                new Object[]{false, new String[]{"Options", "Manage external file types"}, "Manage external file types", "OK", false},
-                new Object[]{false, new String[]{"Options", "Manage external file types"}, "Manage external file types", "Close button", true},
-                new Object[]{false, new String[]{"Options", "Manage journal abbreviations"}, "Journal abbreviations", "Cancel", false},
-                new Object[]{false, new String[]{"Options", "Manage journal abbreviations"}, "Journal abbreviations", "OK", false},
-                new Object[]{false, new String[]{"Options", "Manage journal abbreviations"}, "Journal abbreviations", "Close button", true},
-                new Object[]{true, new String[]{"Options", "Manage content selectors"}, "Manage content selectors", "Cancel", false},
-                // new Object[]{true, new String[]{"Options", "Manage content selectors"}, "Manage content selectors", "OK", false},
-                new Object[]{true, new String[]{"Options", "Manage content selectors"}, "Manage content selectors", "Close button", true},
-                new Object[]{false, new String[]{"Options", "Manage protected terms"}, "Manage protected terms files", "Cancel", false},
-                new Object[]{false, new String[]{"Options", "Manage protected terms"}, "Manage protected terms files", "OK", false},
-                new Object[]{false, new String[]{"Options", "Manage protected terms"}, "Manage protected terms files", "Close button", true},
-                new Object[]{false, new String[]{"Options", "Customize key bindings"}, "Key bindings", "Cancel", false},
-                new Object[]{false, new String[]{"Options", "Customize key bindings"}, "Key bindings", "Close button", true},
-                new Object[]{false, new String[]{"Help", "Show error console"}, "Program output", "OK", false},
-                new Object[]{false, new String[]{"Help", "Show error console"}, "Program output", "Close button", true},
-                new Object[]{false, new String[]{"Help", "About JabRef"}, "About JabRef", "Close button", true}
-        );
-        // @formatter:on
-    }
-}
diff --git a/src/test/java/org/jabref/gui/ParameterizedMenuNewEntryTest.java b/src/test/java/org/jabref/gui/ParameterizedMenuNewEntryTest.java
deleted file mode 100644
index 67efff9e04b..00000000000
--- a/src/test/java/org/jabref/gui/ParameterizedMenuNewEntryTest.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package org.jabref.gui;
-
-import java.util.stream.Stream;
-
-import org.jabref.model.strings.StringUtil;
-
-import org.assertj.swing.fixture.JTableFixture;
-import org.junit.jupiter.api.Tag;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.MethodSource;
-
-@Tag("GUITest")
-public class ParameterizedMenuNewEntryTest extends AbstractUITest {
-
-    // Not working on Travis
-    @ParameterizedTest
-    @MethodSource("instancesToTest")
-    public void addEntryOfGivenType(String databaseMode, String entryType) {
-        mainFrame.menuItemWithPath("File", "New " + databaseMode + " database").click();
-        JTableFixture entryTable = mainFrame.table();
-
-        entryTable.requireRowCount(0);
-        mainFrame.menuItemWithPath("BibTeX", "New entry by type...", StringUtil.capitalizeFirst(entryType)).click();
-        entryTable.requireRowCount(1);
-    }
-
-    public static Stream<Object[]> instancesToTest() {
-        // Create entry from menu
-        // Structure:
-        // {"BibTeX"/"biblatex", "type"}
-        // @formatter:off
-        return Stream.of(
-                new Object[]{"BibTeX", "article"},
-                new Object[]{"BibTeX", "inbook"},
-                new Object[]{"BibTeX", "book"},
-                new Object[]{"BibTeX", "booklet"},
-                new Object[]{"BibTeX", "incollection"},
-                new Object[]{"BibTeX", "conference"},
-                new Object[]{"BibTeX", "inproceedings"},
-                new Object[]{"BibTeX", "proceedings"},
-                new Object[]{"BibTeX", "manual"},
-                new Object[]{"BibTeX", "mastersthesis"},
-                new Object[]{"BibTeX", "phdthesis"},
-                new Object[]{"BibTeX", "techreport"},
-                new Object[]{"BibTeX", "unpublished"},
-                new Object[]{"BibTeX", "misc"},
-                new Object[]{"biblatex", "article"},
-                new Object[]{"biblatex", "inbook"},
-                new Object[]{"biblatex", "book"},
-                new Object[]{"biblatex", "booklet"},
-                new Object[]{"biblatex", "incollection"},
-                new Object[]{"biblatex", "conference"},
-                new Object[]{"biblatex", "inproceedings"},
-                new Object[]{"biblatex", "proceedings"},
-                new Object[]{"biblatex", "manual"},
-                new Object[]{"biblatex", "mastersthesis"},
-                new Object[]{"biblatex", "phdthesis"},
-                new Object[]{"biblatex", "techreport"},
-                new Object[]{"biblatex", "unpublished"},
-                new Object[]{"biblatex", "misc"}
-        );
-        // @formatter:on
-    }
-}
diff --git a/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java b/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java
index df3012e67ad..51a27e3b70a 100644
--- a/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java
+++ b/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java
@@ -13,6 +13,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.util.DummyFileUpdateMonitor;
+import org.jabref.testutils.category.GUITest;
 
 import org.fxmisc.richtext.CodeArea;
 import org.junit.jupiter.api.Test;
@@ -23,6 +24,7 @@
 
 import static org.mockito.Mockito.mock;
 
+@GUITest
 @ExtendWith(ApplicationExtension.class)
 public class SourceTabTest {
 
diff --git a/src/test/java/org/jabref/gui/mergeentries/DiffHighlightingTest.java b/src/test/java/org/jabref/gui/mergeentries/DiffHighlightingTest.java
index 70d0b601cd6..9ed45408946 100644
--- a/src/test/java/org/jabref/gui/mergeentries/DiffHighlightingTest.java
+++ b/src/test/java/org/jabref/gui/mergeentries/DiffHighlightingTest.java
@@ -7,11 +7,14 @@
 
 import javafx.scene.text.Text;
 
+import org.jabref.testutils.category.GUITest;
+
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.testfx.framework.junit5.ApplicationExtension;
 
+@GUITest
 @ExtendWith(ApplicationExtension.class)
 class DiffHighlightingTest {
 
diff --git a/src/test/java/org/jabref/gui/search/ContainsAndRegexBasedSearchRuleDescriberTest.java b/src/test/java/org/jabref/gui/search/ContainsAndRegexBasedSearchRuleDescriberTest.java
index 278556f0db4..cfc515f5949 100644
--- a/src/test/java/org/jabref/gui/search/ContainsAndRegexBasedSearchRuleDescriberTest.java
+++ b/src/test/java/org/jabref/gui/search/ContainsAndRegexBasedSearchRuleDescriberTest.java
@@ -9,12 +9,14 @@
 
 import org.jabref.gui.search.rules.describer.ContainsAndRegexBasedSearchRuleDescriber;
 import org.jabref.gui.util.TooltipTextUtil;
+import org.jabref.testutils.category.GUITest;
 
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.testfx.framework.junit5.ApplicationExtension;
 import org.testfx.framework.junit5.Start;
 
+@GUITest
 @ExtendWith(ApplicationExtension.class)
 class ContainsAndRegexBasedSearchRuleDescriberTest {
 
diff --git a/src/test/java/org/jabref/gui/search/GrammarBasedSearchRuleDescriberTest.java b/src/test/java/org/jabref/gui/search/GrammarBasedSearchRuleDescriberTest.java
index 7855be39bae..36ae0dbea71 100644
--- a/src/test/java/org/jabref/gui/search/GrammarBasedSearchRuleDescriberTest.java
+++ b/src/test/java/org/jabref/gui/search/GrammarBasedSearchRuleDescriberTest.java
@@ -10,6 +10,7 @@
 import org.jabref.gui.search.rules.describer.GrammarBasedSearchRuleDescriber;
 import org.jabref.gui.util.TooltipTextUtil;
 import org.jabref.model.search.rules.GrammarBasedSearchRule;
+import org.jabref.testutils.category.GUITest;
 
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -18,6 +19,7 @@
 
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
+@GUITest
 @ExtendWith(ApplicationExtension.class)
 class GrammarBasedSearchRuleDescriberTest {
 
diff --git a/src/test/java/org/jabref/gui/search/SearchResultsTest.java b/src/test/java/org/jabref/gui/search/SearchResultsTest.java
deleted file mode 100644
index 1e2badcc2ad..00000000000
--- a/src/test/java/org/jabref/gui/search/SearchResultsTest.java
+++ /dev/null
@@ -1,96 +0,0 @@
-package org.jabref.gui.search;
-
-import java.util.concurrent.TimeUnit;
-
-import javax.swing.JFrame;
-
-import org.jabref.testutils.TestUtils;
-
-import org.assertj.swing.core.ComponentFinder;
-import org.assertj.swing.edt.FailOnThreadViolationRepaintManager;
-import org.assertj.swing.finder.WindowFinder;
-import org.assertj.swing.fixture.FrameFixture;
-import org.assertj.swing.fixture.JTextComponentFixture;
-import org.assertj.swing.junit.testcase.AssertJSwingJUnitTestCase;
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Tag;
-import org.junit.jupiter.api.Test;
-
-@Tag("GUITest")
-public class SearchResultsTest extends AssertJSwingJUnitTestCase {
-
-    private FrameFixture frameFixture;
-
-    @BeforeAll
-    public static void before() {
-        FailOnThreadViolationRepaintManager.uninstall();
-    }
-
-    @Override
-    protected void onSetUp() {
-        TestUtils.initJabRef();
-        frameFixture = WindowFinder.findFrame(JFrame.class).withTimeout(15, TimeUnit.SECONDS).using(robot());
-    }
-
-    @Override
-    protected void onTearDown() {
-        frameFixture.close();
-        frameFixture = null;
-
-        TestUtils.closeJabRef();
-    }
-
-    @Test
-    public void testSearchFieldQuery() {
-        frameFixture.menuItemWithPath("Search", "Search").click();
-        JTextComponentFixture searchField = frameFixture.textBox();
-        ComponentFinder finder = robot().finder();
-        /*
-        BasePanel panel = finder.findByType(BasePanel.class);
-        Collection<BibEntry> entries = panel.getDatabase().getEntries();
-
-        searchField.deleteText().enterText("");
-        Assert.assertEquals(19, entries.size());
-
-        searchField.deleteText().enterText("entrytype=article");
-        Assert.assertFalse(entries.stream().noneMatch(entry -> entry.isSearchHit()));
-        Assert.assertEquals(5, entries.stream().filter(entry -> entry.isSearchHit()).count());
-
-        searchField.deleteText().enterText("entrytype=proceedings");
-        Assert.assertFalse(entries.stream().noneMatch(entry -> entry.isSearchHit()));
-        Assert.assertEquals(13, entries.stream().filter(entry -> entry.isSearchHit()).count());
-
-        searchField.deleteText().enterText("entrytype=book");
-        Assert.assertFalse(entries.stream().noneMatch(entry -> entry.isSearchHit()));
-        Assert.assertEquals(1, entries.stream().filter(entry -> entry.isSearchHit()).count());
-        */
-    }
-
-    @Test
-    public void testSeachWithoutResults() {
-        /*
-        frameFixture.menuItemWithPath("Search", "Search").click();
-        JTextComponentFixture searchField = frameFixture.textBox();
-        ComponentFinder finder = robot().finder();
-        BasePanel panel = finder.findByType(BasePanel.class);
-        Collection<BibEntry> entries = panel.getDatabase().getEntries();
-
-        searchField.deleteText().enterText("asdf");
-        Assert.assertTrue(entries.stream().noneMatch(entry -> entry.isSearchHit()));
-        */
-    }
-
-    @Test
-    public void testSearchInvalidQuery() {
-        /*
-        frameFixture.menuItemWithPath("Search", "Search").click();
-        JTextComponentFixture searchField = frameFixture.textBox();
-        ComponentFinder finder = robot().finder();
-        BasePanel panel = finder.findByType(BasePanel.class);
-        Collection<BibEntry> entries = panel.getDatabase().getEntries();
-
-        searchField.deleteText().enterText("asdf[");
-        Assert.assertTrue(entries.stream().noneMatch(entry -> entry.isSearchHit()));
-        */
-    }
-}

From 0a0f4f9b012c9bee5417a11be231b68d13131661 Mon Sep 17 00:00:00 2001
From: Abraham Polk <abepolk@gmail.com>
Date: Fri, 8 Mar 2019 12:59:44 -0500
Subject: [PATCH 092/184] Use action handler (#4726)

* Use actionHandler to update fields

* Add actionHandler

* Add imports

* Final fixes
---
 .../org/jabref/gui/groups/GroupDialog.java    | 28 ++++++++-----------
 1 file changed, 12 insertions(+), 16 deletions(-)

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
index dc7d4ebd615..16b8601a8dd 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDialog.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -7,8 +7,9 @@
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 
-import javafx.beans.value.ChangeListener;
 import javafx.beans.value.ObservableValue;
+import javafx.event.ActionEvent;
+import javafx.event.EventHandler;
 import javafx.geometry.Insets;
 import javafx.geometry.Orientation;
 import javafx.scene.Node;
@@ -329,21 +330,16 @@ groupName, getContext(),
             return null;
         });
 
-        ChangeListener<String> caretListener = (ObservableValue<? extends String> ov, String oldValue,
-                                                String newValue) -> updateComponents();
-        ChangeListener<Boolean> itemListener = (ObservableValue<? extends Boolean> ov, Boolean oldBoolean,
-                                                Boolean newBoolean) -> updateComponents();
-
-        nameField.textProperty().addListener(caretListener);
-        descriptionField.textProperty().addListener(caretListener);
-        iconField.textProperty().addListener(caretListener);
-        keywordGroupSearchField.textProperty().addListener(caretListener);
-        keywordGroupSearchTerm.textProperty().addListener(caretListener);
-        keywordGroupCaseSensitive.selectedProperty().addListener(itemListener);
-        keywordGroupRegExp.selectedProperty().addListener(itemListener);
-        searchGroupSearchExpression.textProperty().addListener(caretListener);
-        searchGroupRegExp.selectedProperty().addListener(itemListener);
-        searchGroupRegExp.selectedProperty().addListener(itemListener);
+        EventHandler<ActionEvent> actionHandler = (ActionEvent e) -> updateComponents();
+        nameField.setOnAction(actionHandler);
+        descriptionField.setOnAction(actionHandler);
+        iconField.setOnAction(actionHandler);
+        keywordGroupSearchField.setOnAction(actionHandler);
+        keywordGroupSearchTerm.setOnAction(actionHandler);
+        keywordGroupCaseSensitive.setOnAction(actionHandler);
+        keywordGroupRegExp.setOnAction(actionHandler);
+        searchGroupSearchExpression.setOnAction(actionHandler);
+        searchGroupRegExp.setOnAction(actionHandler);
 
         // configure for current type
         if (editedGroup == null) {

From 1d4e2d1ad254a32a1444e0515a8bfdef1a812a8c Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Sat, 9 Mar 2019 11:11:41 +0100
Subject: [PATCH 093/184] Rework import inspection dialog in JavaFX (#4692)

* Rework import inspection dialog in JavaFX

* Implement feedback and improve ui design

* Fix build
---
 src/main/java/org/jabref/Globals.java         |    2 +
 src/main/java/org/jabref/gui/Base.css         |   34 +
 .../java/org/jabref/gui/DefaultInjector.java  |    4 +
 .../jabref/gui/DuplicateResolverDialog.java   |   16 +-
 .../java/org/jabref/gui/DuplicateSearch.java  |    2 +-
 .../org/jabref/gui/EntryTypeViewModel.java    |   34 +-
 src/main/java/org/jabref/gui/JabRefFrame.java |   27 +-
 .../FindUnlinkedFilesDialog.java              |    4 +-
 .../gui/externalfiles/ImportHandler.java      |   61 +-
 .../java/org/jabref/gui/icon/IconTheme.java   |    6 +-
 .../org/jabref/gui/importer/ImportAction.java |   80 +-
 .../gui/importer/ImportEntriesDialog.css      |   15 +
 .../gui/importer/ImportEntriesDialog.fxml     |   26 +
 .../gui/importer/ImportEntriesDialog.java     |  168 ++
 .../gui/importer/ImportEntriesViewModel.java  |  183 +++
 .../gui/importer/ImportInspectionDialog.java  | 1411 -----------------
 .../fetcher/WebSearchPaneViewModel.java       |   30 +-
 .../org/jabref/gui/maintable/MainTable.java   |    3 +-
 .../preferences/BibtexKeyPatternPrefTab.java  |    4 -
 .../jabref/gui/search/GlobalSearchBar.java    |   25 +-
 .../gui/search/matchers/SearchMatcher.java    |   19 -
 .../org/jabref/gui/util/BackgroundTask.java   |    5 +
 .../org/jabref/gui/util/NoSelectionModel.java |   75 +
 .../org/jabref/gui/util/TextFlowLimited.java  |   81 +
 .../gui/util/ViewModelListCellFactory.java    |   14 +
 .../jabref/model/database/BibDatabase.java    |    9 +-
 .../java/org/jabref/model/entry/BibEntry.java |   19 -
 .../jabref/preferences/JabRefPreferences.java |   26 +-
 .../preferences/PreferencesService.java       |   10 +
 src/main/resources/l10n/JabRef_en.properties  |   43 +-
 .../l10n/LocalizationConsistencyTest.java     |    4 +-
 .../org/jabref/model/entry/BibEntryTests.java |   13 -
 32 files changed, 804 insertions(+), 1649 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/importer/ImportEntriesDialog.css
 create mode 100644 src/main/java/org/jabref/gui/importer/ImportEntriesDialog.fxml
 create mode 100644 src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java
 create mode 100644 src/main/java/org/jabref/gui/importer/ImportEntriesViewModel.java
 delete mode 100644 src/main/java/org/jabref/gui/importer/ImportInspectionDialog.java
 delete mode 100644 src/main/java/org/jabref/gui/search/matchers/SearchMatcher.java
 create mode 100644 src/main/java/org/jabref/gui/util/NoSelectionModel.java
 create mode 100644 src/main/java/org/jabref/gui/util/TextFlowLimited.java

diff --git a/src/main/java/org/jabref/Globals.java b/src/main/java/org/jabref/Globals.java
index b86cc83cbd2..1a5cc0ee385 100644
--- a/src/main/java/org/jabref/Globals.java
+++ b/src/main/java/org/jabref/Globals.java
@@ -9,6 +9,7 @@
 import org.jabref.gui.ClipBoardManager;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.keyboard.KeyBindingRepository;
+import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.gui.util.DefaultFileUpdateMonitor;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.TaskExecutor;
@@ -57,6 +58,7 @@ public class Globals {
 
     public static StateManager stateManager = new StateManager();
     public static ExporterFactory exportFactory;
+    public static CountingUndoManager undoManager = new CountingUndoManager();
     // Key binding preferences
     private static KeyBindingRepository keyBindingRepository;
     private static DefaultFileUpdateMonitor fileUpdateMonitor;
diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
index 14c7861eb45..8c6b1dbe2d8 100644
--- a/src/main/java/org/jabref/gui/Base.css
+++ b/src/main/java/org/jabref/gui/Base.css
@@ -364,6 +364,11 @@
     -fx-fill: white;
 }
 
+.toggle-button:selected.icon-button:selected {
+    -fx-background-color: transparent;
+    -fx-fill: -jr-selected;
+}
+
 .icon-buttonNoSpaceBottom {
     -fx-padding: 0.5em 0.5em -0.1em 0.5em;
 }
@@ -976,6 +981,35 @@ We want to have a look that matches our icons in the tool-bar */
     -fx-border-width: 0px;
 }
 
+.bibEntry {
+
+}
+
+.bibEntry .type {
+    -fx-font-size: 110%;
+}
+
+.bibEntry .title {
+    -fx-font-size: 110%;
+    -fx-font-weight: bold;
+}
+
+.bibEntry .year {
+    -fx-font-size: 101%;
+    -fx-font-weight: bold;
+}
+
+.bibEntry .journal {
+    -fx-font-size: 101%;
+}
+
+.bibEntry .authors {
+    -fx-font-size: 101%;
+}
+
+.bibEntry .summary {
+    -fx-padding: 1ex 0ex 0ex 0ex;
+}
 
 .warning-icon {
     -fx-fill: -jr-warn;
diff --git a/src/main/java/org/jabref/gui/DefaultInjector.java b/src/main/java/org/jabref/gui/DefaultInjector.java
index 4f18a03b9e6..ee7c8c05839 100644
--- a/src/main/java/org/jabref/gui/DefaultInjector.java
+++ b/src/main/java/org/jabref/gui/DefaultInjector.java
@@ -2,6 +2,8 @@
 
 import java.util.function.Function;
 
+import javax.swing.undo.UndoManager;
+
 import org.jabref.Globals;
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.util.TaskExecutor;
@@ -43,6 +45,8 @@ private static Object createDependency(Class<?> clazz) {
             return Globals.protectedTermsLoader;
         } else if (clazz == ClipBoardManager.class) {
             return Globals.clipboardManager;
+        } else if (clazz == UndoManager.class) {
+            return Globals.undoManager;
         } else {
             try {
                 return clazz.newInstance();
diff --git a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
index 0be0d823c83..858a7c7e7f2 100644
--- a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
+++ b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
@@ -12,10 +12,13 @@
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 
 public class DuplicateResolverDialog extends BaseDialog<DuplicateResolverResult> {
 
+    private final BibDatabaseContext database;
+
     public enum DuplicateResolverType {
         DUPLICATE_SEARCH,
         IMPORT_CHECK,
@@ -32,13 +35,12 @@ public enum DuplicateResolverResult {
         BREAK
     }
 
-    private final JabRefFrame frame;
     private MergeEntries me;
 
-    public DuplicateResolverDialog(JabRefFrame frame, BibEntry one, BibEntry two, DuplicateResolverType type) {
-        this.frame = frame;
+    public DuplicateResolverDialog(BibEntry one, BibEntry two, DuplicateResolverType type, BibDatabaseContext database) {
         this.setTitle(Localization.lang("Possible duplicate entries"));
         init(one, two, type);
+        this.database = database;
     }
 
     private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
@@ -61,14 +63,14 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
                 first = new ButtonType(Localization.lang("Keep left"), ButtonData.APPLY);
                 second = new ButtonType(Localization.lang("Keep right"), ButtonData.APPLY);
                 both = new ButtonType(Localization.lang("Keep both"), ButtonData.APPLY);
-                me = new MergeEntries(one, two, frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
+                me = new MergeEntries(one, two, database.getMode());
                 break;
             case INSPECTION:
                 first = new ButtonType(Localization.lang("Remove old entry"), ButtonData.APPLY);
                 second = new ButtonType(Localization.lang("Remove entry from import"), ButtonData.APPLY);
                 both = new ButtonType(Localization.lang("Keep both"), ButtonData.APPLY);
                 me = new MergeEntries(one, two, Localization.lang("Old entry"),
-                        Localization.lang("From import"), frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
+                        Localization.lang("From import"), database.getMode());
                 break;
             case DUPLICATE_SEARCH_WITH_EXACT:
                 first = new ButtonType(Localization.lang("Keep left"), ButtonData.APPLY);
@@ -77,14 +79,14 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
 
                 removeExactVisible = true;
 
-                me = new MergeEntries(one, two, frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
+                me = new MergeEntries(one, two, database.getMode());
                 break;
             default:
                 first = new ButtonType(Localization.lang("Import and remove old entry"), ButtonData.APPLY);
                 second = new ButtonType(Localization.lang("Do not import entry"), ButtonData.APPLY);
                 both = new ButtonType(Localization.lang("Import and keep old entry"), ButtonData.APPLY);
                 me = new MergeEntries(one, two, Localization.lang("Old entry"),
-                        Localization.lang("From import"), frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
+                        Localization.lang("From import"), database.getMode());
                 break;
         }
         if (removeExactVisible) {
diff --git a/src/main/java/org/jabref/gui/DuplicateSearch.java b/src/main/java/org/jabref/gui/DuplicateSearch.java
index 9e9921f741a..0db4c5df1c2 100644
--- a/src/main/java/org/jabref/gui/DuplicateSearch.java
+++ b/src/main/java/org/jabref/gui/DuplicateSearch.java
@@ -122,7 +122,7 @@ private DuplicateSearchResult verifyDuplicates() {
     }
 
     private void askResolveStrategy(DuplicateSearchResult result, BibEntry first, BibEntry second, DuplicateResolverType resolverType) {
-        DuplicateResolverDialog dialog = new DuplicateResolverDialog(frame, first, second, resolverType);
+        DuplicateResolverDialog dialog = new DuplicateResolverDialog(first, second, resolverType, frame.getCurrentBasePanel().getBibDatabaseContext());
 
         DuplicateResolverResult resolverResult = dialog.showAndWait().orElse(DuplicateResolverResult.BREAK);
 
diff --git a/src/main/java/org/jabref/gui/EntryTypeViewModel.java b/src/main/java/org/jabref/gui/EntryTypeViewModel.java
index d023aa48900..766d449f6c4 100644
--- a/src/main/java/org/jabref/gui/EntryTypeViewModel.java
+++ b/src/main/java/org/jabref/gui/EntryTypeViewModel.java
@@ -1,6 +1,5 @@
 package org.jabref.gui;
 
-import java.util.Arrays;
 import java.util.Optional;
 
 import javafx.beans.property.BooleanProperty;
@@ -15,7 +14,6 @@
 import javafx.concurrent.Task;
 import javafx.concurrent.Worker;
 
-import org.jabref.gui.importer.ImportInspectionDialog;
 import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
 import org.jabref.logic.importer.FetcherException;
@@ -138,18 +136,30 @@ public void runFetcherWorker() {
         fetcherWorker.setOnSucceeded(evt -> {
             Optional<BibEntry> result = fetcherWorker.getValue();
             if (result.isPresent()) {
-                final BibEntry bibEntry = result.get();
-                if ((DuplicateCheck.containsDuplicate(basePanel.getDatabase(), bibEntry, basePanel.getBibDatabaseContext().getMode()).isPresent())) {
-                    //If there are duplicates starts ImportInspectionDialog
-                    ImportInspectionDialog diag = new ImportInspectionDialog(basePanel.frame(), basePanel, Localization.lang("Import"), false);
-                    diag.addEntries(Arrays.asList(bibEntry));
-                    diag.entryListComplete();
-                    diag.setVisible(true);
-                    diag.toFront();
+                final BibEntry entry = result.get();
+                Optional<BibEntry> duplicate = DuplicateCheck.containsDuplicate(basePanel.getDatabase(), entry, basePanel.getBibDatabaseContext().getMode());
+                if ((duplicate.isPresent())) {
+                    DuplicateResolverDialog dialog = new DuplicateResolverDialog(entry, duplicate.get(), DuplicateResolverDialog.DuplicateResolverType.IMPORT_CHECK, basePanel.getBibDatabaseContext());
+                    switch (dialog.showAndWait().orElse(DuplicateResolverDialog.DuplicateResolverResult.BREAK)) {
+                        case KEEP_LEFT:
+                            basePanel.getDatabase().removeEntry(duplicate.get());
+                            basePanel.getDatabase().insertEntry(entry);
+                            break;
+                        case KEEP_BOTH:
+                            basePanel.getDatabase().insertEntry(entry);
+                            break;
+                        case KEEP_MERGE:
+                            basePanel.getDatabase().removeEntry(duplicate.get());
+                            basePanel.getDatabase().insertEntry(dialog.getMergedEntry());
+                            break;
+                        default:
+                            // Do nothing
+                            break;
+                    }
                 } else {
                     // Regenerate CiteKey of imported BibEntry
-                    new BibtexKeyGenerator(basePanel.getBibDatabaseContext(), prefs.getBibtexKeyPatternPreferences()).generateAndSetKey(bibEntry);
-                    basePanel.insertEntry(bibEntry);
+                    new BibtexKeyGenerator(basePanel.getBibDatabaseContext(), prefs.getBibtexKeyPatternPreferences()).generateAndSetKey(entry);
+                    basePanel.insertEntry(entry);
                 }
                 searchSuccesfulProperty.set(true);
 
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index e80c93d9386..74144a9ab42 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -93,7 +93,7 @@
 import org.jabref.gui.help.AboutAction;
 import org.jabref.gui.help.HelpAction;
 import org.jabref.gui.importer.ImportCommand;
-import org.jabref.gui.importer.ImportInspectionDialog;
+import org.jabref.gui.importer.ImportEntriesDialog;
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.gui.integrity.IntegrityCheckAction;
 import org.jabref.gui.keyboard.KeyBinding;
@@ -107,6 +107,7 @@
 import org.jabref.gui.search.GlobalSearchBar;
 import org.jabref.gui.specialfields.SpecialFieldMenuItemFactory;
 import org.jabref.gui.undo.CountingUndoManager;
+import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.autosaveandbackup.AutosaveManager;
 import org.jabref.logic.autosaveandbackup.BackupManager;
@@ -179,7 +180,6 @@ public class JabRefFrame extends BorderPane implements OutputPrinter {
     private SidePaneManager sidePaneManager;
     private TabPane tabbedPane;
     private PushToApplications pushApplications;
-    private final CountingUndoManager undoManager = new CountingUndoManager();
     private final DialogService dialogService;
     private SidePane sidePane;
 
@@ -785,7 +785,7 @@ private MenuBar createMenu() {
         if (Globals.prefs.getBoolean(JabRefPreferences.SPECIALFIELDSENABLED)) {
             boolean menuItemAdded = false;
             if (Globals.prefs.getBoolean(JabRefPreferences.SHOWCOLUMN_RANKING)) {
-                edit.getItems().add(SpecialFieldMenuItemFactory.createSpecialFieldMenuForActiveDatabase(SpecialField.RANKING, factory, undoManager));
+                edit.getItems().add(SpecialFieldMenuItemFactory.createSpecialFieldMenuForActiveDatabase(SpecialField.RANKING, factory, Globals.undoManager));
                 menuItemAdded = true;
             }
 
@@ -805,12 +805,12 @@ private MenuBar createMenu() {
             }
 
             if (Globals.prefs.getBoolean(JabRefPreferences.SHOWCOLUMN_PRIORITY)) {
-                edit.getItems().add(SpecialFieldMenuItemFactory.createSpecialFieldMenuForActiveDatabase(SpecialField.PRIORITY, factory, undoManager));
+                edit.getItems().add(SpecialFieldMenuItemFactory.createSpecialFieldMenuForActiveDatabase(SpecialField.PRIORITY, factory, Globals.undoManager));
                 menuItemAdded = true;
             }
 
             if (Globals.prefs.getBoolean(JabRefPreferences.SHOWCOLUMN_READ)) {
-                edit.getItems().add(SpecialFieldMenuItemFactory.createSpecialFieldMenuForActiveDatabase(SpecialField.READ_STATUS, factory, undoManager));
+                edit.getItems().add(SpecialFieldMenuItemFactory.createSpecialFieldMenuForActiveDatabase(SpecialField.READ_STATUS, factory, Globals.undoManager));
                 menuItemAdded = true;
             }
 
@@ -1204,21 +1204,16 @@ private boolean readyForAutosave(BibDatabaseContext context) {
     }
 
     /**
-     * This method does the job of adding imported entries into the active database, or into a new one. It shows the
-     * ImportInspectionDialog if preferences indicate it should be used. Otherwise it imports directly.
+     * Opens the import inspection dialog to let the user decide which of the given entries to import.
      *
      * @param panel   The BasePanel to add to.
      * @param entries The entries to add.
      */
     private void addImportedEntries(final BasePanel panel, final List<BibEntry> entries) {
-        SwingUtilities.invokeLater(() -> {
-            ImportInspectionDialog diag = new ImportInspectionDialog(JabRefFrame.this, panel,
-                    Localization.lang("Import"), false);
-            diag.addEntries(entries);
-            diag.entryListComplete();
-            diag.setVisible(true);
-            diag.toFront();
-        });
+        BackgroundTask<List<BibEntry>> task = BackgroundTask.wrap(() -> entries);
+        ImportEntriesDialog dialog = new ImportEntriesDialog(panel.getBibDatabaseContext(), task);
+        dialog.setTitle(Localization.lang("Import"));
+        dialog.showAndWait();
     }
 
     public FileHistoryMenu getFileHistory() {
@@ -1389,7 +1384,7 @@ public GlobalSearchBar getGlobalSearchBar() {
     }
 
     public CountingUndoManager getUndoManager() {
-        return undoManager;
+        return Globals.undoManager;
     }
 
     public DialogService getDialogService() {
diff --git a/src/main/java/org/jabref/gui/externalfiles/FindUnlinkedFilesDialog.java b/src/main/java/org/jabref/gui/externalfiles/FindUnlinkedFilesDialog.java
index f9e0e8a689c..a4892565632 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FindUnlinkedFilesDialog.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FindUnlinkedFilesDialog.java
@@ -92,8 +92,8 @@ public FindUnlinkedFilesDialog(JabRefFrame frame) {
                 Globals.prefs.getImportFormatPreferences(),
                 Globals.prefs.getUpdateFieldPreferences(),
                 Globals.getFileUpdateMonitor(),
-                frame.getUndoManager()
-        );
+                frame.getUndoManager(),
+                Globals.stateManager);
 
         initialize();
     }
diff --git a/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java b/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
index 6d0860f53f0..53189b82dbd 100644
--- a/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
@@ -1,6 +1,7 @@
 package org.jabref.gui.externalfiles;
 
 import java.nio.file.Path;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 
@@ -9,19 +10,23 @@
 
 import org.jabref.Globals;
 import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
 import org.jabref.logic.externalfiles.ExternalFilesContentImporter;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.util.UpdateField;
 import org.jabref.logic.util.UpdateFieldPreferences;
 import org.jabref.logic.util.io.FileUtil;
+import org.jabref.model.FieldChange;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
+import org.jabref.model.groups.GroupEntryChanger;
+import org.jabref.model.groups.GroupTreeNode;
 import org.jabref.model.metadata.FilePreferences;
 import org.jabref.model.util.FileUpdateMonitor;
-import org.jabref.preferences.JabRefPreferences;
 
 public class ImportHandler {
 
@@ -32,6 +37,7 @@ public class ImportHandler {
     private final ExternalFilesEntryLinker linker;
     private final ExternalFilesContentImporter contentImporter;
     private final UndoManager undoManager;
+    private final StateManager stateManager;
 
     public ImportHandler(DialogService dialogService,
                          BibDatabaseContext database,
@@ -40,12 +46,14 @@ public ImportHandler(DialogService dialogService,
                          ImportFormatPreferences importFormatPreferences,
                          UpdateFieldPreferences updateFieldPreferences,
                          FileUpdateMonitor fileupdateMonitor,
-                         UndoManager undoManager) {
+                         UndoManager undoManager,
+                         StateManager stateManager) {
 
         this.dialogService = dialogService;
         this.database = database;
         this.updateFieldPreferences = updateFieldPreferences;
         this.fileUpdateMonitor = fileupdateMonitor;
+        this.stateManager = stateManager;
 
         this.linker = new ExternalFilesEntryLinker(externalFileTypes, filePreferences, database);
         this.contentImporter = new ExternalFilesContentImporter(importFormatPreferences);
@@ -83,7 +91,7 @@ public void importAsNewEntries(List<Path> files) {
                 entriesToAdd = Collections.singletonList(createEmptyEntryWithLink(file));
             }
 
-            insertEntries(entriesToAdd);
+            importEntries(entriesToAdd);
             entriesToAdd.forEach(entry -> ce.addEdit(new UndoableInsertEntry(database.getDatabase(), entry)));
         }
         ce.end();
@@ -99,15 +107,52 @@ private BibEntry createEmptyEntryWithLink(Path file) {
 
     public void importEntriesFromBibFiles(Path bibFile) {
         List<BibEntry> entriesToImport = contentImporter.importFromBibFile(bibFile, fileUpdateMonitor);
-        insertEntries(entriesToImport);
+        importEntries(entriesToImport);
     }
 
-    private void insertEntries(List<BibEntry> entries) {
+    public void importEntries(List<BibEntry> entries) {
+        //TODO: Add undo/redo
+        //ce.addEdit(new UndoableInsertEntry(panel.getDatabase(), entry));
+
         database.getDatabase().insertEntries(entries);
 
-        if (Globals.prefs.getBoolean(JabRefPreferences.USE_OWNER)) {
-            // Set owner field to default value
-            UpdateField.setAutomaticFields(entries, true, true, updateFieldPreferences);
+        // Set owner/timestamp
+        UpdateField.setAutomaticFields(entries, updateFieldPreferences);
+
+        // Generate bibtex keys
+        generateKeys(entries);
+
+        // Add to group
+        addToGroups(entries, stateManager.getSelectedGroup(database));
+    }
+
+    private void addToGroups(List<BibEntry> entries, Collection<GroupTreeNode> groups) {
+        for (GroupTreeNode node : groups) {
+            if (node.getGroup() instanceof GroupEntryChanger) {
+                GroupEntryChanger entryChanger = (GroupEntryChanger) node.getGroup();
+                List<FieldChange> undo = entryChanger.add(entries);
+                // TODO: Add undo
+                //if (!undo.isEmpty()) {
+                //    ce.addEdit(UndoableChangeEntriesOfGroup.getUndoableEdit(new GroupTreeNodeViewModel(node),
+                //            undo));
+                //}
+            }
+        }
+    }
+
+    /**
+     * Generate keys for given entries.
+     *
+     * @param entries entries to generate keys for
+     */
+    private void generateKeys(List<BibEntry> entries) {
+        BibtexKeyGenerator keyGenerator = new BibtexKeyGenerator(
+                database.getMetaData().getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern()),
+                database.getDatabase(),
+                Globals.prefs.getBibtexKeyPatternPreferences());
+
+        for (BibEntry entry : entries) {
+            keyGenerator.generateAndSetKey(entry);
         }
     }
 }
diff --git a/src/main/java/org/jabref/gui/icon/IconTheme.java b/src/main/java/org/jabref/gui/icon/IconTheme.java
index 55341a664d0..fbb97842ecf 100644
--- a/src/main/java/org/jabref/gui/icon/IconTheme.java
+++ b/src/main/java/org/jabref/gui/icon/IconTheme.java
@@ -44,6 +44,7 @@ public class IconTheme {
      */
     public static final Color DEFAULT_COLOR = JabRefPreferences.getInstance().getColor(JabRefPreferences.ICON_ENABLED_COLOR);
     public static final Color DEFAULT_DISABLED_COLOR = JabRefPreferences.getInstance().getColor(JabRefPreferences.ICON_DISABLED_COLOR);
+    public static final javafx.scene.paint.Color SELECTED_COLOR = javafx.scene.paint.Color.web("#50618F");
     public static Font FONT;
     private static final String DEFAULT_ICON_PATH = "/images/external/red.png";
     private static final Logger LOGGER = LoggerFactory.getLogger(IconTheme.class);
@@ -179,6 +180,7 @@ public static List<Image> getLogoSetFX() {
     public enum JabRefIcons implements JabRefIcon {
 
         ADD(MaterialDesignIcon.PLUS_CIRCLE_OUTLINE),
+        ADD_FILLED(MaterialDesignIcon.PLUS_CIRCLE),
         ADD_NOBOX(MaterialDesignIcon.PLUS),
         ADD_ENTRY(MaterialDesignIcon.BOOKMARK_PLUS),
         EDIT_ENTRY(MaterialDesignIcon.TOOLTIP_EDIT),
@@ -314,7 +316,9 @@ public enum JabRefIcons implements JabRefIcon {
         NEW_FILE(MaterialDesignIcon.PLUS),
         DOWNLOAD(MaterialDesignIcon.DOWNLOAD),
         OWNER(MaterialDesignIcon.ACCOUNT),
-        CLOSE_JABREF(MaterialDesignIcon.GLASSDOOR);
+        CLOSE_JABREF(MaterialDesignIcon.GLASSDOOR),
+        ARTICLE(MaterialDesignIcon.FILE_DOCUMENT),
+        BOOK(MaterialDesignIcon.BOOK_OPEN_PAGE_VARIANT);
 
         private final JabRefIcon icon;
 
diff --git a/src/main/java/org/jabref/gui/importer/ImportAction.java b/src/main/java/org/jabref/gui/importer/ImportAction.java
index f81bb517c9e..99fa2b36f33 100644
--- a/src/main/java/org/jabref/gui/importer/ImportAction.java
+++ b/src/main/java/org/jabref/gui/importer/ImportAction.java
@@ -9,9 +9,8 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import javax.swing.SwingUtilities;
-
 import org.jabref.Globals;
+import org.jabref.JabRefException;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
@@ -24,6 +23,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.UpdateField;
 import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.KeyCollisionException;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibtexString;
@@ -37,10 +37,6 @@ public class ImportAction {
     private Exception importError;
     private final TaskExecutor taskExecutor = Globals.TASK_EXECUTOR;
 
-    public ImportAction(JabRefFrame frame, boolean openInNew) {
-        this(frame, openInNew, null);
-    }
-
     public ImportAction(JabRefFrame frame, boolean openInNew, Importer importer) {
         this.importer = Optional.ofNullable(importer);
         this.frame = frame;
@@ -54,53 +50,41 @@ public ImportAction(JabRefFrame frame, boolean openInNew, Importer importer) {
      */
     public void automatedImport(List<String> filenames) {
         List<Path> files = filenames.stream().map(Paths::get).collect(Collectors.toList());
-        BackgroundTask.wrap(() -> doImport(files))
-                      .onSuccess(this::reportResult)
-                      .executeWith(taskExecutor);
-    }
-
-    private void reportResult(List<ImportFormatReader.UnknownFormatImport> imports) {
-        // Ok, done. Then try to gather in all we have found. Since we might
-        // have found
-        // one or more bibtex results, it's best to gather them in a
-        // BibDatabase.
-        ParserResult bibtexResult = mergeImportResults(imports);
-
-        /* show parserwarnings, if any. */
-        for (ImportFormatReader.UnknownFormatImport p : imports) {
-            if (p != null) {
-                ParserResult pr = p.parserResult;
-                ParserResultWarningDialog.showParserResultWarningDialog(pr, frame);
-            }
-        }
-
-        if (bibtexResult == null) {
-            if (importer == null) {
-                frame.output(Localization.lang("Could not find a suitable import format."));
-            } else {
-                // Import in a specific format was specified. Check if we have stored error information:
+        BackgroundTask<List<BibEntry>> task = BackgroundTask.wrap(() -> {
+            List<ImportFormatReader.UnknownFormatImport> imports = doImport(files);
+            // Ok, done. Then try to gather in all we have found. Since we might
+            // have found
+            // one or more bibtex results, it's best to gather them in a
+            // BibDatabase.
+            ParserResult bibtexResult = mergeImportResults(imports);
+
+            // TODO: show parserwarnings, if any (not here)
+            // for (ImportFormatReader.UnknownFormatImport p : imports) {
+            //    ParserResultWarningDialog.showParserResultWarningDialog(p.parserResult, frame);
+            //}
+            if (bibtexResult == null) {
                 if (importError == null) {
-                    dialogService.showErrorDialogAndWait(Localization.lang("Import failed"),
-                                                         Localization.lang("No entries found. Please make sure you are using the correct import filter."));
+                    throw new JabRefException(Localization.lang("No entries found. Please make sure you are using the correct import filter."));
                 } else {
-                    dialogService.showErrorDialogAndWait(Localization.lang("Import failed"), importError);
+                    throw importError;
                 }
             }
+
+            return bibtexResult.getDatabase().getEntries();
+        });
+
+        if (openInNew) {
+            task.onSuccess(entries -> {
+                frame.addTab(new BibDatabaseContext(new BibDatabase(entries)), true);
+                dialogService.notify(Localization.lang("Imported entries") + ": " + entries.size());
+            })
+                .executeWith(taskExecutor);
         } else {
-            if (openInNew) {
-                frame.addTab(bibtexResult.getDatabaseContext(), true);
-                frame.output(Localization.lang("Imported entries") + ": " + bibtexResult.getDatabase().getEntryCount());
-            } else {
-                final BasePanel panel = frame.getCurrentBasePanel();
-
-                SwingUtilities.invokeLater(() -> {
-                    ImportInspectionDialog diag = new ImportInspectionDialog(frame, panel, Localization.lang("Import"), false);
-                    diag.addEntries(bibtexResult.getDatabase().getEntries());
-                    diag.entryListComplete();
-                    diag.setVisible(true);
-                    diag.toFront();
-                });
-            }
+            final BasePanel panel = frame.getCurrentBasePanel();
+
+            ImportEntriesDialog dialog = new ImportEntriesDialog(panel.getBibDatabaseContext(), task);
+            dialog.setTitle(Localization.lang("Import"));
+            dialog.showAndWait();
         }
     }
 
diff --git a/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.css b/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.css
new file mode 100644
index 00000000000..81442716e85
--- /dev/null
+++ b/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.css
@@ -0,0 +1,15 @@
+.addEntryButton {
+    -fx-font-size: 2em;
+}
+
+.entry-container {
+    /*-fx-padding: 0.5em 0em 0.5em 0em;*/
+}
+
+.list-cell {
+    -fx-padding: 0.5em 0 1em 0.5em;
+}
+
+.list-cell:entry-selected {
+    -fx-background-color: derive(-jr-selected, 60%);
+}
diff --git a/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.fxml b/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.fxml
new file mode 100644
index 00000000000..005abb8ca28
--- /dev/null
+++ b/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.fxml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.ButtonType?>
+<?import javafx.scene.control.DialogPane?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
+<?import org.controlsfx.control.CheckListView?>
+<DialogPane xmlns:fx="http://javafx.com/fxml"
+            xmlns="http://javafx.com/javafx"
+            fx:controller="org.jabref.gui.importer.ImportEntriesDialog"
+            prefHeight="700.0" prefWidth="1000.0">
+    <content>
+        <VBox spacing="10">
+            <Label text="%Select the entries to be imported:"/>
+            <CheckListView fx:id="entriesListView" VBox.vgrow="ALWAYS"/>
+            <HBox>
+                <Button text="%Select all new entries" styleClass="text-button" onAction="#selectAllNewEntries"/>
+                <Button text="%Unselect all" styleClass="text-button" onAction="#unselectAll"/>
+            </HBox>
+        </VBox>
+    </content>
+    <ButtonType fx:id="importButton" text="%Import entries" buttonData="OK_DONE"/>
+    <ButtonType fx:constant="CANCEL"/>
+</DialogPane>
diff --git a/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java b/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java
new file mode 100644
index 00000000000..bc72cb28fcb
--- /dev/null
+++ b/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java
@@ -0,0 +1,168 @@
+package org.jabref.gui.importer;
+
+import java.util.List;
+
+import javax.inject.Inject;
+import javax.swing.undo.UndoManager;
+
+import javafx.css.PseudoClass;
+import javafx.fxml.FXML;
+import javafx.scene.Node;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.Label;
+import javafx.scene.control.ToggleButton;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.Priority;
+import javafx.scene.layout.VBox;
+import javafx.scene.text.Text;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.icon.IconTheme;
+import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.BindingsHelper;
+import org.jabref.gui.util.NoSelectionModel;
+import org.jabref.gui.util.TaskExecutor;
+import org.jabref.gui.util.TextFlowLimited;
+import org.jabref.gui.util.ViewModelListCellFactory;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.FieldName;
+import org.jabref.model.util.FileUpdateMonitor;
+import org.jabref.preferences.PreferencesService;
+
+import com.airhacks.afterburner.views.ViewLoader;
+import org.controlsfx.control.CheckListView;
+import org.fxmisc.easybind.EasyBind;
+
+public class ImportEntriesDialog extends BaseDialog<Void> {
+
+    public CheckListView<BibEntry> entriesListView;
+    public ButtonType importButton;
+    private final BackgroundTask<List<BibEntry>> task;
+    private ImportEntriesViewModel viewModel;
+    @Inject private TaskExecutor taskExecutor;
+    @Inject private DialogService dialogService;
+    @Inject private UndoManager undoManager;
+    @Inject private PreferencesService preferences;
+    @Inject private StateManager stateManager;
+    @Inject private FileUpdateMonitor fileUpdateMonitor;
+    private BibDatabaseContext database;
+
+    public ImportEntriesDialog(BibDatabaseContext database, BackgroundTask<List<BibEntry>> task) {
+        this.database = database;
+        this.task = task;
+
+        ViewLoader.view(this)
+                  .load()
+                  .setAsDialogPane(this);
+
+        setResultConverter(button -> {
+            if (button == importButton) {
+                viewModel.importEntries(entriesListView.getCheckModel().getCheckedItems());
+            } else {
+                dialogService.notify(Localization.lang("Import canceled"));
+            }
+
+            return null;
+        });
+    }
+
+    @FXML
+    private void initialize() {
+        viewModel = new ImportEntriesViewModel(task, taskExecutor, database, dialogService, undoManager, preferences, stateManager, fileUpdateMonitor);
+
+        Label placeholder = new Label();
+        placeholder.textProperty().bind(viewModel.messageProperty());
+        entriesListView.setPlaceholder(placeholder);
+        entriesListView.setItems(viewModel.getEntries());
+
+        PseudoClass entrySelected = PseudoClass.getPseudoClass("entry-selected");
+        new ViewModelListCellFactory<BibEntry>()
+                .withGraphic(entry -> {
+                    ToggleButton addToggle = IconTheme.JabRefIcons.ADD.asToggleButton();
+                    EasyBind.subscribe(addToggle.selectedProperty(), selected -> {
+                        if (selected) {
+                            addToggle.setGraphic(IconTheme.JabRefIcons.ADD_FILLED.withColor(IconTheme.SELECTED_COLOR).getGraphicNode());
+                        } else {
+                            addToggle.setGraphic(IconTheme.JabRefIcons.ADD.getGraphicNode());
+                        }
+                    });
+                    addToggle.getStyleClass().add("addEntryButton");
+                    addToggle.selectedProperty().bindBidirectional(entriesListView.getItemBooleanProperty(entry));
+                    HBox separator = new HBox();
+                    HBox.setHgrow(separator, Priority.SOMETIMES);
+                    Node entryNode = getEntryNode(entry);
+                    HBox.setHgrow(entryNode, Priority.ALWAYS);
+                    HBox container = new HBox(entryNode, separator, addToggle);
+                    container.getStyleClass().add("entry-container");
+                    BindingsHelper.includePseudoClassWhen(container, entrySelected, addToggle.selectedProperty());
+
+                    if (viewModel.hasDuplicate(entry)) {
+                        Button duplicateButton = IconTheme.JabRefIcons.DUPLICATE.asButton();
+                        duplicateButton.setTooltip(new Tooltip(Localization.lang("Possible duplicate of existing entry. Click to resolve.")));
+                        duplicateButton.setOnAction(event -> viewModel.resolveDuplicate(entry));
+                        container.getChildren().add(1, duplicateButton);
+                    }
+
+                    return container;
+                })
+                .withOnMouseClickedEvent((entry, event) -> entriesListView.getCheckModel().toggleCheckState(entry))
+                .withPseudoClass(entrySelected, entriesListView::getItemBooleanProperty)
+                .install(entriesListView);
+        entriesListView.setSelectionModel(new NoSelectionModel<>());
+    }
+
+    private Node getEntryNode(BibEntry entry) {
+        Node entryType = getIcon(entry.getType()).getGraphicNode();
+        entryType.getStyleClass().add("type");
+        Label authors = new Label(entry.getFieldOrAliasLatexFree(FieldName.AUTHOR).orElse(""));
+        authors.getStyleClass().add("authors");
+        Label title = new Label(entry.getFieldOrAliasLatexFree(FieldName.TITLE).orElse(""));
+        title.getStyleClass().add("title");
+        Label year = new Label(entry.getFieldOrAliasLatexFree(FieldName.YEAR).orElse(""));
+        year.getStyleClass().add("year");
+        Label journal = new Label(entry.getFieldOrAliasLatexFree(FieldName.JOURNAL).orElse(""));
+        journal.getStyleClass().add("journal");
+
+        VBox entryContainer = new VBox(
+                new HBox(10, entryType, title),
+                new HBox(5, year, journal),
+                authors
+        );
+        entry.getFieldOrAliasLatexFree(FieldName.ABSTRACT).ifPresent(summaryText -> {
+            TextFlowLimited summary = new TextFlowLimited(new Text(summaryText));
+            summary.getStyleClass().add("summary");
+            entryContainer.getChildren().add(summary);
+        });
+
+        entryContainer.getStyleClass().add("bibEntry");
+        return entryContainer;
+    }
+
+    private IconTheme.JabRefIcons getIcon(String type) {
+        switch (type.toLowerCase()) {
+            case "book":
+                return IconTheme.JabRefIcons.BOOK;
+            default:
+                return IconTheme.JabRefIcons.ARTICLE;
+        }
+    }
+
+    public void unselectAll() {
+        entriesListView.getCheckModel().clearChecks();
+    }
+
+    public void selectAllNewEntries() {
+        unselectAll();
+        for (BibEntry entry : entriesListView.getItems()) {
+            if (!viewModel.hasDuplicate(entry)) {
+                entriesListView.getCheckModel().check(entry);
+            }
+        }
+    }
+}
diff --git a/src/main/java/org/jabref/gui/importer/ImportEntriesViewModel.java b/src/main/java/org/jabref/gui/importer/ImportEntriesViewModel.java
new file mode 100644
index 00000000000..a28a437400b
--- /dev/null
+++ b/src/main/java/org/jabref/gui/importer/ImportEntriesViewModel.java
@@ -0,0 +1,183 @@
+package org.jabref.gui.importer;
+
+import java.util.List;
+import java.util.Optional;
+
+import javax.swing.undo.UndoManager;
+
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+
+import org.jabref.gui.AbstractViewModel;
+import org.jabref.gui.DialogService;
+import org.jabref.gui.DuplicateResolverDialog;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.externalfiles.ImportHandler;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.TaskExecutor;
+import org.jabref.logic.bibtex.DuplicateCheck;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.util.FileUpdateMonitor;
+import org.jabref.preferences.PreferencesService;
+
+public class ImportEntriesViewModel extends AbstractViewModel {
+
+    private final BackgroundTask<List<BibEntry>> task;
+    private final StringProperty message;
+    private final BibDatabaseContext database;
+    private final DialogService dialogService;
+    private final UndoManager undoManager;
+    private final StateManager stateManager;
+    private final FileUpdateMonitor fileUpdateMonitor;
+    private ObservableList<BibEntry> entries;
+    private PreferencesService preferences;
+
+    public ImportEntriesViewModel(BackgroundTask<List<BibEntry>> task, TaskExecutor taskExecutor, BibDatabaseContext database, DialogService dialogService, UndoManager undoManager, PreferencesService preferences, StateManager stateManager, FileUpdateMonitor fileUpdateMonitor) {
+        this.task = task;
+        this.database = database;
+        this.dialogService = dialogService;
+        this.undoManager = undoManager;
+        this.preferences = preferences;
+        this.stateManager = stateManager;
+        this.fileUpdateMonitor = fileUpdateMonitor;
+        this.entries = FXCollections.observableArrayList();
+        this.message = new SimpleStringProperty();
+        this.message.bind(task.messageProperty());
+
+        task.onSuccess(entriesToImport -> entries.addAll(entriesToImport))
+            .executeWith(taskExecutor);
+    }
+
+    public String getMessage() {
+        return message.get();
+    }
+
+    public StringProperty messageProperty() {
+        return message;
+    }
+
+    public ObservableList<BibEntry> getEntries() {
+        return entries;
+    }
+
+    public boolean hasDuplicate(BibEntry entry) {
+        return findInternalDuplicate(entry).isPresent()
+                ||
+                DuplicateCheck.containsDuplicate(database.getDatabase(), entry, database.getMode()).isPresent();
+    }
+
+    public void importEntries(List<BibEntry> entriesToImport) {
+        // Check if we are supposed to warn about duplicates.
+        // If so, then see if there are duplicates, and warn if yes.
+        if (preferences.shouldWarnAboutDuplicatesForImport()) {
+            boolean containsDuplicate = entriesToImport.stream()
+                                                       .anyMatch(this::hasDuplicate);
+
+            if (containsDuplicate) {
+                boolean continueImport = dialogService.showConfirmationDialogWithOptOutAndWait(Localization.lang("Duplicates found"),
+                        Localization.lang("There are possible duplicates (marked with an icon) that haven't been resolved. Continue?"),
+                        Localization.lang("Continue with import"),
+                        Localization.lang("Cancel import"),
+                        Localization.lang("Disable this confirmation dialog"),
+                        optOut -> preferences.setShouldWarnAboutDuplicatesForImport(!optOut));
+
+                if (!continueImport) {
+                    dialogService.notify(Localization.lang("Import canceled"));
+                    return;
+                }
+            }
+        }
+
+        ImportHandler importHandler = new ImportHandler(
+                dialogService,
+                database,
+                ExternalFileTypes.getInstance(),
+                preferences.getFilePreferences(),
+                preferences.getImportFormatPreferences(),
+                preferences.getUpdateFieldPreferences(),
+                fileUpdateMonitor,
+                undoManager,
+                stateManager);
+        importHandler.importEntries(entriesToImport);
+
+        dialogService.notify(Localization.lang("Number of entries successfully imported") + ": " + entriesToImport.size());
+    }
+
+    /**
+     * Checks if there are duplicates to the given entry in the list of entries to be imported.
+     *
+     * @param entry The entry to search for duplicates of.
+     * @return A possible duplicate, if any, or null if none were found.
+     */
+    private Optional<BibEntry> findInternalDuplicate(BibEntry entry) {
+        for (BibEntry othEntry : entries) {
+            if (othEntry.equals(entry)) {
+                continue; // Don't compare the entry to itself
+            }
+            if (DuplicateCheck.isDuplicate(entry, othEntry, database.getMode())) {
+                return Optional.of(othEntry);
+            }
+        }
+        return Optional.empty();
+    }
+
+    public void resolveDuplicate(BibEntry entry) {
+        // First, try to find duplicate in the existing library
+        Optional<BibEntry> other = DuplicateCheck.containsDuplicate(database.getDatabase(), entry, database.getMode());
+        if (other.isPresent()) {
+            DuplicateResolverDialog dialog = new DuplicateResolverDialog(other.get(),
+                    entry, DuplicateResolverDialog.DuplicateResolverType.INSPECTION, database);
+
+            DuplicateResolverDialog.DuplicateResolverResult result = dialog.showAndWait().orElse(DuplicateResolverDialog.DuplicateResolverResult.BREAK);
+
+            if (result == DuplicateResolverDialog.DuplicateResolverResult.KEEP_LEFT) {
+                // TODO: Remove old entry. Or... add it to a list of entries
+                // to be deleted. We only delete
+                // it after Ok is clicked.
+                // entriesToDelete.add(other.get());
+            } else if (result == DuplicateResolverDialog.DuplicateResolverResult.KEEP_RIGHT) {
+                // Remove the entry from the import inspection dialog.
+                entries.remove(entry);
+            } else if (result == DuplicateResolverDialog.DuplicateResolverResult.KEEP_BOTH) {
+                // Do nothing.
+            } else if (result == DuplicateResolverDialog.DuplicateResolverResult.KEEP_MERGE) {
+                // TODO: Remove old entry. Or... add it to a list of entries
+                // to be deleted. We only delete
+                // it after Ok is clicked.
+                //entriesToDelete.add(other.get());
+
+                // Replace entry by merged entry
+                entries.add(dialog.getMergedEntry());
+                entries.remove(entry);
+            }
+            return;
+        }
+        // Second, check if the duplicate is of another entry in the import:
+        other = findInternalDuplicate(entry);
+        if (other.isPresent()) {
+            DuplicateResolverDialog diag = new DuplicateResolverDialog(entry,
+                    other.get(), DuplicateResolverDialog.DuplicateResolverType.DUPLICATE_SEARCH, database);
+
+            DuplicateResolverDialog.DuplicateResolverResult answer = diag.showAndWait().orElse(DuplicateResolverDialog.DuplicateResolverResult.BREAK);
+            if (answer == DuplicateResolverDialog.DuplicateResolverResult.KEEP_LEFT) {
+                // Remove other entry
+                entries.remove(other.get());
+            } else if (answer == DuplicateResolverDialog.DuplicateResolverResult.KEEP_RIGHT) {
+                // Remove entry
+                entries.remove(entry);
+            } else if (answer == DuplicateResolverDialog.DuplicateResolverResult.KEEP_BOTH) {
+                // Do nothing
+            } else if (answer == DuplicateResolverDialog.DuplicateResolverResult.KEEP_MERGE) {
+                // Replace both entries by merged entry
+                entries.add(diag.getMergedEntry());
+                entries.remove(entry);
+                entries.remove(other.get());
+            }
+        }
+    }
+}
diff --git a/src/main/java/org/jabref/gui/importer/ImportInspectionDialog.java b/src/main/java/org/jabref/gui/importer/ImportInspectionDialog.java
deleted file mode 100644
index 6906a6e36cc..00000000000
--- a/src/main/java/org/jabref/gui/importer/ImportInspectionDialog.java
+++ /dev/null
@@ -1,1411 +0,0 @@
-package org.jabref.gui.importer;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
-import java.util.Set;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JProgressBar;
-import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
-import javax.swing.JTable;
-import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
-import javax.swing.table.TableCellRenderer;
-import javax.swing.table.TableColumnModel;
-import javax.swing.table.TableModel;
-
-import javafx.embed.swing.JFXPanel;
-import javafx.scene.Scene;
-
-import org.jabref.Globals;
-import org.jabref.JabRefExecutorService;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.BasePanelPreferences;
-import org.jabref.gui.DuplicateResolverDialog;
-import org.jabref.gui.DuplicateResolverDialog.DuplicateResolverResult;
-import org.jabref.gui.GUIGlobals;
-import org.jabref.gui.JabRefDialog;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.PreviewPanel;
-import org.jabref.gui.customjfx.CustomJFXPanel;
-import org.jabref.gui.desktop.JabRefDesktop;
-import org.jabref.gui.externalfiles.AutoSetLinks;
-import org.jabref.gui.externalfiles.DownloadExternalFile;
-import org.jabref.gui.externalfiletype.ExternalFileMenuItem;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.filelist.FileListEntry;
-import org.jabref.gui.filelist.FileListTableModel;
-import org.jabref.gui.filelist.LinkedFileEditDialogView;
-import org.jabref.gui.groups.GroupTreeNodeViewModel;
-import org.jabref.gui.groups.UndoableChangeEntriesOfGroup;
-import org.jabref.gui.help.HelpAction;
-import org.jabref.gui.icon.IconTheme;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.renderer.GeneralRenderer;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableInsertEntry;
-import org.jabref.gui.undo.UndoableRemoveEntry;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.gui.util.comparator.IconComparator;
-import org.jabref.logic.bibtex.DuplicateCheck;
-import org.jabref.logic.bibtex.comparator.FieldComparator;
-import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
-import org.jabref.logic.help.HelpFile;
-import org.jabref.logic.importer.OutputPrinter;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.UpdateField;
-import org.jabref.model.Defaults;
-import org.jabref.model.FieldChange;
-import org.jabref.model.database.BibDatabase;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.AuthorList;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FieldName;
-import org.jabref.model.entry.FieldProperty;
-import org.jabref.model.entry.IdGenerator;
-import org.jabref.model.entry.InternalBibtexFields;
-import org.jabref.model.entry.LinkedFile;
-import org.jabref.model.groups.AllEntriesGroup;
-import org.jabref.model.groups.GroupEntryChanger;
-import org.jabref.model.groups.GroupTreeNode;
-import org.jabref.model.metadata.MetaData;
-import org.jabref.model.strings.StringUtil;
-import org.jabref.preferences.JabRefPreferences;
-
-import ca.odell.glazedlists.BasicEventList;
-import ca.odell.glazedlists.EventList;
-import ca.odell.glazedlists.SortedList;
-import ca.odell.glazedlists.event.ListEvent;
-import ca.odell.glazedlists.event.ListEventListener;
-import ca.odell.glazedlists.gui.AbstractTableComparatorChooser;
-import ca.odell.glazedlists.gui.TableFormat;
-import ca.odell.glazedlists.swing.DefaultEventSelectionModel;
-import ca.odell.glazedlists.swing.DefaultEventTableModel;
-import ca.odell.glazedlists.swing.GlazedListsSwing;
-import ca.odell.glazedlists.swing.TableComparatorChooser;
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import com.jgoodies.forms.builder.ButtonStackBuilder;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * Dialog to allow the selection of entries as part of an Import.
- * <p>
- * The usual way to use this class is to pass it to an Importer which will do
- * the following:
- * <ul>
- * <li>Register itself as a callback to get notified if the user wants to stop
- * the import.</li>
- * <li>Call setVisible(true) to display the dialog</li>
- * <li>For each entry that has been found call addEntry(...)</li>
- * <li>Call entryListComplete() after all entries have been fetched</li>
- * </ul>
- * <p>
- * If the importer wants to cancel the import, it should call the dispose()
- * method.
- * <p>
- * If the importer receives the stopFetching-call, it should stop fetching as
- * soon as possible (it is not really critical, but good style to not contribute
- * any more results via addEntry, call entryListComplete() or dispose(), after
- * receiving this call).
- */
-
-public class ImportInspectionDialog extends JabRefDialog implements OutputPrinter {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(ImportInspectionDialog.class);
-    private static final List<String> INSPECTION_FIELDS = Arrays.asList(FieldName.AUTHOR, FieldName.TITLE, FieldName.YEAR, BibEntry.KEY_FIELD);
-    private static final int DUPL_COL = 1;
-    private static final int FILE_COL = 2;
-    private static final int URL_COL = 3;
-    private static final int PAD = 4;
-    private final JabRefFrame frame;
-    private final BibDatabaseContext bibDatabaseContext;
-    private final JSplitPane contentPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
-    private final JTable glTable;
-    private final TableComparatorChooser<BibEntry> comparatorChooser;
-    private final DefaultEventSelectionModel<BibEntry> selectionModel;
-    private final JProgressBar progressBar = new JProgressBar(SwingConstants.HORIZONTAL);
-    private final JButton ok = new JButton(Localization.lang("OK"));
-    private final JButton generate = new JButton(Localization.lang("Generate now"));
-    private final EventList<BibEntry> entries = new BasicEventList<>();
-    private final SortedList<BibEntry> sortedList;
-    /**
-     * Duplicate resolving may require deletion of old entries.
-     */
-    private final List<BibEntry> entriesToDelete = new ArrayList<>();
-    private final String undoName;
-    private final boolean newDatabase;
-    private final JPopupMenu popup = new JPopupMenu();
-    private final JButton deselectAllDuplicates = new JButton(Localization.lang("Deselect all duplicates"));
-    private final JButton stop = new JButton(Localization.lang("Stop"));
-    private final PreviewPanel preview;
-    private final Map<BibEntry, Set<GroupTreeNode>> groupAdditions = new HashMap<>();
-    private final JCheckBox autoGenerate = new JCheckBox(Localization.lang("Generate keys"),
-                                                         Globals.prefs.getBoolean(JabRefPreferences.GENERATE_KEYS_AFTER_INSPECTION));
-    private final JLabel duplLabel = new JLabel(IconTheme.JabRefIcons.DUPLICATE.getSmallIcon());
-    private final JLabel fileLabel = new JLabel(IconTheme.JabRefIcons.FILE.getSmallIcon());
-    private final JLabel urlLabel = new JLabel(IconTheme.JabRefIcons.WWW.getSmallIcon());
-    private BasePanel panel;
-    private boolean generatedKeys; // Set to true after keys have been generated.
-    private boolean defaultSelected = true;
-
-    /**
-     * Creates a dialog that displays the given list of fields in the table. The
-     * dialog allows another process to add entries dynamically while the dialog
-     * is shown.
-     *
-     * @param frame
-     * @param panel
-     */
-    public ImportInspectionDialog(JabRefFrame frame, BasePanel panel, String undoName, boolean newDatabase) {
-        super(ImportInspectionDialog.class);
-        this.frame = frame;
-        this.panel = panel;
-        this.bibDatabaseContext = (panel == null) ? null : panel.getBibDatabaseContext();
-        this.undoName = undoName;
-        this.newDatabase = newDatabase;
-        setIconImages(IconTheme.getLogoSet());
-        preview = DefaultTaskExecutor.runInJavaFXThread(() -> new PreviewPanel(panel, bibDatabaseContext, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), frame.getDialogService(), ExternalFileTypes.getInstance()));
-
-        duplLabel.setToolTipText(Localization.lang("Possible duplicate of existing entry. Click to resolve."));
-
-        sortedList = new SortedList<>(entries);
-        DefaultEventTableModel<BibEntry> tableModelGl = (DefaultEventTableModel<BibEntry>) GlazedListsSwing
-                                                                                                           .eventTableModelWithThreadProxyList(sortedList, new EntryTableFormat());
-        glTable = new EntryTable(tableModelGl);
-        GeneralRenderer renderer = new GeneralRenderer(Color.white);
-        glTable.setDefaultRenderer(JLabel.class, renderer);
-        glTable.setDefaultRenderer(String.class, renderer);
-        glTable.getInputMap().put(Globals.getKeyPrefs().getKey(KeyBinding.DELETE_ENTRY), "delete");
-        DeleteListener deleteListener = new DeleteListener();
-        glTable.getActionMap().put("delete", deleteListener);
-
-        selectionModel = (DefaultEventSelectionModel<BibEntry>) GlazedListsSwing
-                                                                                .eventSelectionModelWithThreadProxyList(sortedList);
-        glTable.setSelectionModel(selectionModel);
-        selectionModel.getSelected().addListEventListener(new EntrySelectionListener());
-        comparatorChooser = TableComparatorChooser.install(glTable, sortedList,
-                                                           AbstractTableComparatorChooser.MULTIPLE_COLUMN_KEYBOARD);
-        setupComparatorChooser();
-        glTable.addMouseListener(new TableClickListener());
-
-        setWidths();
-
-        getContentPane().setLayout(new BorderLayout());
-        progressBar.setIndeterminate(true);
-        JPanel centerPan = new JPanel();
-        centerPan.setLayout(new BorderLayout());
-
-        contentPane.setTopComponent(new JScrollPane(glTable));
-        JFXPanel container = CustomJFXPanel.wrap(new Scene(preview));
-        contentPane.setBottomComponent(container);
-
-        centerPan.add(contentPane, BorderLayout.CENTER);
-        centerPan.add(progressBar, BorderLayout.SOUTH);
-
-        popup.add(deleteListener);
-        popup.addSeparator();
-        if (!newDatabase && (bibDatabaseContext != null) && bibDatabaseContext.getMetaData().getGroups().isPresent()) {
-            GroupTreeNode node = bibDatabaseContext.getMetaData().getGroups().get();
-            JMenu groupsAdd = new JMenu(Localization.lang("Add to group"));
-            groupsAdd.setEnabled(false); // Will get enabled if there are groups that can be added to.
-            insertNodes(groupsAdd, node);
-            popup.add(groupsAdd);
-        }
-
-        // Add "Attach file" menu choices to right click menu:
-        popup.add(new LinkLocalFile());
-        popup.add(new DownloadFile());
-        popup.add(new InternalAutoSetLinks());
-        popup.add(new AttachUrl());
-        getContentPane().add(centerPan, BorderLayout.CENTER);
-
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        bb.addButton(ok);
-        bb.addButton(stop);
-        JButton cancel = new JButton(Localization.lang("Cancel"));
-        bb.addButton(cancel);
-        bb.addRelatedGap();
-        JButton help = new HelpAction(HelpFile.IMPORT_INSPECTION).getHelpButton();
-        bb.addButton(help);
-        bb.addGlue();
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(2, 2, 2, 2));
-
-        ButtonStackBuilder builder = new ButtonStackBuilder();
-        JButton selectAll = new JButton(Localization.lang("Select all"));
-        builder.addButton(selectAll);
-        JButton deselectAll = new JButton(Localization.lang("Deselect all"));
-        builder.addButton(deselectAll);
-        builder.addButton(deselectAllDuplicates);
-        builder.addRelatedGap();
-        JButton delete = new JButton(Localization.lang("Delete"));
-        builder.addButton(delete);
-        builder.addRelatedGap();
-        builder.addFixed(autoGenerate);
-        builder.addButton(generate);
-        builder.getPanel().setBorder(BorderFactory.createEmptyBorder(2, 2, 2, 2));
-        centerPan.add(builder.getPanel(), BorderLayout.WEST);
-
-        ok.setEnabled(false);
-        generate.setEnabled(false);
-        ok.addActionListener(new OkListener());
-        cancel.addActionListener(e -> {
-            dispose();
-            frame.output(Localization.lang("Import canceled by user"));
-        });
-        generate.addActionListener(e -> {
-            generate.setEnabled(false);
-            generatedKeys = true; // To prevent the button from getting
-            // enabled again.
-            generateKeys(); // Generate the keys.
-        });
-        stop.addActionListener(e -> {
-            entryListComplete();
-        });
-        selectAll.addActionListener(new SelectionButton(true));
-        deselectAll.addActionListener(new SelectionButton(false));
-        deselectAllDuplicates.addActionListener(e -> {
-            for (int i = 0; i < glTable.getRowCount(); i++) {
-                if (glTable.getValueAt(i, DUPL_COL) != null) {
-                    glTable.setValueAt(false, i, 0);
-                }
-            }
-            glTable.repaint();
-        });
-        deselectAllDuplicates.setEnabled(false);
-        delete.addActionListener(deleteListener);
-        getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-
-        // Remember and default to last size:
-        setSize(new Dimension(Globals.prefs.getInt(JabRefPreferences.IMPORT_INSPECTION_DIALOG_WIDTH),
-                              Globals.prefs.getInt(JabRefPreferences.IMPORT_INSPECTION_DIALOG_HEIGHT)));
-        addWindowListener(new WindowAdapter() {
-
-            @Override
-            public void windowOpened(WindowEvent e) {
-                contentPane.setDividerLocation(0.5f);
-            }
-
-            @Override
-            public void windowClosed(WindowEvent e) {
-                Globals.prefs.putInt(JabRefPreferences.IMPORT_INSPECTION_DIALOG_WIDTH, getSize().width);
-                Globals.prefs.putInt(JabRefPreferences.IMPORT_INSPECTION_DIALOG_HEIGHT, getSize().height);
-            }
-        });
-        // Key bindings:
-        Action closeAction = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                dispose();
-            }
-        };
-        ActionMap am = contentPane.getActionMap();
-        InputMap im = contentPane.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", closeAction);
-
-    }
-
-    public void addEntries(Collection<BibEntry> entriesToAdd) {
-
-        for (BibEntry entry : entriesToAdd) {
-            // We exploit the entry's search status for indicating "Keep"
-            // status:
-            entry.setSearchHit(defaultSelected);
-            // We exploit the entry's group status for indicating duplicate
-            // status.
-            // Checking duplicates means both checking against the background
-            // database (if
-            // applicable) and against entries already in the table.
-            if ((panel != null) && (DuplicateCheck
-                                                  .containsDuplicate(panel.getDatabase(), entry, panel.getBibDatabaseContext().getMode()).isPresent()
-                                    || (internalDuplicate(this.entries, entry).isPresent()))) {
-                entry.setGroupHit(true);
-                SwingUtilities.invokeLater(() -> deselectAllDuplicates.setEnabled(true));
-            }
-            this.entries.getReadWriteLock().writeLock().lock();
-            try {
-                this.entries.add(entry);
-            } finally {
-                this.entries.getReadWriteLock().writeLock().unlock();
-            }
-        }
-    }
-
-    /**
-     * Checks if there are duplicates to the given entry in the Collection. Does
-     * not report the entry as duplicate of itself if it is in the Collection.
-     *
-     * @param entriesDupe A Collection of BibEntry instances.
-     * @param entry       The entry to search for duplicates of.
-     * @return A possible duplicate, if any, or null if none were found.
-     */
-    private Optional<BibEntry> internalDuplicate(Collection<BibEntry> entriesDupe, BibEntry entry) {
-        for (BibEntry othEntry : entriesDupe) {
-            if (othEntry.equals(entry)) {
-                continue; // Don't compare the entry to itself
-            }
-            if (DuplicateCheck.isDuplicate(entry, othEntry, panel.getBibDatabaseContext().getMode())) {
-                return Optional.of(othEntry);
-            }
-        }
-        return Optional.empty();
-    }
-
-    public void entryListComplete() {
-        SwingUtilities.invokeLater(() -> {
-            progressBar.setIndeterminate(false);
-            progressBar.setVisible(false);
-            ok.setEnabled(true);
-            if (!generatedKeys) {
-                generate.setEnabled(true);
-            }
-            stop.setEnabled(false);
-
-            //This is for selecting and displaying the first entry in the glTable
-            this.glTable.repaint();
-            if ((this.glTable.getSelectedRowCount() == 0) && (this.glTable.getRowCount() > 0)) {
-                this.glTable.setRowSelectionInterval(0, 0); //Select first row in the table
-            }
-        });
-    }
-
-    /**
-     * Generate key for an entry.
-     */
-    private void generateKeyForEntry(BibEntry entry) {
-
-        entries.getReadWriteLock().writeLock().lock();
-        try {
-            BibDatabase database;
-            MetaData localMetaData;
-
-            // Relate to existing database, if any:
-            if (panel == null) {
-                database = new BibDatabase();
-                localMetaData = new MetaData();
-            } else {
-                database = panel.getDatabase();
-                localMetaData = panel.getBibDatabaseContext().getMetaData();
-            }
-
-            entry.setId(IdGenerator.next());
-            // Add the entry to the database we are working with:
-            database.insertEntry(entry);
-
-            // Generate a unique key:
-            new BibtexKeyGenerator(localMetaData.getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern()),
-                                   database, Globals.prefs.getBibtexKeyPatternPreferences()).generateAndSetKey(entry);
-            // Remove the entry from the database again, since we only added it in
-            // order to
-            // make sure the key was unique:
-            database.removeEntry(entry);
-        } finally {
-            entries.getReadWriteLock().writeLock().unlock();
-        }
-        glTable.repaint();
-    }
-
-    /**
-     * Generate keys for all entries. All keys will be unique with respect to
-     * one another, and, if they are destined for an existing database, with
-     * respect to existing keys in the database.
-     */
-    private void generateKeys() {
-        entries.getReadWriteLock().writeLock().lock();
-        try {
-
-            BibDatabase database;
-            MetaData localMetaData;
-
-            // Relate to existing database, if any:
-            if (panel == null) {
-                database = new BibDatabase();
-                localMetaData = new MetaData();
-            } else {
-                database = panel.getDatabase();
-                localMetaData = panel.getBibDatabaseContext().getMetaData();
-            }
-
-            List<Optional<String>> keys = new ArrayList<>(entries.size());
-            // Iterate over the entries, add them to the database we are working
-            // with,
-            // and generate unique keys:
-            for (BibEntry entry : entries) {
-
-                entry.setId(IdGenerator.next());
-                database.insertEntry(entry);
-
-                new BibtexKeyGenerator(localMetaData.getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern()),
-                                       database, Globals.prefs.getBibtexKeyPatternPreferences()).generateAndSetKey(entry);
-                // Add the generated key to our list:   -- TODO: Why??
-                keys.add(entry.getCiteKeyOptional());
-            }
-
-            preview.update();
-            // Remove the entries from the database again, since they are not
-            // supposed to
-            // added yet. They only needed to be in it while we generated the keys,
-            // to keep
-            // control over key uniqueness.
-            for (BibEntry entry : entries) {
-                database.removeEntry(entry);
-            }
-        } finally {
-            entries.getReadWriteLock().writeLock().unlock();
-        }
-
-        glTable.repaint();
-    }
-
-    private void insertNodes(JMenu menu, GroupTreeNode node) {
-        final AbstractAction action = getAction(node);
-
-        if (node.getNumberOfChildren() == 0) {
-            menu.add(action);
-            if (action.isEnabled()) {
-                menu.setEnabled(true);
-            }
-            return;
-        }
-
-        JMenu submenu;
-        if (node.getGroup() instanceof AllEntriesGroup) {
-            for (GroupTreeNode child : node.getChildren()) {
-                insertNodes(menu, child);
-            }
-        } else {
-            submenu = new JMenu('[' + node.getName() + ']');
-            // setEnabled(true) is done above/below if at least one menu
-            // entry (item or submenu) is enabled
-            submenu.setEnabled(action.isEnabled());
-            submenu.add(action);
-            submenu.add(new JPopupMenu.Separator());
-            for (GroupTreeNode child : node.getChildren()) {
-                insertNodes(submenu, child);
-            }
-            menu.add(submenu);
-            if (submenu.isEnabled()) {
-                menu.setEnabled(true);
-            }
-        }
-    }
-
-    private AbstractAction getAction(GroupTreeNode node) {
-        AbstractAction action = new AddToGroupAction(node);
-        action.setEnabled(node.getGroup() instanceof GroupEntryChanger);
-        return action;
-    }
-
-    private void setWidths() {
-        TableColumnModel cm = glTable.getColumnModel();
-        cm.getColumn(0).setPreferredWidth(55);
-        cm.getColumn(0).setMinWidth(55);
-        cm.getColumn(0).setMaxWidth(55);
-        for (int i = 1; i < PAD; i++) {
-            // Lock the width of icon columns.
-            cm.getColumn(i).setPreferredWidth(GUIGlobals.WIDTH_ICON_COL);
-            cm.getColumn(i).setMinWidth(GUIGlobals.WIDTH_ICON_COL);
-            cm.getColumn(i).setMaxWidth(GUIGlobals.WIDTH_ICON_COL);
-        }
-
-        for (int i = 0; i < INSPECTION_FIELDS.size(); i++) {
-            Double width = InternalBibtexFields.getFieldLength(INSPECTION_FIELDS.get(i));
-            glTable.getColumnModel().getColumn(i + PAD).setPreferredWidth(width.intValue());
-        }
-    }
-
-    private void setupComparatorChooser() {
-        // First column:
-
-        List<Comparator> comparators = comparatorChooser.getComparatorsForColumn(0);
-        comparators.clear();
-
-        comparators = comparatorChooser.getComparatorsForColumn(1);
-        comparators.clear();
-
-        // Icon columns:
-        for (int i = 2; i < PAD; i++) {
-            comparators = comparatorChooser.getComparatorsForColumn(i);
-            comparators.clear();
-            if (i == FILE_COL) {
-                comparators.add(new IconComparator(Collections.singletonList(FieldName.FILE)));
-            } else if (i == URL_COL) {
-                comparators.add(new IconComparator(Collections.singletonList(FieldName.URL)));
-            }
-        }
-        // Remaining columns:
-        for (int i = PAD; i < (PAD + INSPECTION_FIELDS.size()); i++) {
-            comparators = comparatorChooser.getComparatorsForColumn(i);
-            comparators.clear();
-            comparators.add(new FieldComparator(INSPECTION_FIELDS.get(i - PAD)));
-        }
-
-        sortedList.getReadWriteLock().writeLock().lock();
-        try {
-            comparatorChooser.appendComparator(PAD, 0, false);
-        } finally {
-            sortedList.getReadWriteLock().writeLock().unlock();
-        }
-    }
-
-    /**
-     * The "defaultSelected" boolean value determines if new entries added are
-     * selected for import or not. This value is true by default.
-     *
-     * @param defaultSelected The desired value.
-     */
-    public void setDefaultSelected(boolean defaultSelected) {
-        this.defaultSelected = defaultSelected;
-    }
-
-    @Override
-    public void setStatus(String s) {
-        frame.setStatus(s);
-    }
-
-    @Override
-    public void showMessage(String message, String title, int msgType) {
-        JOptionPane.showMessageDialog(this, message, title, msgType);
-    }
-
-    @Override
-    public void showMessage(String message) {
-        JOptionPane.showMessageDialog(this, message);
-    }
-
-    /**
-     * Displays a dialog which tells the user that an error occurred while fetching entries
-     */
-    public void showErrorMessage(String fetcherTitle, String localizedException) {
-        showMessage(Localization.lang("Error while fetching from %0", fetcherTitle) + "\n" +
-                    Localization.lang("Please try again later and/or check your network connection.") + "\n" +
-                    localizedException,
-                    Localization.lang("Search %0", fetcherTitle), JOptionPane.ERROR_MESSAGE);
-    }
-
-    public JabRefFrame getFrame() {
-        return frame;
-    }
-
-    @FunctionalInterface
-    public interface CallBack {
-
-        /**
-         * This method is called by the dialog when the user has canceled or
-         * signaled a stop. It is expected that any long-running fetch
-         * operations will stop after this method is called.
-         */
-        void stopFetching();
-    }
-
-    /**
-     * Stores the information about the selected entries being scheduled for
-     * addition to this group. The entries are *not* added to the group at this
-     * time. <p/> Synchronizes on this.entries to prevent conflict with threads
-     * that modify the entry list.
-     */
-    class AddToGroupAction extends AbstractAction {
-
-        private final GroupTreeNode node;
-
-        public AddToGroupAction(GroupTreeNode node) {
-            super(node.getName());
-            this.node = node;
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent event) {
-
-            selectionModel.getSelected().getReadWriteLock().writeLock().lock();
-            try {
-                for (BibEntry entry : selectionModel.getSelected()) {
-                    // We store the groups this entry should be added to in a Set in
-                    // the Map:
-                    Set<GroupTreeNode> groups = groupAdditions.get(entry);
-                    if (groups == null) {
-                        // No previous definitions, so we create the Set now:
-                        groups = new HashSet<>();
-                        groupAdditions.put(entry, groups);
-                    }
-                    // Add the group:
-                    groups.add(node);
-                }
-            } finally {
-                selectionModel.getSelected().getReadWriteLock().writeLock().unlock();
-            }
-        }
-    }
-
-    private class OkListener implements ActionListener {
-
-        @Override
-        public void actionPerformed(ActionEvent event) {
-
-            // First check if we are supposed to warn about duplicates. If so,
-            // see if there
-            // are unresolved duplicates, and warn if yes.
-            if (Globals.prefs.getBoolean(JabRefPreferences.WARN_ABOUT_DUPLICATES_IN_INSPECTION)) {
-                for (BibEntry entry : entries) {
-
-                    // Only check entries that are to be imported. Keep status
-                    // is indicated
-                    // through the search hit status of the entry:
-                    if (!entry.isSearchHit()) {
-                        continue;
-                    }
-
-                    // Check if the entry is a suspected, unresolved, duplicate.
-                    // This status
-                    // is indicated by the entry's group hit status:
-                    if (entry.isGroupHit()) {
-
-                        boolean continuePressed = DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().showConfirmationDialogWithOptOutAndWait(Localization.lang("Duplicates found"),
-                                Localization.lang("There are possible duplicates (marked with an icon) that haven't been resolved. Continue?"),
-                                Localization.lang("Continue"),
-                                Localization.lang("Cancel"),
-                                Localization.lang("Disable this confirmation dialog"),
-                                optOut -> Globals.prefs.putBoolean(JabRefPreferences.WARN_ABOUT_DUPLICATES_IN_INSPECTION, !optOut)));
-
-                        if (!continuePressed) {
-                            return;
-                        }
-                        break;
-                    }
-                }
-            }
-
-            // The compund undo action used to contain all changes made by this
-            // dialog.
-            NamedCompound ce = new NamedCompound(undoName);
-
-            // See if we should remove any old entries for duplicate resolving:
-            if (!entriesToDelete.isEmpty()) {
-                removeEntriesToDelete(ce);
-            }
-
-            // If "Generate keys" is checked, generate keys unless it's already
-            // been done:
-            if (autoGenerate.isSelected() && !generatedKeys) {
-                generateKeys();
-            }
-            // Remember the choice until next time:
-            Globals.prefs.putBoolean(JabRefPreferences.GENERATE_KEYS_AFTER_INSPECTION, autoGenerate.isSelected());
-
-            final List<BibEntry> selected = getSelectedEntries();
-
-            if (!selected.isEmpty()) {
-                addSelectedEntries(ce, selected);
-            }
-
-            dispose();
-            SwingUtilities.invokeLater(() -> updateGUI(selected.size()));
-        }
-
-        private void updateGUI(int entryCount) {
-            if (newDatabase) {
-                frame.addTab(panel, true);
-            }
-            panel.markBaseChanged();
-
-            if (entryCount == 0) {
-                frame.output(Localization.lang("No entries imported."));
-            } else {
-                frame.output(Localization.lang("Number of entries successfully imported") + ": " + entryCount);
-            }
-        }
-
-        private void removeEntriesToDelete(NamedCompound ce) {
-            for (BibEntry entry : entriesToDelete) {
-                ce.addEdit(new UndoableRemoveEntry(panel.getDatabase(), entry, panel));
-                panel.getDatabase().removeEntry(entry);
-            }
-        }
-
-        private void addSelectedEntries(NamedCompound ce, final List<BibEntry> selected) {
-            if (newDatabase) {
-                // Create a new BasePanel for the entries:
-                Defaults defaults = new Defaults(Globals.prefs.getDefaultBibDatabaseMode());
-                panel = new BasePanel(frame, BasePanelPreferences.from(Globals.prefs), new BibDatabaseContext(defaults), ExternalFileTypes.getInstance());
-            }
-
-            boolean groupingCanceled = false;
-
-            // Set owner/timestamp if options are enabled:
-            UpdateField.setAutomaticFields(selected, Globals.prefs.getUpdateFieldPreferences());
-
-            for (BibEntry entry : selected) {
-                // Remove settings to group/search hit status:
-                entry.setSearchHit(false);
-                entry.setGroupHit(false);
-
-                // If this entry should be added to any groups, do it now:
-                Set<GroupTreeNode> groups = groupAdditions.get(entry);
-                if (!groupingCanceled && (groups != null)) {
-                    groupingCanceled = addToGroups(ce, entry, groups);
-                }
-
-                entry.setId(IdGenerator.next());
-                ce.addEdit(new UndoableInsertEntry(panel.getDatabase(), entry));
-            }
-            panel.getDatabase().insertEntries(selected);
-
-            ce.end();
-            panel.getUndoManager().addEdit(ce);
-        }
-
-        private boolean addToGroups(NamedCompound ce, BibEntry entry, Set<GroupTreeNode> groups) {
-            boolean groupingCanceled = false;
-            if (!entry.hasCiteKey()) {
-                // The entry has no key, so it can't be added to the
-                // group.
-                // The best course of action is probably to ask the
-                // user if a key should be generated
-                // immediately.
-
-                boolean generateKeysPressed = frame.getDialogService().showConfirmationDialogAndWait(Localization.lang("Add to group"),
-                                                                                                     Localization.lang("Cannot add entries to group without generating keys. Generate keys now?"),
-                                                                                                     Localization.lang("Generate keys"),
-                                                                                                     Localization.lang("Cancel"));
-
-                if (generateKeysPressed) {
-                    generateKeys();
-                } else {
-                    groupingCanceled = true;
-                }
-            }
-
-            // If the key existed, or exists now, go ahead:
-            if (entry.hasCiteKey()) {
-                for (GroupTreeNode node : groups) {
-                    if (node.getGroup() instanceof GroupEntryChanger) {
-                        // Add the entry:
-                        GroupEntryChanger entryChanger = (GroupEntryChanger) node.getGroup();
-                        List<FieldChange> undo = entryChanger.add(Collections.singletonList(entry));
-                        if (!undo.isEmpty()) {
-                            ce.addEdit(UndoableChangeEntriesOfGroup.getUndoableEdit(new GroupTreeNodeViewModel(node),
-                                                                                    undo));
-                        }
-                    }
-                }
-            }
-            return groupingCanceled;
-        }
-
-        /**
-         * This method returns a List containing all entries that are selected
-         * (checkbox checked).
-         *
-         * @return a List containing the selected entries.
-         */
-        private List<BibEntry> getSelectedEntries() {
-            List<BibEntry> selected = new ArrayList<>();
-            for (BibEntry entry : entries) {
-                if (entry.isSearchHit()) {
-                    selected.add(entry);
-                }
-            }
-
-            return selected;
-        }
-
-    }
-
-    private class DeleteListener extends AbstractAction {
-
-        public DeleteListener() {
-            super(Localization.lang("Delete"), IconTheme.JabRefIcons.DELETE_ENTRY.getSmallIcon());
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent event) {
-            removeSelectedEntries();
-        }
-
-        /**
-         * Removes all selected entries from the table. Synchronizes on this.entries
-         * to prevent conflict with addition of new entries.
-         */
-        private void removeSelectedEntries() {
-            int row = glTable.getSelectedRow();
-            List<BibEntry> toRemove = new ArrayList<>();
-            toRemove.addAll(selectionModel.getSelected());
-
-            entries.getReadWriteLock().writeLock().lock();
-            try {
-                for (BibEntry entry : toRemove) {
-                    entries.remove(entry);
-                }
-            } finally {
-                entries.getReadWriteLock().writeLock().unlock();
-            }
-            glTable.clearSelection();
-            if ((row >= 0) && (!entries.isEmpty())) {
-                row = Math.min(entries.size() - 1, row);
-                glTable.addRowSelectionInterval(row, row);
-            }
-        }
-    }
-
-    private class SelectionButton implements ActionListener {
-
-        private final Boolean enable;
-
-        public SelectionButton(boolean enable) {
-            this.enable = enable;
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent event) {
-            for (int i = 0; i < glTable.getRowCount(); i++) {
-                glTable.setValueAt(enable, i, 0);
-            }
-            glTable.repaint();
-        }
-    }
-
-    private class EntrySelectionListener implements ListEventListener<BibEntry> {
-
-        @Override
-        public void listChanged(ListEvent<BibEntry> listEvent) {
-            if (listEvent.getSourceList().size() == 1) {
-                preview.setEntry(listEvent.getSourceList().get(0));
-            }
-        }
-    }
-
-    /**
-     * This class handles clicks on the table that should trigger specific
-     * events, like opening the popup menu.
-     */
-    private class TableClickListener implements MouseListener {
-
-        private boolean isIconColumn(int col) {
-            return (col == FILE_COL) || (col == URL_COL);
-        }
-
-        @Override
-        public void mouseClicked(MouseEvent e) {
-            final int col = glTable.columnAtPoint(e.getPoint());
-            final int row = glTable.rowAtPoint(e.getPoint());
-            if (isIconColumn(col)) {
-                BibEntry entry = sortedList.get(row);
-
-                if (col == FILE_COL) {
-                    if (entry.hasField(FieldName.FILE)) {
-                        FileListTableModel tableModel = new FileListTableModel();
-                        entry.getField(FieldName.FILE).ifPresent(tableModel::setContent);
-                        if (tableModel.getRowCount() == 0) {
-                            return;
-                        }
-                        FileListEntry fl = tableModel.getEntry(0);
-                        (new ExternalFileMenuItem(frame, "", fl.getLink(), null, panel.getBibDatabaseContext(),
-                                                  fl.getType())).actionPerformed(null);
-                    }
-                } else { // Must be URL_COL
-                    openExternalLink(FieldName.URL, e);
-                }
-            }
-        }
-
-        @Override
-        public void mouseEntered(MouseEvent e) {
-            // Nothing
-        }
-
-        @Override
-        public void mouseExited(MouseEvent e) {
-            // Nothing
-        }
-
-        /**
-         * Show right-click menu. If the click happened in an icon column that
-         * presents its own popup menu, show that. Otherwise, show the ordinary
-         * popup menu.
-         *
-         * @param e The mouse event that triggered the popup.
-         */
-        private void showPopup(MouseEvent e) {
-            final int col = glTable.columnAtPoint(e.getPoint());
-            if (col == FILE_COL) {
-                showFileFieldMenu(e);
-            } else {
-                showOrdinaryRightClickMenu(e);
-            }
-        }
-
-        private void showOrdinaryRightClickMenu(MouseEvent e) {
-            popup.show(glTable, e.getX(), e.getY());
-        }
-
-        /**
-         * Show the popup menu for the FILE field.
-         *
-         * @param e The mouse event that triggered the popup.
-         */
-        private void showFileFieldMenu(MouseEvent e) {
-            final int row = glTable.rowAtPoint(e.getPoint());
-            BibEntry entry = sortedList.get(row);
-            JPopupMenu menu = new JPopupMenu();
-            int count = 0;
-            FileListTableModel fileList = new FileListTableModel();
-            entry.getField(FieldName.FILE).ifPresent(fileList::setContent);
-            // If there are one or more links, open the first one:
-            for (int i = 0; i < fileList.getRowCount(); i++) {
-                FileListEntry flEntry = fileList.getEntry(i);
-                String description = flEntry.getDescription();
-                if ((description == null) || (description.trim().isEmpty())) {
-                    description = flEntry.getLink();
-                }
-                menu.add(new ExternalFileMenuItem(panel.frame(), description, flEntry.getLink(),
-                                                  flEntry.getType().get().getIcon().getSmallIcon(), panel.getBibDatabaseContext(), flEntry.getType()));
-                count++;
-            }
-            if (count == 0) {
-                showOrdinaryRightClickMenu(e);
-            } else {
-                menu.show(glTable, e.getX(), e.getY());
-            }
-        }
-
-        /**
-         * Open old-style external links after user clicks icon.
-         *
-         * @param fieldName The name of the BibTeX field this icon is used for.
-         * @param e         The MouseEvent that triggered this operation.
-         */
-        private void openExternalLink(String fieldName, MouseEvent e) {
-            final int row = glTable.rowAtPoint(e.getPoint());
-            BibEntry entry = sortedList.get(row);
-
-            entry.getField(fieldName).ifPresent(link -> {
-                try {
-                    JabRefDesktop.openExternalViewer(panel.getBibDatabaseContext(), link, fieldName);
-                } catch (IOException ex) {
-                    LOGGER.warn("Could not open link", ex);
-                }
-            });
-        }
-
-        @Override
-        public void mouseReleased(MouseEvent e) {
-            // Check if the user has right-clicked. If so, open the right-click
-            // menu.
-            if (e.isPopupTrigger()) {
-                showPopup(e);
-            }
-        }
-
-        @Override
-        public void mousePressed(MouseEvent e) {
-            // Check if the user has right-clicked. If so, open the right-click
-            // menu.
-            if (e.isPopupTrigger()) {
-                showPopup(e);
-                return;
-            }
-
-            // Check if any other action should be taken:
-            final int col = glTable.columnAtPoint(e.getPoint());
-            final int row = glTable.rowAtPoint(e.getPoint());
-            // Is this the duplicate icon column, and is there an icon?
-            if ((col == DUPL_COL) && (glTable.getValueAt(row, col) != null)) {
-                BibEntry first = sortedList.get(row);
-                Optional<BibEntry> other = DuplicateCheck.containsDuplicate(panel.getDatabase(), first,
-                                                                            panel.getBibDatabaseContext().getMode());
-                if (other.isPresent()) {
-                    // This will be true if the duplicate is in the existing
-                    // database.
-                    DuplicateResolverDialog diag = new DuplicateResolverDialog(getFrame(), other.get(),
-                                                                               first, DuplicateResolverDialog.DuplicateResolverType.INSPECTION);
-
-                    DuplicateResolverResult result = diag.showAndWait().orElse(DuplicateResolverResult.BREAK);
-
-                    ImportInspectionDialog.this.toFront();
-                    if (result == DuplicateResolverResult.KEEP_LEFT) {
-                        // Remove old entry. Or... add it to a list of entries
-                        // to be deleted. We only delete
-                        // it after Ok is clicked.
-                        entriesToDelete.add(other.get());
-                        // Clear duplicate icon, which is controlled by the
-                        // group hit
-                        // field of the entry:
-
-                        entries.getReadWriteLock().writeLock().lock();
-                        try {
-                            first.setGroupHit(false);
-                        } finally {
-                            entries.getReadWriteLock().writeLock().unlock();
-                        }
-                    } else if (result == DuplicateResolverResult.KEEP_RIGHT) {
-                        // Remove the entry from the import inspection dialog.
-                        entries.getReadWriteLock().writeLock().lock();
-                        try {
-                            entries.remove(first);
-                        } finally {
-                            entries.getReadWriteLock().writeLock().unlock();
-                        }
-                    } else if (result == DuplicateResolverResult.KEEP_BOTH) {
-                        // Do nothing.
-                        entries.getReadWriteLock().writeLock().lock();
-                        try {
-                            first.setGroupHit(false);
-                        } finally {
-                            entries.getReadWriteLock().writeLock().unlock();
-                        }
-                    } else if (result == DuplicateResolverResult.KEEP_MERGE) {
-                        // Remove old entry. Or... add it to a list of entries
-                        // to be deleted. We only delete
-                        // it after Ok is clicked.
-                        entriesToDelete.add(other.get());
-                        // Store merged entry for later adding
-                        // Clear duplicate icon, which is controlled by the
-                        // group hit
-                        // field of the entry:
-                        entries.getReadWriteLock().writeLock().lock();
-                        try {
-                            diag.getMergedEntry().setGroupHit(false);
-                            diag.getMergedEntry().setSearchHit(true);
-                            entries.add(diag.getMergedEntry());
-                            entries.remove(first);
-                            first = new BibEntry(); // Reset first so the next duplicate doesn't trigger
-                        } finally {
-                            entries.getReadWriteLock().writeLock().unlock();
-                        }
-                    }
-                }
-                // Check if the duplicate is of another entry in the import:
-                other = internalDuplicate(entries, first);
-                if (other.isPresent()) {
-                    DuplicateResolverDialog diag = new DuplicateResolverDialog(getFrame(), first,
-                                                                               other.get(), DuplicateResolverDialog.DuplicateResolverType.DUPLICATE_SEARCH);
-
-                    ImportInspectionDialog.this.toFront();
-                    DuplicateResolverResult answer = diag.showAndWait().get();
-                    if (answer == DuplicateResolverResult.KEEP_LEFT) {
-                        entries.remove(other.get());
-                        first.setGroupHit(false);
-                    } else if (answer == DuplicateResolverResult.KEEP_RIGHT) {
-                        entries.remove(first);
-                    } else if (answer == DuplicateResolverResult.KEEP_BOTH) {
-                        first.setGroupHit(false);
-                    } else if (answer == DuplicateResolverResult.KEEP_MERGE) {
-                        diag.getMergedEntry().setGroupHit(false);
-                        diag.getMergedEntry().setSearchHit(true);
-                        entries.add(diag.getMergedEntry());
-                        entries.remove(first);
-                        entries.remove(other.get());
-                    }
-                }
-            }
-        }
-    }
-
-    class AttachUrl extends JMenuItem implements ActionListener {
-
-        public AttachUrl() {
-            super(Localization.lang("Attach URL"));
-            addActionListener(this);
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent event) {
-            if (selectionModel.getSelected().size() != 1) {
-                return;
-            }
-            BibEntry entry = selectionModel.getSelected().get(0);
-
-            Optional<String> result = frame.getDialogService().showInputDialogAndWait(Localization.lang("Enter URL"), Localization.lang("Enter URL"));
-
-            entries.getReadWriteLock().writeLock().lock();
-            try {
-                if (result.isPresent()) {
-                    if (result.get().isEmpty()) {
-                        entry.clearField(FieldName.URL);
-                    } else {
-                        entry.setField(FieldName.URL, result.get());
-                    }
-                }
-            } finally {
-                entries.getReadWriteLock().writeLock().unlock();
-            }
-            glTable.repaint();
-        }
-    }
-
-    class DownloadFile extends JMenuItem implements ActionListener, DownloadExternalFile.DownloadCallback {
-
-        private BibEntry entry;
-
-        public DownloadFile() {
-            super(Localization.lang("Download file"));
-            addActionListener(this);
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent actionEvent) {
-            if (selectionModel.getSelected().size() != 1) {
-                return;
-            }
-            entry = selectionModel.getSelected().get(0);
-            if (!entry.getCiteKeyOptional().isPresent()) {
-
-                boolean generateKeyPressed = frame.getDialogService().showConfirmationDialogAndWait(Localization.lang("Download file"),
-                                                                                                    Localization.lang("This entry has no BibTeX key. Generate key now?"),
-                                                                                                    Localization.lang("Generate key"),
-                                                                                                    Localization.lang("Cancel"));
-
-                if (generateKeyPressed) {
-                    generateKeyForEntry(entry);
-                }
-            }
-            DownloadExternalFile def = new DownloadExternalFile(frame.getDialogService(), bibDatabaseContext, entry);
-            try {
-                def.download(this);
-            } catch (IOException ex) {
-                LOGGER.warn("Could not download file", ex);
-            }
-        }
-
-        @Override
-        public void downloadComplete(LinkedFile file) {
-            ImportInspectionDialog.this.toFront(); // Hack
-            entries.getReadWriteLock().writeLock().lock();
-            try {
-                entry.addFile(file);
-            } finally {
-                entries.getReadWriteLock().writeLock().unlock();
-            }
-            glTable.repaint();
-        }
-    }
-
-    private class InternalAutoSetLinks extends JMenuItem implements ActionListener {
-
-        public InternalAutoSetLinks() {
-            super(Localization.lang("Automatically set file links"));
-            addActionListener(this);
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent actionEvent) {
-            if (selectionModel.getSelected().size() != 1) {
-                return;
-            }
-            final BibEntry entry = selectionModel.getSelected().get(0);
-            if (!entry.hasCiteKey()) {
-
-                boolean generateKeyPressed = frame.getDialogService().showConfirmationDialogAndWait(Localization.lang("Download file"),
-                                                                                                    Localization.lang("This entry has no BibTeX key. Generate key now?"),
-                                                                                                    Localization.lang("Generate key"),
-                                                                                                    Localization.lang("Cancel"));
-
-                if (generateKeyPressed) {
-                    generateKeyForEntry(entry);
-                } else {
-                    return; // Can't go on without the bibtex key.
-                }
-            }
-            final FileListTableModel localModel = new FileListTableModel();
-            entry.getField(FieldName.FILE).ifPresent(localModel::setContent);
-            // We have a static utility method for searching for all relevant
-            // links:
-            JDialog diag = new JDialog(ImportInspectionDialog.this, true);
-            JabRefExecutorService.INSTANCE
-                                          .execute(AutoSetLinks.autoSetLinks(entry, bibDatabaseContext, e -> {
-                                              if (e.getID() > 0) {
-
-                                                  entries.getReadWriteLock().writeLock().lock();
-                                                  try {
-                                                      entry.setField(FieldName.FILE, localModel.getStringRepresentation());
-                                                  } finally {
-                                                      entries.getReadWriteLock().writeLock().unlock();
-                                                  }
-                                                  glTable.repaint();
-                                              }
-                                          }, diag));
-
-        }
-    }
-
-    private class LinkLocalFile extends JMenuItem implements ActionListener, DownloadExternalFile.DownloadCallback {
-
-        private BibEntry entry;
-
-        public LinkLocalFile() {
-            super(Localization.lang("Link local file"));
-            addActionListener(this);
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent actionEvent) {
-            if (selectionModel.getSelected().size() != 1) {
-                return;
-            }
-            entry = selectionModel.getSelected().get(0);
-            LinkedFile linkedFile = new LinkedFile("", "", "");
-
-            LinkedFileEditDialogView dialog = new LinkedFileEditDialogView(linkedFile);
-
-            Optional<LinkedFile> editedLinkedFile = DefaultTaskExecutor.runInJavaFXThread(() -> dialog.showAndWait());
-            editedLinkedFile.ifPresent(file -> entry.addFile(linkedFile));
-        }
-
-        @Override
-        public void downloadComplete(LinkedFile file) {
-            ImportInspectionDialog.this.toFront(); // Hack
-            entries.getReadWriteLock().writeLock().lock();
-            try {
-                entry.addFile(file);
-            } finally {
-                entries.getReadWriteLock().writeLock().unlock();
-            }
-            glTable.repaint();
-        }
-    }
-
-    class EntryTable extends JTable {
-
-        private final GeneralRenderer renderer = new GeneralRenderer(Color.white);
-
-        public EntryTable(TableModel model) {
-            super(model);
-            getTableHeader().setReorderingAllowed(false);
-
-            setFont(GUIGlobals.currentFont);
-            int maxOfIconsAndFontSize = GUIGlobals.currentFont.getSize();
-            setRowHeight(maxOfIconsAndFontSize);
-            // Update Table header with new settings
-            this.getTableHeader().resizeAndRepaint();
-        }
-
-        @Override
-        public TableCellRenderer getCellRenderer(int row, int column) {
-            return column == 0 ? getDefaultRenderer(Boolean.class) : renderer;
-        }
-
-        @Override
-        public Class<?> getColumnClass(int col) {
-            if (col == 0) {
-                return Boolean.class;
-            } else if (col < PAD) {
-                return JLabel.class;
-            } else {
-                return String.class;
-            }
-        }
-
-        @Override
-        public boolean isCellEditable(int row, int column) {
-            return column == 0;
-        }
-
-        @Override
-        public void setValueAt(Object value, int row, int column) {
-            // Only column 0, which is controlled by BibEntry.searchHit, is
-            // editable:
-            entries.getReadWriteLock().writeLock().lock();
-            try {
-                BibEntry entry = sortedList.get(row);
-                entry.setSearchHit((Boolean) value);
-            } finally {
-                entries.getReadWriteLock().writeLock().unlock();
-            }
-        }
-    }
-
-    private class EntryTableFormat implements TableFormat<BibEntry> {
-
-        @Override
-        public int getColumnCount() {
-            return PAD + INSPECTION_FIELDS.size();
-        }
-
-        @Override
-        public String getColumnName(int i) {
-            if (i == 0) {
-                return Localization.lang("Keep");
-            }
-            if (i >= PAD) {
-                return StringUtil.capitalizeFirst(INSPECTION_FIELDS.get(i - PAD));
-            }
-            return "";
-        }
-
-        @Override
-        public Object getColumnValue(BibEntry entry, int i) {
-            if (i == 0) {
-                return entry.isSearchHit() ? Boolean.TRUE : Boolean.FALSE;
-            } else if (i < PAD) {
-                switch (i) {
-                    case DUPL_COL:
-                        return entry.isGroupHit() ? duplLabel : null;
-                    case FILE_COL:
-                        if (entry.hasField(FieldName.FILE)) {
-                            FileListTableModel model = new FileListTableModel();
-                            entry.getField(FieldName.FILE).ifPresent(model::setContent);
-                            fileLabel.setToolTipText(model.getToolTipHTMLRepresentation());
-                            if ((model.getRowCount() > 0) && model.getEntry(0).getType().isPresent()) {
-                                fileLabel.setIcon(model.getEntry(0).getType().get().getIcon().getSmallIcon());
-                            }
-                            return fileLabel;
-                        } else {
-                            return null;
-                        }
-                    case URL_COL:
-                        if (entry.hasField(FieldName.URL)) {
-                            urlLabel.setToolTipText(entry.getField(FieldName.URL).orElse(""));
-                            return urlLabel;
-                        } else {
-                            return null;
-                        }
-                    default:
-                        return null;
-                }
-            } else {
-                String field = INSPECTION_FIELDS.get(i - PAD);
-                if (InternalBibtexFields.getFieldProperties(field).contains(FieldProperty.PERSON_NAMES)) {
-                    return entry.getField(field).map(AuthorList::fixAuthorNatbib).orElse("");
-                } else {
-                    return entry.getField(field).orElse(null);
-                }
-            }
-        }
-
-    }
-}
diff --git a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java
index 984b11025d9..77354393115 100644
--- a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java
+++ b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java
@@ -3,8 +3,6 @@
 import java.util.Comparator;
 import java.util.List;
 
-import javax.swing.SwingUtilities;
-
 import javafx.beans.property.ListProperty;
 import javafx.beans.property.ObjectProperty;
 import javafx.beans.property.SimpleListProperty;
@@ -14,10 +12,9 @@
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 
-import org.jabref.JabRefExecutorService;
 import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.importer.ImportInspectionDialog;
-import org.jabref.logic.importer.FetcherException;
+import org.jabref.gui.importer.ImportEntriesDialog;
+import org.jabref.gui.util.BackgroundTask;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.SearchBasedFetcher;
 import org.jabref.logic.importer.WebFetcher;
@@ -97,21 +94,12 @@ public void search() {
         }
 
         SearchBasedFetcher activeFetcher = getSelectedFetcher();
-        final ImportInspectionDialog dialog = new ImportInspectionDialog(frame, frame.getCurrentBasePanel(),
-                activeFetcher.getName(), false);
-
-        SwingUtilities.invokeLater(() -> dialog.setVisible(true));
-
-        JabRefExecutorService.INSTANCE.execute(() -> {
-            dialog.setStatus(Localization.lang("Processing %0", getQuery()));
-            try {
-                List<BibEntry> matches = activeFetcher.performSearch(getQuery().trim());
-                dialog.addEntries(matches);
-                dialog.entryListComplete();
-            } catch (FetcherException e) {
-                LOGGER.error("Error while fetching from " + activeFetcher.getName(), e);
-                dialog.showErrorMessage(activeFetcher.getName(), e.getLocalizedMessage());
-            }
-        });
+
+        BackgroundTask<List<BibEntry>> task = BackgroundTask.wrap(() -> activeFetcher.performSearch(getQuery().trim()))
+                                                            .withInitialMessage(Localization.lang("Processing %0", getQuery()));
+
+        ImportEntriesDialog dialog = new ImportEntriesDialog(frame.getCurrentBasePanel().getBibDatabaseContext(), task);
+        dialog.setTitle(activeFetcher.getName());
+        dialog.showAndWait();
     }
 }
diff --git a/src/main/java/org/jabref/gui/maintable/MainTable.java b/src/main/java/org/jabref/gui/maintable/MainTable.java
index 7ff9de40304..d852104c1fd 100644
--- a/src/main/java/org/jabref/gui/maintable/MainTable.java
+++ b/src/main/java/org/jabref/gui/maintable/MainTable.java
@@ -77,7 +77,8 @@ public MainTable(MainTableDataModel model, JabRefFrame frame,
                 Globals.prefs.getImportFormatPreferences(),
                 Globals.prefs.getUpdateFieldPreferences(),
                 Globals.getFileUpdateMonitor(),
-                undoManager);
+                undoManager,
+                Globals.stateManager);
 
         this.getColumns().addAll(new MainTableColumnFactory(database, preferences.getColumnPreferences(), externalFileTypes, panel.getUndoManager(), frame.getDialogService()).createColumns());
 
diff --git a/src/main/java/org/jabref/gui/preferences/BibtexKeyPatternPrefTab.java b/src/main/java/org/jabref/gui/preferences/BibtexKeyPatternPrefTab.java
index 3dabc05b209..8240accc730 100644
--- a/src/main/java/org/jabref/gui/preferences/BibtexKeyPatternPrefTab.java
+++ b/src/main/java/org/jabref/gui/preferences/BibtexKeyPatternPrefTab.java
@@ -24,7 +24,6 @@ class BibtexKeyPatternPrefTab extends BibtexKeyPatternPanel implements PrefsTab
     private final CheckBox dontOverwrite = new CheckBox(Localization.lang("Do not overwrite existing keys"));
     private final CheckBox warnBeforeOverwriting = new CheckBox(Localization.lang("Warn before overwriting existing keys"));
     private final CheckBox generateOnSave = new CheckBox(Localization.lang("Generate keys before saving (for entries without a key)"));
-    private final CheckBox autoGenerateOnImport = new CheckBox(Localization.lang("Generate keys for imported entries"));
 
     private final RadioButton letterStartA = new RadioButton(Localization.lang("Ensure unique keys using letters (a, b, ...)"));
     private final RadioButton letterStartB = new RadioButton(Localization.lang("Ensure unique keys using letters (b, c, ...)"));
@@ -57,7 +56,6 @@ public void storeSettings() {
 
         Globals.prefs.put(JabRefPreferences.KEY_PATTERN_REGEX, keyPatternRegex.getText());
         Globals.prefs.put(JabRefPreferences.KEY_PATTERN_REPLACEMENT, keyPatternReplacement.getText());
-        Globals.prefs.putBoolean(JabRefPreferences.GENERATE_KEYS_AFTER_INSPECTION, autoGenerateOnImport.isSelected());
         Globals.prefs.putBoolean(JabRefPreferences.GENERATE_KEYS_BEFORE_SAVING, generateOnSave.isSelected());
 
         if (alwaysAddLetter.isSelected()) {
@@ -82,7 +80,6 @@ private void appendKeyGeneratorSettings() {
         Label keyGeneratorSettings = new Label(Localization.lang("Key generator settings"));
         keyGeneratorSettings.getStyleClass().add("sectionHeader");
         builder.add(keyGeneratorSettings, 1, 10);
-        builder.add(autoGenerateOnImport, 1, 11);
         builder.add(letterStartA, 2, 11);
         builder.add(warnBeforeOverwriting, 1, 12);
         builder.add(letterStartB, 2, 12);
@@ -116,7 +113,6 @@ public void setValues() {
         defaultPat.setText(Globals.prefs.get(JabRefPreferences.DEFAULT_BIBTEX_KEY_PATTERN));
         dontOverwrite.setSelected(Globals.prefs.getBoolean(JabRefPreferences.AVOID_OVERWRITING_KEY));
         generateOnSave.setSelected(Globals.prefs.getBoolean(JabRefPreferences.GENERATE_KEYS_BEFORE_SAVING));
-        autoGenerateOnImport.setSelected(Globals.prefs.getBoolean(JabRefPreferences.GENERATE_KEYS_AFTER_INSPECTION));
         warnBeforeOverwriting.setSelected(Globals.prefs.getBoolean(JabRefPreferences.WARN_BEFORE_OVERWRITING_KEY));
 
         boolean prefAlwaysAddLetter = Globals.prefs.getBoolean(JabRefPreferences.KEY_GEN_ALWAYS_ADD_LETTER);
diff --git a/src/main/java/org/jabref/gui/search/GlobalSearchBar.java b/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
index e0fb4494af1..3f18ba400c6 100644
--- a/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
+++ b/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
@@ -2,10 +2,8 @@
 
 import java.lang.reflect.Field;
 import java.nio.file.Path;
-import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
-import java.util.stream.Collectors;
 
 import javafx.animation.KeyFrame;
 import javafx.animation.KeyValue;
@@ -53,7 +51,6 @@
 import org.jabref.logic.search.SearchQuery;
 import org.jabref.logic.search.SearchQueryHighlightObservable;
 import org.jabref.model.entry.Author;
-import org.jabref.model.entry.BibEntry;
 import org.jabref.preferences.SearchPreferences;
 
 import impl.org.controlsfx.skin.AutoCompletePopup;
@@ -226,18 +223,16 @@ private void openLocalFindingsInExternalPanel() {
             return;
         }
 
-        SearchResultFrame searchDialog = new SearchResultFrame(currentBasePanel.frame(), Localization.lang("Search results in library %0 for %1", currentBasePanel.getBibDatabaseContext()
-                                                                                                                                                                  .getDatabasePath()
-                                                                                                                                                                  .map(Path::getFileName)
-                                                                                                                                                                  .map(Path::toString)
-                                                                                                                                                                  .orElse(GUIGlobals.UNTITLED_TITLE),
-                                                                                                           this.getSearchQuery().localize()), getSearchQuery(), false);
-        List<BibEntry> entries = currentBasePanel.getDatabase()
-                                                 .getEntries()
-                                                 .stream()
-                                                 .filter(BibEntry::isSearchHit)
-                                                 .collect(Collectors.toList());
-        searchDialog.addEntries(entries, currentBasePanel);
+        SearchResultFrame searchDialog = new SearchResultFrame(
+                currentBasePanel.frame(),
+                Localization.lang("Search results in library %0 for %1",
+                        currentBasePanel.getBibDatabaseContext()
+                                        .getDatabasePath()
+                                        .map(Path::getFileName)
+                                        .map(Path::toString)
+                                        .orElse(GUIGlobals.UNTITLED_TITLE),
+                        this.getSearchQuery().localize()), getSearchQuery(), false);
+        searchDialog.addEntries(currentBasePanel.getDatabase().getEntries(), currentBasePanel);
         searchDialog.selectFirstEntry();
         searchDialog.setVisible(true);
     }
diff --git a/src/main/java/org/jabref/gui/search/matchers/SearchMatcher.java b/src/main/java/org/jabref/gui/search/matchers/SearchMatcher.java
deleted file mode 100644
index 232f022ae71..00000000000
--- a/src/main/java/org/jabref/gui/search/matchers/SearchMatcher.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package org.jabref.gui.search.matchers;
-
-import org.jabref.model.entry.BibEntry;
-
-import ca.odell.glazedlists.matchers.Matcher;
-
-/**
- * Matcher for filtering or sorting the table according to whether entries are
- * tagged as search matches.
- */
-public class SearchMatcher implements Matcher<BibEntry> {
-
-    public static final Matcher<BibEntry> INSTANCE = new SearchMatcher();
-
-    @Override
-    public boolean matches(BibEntry entry) {
-        return entry.isSearchHit();
-    }
-}
diff --git a/src/main/java/org/jabref/gui/util/BackgroundTask.java b/src/main/java/org/jabref/gui/util/BackgroundTask.java
index bab42164053..7b0b8df1424 100644
--- a/src/main/java/org/jabref/gui/util/BackgroundTask.java
+++ b/src/main/java/org/jabref/gui/util/BackgroundTask.java
@@ -223,6 +223,11 @@ protected void updateMessage(String newMessage) {
         message.setValue(newMessage);
     }
 
+    public BackgroundTask<V> withInitialMessage(String message) {
+        updateMessage(message);
+        return this;
+    }
+
     class BackgroundProgress {
 
         private final double workDone;
diff --git a/src/main/java/org/jabref/gui/util/NoSelectionModel.java b/src/main/java/org/jabref/gui/util/NoSelectionModel.java
new file mode 100644
index 00000000000..88cba6e413c
--- /dev/null
+++ b/src/main/java/org/jabref/gui/util/NoSelectionModel.java
@@ -0,0 +1,75 @@
+package org.jabref.gui.util;
+
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+import javafx.scene.control.MultipleSelectionModel;
+
+/**
+ * Disables selection
+ */
+public class NoSelectionModel<T> extends MultipleSelectionModel<T> {
+
+    @Override
+    public ObservableList<Integer> getSelectedIndices() {
+        return FXCollections.emptyObservableList();
+    }
+
+    @Override
+    public ObservableList<T> getSelectedItems() {
+        return FXCollections.emptyObservableList();
+    }
+
+    @Override
+    public void selectIndices(int index, int... indices) {
+    }
+
+    @Override
+    public void selectAll() {
+    }
+
+    @Override
+    public void selectFirst() {
+    }
+
+    @Override
+    public void selectLast() {
+    }
+
+    @Override
+    public void clearAndSelect(int index) {
+    }
+
+    @Override
+    public void select(int index) {
+    }
+
+    @Override
+    public void select(T obj) {
+    }
+
+    @Override
+    public void clearSelection(int index) {
+    }
+
+    @Override
+    public void clearSelection() {
+    }
+
+    @Override
+    public boolean isSelected(int index) {
+        return false;
+    }
+
+    @Override
+    public boolean isEmpty() {
+        return true;
+    }
+
+    @Override
+    public void selectPrevious() {
+    }
+
+    @Override
+    public void selectNext() {
+    }
+}
diff --git a/src/main/java/org/jabref/gui/util/TextFlowLimited.java b/src/main/java/org/jabref/gui/util/TextFlowLimited.java
new file mode 100644
index 00000000000..42638536c66
--- /dev/null
+++ b/src/main/java/org/jabref/gui/util/TextFlowLimited.java
@@ -0,0 +1,81 @@
+package org.jabref.gui.util;
+
+import javafx.animation.Animation;
+import javafx.animation.Transition;
+import javafx.geometry.HPos;
+import javafx.geometry.VPos;
+import javafx.scene.control.Hyperlink;
+import javafx.scene.layout.Region;
+import javafx.scene.shape.Rectangle;
+import javafx.scene.text.Text;
+import javafx.scene.text.TextFlow;
+import javafx.util.Duration;
+
+import org.jabref.logic.l10n.Localization;
+
+public class TextFlowLimited extends TextFlow {
+    private boolean isCollapsed = true;
+    private Hyperlink moreLink = new Hyperlink(Localization.lang("(more)"));
+    private Rectangle clip = new Rectangle();
+
+    public TextFlowLimited(Text... texts) {
+        super(texts);
+
+        this.setPrefWidth(Region.USE_PREF_SIZE);
+
+        moreLink.setOnAction(event -> expand());
+        moreLink.setStyle("-fx-background-color: white");
+
+        this.setOnMouseClicked(event -> expand());
+    }
+
+    private void expand() {
+        double newPrefHeight = super.computePrefHeight(getWidth());
+        final Animation expandPanel = new Transition() {
+            {
+                setCycleDuration(Duration.millis(200));
+            }
+
+            @Override
+            protected void interpolate(double fraction) {
+                setPrefHeight(newPrefHeight * fraction);
+            }
+        };
+
+        expandPanel.setOnFinished(event -> {
+            isCollapsed = false;
+            requestLayout();
+        });
+        expandPanel.play();
+    }
+
+    @Override
+    protected double computePrefHeight(double width) {
+        if (isCollapsed) {
+            return 38;
+        } else {
+            return super.computePrefHeight(width);
+        }
+    }
+
+    @Override
+    protected void layoutChildren() {
+        super.layoutChildren();
+
+        if (isCollapsed) {
+            // Display link to expand text
+            if (!this.getChildren().contains(moreLink)) {
+                this.getChildren().add(moreLink);
+            }
+            layoutInArea(moreLink, 0, 0, getWidth(), getHeight(), getBaselineOffset(), HPos.RIGHT, VPos.BOTTOM);
+
+            // Clip content if it expands above pref height (no idea why this is needed, but otherwise sometimes the text is still visible)
+            clip.setHeight(computePrefHeight(this.getWidth()));
+            clip.setWidth(this.getWidth());
+            this.setClip(clip);
+        } else {
+            this.getChildren().remove(moreLink);
+            this.setClip(null);
+        }
+    }
+}
diff --git a/src/main/java/org/jabref/gui/util/ViewModelListCellFactory.java b/src/main/java/org/jabref/gui/util/ViewModelListCellFactory.java
index 983e4c4b29e..3f58f3cc9b3 100644
--- a/src/main/java/org/jabref/gui/util/ViewModelListCellFactory.java
+++ b/src/main/java/org/jabref/gui/util/ViewModelListCellFactory.java
@@ -1,7 +1,11 @@
 package org.jabref.gui.util;
 
+import java.util.HashMap;
+import java.util.Map;
 import java.util.function.BiConsumer;
 
+import javafx.beans.value.ObservableValue;
+import javafx.css.PseudoClass;
 import javafx.scene.Node;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.ContextMenu;
@@ -37,6 +41,7 @@ public class ViewModelListCellFactory<T> implements Callback<ListView<T>, ListCe
     private BiConsumer<T, ? super DragEvent> toOnDragEntered;
     private BiConsumer<T, ? super DragEvent> toOnDragExited;
     private BiConsumer<T, ? super DragEvent> toOnDragOver;
+    private Map<PseudoClass, Callback<T, ObservableValue<Boolean>>> pseudoClasses = new HashMap<>();
 
     public ViewModelListCellFactory<T> withText(Callback<T, String> toText) {
         this.toText = toText;
@@ -115,6 +120,11 @@ public ViewModelListCellFactory<T> setOnDragOver(BiConsumer<T, ? super DragEvent
         return this;
     }
 
+    public ViewModelListCellFactory<T> withPseudoClass(PseudoClass pseudoClass, Callback<T, ObservableValue<Boolean>> toCondition) {
+        this.pseudoClasses.putIfAbsent(pseudoClass, toCondition);
+        return this;
+    }
+
     public void install(ComboBox<T> comboBox) {
         comboBox.setButtonCell(this.call(null));
         comboBox.setCellFactory(this);
@@ -176,6 +186,10 @@ protected void updateItem(T item, boolean empty) {
                     if (toOnDragOver != null) {
                         setOnDragOver(event -> toOnDragOver.accept(viewModel, event));
                     }
+                    for (Map.Entry<PseudoClass, Callback<T, ObservableValue<Boolean>>> pseudoClassWithCondition : pseudoClasses.entrySet()) {
+                        ObservableValue<Boolean> condition = pseudoClassWithCondition.getValue().call(viewModel);
+                        BindingsHelper.includePseudoClassWhen(this, pseudoClassWithCondition.getKey(), condition);
+                    }
                 }
                 getListView().refresh();
             }
diff --git a/src/main/java/org/jabref/model/database/BibDatabase.java b/src/main/java/org/jabref/model/database/BibDatabase.java
index e986136fad2..8ec6ad73bae 100644
--- a/src/main/java/org/jabref/model/database/BibDatabase.java
+++ b/src/main/java/org/jabref/model/database/BibDatabase.java
@@ -69,6 +69,11 @@ public BibDatabase() {
         this.registerListener(new KeyChangeListener(this));
     }
 
+    public BibDatabase(List<BibEntry> entries) {
+        this();
+        insertEntries(entries);
+    }
+
     /**
      * @param toResolve maybenull The text to resolve.
      * @param database  maybenull The database to use for resolving the text.
@@ -506,7 +511,7 @@ private String resolveContent(String result, Set<String> usedIds, Set<String> al
                 // We found the next string ref. Append the text
                 // up to it.
                 if (next > 0) {
-                    newRes.append(res.substring(piv, next));
+                    newRes.append(res, piv, next);
                 }
                 int stringEnd = res.indexOf('#', next + 1);
                 if (stringEnd >= 0) {
@@ -518,7 +523,7 @@ private String resolveContent(String result, Set<String> usedIds, Set<String> al
                     if (resolved == null) {
                         // Could not resolve string. Display the #
                         // characters rather than removing them:
-                        newRes.append(res.substring(next, stringEnd + 1));
+                        newRes.append(res, next, stringEnd + 1);
                     } else {
                         // The string was resolved, so we display its meaning only,
                         // stripping the # characters signifying the string label:
diff --git a/src/main/java/org/jabref/model/entry/BibEntry.java b/src/main/java/org/jabref/model/entry/BibEntry.java
index 3f901d9b4cc..6351d9bde36 100644
--- a/src/main/java/org/jabref/model/entry/BibEntry.java
+++ b/src/main/java/org/jabref/model/entry/BibEntry.java
@@ -62,9 +62,6 @@ public class BibEntry implements Cloneable {
     private final StringProperty type = new SimpleStringProperty();
 
     private ObservableMap<String, String> fields = FXCollections.observableMap(new ConcurrentHashMap<>());
-    // Search and grouping status is stored in boolean fields for quick reference:
-    private boolean searchHit;
-    private boolean groupHit;
     private String parsedSerialization = "";
     private String commentsBeforeEntry = "";
     /**
@@ -549,22 +546,6 @@ public String toString() {
         return CanonicalBibtexEntry.getCanonicalRepresentation(this);
     }
 
-    public boolean isSearchHit() {
-        return searchHit;
-    }
-
-    public void setSearchHit(boolean searchHit) {
-        this.searchHit = searchHit;
-    }
-
-    public boolean isGroupHit() {
-        return groupHit;
-    }
-
-    public void setGroupHit(boolean groupHit) {
-        this.groupHit = groupHit;
-    }
-
     /**
      * @param maxCharacters The maximum number of characters (additional
      *                      characters are replaced with "..."). Set to 0 to disable truncation.
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index a5aaf265c09..4970e4de5c2 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -185,8 +185,6 @@ public class JabRefPreferences implements PreferencesService {
     public static final String PREAMBLE_POS_X = "preamblePosX";
     public static final String SEARCH_DIALOG_HEIGHT = "searchDialogHeight";
     public static final String SEARCH_DIALOG_WIDTH = "searchDialogWidth";
-    public static final String IMPORT_INSPECTION_DIALOG_HEIGHT = "importInspectionDialogHeight";
-    public static final String IMPORT_INSPECTION_DIALOG_WIDTH = "importInspectionDialogWidth";
     public static final String LAST_EDITED = "lastEdited";
     public static final String OPEN_LAST_EDITED = "openLastEdited";
     public static final String LAST_FOCUSED = "lastFocused";
@@ -233,7 +231,6 @@ public class JabRefPreferences implements PreferencesService {
     public static final String OVERWRITE_TIME_STAMP = "overwriteTimeStamp";
 
     public static final String WARN_ABOUT_DUPLICATES_IN_INSPECTION = "warnAboutDuplicatesInInspection";
-    public static final String GENERATE_KEYS_AFTER_INSPECTION = "generateKeysAfterInspection";
     public static final String NON_WRAPPABLE_FIELDS = "nonWrappableFields";
     public static final String RESOLVE_STRINGS_ALL_FIELDS = "resolveStringsAllFields";
     public static final String DO_NOT_RESOLVE_STRINGS_FOR = "doNotResolveStringsFor";
@@ -659,7 +656,6 @@ private JabRefPreferences() {
         defaults.put(DO_NOT_RESOLVE_STRINGS_FOR, FieldName.URL);
         defaults.put(RESOLVE_STRINGS_ALL_FIELDS, Boolean.FALSE);
         defaults.put(NON_WRAPPABLE_FIELDS, "pdf;ps;url;doi;file;isbn;issn");
-        defaults.put(GENERATE_KEYS_AFTER_INSPECTION, Boolean.TRUE);
         defaults.put(WARN_ABOUT_DUPLICATES_IN_INSPECTION, Boolean.TRUE);
         defaults.put(USE_TIME_STAMP, Boolean.FALSE);
         defaults.put(OVERWRITE_TIME_STAMP, Boolean.FALSE);
@@ -685,8 +681,6 @@ private JabRefPreferences() {
         defaults.put(MAIN_FONT_SIZE, 9);
         defaults.put(OVERRIDE_DEFAULT_FONT_SIZE, false);
 
-        defaults.put(IMPORT_INSPECTION_DIALOG_WIDTH, 650);
-        defaults.put(IMPORT_INSPECTION_DIALOG_HEIGHT, 650);
         defaults.put(SHOW_FILE_LINKS_UPGRADE_WARNING, Boolean.TRUE);
         defaults.put(AUTOLINK_EXACT_KEY_ONLY, Boolean.FALSE);
         defaults.put(NUMERIC_FIELDS, "mittnum;author");
@@ -1432,10 +1426,11 @@ public FilePreferences getFilePreferences() {
                                    get(IMPORT_FILEDIRPATTERN));
     }
 
+    @Override
     public UpdateFieldPreferences getUpdateFieldPreferences() {
         return new UpdateFieldPreferences(getBoolean(USE_OWNER), getBoolean(OVERWRITE_OWNER), get(DEFAULT_OWNER),
-                                          getBoolean(USE_TIME_STAMP), getBoolean(OVERWRITE_TIME_STAMP), get(TIME_STAMP_FIELD),
-                                          get(TIME_STAMP_FORMAT));
+                getBoolean(USE_TIME_STAMP), getBoolean(OVERWRITE_TIME_STAMP), get(TIME_STAMP_FIELD),
+                get(TIME_STAMP_FORMAT));
     }
 
     public LatexFieldFormatterPreferences getLatexFieldFormatterPreferences() {
@@ -1453,10 +1448,11 @@ public boolean isKeywordSyncEnabled() {
                 && getBoolean(JabRefPreferences.AUTOSYNCSPECIALFIELDSTOKEYWORDS);
     }
 
+    @Override
     public ImportFormatPreferences getImportFormatPreferences() {
         return new ImportFormatPreferences(customImports, getDefaultEncoding(), getKeywordDelimiter(),
-                                           getBibtexKeyPatternPreferences(), getFieldContentParserPreferences(), getXMPPreferences(),
-                                           isKeywordSyncEnabled());
+                getBibtexKeyPatternPreferences(), getFieldContentParserPreferences(), getXMPPreferences(),
+                isKeywordSyncEnabled());
     }
 
     @Override
@@ -2042,4 +2038,14 @@ public String getExportWorkingDirectory() {
     public void setExportWorkingDirectory(String layoutFileDirString) {
         put(EXPORT_WORKING_DIRECTORY, layoutFileDirString);
     }
+
+    @Override
+    public boolean shouldWarnAboutDuplicatesForImport() {
+        return getBoolean(JabRefPreferences.WARN_ABOUT_DUPLICATES_IN_INSPECTION);
+    }
+
+    @Override
+    public void setShouldWarnAboutDuplicatesForImport(boolean value) {
+        putBoolean(JabRefPreferences.WARN_ABOUT_DUPLICATES_IN_INSPECTION, value);
+    }
 }
diff --git a/src/main/java/org/jabref/preferences/PreferencesService.java b/src/main/java/org/jabref/preferences/PreferencesService.java
index 21550d547cb..726b2ec4966 100644
--- a/src/main/java/org/jabref/preferences/PreferencesService.java
+++ b/src/main/java/org/jabref/preferences/PreferencesService.java
@@ -7,11 +7,13 @@
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.logic.exporter.SavePreferences;
 import org.jabref.logic.exporter.TemplateExporter;
+import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.journals.JournalAbbreviationPreferences;
 import org.jabref.logic.layout.LayoutFormatterPreferences;
 import org.jabref.logic.openoffice.OpenOfficePreferences;
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
+import org.jabref.logic.util.UpdateFieldPreferences;
 import org.jabref.model.metadata.FilePreferences;
 
 public interface PreferencesService {
@@ -58,6 +60,10 @@ public interface PreferencesService {
 
     LayoutFormatterPreferences getLayoutFormatterPreferences(JournalAbbreviationLoader loader);
 
+    UpdateFieldPreferences getUpdateFieldPreferences();
+
+    ImportFormatPreferences getImportFormatPreferences();
+
     boolean isKeywordSyncEnabled();
 
     SavePreferences loadForExportFromPreferences();
@@ -65,4 +71,8 @@ public interface PreferencesService {
     String getExportWorkingDirectory();
 
     void setExportWorkingDirectory(String layoutFileDirString);
+
+    boolean shouldWarnAboutDuplicatesForImport();
+
+    void setShouldWarnAboutDuplicatesForImport(boolean value);
 }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index b8bfd4a718d..0a4929876ab 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -43,8 +43,6 @@ Add\ selected\ entries\ to\ this\ group=Add selected entries to this group
 
 Add\ subgroup=Add subgroup
 
-Add\ to\ group=Add to group
-
 Added\ group\ "%0".=Added group "%0".
 
 Added\ string=Added string
@@ -81,8 +79,6 @@ Assigned\ %0\ entries\ to\ group\ "%1".=Assigned %0 entries to group "%1".
 
 Assigned\ 1\ entry\ to\ group\ "%0".=Assigned 1 entry to group "%0".
 
-Attach\ URL=Attach URL
-
 Autogenerate\ BibTeX\ keys=Autogenerate BibTeX keys
 
 Autolink\ files\ with\ names\ starting\ with\ the\ BibTeX\ key=Autolink files with names starting with the BibTeX key
@@ -111,9 +107,6 @@ by=by
 The\ conflicting\ fields\ of\ these\ entries\ will\ be\ merged\ into\ the\ 'Comment'\ field.=The conflicting fields of these entries will be merged into the 'Comment' field.
 
 Cancel=Cancel
-
-Cannot\ add\ entries\ to\ group\ without\ generating\ keys.\ Generate\ keys\ now?=Cannot add entries to group without generating keys. Generate keys now?
-
 Cannot\ create\ group=Cannot create group
 
 Cannot\ create\ group.\ Please\ create\ a\ library\ first.=Cannot create group. Please create a library first.
@@ -260,9 +253,6 @@ Descending=Descending
 
 Description=Description
 
-Deselect\ all=Deselect all
-Deselect\ all\ duplicates=Deselect all duplicates
-
 Disable\ this\ confirmation\ dialog=Disable this confirmation dialog
 
 Display\ all\ entries\ belonging\ to\ one\ or\ more\ of\ the\ selected\ groups.=Display all entries belonging to one or more of the selected groups.
@@ -323,8 +313,6 @@ Editor\ options=Editor options
 empty\ library=empty library
 Enable\ word/name\ autocompletion=Enable word/name autocompletion
 
-Enter\ URL=Enter URL
-
 Enter\ URL\ to\ download=Enter URL to download
 
 entries=entries
@@ -447,9 +435,6 @@ Generate\ BibTeX\ key=Generate BibTeX key
 Generate\ keys=Generate keys
 
 Generate\ keys\ before\ saving\ (for\ entries\ without\ a\ key)=Generate keys before saving (for entries without a key)
-Generate\ keys\ for\ imported\ entries=Generate keys for imported entries
-
-Generate\ now=Generate now
 
 Generated\ BibTeX\ key\ for=Generated BibTeX key for
 
@@ -495,9 +480,6 @@ Import\ and\ keep\ old\ entry=Import and keep old entry
 Import\ and\ remove\ old\ entry=Import and remove old entry
 
 Import\ entries=Import entries
-
-Import\ failed=Import failed
-
 Import\ file=Import file
 
 Import\ group\ definitions=Import group definitions
@@ -552,9 +534,6 @@ JabRef\ requests\ recommendations\ from\ Mr.\ DLib,\ which\ is\ an\ external\ se
 JabRef\ Version\ (Required\ to\ ensure\ backwards\ compatibility\ with\ Mr.\ DLib's\ Web\ Service)=JabRef Version (Required to ensure backwards compatibility with Mr. DLib's Web Service)
 
 Journal\ abbreviations=Journal abbreviations
-
-Keep=Keep
-
 Keep\ both=Keep both
 
 Key\ bindings=Key bindings
@@ -579,8 +558,6 @@ LaTeX\ AUX\ file\:=LaTeX AUX file\:
 Left=Left
 
 Link=Link
-Link\ local\ file=Link local file
-
 Listen\ for\ remote\ operation\ on\ port=Listen for remote operation on port
 Load\ and\ Save\ preferences\ from/to\ jabref.xml\ on\ start-up\ (memory\ stick\ mode)=Load and Save preferences from/to jabref.xml on start-up (memory stick mode)
 
@@ -645,9 +622,6 @@ no\ base-BibTeX-file\ specified=no base-BibTeX-file specified
 no\ library\ generated=no library generated
 
 No\ entries\ found.\ Please\ make\ sure\ you\ are\ using\ the\ correct\ import\ filter.=No entries found. Please make sure you are using the correct import filter.
-
-No\ entries\ imported.=No entries imported.
-
 No\ files\ found.=No files found.
 
 No\ GUI.\ Only\ process\ command\ line\ options.=No GUI. Only process command line options.
@@ -955,9 +929,6 @@ Special\ table\ columns=Special table columns
 Statically\ group\ entries\ by\ manual\ assignment=Statically group entries by manual assignment
 
 Status=Status
-
-Stop=Stop
-
 Strings\ for\ library=Strings for library
 
 Sublibrary\ from\ AUX=Sublibrary from AUX
@@ -1001,9 +972,6 @@ The\ search\ is\ case\ sensitive.=The search is case sensitive.
 The\ string\ has\ been\ removed\ locally=The string has been removed locally
 
 There\ are\ possible\ duplicates\ (marked\ with\ an\ icon)\ that\ haven't\ been\ resolved.\ Continue?=There are possible duplicates (marked with an icon) that haven't been resolved. Continue?
-
-This\ entry\ has\ no\ BibTeX\ key.\ Generate\ key\ now?=This entry has no BibTeX key. Generate key now?
-
 This\ entry\ type\ cannot\ be\ removed.=This entry type cannot be removed.
 
 This\ group\ contains\ entries\ based\ on\ manual\ assignment.\ Entries\ can\ be\ assigned\ to\ this\ group\ by\ selecting\ them\ then\ using\ either\ drag\ and\ drop\ or\ the\ context\ menu.\ Entries\ can\ be\ removed\ from\ this\ group\ by\ selecting\ them\ then\ using\ the\ context\ menu.=This group contains entries based on manual assignment. Entries can be assigned to this group by selecting them then using either drag and drop or the context menu. Entries can be removed from this group by selecting them then using the context menu.
@@ -1115,7 +1083,6 @@ Move\ file\ to\ file\ directory\ and\ rename\ file=Move file to file directory a
 Could\ not\ move\ file\ '%0'.=Could not move file '%0'.
 Could\ not\ find\ file\ '%0'.=Could not find file '%0'.
 Number\ of\ entries\ successfully\ imported=Number of entries successfully imported
-Import\ canceled\ by\ user=Import canceled by user
 Error\ while\ fetching\ from\ %0=Error while fetching from %0
 
 Show\ search\ results\ in\ a\ window=Show search results in a window
@@ -2047,8 +2014,6 @@ Keep\ entry=Keep entry
 Ignore\ backup=Ignore backup
 Restore\ from\ backup=Restore from backup
 
-Continue=Continue
-Generate\ key=Generate key
 Overwrite\ file=Overwrite file
 Shared\ database\ connection=Shared database connection
 
@@ -2132,12 +2097,16 @@ File\ extension\:=File extension\:
 Export\ format\ name\:=Export format name\:
 Cleared\ connection\ settings=Cleared connection settings
 Error\ adding\ discovered\ CitationStyles=Error adding discovered CitationStyles
-
+(more)=(more)
+Cancel\ import=Cancel import
+Continue\ with\ import=Continue with import
+Import\ canceled=Import canceled
+Select\ all\ new\ entries=Select all new entries
+Select\ the\ entries\ to\ be\ imported\:=Select the entries to be imported\:
 Add\ new\ String=Add new String
 Remove\ selected\ Strings=Remove selected Strings
 Must\ not\ be\ empty\!=Must not be empty\!
 Open\ Help\ page=Open Help page
-
 Active\ database\ connection\ do\ not\ exists\!=Active database connection do not exists!
 Add\ new\ field\ name=Add new field name
 Field\ name\:=Field name:
diff --git a/src/test/java/org/jabref/logic/l10n/LocalizationConsistencyTest.java b/src/test/java/org/jabref/logic/l10n/LocalizationConsistencyTest.java
index 6f8aa2c15de..7e8ef1db2d9 100644
--- a/src/test/java/org/jabref/logic/l10n/LocalizationConsistencyTest.java
+++ b/src/test/java/org/jabref/logic/l10n/LocalizationConsistencyTest.java
@@ -112,8 +112,8 @@ void findMissingLocalizationKeys() throws IOException {
                 "DETECTED LANGUAGE KEYS WHICH ARE NOT IN THE ENGLISH LANGUAGE FILE\n" +
                         "PASTE THESE INTO THE ENGLISH LANGUAGE FILE\n" +
                         missingKeys.parallelStream()
-                                   .map(key -> String.format("\n%s=%s\n", key.getKey(), key.getKey().replaceAll("\\\\ ", " ")))
-                                   .collect(Collectors.joining("\n")));
+                                   .map(key -> String.format("%s=%s", key.getKey(), key.getKey().replaceAll("\\\\ ", " ")))
+                                   .collect(Collectors.joining("\n", "\n", "\n")));
     }
 
     @Test
diff --git a/src/test/java/org/jabref/model/entry/BibEntryTests.java b/src/test/java/org/jabref/model/entry/BibEntryTests.java
index 872ba189f65..b2e0d35cdaf 100644
--- a/src/test/java/org/jabref/model/entry/BibEntryTests.java
+++ b/src/test/java/org/jabref/model/entry/BibEntryTests.java
@@ -396,19 +396,6 @@ public void removeKeywordsWithExistingKeywordsRemovesThem() {
         assertEquals(KeywordList.parse("kw3", ','), keywordEntry.getKeywords(','));
     }
 
-    @Test
-    public void testGroupAndSearchHits() {
-        BibEntry be = new BibEntry();
-        be.setGroupHit(true);
-        assertTrue(be.isGroupHit());
-        be.setGroupHit(false);
-        assertFalse(be.isGroupHit());
-        be.setSearchHit(true);
-        assertTrue(be.isSearchHit());
-        be.setSearchHit(false);
-        assertFalse(be.isSearchHit());
-    }
-
     @Test
     public void setCiteKey() {
         BibEntry be = new BibEntry();

From e214240379289b458dafd2e26f222afcf3f5ae25 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sat, 9 Mar 2019 12:47:06 +0100
Subject: [PATCH 094/184] fix css

---
 src/main/java/org/jabref/gui/Base.css | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
index f2d02b9cc95..dba1545c494 100644
--- a/src/main/java/org/jabref/gui/Base.css
+++ b/src/main/java/org/jabref/gui/Base.css
@@ -997,4 +997,4 @@ We want to have a look that matches our icons in the tool-bar */
 .sectionHeader {
     -fx-font-size: 1.5em;
     -fx-padding: 1em 0em 1em 0em;
-}
\ No newline at end of file
+}

From 28d46fd95a3f98ac60046436bb08a941ecc91207 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sat, 9 Mar 2019 13:47:06 +0100
Subject: [PATCH 095/184] introduce second boolean for export in specified
 order to reflect table order adjust tests format fxml

---
 .../jabref/gui/SaveOrderConfigDisplay.fxml    | 60 +++++++-------
 .../gui/SaveOrderConfigDisplayView.java       |  5 --
 .../gui/SaveOrderConfigDisplayViewModel.java  |  2 +-
 .../LibraryPropertiesDialog.fxml              | 80 +++++++++----------
 .../preferences/ExportSortingPrefsTab.java    |  4 +-
 .../model/metadata/SaveOrderConfig.java       | 14 ++--
 .../jabref/preferences/JabRefPreferences.java |  2 +-
 .../exporter/BibtexDatabaseWriterTest.java    |  4 +-
 .../importer/fileformat/BibtexParserTest.java |  4 +-
 9 files changed, 87 insertions(+), 88 deletions(-)

diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
index 6fab26dcfd1..4bee6851ab0 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplay.fxml
@@ -10,34 +10,34 @@
 <?import javafx.scene.layout.RowConstraints?>
 
 <fx:root prefHeight="200.0" prefWidth="600.0" type="javafx.scene.layout.GridPane" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.SaveOrderConfigDisplayView">
-  <columnConstraints>
-    <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="100.0" />
-    <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
-      <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
-  </columnConstraints>
-  <rowConstraints>
-    <RowConstraints prefHeight="30.0" />
-    <RowConstraints prefHeight="30.0" />
-      <RowConstraints prefHeight="30.0" />
-      <RowConstraints prefHeight="30.0" />
-      <RowConstraints prefHeight="30.0" />
-      <RowConstraints prefHeight="30.0" />
-  </rowConstraints>
-     <fx:define>
-       <ToggleGroup fx:id="saveOrderToggleGroup" />
-     </fx:define>
-   <children>
-      <ComboBox fx:id="savePriSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="3" />
-      <ComboBox fx:id="saveSecSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="4" />
-      <ComboBox fx:id="saveTerSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="5" />
-      <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" GridPane.rowIndex="2"/>
-      <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" GridPane.rowIndex="1" />
-      <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" />
-      <CheckBox fx:id="savePriDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" />
-      <CheckBox fx:id="saveSecDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" />
-      <CheckBox fx:id="saveTerDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" />
-      <Label disabled="${!exportInSpecifiedOrder.selected}" text="%Primary sort criterion" GridPane.rowIndex="3" />
-      <Label disabled="${!exportInSpecifiedOrder.selected}" text="%Secondary sort criterion" GridPane.rowIndex="4" />
-      <Label disabled="${!exportInSpecifiedOrder.selected}" text="%Tertiary sort criterion" GridPane.rowIndex="5" />
-   </children>
+    <columnConstraints>
+        <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="100.0" />
+        <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
+        <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
+    </columnConstraints>
+    <rowConstraints>
+        <RowConstraints prefHeight="30.0" />
+        <RowConstraints prefHeight="30.0" />
+        <RowConstraints prefHeight="30.0" />
+        <RowConstraints prefHeight="30.0" />
+        <RowConstraints prefHeight="30.0" />
+        <RowConstraints prefHeight="30.0" />
+    </rowConstraints>
+    <fx:define>
+        <ToggleGroup fx:id="saveOrderToggleGroup" />
+    </fx:define>
+    <children>
+        <ComboBox fx:id="savePriSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="3" />
+        <ComboBox fx:id="saveSecSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="4" />
+        <ComboBox fx:id="saveTerSort" editable="true" GridPane.columnIndex="1" GridPane.rowIndex="5" />
+        <RadioButton fx:id="exportInSpecifiedOrder" mnemonicParsing="false" prefHeight="5.0" prefWidth="206.0" text="%Export entries ordered as specified" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" GridPane.rowIndex="2" />
+        <RadioButton fx:id="exportInTableOrder" mnemonicParsing="false" text="%Export in current table sort order" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" GridPane.rowIndex="1" />
+        <RadioButton fx:id="exportInOriginalOrder" mnemonicParsing="false" text="%Export entries in their original order" toggleGroup="$saveOrderToggleGroup" GridPane.columnSpan="3" />
+        <CheckBox fx:id="savePriDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="3" />
+        <CheckBox fx:id="saveSecDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="4" />
+        <CheckBox fx:id="saveTerDesc" disable="${!exportInSpecifiedOrder.selected}" mnemonicParsing="false" text="%Descending" GridPane.columnIndex="2" GridPane.rowIndex="5" />
+        <Label disabled="${!exportInSpecifiedOrder.selected}" text="%Primary sort criterion" GridPane.rowIndex="3" />
+        <Label disabled="${!exportInSpecifiedOrder.selected}" text="%Secondary sort criterion" GridPane.rowIndex="4" />
+        <Label disabled="${!exportInSpecifiedOrder.selected}" text="%Tertiary sort criterion" GridPane.rowIndex="5" />
+    </children>
 </fx:root>
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
index 3f7e253f231..aeca6f4ddad 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayView.java
@@ -3,7 +3,6 @@
 import javax.inject.Inject;
 
 import javafx.fxml.FXML;
-import javafx.scene.Node;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.RadioButton;
@@ -39,7 +38,6 @@ public SaveOrderConfigDisplayView(SaveOrderConfig config) {
 
         ViewLoader.view(this)
                   .root(this)
-                  .controller(this)
                   .load();
     }
 
@@ -80,7 +78,4 @@ public SaveOrderConfig getSaveOrderConfig() {
         return viewModel.getSaveOrderConfig();
     }
 
-    public Node getJFXPanel() {
-        return this;
-    }
 }
diff --git a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
index a653a10e319..0846ee4866c 100644
--- a/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
+++ b/src/main/java/org/jabref/gui/SaveOrderConfigDisplayViewModel.java
@@ -70,7 +70,7 @@ public SaveOrderConfig getSaveOrderConfig() {
         SortCriterion secondary = new SortCriterion(getSelectedItemAsLowerCaseTrim(saveSecSortSelectedValueProperty), saveSecDescPropertySelected.getValue());
         SortCriterion tertiary = new SortCriterion(getSelectedItemAsLowerCaseTrim(saveTerSortSelectedValueProperty), saveTerDescPropertySelected.getValue());
 
-        SaveOrderConfig saveOrderConfig = new SaveOrderConfig(saveInOriginalProperty.getValue(), primary, secondary, tertiary);
+        SaveOrderConfig saveOrderConfig = new SaveOrderConfig(saveInOriginalProperty.getValue(), saveInSpecifiedOrderProperty.getValue(), primary, secondary, tertiary);
 
         return saveOrderConfig;
     }
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
index 980e13f0560..126d9e959b6 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
@@ -13,44 +13,44 @@
 <?import javafx.scene.layout.VBox?>
 
 <DialogPane minHeight="-Infinity" prefHeight="784.0" prefWidth="921.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.libraryproperties.LibraryPropertiesDialogView">
-   <content>
-      <VBox fx:id="contentVbox" minHeight="-Infinity" prefHeight="200.0" prefWidth="100.0">
-         <children>
-            <GridPane minHeight="-Infinity">
-              <columnConstraints>
-                <ColumnConstraints hgrow="SOMETIMES" maxWidth="218.0" minWidth="10.0" prefWidth="200.0" />
-                <ColumnConstraints hgrow="SOMETIMES" maxWidth="797.0" minWidth="10.0" prefWidth="529.0" />
-                  <ColumnConstraints hgrow="SOMETIMES" maxWidth="797.0" minWidth="10.0" prefWidth="100.0" />
-              </columnConstraints>
-              <rowConstraints>
-                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="SOMETIMES" />
-                <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="ALWAYS" />
-                  <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                  <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="ALWAYS" />
-                  <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                  <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="SOMETIMES" />
-              </rowConstraints>
-               <children>
-                  <Label text="%Library encoding" />
-                  <ComboBox fx:id="encoding" prefWidth="250.0" GridPane.columnIndex="1" GridPane.hgrow="ALWAYS" />
-                  <Label text="%General file directory" GridPane.rowIndex="2" />
-                  <TextField fx:id="generalFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="2" />
-                  <Button fx:id="browseGeneralFileDir" mnemonicParsing="false" onAction="#browseGeneralFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="2" />
-                  <Label text="%User-specific file directory" GridPane.rowIndex="3" />
-                  <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
-                  <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
-                  <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Override default file directories" GridPane.columnSpan="3" GridPane.rowIndex="1" />
-                  <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Library protection" GridPane.columnSpan="3" GridPane.rowIndex="4" />
-                  <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." GridPane.columnSpan="3" GridPane.rowIndex="5" />
-                  <Label styleClass="sectionHeader" text="%Export sort order" GridPane.rowIndex="6" />
-               </children>
-            </GridPane>
-         </children>
-      </VBox>
-   </content>
-  <buttonTypes>
-    <ButtonType fx:constant="CANCEL" />
-    <ButtonType fx:constant="OK" />
-  </buttonTypes>
+    <content>
+        <VBox fx:id="contentVbox" minHeight="-Infinity" prefHeight="200.0" prefWidth="100.0">
+            <children>
+                <GridPane minHeight="-Infinity">
+                    <columnConstraints>
+                        <ColumnConstraints hgrow="SOMETIMES" maxWidth="218.0" minWidth="10.0" prefWidth="200.0" />
+                        <ColumnConstraints hgrow="SOMETIMES" maxWidth="797.0" minWidth="10.0" prefWidth="529.0" />
+                        <ColumnConstraints hgrow="SOMETIMES" maxWidth="797.0" minWidth="10.0" prefWidth="100.0" />
+                    </columnConstraints>
+                    <rowConstraints>
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                        <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="SOMETIMES" />
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="ALWAYS" />
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                        <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="ALWAYS" />
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                        <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="SOMETIMES" />
+                    </rowConstraints>
+                    <children>
+                        <Label text="%Library encoding" />
+                        <ComboBox fx:id="encoding" prefWidth="250.0" GridPane.columnIndex="1" GridPane.hgrow="ALWAYS" />
+                        <Label text="%General file directory" GridPane.rowIndex="2" />
+                        <TextField fx:id="generalFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="2" />
+                        <Button fx:id="browseGeneralFileDir" mnemonicParsing="false" onAction="#browseGeneralFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="2" />
+                        <Label text="%User-specific file directory" GridPane.rowIndex="3" />
+                        <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
+                        <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
+                        <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Override default file directories" GridPane.columnSpan="3" GridPane.rowIndex="1" />
+                        <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Library protection" GridPane.columnSpan="3" GridPane.rowIndex="4" />
+                        <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." GridPane.columnSpan="3" GridPane.rowIndex="5" />
+                        <Label styleClass="sectionHeader" text="%Export sort order" GridPane.rowIndex="6" />
+                    </children>
+                </GridPane>
+            </children>
+        </VBox>
+    </content>
+    <buttonTypes>
+        <ButtonType fx:constant="CANCEL" />
+        <ButtonType fx:constant="OK" />
+    </buttonTypes>
 </DialogPane>
diff --git a/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java b/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
index d6482f567ce..000f2bd8053 100644
--- a/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExportSortingPrefsTab.java
@@ -20,7 +20,7 @@ class ExportSortingPrefsTab extends Pane implements PrefsTab {
     public ExportSortingPrefsTab(JabRefPreferences prefs) {
         exportOrderPanel = new SaveOrderConfigDisplayView(prefs.loadExportSaveOrder());
 
-        builder.add(exportOrderPanel.getJFXPanel(), 1, 8);
+        builder.add(exportOrderPanel, 1, 8);
         builder.add(new Line(), 2, 9);
     }
 
@@ -31,7 +31,7 @@ public Node getBuilder() {
 
     @Override
     public void setValues() {
-
+        //empty
     }
 
     @Override
diff --git a/src/main/java/org/jabref/model/metadata/SaveOrderConfig.java b/src/main/java/org/jabref/model/metadata/SaveOrderConfig.java
index 59fbfaa2d42..8bc318987a3 100644
--- a/src/main/java/org/jabref/model/metadata/SaveOrderConfig.java
+++ b/src/main/java/org/jabref/model/metadata/SaveOrderConfig.java
@@ -16,13 +16,15 @@ public class SaveOrderConfig {
     private static final String SPECIFIED = "specified";
     private final LinkedList<SortCriterion> sortCriteria = new LinkedList<>();
     private boolean saveInOriginalOrder;
+    private boolean saveInSpecifiedOrder;
 
     public SaveOrderConfig() {
         setSaveInOriginalOrder();
     }
 
-    public SaveOrderConfig(boolean saveInOriginalOrder, SortCriterion first, SortCriterion second, SortCriterion third) {
+    public SaveOrderConfig(boolean saveInOriginalOrder, boolean saveInSpecifiedOrder, SortCriterion first, SortCriterion second, SortCriterion third) {
         this.saveInOriginalOrder = saveInOriginalOrder;
+        this.saveInSpecifiedOrder = saveInSpecifiedOrder;
         sortCriteria.add(first);
         sortCriteria.add(second);
         sortCriteria.add(third);
@@ -62,7 +64,7 @@ public boolean saveInOriginalOrder() {
     }
 
     public boolean saveInSpecifiedOrder() {
-        return !saveInOriginalOrder;
+        return saveInSpecifiedOrder;
     }
 
     public LinkedList<SortCriterion> getSortCriteria() {
@@ -83,13 +85,14 @@ public boolean equals(Object o) {
 
     @Override
     public int hashCode() {
-        return Objects.hash(saveInOriginalOrder, sortCriteria);
+        return Objects.hash(saveInOriginalOrder, saveInSpecifiedOrder, sortCriteria);
     }
 
     @Override
     public String toString() {
-        return "SaveOrderConfig{" + "saveInOriginalOrder=" + saveInOriginalOrder +
-               ", sortCriteria=" + sortCriteria +
+        return "SaveOrderConfig{" + "saveInOriginalOrder=" + saveInOriginalOrder
+               + "saveInSpecifiedOrder =" + saveInSpecifiedOrder
+               + ", sortCriteria=" + sortCriteria +
                '}';
     }
 
@@ -99,6 +102,7 @@ public void setSaveInOriginalOrder() {
 
     public void setSaveInSpecifiedOrder() {
         this.saveInOriginalOrder = false;
+        this.saveInSpecifiedOrder = true;
     }
 
     /**
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index d088a64fa86..88eae71f20a 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -1722,7 +1722,7 @@ private SaveOrderConfig loadTableSaveOrder() {
 
     @Override
     public SaveOrderConfig loadExportSaveOrder() {
-        return new SaveOrderConfig(getBoolean(EXPORT_IN_ORIGINAL_ORDER),
+        return new SaveOrderConfig(getBoolean(EXPORT_IN_ORIGINAL_ORDER), getBoolean(EXPORT_IN_SPECIFIED_ORDER),
                 new SaveOrderConfig.SortCriterion(get(EXPORT_PRIMARY_SORT_FIELD), getBoolean(EXPORT_PRIMARY_SORT_DESCENDING)),
                 new SaveOrderConfig.SortCriterion(get(EXPORT_SECONDARY_SORT_FIELD), getBoolean(EXPORT_SECONDARY_SORT_DESCENDING)),
                 new SaveOrderConfig.SortCriterion(get(EXPORT_TERTIARY_SORT_FIELD), getBoolean(EXPORT_TERTIARY_SORT_DESCENDING))
diff --git a/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java b/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java
index e30ecf77ca8..a7f2ef36a4c 100644
--- a/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java
+++ b/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java
@@ -435,7 +435,7 @@ void writeSaveActions() throws Exception {
 
     @Test
     void writeSaveOrderConfig() throws Exception {
-        SaveOrderConfig saveOrderConfig = new SaveOrderConfig(false, new SaveOrderConfig.SortCriterion("author", false),
+        SaveOrderConfig saveOrderConfig = new SaveOrderConfig(false, true, new SaveOrderConfig.SortCriterion("author", false),
                 new SaveOrderConfig.SortCriterion("year", true),
                 new SaveOrderConfig.SortCriterion("abstract", false));
         metaData.setSaveOrderConfig(saveOrderConfig);
@@ -495,7 +495,7 @@ void writeFileDirectories() throws Exception {
 
     @Test
     void writeEntriesSorted() throws Exception {
-        SaveOrderConfig saveOrderConfig = new SaveOrderConfig(false,
+        SaveOrderConfig saveOrderConfig = new SaveOrderConfig(false, true,
                 new SaveOrderConfig.SortCriterion("author", false),
                 new SaveOrderConfig.SortCriterion("year", true),
                 new SaveOrderConfig.SortCriterion("abstract", false));
diff --git a/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java b/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
index 59e5d7d250e..116cfd198aa 100644
--- a/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
+++ b/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
@@ -57,7 +57,7 @@ class BibtexParserTest {
 
     private ImportFormatPreferences importFormatPreferences;
     private BibtexParser parser;
-    private FileUpdateMonitor fileMonitor = new DummyFileUpdateMonitor();
+    private final FileUpdateMonitor fileMonitor = new DummyFileUpdateMonitor();
 
     @BeforeEach
     void setUp() {
@@ -1338,7 +1338,7 @@ void integrationTestSaveOrderConfig() throws IOException {
 
         Optional<SaveOrderConfig> saveOrderConfig = result.getMetaData().getSaveOrderConfig();
 
-        assertEquals(new SaveOrderConfig(false, new SaveOrderConfig.SortCriterion("author", false),
+        assertEquals(new SaveOrderConfig(false, true, new SaveOrderConfig.SortCriterion("author", false),
                         new SaveOrderConfig.SortCriterion("year", true), new SaveOrderConfig.SortCriterion("abstract", false)),
                 saveOrderConfig.get());
     }

From ab9de54d17814ad6488b4d5c60c15f30608a907b Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sat, 9 Mar 2019 13:54:26 +0100
Subject: [PATCH 096/184] remove empty line

---
 src/main/java/org/jabref/gui/JabRefFrame.java | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 5f3d0624937..ffdeb573738 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -838,7 +838,6 @@ private MenuBar createMenu() {
             lookupIdentifiers.getItems().add(factory.createMenuItem(identifierAction.getAction(), identifierAction));
         }
 
-
         quality.getItems().addAll(
                 factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(this, dialogService)),
                 factory.createMenuItem(StandardActions.MERGE_ENTRIES, new MergeEntriesAction(this)),

From 06540939946648cff2428e5c5ff4d2ac69c8be19 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Sat, 9 Mar 2019 14:42:39 +0100
Subject: [PATCH 097/184] Fix NotOnJavaFXThread exception for remote import

---
 .../java/org/jabref/gui/remote/JabRefMessageHandler.java  | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/remote/JabRefMessageHandler.java b/src/main/java/org/jabref/gui/remote/JabRefMessageHandler.java
index 364052baa2d..8033c9343d9 100644
--- a/src/main/java/org/jabref/gui/remote/JabRefMessageHandler.java
+++ b/src/main/java/org/jabref/gui/remote/JabRefMessageHandler.java
@@ -3,6 +3,8 @@
 import java.util.Arrays;
 import java.util.List;
 
+import javafx.application.Platform;
+
 import org.jabref.JabRefGUI;
 import org.jabref.cli.ArgumentProcessor;
 import org.jabref.logic.importer.ParserResult;
@@ -20,7 +22,11 @@ public void handleCommandLineArguments(String[] message) {
         List<ParserResult> loaded = argumentProcessor.getParserResults();
         for (int i = 0; i < loaded.size(); i++) {
             ParserResult pr = loaded.get(i);
-            JabRefGUI.getMainFrame().addParserResult(pr, i == 0);
+            boolean focusPanel = i == 0;
+            Platform.runLater(() ->
+                    // Need to run this on the JavaFX thread
+                    JabRefGUI.getMainFrame().addParserResult(pr, focusPanel)
+            );
         }
     }
 }

From 03fc076324c4d57e40a663f962d050bafac15f08 Mon Sep 17 00:00:00 2001
From: Chelsey Ong <chelseyong@gmail.com>
Date: Sun, 10 Mar 2019 09:56:14 +0800
Subject: [PATCH 098/184] Filter unwanted characters before removing
 whitespaces

---
 .../logic/bibtexkeypattern/BibtexKeyGenerator.java     | 10 +++++++---
 .../logic/bibtexkeypattern/BracketedPattern.java       |  2 +-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
index ffea572e61e..35b4c5f6524 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
@@ -72,7 +72,7 @@ private static String getAppendix(int number) {
         }
     }
 
-    public static String cleanKey(String key, boolean enforceLegalKey) {
+    public static String filterUnwantedCharacters(String key, boolean enforceLegalKey) {
         if (!enforceLegalKey) {
             // User doesn't want us to enforce legal characters. We must still look
             // for whitespace and some characters such as commas, since these would
@@ -80,7 +80,7 @@ public static String cleanKey(String key, boolean enforceLegalKey) {
             StringBuilder newKey = new StringBuilder();
             for (int i = 0; i < key.length(); i++) {
                 char c = key.charAt(i);
-                if (!Character.isWhitespace(c) && (KEY_UNWANTED_CHARACTERS.indexOf(c) == -1)) {
+                if (KEY_UNWANTED_CHARACTERS.indexOf(c) == -1) {
                     newKey.append(c);
                 }
             }
@@ -90,7 +90,7 @@ public static String cleanKey(String key, boolean enforceLegalKey) {
         StringBuilder newKey = new StringBuilder();
         for (int i = 0; i < key.length(); i++) {
             char c = key.charAt(i);
-            if (!Character.isWhitespace(c) && (KEY_ILLEGAL_CHARACTERS.indexOf(c) == -1)) {
+            if (KEY_ILLEGAL_CHARACTERS.indexOf(c) == -1) {
                 newKey.append(c);
             }
         }
@@ -100,6 +100,10 @@ public static String cleanKey(String key, boolean enforceLegalKey) {
         return StringUtil.replaceSpecialCharacters(newKey.toString());
     }
 
+    public static String cleanKey(String key, boolean enforceLegalKey) {
+        return filterUnwantedCharacters(key, enforceLegalKey).replaceAll("\\s","");
+    }
+
     public String generateKey(BibEntry entry) {
         String key;
         StringBuilder stringBuilder = new StringBuilder();
diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
index 36e11757552..c6a8d292ae5 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
@@ -841,7 +841,7 @@ public static String authNofMth(String authorField, int n, int m) {
      * First N chars of the first author's last name.
      */
     public static String authN(String authString, int num, boolean isEnforceLegalKey) {
-        authString = BibtexKeyGenerator.cleanKey(authString, isEnforceLegalKey);
+        authString = BibtexKeyGenerator.filterUnwantedCharacters(authString, isEnforceLegalKey);
         String fa = firstAuthor(authString);
         if (num > fa.length()) {
             num = fa.length();

From a0219f384719159bc067e03784348662332ad8ef Mon Sep 17 00:00:00 2001
From: Chelsey Ong <chelseyong@gmail.com>
Date: Sun, 10 Mar 2019 10:10:01 +0800
Subject: [PATCH 099/184] Update test cases

---
 .../BibtexKeyGeneratorTest.java               | 46 ++++++++++++-------
 1 file changed, 29 insertions(+), 17 deletions(-)

diff --git a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
index 4ed5b5bb728..6c2a319c798 100644
--- a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
+++ b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
@@ -119,73 +119,73 @@ public void testMakeLabelAndCheckLegalKeys() throws ParseException {
 
         Optional<BibEntry> entry0 = BibtexParser.singleFromString(
                 "@ARTICLE{kohn, author={Andreas Köning}, year={2000}}", importFormatPreferences, fileMonitor);
-        assertEquals("Koen",
+        assertEquals("Koe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Áöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Aoen",
+        assertEquals("Aoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Éöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Eoen",
+        assertEquals("Eoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Íöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ioen",
+        assertEquals("Ioe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ĺöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Loen",
+        assertEquals("Loe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ńöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Noen",
+        assertEquals("Noe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Óöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ooen",
+        assertEquals("Ooe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ŕöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Roen",
+        assertEquals("Roe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Śöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Soen",
+        assertEquals("Soe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Úöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Uoen",
+        assertEquals("Uoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ýöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Yoen",
+        assertEquals("Yoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Źöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Zoen",
+        assertEquals("Zoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
     }
@@ -197,31 +197,43 @@ public void testMakeLabelAndCheckLegalKeys() throws ParseException {
     public void testMakeLabelAndCheckLegalKeysAccentGrave() throws ParseException {
         Optional<BibEntry> entry0 = BibtexParser.singleFromString(
                 "@ARTICLE{kohn, author={Andreas Àöning}, year={2000}}", importFormatPreferences, fileMonitor);
-        assertEquals("Aoen",
+        assertEquals("Aoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Èöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Eoen",
+        assertEquals("Eoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ìöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ioen",
+        assertEquals("Ioe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Òöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ooen",
+        assertEquals("Ooe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ùöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Uoen",
+        assertEquals("Uoe",
+                BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
+                        new BibDatabase()), true));
+
+        entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Oraib Al-Ketan}, year={2000}}",
+                importFormatPreferences, fileMonitor);
+        assertEquals("AlK",
+                BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
+                        new BibDatabase()), true));
+
+        entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andrés D'Alessandro}, year={2000}}",
+                importFormatPreferences, fileMonitor);
+        assertEquals("DAl",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
     }

From 89a398b5951659d11e81aa4ad9979deb0150ffc2 Mon Sep 17 00:00:00 2001
From: Chelsey Ong <chelseyong@gmail.com>
Date: Sun, 10 Mar 2019 10:10:30 +0800
Subject: [PATCH 100/184] Remove -s from key

---
 .../org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
index 35b4c5f6524..f1a7306b558 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
@@ -26,8 +26,8 @@ public class BibtexKeyGenerator extends BracketedPattern {
      */
     public static final String APPENDIX_CHARACTERS = "abcdefghijklmnopqrstuvwxyz";
     private static final Logger LOGGER = LoggerFactory.getLogger(BibtexKeyGenerator.class);
-    private static final String KEY_ILLEGAL_CHARACTERS = "{}(),\\\"#~^':`";
-    private static final String KEY_UNWANTED_CHARACTERS = "{}(),\\\"";
+    private static final String KEY_ILLEGAL_CHARACTERS = "{}(),\\\"-#~^':`";
+    private static final String KEY_UNWANTED_CHARACTERS = "{}(),\\\"-";
     private final AbstractBibtexKeyPattern citeKeyPattern;
     private final BibDatabase database;
     private final BibtexKeyPatternPreferences bibtexKeyPatternPreferences;

From e3e696113b1877d856abbcfbaf80ef04a0ca77b2 Mon Sep 17 00:00:00 2001
From: Chelsey Ong <chelseyong@gmail.com>
Date: Sun, 10 Mar 2019 10:36:33 +0800
Subject: [PATCH 101/184] Remove the dashes from test case

---
 .../logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java b/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java
index a28d412bc35..88345234b72 100644
--- a/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java
+++ b/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java
@@ -397,7 +397,7 @@ void generateKeyTitleRegexe() {
         bibtexKeyPattern.setDefaultValue("[title:regex(\" \",\"-\")]");
         entry.setField("title", "Please replace the spaces");
         new BibtexKeyGenerator(bibtexKeyPattern, database, preferences).generateAndSetKey(entry);
-        assertEquals(Optional.of("Please-Replace-the-Spaces"), entry.getCiteKeyOptional());
+        assertEquals(Optional.of("PleaseReplacetheSpaces"), entry.getCiteKeyOptional());
     }
 
     @Test

From f414a9643f519e12553328ef9c00fd51e15fb7dc Mon Sep 17 00:00:00 2001
From: Chelsey Ong <chelseyong@gmail.com>
Date: Sun, 10 Mar 2019 18:18:21 +0800
Subject: [PATCH 102/184] Rename method to removeUnwantedCharacters

---
 .../org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java | 4 ++--
 .../org/jabref/logic/bibtexkeypattern/BracketedPattern.java   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
index f1a7306b558..6e10ac5ff8f 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
@@ -72,7 +72,7 @@ private static String getAppendix(int number) {
         }
     }
 
-    public static String filterUnwantedCharacters(String key, boolean enforceLegalKey) {
+    public static String removeUnwantedCharacters(String key, boolean enforceLegalKey) {
         if (!enforceLegalKey) {
             // User doesn't want us to enforce legal characters. We must still look
             // for whitespace and some characters such as commas, since these would
@@ -101,7 +101,7 @@ public static String filterUnwantedCharacters(String key, boolean enforceLegalKe
     }
 
     public static String cleanKey(String key, boolean enforceLegalKey) {
-        return filterUnwantedCharacters(key, enforceLegalKey).replaceAll("\\s","");
+        return removeUnwantedCharacters(key, enforceLegalKey).replaceAll("\\s","");
     }
 
     public String generateKey(BibEntry entry) {
diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
index c6a8d292ae5..25f214ab164 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
@@ -841,7 +841,7 @@ public static String authNofMth(String authorField, int n, int m) {
      * First N chars of the first author's last name.
      */
     public static String authN(String authString, int num, boolean isEnforceLegalKey) {
-        authString = BibtexKeyGenerator.filterUnwantedCharacters(authString, isEnforceLegalKey);
+        authString = BibtexKeyGenerator.removeUnwantedCharacters(authString, isEnforceLegalKey);
         String fa = firstAuthor(authString);
         if (num > fa.length()) {
             num = fa.length();

From 26f7865c64132ce619a656781a2e03525728f57a Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Sun, 10 Mar 2019 13:40:53 +0100
Subject: [PATCH 103/184] Revert "Fix: bibkey generated does not handle
 diacritics" (#4741)

---
 .../bibtexkeypattern/BibtexKeyGenerator.java  | 16 +++----
 .../bibtexkeypattern/BracketedPattern.java    | 33 +++++--------
 .../BibtexKeyGeneratorTest.java               | 46 +++++++------------
 .../MakeLabelWithDatabaseTest.java            |  2 +-
 4 files changed, 36 insertions(+), 61 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
index 6e10ac5ff8f..ff61a9035da 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
@@ -26,8 +26,8 @@ public class BibtexKeyGenerator extends BracketedPattern {
      */
     public static final String APPENDIX_CHARACTERS = "abcdefghijklmnopqrstuvwxyz";
     private static final Logger LOGGER = LoggerFactory.getLogger(BibtexKeyGenerator.class);
-    private static final String KEY_ILLEGAL_CHARACTERS = "{}(),\\\"-#~^':`";
-    private static final String KEY_UNWANTED_CHARACTERS = "{}(),\\\"-";
+    private static final String KEY_ILLEGAL_CHARACTERS = "{}(),\\\"#~^':`";
+    private static final String KEY_UNWANTED_CHARACTERS = "{}(),\\\"";
     private final AbstractBibtexKeyPattern citeKeyPattern;
     private final BibDatabase database;
     private final BibtexKeyPatternPreferences bibtexKeyPatternPreferences;
@@ -72,7 +72,7 @@ private static String getAppendix(int number) {
         }
     }
 
-    public static String removeUnwantedCharacters(String key, boolean enforceLegalKey) {
+    public static String cleanKey(String key, boolean enforceLegalKey) {
         if (!enforceLegalKey) {
             // User doesn't want us to enforce legal characters. We must still look
             // for whitespace and some characters such as commas, since these would
@@ -80,7 +80,7 @@ public static String removeUnwantedCharacters(String key, boolean enforceLegalKe
             StringBuilder newKey = new StringBuilder();
             for (int i = 0; i < key.length(); i++) {
                 char c = key.charAt(i);
-                if (KEY_UNWANTED_CHARACTERS.indexOf(c) == -1) {
+                if (!Character.isWhitespace(c) && (KEY_UNWANTED_CHARACTERS.indexOf(c) == -1)) {
                     newKey.append(c);
                 }
             }
@@ -90,7 +90,7 @@ public static String removeUnwantedCharacters(String key, boolean enforceLegalKe
         StringBuilder newKey = new StringBuilder();
         for (int i = 0; i < key.length(); i++) {
             char c = key.charAt(i);
-            if (KEY_ILLEGAL_CHARACTERS.indexOf(c) == -1) {
+            if (!Character.isWhitespace(c) && (KEY_ILLEGAL_CHARACTERS.indexOf(c) == -1)) {
                 newKey.append(c);
             }
         }
@@ -100,10 +100,6 @@ public static String removeUnwantedCharacters(String key, boolean enforceLegalKe
         return StringUtil.replaceSpecialCharacters(newKey.toString());
     }
 
-    public static String cleanKey(String key, boolean enforceLegalKey) {
-        return removeUnwantedCharacters(key, enforceLegalKey).replaceAll("\\s","");
-    }
-
     public String generateKey(BibEntry entry) {
         String key;
         StringBuilder stringBuilder = new StringBuilder();
@@ -127,7 +123,7 @@ public String generateKey(BibEntry entry) {
                     List<String> parts = parseFieldMarker(typeListEntry);
                     Character delimiter = bibtexKeyPatternPreferences.getKeywordDelimiter();
                     String pattern = "[" + parts.get(0) + "]";
-                    String label = expandBrackets(pattern, delimiter, entry, database, bibtexKeyPatternPreferences.isEnforceLegalKey());
+                    String label = expandBrackets(pattern, delimiter, entry, database);
                     // apply modifier if present
                     if (parts.size() > 1) {
                         label = applyModifiers(label, parts, 1);
diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
index 25f214ab164..f88e98b3842 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
@@ -92,10 +92,6 @@ public String expand(BibEntry bibentry, Character keywordDelimiter, BibDatabase
         return expandBrackets(this.pattern, keywordDelimiter, bibentry, database);
     }
 
-    public static String expandBrackets(String pattern, Character keywordDelimiter, BibEntry entry, BibDatabase database) {
-        return expandBrackets(pattern, keywordDelimiter, entry, database, false);
-    }
-
     /**
      * Expands a pattern
      *
@@ -105,7 +101,7 @@ public static String expandBrackets(String pattern, Character keywordDelimiter,
      * @param database The database for field resolving. May be null.
      * @return The expanded pattern. Not null.
      */
-    public static String expandBrackets(String pattern, Character keywordDelimiter, BibEntry entry, BibDatabase database, boolean isEnforceLegalKey) {
+    public static String expandBrackets(String pattern, Character keywordDelimiter, BibEntry entry, BibDatabase database) {
         Objects.requireNonNull(pattern);
         Objects.requireNonNull(entry);
         StringBuilder sb = new StringBuilder();
@@ -126,10 +122,10 @@ public static String expandBrackets(String pattern, Character keywordDelimiter,
                     // check whether there is a modifier on the end such as
                     // ":lower":
                     if (fieldParts.size() <= 1) {
-                        sb.append(getFieldValue(entry, token, keywordDelimiter, database, isEnforceLegalKey));
+                        sb.append(getFieldValue(entry, token, keywordDelimiter, database));
                     } else {
                         // apply modifiers:
-                        String fieldValue = getFieldValue(entry, fieldParts.get(0), keywordDelimiter, database, isEnforceLegalKey);
+                        String fieldValue = getFieldValue(entry, fieldParts.get(0), keywordDelimiter, database);
                         sb.append(applyModifiers(fieldValue, fieldParts, 1));
                     }
                     // Fetch and discard the closing ']'
@@ -160,7 +156,7 @@ public static String expandBrackets(String pattern, Character keywordDelimiter,
      *
      * @return String containing the evaluation result. Empty string if the pattern cannot be resolved.
      */
-    public static String getFieldValue(BibEntry entry, String value, Character keywordDelimiter, BibDatabase database, boolean isEnforceLegalKey) {
+    public static String getFieldValue(BibEntry entry, String value, Character keywordDelimiter, BibDatabase database) {
 
         String val = value;
         try {
@@ -228,8 +224,15 @@ else if ("authorLast".equals(val)) {
                     return authNofMth(authString, Integer.parseInt(nums[0]),
                             Integer.parseInt(nums[1]));
                 } else if (val.matches("auth\\d+")) {
+                    // authN. First N chars of the first author's last
+                    // name.
+
+                    String fa = firstAuthor(authString);
                     int num = Integer.parseInt(val.substring(4));
-                    return authN(authString, num, isEnforceLegalKey);
+                    if (num > fa.length()) {
+                        num = fa.length();
+                    }
+                    return fa.substring(0, num);
                 } else if (val.matches("authors\\d+")) {
                     return nAuthors(authString, Integer.parseInt(val.substring(7)));
                 } else {
@@ -837,18 +840,6 @@ public static String authNofMth(String authorField, int n, int m) {
         }
     }
 
-    /**
-     * First N chars of the first author's last name.
-     */
-    public static String authN(String authString, int num, boolean isEnforceLegalKey) {
-        authString = BibtexKeyGenerator.removeUnwantedCharacters(authString, isEnforceLegalKey);
-        String fa = firstAuthor(authString);
-        if (num > fa.length()) {
-            num = fa.length();
-        }
-        return fa.substring(0, num);
-    }
-
     /**
      * authshort format:
      * added by Kolja Brix, kbx@users.sourceforge.net
diff --git a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
index 3857cfb6c8b..f09b091fb7e 100644
--- a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
+++ b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
@@ -119,73 +119,73 @@ public void testMakeLabelAndCheckLegalKeys() throws ParseException {
 
         Optional<BibEntry> entry0 = BibtexParser.singleFromString(
                 "@ARTICLE{kohn, author={Andreas Köning}, year={2000}}", importFormatPreferences, fileMonitor);
-        assertEquals("Koe",
+        assertEquals("Koen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Áöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Aoe",
+        assertEquals("Aoen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Éöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Eoe",
+        assertEquals("Eoen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Íöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ioe",
+        assertEquals("Ioen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ĺöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Loe",
+        assertEquals("Loen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ńöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Noe",
+        assertEquals("Noen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Óöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ooe",
+        assertEquals("Ooen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ŕöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Roe",
+        assertEquals("Roen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Śöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Soe",
+        assertEquals("Soen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Úöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Uoe",
+        assertEquals("Uoen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ýöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Yoe",
+        assertEquals("Yoen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Źöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Zoe",
+        assertEquals("Zoen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
     }
@@ -197,43 +197,31 @@ public void testMakeLabelAndCheckLegalKeys() throws ParseException {
     public void testMakeLabelAndCheckLegalKeysAccentGrave() throws ParseException {
         Optional<BibEntry> entry0 = BibtexParser.singleFromString(
                 "@ARTICLE{kohn, author={Andreas Àöning}, year={2000}}", importFormatPreferences, fileMonitor);
-        assertEquals("Aoe",
+        assertEquals("Aoen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Èöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Eoe",
+        assertEquals("Eoen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ìöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ioe",
+        assertEquals("Ioen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Òöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ooe",
+        assertEquals("Ooen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ùöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Uoe",
-                BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
-                        new BibDatabase()), true));
-
-        entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Oraib Al-Ketan}, year={2000}}",
-                importFormatPreferences, fileMonitor);
-        assertEquals("AlK",
-                BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
-                        new BibDatabase()), true));
-
-        entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andrés D'Alessandro}, year={2000}}",
-                importFormatPreferences, fileMonitor);
-        assertEquals("DAl",
+        assertEquals("Uoen",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
     }
diff --git a/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java b/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java
index 88345234b72..a28d412bc35 100644
--- a/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java
+++ b/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java
@@ -397,7 +397,7 @@ void generateKeyTitleRegexe() {
         bibtexKeyPattern.setDefaultValue("[title:regex(\" \",\"-\")]");
         entry.setField("title", "Please replace the spaces");
         new BibtexKeyGenerator(bibtexKeyPattern, database, preferences).generateAndSetKey(entry);
-        assertEquals(Optional.of("PleaseReplacetheSpaces"), entry.getCiteKeyOptional());
+        assertEquals(Optional.of("Please-Replace-the-Spaces"), entry.getCiteKeyOptional());
     }
 
     @Test

From fac6e625dba9182d3fd78e66380b307e3406eab5 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Sun, 10 Mar 2019 13:46:55 +0100
Subject: [PATCH 104/184] Revert "Revert "Fix: bibkey generated does not handle
 diacritics" (#4741)" (#4742)

This reverts commit 26f7865c64132ce619a656781a2e03525728f57a.
---
 .../bibtexkeypattern/BibtexKeyGenerator.java  | 16 ++++---
 .../bibtexkeypattern/BracketedPattern.java    | 33 ++++++++-----
 .../BibtexKeyGeneratorTest.java               | 46 ++++++++++++-------
 .../MakeLabelWithDatabaseTest.java            |  2 +-
 4 files changed, 61 insertions(+), 36 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
index ff61a9035da..6e10ac5ff8f 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
@@ -26,8 +26,8 @@ public class BibtexKeyGenerator extends BracketedPattern {
      */
     public static final String APPENDIX_CHARACTERS = "abcdefghijklmnopqrstuvwxyz";
     private static final Logger LOGGER = LoggerFactory.getLogger(BibtexKeyGenerator.class);
-    private static final String KEY_ILLEGAL_CHARACTERS = "{}(),\\\"#~^':`";
-    private static final String KEY_UNWANTED_CHARACTERS = "{}(),\\\"";
+    private static final String KEY_ILLEGAL_CHARACTERS = "{}(),\\\"-#~^':`";
+    private static final String KEY_UNWANTED_CHARACTERS = "{}(),\\\"-";
     private final AbstractBibtexKeyPattern citeKeyPattern;
     private final BibDatabase database;
     private final BibtexKeyPatternPreferences bibtexKeyPatternPreferences;
@@ -72,7 +72,7 @@ private static String getAppendix(int number) {
         }
     }
 
-    public static String cleanKey(String key, boolean enforceLegalKey) {
+    public static String removeUnwantedCharacters(String key, boolean enforceLegalKey) {
         if (!enforceLegalKey) {
             // User doesn't want us to enforce legal characters. We must still look
             // for whitespace and some characters such as commas, since these would
@@ -80,7 +80,7 @@ public static String cleanKey(String key, boolean enforceLegalKey) {
             StringBuilder newKey = new StringBuilder();
             for (int i = 0; i < key.length(); i++) {
                 char c = key.charAt(i);
-                if (!Character.isWhitespace(c) && (KEY_UNWANTED_CHARACTERS.indexOf(c) == -1)) {
+                if (KEY_UNWANTED_CHARACTERS.indexOf(c) == -1) {
                     newKey.append(c);
                 }
             }
@@ -90,7 +90,7 @@ public static String cleanKey(String key, boolean enforceLegalKey) {
         StringBuilder newKey = new StringBuilder();
         for (int i = 0; i < key.length(); i++) {
             char c = key.charAt(i);
-            if (!Character.isWhitespace(c) && (KEY_ILLEGAL_CHARACTERS.indexOf(c) == -1)) {
+            if (KEY_ILLEGAL_CHARACTERS.indexOf(c) == -1) {
                 newKey.append(c);
             }
         }
@@ -100,6 +100,10 @@ public static String cleanKey(String key, boolean enforceLegalKey) {
         return StringUtil.replaceSpecialCharacters(newKey.toString());
     }
 
+    public static String cleanKey(String key, boolean enforceLegalKey) {
+        return removeUnwantedCharacters(key, enforceLegalKey).replaceAll("\\s","");
+    }
+
     public String generateKey(BibEntry entry) {
         String key;
         StringBuilder stringBuilder = new StringBuilder();
@@ -123,7 +127,7 @@ public String generateKey(BibEntry entry) {
                     List<String> parts = parseFieldMarker(typeListEntry);
                     Character delimiter = bibtexKeyPatternPreferences.getKeywordDelimiter();
                     String pattern = "[" + parts.get(0) + "]";
-                    String label = expandBrackets(pattern, delimiter, entry, database);
+                    String label = expandBrackets(pattern, delimiter, entry, database, bibtexKeyPatternPreferences.isEnforceLegalKey());
                     // apply modifier if present
                     if (parts.size() > 1) {
                         label = applyModifiers(label, parts, 1);
diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
index f88e98b3842..25f214ab164 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java
@@ -92,6 +92,10 @@ public String expand(BibEntry bibentry, Character keywordDelimiter, BibDatabase
         return expandBrackets(this.pattern, keywordDelimiter, bibentry, database);
     }
 
+    public static String expandBrackets(String pattern, Character keywordDelimiter, BibEntry entry, BibDatabase database) {
+        return expandBrackets(pattern, keywordDelimiter, entry, database, false);
+    }
+
     /**
      * Expands a pattern
      *
@@ -101,7 +105,7 @@ public String expand(BibEntry bibentry, Character keywordDelimiter, BibDatabase
      * @param database The database for field resolving. May be null.
      * @return The expanded pattern. Not null.
      */
-    public static String expandBrackets(String pattern, Character keywordDelimiter, BibEntry entry, BibDatabase database) {
+    public static String expandBrackets(String pattern, Character keywordDelimiter, BibEntry entry, BibDatabase database, boolean isEnforceLegalKey) {
         Objects.requireNonNull(pattern);
         Objects.requireNonNull(entry);
         StringBuilder sb = new StringBuilder();
@@ -122,10 +126,10 @@ public static String expandBrackets(String pattern, Character keywordDelimiter,
                     // check whether there is a modifier on the end such as
                     // ":lower":
                     if (fieldParts.size() <= 1) {
-                        sb.append(getFieldValue(entry, token, keywordDelimiter, database));
+                        sb.append(getFieldValue(entry, token, keywordDelimiter, database, isEnforceLegalKey));
                     } else {
                         // apply modifiers:
-                        String fieldValue = getFieldValue(entry, fieldParts.get(0), keywordDelimiter, database);
+                        String fieldValue = getFieldValue(entry, fieldParts.get(0), keywordDelimiter, database, isEnforceLegalKey);
                         sb.append(applyModifiers(fieldValue, fieldParts, 1));
                     }
                     // Fetch and discard the closing ']'
@@ -156,7 +160,7 @@ public static String expandBrackets(String pattern, Character keywordDelimiter,
      *
      * @return String containing the evaluation result. Empty string if the pattern cannot be resolved.
      */
-    public static String getFieldValue(BibEntry entry, String value, Character keywordDelimiter, BibDatabase database) {
+    public static String getFieldValue(BibEntry entry, String value, Character keywordDelimiter, BibDatabase database, boolean isEnforceLegalKey) {
 
         String val = value;
         try {
@@ -224,15 +228,8 @@ else if ("authorLast".equals(val)) {
                     return authNofMth(authString, Integer.parseInt(nums[0]),
                             Integer.parseInt(nums[1]));
                 } else if (val.matches("auth\\d+")) {
-                    // authN. First N chars of the first author's last
-                    // name.
-
-                    String fa = firstAuthor(authString);
                     int num = Integer.parseInt(val.substring(4));
-                    if (num > fa.length()) {
-                        num = fa.length();
-                    }
-                    return fa.substring(0, num);
+                    return authN(authString, num, isEnforceLegalKey);
                 } else if (val.matches("authors\\d+")) {
                     return nAuthors(authString, Integer.parseInt(val.substring(7)));
                 } else {
@@ -840,6 +837,18 @@ public static String authNofMth(String authorField, int n, int m) {
         }
     }
 
+    /**
+     * First N chars of the first author's last name.
+     */
+    public static String authN(String authString, int num, boolean isEnforceLegalKey) {
+        authString = BibtexKeyGenerator.removeUnwantedCharacters(authString, isEnforceLegalKey);
+        String fa = firstAuthor(authString);
+        if (num > fa.length()) {
+            num = fa.length();
+        }
+        return fa.substring(0, num);
+    }
+
     /**
      * authshort format:
      * added by Kolja Brix, kbx@users.sourceforge.net
diff --git a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
index f09b091fb7e..3857cfb6c8b 100644
--- a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
+++ b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
@@ -119,73 +119,73 @@ public void testMakeLabelAndCheckLegalKeys() throws ParseException {
 
         Optional<BibEntry> entry0 = BibtexParser.singleFromString(
                 "@ARTICLE{kohn, author={Andreas Köning}, year={2000}}", importFormatPreferences, fileMonitor);
-        assertEquals("Koen",
+        assertEquals("Koe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Áöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Aoen",
+        assertEquals("Aoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Éöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Eoen",
+        assertEquals("Eoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Íöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ioen",
+        assertEquals("Ioe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ĺöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Loen",
+        assertEquals("Loe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ńöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Noen",
+        assertEquals("Noe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Óöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ooen",
+        assertEquals("Ooe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ŕöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Roen",
+        assertEquals("Roe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Śöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Soen",
+        assertEquals("Soe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Úöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Uoen",
+        assertEquals("Uoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ýöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Yoen",
+        assertEquals("Yoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Źöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Zoen",
+        assertEquals("Zoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
     }
@@ -197,31 +197,43 @@ public void testMakeLabelAndCheckLegalKeys() throws ParseException {
     public void testMakeLabelAndCheckLegalKeysAccentGrave() throws ParseException {
         Optional<BibEntry> entry0 = BibtexParser.singleFromString(
                 "@ARTICLE{kohn, author={Andreas Àöning}, year={2000}}", importFormatPreferences, fileMonitor);
-        assertEquals("Aoen",
+        assertEquals("Aoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Èöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Eoen",
+        assertEquals("Eoe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ìöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ioen",
+        assertEquals("Ioe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Òöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Ooen",
+        assertEquals("Ooe",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
 
         entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andreas Ùöning}, year={2000}}",
                 importFormatPreferences, fileMonitor);
-        assertEquals("Uoen",
+        assertEquals("Uoe",
+                BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
+                        new BibDatabase()), true));
+
+        entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Oraib Al-Ketan}, year={2000}}",
+                importFormatPreferences, fileMonitor);
+        assertEquals("AlK",
+                BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
+                        new BibDatabase()), true));
+
+        entry0 = BibtexParser.singleFromString("@ARTICLE{kohn, author={Andrés D'Alessandro}, year={2000}}",
+                importFormatPreferences, fileMonitor);
+        assertEquals("DAl",
                 BibtexKeyGenerator.cleanKey(BibtexKeyGenerator.generateKey(entry0.get(), "auth3",
                         new BibDatabase()), true));
     }
diff --git a/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java b/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java
index a28d412bc35..88345234b72 100644
--- a/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java
+++ b/src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java
@@ -397,7 +397,7 @@ void generateKeyTitleRegexe() {
         bibtexKeyPattern.setDefaultValue("[title:regex(\" \",\"-\")]");
         entry.setField("title", "Please replace the spaces");
         new BibtexKeyGenerator(bibtexKeyPattern, database, preferences).generateAndSetKey(entry);
-        assertEquals(Optional.of("Please-Replace-the-Spaces"), entry.getCiteKeyOptional());
+        assertEquals(Optional.of("PleaseReplacetheSpaces"), entry.getCiteKeyOptional());
     }
 
     @Test

From d46725a663f06f81e29743c361c97d0b9c689ef9 Mon Sep 17 00:00:00 2001
From: Matthias Geiger <matthias.geiger@uni-bamberg.de>
Date: Sun, 10 Mar 2019 18:23:42 +0100
Subject: [PATCH 105/184] Move library specific key pattern dialog call to
 library menu (#4744)

---
 src/main/java/org/jabref/gui/JabRefFrame.java                 | 4 ++--
 .../jabref/gui/bibtexkeypattern/BibtexKeyPatternDialog.java   | 3 +++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index ffdeb573738..9a1a2bdb735 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -829,6 +829,7 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.LIBRARY_PROPERTIES, new LibraryPropertiesAction(this, dialogService)),
                 factory.createMenuItem(StandardActions.EDIT_PREAMBLE, new PreambleEditor(this)),
                 factory.createMenuItem(StandardActions.EDIT_STRINGS, new BibtexStringEditorAction(this)),
+                factory.createMenuItem(StandardActions.MANAGE_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this)),
                 factory.createMenuItem(StandardActions.MASS_SET_FIELDS, new MassSetFieldsAction(this))
         );
 
@@ -916,10 +917,9 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.MANAGE_CONTENT_SELECTORS, new ManageContentSelectorAction(this)),
+                factory.createMenuItem(StandardActions.MANAGE_CONTENT_SELECTORS, new ManageContentSelectorAction(this))
                 // TODO: Reenable customize entry types feature (https://github.com/JabRef/jabref/issues/4719)
                 //factory.createMenuItem(StandardActions.CUSTOMIZE_ENTRY_TYPES, new CustomizeEntryAction(this)),
-                factory.createMenuItem(StandardActions.MANAGE_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this))
         );
 
         help.getItems().addAll(
diff --git a/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternDialog.java b/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternDialog.java
index 647c54a1fc0..3246ff21267 100644
--- a/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternDialog.java
+++ b/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternDialog.java
@@ -5,6 +5,7 @@
 import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.util.BaseDialog;
+import org.jabref.logic.l10n.Localization;
 import org.jabref.model.bibtexkeypattern.AbstractBibtexKeyPattern;
 import org.jabref.model.metadata.MetaData;
 
@@ -25,6 +26,8 @@ public BibtexKeyPatternDialog(BasePanel panel) {
 
     private void init() {
 
+        this.setTitle(Localization.lang("BibTeX key patterns"));
+
         this.getDialogPane().setContent(bibtexKeyPatternPanel.getPanel());
         this.getDialogPane().getButtonTypes().addAll(ButtonType.APPLY, ButtonType.CANCEL);
 

From 864d5c86ca6edb46fa5101c04b306dde74274798 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Sun, 10 Mar 2019 20:06:01 +0100
Subject: [PATCH 106/184] Remove obsolete swing components in Preferences and
 OpenOffice (#4740)

* remove old swing help action code

* replace OO swing dialog for document chosing with javafx choice dialog

* add missing l10n

* refactor: Call selectDocument dialog when background task is finished
set title of choice dialog

* add newline
---
 .../java/org/jabref/gui/FXDialogService.java  |   1 +
 .../java/org/jabref/gui/help/HelpAction.java  |  10 -
 .../org/jabref/gui/openoffice/OOBibBase.java  | 184 +++++++++---------
 .../gui/openoffice/OpenOfficePanel.java       |  99 +++++-----
 .../gui/preferences/AppearancePrefsTab.java   |   1 +
 .../preferences/BibtexKeyPatternPrefTab.java  |   2 +-
 .../org/jabref/gui/preferences/FileTab.java   |  45 +++--
 .../jabref/gui/preferences/GeneralTab.java    |  16 +-
 .../gui/preferences/NameFormatterTab.java     |  78 ++++----
 .../gui/preferences/TableColumnsTab.java      |  76 ++++----
 src/main/resources/l10n/JabRef_en.properties  |   3 +
 11 files changed, 270 insertions(+), 245 deletions(-)

diff --git a/src/main/java/org/jabref/gui/FXDialogService.java b/src/main/java/org/jabref/gui/FXDialogService.java
index 0d6bc1fecd0..f3edaba275a 100644
--- a/src/main/java/org/jabref/gui/FXDialogService.java
+++ b/src/main/java/org/jabref/gui/FXDialogService.java
@@ -112,6 +112,7 @@ public <T> Optional<T> showChoiceDialogAndWait(String title, String content, Str
         ButtonType okButtonType = new ButtonType(okButtonLabel, ButtonBar.ButtonData.OK_DONE);
         choiceDialog.getDialogPane().getButtonTypes().setAll(ButtonType.CANCEL, okButtonType);
         choiceDialog.setHeaderText(title);
+        choiceDialog.setTitle(title);
         choiceDialog.setContentText(content);
         return choiceDialog.showAndWait();
 
diff --git a/src/main/java/org/jabref/gui/help/HelpAction.java b/src/main/java/org/jabref/gui/help/HelpAction.java
index e8d410de343..d18d3f0b34b 100644
--- a/src/main/java/org/jabref/gui/help/HelpAction.java
+++ b/src/main/java/org/jabref/gui/help/HelpAction.java
@@ -1,6 +1,5 @@
 package org.jabref.gui.help;
 
-import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.util.HashSet;
 import java.util.Set;
@@ -9,7 +8,6 @@
 
 import javax.swing.Action;
 import javax.swing.Icon;
-import javax.swing.JButton;
 import javax.swing.KeyStroke;
 
 import org.jabref.Globals;
@@ -60,14 +58,6 @@ public HelpAction(HelpFile helpPage) {
         this(Localization.lang("Help"), Localization.lang("Help"), helpPage, IconTheme.JabRefIcons.HELP.getSmallIcon());
     }
 
-    public JButton getHelpButton() {
-        JButton button = new JButton(this);
-        button.setText(null);
-        button.setPreferredSize(new Dimension(24, 24));
-        button.setToolTipText(getValue(Action.SHORT_DESCRIPTION).toString());
-        return button;
-    }
-
     public static void openHelpPage(HelpFile helpPage) {
         String lang = Globals.prefs.get(JabRefPreferences.LANGUAGE);
         StringBuilder sb = new StringBuilder("https://help.jabref.org/");
diff --git a/src/main/java/org/jabref/gui/openoffice/OOBibBase.java b/src/main/java/org/jabref/gui/openoffice/OOBibBase.java
index 39f99b03e9c..26cf2ee6b40 100644
--- a/src/main/java/org/jabref/gui/openoffice/OOBibBase.java
+++ b/src/main/java/org/jabref/gui/openoffice/OOBibBase.java
@@ -26,11 +26,7 @@
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
-import javax.swing.JList;
-import javax.swing.JOptionPane;
-import javax.swing.JScrollPane;
-import javax.swing.ListSelectionModel;
-
+import org.jabref.gui.DialogService;
 import org.jabref.logic.bibtex.comparator.FieldComparator;
 import org.jabref.logic.bibtex.comparator.FieldComparatorStack;
 import org.jabref.logic.l10n.Localization;
@@ -130,14 +126,15 @@ class OOBibBase {
     private final List<Comparator<BibEntry>> authorYearTitleList = new ArrayList<>(3);
 
     private final List<Comparator<BibEntry>> yearAuthorTitleList = new ArrayList<>(3);
-
     private final Map<String, String> uniquefiers = new HashMap<>();
-
     private List<String> sortedReferenceMarks;
 
-    public OOBibBase(String pathToOO, boolean atEnd) throws IOException, IllegalAccessException,
-            InvocationTargetException, BootstrapException, CreationException, UnknownPropertyException,
-            WrappedTargetException, IndexOutOfBoundsException, NoSuchElementException, NoDocumentException {
+    private final DialogService dialogService;
+
+    public OOBibBase(String pathToOO, boolean atEnd, DialogService dialogService) throws IllegalAccessException, InvocationTargetException, BootstrapException, CreationException, IOException {
+
+        this.dialogService = dialogService;
+
         authorYearTitleList.add(authComp);
         authorYearTitleList.add(yearComp);
         authorYearTitleList.add(titleComp);
@@ -151,40 +148,30 @@ public OOBibBase(String pathToOO, boolean atEnd) throws IOException, IllegalAcce
 
         this.atEnd = atEnd;
         xDesktop = simpleBootstrap(pathToOO);
-        selectDocument();
+
     }
 
     public boolean isConnectedToDocument() {
         return xCurrentComponent != null;
     }
 
-    public static XTextDocument selectComponent(List<XTextDocument> list)
-            throws UnknownPropertyException, WrappedTargetException, IndexOutOfBoundsException {
-        String[] values = new String[list.size()];
-        int ii = 0;
-        for (XTextDocument doc : list) {
-            values[ii] = String.valueOf(OOUtil.getProperty(doc.getCurrentController().getFrame(), "Title"));
-            ii++;
-        }
-        JList<String> sel = new JList<>(values);
-        sel.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        sel.setSelectedIndex(0);
-        int ans = JOptionPane.showConfirmDialog(null, new JScrollPane(sel), Localization.lang("Select document"),
-                JOptionPane.OK_CANCEL_OPTION);
-        if (ans == JOptionPane.OK_OPTION) {
-            return list.get(sel.getSelectedIndex());
-        } else {
-            return null;
-        }
+    public XTextDocument selectComponent(List<XTextDocument> list) {
+        List<DocumentTitleViewModel> viewModel = list.stream().map(DocumentTitleViewModel::new).collect(Collectors.toList());
+        //this whole method is part of a background task when autodecting instances, so we need to show dialog in FX thread
+        Optional<DocumentTitleViewModel> selectedDocument = dialogService.showChoiceDialogAndWait(Localization.lang("Select document"), Localization.lang("Found documents:"), Localization.lang("Use selected document"), viewModel);
+        return selectedDocument.map(DocumentTitleViewModel::getXtextDocument).orElse(null);
     }
 
     public Optional<String> getCurrentDocumentTitle() {
-        if (mxDoc == null) {
+        return getDocumentTitle(mxDoc);
+    }
+
+    private Optional<String> getDocumentTitle(XTextDocument doc) {
+        if (doc == null) {
             return Optional.empty();
         } else {
             try {
-                return Optional
-                        .of(String.valueOf(OOUtil.getProperty(mxDoc.getCurrentController().getFrame(), "Title")));
+                return Optional.of(String.valueOf(OOUtil.getProperty(doc.getCurrentController().getFrame(), "Title")));
             } catch (UnknownPropertyException | WrappedTargetException e) {
                 LOGGER.warn("Could not get document title", e);
                 return Optional.empty();
@@ -192,8 +179,7 @@ public Optional<String> getCurrentDocumentTitle() {
         }
     }
 
-    public void selectDocument() throws UnknownPropertyException, WrappedTargetException, IndexOutOfBoundsException,
-            NoSuchElementException, NoDocumentException {
+    public void selectDocument() throws NoDocumentException, NoSuchElementException, WrappedTargetException {
         List<XTextDocument> textDocumentList = getTextDocuments();
         XTextDocument selected;
         if (textDocumentList.isEmpty()) {
@@ -250,8 +236,8 @@ private List<XTextDocument> getTextDocuments() throws NoSuchElementException, Wr
     }
 
     private XDesktop simpleBootstrap(String pathToExecutable)
-            throws IllegalAccessException, InvocationTargetException, BootstrapException,
-            CreationException, IOException {
+        throws IllegalAccessException, InvocationTargetException, BootstrapException,
+        CreationException, IOException {
 
         ClassLoader loader = ClassLoader.getSystemClassLoader();
         if (loader instanceof URLClassLoader) {
@@ -268,7 +254,7 @@ private XDesktop simpleBootstrap(String pathToExecutable)
             }
         } else {
             LOGGER.error("Error occured, URLClassLoader expected but " + loader.getClass()
-                    + " received. Could not continue.");
+                         + " received. Could not continue.");
         }
 
         //Get the office component context:
@@ -302,13 +288,13 @@ public void updateSortedReferenceMarks() throws WrappedTargetException, NoSuchEl
     }
 
     public void setCustomProperty(String property, String value) throws UnknownPropertyException,
-            NotRemoveableException, PropertyExistException, IllegalTypeException, IllegalArgumentException {
+        NotRemoveableException, PropertyExistException, IllegalTypeException, IllegalArgumentException {
         if (propertySet.getPropertySetInfo().hasPropertyByName(property)) {
             userProperties.removeProperty(property);
         }
         if (value != null) {
             userProperties.addProperty(property, com.sun.star.beans.PropertyAttribute.REMOVEABLE,
-                    new Any(Type.STRING, value));
+                                       new Any(Type.STRING, value));
         }
     }
 
@@ -339,10 +325,10 @@ public void setCustomProperty(String property, String value) throws UnknownPrope
     public void insertEntry(List<BibEntry> entries, BibDatabase database,
                             List<BibDatabase> allBases, OOBibStyle style,
                             boolean inParenthesis, boolean withText, String pageInfo, boolean sync)
-            throws IllegalArgumentException,
-            UnknownPropertyException, NotRemoveableException, PropertyExistException, IllegalTypeException,
-            UndefinedCharacterFormatException, WrappedTargetException, NoSuchElementException, PropertyVetoException,
-            IOException, CreationException, BibEntryNotFoundException, UndefinedParagraphFormatException {
+        throws IllegalArgumentException,
+        UnknownPropertyException, NotRemoveableException, PropertyExistException, IllegalTypeException,
+        UndefinedCharacterFormatException, WrappedTargetException, NoSuchElementException, PropertyVetoException,
+        IOException, CreationException, BibEntryNotFoundException, UndefinedParagraphFormatException {
 
         try {
 
@@ -357,10 +343,10 @@ public void insertEntry(List<BibEntry> entries, BibDatabase database,
             }
 
             String keyString = String.join(",",
-                    entries.stream().map(entry -> entry.getCiteKeyOptional().orElse("")).collect(Collectors.toList()));
+                                           entries.stream().map(entry -> entry.getCiteKeyOptional().orElse("")).collect(Collectors.toList()));
             // Insert bookmark:
             String bName = getUniqueReferenceMarkName(keyString,
-                    withText ? inParenthesis ? OOBibBase.AUTHORYEAR_PAR : OOBibBase.AUTHORYEAR_INTEXT : OOBibBase.INVISIBLE_CIT);
+                                                      withText ? inParenthesis ? OOBibBase.AUTHORYEAR_PAR : OOBibBase.AUTHORYEAR_INTEXT : OOBibBase.INVISIBLE_CIT);
 
             // If we should store metadata for page info, do that now:
             if (pageInfo != null) {
@@ -375,7 +361,7 @@ public void insertEntry(List<BibEntry> entries, BibDatabase database,
                 try {
                     xCursorProps.setPropertyValue(CHAR_STYLE_NAME, charStyle);
                 } catch (UnknownPropertyException | PropertyVetoException | IllegalArgumentException |
-                        WrappedTargetException ex) {
+                         WrappedTargetException ex) {
                     // Setting the character format failed, so we throw an exception that
                     // will result in an error message for the user. Before that,
                     // delete the space we inserted:
@@ -390,7 +376,7 @@ public void insertEntry(List<BibEntry> entries, BibDatabase database,
                 databaseMap.put(entry, database);
             }
             String citeText = style.isNumberEntries() ? "-" : style.getCitationMarker(entries, databaseMap,
-                    inParenthesis, null, null);
+                                                                                      inParenthesis, null, null);
             insertReferenceMark(bName, citeText, xViewCursor, withText, style);
 
             xViewCursor.collapseToEnd();
@@ -447,9 +433,9 @@ public List<String> getJabRefReferenceMarks(XNameAccess nameAccess) {
      * @throws UnknownPropertyException
      */
     public List<String> refreshCiteMarkers(List<BibDatabase> databases, OOBibStyle style)
-            throws WrappedTargetException, IllegalArgumentException, NoSuchElementException,
-            UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException, IOException,
-            CreationException, BibEntryNotFoundException {
+        throws WrappedTargetException, IllegalArgumentException, NoSuchElementException,
+        UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException, IOException,
+        CreationException, BibEntryNotFoundException {
         try {
             return refreshCiteMarkersInternal(databases, style);
         } catch (DisposedException ex) {
@@ -461,9 +447,9 @@ public List<String> refreshCiteMarkers(List<BibDatabase> databases, OOBibStyle s
     }
 
     private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOBibStyle style)
-            throws WrappedTargetException, IllegalArgumentException, NoSuchElementException,
-            UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException,
-            CreationException, BibEntryNotFoundException {
+        throws WrappedTargetException, IllegalArgumentException, NoSuchElementException,
+        UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException,
+        CreationException, BibEntryNotFoundException {
 
         List<String> cited = findCitedKeys();
         Map<String, BibDatabase> linkSourceBase = new HashMap<>();
@@ -570,7 +556,7 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
                         citationMarker = style.getNumCitationMarker(num, minGroupingCount, false);
                         for (int j = 0; j < keys.length; j++) {
                             normCitMarker[j] = style.getNumCitationMarker(Collections.singletonList(num.get(j)),
-                                    minGroupingCount, false);
+                                                                          minGroupingCount, false);
                         }
                     } else {
                         // We need to find the number of the cited entry in the bibliography,
@@ -579,7 +565,7 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
 
                         if (num.isEmpty()) {
                             throw new BibEntryNotFoundException(names.get(i), Localization
-                                    .lang("Could not resolve BibTeX entry for citation marker '%0'.", names.get(i)));
+                                                                                          .lang("Could not resolve BibTeX entry for citation marker '%0'.", names.get(i)));
                         } else {
                             citationMarker = style.getNumCitationMarker(num, minGroupingCount, false);
                         }
@@ -605,11 +591,11 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
                     }
 
                     citationMarker = style.getCitationMarker(Arrays.asList(cEntries), entries,
-                            type == OOBibBase.AUTHORYEAR_PAR, null, null);
+                                                             type == OOBibBase.AUTHORYEAR_PAR, null, null);
                     // We need "normalized" (in parenthesis) markers for uniqueness checking purposes:
                     for (int j = 0; j < cEntries.length; j++) {
                         normCitMarker[j] = style.getCitationMarker(Collections.singletonList(cEntries[j]), entries,
-                                true, null, new int[]{-1});
+                                                                   true, null, new int[] {-1});
                     }
                 }
                 citMarkers[i] = citationMarker;
@@ -709,7 +695,7 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
                 }
                 if (needsChange) {
                     citMarkers[j] = style.getCitationMarker(Arrays.asList(cEntries), entries,
-                            types[j] == OOBibBase.AUTHORYEAR_PAR, uniquif, firstLimAuthors);
+                                                            types[j] == OOBibBase.AUTHORYEAR_PAR, uniquif, firstLimAuthors);
                 }
             }
         }
@@ -735,7 +721,7 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
                 try {
                     xCursorProps.setPropertyValue(CHAR_STYLE_NAME, charStyle);
                 } catch (UnknownPropertyException | PropertyVetoException | IllegalArgumentException |
-                        WrappedTargetException ex) {
+                         WrappedTargetException ex) {
                     throw new UndefinedCharacterFormatException(charStyle);
                 }
             }
@@ -765,9 +751,9 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
     }
 
     private List<String> getSortedReferenceMarks(final XNameAccess nameAccess)
-            throws WrappedTargetException, NoSuchElementException {
+        throws WrappedTargetException, NoSuchElementException {
         XTextViewCursorSupplier cursorSupplier = UnoRuntime.queryInterface(XTextViewCursorSupplier.class,
-                mxDoc.getCurrentController());
+                                                                           mxDoc.getCurrentController());
 
         XTextViewCursor viewCursor = cursorSupplier.getViewCursor();
         XTextRange initialPos = viewCursor.getStart();
@@ -817,8 +803,8 @@ private String getUniqueReferenceMarkName(String bibtexKey, int type) {
     }
 
     public void rebuildBibTextSection(List<BibDatabase> databases, OOBibStyle style)
-            throws NoSuchElementException, WrappedTargetException, IllegalArgumentException,
-            CreationException, PropertyVetoException, UnknownPropertyException, UndefinedParagraphFormatException {
+        throws NoSuchElementException, WrappedTargetException, IllegalArgumentException,
+        CreationException, PropertyVetoException, UnknownPropertyException, UndefinedParagraphFormatException {
         List<String> cited = findCitedKeys();
         Map<String, BibDatabase> linkSourceBase = new HashMap<>();
         Map<BibEntry, BibDatabase> entries = findCitedEntries(databases, cited, linkSourceBase); // Although entries are redefined without use, this also updates linkSourceBase
@@ -831,7 +817,7 @@ public void rebuildBibTextSection(List<BibDatabase> databases, OOBibStyle style)
         } else {
             SortedMap<BibEntry, BibDatabase> newMap = new TreeMap<>(entryComparator);
             for (Map.Entry<BibEntry, BibDatabase> bibtexEntryBibtexDatabaseEntry : findCitedEntries(databases, cited,
-                    linkSourceBase).entrySet()) {
+                                                                                                    linkSourceBase).entrySet()) {
                 newMap.put(bibtexEntryBibtexDatabaseEntry.getKey(), bibtexEntryBibtexDatabaseEntry.getValue());
             }
             entries = newMap;
@@ -961,7 +947,7 @@ private Map<BibEntry, BibDatabase> getSortedEntriesFromSortedRefMarks(List<Strin
 
     public String getCitationContext(XNameAccess nameAccess, String refMarkName, int charBefore, int charAfter,
                                      boolean htmlMarkup)
-            throws NoSuchElementException, WrappedTargetException {
+        throws NoSuchElementException, WrappedTargetException {
         Object referenceMark = nameAccess.getByName(refMarkName);
         XTextContent bookmark = UnoRuntime.queryInterface(XTextContent.class, referenceMark);
 
@@ -1004,8 +990,8 @@ public String getCitationContext(XNameAccess nameAccess, String refMarkName, int
 
     private void insertFullReferenceAtCursor(XTextCursor cursor, Map<BibEntry, BibDatabase> entries, OOBibStyle style,
                                              String parFormat)
-            throws UndefinedParagraphFormatException, IllegalArgumentException,
-            UnknownPropertyException, PropertyVetoException, WrappedTargetException {
+        throws UndefinedParagraphFormatException, IllegalArgumentException,
+        UnknownPropertyException, PropertyVetoException, WrappedTargetException {
         Map<BibEntry, BibDatabase> correctEntries;
         // If we don't have numbered entries, we need to sort the entries before adding them:
         if (style.isSortByPosition()) {
@@ -1026,18 +1012,18 @@ private void insertFullReferenceAtCursor(XTextCursor cursor, Map<BibEntry, BibDa
             if (style.isNumberEntries()) {
                 int minGroupingCount = style.getIntCitProperty(OOBibStyle.MINIMUM_GROUPING_COUNT);
                 OOUtil.insertTextAtCurrentLocation(text, cursor,
-                        style.getNumCitationMarker(Collections.singletonList(number++), minGroupingCount, true), Collections.emptyList());
+                                                   style.getNumCitationMarker(Collections.singletonList(number++), minGroupingCount, true), Collections.emptyList());
             }
             Layout layout = style.getReferenceFormat(entry.getKey().getType());
             layout.setPostFormatter(POSTFORMATTER);
             OOUtil.insertFullReferenceAtCurrentLocation(text, cursor, layout, parFormat, entry.getKey(),
-                    entry.getValue(), uniquefiers.get(entry.getKey().getCiteKeyOptional().orElse(null)));
+                                                        entry.getValue(), uniquefiers.get(entry.getKey().getCiteKeyOptional().orElse(null)));
         }
 
     }
 
     private void createBibTextSection2(boolean end)
-            throws IllegalArgumentException, CreationException {
+        throws IllegalArgumentException, CreationException {
 
         XTextCursor mxDocCursor = text.createTextCursor();
         if (end) {
@@ -1048,7 +1034,7 @@ private void createBibTextSection2(boolean end)
         XNamed xChildNamed;
         try {
             xChildNamed = UnoRuntime.queryInterface(XNamed.class,
-                    mxDocFactory.createInstance("com.sun.star.text.TextSection"));
+                                                    mxDocFactory.createInstance("com.sun.star.text.TextSection"));
         } catch (Exception e) {
             throw new CreationException(e.getMessage());
         }
@@ -1061,13 +1047,13 @@ private void createBibTextSection2(boolean end)
     }
 
     private void clearBibTextSectionContent2()
-            throws NoSuchElementException, WrappedTargetException, IllegalArgumentException, CreationException {
+        throws NoSuchElementException, WrappedTargetException, IllegalArgumentException, CreationException {
 
         // Check if the section exists:
         XTextSectionsSupplier supplier = UnoRuntime.queryInterface(XTextSectionsSupplier.class, mxDoc);
         if (supplier.getTextSections().hasByName(OOBibBase.BIB_SECTION_NAME)) {
             XTextSection section = (XTextSection) ((Any) supplier.getTextSections().getByName(OOBibBase.BIB_SECTION_NAME))
-                    .getObject();
+                                                                                                                          .getObject();
             // Clear it:
             XTextCursor cursor = text.createTextCursorByRange(section.getAnchor());
             cursor.gotoRange(section.getAnchor(), false);
@@ -1078,21 +1064,21 @@ private void clearBibTextSectionContent2()
     }
 
     private void populateBibTextSection(Map<BibEntry, BibDatabase> entries, OOBibStyle style)
-            throws NoSuchElementException, WrappedTargetException, PropertyVetoException,
-            UnknownPropertyException, UndefinedParagraphFormatException, IllegalArgumentException, CreationException {
+        throws NoSuchElementException, WrappedTargetException, PropertyVetoException,
+        UnknownPropertyException, UndefinedParagraphFormatException, IllegalArgumentException, CreationException {
         XTextSectionsSupplier supplier = UnoRuntime.queryInterface(XTextSectionsSupplier.class, mxDoc);
         XTextSection section = (XTextSection) ((Any) supplier.getTextSections().getByName(OOBibBase.BIB_SECTION_NAME))
-                .getObject();
+                                                                                                                      .getObject();
         XTextCursor cursor = text.createTextCursorByRange(section.getAnchor());
         OOUtil.insertTextAtCurrentLocation(text, cursor, (String) style.getProperty(OOBibStyle.TITLE),
-                (String) style.getProperty(OOBibStyle.REFERENCE_HEADER_PARAGRAPH_FORMAT));
+                                           (String) style.getProperty(OOBibStyle.REFERENCE_HEADER_PARAGRAPH_FORMAT));
         insertFullReferenceAtCursor(cursor, entries, style,
-                (String) style.getProperty(OOBibStyle.REFERENCE_PARAGRAPH_FORMAT));
+                                    (String) style.getProperty(OOBibStyle.REFERENCE_PARAGRAPH_FORMAT));
         insertBookMark(OOBibBase.BIB_SECTION_END_NAME, cursor);
     }
 
     private XTextContent insertBookMark(String name, XTextCursor position)
-            throws IllegalArgumentException, CreationException {
+        throws IllegalArgumentException, CreationException {
         Object bookmark;
         try {
             bookmark = mxDocFactory.createInstance("com.sun.star.text.Bookmark");
@@ -1113,8 +1099,8 @@ private XTextContent insertBookMark(String name, XTextCursor position)
 
     private void insertReferenceMark(String name, String citationText, XTextCursor position, boolean withText,
                                      OOBibStyle style)
-            throws UnknownPropertyException, WrappedTargetException,
-            PropertyVetoException, IllegalArgumentException, UndefinedCharacterFormatException, CreationException {
+        throws UnknownPropertyException, WrappedTargetException,
+        PropertyVetoException, IllegalArgumentException, UndefinedCharacterFormatException, CreationException {
 
         // Check if there is "page info" stored for this citation. If so, insert it into
         // the citation text before inserting the citation:
@@ -1147,7 +1133,7 @@ private void insertReferenceMark(String name, String citationText, XTextCursor p
                 try {
                     xCursorProps.setPropertyValue(CHAR_STYLE_NAME, charStyle);
                 } catch (UnknownPropertyException | PropertyVetoException | IllegalArgumentException |
-                        WrappedTargetException ex) {
+                         WrappedTargetException ex) {
                     throw new UndefinedCharacterFormatException(charStyle);
                 }
             }
@@ -1210,7 +1196,7 @@ private XNameAccess getBookmarks() {
     }
 
     private void italicizeOrBold(XTextCursor position, boolean italicize, int start, int end)
-            throws UnknownPropertyException, PropertyVetoException, IllegalArgumentException, WrappedTargetException {
+        throws UnknownPropertyException, PropertyVetoException, IllegalArgumentException, WrappedTargetException {
         XTextRange range = position.getStart();
         XTextCursor cursor = position.getText().createTextCursorByRange(range);
         cursor.goRight((short) start, false);
@@ -1224,9 +1210,9 @@ private void italicizeOrBold(XTextCursor position, boolean italicize, int start,
     }
 
     public void combineCiteMarkers(List<BibDatabase> databases, OOBibStyle style)
-            throws IOException, WrappedTargetException, NoSuchElementException, IllegalArgumentException,
-            UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException, CreationException,
-            BibEntryNotFoundException {
+        throws IOException, WrappedTargetException, NoSuchElementException, IllegalArgumentException,
+        UndefinedCharacterFormatException, UnknownPropertyException, PropertyVetoException, CreationException,
+        BibEntryNotFoundException {
         XNameAccess nameAccess = getReferenceMarks();
         // TODO: doesn't work for citations in footnotes/tables
         List<String> names = getSortedReferenceMarks(nameAccess);
@@ -1263,7 +1249,7 @@ public void combineCiteMarkers(List<BibDatabase> databases, OOBibStyle style)
                     try {
                         xCursorProps.setPropertyValue(CHAR_STYLE_NAME, charStyle);
                     } catch (UnknownPropertyException | PropertyVetoException | IllegalArgumentException |
-                            WrappedTargetException ex) {
+                             WrappedTargetException ex) {
                         // Setting the character format failed, so we throw an exception that
                         // will result in an error message for the user:
                         throw new UndefinedCharacterFormatException(charStyle);
@@ -1303,7 +1289,7 @@ public void combineCiteMarkers(List<BibDatabase> databases, OOBibStyle style)
     }
 
     public BibDatabase generateDatabase(List<BibDatabase> databases)
-            throws NoSuchElementException, WrappedTargetException {
+        throws NoSuchElementException, WrappedTargetException {
         BibDatabase resultDatabase = new BibDatabase();
         List<String> cited = findCitedKeys();
 
@@ -1363,7 +1349,7 @@ public boolean equals(Object o) {
             if (o instanceof ComparableMark) {
                 ComparableMark other = (ComparableMark) o;
                 return (this.position.X == other.position.X) && (this.position.Y == other.position.Y)
-                        && Objects.equals(this.name, other.name);
+                       && Objects.equals(this.name, other.name);
             }
             return false;
         }
@@ -1376,7 +1362,25 @@ public String getName() {
         public int hashCode() {
             return Objects.hash(position, name);
         }
-
     }
 
+    private class DocumentTitleViewModel {
+
+        private final XTextDocument xTextDocument;
+        private final String description;
+
+        public DocumentTitleViewModel(XTextDocument xTextDocument) {
+            this.xTextDocument = xTextDocument;
+            this.description = getDocumentTitle(xTextDocument).orElse("");
+        }
+
+        public XTextDocument getXtextDocument() {
+            return xTextDocument;
+        }
+
+        @Override
+        public String toString() {
+            return description;
+        }
+    }
 }
diff --git a/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java b/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
index 9f31cc17a8b..7d2c1c20e70 100644
--- a/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
+++ b/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
@@ -133,8 +133,8 @@ public OpenOfficePanel(JabRefFrame frame, JabRefPreferences jabRefPreferences, O
         update.setMaxWidth(Double.MAX_VALUE);
 
         loader = new StyleLoader(ooPrefs,
-                Globals.prefs.getLayoutFormatterPreferences(Globals.journalAbbreviationLoader),
-                Globals.prefs.getDefaultEncoding());
+                                 Globals.prefs.getLayoutFormatterPreferences(Globals.journalAbbreviationLoader),
+                                 Globals.prefs.getDefaultEncoding());
 
         initPanel();
     }
@@ -149,7 +149,7 @@ private static void addURL(List<URL> jarList) throws IOException {
                 method.invoke(sysloader, anU);
             }
         } catch (SecurityException | NoSuchMethodException | IllegalAccessException | IllegalArgumentException |
-                InvocationTargetException e) {
+                 InvocationTargetException e) {
             LOGGER.error("Could not add URL to system classloader", e);
             sysloader.close();
             throw new IOException("Error, could not add URL to system classloader", e);
@@ -171,9 +171,9 @@ private void initPanel() {
             try {
                 ooBase.selectDocument();
                 dialogService.notify(Localization.lang("Connected to document") + ": "
-                        + ooBase.getCurrentDocumentTitle().orElse(""));
-            } catch (UnknownPropertyException | WrappedTargetException | IndexOutOfBoundsException |
-                    NoSuchElementException | NoDocumentException ex) {
+                                     + ooBase.getCurrentDocumentTitle().orElse(""));
+            } catch (WrappedTargetException | IndexOutOfBoundsException |
+                     NoSuchElementException | NoDocumentException ex) {
                 LOGGER.warn("Problem connecting", ex);
                 dialogService.showErrorDialogAndWait(ex);
             }
@@ -226,8 +226,8 @@ private void initPanel() {
                 ooBase.rebuildBibTextSection(databases, style);
                 if (!unresolvedKeys.isEmpty()) {
                     dialogService.showErrorDialogAndWait(Localization.lang("Unable to synchronize bibliography"),
-                            Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
-                                    unresolvedKeys.get(0)));
+                                                         Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
+                                                                           unresolvedKeys.get(0)));
                 }
             } catch (UndefinedCharacterFormatException ex) {
                 reportUndefinedCharacterFormat(ex);
@@ -238,14 +238,14 @@ private void initPanel() {
             } catch (IOException ex) {
                 LOGGER.warn("Problem with style file", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("No valid style file defined"),
-                        Localization.lang("You must select either a valid style file, or use one of the default styles."));
+                                                     Localization.lang("You must select either a valid style file, or use one of the default styles."));
             } catch (BibEntryNotFoundException ex) {
                 LOGGER.debug("BibEntry not found", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("Unable to synchronize bibliography"), Localization.lang(
-                        "Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
-                        ex.getBibtexKey()));
+                                                                                                                                "Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
+                                                                                                                                ex.getBibtexKey()));
             } catch (com.sun.star.lang.IllegalArgumentException | PropertyVetoException | UnknownPropertyException | WrappedTargetException | NoSuchElementException |
-                    CreationException ex) {
+                     CreationException ex) {
                 LOGGER.warn("Could not update bibliography", ex);
             }
         });
@@ -258,8 +258,8 @@ private void initPanel() {
             } catch (UndefinedCharacterFormatException ex) {
                 reportUndefinedCharacterFormat(ex);
             } catch (com.sun.star.lang.IllegalArgumentException | UnknownPropertyException | PropertyVetoException |
-                    CreationException | NoSuchElementException | WrappedTargetException | IOException |
-                    BibEntryNotFoundException ex) {
+                     CreationException | NoSuchElementException | WrappedTargetException | IOException |
+                     BibEntryNotFoundException ex) {
                 LOGGER.warn("Problem combining cite markers", ex);
             }
 
@@ -311,8 +311,8 @@ private void exportEntries() {
             if (!unresolvedKeys.isEmpty()) {
 
                 dialogService.showErrorDialogAndWait(Localization.lang("Unable to generate new library"),
-                        Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
-                                unresolvedKeys.get(0)));
+                                                     Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
+                                                                       unresolvedKeys.get(0)));
 
             }
 
@@ -323,12 +323,12 @@ private void exportEntries() {
         } catch (BibEntryNotFoundException ex) {
             LOGGER.debug("BibEntry not found", ex);
             dialogService.showErrorDialogAndWait(Localization.lang("Unable to synchronize bibliography"),
-                    Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
-                            ex.getBibtexKey()));
+                                                 Localization.lang("Your OpenOffice/LibreOffice document references the BibTeX key '%0', which could not be found in your current library.",
+                                                                   ex.getBibtexKey()));
 
         } catch (com.sun.star.lang.IllegalArgumentException | UnknownPropertyException | PropertyVetoException |
-                UndefinedCharacterFormatException | NoSuchElementException | WrappedTargetException | IOException |
-                CreationException e) {
+                 UndefinedCharacterFormatException | NoSuchElementException | WrappedTargetException | IOException |
+                 CreationException e) {
             LOGGER.warn("Problem generating new database.", e);
         }
 
@@ -397,6 +397,12 @@ protected OOBibBase call() throws Exception {
         connectTask.setOnSucceeded(value -> {
             ooBase = connectTask.getValue();
 
+            try {
+                ooBase.selectDocument();
+            } catch (WrappedTargetException | NoSuchElementException | NoDocumentException e) {
+                LOGGER.error("Error getting open writer documents", e);
+            }
+
             if (ooBase.isConnectedToDocument()) {
                 dialogService.notify(Localization.lang("Connected to document") + ": " + ooBase.getCurrentDocumentTitle().orElse(""));
             }
@@ -418,16 +424,16 @@ protected OOBibBase call() throws Exception {
                 LOGGER.warn("Could not connect to running OpenOffice/LibreOffice", ex);
 
                 dialogService.showErrorDialogAndWait(Localization.lang("Unable to connect. One possible reason is that JabRef "
-                        + "and OpenOffice/LibreOffice are not both running in either 32 bit mode or 64 bit mode."));
+                                                                       + "and OpenOffice/LibreOffice are not both running in either 32 bit mode or 64 bit mode."));
             } else if (ex instanceof IOException) {
                 LOGGER.warn("Could not connect to running OpenOffice/LibreOffice", ex);
 
                 dialogService.showErrorDialogAndWait(Localization.lang("Could not connect to running OpenOffice/LibreOffice."),
-                        Localization.lang("Could not connect to running OpenOffice/LibreOffice.")
-                                + "\n"
-                                + Localization.lang("Make sure you have installed OpenOffice/LibreOffice with Java support.") + "\n"
-                                + Localization.lang("If connecting manually, please verify program and library paths.") + "\n" + "\n" + Localization.lang("Error message:"),
-                        ex);
+                                                     Localization.lang("Could not connect to running OpenOffice/LibreOffice.")
+                                                                                                                                + "\n"
+                                                                                                                                + Localization.lang("Make sure you have installed OpenOffice/LibreOffice with Java support.") + "\n"
+                                                                                                                                + Localization.lang("If connecting manually, please verify program and library paths.") + "\n" + "\n" + Localization.lang("Error message:"),
+                                                     ex);
             } else {
                 dialogService.showErrorDialogAndWait(Localization.lang("Autodetection failed"), Localization.lang("Autodetection failed"), ex);
             }
@@ -453,10 +459,9 @@ private void loadOpenOfficeJars(Path configurationPath) throws IOException {
     }
 
     private OOBibBase createBibBase() throws IOException, InvocationTargetException, IllegalAccessException,
-            WrappedTargetException, BootstrapException, UnknownPropertyException, NoDocumentException,
-            NoSuchElementException, CreationException {
+        BootstrapException, CreationException {
         // Connect
-        return new OOBibBase(ooPrefs.getExecutablePath(), true);
+        return new OOBibBase(ooPrefs.getExecutablePath(), true, dialogService);
     }
 
     private Optional<Boolean> showManualConnectionDialog() {
@@ -497,12 +502,12 @@ private void pushEntries(boolean inParenthesisIn, boolean withText, boolean addP
                         style = loader.getUsedStyle();
                     }
                     ooBase.insertEntry(entries, database, getBaseList(), style, inParenthesis, withText, pageInfo,
-                            ooPrefs.getSyncWhenCiting());
+                                       ooPrefs.getSyncWhenCiting());
                 } catch (FileNotFoundException ex) {
 
                     dialogService.showErrorDialogAndWait(
-                            Localization.lang("No valid style file defined"),
-                            Localization.lang("You must select either a valid style file, or use one of the default styles."));
+                                                         Localization.lang("No valid style file defined"),
+                                                         Localization.lang("You must select either a valid style file, or use one of the default styles."));
 
                     LOGGER.warn("Problem with style file", ex);
                 } catch (ConnectionLostException ex) {
@@ -512,9 +517,9 @@ private void pushEntries(boolean inParenthesisIn, boolean withText, boolean addP
                 } catch (UndefinedParagraphFormatException ex) {
                     reportUndefinedParagraphFormat(ex);
                 } catch (com.sun.star.lang.IllegalArgumentException | UnknownPropertyException | PropertyVetoException |
-                        CreationException | NoSuchElementException | WrappedTargetException | IOException |
-                        BibEntryNotFoundException | IllegalTypeException | PropertyExistException |
-                        NotRemoveableException ex) {
+                         CreationException | NoSuchElementException | WrappedTargetException | IOException |
+                         BibEntryNotFoundException | IllegalTypeException | PropertyExistException |
+                         NotRemoveableException ex) {
                     LOGGER.warn("Could not insert entry", ex);
                 }
             }
@@ -547,9 +552,9 @@ private boolean checkThatEntriesHaveKeys(List<BibEntry> entries) {
 
         // Ask if keys should be generated
         boolean citePressed = dialogService.showConfirmationDialogAndWait(Localization.lang("Cite"),
-                Localization.lang("Cannot cite entries without BibTeX keys. Generate keys now?"),
-                Localization.lang("Generate keys"),
-                Localization.lang("Cancel"));
+                                                                          Localization.lang("Cannot cite entries without BibTeX keys. Generate keys now?"),
+                                                                          Localization.lang("Generate keys"),
+                                                                          Localization.lang("Cancel"));
 
         BasePanel panel = frame.getCurrentBasePanel();
         if (citePressed && (panel != null)) {
@@ -560,8 +565,8 @@ private boolean checkThatEntriesHaveKeys(List<BibEntry> entries) {
                 if (!entry.getCiteKeyOptional().isPresent()) {
                     // Generate key
                     new BibtexKeyGenerator(panel.getBibDatabaseContext(), prefs)
-                            .generateAndSetKey(entry)
-                            .ifPresent(change -> undoCompound.addEdit(new UndoableKeyChange(change)));
+                                                                                .generateAndSetKey(entry)
+                                                                                .ifPresent(change -> undoCompound.addEdit(new UndoableKeyChange(change)));
                 }
             }
             undoCompound.end();
@@ -577,23 +582,23 @@ private boolean checkThatEntriesHaveKeys(List<BibEntry> entries) {
 
     private void showConnectionLostErrorMessage() {
         dialogService.showErrorDialogAndWait(Localization.lang("Connection lost"),
-                Localization.lang("Connection to OpenOffice/LibreOffice has been lost. " + "Please make sure OpenOffice/LibreOffice is running, and try to reconnect."));
+                                             Localization.lang("Connection to OpenOffice/LibreOffice has been lost. " + "Please make sure OpenOffice/LibreOffice is running, and try to reconnect."));
 
     }
 
     private void reportUndefinedParagraphFormat(UndefinedParagraphFormatException ex) {
         dialogService.showErrorDialogAndWait(Localization.lang("Undefined paragraph format"),
-                Localization.lang("Your style file specifies the paragraph format '%0', "
-                                + "which is undefined in your current OpenOffice/LibreOffice document.",
-                        ex.getFormatName()) + "\n" + Localization.lang("The paragraph format is controlled by the property 'ReferenceParagraphFormat' or 'ReferenceHeaderParagraphFormat' in the style file."));
+                                             Localization.lang("Your style file specifies the paragraph format '%0', "
+                                                               + "which is undefined in your current OpenOffice/LibreOffice document.",
+                                                               ex.getFormatName()) + "\n" + Localization.lang("The paragraph format is controlled by the property 'ReferenceParagraphFormat' or 'ReferenceHeaderParagraphFormat' in the style file."));
 
     }
 
     private void reportUndefinedCharacterFormat(UndefinedCharacterFormatException ex) {
         dialogService.showErrorDialogAndWait(Localization.lang("Undefined character format"),
-                Localization.lang("Your style file specifies the character format '%0', "
-                                + "which is undefined in your current OpenOffice/LibreOffice document.",
-                        ex.getFormatName()) + "\n" + Localization.lang("The character format is controlled by the citation property 'CitationCharacterFormat' in the style file.")
+                                             Localization.lang("Your style file specifies the character format '%0', "
+                                                               + "which is undefined in your current OpenOffice/LibreOffice document.",
+                                                               ex.getFormatName()) + "\n" + Localization.lang("The character format is controlled by the citation property 'CitationCharacterFormat' in the style file.")
 
         );
     }
diff --git a/src/main/java/org/jabref/gui/preferences/AppearancePrefsTab.java b/src/main/java/org/jabref/gui/preferences/AppearancePrefsTab.java
index 917b88b3ea4..1ad4e79b854 100644
--- a/src/main/java/org/jabref/gui/preferences/AppearancePrefsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/AppearancePrefsTab.java
@@ -63,6 +63,7 @@ public AppearancePrefsTab(DialogService dialogService, JabRefPreferences prefs)
         container.getChildren().addAll(overrideFonts, fontSizeContainer, fontTweaksLAF, lightTheme, darkTheme);
     }
 
+    @Override
     public Node getBuilder() {
         return container;
     }
diff --git a/src/main/java/org/jabref/gui/preferences/BibtexKeyPatternPrefTab.java b/src/main/java/org/jabref/gui/preferences/BibtexKeyPatternPrefTab.java
index 8240accc730..2cf6495d54d 100644
--- a/src/main/java/org/jabref/gui/preferences/BibtexKeyPatternPrefTab.java
+++ b/src/main/java/org/jabref/gui/preferences/BibtexKeyPatternPrefTab.java
@@ -48,7 +48,6 @@ public BibtexKeyPatternPrefTab(JabRefPreferences prefs, BasePanel panel) {
      */
     @Override
     public void storeSettings() {
-
         // Set the default value:
         Globals.prefs.put(JabRefPreferences.DEFAULT_BIBTEX_KEY_PATTERN, defaultPat.getText());
         Globals.prefs.putBoolean(JabRefPreferences.WARN_BEFORE_OVERWRITING_KEY, warnBeforeOverwriting.isSelected());
@@ -98,6 +97,7 @@ private void appendKeyGeneratorSettings() {
         warnBeforeOverwriting.setDisable(dontOverwrite.isSelected()));
     }
 
+    @Override
     public Node getBuilder() {
         return builder;
     }
diff --git a/src/main/java/org/jabref/gui/preferences/FileTab.java b/src/main/java/org/jabref/gui/preferences/FileTab.java
index 3bbc387f130..4067cf08751 100644
--- a/src/main/java/org/jabref/gui/preferences/FileTab.java
+++ b/src/main/java/org/jabref/gui/preferences/FileTab.java
@@ -17,6 +17,8 @@
 import javafx.scene.layout.Pane;
 
 import org.jabref.gui.DialogService;
+import org.jabref.gui.actions.ActionFactory;
+import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.help.HelpAction;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.logic.help.HelpFile;
@@ -52,22 +54,26 @@ class FileTab extends Pane implements PrefsTab {
     private final CheckBox allowFileAutoOpenBrowse;
     private final RadioButton useRegExpComboBox;
     private final RadioButton matchExactKeyOnly = new RadioButton(
-            Localization.lang("Autolink only files that match the BibTeX key"));
+                                                                  Localization.lang("Autolink only files that match the BibTeX key"));
     private final RadioButton matchStartsWithKey = new RadioButton(
-            Localization.lang("Autolink files with names starting with the BibTeX key"));
+                                                                   Localization.lang("Autolink files with names starting with the BibTeX key"));
     private final TextField regExpTextField;
 
     public FileTab(DialogService dialogService, JabRefPreferences prefs) {
         this.dialogService = dialogService;
         this.prefs = prefs;
+
+        ActionFactory factory = new ActionFactory(prefs.getKeyBindingRepository());
+
         fileDir = new TextField();
+
         bibLocAsPrimaryDir = new CheckBox(Localization.lang("Use the BIB file location as primary file directory"));
         bibLocAsPrimaryDir.setAccessibleText(Localization.lang("When downloading files, or moving linked files to the "
-                + "file directory, prefer the BIB file location rather than the file directory set above"));
+                                                               + "file directory, prefer the BIB file location rather than the file directory set above"));
         runAutoFileSearch = new CheckBox(
-                Localization.lang("When opening file link, search for matching file if no link is defined"));
+                                         Localization.lang("When opening file link, search for matching file if no link is defined"));
         allowFileAutoOpenBrowse = new CheckBox(
-                Localization.lang("Automatically open browse dialog when creating new file link"));
+                                               Localization.lang("Automatically open browse dialog when creating new file link"));
         regExpTextField = new TextField();
         useRegExpComboBox = new RadioButton(Localization.lang("Use regular expression search"));
         useRegExpComboBox.setOnAction(e -> regExpTextField.setEditable(useRegExpComboBox.isSelected()));
@@ -92,13 +98,13 @@ public FileTab(DialogService dialogService, JabRefPreferences prefs) {
         Label general = new Label(Localization.lang("General"));
         general.getStyleClass().add("sectionHeader");
         builder.add(general, 1, 1);
-        builder.add(openLast,  1, 2);
+        builder.add(openLast, 1, 2);
         builder.add(backup, 1, 3);
         Label label = new Label(Localization.lang("Do not wrap the following fields when saving") + ":");
         builder.add(label, 1, 4);
         final ToggleGroup resolveGroup = new ToggleGroup();
         builder.add(nonWrappableFields, 2, 4);
-        builder.add(resolveStringsStandard,  1, 5);
+        builder.add(resolveStringsStandard, 1, 5);
         builder.add(resolveStringsAll, 1, 6);
         builder.add(doNotResolveStringsFor, 2, 6);
         resolveStringsStandard.setToggleGroup(resolveGroup);
@@ -122,25 +128,23 @@ public FileTab(DialogService dialogService, JabRefPreferences prefs) {
         browse.setPrefSize(80, 20);
         browse.setOnAction(e -> {
             DirectoryDialogConfiguration dirDialogConfiguration = new DirectoryDialogConfiguration.Builder()
-                    .withInitialDirectory(Paths.get(fileDir.getText())).build();
+                                                                                                            .withInitialDirectory(Paths.get(fileDir.getText())).build();
             dialogService.showDirectorySelectionDialog(dirDialogConfiguration)
                          .ifPresent(f -> fileDir.setText(f.toString()));
         });
         builder.add(browse, 3, 12);
         builder.add(bibLocAsPrimaryDir, 1, 13);
         final ToggleGroup autolinkGroup = new ToggleGroup();
-        builder.add(matchStartsWithKey,  1, 14);
-        builder.add(matchExactKeyOnly,  1, 15);
+        builder.add(matchStartsWithKey, 1, 14);
+        builder.add(matchExactKeyOnly, 1, 15);
         builder.add(useRegExpComboBox, 1, 16);
         builder.add(regExpTextField, 2, 16);
         matchStartsWithKey.setToggleGroup(autolinkGroup);
         matchExactKeyOnly.setToggleGroup(autolinkGroup);
         useRegExpComboBox.setToggleGroup(autolinkGroup);
 
-        Button help = new Button("?");
-        help.setOnAction(event -> new HelpAction(Localization.lang("Help on regular expression search"),
-                HelpFile.REGEX_SEARCH).getHelpButton().doClick());
-
+        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on regular expression search"),
+                                                                                    HelpFile.REGEX_SEARCH).getCommand());
         builder.add(help, 3, 16);
         builder.add(runAutoFileSearch, 1, 17);
         builder.add(allowFileAutoOpenBrowse, 1, 18);
@@ -151,10 +155,10 @@ public FileTab(DialogService dialogService, JabRefPreferences prefs) {
         Label autosave = new Label(Localization.lang("Autosave"));
         autosave.getStyleClass().add("sectionHeader");
         builder.add(autosave, 1, 20);
-        builder.add(localAutoSave,  1, 21);
-        Button help1 = new Button("?");
-        help1.setOnAction(event -> new HelpAction(HelpFile.AUTOSAVE).getHelpButton().doClick());
-        builder.add(help1, 2, 21);
+        builder.add(localAutoSave, 1, 21);
+
+        Button helpAutosave = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.AUTOSAVE).getCommand());
+        builder.add(helpAutosave, 2, 21);
     }
 
     @Override
@@ -194,6 +198,7 @@ public void setValues() {
         localAutoSave.setSelected(prefs.getBoolean(JabRefPreferences.LOCAL_AUTO_SAVE));
     }
 
+    @Override
     public Node getBuilder() {
         return builder;
     }
@@ -247,8 +252,8 @@ public boolean validateSettings() {
         boolean valid = Files.exists(path) && Files.isDirectory(path);
         if (!valid) {
             dialogService.showErrorDialogAndWait(
-                    String.format("%s -> %s %n %n %s: %n %s", Localization.lang("File"),
-                            Localization.lang("Main file directory"), Localization.lang("Directory not found"), path));
+                                                 String.format("%s -> %s %n %n %s: %n %s", Localization.lang("File"),
+                                                               Localization.lang("Main file directory"), Localization.lang("Directory not found"), path));
         }
         return valid;
     }
diff --git a/src/main/java/org/jabref/gui/preferences/GeneralTab.java b/src/main/java/org/jabref/gui/preferences/GeneralTab.java
index d2c27c1a97c..c7f3759755d 100644
--- a/src/main/java/org/jabref/gui/preferences/GeneralTab.java
+++ b/src/main/java/org/jabref/gui/preferences/GeneralTab.java
@@ -15,6 +15,8 @@
 import javafx.scene.shape.Line;
 
 import org.jabref.gui.DialogService;
+import org.jabref.gui.actions.ActionFactory;
+import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.help.HelpAction;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.ViewModelListCellFactory;
@@ -55,6 +57,9 @@ class GeneralTab extends Pane implements PrefsTab {
     public GeneralTab(DialogService dialogService, JabRefPreferences prefs) {
         this.prefs = prefs;
         this.dialogService = dialogService;
+
+        ActionFactory factory = new ActionFactory(prefs.getKeyBindingRepository());
+
         biblatexMode = new ComboBox<>(FXCollections.observableArrayList(BibDatabaseMode.values()));
         memoryStick = new CheckBox(Localization.lang("Load and Save preferences from/to jabref.xml on start-up (memory stick mode)"));
         useOwner = new CheckBox(Localization.lang("Mark new entries with owner name") + ':');
@@ -90,10 +95,8 @@ public GeneralTab(DialogService dialogService, JabRefPreferences prefs) {
         builder.add(defOwnerField, 2, 10);
         builder.add(overwriteOwner, 3, 10);
 
-        Button help = new Button("?");
-        help.setPrefSize(10, 10);
-        help.setOnAction(event -> new HelpAction(HelpFile.OWNER).getHelpButton().doClick());
-        builder.add(help, 4, 10);
+        Button helpOwner = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.OWNER).getCommand());
+        builder.add(helpOwner, 4, 10);
 
         builder.add(useTimeStamp, 1, 13);
         builder.add(timeStampFormat, 2, 13);
@@ -102,9 +105,8 @@ public GeneralTab(DialogService dialogService, JabRefPreferences prefs) {
         builder.add(fieldName, 3, 13);
         builder.add(timeStampField, 4, 13);
 
-        Button help1 = new Button("?");
-        help1.setOnAction(event -> new HelpAction(HelpFile.TIMESTAMP).getHelpButton().doClick());
-        builder.add(help1, 6, 13);
+        Button helpTimestamp = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.TIMESTAMP).getCommand());
+        builder.add(helpTimestamp, 6, 13);
 
         builder.add(updateTimeStamp, 1, 14);
         builder.add(new Line(), 1, 15);
diff --git a/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java b/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java
index bac74718d33..da1f649fb2c 100644
--- a/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java
+++ b/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java
@@ -1,6 +1,7 @@
 package org.jabref.gui.preferences;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Objects;
 
@@ -21,6 +22,8 @@
 import javafx.scene.layout.HBox;
 import javafx.scene.layout.Pane;
 
+import org.jabref.gui.actions.ActionFactory;
+import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.help.HelpAction;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.l10n.Localization;
@@ -31,24 +34,25 @@ public class NameFormatterTab extends Pane implements PrefsTab {
 
     private final JabRefPreferences prefs;
     private boolean tableChanged;
-    private final TableView table;
+    private final TableView<NameFormatterViewModel> table;
     private final GridPane builder = new GridPane();
-    private final List<TableRow> tableRows = new ArrayList<>(10);
-    private final ObservableList<TableRow> data = FXCollections.observableArrayList();
+    private final List<NameFormatterViewModel> tableRows = new ArrayList<>(10);
+    private final ObservableList<NameFormatterViewModel> data = FXCollections.observableArrayList();
 
-    public static class TableRow {
-        private SimpleStringProperty name;
-        private SimpleStringProperty format;
+    public static class NameFormatterViewModel {
 
-        TableRow() {
+        private final SimpleStringProperty name;
+        private final SimpleStringProperty format;
+
+        NameFormatterViewModel() {
             this("");
         }
 
-        TableRow(String name) {
+        NameFormatterViewModel(String name) {
             this(name, NameFormatter.DEFAULT_FORMAT);
         }
 
-        TableRow(String name, String format) {
+        NameFormatterViewModel(String name, String format) {
             this.name = new SimpleStringProperty(name);
             this.format = new SimpleStringProperty(format);
         }
@@ -77,28 +81,32 @@ public void setFormat(String format) {
     public NameFormatterTab(JabRefPreferences prefs) {
         this.prefs = Objects.requireNonNull(prefs);
 
-        TableColumn<TableRow,String> firstCol = new TableColumn<>(Localization.lang("Formatter name"));
-        TableColumn<TableRow,String> lastCol = new TableColumn<>(Localization.lang("Format string"));
-        table = new TableView();
+        ActionFactory factory = new ActionFactory(prefs.getKeyBindingRepository());
+
+        TableColumn<NameFormatterViewModel, String> firstCol = new TableColumn<>(Localization.lang("Formatter name"));
+        TableColumn<NameFormatterViewModel, String> lastCol = new TableColumn<>(Localization.lang("Format string"));
+        table = new TableView<>();
         table.setEditable(true);
         firstCol.setCellValueFactory(new PropertyValueFactory<>("name"));
         firstCol.setCellFactory(TextFieldTableCell.forTableColumn());
         firstCol.setOnEditCommit(
-                (TableColumn.CellEditEvent<TableRow, String> t) -> {
-                    t.getTableView().getItems().get(
-                            t.getTablePosition().getRow()).setName(t.getNewValue());
-                });
+                                 (TableColumn.CellEditEvent<NameFormatterViewModel, String> t) -> {
+                                     t.getTableView().getItems().get(
+                                                                     t.getTablePosition().getRow())
+                                      .setName(t.getNewValue());
+                                 });
         lastCol.setCellValueFactory(new PropertyValueFactory<>("format"));
         lastCol.setCellFactory(TextFieldTableCell.forTableColumn());
         lastCol.setOnEditCommit(
-                (TableColumn.CellEditEvent<TableRow, String> t) -> {
-                    t.getTableView().getItems().get(
-                            t.getTablePosition().getRow()).setFormat(t.getNewValue());
-                });
+                                (TableColumn.CellEditEvent<NameFormatterViewModel, String> t) -> {
+                                    t.getTableView().getItems().get(
+                                                                    t.getTablePosition().getRow())
+                                     .setFormat(t.getNewValue());
+                                });
         firstCol.setPrefWidth(140);
         lastCol.setPrefWidth(200);
         table.setItems(data);
-        table.getColumns().addAll(firstCol, lastCol);
+        table.getColumns().addAll(Arrays.asList(firstCol, lastCol));
         final TextField addName = new TextField();
         addName.setPromptText("name");
         addName.setMaxWidth(100);
@@ -116,9 +124,9 @@ public NameFormatterTab(JabRefPreferences prefs) {
         Label insertRows = new Label(Localization.lang("Insert rows"));
         insertRows.setVisible(false);
         Button add = new Button("Insert");
-        add.setOnAction(e-> {
+        add.setOnAction(e -> {
             if (!addName.getText().isEmpty() && !addLast.getText().isEmpty()) {
-                TableRow tableRow = new TableRow(addName.getText(), addLast.getText());
+                NameFormatterViewModel tableRow = new NameFormatterViewModel(addName.getText(), addLast.getText());
                 addName.clear();
                 addLast.clear();
                 data.add(tableRow);
@@ -131,21 +139,22 @@ public NameFormatterTab(JabRefPreferences prefs) {
         Label deleteRows = new Label(Localization.lang("Delete rows"));
         deleteRows.setVisible(false);
         Button delete = new Button("Delete");
-        delete.setOnAction(e-> {
-            if (table.getFocusModel() != null && table.getFocusModel().getFocusedIndex() != -1) {
+        delete.setOnAction(e -> {
+            if ((table.getFocusModel() != null) && (table.getFocusModel().getFocusedIndex() != -1)) {
                 tableChanged = true;
                 int row = table.getFocusModel().getFocusedIndex();
-                TableRow tableRow = tableRows.get(row);
+                NameFormatterViewModel tableRow = tableRows.get(row);
                 tableRows.remove(tableRow);
                 data.remove(tableRow);
                 table.setItems(data);
                 table.refresh();
-            }});
-        Button help = new Button("?");
-        help.setOnAction(e-> new HelpAction(Localization.lang("Help on Name Formatting"),
-                HelpFile.CUSTOM_EXPORTS_NAME_FORMATTER).getHelpButton().doClick());
+            }
+        });
+
+        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on Name Formatting"),
+                                                                                    HelpFile.CUSTOM_EXPORTS_NAME_FORMATTER).getCommand());
         HBox toolbar = new HBox();
-        toolbar.getChildren().addAll(addName, addLast,add,delete,help);
+        toolbar.getChildren().addAll(addName, addLast, add, delete, help);
         tabPanel.setBottom(toolbar);
 
         Label specialNameFormatters = new Label(Localization.lang("Special name formatters"));
@@ -154,6 +163,7 @@ public NameFormatterTab(JabRefPreferences prefs) {
         builder.add(tabPanel, 1, 2);
     }
 
+    @Override
     public Node getBuilder() {
         return builder;
     }
@@ -166,9 +176,9 @@ public void setValues() {
 
         for (int i = 0; i < names.size(); i++) {
             if (i < formats.size()) {
-                tableRows.add(new TableRow(names.get(i), formats.get(i)));
+                tableRows.add(new NameFormatterViewModel(names.get(i), formats.get(i)));
             } else {
-                tableRows.add(new TableRow(names.get(i)));
+                tableRows.add(new NameFormatterViewModel(names.get(i)));
             }
         }
     }
@@ -198,7 +208,7 @@ public void storeSettings() {
             List<String> names = new ArrayList<>(tableRows.size());
             List<String> formats = new ArrayList<>(tableRows.size());
 
-            for (TableRow tr : tableRows) {
+            for (NameFormatterViewModel tr : tableRows) {
                 names.add(tr.getName());
                 formats.add(tr.getFormat());
             }
diff --git a/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java b/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
index 090f22d3020..fe9dd582df7 100644
--- a/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
@@ -35,6 +35,8 @@
 
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.actions.ActionFactory;
+import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.help.HelpAction;
@@ -113,16 +115,17 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
         field.setCellFactory(TextFieldTableCell.forTableColumn());
         field.setEditable(true);
         field.setOnEditCommit(
-                (TableColumn.CellEditEvent<TableRow, String> t) -> {
-                    t.getTableView().getItems().get(
-                            t.getTablePosition().getRow()).setName(t.getNewValue());
-                    // Since data is an ObservableList, updating it updates the displayed field name.
-                    this.data.set(t.getTablePosition().getRow(), new TableRow(t.getNewValue()));
-                    // Update the User Preference of COLUMN_NAMES
-                    List<String> tempColumnNames = this.prefs.getStringList(JabRefPreferences.COLUMN_NAMES);
-                    tempColumnNames.set(t.getTablePosition().getRow(), t.getNewValue());
-                    this.prefs.putStringList(JabRefPreferences.COLUMN_NAMES, tempColumnNames);
-                });
+                              (TableColumn.CellEditEvent<TableRow, String> t) -> {
+                                  t.getTableView().getItems().get(
+                                                                  t.getTablePosition().getRow())
+                                   .setName(t.getNewValue());
+                                  // Since data is an ObservableList, updating it updates the displayed field name.
+                                  this.data.set(t.getTablePosition().getRow(), new TableRow(t.getNewValue()));
+                                  // Update the User Preference of COLUMN_NAMES
+                                  List<String> tempColumnNames = this.prefs.getStringList(JabRefPreferences.COLUMN_NAMES);
+                                  tempColumnNames.set(t.getTablePosition().getRow(), t.getNewValue());
+                                  this.prefs.putStringList(JabRefPreferences.COLUMN_NAMES, tempColumnNames);
+                              });
 
         colSetup.setItems(data);
         colSetup.getColumns().add(field);
@@ -150,7 +153,7 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
         deleteRow = new Button("Delete");
         deleteRow.setPrefSize(80, 20);
         deleteRow.setOnAction(e -> {
-            if (colSetup.getFocusModel() != null && colSetup.getFocusModel().getFocusedIndex() != -1) {
+            if ((colSetup.getFocusModel() != null) && (colSetup.getFocusModel().getFocusedIndex() != -1)) {
                 tableChanged = true;
                 int row = colSetup.getFocusModel().getFocusedIndex();
                 TableRow tableRow = data.get(row);
@@ -162,7 +165,7 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
         up.setOnAction(e -> {
             if (colSetup.getFocusModel() != null) {
                 int row = colSetup.getFocusModel().getFocusedIndex();
-                if (row > data.size() || row == 0) {
+                if ((row > data.size()) || (row == 0)) {
                     return;
                 }
                 TableRow tableRow1 = data.get(row);
@@ -178,7 +181,7 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
         down.setOnAction(e -> {
             if (colSetup.getFocusModel() != null) {
                 int row = colSetup.getFocusModel().getFocusedIndex();
-                if (row + 1 > data.size()) {
+                if ((row + 1) > data.size()) {
                     return;
                 }
                 TableRow tableRow1 = data.get(row);
@@ -224,10 +227,10 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
 
         /** begin: special table columns and special fields ***/
 
-        Button helpButton = new Button("?");
-        helpButton.setPrefSize(20, 20);
-        helpButton.setOnAction(e -> new HelpAction(Localization.lang("Help on special fields"),
-                HelpFile.SPECIAL_FIELDS).getHelpButton().doClick());
+        ActionFactory factory = new ActionFactory(prefs.getKeyBindingRepository());
+
+        Button helpButton = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on special fields"),
+                                                                                          HelpFile.SPECIAL_FIELDS).getCommand());
 
         rankingColumn = new CheckBox(Localization.lang("Show rank"));
         qualityColumn = new CheckBox(Localization.lang("Show quality"));
@@ -300,6 +303,7 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
         builder.add(buttonOrder, 1, 7);
     }
 
+    @Override
     public Node getBuilder() {
         return builder;
     }
@@ -331,7 +335,7 @@ public void setValues() {
                 listOfFileColumns.getSelectionModel().select(indicesToSelect[i]);
             }
         } else {
-            listOfFileColumns.getSelectionModel().select(new int[]{});
+            listOfFileColumns.getSelectionModel().select(new int[] {});
         }
 
         /*** begin: special fields ***/
@@ -379,8 +383,8 @@ public void setValues() {
 
     public static class TableRow {
 
-        private SimpleStringProperty name;
-        private SimpleDoubleProperty length;
+        private final SimpleStringProperty name;
+        private final SimpleDoubleProperty length;
 
         public TableRow() {
             name = new SimpleStringProperty("");
@@ -447,19 +451,19 @@ public void storeSettings() {
 
         boolean restartRequired;
         restartRequired = (oldSpecialFieldsEnabled != newSpecialFieldsEnabled) ||
-                (oldRankingColumn != newRankingColumn) ||
-                (oldQualityColumn != newQualityColumn) ||
-                (oldPriorityColumn != newPriorityColumn) ||
-                (oldRelevanceColumn != newRelevanceColumn) ||
-                (oldPrintedColumn != newPrintedColumn) ||
-                (oldReadStatusColumn != newReadStatusColumn) ||
-                (oldSyncKeyWords != newSyncKeyWords) ||
-                (oldWriteSpecialFields != newWriteSpecialFields);
+                          (oldRankingColumn != newRankingColumn) ||
+                          (oldQualityColumn != newQualityColumn) ||
+                          (oldPriorityColumn != newPriorityColumn) ||
+                          (oldRelevanceColumn != newRelevanceColumn) ||
+                          (oldPrintedColumn != newPrintedColumn) ||
+                          (oldReadStatusColumn != newReadStatusColumn) ||
+                          (oldSyncKeyWords != newSyncKeyWords) ||
+                          (oldWriteSpecialFields != newWriteSpecialFields);
         if (restartRequired) {
             DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().showWarningDialogAndWait(Localization.lang("Changed special field settings"),
-                    Localization.lang("You have changed settings for special fields.")
-                            .concat(" ")
-                            .concat(Localization.lang("You must restart JabRef for this to come into effect."))));
+                                                                                                          Localization.lang("You have changed settings for special fields.")
+                                                                                                                      .concat(" ")
+                                                                                                                      .concat(Localization.lang("You must restart JabRef for this to come into effect."))));
 
         }
 
@@ -479,11 +483,11 @@ public void storeSettings() {
 
         /*** end: special fields ***/
 
-//        if (colSetup.isEditing()) {
-//            int col = colSetup.getEditingColumn();
-//            int row = colSetup.getEditingRow();
-//            colSetup.getCellEditor(row, col).stopCellEditing();
-//        }
+        //        if (colSetup.isEditing()) {
+        //            int col = colSetup.getEditingColumn();
+        //            int row = colSetup.getEditingRow();
+        //            colSetup.getCellEditor(row, col).stopCellEditing();
+        //        }
 
         // Now we need to make sense of the contents the user has made to the
         // table setup table.
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 1c95118f7c1..2f5131a84a9 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2135,3 +2135,6 @@ Search\ document\ identifier\ online=Search document identifier online
 Search\ for\ unlinked\ local\ files=Search for unlinked local files
 Search\ full\ text\ documents\ online=Search full text documents online
 Find\ and\ replace=Find and replace
+
+Found\ documents\:=Found documents\:
+Use\ selected\ document=Use selected document

From 53bd0ea6d6b21500de099ec174176492b8ec55fe Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Mar 2019 08:12:20 +0100
Subject: [PATCH 107/184] Bump mvvmfx-validation from 1.7.0 to 1.8.0 (#4749)

Bumps [mvvmfx-validation](https://github.com/sialcasa/mvvmFX) from 1.7.0 to 1.8.0.
- [Release notes](https://github.com/sialcasa/mvvmFX/releases)
- [Commits](https://github.com/sialcasa/mvvmFX/commits)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index a3a9a3f66ab..9e22520ad4c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -130,7 +130,7 @@ dependencies {
 
     // JavaFX stuff
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
-    compile 'de.saxsys:mvvmfx-validation:1.7.0'
+    compile 'de.saxsys:mvvmfx-validation:1.8.0'
     compile 'de.saxsys:mvvmfx:1.7.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'

From 2f022f75c1eaa2d8e1eeacf3ac3b25fa110daf05 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Mar 2019 08:12:32 +0100
Subject: [PATCH 108/184] Bump guava from 27.0.1-jre to 27.1-jre (#4748)

Bumps [guava](https://github.com/google/guava) from 27.0.1-jre to 27.1-jre.
- [Release notes](https://github.com/google/guava/releases)
- [Commits](https://github.com/google/guava/commits)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9e22520ad4c..0a45aab3885 100644
--- a/build.gradle
+++ b/build.gradle
@@ -126,7 +126,7 @@ dependencies {
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:27.0.1-jre'
+    compile 'com.google.guava:guava:27.1-jre'
 
     // JavaFX stuff
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'

From b3e5b5126474137e57ff258d4d176253f5345e89 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Mar 2019 08:14:19 +0100
Subject: [PATCH 109/184] Bump mvvmfx from 1.7.0 to 1.8.0 (#4747)

Bumps [mvvmfx](https://github.com/sialcasa/mvvmFX) from 1.7.0 to 1.8.0.
- [Release notes](https://github.com/sialcasa/mvvmFX/releases)
- [Commits](https://github.com/sialcasa/mvvmFX/commits)

Signed-off-by: dependabot[bot] <support@dependabot.com>

From 7c8441db970b9e8e142faf329ec7f9b3c11fb3d3 Mon Sep 17 00:00:00 2001
From: Chamod Shehanka <hcsperera@outlook.com>
Date: Tue, 12 Mar 2019 01:12:07 +0530
Subject: [PATCH 110/184] Code optimized and created a reusable method to get
 writer output (#4750)

---
 .../org/jabref/benchmarks/Benchmarks.java     | 20 ++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/src/jmh/java/org/jabref/benchmarks/Benchmarks.java b/src/jmh/java/org/jabref/benchmarks/Benchmarks.java
index c17b4c6e76b..a7316584eee 100644
--- a/src/jmh/java/org/jabref/benchmarks/Benchmarks.java
+++ b/src/jmh/java/org/jabref/benchmarks/Benchmarks.java
@@ -62,17 +62,22 @@ public void init() throws Exception {
             entry.setField("rnd", "2" + randomizer.nextInt());
             database.insertEntry(entry);
         }
-        StringWriter outputWriter = new StringWriter();
-        BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(outputWriter, mock(SavePreferences.class));
-        databaseWriter.savePartOfDatabase(
-                new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries());
-        bibtexString = outputWriter.toString();
+
+        bibtexString = getOutputWriter().toString();
 
         latexConversionString = "{A} \\textbf{bold} approach {\\it to} ${{\\Sigma}}{\\Delta}$ modulator \\textsuperscript{2} \\$";
 
         htmlConversionString = "<b>&Ouml;sterreich</b> &#8211; &amp; characters &#x2aa2; <i>italic</i>";
     }
 
+    private StringWriter getOutputWriter() throws IOException {
+        StringWriter outputWriter = new StringWriter();
+        BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(outputWriter, mock(SavePreferences.class));
+        databaseWriter.savePartOfDatabase(
+                new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries());
+        return outputWriter;
+    }
+
     @Benchmark
     public ParserResult parse() throws IOException {
         BibtexParser parser = new BibtexParser(Globals.prefs.getImportFormatPreferences(), new DummyFileUpdateMonitor());
@@ -81,10 +86,7 @@ public ParserResult parse() throws IOException {
 
     @Benchmark
     public String write() throws Exception {
-        StringWriter outputWriter = new StringWriter();
-        BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(outputWriter, mock(SavePreferences.class));
-        databaseWriter.savePartOfDatabase(new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries());
-        return outputWriter.toString();
+        return getOutputWriter().toString();
     }
 
     @Benchmark

From 3d3eecc0a01b7d419681457bc46eb809b25982f0 Mon Sep 17 00:00:00 2001
From: Yash  Kothari <yashkothari199767@gmail.com>
Date: Tue, 12 Mar 2019 03:02:14 +0530
Subject: [PATCH 111/184] Saving changes and exiting application (#4729)

* [WIP] Saving changes and exiting application

Fixes #4728

When the user clicks _Save changes_ option, the status of
saving is not shown unlike before. I am not sure what might be
the cause of that.

* Refactored confirmClose() method

* Display dialog in case of save exception, and remove runInJavaFXThread
---
 src/main/java/org/jabref/gui/JabRefFrame.java  | 18 ++++++++++--------
 .../gui/exporter/SaveDatabaseAction.java       | 17 +++++++----------
 2 files changed, 17 insertions(+), 18 deletions(-)

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 9a1a2bdb735..ff496a25e09 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -1313,18 +1313,20 @@ private boolean confirmClose(BasePanel panel) {
             // The user wants to save.
             try {
                 SaveDatabaseAction saveAction = new SaveDatabaseAction(panel, Globals.prefs);
-                if (!saveAction.save()) {
-                    // The action was either canceled or unsuccessful.
-                    output(Localization.lang("Unable to save library"));
-                    return false;
+                if (saveAction.save()) {
+                    // Saved, now exit.
+                    return true;
                 }
+                // The action was either canceled or unsuccessful.
+                output(Localization.lang("Unable to save library"));
             } catch (Throwable ex) {
-                return false;
+                LOGGER.error("A problem occurred when trying to save the file", ex);
+                dialogService.showErrorDialogAndWait(Localization.lang("Save library"), Localization.lang("Could not save file."), ex);
             }
-        } else {
-            return !response.isPresent() || !response.get().equals(cancel);
+            // Save was cancelled or an error occurred.
+            return false;
         }
-        return false;
+        return !response.isPresent() || !response.get().equals(cancel);
     }
 
     private void closeTab(BasePanel panel) {
diff --git a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
index 681cf946275..f1bfe5c0739 100644
--- a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
@@ -19,7 +19,6 @@
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.dialogs.AutosaveUIManager;
 import org.jabref.gui.util.BackgroundTask;
-import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.autosaveandbackup.AutosaveManager;
 import org.jabref.logic.autosaveandbackup.BackupManager;
@@ -138,15 +137,13 @@ private boolean doSave() {
                 panel.setBaseChanged(false);
                 panel.markExternalChangesAsResolved();
 
-                DefaultTaskExecutor.runInJavaFXThread(() -> {
-                    // Reset title of tab
-                    frame.setTabTitle(panel, panel.getTabTitle(),
-                            panel.getBibDatabaseContext().getDatabaseFile().get().getAbsolutePath());
-                    frame.output(Localization.lang("Saved library") + " '"
-                            + panel.getBibDatabaseContext().getDatabaseFile().get().getPath() + "'.");
-                    frame.setWindowTitle();
-                    frame.updateAllTabTitles();
-                });
+                // Reset title of tab
+                frame.setTabTitle(panel, panel.getTabTitle(),
+                                  panel.getBibDatabaseContext().getDatabaseFile().get().getAbsolutePath());
+                frame.output(Localization.lang("Saved library") + " '"
+                             + panel.getBibDatabaseContext().getDatabaseFile().get().getPath() + "'.");
+                frame.setWindowTitle();
+                frame.updateAllTabTitles();
             }
             return success;
         } catch (SaveException ex) {

From fa984a743b5d834867daaac7200e0fd74035bd4b Mon Sep 17 00:00:00 2001
From: Samiya Caur <36728314+samiyac@users.noreply.github.com>
Date: Tue, 12 Mar 2019 03:04:24 +0530
Subject: [PATCH 112/184] Adds a browse button next to the path text field for
 aux-based groups (#4743)

* Fixes #4586

* implementing suggestions from code review

* Updated constructor to remove JabRefFrame object

* Using DialogService to show warnings/errors

* changes implemented
---
 CHANGELOG.md                                  |  1 +
 .../org/jabref/gui/groups/GroupDialog.java    | 50 +++++++++++++------
 .../jabref/gui/groups/GroupTreeViewModel.java |  4 +-
 3 files changed, 39 insertions(+), 16 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index eecbaff3814..4efb45787a6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -55,6 +55,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We grouped and reordered the Main Menu (File, Edit, Library, Quality, Tools, and View tabs & icons). [#4666](https://github.com/JabRef/jabref/issues/4666) [#4667](https://github.com/JabRef/jabref/issues/4667) [#4668](https://github.com/JabRef/jabref/issues/4668) [#4669](https://github.com/JabRef/jabref/issues/4669) [#4670](https://github.com/JabRef/jabref/issues/4670) [#4671](https://github.com/JabRef/jabref/issues/4671) [#4672](https://github.com/JabRef/jabref/issues/4672) [#4673](https://github.com/JabRef/jabref/issues/4673)
 - We added additional modifiers (capitalize, titlecase and sentencecase) to the Bibtex key generator. [#1506](https://github.com/JabRef/jabref/issues/1506)
 - We grouped the toolbar icons and changed the Open Library and Copy icons. [#4584](https://github.com/JabRef/jabref/issues/4584) 
+- We added a browse button next to the path text field for aux-based groups. [#4586](https://github.com/JabRef/jabref/issues/4586)
 
 
 ### Fixed
diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
index 16b8601a8dd..9859213c926 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDialog.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -13,6 +13,7 @@
 import javafx.geometry.Insets;
 import javafx.geometry.Orientation;
 import javafx.scene.Node;
+import javafx.scene.control.Button;
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.Label;
@@ -24,6 +25,7 @@
 import javafx.scene.control.Toggle;
 import javafx.scene.control.ToggleGroup;
 import javafx.scene.layout.HBox;
+import javafx.scene.layout.Priority;
 import javafx.scene.layout.StackPane;
 import javafx.scene.layout.VBox;
 import javafx.scene.text.Font;
@@ -33,13 +35,16 @@
 
 import org.jabref.Globals;
 import org.jabref.JabRefGUI;
-import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.BasePanel;
+import org.jabref.gui.DialogService;
 import org.jabref.gui.search.rules.describer.SearchDescribers;
 import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.gui.util.TooltipTextUtil;
 import org.jabref.logic.auxparser.DefaultAuxParser;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.search.SearchQuery;
+import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.Keyword;
@@ -83,6 +88,8 @@ class GroupDialog extends BaseDialog<AbstractGroup> {
     private final RadioButton independentButton = new RadioButton(Localization.lang("Independent group: When selected, view only this group's entries"));
     private final RadioButton intersectionButton = new RadioButton(Localization.lang("Refine supergroup: When selected, view entries contained in both this group and its supergroup"));
     private final RadioButton unionButton = new RadioButton(Localization.lang("Include subgroups: When selected, view entries contained in this group or its subgroups"));
+    private final DialogService dialogService;
+    private final JabRefPreferences prefs;
 
     // for KeywordGroup
     private final TextField keywordGroupSearchTerm = new TextField();
@@ -105,6 +112,8 @@ class GroupDialog extends BaseDialog<AbstractGroup> {
 
     // for TexGroup
     private final TextField texGroupFilePath = new TextField();
+    private final Button texGroupBrowseButton = new Button("Browse");
+    private final HBox texGroupHBox = new HBox(10);
 
     // for all types
     private final TextFlow descriptionTextFlow = new TextFlow();
@@ -118,7 +127,7 @@ class GroupDialog extends BaseDialog<AbstractGroup> {
      * @param editedGroup The group being edited, or null if a new group is to be
      *                    created.
      */
-    public GroupDialog(JabRefFrame jabrefFrame, AbstractGroup editedGroup) {
+    public GroupDialog(DialogService dialogService, BasePanel basePanel, JabRefPreferences prefs, AbstractGroup editedGroup) {
         this.setTitle(Localization.lang("Edit group"));
 
         explicitRadioButton.setSelected(true);
@@ -128,8 +137,11 @@ public GroupDialog(JabRefFrame jabrefFrame, AbstractGroup editedGroup) {
         descriptionTextFlow.setMinHeight(180);
         descriptionTextFlow.setPrefHeight(180);
 
+        this.dialogService = dialogService;
+        this.prefs = prefs;
+
         // set default values (overwritten if editedGroup != null)
-        keywordGroupSearchField.setText(jabrefFrame.prefs().get(JabRefPreferences.GROUPS_DEFAULT_FIELD));
+        keywordGroupSearchField.setText(prefs.get(JabRefPreferences.GROUPS_DEFAULT_FIELD));
 
         // configure elements
         ToggleGroup groupType = new ToggleGroup();
@@ -261,11 +273,10 @@ public GroupDialog(JabRefFrame jabrefFrame, AbstractGroup editedGroup) {
                     if (explicitRadioButton.isSelected()) {
                         Character keywordDelimiter = Globals.prefs.getKeywordDelimiter();
                         if (groupName.contains(Character.toString(keywordDelimiter))) {
-                            jabrefFrame.showMessage(
-                                    Localization.lang("The group name contains the keyword separator \"%0\" and thus probably does not work as expected.", Character.toString(keywordDelimiter)));
+                            dialogService.showWarningDialogAndWait(null, Localization.lang("The group name contains the keyword separator \"%0\" and thus probably does not work as expected.", Character.toString(keywordDelimiter)));
                         }
 
-                        Optional<GroupTreeNode> rootGroup = jabrefFrame.getCurrentBasePanel().getBibDatabaseContext().getMetaData().getGroups();
+                        Optional<GroupTreeNode> rootGroup = basePanel.getBibDatabaseContext().getMetaData().getGroups();
                         if (rootGroup.isPresent()) {
                             int groupsWithSameName = rootGroup.get().findChildrenSatisfying(group -> group.getName().equals(groupName)).size();
                             boolean warnAboutSameName = false;
@@ -279,8 +290,7 @@ public GroupDialog(JabRefFrame jabrefFrame, AbstractGroup editedGroup) {
                             }
 
                             if (warnAboutSameName) {
-                                jabrefFrame.showMessage(
-                                        Localization.lang("There exists already a group with the same name.", Character.toString(keywordDelimiter)));
+                                dialogService.showErrorDialogAndWait(Localization.lang("There exists already a group with the same name.", Character.toString(keywordDelimiter)));
                                 return null;
                             }
                         }
@@ -323,7 +333,7 @@ groupName, getContext(),
                     resultingGroup.setIconName(iconField.getText());
                     return resultingGroup;
                 } catch (IllegalArgumentException | IOException exception) {
-                    jabrefFrame.showMessage(exception.getLocalizedMessage());
+                    dialogService.showErrorDialogAndWait(exception.getLocalizedMessage(), exception);
                     return null;
                 }
             }
@@ -404,12 +414,12 @@ groupName, getContext(),
         getDialogPane().getScene().getWindow().sizeToScene();
     }
 
-    public GroupDialog() {
-        this(JabRefGUI.getMainFrame(), null);
+    public GroupDialog(DialogService dialogService) {
+        this(dialogService, JabRefGUI.getMainFrame().getCurrentBasePanel(), Globals.prefs, null);
     }
 
-    public GroupDialog(AbstractGroup editedGroup) {
-        this(JabRefGUI.getMainFrame(), editedGroup);
+    public GroupDialog(DialogService dialogService, AbstractGroup editedGroup) {
+        this(dialogService, JabRefGUI.getMainFrame().getCurrentBasePanel(), Globals.prefs, editedGroup);
     }
 
     private static String formatRegExException(String regExp, Exception e) {
@@ -442,7 +452,11 @@ private VBox createOptionsTexGroup() {
         VBox texPanel = new VBox();
         texPanel.setVisible(false);
         texPanel.getChildren().add(new Label(Localization.lang("Aux file")));
-        texPanel.getChildren().add(texGroupFilePath);
+        texGroupBrowseButton.setOnAction((ActionEvent e) -> openBrowseDialog());
+        texGroupHBox.getChildren().add(texGroupFilePath);
+        texGroupHBox.getChildren().add(texGroupBrowseButton);
+        texGroupHBox.setHgrow(texGroupFilePath, Priority.ALWAYS);
+        texPanel.getChildren().add(texGroupHBox);
         return texPanel;
     }
 
@@ -586,6 +600,14 @@ private void updateComponents() {
         getDialogPane().lookupButton(ButtonType.OK).setDisable(!okEnabled);
     }
 
+    private void openBrowseDialog() {
+        FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
+            .addExtensionFilter(StandardFileType.AUX)
+            .withDefaultExtension(StandardFileType.AUX)
+            .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)).build();
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> texGroupFilePath.setText(file.toAbsolutePath().toString()));
+    }
+
     private String fromTextFlowToHTMLString(TextFlow textFlow) {
         StringBuilder htmlStringBuilder = new StringBuilder();
         for (Node node : textFlow.getChildren()) {
diff --git a/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java b/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java
index de4c279e59c..bccddf297e5 100644
--- a/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java
+++ b/src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java
@@ -141,7 +141,7 @@ private void onActiveDatabaseChanged(Optional<BibDatabaseContext> newDatabase) {
      * Opens "New Group Dialog" and add the resulting group to the specified group
      */
     public void addNewSubgroup(GroupNodeViewModel parent) {
-        Optional<AbstractGroup> newGroup = dialogService.showCustomDialogAndWait(new GroupDialog());
+        Optional<AbstractGroup> newGroup = dialogService.showCustomDialogAndWait(new GroupDialog(dialogService));
         newGroup.ifPresent(group -> {
             parent.addSubgroup(group);
 
@@ -166,7 +166,7 @@ private void writeGroupChangesToMetaData() {
      */
     public void editGroup(GroupNodeViewModel oldGroup) {
         Optional<AbstractGroup> newGroup = dialogService
-                .showCustomDialogAndWait(new GroupDialog(oldGroup.getGroupNode().getGroup()));
+                .showCustomDialogAndWait(new GroupDialog(dialogService, oldGroup.getGroupNode().getGroup()));
         newGroup.ifPresent(group -> {
             // TODO: Keep assignments
             boolean keepPreviousAssignments = dialogService.showConfirmationDialogAndWait(

From b906e69449d70857d8a46b2139032f47fa2a06b3 Mon Sep 17 00:00:00 2001
From: Ali <alijakparov.kz@gmail.com>
Date: Tue, 12 Mar 2019 00:35:49 +0300
Subject: [PATCH 113/184] Optimize data fetching (#4520)

* optimize data fetching from database

* delete time measure code

* revert code style

* fix checkstyle

* put columns name instead of *

* revert checkstyle

* change for to stream

* refactor variable name

* create simple test

* fix test

* rename method name

* refactor

* create test

* Fix formatting

* Remove obsolete method by slight refactoring

Co-authored-by: Tobias Diez <tobiasdiez@gmx.de>
---
 .../jabref/logic/shared/DBMSProcessor.java    | 131 +++++++++---------
 .../jabref/logic/shared/DBMSSynchronizer.java |  20 +--
 .../logic/shared/DBMSProcessorTest.java       |  18 +++
 3 files changed, 94 insertions(+), 75 deletions(-)

diff --git a/src/main/java/org/jabref/logic/shared/DBMSProcessor.java b/src/main/java/org/jabref/logic/shared/DBMSProcessor.java
index 9ebf92f0d33..59d3deed123 100644
--- a/src/main/java/org/jabref/logic/shared/DBMSProcessor.java
+++ b/src/main/java/org/jabref/logic/shared/DBMSProcessor.java
@@ -6,6 +6,7 @@
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -14,6 +15,7 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.UUID;
+import java.util.stream.Collectors;
 
 import org.jabref.logic.shared.exception.OfflineLockException;
 import org.jabref.model.database.shared.DBMSType;
@@ -52,7 +54,7 @@ protected DBMSProcessor(DatabaseConnection dbmsConnection) {
      * @throws SQLException
      */
     public boolean checkBaseIntegrity() throws SQLException {
-        return checkTableAvailibility("ENTRY", "FIELD", "METADATA");
+        return checkTableAvailability("ENTRY", "FIELD", "METADATA");
     }
 
     /**
@@ -60,8 +62,8 @@ public boolean checkBaseIntegrity() throws SQLException {
      *
      * @return <code>true</code> if the structure is old, else <code>false</code>.
      */
-    public boolean checkForPre3Dot6Intergrity() throws SQLException {
-        return checkTableAvailibility(
+    public boolean checkForPare3Dot6Integrity() throws SQLException {
+        return checkTableAvailability(
                 "ENTRIES",
                 "ENTRY_GROUP",
                 "ENTRY_TYPES",
@@ -77,7 +79,7 @@ public boolean checkForPre3Dot6Intergrity() throws SQLException {
      * @param tableNames Table names to be checked
      * @return <code>true</code> if <b>all</b> given tables are present, else <code>false</code>.
      */
-    private boolean checkTableAvailibility(String... tableNames) throws SQLException {
+    private boolean checkTableAvailability(String... tableNames) throws SQLException {
         List<String> requiredTables = new ArrayList<>();
         for (String name : tableNames) {
             requiredTables.add(name.toUpperCase(Locale.ENGLISH));
@@ -147,16 +149,15 @@ public void insertEntry(BibEntry bibEntry) {
      * @param bibEntry {@link BibEntry} to be inserted
      */
     protected void insertIntoEntryTable(BibEntry bibEntry) {
-        // Inserting into ENTRY table
-        StringBuilder insertIntoEntryQuery = new StringBuilder()
-                .append("INSERT INTO ")
-                .append(escape("ENTRY"))
-                .append("(")
-                .append(escape("TYPE"))
-                .append(") VALUES(?)");
-
         // This is the only method to get generated keys which is accepted by MySQL, PostgreSQL and Oracle.
-        try (PreparedStatement preparedEntryStatement = connection.prepareStatement(insertIntoEntryQuery.toString(),
+        String insertIntoEntryQuery =
+                "INSERT INTO " +
+                        escape("ENTRY") +
+                        "(" +
+                        escape("TYPE") +
+                        ") VALUES(?)";
+
+        try (PreparedStatement preparedEntryStatement = connection.prepareStatement(insertIntoEntryQuery,
                 new String[] {"SHARED_ID"})) {
 
             preparedEntryStatement.setString(1, bibEntry.getType());
@@ -182,14 +183,14 @@ private boolean checkForBibEntryExistence(BibEntry bibEntry) {
             // Check if already exists
             int sharedID = bibEntry.getSharedBibEntryData().getSharedID();
             if (sharedID != -1) {
-                StringBuilder selectQuery = new StringBuilder()
-                        .append("SELECT * FROM ")
-                        .append(escape("ENTRY"))
-                        .append(" WHERE ")
-                        .append(escape("SHARED_ID"))
-                        .append(" = ?");
-
-                try (PreparedStatement preparedSelectStatement = connection.prepareStatement(selectQuery.toString())) {
+                String selectQuery =
+                        "SELECT * FROM " +
+                                escape("ENTRY") +
+                                " WHERE " +
+                                escape("SHARED_ID") +
+                                " = ?";
+
+                try (PreparedStatement preparedSelectStatement = connection.prepareStatement(selectQuery)) {
                     preparedSelectStatement.setInt(1, sharedID);
                     try (ResultSet resultSet = preparedSelectStatement.executeQuery()) {
                         if (resultSet.next()) {
@@ -420,63 +421,57 @@ public void removeEntry(BibEntry bibEntry) {
      * @return instance of {@link BibEntry}
      */
     public Optional<BibEntry> getSharedEntry(int sharedID) {
-        List<BibEntry> sharedEntries = getSharedEntryList(sharedID);
+        List<BibEntry> sharedEntries = getSharedEntries(Collections.singletonList(sharedID));
         if (!sharedEntries.isEmpty()) {
             return Optional.of(sharedEntries.get(0));
         }
         return Optional.empty();
     }
 
-    public List<BibEntry> getSharedEntries() {
-        return getSharedEntryList(0);
-    }
-
-    /**
-     * @param sharedID Entry ID. If 0, all entries are going to be fetched.
-     * @return List of {@link BibEntry} instances
-     */
-    private List<BibEntry> getSharedEntryList(int sharedID) {
+    public List<BibEntry> getSharedEntries(List<Integer> sharedIDs) {
         List<BibEntry> sharedEntries = new ArrayList<>();
 
-        StringBuilder selectEntryQuery = new StringBuilder();
-        selectEntryQuery.append("SELECT * FROM ");
-        selectEntryQuery.append(escape("ENTRY"));
-
-        if (sharedID != 0) {
-            selectEntryQuery.append(" WHERE ");
-            selectEntryQuery.append(escape("SHARED_ID"));
-            selectEntryQuery.append(" = ");
-            selectEntryQuery.append(sharedID);
+        StringBuilder query = new StringBuilder();
+        query.append("SELECT ")
+             .append(escape("ENTRY")).append(".").append(escape("SHARED_ID")).append(", ")
+             .append(escape("ENTRY")).append(".").append(escape("TYPE")).append(", ")
+             .append(escape("ENTRY")).append(".").append(escape("VERSION")).append(", ")
+             .append("F.").append(escape("ENTRY_SHARED_ID")).append(", ")
+             .append("F.").append(escape("NAME")).append(", ")
+             .append("F.").append(escape("VALUE"))
+             .append(" FROM ")
+             .append(escape("ENTRY"))
+             .append(" inner join ")
+             .append(escape("FIELD"))
+             .append(" F on ")
+             .append(escape("ENTRY")).append(".").append(escape("SHARED_ID"))
+             .append(" = F.").append(escape("ENTRY_SHARED_ID"));
+
+        if (!sharedIDs.isEmpty()) {
+            String idListAsString = sharedIDs.stream().map(String::valueOf).collect(Collectors.joining(", "));
+            query.append(" where ")
+                 .append(escape("SHARED_ID")).append(" in (")
+                 .append(idListAsString)
+                 .append(")");
         }
+        query.append(" order by ")
+             .append(escape("SHARED_ID"))
+             .append(";");
 
-        selectEntryQuery.append(" ORDER BY ");
-        selectEntryQuery.append(escape("SHARED_ID"));
-
-        try (ResultSet selectEntryResultSet = connection.createStatement().executeQuery(selectEntryQuery.toString())) {
+        try (ResultSet selectEntryResultSet = connection.createStatement().executeQuery(query.toString())) {
+            BibEntry bibEntry = null;
+            int lastId = -1;
             while (selectEntryResultSet.next()) {
-                BibEntry bibEntry = new BibEntry();
-                // setting the base attributes once
-                bibEntry.getSharedBibEntryData().setSharedID(selectEntryResultSet.getInt("SHARED_ID"));
-                bibEntry.setType(selectEntryResultSet.getString("TYPE"));
-                bibEntry.getSharedBibEntryData().setVersion(selectEntryResultSet.getInt("VERSION"));
-
-                StringBuilder selectFieldQuery = new StringBuilder()
-                    .append("SELECT * FROM ")
-                    .append(escape("FIELD"))
-                    .append(" WHERE ")
-                    .append(escape("ENTRY_SHARED_ID"))
-                    .append(" = ?");
-
-                try (PreparedStatement preparedSelectFieldStatement = connection.prepareStatement(selectFieldQuery.toString())) {
-                    preparedSelectFieldStatement.setInt(1, selectEntryResultSet.getInt("SHARED_ID"));
-                    try (ResultSet selectFieldResultSet = preparedSelectFieldStatement.executeQuery()) {
-                        while (selectFieldResultSet.next()) {
-                            bibEntry.setField(selectFieldResultSet.getString("NAME"),
-                                    Optional.ofNullable(selectFieldResultSet.getString("VALUE")), EntryEventSource.SHARED);
-                        }
-                    }
+                if (selectEntryResultSet.getInt("SHARED_ID") > lastId) {
+                    bibEntry = new BibEntry();
+                    bibEntry.getSharedBibEntryData().setSharedID(selectEntryResultSet.getInt("SHARED_ID"));
+                    bibEntry.setType(selectEntryResultSet.getString("TYPE"));
+                    bibEntry.getSharedBibEntryData().setVersion(selectEntryResultSet.getInt("VERSION"));
+                    sharedEntries.add(bibEntry);
+                    lastId = selectEntryResultSet.getInt("SHARED_ID");
                 }
-                sharedEntries.add(bibEntry);
+
+                bibEntry.setField(selectEntryResultSet.getString("NAME"), Optional.ofNullable(selectEntryResultSet.getString("VALUE")), EntryEventSource.SHARED);
             }
         } catch (SQLException e) {
             LOGGER.error("SQL Error", e);
@@ -485,6 +480,10 @@ private List<BibEntry> getSharedEntryList(int sharedID) {
         return sharedEntries;
     }
 
+    public List<BibEntry> getSharedEntries() {
+        return getSharedEntries(Collections.emptyList());
+    }
+
     /**
      * Retrieves a mapping between the columns SHARED_ID and VERSION.
      */
diff --git a/src/main/java/org/jabref/logic/shared/DBMSSynchronizer.java b/src/main/java/org/jabref/logic/shared/DBMSSynchronizer.java
index 64ede9203ba..94edfe1c93d 100644
--- a/src/main/java/org/jabref/logic/shared/DBMSSynchronizer.java
+++ b/src/main/java/org/jabref/logic/shared/DBMSSynchronizer.java
@@ -2,6 +2,7 @@
 
 import java.sql.Connection;
 import java.sql.SQLException;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
@@ -147,7 +148,7 @@ public void initializeDatabases() throws DatabaseNotSupportedException {
 
                 // This check should only be performed once on initial database setup.
                 // Calling dbmsProcessor.setupSharedDatabase() lets dbmsProcessor.checkBaseIntegrity() be true.
-                if (dbmsProcessor.checkForPre3Dot6Intergrity()) {
+                if (dbmsProcessor.checkForPare3Dot6Integrity()) {
                     throw new DatabaseNotSupportedException();
                 }
             }
@@ -175,7 +176,7 @@ public void synchronizeLocalDatabase() {
 
         // remove old entries locally
         removeNotSharedEntries(localEntries, idVersionMap.keySet());
-
+        List<Integer> entriesToDrag = new ArrayList<>();
         // compare versions and update local entry if needed
         for (Map.Entry<Integer, Integer> idVersionEntry : idVersionMap.entrySet()) {
             boolean match = false;
@@ -205,12 +206,13 @@ public void synchronizeLocalDatabase() {
                 }
             }
             if (!match) {
-                Optional<BibEntry> bibEntry = dbmsProcessor.getSharedEntry(idVersionEntry.getKey());
-                if (bibEntry.isPresent()) {
-                    bibDatabase.insertEntry(bibEntry.get(), EntryEventSource.SHARED);
-                }
+                entriesToDrag.add(idVersionEntry.getKey());
             }
         }
+
+        for (BibEntry bibEntry : dbmsProcessor.getSharedEntries(entriesToDrag)) {
+            bibDatabase.insertEntry(bibEntry, EntryEventSource.SHARED);
+        }
     }
 
     /**
@@ -322,10 +324,10 @@ public void pullChanges() {
     }
 
     /**
-     *  Checks whether the current SQL connection is valid.
-     *  In case that the connection is not valid a new {@link ConnectionLostEvent} is going to be sent.
+     * Checks whether the current SQL connection is valid.
+     * In case that the connection is not valid a new {@link ConnectionLostEvent} is going to be sent.
      *
-     *  @return <code>true</code> if the connection is valid, else <code>false</code>.
+     * @return <code>true</code> if the connection is valid, else <code>false</code>.
      */
     public boolean checkCurrentConnection() {
         try {
diff --git a/src/test/java/org/jabref/logic/shared/DBMSProcessorTest.java b/src/test/java/org/jabref/logic/shared/DBMSProcessorTest.java
index 1d84949752b..088ff3c9988 100644
--- a/src/test/java/org/jabref/logic/shared/DBMSProcessorTest.java
+++ b/src/test/java/org/jabref/logic/shared/DBMSProcessorTest.java
@@ -113,6 +113,24 @@ void testUpdateEntry(DBMSType dbmsType, DBMSConnection dbmsConnection, DBMSProce
         assertEquals(expectedEntry, actualEntryOptional.get());
     }
 
+    @ParameterizedTest
+    @MethodSource("getTestingDatabaseSystems")
+    void testGetEntriesByIdList(DBMSType dbmsType, DBMSConnection dbmsConnection, DBMSProcessor dbmsProcessor) throws OfflineLockException, SQLException {
+        dbmsProcessor.setupSharedDatabase();
+        BibEntry firstEntry = getBibEntryExample();
+        firstEntry.setId("1");
+        BibEntry secondEntry = getBibEntryExample();
+        secondEntry.setId("2");
+
+        dbmsProcessor.insertEntry(firstEntry);
+        dbmsProcessor.insertEntry(secondEntry);
+
+        List<BibEntry> sharedEntriesByIdList = dbmsProcessor.getSharedEntries(Arrays.asList(1, 2));
+
+        assertEquals(firstEntry.getId(), sharedEntriesByIdList.get(0).getId());
+        assertEquals(secondEntry.getId(), sharedEntriesByIdList.get(1).getId());
+    }
+
     @ParameterizedTest
     @MethodSource("getTestingDatabaseSystems")
     void testUpdateNewerEntry(DBMSType dbmsType, DBMSConnection dbmsConnection, DBMSProcessor dbmsProcessor) throws OfflineLockException, SQLException {

From 74de6b8c8b3876304ab7254d37d68a89f1d4b03a Mon Sep 17 00:00:00 2001
From: Samiya Caur <36728314+samiyac@users.noreply.github.com>
Date: Wed, 13 Mar 2019 00:52:12 +0530
Subject: [PATCH 114/184] Changes the title of Group Dialog to Add subgroup
 when adding a new subgroup (#4757)

---
 CHANGELOG.md                                         | 1 +
 src/main/java/org/jabref/gui/groups/GroupDialog.java | 7 ++++++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4efb45787a6..93ba052512e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -56,6 +56,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added additional modifiers (capitalize, titlecase and sentencecase) to the Bibtex key generator. [#1506](https://github.com/JabRef/jabref/issues/1506)
 - We grouped the toolbar icons and changed the Open Library and Copy icons. [#4584](https://github.com/JabRef/jabref/issues/4584) 
 - We added a browse button next to the path text field for aux-based groups. [#4586](https://github.com/JabRef/jabref/issues/4586)
+- We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
 
 
 ### Fixed
diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
index 9859213c926..94c9f519fa7 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDialog.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -128,7 +128,12 @@ class GroupDialog extends BaseDialog<AbstractGroup> {
      *                    created.
      */
     public GroupDialog(DialogService dialogService, BasePanel basePanel, JabRefPreferences prefs, AbstractGroup editedGroup) {
-        this.setTitle(Localization.lang("Edit group"));
+
+        if (editedGroup == null) {
+            this.setTitle(Localization.lang("Add subgroup"));
+        } else {
+            this.setTitle(Localization.lang("Edit group"));
+        }
 
         explicitRadioButton.setSelected(true);
 

From 930fa4efb4d59b021b69321aaff164010f081c51 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 12 Mar 2019 21:47:15 +0100
Subject: [PATCH 115/184] Rework external changes dialog in JavaFX (#4693)

* Rework external changes dialog in JavaFX

* fix exception by running in FX thread

* Fix appearance

* Improve display
---
 src/main/java/org/jabref/gui/BasePanel.java   |  26 +--
 .../java/org/jabref/gui/SidePaneManager.java  |   2 -
 .../java/org/jabref/gui/SidePaneType.java     |   4 +-
 .../gui/collab/ChangeDisplayDialog.java       | 194 ++++++------------
 .../org/jabref/gui/collab/ChangeScanner.java  | 124 +++--------
 .../jabref/gui/collab/ChangeViewModel.java    |  67 ------
 .../gui/collab/DatabaseChangeListener.java    |   7 +
 .../gui/collab/DatabaseChangeMonitor.java     | 119 +++--------
 .../jabref/gui/collab/DatabaseChangePane.java |  46 +++++
 .../gui/collab/DatabaseChangeViewModel.java   |  49 +++++
 .../gui/collab/EntryAddChangeViewModel.java   |  33 +--
 .../gui/collab/EntryChangeViewModel.java      | 119 +++++------
 .../collab/EntryDeleteChangeViewModel.java    |  32 +--
 .../jabref/gui/collab/FileUpdatePanel.java    | 129 ------------
 .../gui/collab/GroupChangeViewModel.java      |  43 ++--
 .../java/org/jabref/gui/collab/InfoPane.java  |  23 ---
 .../gui/collab/MetaDataChangeViewModel.java   |  22 +-
 .../gui/collab/PreambleChangeViewModel.java   |  62 +++---
 .../gui/collab/StringAddChangeViewModel.java  |  51 ++---
 .../gui/collab/StringChangeViewModel.java     |  68 +++---
 .../gui/collab/StringNameChangeViewModel.java |  37 +---
 .../collab/StringRemoveChangeViewModel.java   |  42 ++--
 .../logic/bibtex/comparator/PreambleDiff.java |  12 +-
 src/main/resources/l10n/JabRef_en.properties  |  15 +-
 24 files changed, 431 insertions(+), 895 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/collab/ChangeViewModel.java
 create mode 100644 src/main/java/org/jabref/gui/collab/DatabaseChangeListener.java
 create mode 100644 src/main/java/org/jabref/gui/collab/DatabaseChangePane.java
 create mode 100644 src/main/java/org/jabref/gui/collab/DatabaseChangeViewModel.java
 delete mode 100644 src/main/java/org/jabref/gui/collab/FileUpdatePanel.java
 delete mode 100644 src/main/java/org/jabref/gui/collab/InfoPane.java

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index 89d54058434..ea88315f304 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -41,7 +41,7 @@
 import org.jabref.gui.autocompleter.PersonNameSuggestionProvider;
 import org.jabref.gui.autocompleter.SuggestionProviders;
 import org.jabref.gui.collab.DatabaseChangeMonitor;
-import org.jabref.gui.collab.FileUpdatePanel;
+import org.jabref.gui.collab.DatabaseChangePane;
 import org.jabref.gui.desktop.JabRefDesktop;
 import org.jabref.gui.edit.ReplaceStringAction;
 import org.jabref.gui.entryeditor.EntryEditor;
@@ -116,6 +116,7 @@ public class BasePanel extends StackPane {
 
     private final BibDatabaseContext bibDatabaseContext;
     private final MainTableDataModel tableModel;
+    private final DatabaseChangePane changePane;
 
     private final CitationStyleCache citationStyleCache;
     private final FileAnnotationCache annotationCache;
@@ -189,7 +190,9 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         Optional<File> file = bibDatabaseContext.getDatabaseFile();
         if (file.isPresent()) {
             // Register so we get notifications about outside changes to the file.
-            changeMonitor = Optional.of(new DatabaseChangeMonitor(bibDatabaseContext, Globals.getFileUpdateMonitor(), this));
+            changeMonitor = Optional.of(new DatabaseChangeMonitor(bibDatabaseContext, Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR));
+            changePane = new DatabaseChangePane(mainTable.getPane(), bibDatabaseContext, changeMonitor.get());
+            getChildren().add(changePane);
         } else {
             if (bibDatabaseContext.getDatabase().hasEntries()) {
                 // if the database is not empty and no file is assigned,
@@ -197,6 +200,7 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
                 // -> mark as changed
                 this.baseChanged = true;
             }
+            changePane = null;
         }
 
         this.getDatabase().registerListener(new UpdateTimestampListener(Globals.prefs));
@@ -1098,14 +1102,6 @@ private void saveDividerLocation(Number position) {
      */
     public void cleanUp() {
         changeMonitor.ifPresent(DatabaseChangeMonitor::unregister);
-
-        // Check if there is a FileUpdatePanel for this BasePanel being shown. If so remove it:
-        if (sidePaneManager.isComponentVisible(SidePaneType.FILE_UPDATE_NOTIFICATION)) {
-            FileUpdatePanel fup = (FileUpdatePanel) sidePaneManager.getComponent(SidePaneType.FILE_UPDATE_NOTIFICATION);
-            if (fup.getPanel() == this) {
-                sidePaneManager.hide(SidePaneType.FILE_UPDATE_NOTIFICATION);
-            }
-        }
     }
 
     /**
@@ -1122,10 +1118,6 @@ public BibDatabaseContext getBibDatabaseContext() {
         return this.bibDatabaseContext;
     }
 
-    public boolean isUpdatedExternally() {
-        return changeMonitor.map(DatabaseChangeMonitor::hasBeenModifiedExternally).orElse(false);
-    }
-
     public void markExternalChangesAsResolved() {
         changeMonitor.ifPresent(DatabaseChangeMonitor::markExternalChangesAsResolved);
     }
@@ -1210,17 +1202,13 @@ public FileAnnotationCache getAnnotationCache() {
 
     public void resetChangeMonitor() {
         changeMonitor.ifPresent(DatabaseChangeMonitor::unregister);
-        changeMonitor = Optional.of(new DatabaseChangeMonitor(bibDatabaseContext, Globals.getFileUpdateMonitor(), this));
+        changeMonitor = Optional.of(new DatabaseChangeMonitor(bibDatabaseContext, Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR));
     }
 
     public void updateTimeStamp() {
         changeMonitor.ifPresent(DatabaseChangeMonitor::markAsSaved);
     }
 
-    public Path getTempFile() {
-        return changeMonitor.map(DatabaseChangeMonitor::getTempFile).orElse(null);
-    }
-
     public void copy() {
         mainTable.copy();
     }
diff --git a/src/main/java/org/jabref/gui/SidePaneManager.java b/src/main/java/org/jabref/gui/SidePaneManager.java
index 173a11a07c3..324810dd6ed 100644
--- a/src/main/java/org/jabref/gui/SidePaneManager.java
+++ b/src/main/java/org/jabref/gui/SidePaneManager.java
@@ -8,7 +8,6 @@
 import java.util.stream.Stream;
 
 import org.jabref.Globals;
-import org.jabref.gui.collab.FileUpdatePanel;
 import org.jabref.gui.groups.GroupSidePane;
 import org.jabref.gui.importer.fetcher.WebSearchPane;
 import org.jabref.gui.openoffice.OpenOfficeSidePanel;
@@ -31,7 +30,6 @@ public SidePaneManager(JabRefPreferences preferences, JabRefFrame frame) {
 
         OpenOfficePreferences openOfficePreferences = preferences.getOpenOfficePreferences();
         Stream.of(
-                new FileUpdatePanel(this),
                 new GroupSidePane(this, preferences, frame.getDialogService()),
                 new WebSearchPane(this, preferences, frame),
                 new OpenOfficeSidePanel(this, preferences, frame))
diff --git a/src/main/java/org/jabref/gui/SidePaneType.java b/src/main/java/org/jabref/gui/SidePaneType.java
index cd60411cf61..01cec0cedb1 100644
--- a/src/main/java/org/jabref/gui/SidePaneType.java
+++ b/src/main/java/org/jabref/gui/SidePaneType.java
@@ -4,5 +4,7 @@
  * Definition of all possible components in the side pane.
  */
 public enum SidePaneType {
-    OPEN_OFFICE, WEB_SEARCH, FILE_UPDATE_NOTIFICATION, GROUPS
+    OPEN_OFFICE,
+    WEB_SEARCH,
+    GROUPS
 }
diff --git a/src/main/java/org/jabref/gui/collab/ChangeDisplayDialog.java b/src/main/java/org/jabref/gui/collab/ChangeDisplayDialog.java
index ff67d3e19bb..1a522953e24 100644
--- a/src/main/java/org/jabref/gui/collab/ChangeDisplayDialog.java
+++ b/src/main/java/org/jabref/gui/collab/ChangeDisplayDialog.java
@@ -1,145 +1,81 @@
 package org.jabref.gui.collab;
 
-import java.awt.BorderLayout;
-import java.awt.Insets;
-import java.util.Collections;
-import java.util.Enumeration;
+import java.util.List;
+
+import javafx.collections.FXCollections;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.Label;
+import javafx.scene.control.ListView;
+import javafx.scene.control.ScrollPane;
+import javafx.scene.control.SplitPane;
+import javafx.scene.layout.BorderPane;
 
-import javax.swing.BorderFactory;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComponent;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
-import javax.swing.JTree;
-import javax.swing.event.TreeSelectionEvent;
-import javax.swing.event.TreeSelectionListener;
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.JabRefDialog;
 import org.jabref.gui.undo.NamedCompound;
+import org.jabref.gui.util.BaseDialog;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
-
-class ChangeDisplayDialog extends JabRefDialog implements TreeSelectionListener {
-
-    private final JTree tree;
-    private final JPanel infoPanel = new JPanel();
-    private final JCheckBox cb = new JCheckBox(Localization.lang("Accept change"));
-    private final JLabel rootInfo = new JLabel(Localization.lang("Select the tree nodes to view and accept or reject changes") + '.');
-    private ChangeViewModel selected;
-    private JComponent infoShown;
-    private boolean okPressed;
-
-    public ChangeDisplayDialog(final BasePanel panel,
-                               BibDatabase secondary, final DefaultMutableTreeNode root) {
-        super(Localization.lang("External changes"), true, ChangeDisplayDialog.class);
-        BibDatabase localSecondary;
-
-        // Just to be sure, put in an empty secondary base if none is given:
-        if (secondary == null) {
-            localSecondary = new BibDatabase();
-        } else {
-            localSecondary = secondary;
-        }
-        tree = new JTree(root);
-        tree.addTreeSelectionListener(this);
-
-        JSplitPane pane = new JSplitPane();
-        pane.setLeftComponent(new JScrollPane(tree));
-        JPanel infoBorder = new JPanel();
-        pane.setRightComponent(infoBorder);
-
-        cb.setMargin(new Insets(2, 2, 2, 2));
-        cb.setEnabled(false);
-        infoPanel.setLayout(new BorderLayout());
-        infoBorder.setLayout(new BorderLayout());
-        infoBorder.setBorder(BorderFactory.createEtchedBorder());
-        infoBorder.add(infoPanel, BorderLayout.CENTER);
-        setInfo(rootInfo);
-        infoPanel.add(cb, BorderLayout.SOUTH);
-
-        JButton ok = new JButton(Localization.lang("OK"));
-        JPanel buttonPanel = new JPanel();
-        buttonPanel.add(ok);
-        JButton cancel = new JButton(Localization.lang("Cancel"));
-        buttonPanel.add(cancel);
-
-        getContentPane().add(pane, BorderLayout.CENTER);
-        getContentPane().add(buttonPanel, BorderLayout.SOUTH);
+import org.jabref.model.database.BibDatabaseContext;
+
+import org.fxmisc.easybind.EasyBind;
+
+class ChangeDisplayDialog extends BaseDialog<Boolean> {
+
+    private final ListView<DatabaseChangeViewModel> tree;
+    private final BorderPane infoPanel = new BorderPane();
+    private final CheckBox cb = new CheckBox(Localization.lang("Accept change"));
+
+    public ChangeDisplayDialog(BibDatabaseContext database, List<DatabaseChangeViewModel> changes) {
+        this.setTitle(Localization.lang("External changes"));
+        this.getDialogPane().setPrefSize(800, 600);
+
+        tree = new ListView<>(FXCollections.observableArrayList(changes));
+        tree.setPrefWidth(190);
+        EasyBind.subscribe(tree.getSelectionModel().selectedItemProperty(), this::selectedChangeChanged);
+
+        SplitPane pane = new SplitPane();
+        pane.setDividerPositions(0.25);
+        pane.getItems().addAll(new ScrollPane(tree), infoPanel);
+        getDialogPane().setContent(pane);
+
+        infoPanel.setBottom(cb);
+        Label rootInfo = new Label(Localization.lang("Select the tree nodes to view and accept or reject changes") + '.');
+        infoPanel.setCenter(rootInfo);
+
+        getDialogPane().getButtonTypes().setAll(
+                new ButtonType(Localization.lang("Accept changes"), ButtonBar.ButtonData.APPLY),
+                ButtonType.CANCEL
+        );
+
+        setResultConverter(button -> {
+            if (button == ButtonType.CANCEL) {
+                return false;
+            } else {
+                // Perform all accepted changes
+                NamedCompound ce = new NamedCompound(Localization.lang("Merged external changes"));
+                for (DatabaseChangeViewModel change : changes) {
+                    if (change.isAccepted()) {
+                        change.makeChange(database, ce);
+                    }
+                }
+                ce.end();
+                //TODO: panel.getUndoManager().addEdit(ce);
 
-        cb.addChangeListener(e -> {
-            if (selected != null) {
-                selected.setAccepted(cb.isSelected());
+                return true;
             }
         });
 
-        cancel.addActionListener(e -> dispose());
-
-        ok.addActionListener(e -> {
-
-            // Perform all accepted changes:
-            // Store all edits in an Undoable object:
-            NamedCompound ce = new NamedCompound(Localization.lang("Merged external changes"));
-            Enumeration<ChangeViewModel> enumer = root.children();
-            boolean anyDisabled = false;
-            for (ChangeViewModel c : Collections.list(enumer)) {
-                boolean allAccepted = false;
-                if (c.isAcceptable() && c.isAccepted()) {
-                    allAccepted = c.makeChange(panel, localSecondary, ce);
-                }
-
-                if (!allAccepted) {
-                    anyDisabled = true;
-                }
-            }
-            ce.end();
-            panel.getUndoManager().addEdit(ce);
-            if (anyDisabled) {
-                panel.markBaseChanged();
+        EasyBind.subscribe(cb.selectedProperty(), selected -> {
+            if (selected != null && tree.getSelectionModel().getSelectedItem() != null) {
+                tree.getSelectionModel().getSelectedItem().setAccepted(selected);
             }
-            panel.markExternalChangesAsResolved();
-            dispose();
-            okPressed = true;
         });
-
-        pack();
-    }
-
-    public boolean isOkPressed() {
-        return okPressed;
-    }
-
-    private void setInfo(JComponent comp) {
-        if (infoShown != null) {
-            infoPanel.remove(infoShown);
-        }
-        infoShown = comp;
-        infoPanel.add(infoShown, BorderLayout.CENTER);
-        infoPanel.revalidate();
-        infoPanel.repaint();
     }
 
-    /**
-     * valueChanged
-     *
-     * @param e TreeSelectionEvent
-     */
-    @Override
-    public void valueChanged(TreeSelectionEvent e) {
-        Object o = tree.getLastSelectedPathComponent();
-        if (o instanceof ChangeViewModel) {
-            selected = (ChangeViewModel) o;
-            setInfo(selected.description());
-            cb.setSelected(selected.isAccepted());
-            cb.setEnabled(selected.isAcceptable());
-        } else {
-            setInfo(rootInfo);
-            selected = null;
-            cb.setEnabled(false);
+    private void selectedChangeChanged(DatabaseChangeViewModel currentChange) {
+        if (currentChange != null) {
+            infoPanel.setCenter(currentChange.description());
+            cb.setSelected(currentChange.isAccepted());
         }
     }
 }
diff --git a/src/main/java/org/jabref/gui/collab/ChangeScanner.java b/src/main/java/org/jabref/gui/collab/ChangeScanner.java
index 7fb1b74e388..021a941c87f 100644
--- a/src/main/java/org/jabref/gui/collab/ChangeScanner.java
+++ b/src/main/java/org/jabref/gui/collab/ChangeScanner.java
@@ -1,68 +1,33 @@
 package org.jabref.gui.collab;
 
-import java.io.IOException;
 import java.nio.file.Path;
+import java.util.ArrayList;
 import java.util.Comparator;
 import java.util.List;
 import java.util.Optional;
 
-import javax.swing.SwingUtilities;
-import javax.swing.tree.DefaultMutableTreeNode;
-
 import org.jabref.Globals;
-import org.jabref.JabRefExecutorService;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.JabRefFrame;
 import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.bibtex.comparator.BibDatabaseDiff;
 import org.jabref.logic.bibtex.comparator.BibEntryDiff;
 import org.jabref.logic.bibtex.comparator.BibStringDiff;
-import org.jabref.logic.exporter.AtomicFileWriter;
-import org.jabref.logic.exporter.BibDatabaseWriter;
-import org.jabref.logic.exporter.BibtexDatabaseWriter;
-import org.jabref.logic.exporter.SavePreferences;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.OpenDatabase;
 import org.jabref.logic.importer.ParserResult;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibtexString;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class ChangeScanner implements Runnable {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(ChangeScanner.class);
+public class ChangeScanner {
 
-    private final Optional<Path> file;
-    private final Path tempFile;
-    private final BibDatabaseContext databaseInMemory;
+    private final Path referenceFile;
+    private final BibDatabaseContext database;
+    private final List<DatabaseChangeViewModel> changes = new ArrayList<>();
+    private BibDatabaseContext referenceDatabase;
 
-    private final BasePanel panel;
-    private final JabRefFrame frame;
-    private BibDatabaseContext databaseInTemp;
-
-    /**
-     * We create an ArrayList to hold the changes we find. These will be added in the form
-     * of UndoEdit objects. We instantiate these so that the changes found in the file on disk
-     * can be reproduced in memory by calling redo() on them. REDO, not UNDO!
-     */
-    private final DefaultMutableTreeNode changes = new DefaultMutableTreeNode(Localization.lang("External changes"));
-
-    //  NamedCompound edit = new NamedCompound("Merged external changes")
-
-    public ChangeScanner(JabRefFrame frame, BasePanel bp, Path file, Path tempFile) {
-        this.panel = bp;
-        this.frame = frame;
-        this.databaseInMemory = bp.getBibDatabaseContext();
-        this.file = Optional.ofNullable(file);
-        this.tempFile = tempFile;
-    }
-
-    public boolean changesFound() {
-        return changes.getChildCount() > 0;
+    public ChangeScanner(BibDatabaseContext database, Path referenceFile) {
+        this.database = database;
+        this.referenceFile = referenceFile;
     }
 
     /**
@@ -75,101 +40,58 @@ private static BibEntry bestFit(BibEntry targetEntry, List<BibEntry> entries) {
                       .orElse(null);
     }
 
-    public void displayResult(final DisplayResultCallback fup) {
-        if (changes.getChildCount() > 0) {
-            SwingUtilities.invokeLater(() -> {
-                ChangeDisplayDialog changeDialog = new ChangeDisplayDialog(panel, databaseInTemp.getDatabase(), changes);
-                changeDialog.setVisible(true);
-                fup.scanResultsResolved(changeDialog.isOkPressed());
-                if (changeDialog.isOkPressed()) {
-                    // Overwrite the temp database:
-                    storeTempDatabase();
-                }
-            });
-        } else {
-            frame.getDialogService().showInformationDialogAndWait(Localization.lang("External changes"),
-                                                                  Localization.lang("No actual changes found."));
-
-            fup.scanResultsResolved(true);
-        }
-    }
-
-    private void storeTempDatabase() {
-        JabRefExecutorService.INSTANCE.execute(() -> {
-            try {
-                SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences()
-                                                     .withMakeBackup(false)
-                                                     .withEncoding(panel.getBibDatabaseContext()
-                                                                        .getMetaData()
-                                                                        .getEncoding()
-                                                                        .orElse(Globals.prefs.getDefaultEncoding()));
-
-                BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(new AtomicFileWriter(tempFile, prefs.getEncoding()), prefs);
-                databaseWriter.saveDatabase(databaseInTemp);
-            } catch (IOException ex) {
-                LOGGER.warn("Problem updating tmp file after accepting external changes", ex);
-            }
-        });
-    }
-
-    @Override
-    public void run() {
-        file.ifPresent(diskdb -> {
+    public List<DatabaseChangeViewModel> scanForChanges() {
+        database.getDatabasePath().ifPresent(diskdb -> {
             // Parse the temporary file.
             ImportFormatPreferences importFormatPreferences = Globals.prefs.getImportFormatPreferences();
-            ParserResult result = OpenDatabase.loadDatabase(tempFile.toAbsolutePath().toString(), importFormatPreferences, Globals.getFileUpdateMonitor());
-            databaseInTemp = result.getDatabaseContext();
+            ParserResult result = OpenDatabase.loadDatabase(referenceFile.toAbsolutePath().toString(), importFormatPreferences, Globals.getFileUpdateMonitor());
+            referenceDatabase = result.getDatabaseContext();
 
             // Parse the modified file.
             result = OpenDatabase.loadDatabase(diskdb.toAbsolutePath().toString(), importFormatPreferences, Globals.getFileUpdateMonitor());
             BibDatabaseContext databaseOnDisk = result.getDatabaseContext();
 
             // Start looking at changes.
-            BibDatabaseDiff differences = BibDatabaseDiff.compare(databaseInTemp, databaseOnDisk);
+            BibDatabaseDiff differences = BibDatabaseDiff.compare(referenceDatabase, databaseOnDisk);
             differences.getMetaDataDifferences().ifPresent(diff -> {
                 changes.add(new MetaDataChangeViewModel(diff));
                 diff.getGroupDifferences().ifPresent(groupDiff -> changes.add(new GroupChangeViewModel(groupDiff)));
             });
-            differences.getPreambleDifferences().ifPresent(diff -> changes.add(new PreambleChangeViewModel(databaseInMemory.getDatabase().getPreamble().orElse(""), diff)));
+            differences.getPreambleDifferences().ifPresent(diff -> changes.add(new PreambleChangeViewModel(diff)));
             differences.getBibStringDifferences().forEach(diff -> changes.add(createBibStringDiff(diff)));
             differences.getEntryDifferences().forEach(diff -> changes.add(createBibEntryDiff(diff)));
         });
+        return changes;
     }
 
-    private ChangeViewModel createBibStringDiff(BibStringDiff diff) {
+    private DatabaseChangeViewModel createBibStringDiff(BibStringDiff diff) {
         if (diff.getOriginalString() == null) {
             return new StringAddChangeViewModel(diff.getNewString());
         }
 
         if (diff.getNewString() == null) {
-            Optional<BibtexString> current = databaseInMemory.getDatabase().getStringByName(diff.getOriginalString().getName());
+            Optional<BibtexString> current = database.getDatabase().getStringByName(diff.getOriginalString().getName());
             return new StringRemoveChangeViewModel(diff.getOriginalString(), current.orElse(null));
         }
 
         if (diff.getOriginalString().getName().equals(diff.getNewString().getName())) {
-            Optional<BibtexString> current = databaseInMemory.getDatabase().getStringByName(diff.getOriginalString().getName());
+            Optional<BibtexString> current = database.getDatabase().getStringByName(diff.getOriginalString().getName());
             return new StringChangeViewModel(current.orElse(null), diff.getOriginalString(), diff.getNewString().getContent());
         }
 
-        Optional<BibtexString> current = databaseInMemory.getDatabase().getStringByName(diff.getOriginalString().getName());
+        Optional<BibtexString> current = database.getDatabase().getStringByName(diff.getOriginalString().getName());
         return new StringNameChangeViewModel(current.orElse(null), diff.getOriginalString(), current.map(BibtexString::getName).orElse(""), diff.getNewString().getName());
     }
 
-    private ChangeViewModel createBibEntryDiff(BibEntryDiff diff) {
+    private DatabaseChangeViewModel createBibEntryDiff(BibEntryDiff diff) {
         if (diff.getOriginalEntry() == null) {
             return new EntryAddChangeViewModel(diff.getNewEntry());
         }
 
         if (diff.getNewEntry() == null) {
-            return new EntryDeleteChangeViewModel(bestFit(diff.getOriginalEntry(), databaseInMemory.getEntries()), diff.getOriginalEntry());
+            return new EntryDeleteChangeViewModel(bestFit(diff.getOriginalEntry(), database.getEntries()), diff.getOriginalEntry());
         }
 
-        return new EntryChangeViewModel(bestFit(diff.getOriginalEntry(), databaseInMemory.getEntries()), diff.getOriginalEntry(), diff.getNewEntry());
-    }
-
-    @FunctionalInterface
-    public interface DisplayResultCallback {
-
-        void scanResultsResolved(boolean resolved);
+        return new EntryChangeViewModel(bestFit(diff.getOriginalEntry(), database.getEntries()), diff.getOriginalEntry(), diff.getNewEntry());
     }
 }
diff --git a/src/main/java/org/jabref/gui/collab/ChangeViewModel.java b/src/main/java/org/jabref/gui/collab/ChangeViewModel.java
deleted file mode 100644
index 0561a799b24..00000000000
--- a/src/main/java/org/jabref/gui/collab/ChangeViewModel.java
+++ /dev/null
@@ -1,67 +0,0 @@
-package org.jabref.gui.collab;
-
-import javax.swing.JComponent;
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.model.database.BibDatabase;
-
-abstract class ChangeViewModel extends DefaultMutableTreeNode {
-
-    protected String name;
-    private boolean accepted = true;
-
-
-    ChangeViewModel() {
-        name = "";
-    }
-
-    ChangeViewModel(String name) {
-        this.name = name;
-    }
-
-    @Override
-    public String toString() {
-        return name;
-    }
-
-    public boolean isAccepted() {
-        return accepted;
-    }
-
-    public void setAccepted(boolean a) {
-        accepted = a;
-    }
-
-    /**
-     * This method is used to disable the "accept" box if the parent has been set to "not accepted".
-     * Thus the user can disable e.g. an entry change without having to disable all field changes.
-     * @return boolean false if the parent overrides by not being accepted.
-     */
-    public boolean isAcceptable() {
-        if ((getParent() != null) && (getParent() instanceof ChangeViewModel)) {
-            return ((ChangeViewModel) getParent()).isAccepted();
-        } else {
-            return true;
-        }
-    }
-
-    /**
-     * This method returns a JComponent detailing the nature of the change.
-     * @return JComponent
-     */
-    public abstract JComponent description();
-
-    /**
-     * Perform the change. This method is responsible for adding a proper undo edit to
-     * the NamedCompound, so the change can be undone.
-     * @param panel BasePanel The tab where the database lives.
-     * @param secondary BibDatabase The "tmp" database for which the change
-     *   should also be made.
-     * @param undoEdit NamedCompound The compound to hold the undo edits.
-     * @return true if all changes were made, false if not all were accepted.
-     */
-    public abstract boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit);
-
-}
diff --git a/src/main/java/org/jabref/gui/collab/DatabaseChangeListener.java b/src/main/java/org/jabref/gui/collab/DatabaseChangeListener.java
new file mode 100644
index 00000000000..cfb9ac2e1ff
--- /dev/null
+++ b/src/main/java/org/jabref/gui/collab/DatabaseChangeListener.java
@@ -0,0 +1,7 @@
+package org.jabref.gui.collab;
+
+import java.util.List;
+
+public interface DatabaseChangeListener {
+    void databaseChanged(List<DatabaseChangeViewModel> changes);
+}
diff --git a/src/main/java/org/jabref/gui/collab/DatabaseChangeMonitor.java b/src/main/java/org/jabref/gui/collab/DatabaseChangeMonitor.java
index 701679fed5f..2bf20a9b69d 100644
--- a/src/main/java/org/jabref/gui/collab/DatabaseChangeMonitor.java
+++ b/src/main/java/org/jabref/gui/collab/DatabaseChangeMonitor.java
@@ -3,14 +3,11 @@
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.Optional;
+import java.util.ArrayList;
+import java.util.List;
 
-import javax.swing.SwingUtilities;
-
-import org.jabref.JabRefExecutorService;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.SidePaneManager;
-import org.jabref.gui.SidePaneType;
+import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.util.FileUpdateListener;
@@ -24,25 +21,22 @@ public class DatabaseChangeMonitor implements FileUpdateListener {
 
     private final BibDatabaseContext database;
     private final FileUpdateMonitor fileMonitor;
-    private final BasePanel panel;
-    private boolean updatedExternally;
-    private Path tmpFile;
-    private long timeStamp;
-    private long fileSize;
+    private final List<DatabaseChangeListener> listeners;
+    private Path referenceFile;
+    private TaskExecutor taskExecutor;
 
-    public DatabaseChangeMonitor(BibDatabaseContext database, FileUpdateMonitor fileMonitor, BasePanel panel) {
+    public DatabaseChangeMonitor(BibDatabaseContext database, FileUpdateMonitor fileMonitor, TaskExecutor taskExecutor) {
         this.database = database;
         this.fileMonitor = fileMonitor;
-        this.panel = panel;
+        this.taskExecutor = taskExecutor;
+        this.listeners = new ArrayList<>();
 
         this.database.getDatabasePath().ifPresent(path -> {
             try {
                 fileMonitor.addListenerForFile(path, this);
-                timeStamp = Files.getLastModifiedTime(path).toMillis();
-                fileSize = Files.size(path);
-                tmpFile = Files.createTempFile("jabref", ".bib");
-                tmpFile.toFile().deleteOnExit();
-                copyToTemp(path);
+                referenceFile = Files.createTempFile("jabref", ".bib");
+                referenceFile.toFile().deleteOnExit();
+                setAsReference(path);
             } catch (IOException e) {
                 LOGGER.error("Error while trying to monitor " + path, e);
             }
@@ -51,93 +45,34 @@ public DatabaseChangeMonitor(BibDatabaseContext database, FileUpdateMonitor file
 
     @Override
     public void fileUpdated() {
-        if (panel.isSaving()) {
-            // We are just saving the file, so this message is most likely due to bad timing.
-            // If not, we'll handle it on the next polling.
-            return;
-        }
-
-        updatedExternally = true;
-
-        final ChangeScanner scanner = new ChangeScanner(panel.frame(), panel, database.getDatabasePath().orElse(null), tmpFile);
-        JabRefExecutorService.INSTANCE.executeInterruptableTaskAndWait(scanner);
-
-        // Adding the sidepane component is Swing work, so we must do this in the Swing
-        // thread:
-        Runnable t = () -> {
-
-            // Check if there is already a notification about external changes:
-            SidePaneManager sidePaneManager = panel.getSidePaneManager();
-            boolean hasAlready = sidePaneManager.isComponentVisible(SidePaneType.FILE_UPDATE_NOTIFICATION);
-            if (hasAlready) {
-                sidePaneManager.hide(SidePaneType.FILE_UPDATE_NOTIFICATION);
-            }
-
-            FileUpdatePanel component = (FileUpdatePanel) sidePaneManager.getComponent(SidePaneType.FILE_UPDATE_NOTIFICATION);
-            component.showForFile(panel, database.getDatabaseFile().orElse(null), scanner);
-        };
-
-        if (scanner.changesFound()) {
-            SwingUtilities.invokeLater(t);
-        } else {
-            updatedExternally = false;
-        }
+        // File on disk has changed, thus look for notable changes and notify listeners in case there are such changes
+        ChangeScanner scanner = new ChangeScanner(database, referenceFile);
+        BackgroundTask.wrap(scanner::scanForChanges)
+                      .onSuccess(changes -> {
+                          if (!changes.isEmpty()) {
+                              listeners.forEach(listener -> listener.databaseChanged(changes));
+                          }
+                      })
+                      .executeWith(taskExecutor);
     }
 
-    /**
-     * Forces a check on the file, and returns the result. Check if time stamp or the file size has changed.
-     *
-     * @return boolean true if the file has changed.
-     */
-    private boolean hasBeenModified() {
-        Optional<Path> file = database.getDatabasePath();
-        if (file.isPresent()) {
-            try {
-                long modified = Files.getLastModifiedTime(file.get()).toMillis();
-                if (modified == 0L) {
-                    // File deleted
-                    return false;
-                }
-                long fileSizeNow = Files.size(file.get());
-                return (timeStamp != modified) || (fileSize != fileSizeNow);
-            } catch (IOException ex) {
-                return false;
-            }
-        }
-        return false;
+    public void addListener(DatabaseChangeListener listener) {
+        listeners.add(listener);
     }
 
     public void unregister() {
         database.getDatabasePath().ifPresent(file -> fileMonitor.removeListener(file, this));
     }
 
-    public boolean hasBeenModifiedExternally() {
-        return updatedExternally || hasBeenModified();
-    }
-
     public void markExternalChangesAsResolved() {
-        updatedExternally = false;
         markAsSaved();
     }
 
     public void markAsSaved() {
-        database.getDatabasePath().ifPresent(file -> {
-            try {
-                timeStamp = Files.getLastModifiedTime(file).toMillis();
-                fileSize = Files.size(file);
-
-                copyToTemp(file);
-            } catch (IOException ex) {
-                LOGGER.error("Error while getting file information", ex);
-            }
-        });
-    }
-
-    private void copyToTemp(Path file) {
-        FileUtil.copyFile(file, tmpFile, true);
+        database.getDatabasePath().ifPresent(this::setAsReference);
     }
 
-    public Path getTempFile() {
-        return tmpFile;
+    private void setAsReference(Path file) {
+        FileUtil.copyFile(file, referenceFile, true);
     }
 }
diff --git a/src/main/java/org/jabref/gui/collab/DatabaseChangePane.java b/src/main/java/org/jabref/gui/collab/DatabaseChangePane.java
new file mode 100644
index 00000000000..17582a41ba9
--- /dev/null
+++ b/src/main/java/org/jabref/gui/collab/DatabaseChangePane.java
@@ -0,0 +1,46 @@
+package org.jabref.gui.collab;
+
+import java.util.List;
+
+import javafx.scene.Node;
+
+import org.jabref.gui.icon.IconTheme;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.BibDatabaseContext;
+
+import org.controlsfx.control.NotificationPane;
+import org.controlsfx.control.action.Action;
+
+public class DatabaseChangePane extends NotificationPane {
+
+    private final DatabaseChangeMonitor monitor;
+    private final BibDatabaseContext database;
+
+    public DatabaseChangePane(Node parent, BibDatabaseContext database, DatabaseChangeMonitor monitor) {
+        super(parent);
+        this.database = database;
+        this.monitor = monitor;
+
+        this.setGraphic(IconTheme.JabRefIcons.SAVE.getGraphicNode());
+        this.setText(Localization.lang("The library has been modified by another program."));
+
+        monitor.addListener(this::onDatabaseChanged);
+    }
+
+    private void onDatabaseChanged(List<DatabaseChangeViewModel> changes) {
+        this.getActions().setAll(
+                new Action(Localization.lang("Dismiss changes"), event -> {
+                    monitor.markExternalChangesAsResolved();
+                    this.hide();
+                }),
+                new Action(Localization.lang("Review changes"), event -> {
+                    ChangeDisplayDialog changeDialog = new ChangeDisplayDialog(database, changes);
+                    boolean changesHandled = changeDialog.showAndWait().orElse(false);
+                    if (changesHandled) {
+                        monitor.markExternalChangesAsResolved();
+                        this.hide();
+                    }
+                }));
+        this.show();
+    }
+}
diff --git a/src/main/java/org/jabref/gui/collab/DatabaseChangeViewModel.java b/src/main/java/org/jabref/gui/collab/DatabaseChangeViewModel.java
new file mode 100644
index 00000000000..88f4d200ed5
--- /dev/null
+++ b/src/main/java/org/jabref/gui/collab/DatabaseChangeViewModel.java
@@ -0,0 +1,49 @@
+package org.jabref.gui.collab;
+
+import javafx.scene.Node;
+
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.model.database.BibDatabaseContext;
+
+abstract class DatabaseChangeViewModel {
+
+    protected String name;
+    private boolean accepted = true;
+
+    DatabaseChangeViewModel() {
+        name = "";
+    }
+
+    DatabaseChangeViewModel(String name) {
+        this.name = name;
+    }
+
+    @Override
+    public String toString() {
+        return name;
+    }
+
+    public boolean isAccepted() {
+        return accepted;
+    }
+
+    public void setAccepted(boolean a) {
+        accepted = a;
+    }
+
+
+    /**
+     * This method returns a JComponent detailing the nature of the change.
+     * @return JComponent
+     */
+    public abstract Node description();
+
+    /**
+     * Performs the change. This method is responsible for adding a proper undo edit to
+     * the NamedCompound, so the change can be undone.
+     * @param database the database that should be modified accordingly.
+     * @param undoEdit NamedCompound The compound to hold the undo edits.
+     */
+    public abstract void makeChange(BibDatabaseContext database, NamedCompound undoEdit);
+
+}
diff --git a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
index 622dc4142cf..8284f544cab 100644
--- a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
@@ -1,49 +1,36 @@
 package org.jabref.gui.collab;
 
-import javax.swing.JComponent;
-
-import javafx.embed.swing.JFXPanel;
-import javafx.scene.Scene;
+import javafx.scene.Node;
 
 import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.FXDialogService;
 import org.jabref.gui.PreviewPanel;
-import org.jabref.gui.customjfx.CustomJFXPanel;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableInsertEntry;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.IdGenerator;
 
-class EntryAddChangeViewModel extends ChangeViewModel {
+class EntryAddChangeViewModel extends DatabaseChangeViewModel {
 
     private final BibEntry diskEntry;
-    private final JFXPanel container;
-
 
     public EntryAddChangeViewModel(BibEntry diskEntry) {
         super(Localization.lang("Added entry"));
         this.diskEntry = diskEntry;
-
-        PreviewPanel previewPanel = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
-        previewPanel.setEntry(diskEntry);
-        container = CustomJFXPanel.wrap(new Scene(previewPanel));
     }
 
     @Override
-    public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
-        diskEntry.setId(IdGenerator.next());
-        panel.getDatabase().insertEntry(diskEntry);
-        secondary.insertEntry(diskEntry);
-        undoEdit.addEdit(new UndoableInsertEntry(panel.getDatabase(), diskEntry));
-        return true;
+    public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
+        database.getDatabase().insertEntry(diskEntry);
+        undoEdit.addEdit(new UndoableInsertEntry(database.getDatabase(), diskEntry));
     }
 
     @Override
-    public JComponent description() {
-        return container;
+    public Node description() {
+        PreviewPanel previewPanel = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        previewPanel.setEntry(diskEntry);
+        return previewPanel;
     }
 }
diff --git a/src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java
index 7a63b4aed8f..fcad087163d 100644
--- a/src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java
@@ -1,38 +1,36 @@
 package org.jabref.gui.collab;
 
-import java.util.Collections;
-import java.util.Enumeration;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Optional;
 import java.util.Set;
 import java.util.TreeSet;
 
-import javax.swing.JComponent;
-import javax.swing.JLabel;
-import javax.swing.JScrollPane;
+import javafx.scene.Node;
+import javafx.scene.control.Label;
+import javafx.scene.layout.VBox;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-class EntryChangeViewModel extends ChangeViewModel {
+class EntryChangeViewModel extends DatabaseChangeViewModel {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(EntryChangeViewModel.class);
 
+    private final List<FieldChangeViewModel> fieldChanges = new ArrayList<>();
+
     public EntryChangeViewModel(BibEntry memEntry, BibEntry tmpEntry, BibEntry diskEntry) {
         super();
-        Optional<String> key = tmpEntry.getCiteKeyOptional();
-        if (key.isPresent()) {
-            name = Localization.lang("Modified entry") + ": '" + key.get() + '\'';
-        } else {
-            name = Localization.lang("Modified entry");
-        }
+        name = tmpEntry.getCiteKeyOptional()
+                       .map(key -> Localization.lang("Modified entry") + ": '" + key + '\'')
+                       .orElse(Localization.lang("Modified entry"));
 
         // We know that tmpEntry is not equal to diskEntry. Check if it has been modified
         // locally as well, since last tempfile was saved.
@@ -58,55 +56,48 @@ public EntryChangeViewModel(BibEntry memEntry, BibEntry tmpEntry, BibEntry diskE
             if ((tmp.isPresent()) && (disk.isPresent())) {
                 if (!tmp.equals(disk)) {
                     // Modified externally.
-                    add(new FieldChangeViewModel(field, memEntry, tmpEntry, mem.orElse(null), tmp.get(), disk.get()));
+                    fieldChanges.add(new FieldChangeViewModel(field, memEntry, tmpEntry, mem.orElse(null), tmp.get(), disk.get()));
                 }
             } else if (((!tmp.isPresent()) && (disk.isPresent()) && !disk.get().isEmpty())
                     || ((!disk.isPresent()) && (tmp.isPresent()) && !tmp.get().isEmpty()
                             && (mem.isPresent()) && !mem.get().isEmpty())) {
                 // Added externally.
-                add(new FieldChangeViewModel(field, memEntry, tmpEntry, mem.orElse(null), tmp.orElse(null),
-                        disk.orElse(null)));
+                fieldChanges.add(new FieldChangeViewModel(field, memEntry, tmpEntry, mem.orElse(null), tmp.orElse(null), disk.orElse(null)));
             }
         }
     }
 
     @Override
-    public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
-        boolean allAccepted = true;
-
-        Enumeration<ChangeViewModel> e = children();
-        for (ChangeViewModel c : Collections.list(e)) {
-            if (c.isAcceptable() && c.isAccepted()) {
-                c.makeChange(panel, secondary, undoEdit);
-            } else {
-                allAccepted = false;
+    public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
+        for (DatabaseChangeViewModel c : fieldChanges) {
+            if (c.isAccepted()) {
+                c.makeChange(database, undoEdit);
             }
         }
-
-        /*panel.database().removeEntry(memEntry.getId());
-        try {
-          diskEntry.setId(Util.next());
-        } catch (KeyCollisionException ex) {}
-        panel.database().removeEntry(memEntry.getId());*/
-
-        return allAccepted;
     }
 
     @Override
-    public JComponent description() {
-        return new JLabel(name);
+    public Node description() {
+        VBox container = new VBox();
+        Label header = new Label(name);
+        header.getStyleClass().add("sectionHeader");
+        container.getChildren().add(header);
+
+        for (FieldChangeViewModel change : fieldChanges) {
+            container.getChildren().add(change.description());
+        }
+
+        return container;
     }
 
-    static class FieldChangeViewModel extends ChangeViewModel {
+    static class FieldChangeViewModel extends DatabaseChangeViewModel {
 
         private final BibEntry entry;
         private final BibEntry tmpEntry;
         private final String field;
         private final String inMem;
+        private final String onTmp;
         private final String onDisk;
-        private final InfoPane tp = new InfoPane();
-        private final JScrollPane sp = new JScrollPane(tp);
-
 
         public FieldChangeViewModel(String field, BibEntry memEntry, BibEntry tmpEntry, String inMem, String onTmp, String onDisk) {
             super(field);
@@ -114,47 +105,39 @@ public FieldChangeViewModel(String field, BibEntry memEntry, BibEntry tmpEntry,
             this.tmpEntry = tmpEntry;
             this.field = field;
             this.inMem = inMem;
+            this.onTmp = onTmp;
             this.onDisk = onDisk;
-
-            StringBuilder text = new StringBuilder(36);
-            text.append("<FONT SIZE=10><H2>").append(Localization.lang("Modification of field"))
-                    .append(" <I>").append(field).append("</I></H2>");
-
-            if ((onDisk != null) && !onDisk.isEmpty()) {
-                text.append("<H3>").append(Localization.lang("Value set externally")).append(":</H3> ").append(onDisk);
-            } else {
-                text.append("<H3>").append(Localization.lang("Value cleared externally")).append("</H3>");
-            }
-
-            if ((inMem != null) && !inMem.isEmpty()) {
-                text.append("<H3>").append(Localization.lang("Current value")).append(":</H3> ").append(inMem);
-            }
-            if ((onTmp != null) && !onTmp.isEmpty()) {
-                text.append("<H3>").append(Localization.lang("Current tmp value")).append(":</H3> ").append(onTmp);
-            }
-            tp.setContentType("text/html");
-            tp.setText(text.toString());
         }
 
         @Override
-        public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
+        public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
             if (onDisk == null) {
                 entry.clearField(field);
             } else {
                 entry.setField(field, onDisk);
             }
             undoEdit.addEdit(new UndoableFieldChange(entry, field, inMem, onDisk));
-            if (onDisk == null) {
-                tmpEntry.clearField(field);
-            } else {
-                tmpEntry.setField(field, onDisk);
-            }
-            return true;
         }
 
         @Override
-        public JComponent description() {
-            return sp;
+        public Node description() {
+            VBox container = new VBox();
+            container.getChildren().add(new Label(Localization.lang("Modification of field") + " " + field));
+
+            if ((onDisk != null) && !onDisk.isEmpty()) {
+                container.getChildren().add(new Label(Localization.lang("Value set externally") + ": " + onDisk));
+            } else {
+                container.getChildren().add(new Label(Localization.lang("Value cleared externally")));
+            }
+
+            if ((inMem != null) && !inMem.isEmpty()) {
+                container.getChildren().add(new Label(Localization.lang("Current value") + ": " + inMem));
+            }
+            if ((onTmp != null) && !onTmp.isEmpty()) {
+                container.getChildren().add(new Label(Localization.lang("Current tmp value") + ": " + onTmp));
+            }
+
+            return container;
         }
 
     }
diff --git a/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
index 37511d67830..22f4c9a80b9 100644
--- a/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
@@ -1,35 +1,27 @@
 package org.jabref.gui.collab;
 
-import javax.swing.JComponent;
-
-import javafx.embed.swing.JFXPanel;
-import javafx.scene.Scene;
+import javafx.scene.Node;
 
 import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.FXDialogService;
 import org.jabref.gui.PreviewPanel;
-import org.jabref.gui.customjfx.CustomJFXPanel;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableRemoveEntry;
 import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-class EntryDeleteChangeViewModel extends ChangeViewModel {
+class EntryDeleteChangeViewModel extends DatabaseChangeViewModel {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(EntryDeleteChangeViewModel.class);
     private final BibEntry memEntry;
     private final BibEntry tmpEntry;
 
-    private final JFXPanel container;
-
-
     public EntryDeleteChangeViewModel(BibEntry memEntry, BibEntry tmpEntry) {
         super(Localization.lang("Deleted entry"));
         this.memEntry = memEntry;
@@ -44,22 +36,18 @@ public EntryDeleteChangeViewModel(BibEntry memEntry, BibEntry tmpEntry) {
 
         LOGGER.debug("Modified entry: " + memEntry.getCiteKeyOptional().orElse("<no BibTeX key set>")
                 + "\n Modified locally: " + isModifiedLocally);
-
-        PreviewPanel previewPanel = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
-        previewPanel.setEntry(memEntry);
-        container = CustomJFXPanel.wrap(new Scene(previewPanel));
     }
 
     @Override
-    public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
-        panel.getDatabase().removeEntry(memEntry);
-        undoEdit.addEdit(new UndoableRemoveEntry(panel.getDatabase(), memEntry, panel));
-        secondary.removeEntry(tmpEntry);
-        return true;
+    public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
+        database.getDatabase().removeEntry(memEntry);
+        undoEdit.addEdit(new UndoableRemoveEntry(database.getDatabase(), memEntry, null));
     }
 
     @Override
-    public JComponent description() {
-        return container;
+    public Node description() {
+        PreviewPanel previewPanel = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        previewPanel.setEntry(memEntry);
+        return previewPanel;
     }
 }
diff --git a/src/main/java/org/jabref/gui/collab/FileUpdatePanel.java b/src/main/java/org/jabref/gui/collab/FileUpdatePanel.java
deleted file mode 100644
index ea270674a02..00000000000
--- a/src/main/java/org/jabref/gui/collab/FileUpdatePanel.java
+++ /dev/null
@@ -1,129 +0,0 @@
-package org.jabref.gui.collab;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.File;
-
-import javax.swing.BorderFactory;
-import javax.swing.JButton;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
-
-import javafx.embed.swing.SwingNode;
-import javafx.scene.Node;
-import javafx.scene.layout.Priority;
-
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.SidePaneComponent;
-import org.jabref.gui.SidePaneManager;
-import org.jabref.gui.SidePaneType;
-import org.jabref.gui.actions.Action;
-import org.jabref.gui.icon.IconTheme;
-import org.jabref.logic.l10n.Localization;
-
-public class FileUpdatePanel extends SidePaneComponent implements ActionListener, ChangeScanner.DisplayResultCallback {
-
-    private final SidePaneManager manager;
-    private ChangeScanner scanner;
-    private File file;
-    private BasePanel panel;
-
-    public FileUpdatePanel(SidePaneManager manager) {
-        super(manager, IconTheme.JabRefIcons.SAVE, Localization.lang("File changed"));
-
-        this.manager = manager;
-    }
-
-    public void showForFile(BasePanel panel, File file, ChangeScanner scanner) {
-        this.file = file;
-        this.panel = panel;
-        this.scanner = scanner;
-
-        this.show();
-    }
-
-    /**
-     * We include a getter for the BasePanel this component refers to, because this
-     * component needs to be closed if the BasePanel is closed.
-     * @return the base panel this component refers to.
-     */
-    public BasePanel getPanel() {
-        return panel;
-    }
-
-    @Override
-    public Priority getResizePolicy() {
-        return Priority.NEVER;
-    }
-
-    @Override
-    public ToggleCommand getToggleCommand() {
-        throw new UnsupportedOperationException();
-    }
-
-    @Override
-    public Action getToggleAction() {
-        throw new UnsupportedOperationException();
-    }
-
-    @Override
-    protected Node createContentPane() {
-        JPanel main = new JPanel();
-        main.setLayout(new BorderLayout());
-
-        JLabel message = new JLabel("<html><center>"
-                + Localization.lang("The file<BR>'%0'<BR>has been modified<BR>externally!", file.getName())
-                + "</center></html>", SwingConstants.CENTER);
-
-        main.add(message, BorderLayout.CENTER);
-        JButton reviewChanges = new JButton(Localization.lang("Review changes"));
-        reviewChanges.addActionListener(this);
-        main.add(reviewChanges, BorderLayout.SOUTH);
-        main.setBorder(BorderFactory.createEmptyBorder(1, 1, 1, 1));
-
-        SwingNode swingNode = new SwingNode();
-        SwingUtilities.invokeLater(() -> swingNode.setContent(main));
-        return swingNode;
-    }
-
-    @Override
-    public SidePaneType getType() {
-        return SidePaneType.FILE_UPDATE_NOTIFICATION;
-    }
-
-    /**
-     * actionPerformed
-     *
-     * @param e
-     *            ActionEvent
-     */
-    @Override
-    public void actionPerformed(ActionEvent e) {
-
-        // ChangeScanner scanner = new ChangeScanner(frame, panel); //,
-        // panel.database(), panel.metaData());
-        // try {
-        scanner.displayResult(this);
-        // scanner.changeScan(panel.file());
-
-        // } catch (IOException ex) {
-        // ex.printStackTrace();
-        // }
-    }
-
-    /**
-     * Callback method for signalling that the change scanner has displayed the
-     * scan results to the user.
-     * @param resolved true if there were no changes, or if the user has resolved them.
-     */
-    @Override
-    public void scanResultsResolved(boolean resolved) {
-        if (resolved) {
-            manager.hide(this.getType());
-            panel.markExternalChangesAsResolved();
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/gui/collab/GroupChangeViewModel.java b/src/main/java/org/jabref/gui/collab/GroupChangeViewModel.java
index 99826a5886c..e6b75feaa38 100644
--- a/src/main/java/org/jabref/gui/collab/GroupChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/GroupChangeViewModel.java
@@ -1,40 +1,36 @@
 package org.jabref.gui.collab;
 
-import javax.swing.JComponent;
-import javax.swing.JLabel;
+import javafx.scene.Node;
+import javafx.scene.control.Label;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.groups.GroupTreeNodeViewModel;
 import org.jabref.gui.groups.UndoableModifySubtree;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.logic.bibtex.comparator.GroupDiff;
 import org.jabref.logic.groups.DefaultGroupsFactory;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.groups.GroupTreeNode;
 
-class GroupChangeViewModel extends ChangeViewModel {
+class GroupChangeViewModel extends DatabaseChangeViewModel {
 
     private final GroupTreeNode changedGroups;
-    private final GroupTreeNode tmpGroupRoot;
-
 
     public GroupChangeViewModel(GroupDiff diff) {
         super(diff.getOriginalGroupRoot() == null ? Localization.lang("Removed all groups") : Localization
                 .lang("Modified groups tree"));
-        this.changedGroups = diff.getOriginalGroupRoot();
-        this.tmpGroupRoot = diff.getNewGroupRoot();
+        this.changedGroups = diff.getNewGroupRoot();
     }
 
     @Override
-    public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
-        GroupTreeNode root = panel.getBibDatabaseContext().getMetaData().getGroups().orElse(null);
+    public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
+        GroupTreeNode root = database.getMetaData().getGroups().orElse(null);
         if (root == null) {
             root = new GroupTreeNode(DefaultGroupsFactory.getAllEntriesGroup());
-            panel.getBibDatabaseContext().getMetaData().setGroups(root);
+            database.getMetaData().setGroups(root);
         }
         final UndoableModifySubtree undo = new UndoableModifySubtree(
-                new GroupTreeNodeViewModel(panel.getBibDatabaseContext().getMetaData().getGroups().orElse(null)),
+                new GroupTreeNodeViewModel(database.getMetaData().getGroups().orElse(null)),
                 new GroupTreeNodeViewModel(root), Localization.lang("Modified groups"));
         root.removeAllChildren();
         if (changedGroups == null) {
@@ -49,28 +45,13 @@ public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound
         }
 
         undoEdit.addEdit(undo);
-
-        // Update tmp database:
-        if (tmpGroupRoot != null) {
-            tmpGroupRoot.removeAllChildren();
-            if (changedGroups != null) {
-                GroupTreeNode copied = changedGroups.copySubtree();
-                tmpGroupRoot.setGroup(copied.getGroup());
-                for (GroupTreeNode child : copied.getChildren()) {
-                    child.copySubtree().moveTo(tmpGroupRoot);
-                }
-            }
-        }
-
-        return true;
     }
 
     @Override
-    public JComponent description() {
-        return new JLabel("<html>" + toString() + '.'
+    public Node description() {
+        return new Label(toString() + '.'
                 + (changedGroups == null ? "" : ' ' + Localization
-                        .lang("Accepting the change replaces the complete groups tree with the externally modified groups tree."))
-                + "</html>");
+                .lang("Accepting the change replaces the complete groups tree with the externally modified groups tree.")));
 
     }
 }
diff --git a/src/main/java/org/jabref/gui/collab/InfoPane.java b/src/main/java/org/jabref/gui/collab/InfoPane.java
deleted file mode 100644
index cec4658a5de..00000000000
--- a/src/main/java/org/jabref/gui/collab/InfoPane.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.jabref.gui.collab;
-
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-
-import javax.swing.JEditorPane;
-
-class InfoPane extends JEditorPane {
-
-    public InfoPane() {
-        setEditable(false);
-        setContentType("text/html");
-    }
-
-    @Override
-    public void paint(Graphics g) {
-        Graphics2D g2 = (Graphics2D) g;
-        g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                RenderingHints.VALUE_ANTIALIAS_ON);
-        super.paint(g2);
-    }
-}
diff --git a/src/main/java/org/jabref/gui/collab/MetaDataChangeViewModel.java b/src/main/java/org/jabref/gui/collab/MetaDataChangeViewModel.java
index 7418ff1695f..83b5b7f7b56 100644
--- a/src/main/java/org/jabref/gui/collab/MetaDataChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/MetaDataChangeViewModel.java
@@ -1,30 +1,25 @@
 package org.jabref.gui.collab;
 
-import javax.swing.JComponent;
-import javax.swing.JScrollPane;
+import javafx.scene.Node;
+import javafx.scene.control.Label;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.logic.bibtex.comparator.MetaDataDiff;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.metadata.MetaData;
 
-class MetaDataChangeViewModel extends ChangeViewModel {
+class MetaDataChangeViewModel extends DatabaseChangeViewModel {
 
-    private final InfoPane infoPane = new InfoPane();
-    private final JScrollPane sp = new JScrollPane(infoPane);
     private final MetaData newMetaData;
 
     public MetaDataChangeViewModel(MetaDataDiff metaDataDiff) {
         super(Localization.lang("Metadata change"));
         this.newMetaData = metaDataDiff.getNewMetaData();
-
-        infoPane.setText("<html>" + Localization.lang("Metadata change") + "</html>");
     }
 
     @Override
-    public JComponent description() {
+    public Node description() {
         /*
         // TODO: Show detailed description of the changes
         StringBuilder sb = new StringBuilder(
@@ -34,12 +29,11 @@ public JComponent description() {
         sb.append("</html>");
         infoPane.setText(sb.toString());
         */
-        return sp;
+        return new Label(Localization.lang("Metadata change"));
     }
 
     @Override
-    public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
-        panel.getBibDatabaseContext().setMetaData(newMetaData);
-        return true;
+    public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
+        database.setMetaData(newMetaData);
     }
 }
diff --git a/src/main/java/org/jabref/gui/collab/PreambleChangeViewModel.java b/src/main/java/org/jabref/gui/collab/PreambleChangeViewModel.java
index a3f707b5cd5..b8a17ccb840 100644
--- a/src/main/java/org/jabref/gui/collab/PreambleChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/PreambleChangeViewModel.java
@@ -1,54 +1,48 @@
 package org.jabref.gui.collab;
 
-import javax.swing.JComponent;
-import javax.swing.JScrollPane;
+import javafx.scene.Node;
+import javafx.scene.control.Label;
+import javafx.scene.layout.VBox;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoablePreambleChange;
 import org.jabref.logic.bibtex.comparator.PreambleDiff;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.strings.StringUtil;
 
-class PreambleChangeViewModel extends ChangeViewModel {
+class PreambleChangeViewModel extends DatabaseChangeViewModel {
 
-    private final String mem;
-    private final String disk;
-    private final InfoPane tp = new InfoPane();
-    private final JScrollPane sp = new JScrollPane(tp);
+    private final PreambleDiff change;
 
-    public PreambleChangeViewModel(String mem, PreambleDiff diff) {
+    public PreambleChangeViewModel(PreambleDiff change) {
         super(Localization.lang("Changed preamble"));
-        this.disk = diff.getNewPreamble();
-        this.mem = mem;
-
-        StringBuilder text = new StringBuilder(34);
-        text.append("<FONT SIZE=3><H2>").append(Localization.lang("Changed preamble")).append("</H2>");
-
-        if (StringUtil.isNotBlank(disk)) {
-            text.append("<H3>").append(Localization.lang("Value set externally")).append(":</H3>" + "<CODE>").append(disk).append("</CODE>");
-        } else {
-            text.append("<H3>").append(Localization.lang("Value cleared externally")).append("</H3>");
-        }
-
-        if (StringUtil.isNotBlank(mem)) {
-            text.append("<H3>").append(Localization.lang("Current value")).append(":</H3>" + "<CODE>").append(mem).append("</CODE>");
-        }
-
-        tp.setText(text.toString());
+        this.change = change;
     }
 
     @Override
-    public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
-        panel.getDatabase().setPreamble(disk);
-        undoEdit.addEdit(new UndoablePreambleChange(panel.getDatabase(), mem, disk));
-        secondary.setPreamble(disk);
-        return true;
+    public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
+        database.getDatabase().setPreamble(change.getNewPreamble());
+        undoEdit.addEdit(new UndoablePreambleChange(database.getDatabase(), change.getOriginalPreamble(), change.getNewPreamble()));
     }
 
     @Override
-    public JComponent description() {
-        return sp;
+    public Node description() {
+        VBox container = new VBox();
+        Label header = new Label(Localization.lang("Changed preamble"));
+        header.getStyleClass().add("sectionHeader");
+        container.getChildren().add(header);
+
+        if (StringUtil.isNotBlank(change.getOriginalPreamble())) {
+            container.getChildren().add(new Label(Localization.lang("Current value") + ": " + change.getOriginalPreamble()));
+        }
+
+        if (StringUtil.isNotBlank(change.getNewPreamble())) {
+            container.getChildren().add(new Label(Localization.lang("Value set externally") + ": " + change.getNewPreamble()));
+        } else {
+            container.getChildren().add(new Label(Localization.lang("Value cleared externally")));
+        }
+
+        return container;
     }
 }
diff --git a/src/main/java/org/jabref/gui/collab/StringAddChangeViewModel.java b/src/main/java/org/jabref/gui/collab/StringAddChangeViewModel.java
index dafb80b125f..f22535b875b 100644
--- a/src/main/java/org/jabref/gui/collab/StringAddChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/StringAddChangeViewModel.java
@@ -1,63 +1,50 @@
 package org.jabref.gui.collab;
 
-import javax.swing.JComponent;
-import javax.swing.JScrollPane;
+import javafx.scene.Node;
+import javafx.scene.control.Label;
+import javafx.scene.layout.VBox;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableInsertString;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.KeyCollisionException;
 import org.jabref.model.entry.BibtexString;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-class StringAddChangeViewModel extends ChangeViewModel {
+class StringAddChangeViewModel extends DatabaseChangeViewModel {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(StringAddChangeViewModel.class);
-
     private final BibtexString string;
-    private final InfoPane tp = new InfoPane();
-
-    private final JScrollPane sp = new JScrollPane(tp);
-
 
     public StringAddChangeViewModel(BibtexString string) {
         super(Localization.lang("Added string") + ": '" + string.getName() + '\'');
         this.string = string;
-        tp.setText("<HTML><H2>" + Localization.lang("Added string") + "</H2><H3>" +
-                Localization.lang("Label") + ":</H3>" + string.getName() + "<H3>" +
-                Localization.lang("Content") + ":</H3>" + string.getContent() + "</HTML>");
     }
 
     @Override
-    public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
-
-        if (panel.getDatabase().hasStringLabel(string.getName())) {
-            // The name to change to is already in the database, so we can't comply.
-            LOGGER.info("Cannot add string '" + string.getName() + "' because the name "
-                    + "is already in use.");
-        }
-
-        try {
-            panel.getDatabase().addString(string);
-            undoEdit.addEdit(new UndoableInsertString(panel.getDatabase(), string));
-        } catch (KeyCollisionException ex) {
-            LOGGER.info("Error: could not add string '" + string.getName() + "': " + ex.getMessage(), ex);
-        }
+    public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
         try {
-            secondary.addString(new BibtexString(string.getName(), string.getContent()));
+            database.getDatabase().addString(string);
+            undoEdit.addEdit(new UndoableInsertString(database.getDatabase(), string));
         } catch (KeyCollisionException ex) {
-            LOGGER.info("Error: could not add string '" + string.getName() + "' to tmp database: " + ex.getMessage(), ex);
+            LOGGER.warn("Error: could not add string '" + string.getName() + "': " + ex.getMessage(), ex);
         }
-        return true;
     }
 
     @Override
-    public JComponent description() {
-        return sp;
+    public Node description() {
+        VBox container = new VBox();
+        Label header = new Label(Localization.lang("Added string"));
+        header.getStyleClass().add("sectionHeader");
+        container.getChildren().addAll(
+                header,
+                new Label(Localization.lang("Label") + ": " + string.getName()),
+                new Label(Localization.lang("Content") + ": " + string.getContent())
+        );
+        return container;
     }
 
 }
diff --git a/src/main/java/org/jabref/gui/collab/StringChangeViewModel.java b/src/main/java/org/jabref/gui/collab/StringChangeViewModel.java
index d44ac099658..278715f4b43 100644
--- a/src/main/java/org/jabref/gui/collab/StringChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/StringChangeViewModel.java
@@ -1,88 +1,70 @@
 package org.jabref.gui.collab;
 
-import javax.swing.JComponent;
-import javax.swing.JScrollPane;
+import javafx.scene.Node;
+import javafx.scene.control.Label;
+import javafx.scene.layout.VBox;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableInsertString;
 import org.jabref.gui.undo.UndoableStringChange;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.KeyCollisionException;
 import org.jabref.model.entry.BibtexString;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-class StringChangeViewModel extends ChangeViewModel {
+class StringChangeViewModel extends DatabaseChangeViewModel {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(StringChangeViewModel.class);
     private final BibtexString string;
     private final String disk;
-
     private final String label;
-    private final InfoPane tp = new InfoPane();
-    private final JScrollPane sp = new JScrollPane(tp);
-
-    private final BibtexString tmpString;
-
 
     public StringChangeViewModel(BibtexString string, BibtexString tmpString, String disk) {
         super(Localization.lang("Modified string") + ": '" + tmpString.getName() + '\'');
-        this.tmpString = tmpString;
         this.string = string;
         this.label = tmpString.getName();
         this.disk = disk;
-
-        StringBuilder sb = new StringBuilder(46);
-        sb.append("<HTML><H2>").append(Localization.lang("Modified string")).append("</H2><H3>")
-                .append(Localization.lang("Label")).append(":</H3>").append(label).append("<H3>")
-                .append(Localization.lang("New content")).append(":</H3>").append(disk);
-        if (string == null) {
-            sb.append("<P><I>");
-            sb.append(Localization.lang("Cannot merge this change")).append(": ");
-            sb.append(Localization.lang("The string has been removed locally")).append("</I>");
-        } else {
-            sb.append("<H3>");
-            sb.append(Localization.lang("Current content")).append(":</H3>");
-            sb.append(string.getContent());
-        }
-        sb.append("</HTML>");
-        tp.setText(sb.toString());
     }
 
     @Override
-    public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
+    public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
         if (string == null) {
             // The string was removed or renamed locally. We guess that it was removed.
             BibtexString bs = new BibtexString(label, disk);
             try {
-                panel.getDatabase().addString(bs);
-                undoEdit.addEdit(new UndoableInsertString(panel.getDatabase(), bs));
+                database.getDatabase().addString(bs);
+                undoEdit.addEdit(new UndoableInsertString(database.getDatabase(), bs));
             } catch (KeyCollisionException ex) {
-                LOGGER.info("Error: could not add string '" + bs.getName() + "': " + ex.getMessage(), ex);
+                LOGGER.warn("Error: could not add string '" + bs.getName() + "': " + ex.getMessage(), ex);
             }
         } else {
             String mem = string.getContent();
             string.setContent(disk);
             undoEdit.addEdit(new UndoableStringChange(string, false, mem, disk));
         }
+    }
 
-        // Update tmp database:
-        if (tmpString == null) {
-            BibtexString bs = new BibtexString(label, disk);
-            secondary.addString(bs);
+    @Override
+    public Node description() {
+        VBox container = new VBox();
+        Label header = new Label(Localization.lang("Modified string"));
+        header.getStyleClass().add("sectionHeader");
+        container.getChildren().addAll(
+                header,
+                new Label(Localization.lang("Label") + ": " + label),
+                new Label(Localization.lang("Content") + ": " + disk)
+        );
+
+        if (string == null) {
+            container.getChildren().add(new Label(Localization.lang("Cannot merge this change") + ": " + Localization.lang("The string has been removed locally")));
         } else {
-            tmpString.setContent(disk);
+            container.getChildren().add(new Label(Localization.lang("Current content") + ": " + string.getContent()));
         }
 
-        return true;
-    }
-
-    @Override
-    public JComponent description() {
-        return sp;
+        return container;
     }
 
 }
diff --git a/src/main/java/org/jabref/gui/collab/StringNameChangeViewModel.java b/src/main/java/org/jabref/gui/collab/StringNameChangeViewModel.java
index b9cd5bb80fe..77aebba89e1 100644
--- a/src/main/java/org/jabref/gui/collab/StringNameChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/StringNameChangeViewModel.java
@@ -1,21 +1,20 @@
 package org.jabref.gui.collab;
 
-import javax.swing.JComponent;
-import javax.swing.JLabel;
+import javafx.scene.Node;
+import javafx.scene.control.Label;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableInsertString;
 import org.jabref.gui.undo.UndoableStringChange;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.KeyCollisionException;
 import org.jabref.model.entry.BibtexString;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-class StringNameChangeViewModel extends ChangeViewModel {
+class StringNameChangeViewModel extends DatabaseChangeViewModel {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(StringNameChangeViewModel.class);
     private final BibtexString string;
@@ -23,23 +22,17 @@ class StringNameChangeViewModel extends ChangeViewModel {
     private final String disk;
     private final String content;
 
-    private final BibtexString tmpString;
-
-
     public StringNameChangeViewModel(BibtexString string, BibtexString tmpString, String mem, String disk) {
         super(Localization.lang("Renamed string") + ": '" + tmpString.getName() + '\'');
-        this.tmpString = tmpString;
         this.string = string;
         this.content = tmpString.getContent();
         this.mem = mem;
         this.disk = disk;
-
     }
 
     @Override
-    public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
-
-        if (panel.getDatabase().hasStringLabel(disk)) {
+    public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
+        if (database.getDatabase().hasStringLabel(disk)) {
             // The name to change to is already in the database, so we can't comply.
             LOGGER.info("Cannot rename string '" + mem + "' to '" + disk + "' because the name "
                     + "is already in use.");
@@ -49,8 +42,8 @@ public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound
             // The string was removed or renamed locally. We guess that it was removed.
             BibtexString bs = new BibtexString(disk, content);
             try {
-                panel.getDatabase().addString(bs);
-                undoEdit.addEdit(new UndoableInsertString(panel.getDatabase(), bs));
+                database.getDatabase().addString(bs);
+                undoEdit.addEdit(new UndoableInsertString(database.getDatabase(), bs));
             } catch (KeyCollisionException ex) {
                 LOGGER.info("Error: could not add string '" + bs.getName() + "': " + ex.getMessage(), ex);
             }
@@ -58,21 +51,11 @@ public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound
             string.setName(disk);
             undoEdit.addEdit(new UndoableStringChange(string, true, mem, disk));
         }
-
-        // Update tmp database:
-        if (tmpString == null) {
-            BibtexString bs = new BibtexString(disk, content);
-            secondary.addString(bs);
-        } else {
-            tmpString.setName(disk);
-        }
-
-        return true;
     }
 
     @Override
-    public JComponent description() {
-        return new JLabel(disk + " : " + content);
+    public Node description() {
+        return new Label(disk + " : " + content);
     }
 
 }
diff --git a/src/main/java/org/jabref/gui/collab/StringRemoveChangeViewModel.java b/src/main/java/org/jabref/gui/collab/StringRemoveChangeViewModel.java
index eaf66d47304..ba1b8066afb 100644
--- a/src/main/java/org/jabref/gui/collab/StringRemoveChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/StringRemoveChangeViewModel.java
@@ -1,55 +1,51 @@
 package org.jabref.gui.collab;
 
-import javax.swing.JComponent;
-import javax.swing.JScrollPane;
+import javafx.scene.Node;
+import javafx.scene.control.Label;
+import javafx.scene.layout.VBox;
 
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableRemoveString;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibtexString;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-class StringRemoveChangeViewModel extends ChangeViewModel {
+class StringRemoveChangeViewModel extends DatabaseChangeViewModel {
     private static final Logger LOGGER = LoggerFactory.getLogger(StringRemoveChangeViewModel.class);
     private final BibtexString string;
 
     private final BibtexString inMem;
-    private final InfoPane tp = new InfoPane();
-    private final JScrollPane sp = new JScrollPane(tp);
 
     public StringRemoveChangeViewModel(BibtexString string, BibtexString inMem) {
         super(Localization.lang("Removed string") + ": '" + string.getName() + '\'');
         this.string = string;
         this.inMem = inMem; // Holds the version in memory. Check if it has been modified...?
-
-        tp.setText("<HTML><H2>" + Localization.lang("Removed string") + "</H2><H3>" +
-                Localization.lang("Label") + ":</H3>" + string.getName() + "<H3>" +
-                Localization.lang("Content") + ":</H3>" + string.getContent() + "</HTML>");
     }
 
     @Override
-    public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
-
+    public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
         try {
-            panel.getDatabase().removeString(inMem.getId());
-            undoEdit.addEdit(new UndoableRemoveString(panel.getDatabase(), string));
+            database.getDatabase().removeString(inMem.getId());
+            undoEdit.addEdit(new UndoableRemoveString(database.getDatabase(), string));
         } catch (Exception ex) {
-            LOGGER.info("Error: could not add string '" + string.getName() + "': " + ex.getMessage(), ex);
+            LOGGER.warn("Error: could not add string '" + string.getName() + "': " + ex.getMessage(), ex);
         }
-
-        // Update tmp database:
-        secondary.removeString(string.getId());
-
-        return true;
     }
 
     @Override
-    public JComponent description() {
-        return sp;
+    public Node description() {
+        VBox container = new VBox();
+        Label header = new Label(Localization.lang("Removed string"));
+        header.getStyleClass().add("sectionHeader");
+        container.getChildren().addAll(
+                header,
+                new Label(Localization.lang("Label") + ": " + string.getName()),
+                new Label(Localization.lang("Content") + ": " + string.getContent())
+        );
+        return container;
     }
 
 }
diff --git a/src/main/java/org/jabref/logic/bibtex/comparator/PreambleDiff.java b/src/main/java/org/jabref/logic/bibtex/comparator/PreambleDiff.java
index b7bb0f56d31..e54074a1f40 100644
--- a/src/main/java/org/jabref/logic/bibtex/comparator/PreambleDiff.java
+++ b/src/main/java/org/jabref/logic/bibtex/comparator/PreambleDiff.java
@@ -6,9 +6,11 @@
 
 public class PreambleDiff {
 
-    private String newPreamble;
+    private final String originalPreamble;
+    private final String newPreamble;
 
-    private PreambleDiff(String newPreamble) {
+    private PreambleDiff(String originalPreamble, String newPreamble) {
+        this.originalPreamble = originalPreamble;
         this.newPreamble = newPreamble;
     }
 
@@ -18,11 +20,15 @@ public static Optional<PreambleDiff> compare(BibDatabaseContext originalDatabase
         if (originalPreamble.equals(newPreamble)) {
             return Optional.empty();
         } else {
-            return Optional.of(new PreambleDiff(newPreamble.orElse("")));
+            return Optional.of(new PreambleDiff(originalPreamble.orElse(""), newPreamble.orElse("")));
         }
     }
 
     public String getNewPreamble() {
         return newPreamble;
     }
+
+    public String getOriginalPreamble() {
+        return originalPreamble;
+    }
 }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 2f5131a84a9..6f889dd0133 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -385,9 +385,6 @@ File=File
 
 file=file
 File\ '%0'\ is\ already\ open.=File '%0' is already open.
-
-File\ changed=File changed
-
 File\ directory\ is\ not\ set\ or\ does\ not\ exist\!=File directory is not set or does not exist!
 
 File\ exists=File exists
@@ -604,9 +601,6 @@ nested\ AUX\ files=nested AUX files
 new=new
 
 New\ BibTeX\ sublibrary=New BibTeX sublibrary
-
-New\ content=New content
-
 New\ library\ created.=New library created.
 
 New\ group=New group
@@ -614,9 +608,6 @@ New\ group=New group
 New\ string=New string
 
 Next\ entry=Next entry
-
-No\ actual\ changes\ found.=No actual changes found.
-
 no\ base-BibTeX-file\ specified=no base-BibTeX-file specified
 
 no\ library\ generated=no library generated
@@ -950,9 +941,6 @@ The\ chosen\ encoding\ '%0'\ could\ not\ encode\ the\ following\ characters\:=Th
 
 
 the\ field\ <b>%0</b>=the field <b>%0</b>
-
-The\ file<BR>'%0'<BR>has\ been\ modified<BR>externally\!=The file<BR>'%0'<BR>has been modified<BR>externally!
-
 The\ group\ "%0"\ already\ contains\ the\ selection.=The group "%0" already contains the selection.
 
 The\ label\ of\ the\ string\ cannot\ be\ a\ number.=The label of the string cannot be a number.
@@ -2138,3 +2126,6 @@ Find\ and\ replace=Find and replace
 
 Found\ documents\:=Found documents\:
 Use\ selected\ document=Use selected document
+Accept\ changes=Accept changes
+Dismiss\ changes=Dismiss changes
+The\ library\ has\ been\ modified\ by\ another\ program.=The library has been modified by another program.

From bd5b67b42fa8f657bdc4667cbed9b403c2e4b6e9 Mon Sep 17 00:00:00 2001
From: Samiya Caur <36728314+samiyac@users.noreply.github.com>
Date: Fri, 15 Mar 2019 01:40:20 +0530
Subject: [PATCH 116/184] Modifications to improve contrast of UI elements
 (#4758)

---
 CHANGELOG.md                                      |  2 +-
 src/main/java/org/jabref/gui/Base.css             | 10 +++++-----
 src/main/java/org/jabref/gui/groups/GroupTree.css |  2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 93ba052512e..28d10b93720 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -57,7 +57,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We grouped the toolbar icons and changed the Open Library and Copy icons. [#4584](https://github.com/JabRef/jabref/issues/4584) 
 - We added a browse button next to the path text field for aux-based groups. [#4586](https://github.com/JabRef/jabref/issues/4586)
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
-
+- We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
 
 ### Fixed
 - We fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries [#3112](https://github.com/JabRef/jabref/issues/3112)
diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
index 8b2cd80f7b1..642fe8dcf88 100644
--- a/src/main/java/org/jabref/gui/Base.css
+++ b/src/main/java/org/jabref/gui/Base.css
@@ -18,7 +18,7 @@
 
     -jr-white: #ffffff;
     -jr-gray-0: #f2f2f2;
-    -jr-gray-1: #e6e6e6;
+    -jr-gray-1: #dddddd;
     -jr-gray-2: #808080;
     -jr-gray-3: #404040;
     -jr-black: #000;
@@ -70,7 +70,7 @@
     -jr-error: -jr-light-red;
 
     /* Color for the small group view indicator for the number of hits */
-    -jr-group-hits-bg: derive(-jr-sidepane-background, -5%);
+    -jr-group-hits-bg: derive(-jr-sidepane-background, -50%);
     -jr-group-hits-fg: ladder(
             -jr-group-hits-bg,
             -fx-light-text-color 45%,
@@ -84,8 +84,8 @@
     -jr-tooltip-fg: -jr-black;
 
     /* Finally, some specific jr styles that depend on -fx definitions in *this* style */
-    -jr-sidepane-background: -jr-gray-0;
-    -jr-sidepane-header-background: -jr-gray-0;
+    -jr-sidepane-background: -jr-gray-1;
+    -jr-sidepane-header-background: -jr-gray-1;
     -jr-sidepane-header-color: -jr-theme-text;
 
     /* Specs for the scrollbars */
@@ -116,7 +116,7 @@
      */
     -fx-control-inner-background: derive(-fx-base, 95%);
     /* Version of -fx-control-inner-background for alternative rows */
-    -fx-control-inner-background-alt: derive(-fx-control-inner-background, -2%);
+    -fx-control-inner-background-alt: derive(-fx-control-inner-background, -6%);
 
     /* One of these colors will be chosen based upon a ladder calculation
      * that uses the brightness of a background color.  Instead of using these
diff --git a/src/main/java/org/jabref/gui/groups/GroupTree.css b/src/main/java/org/jabref/gui/groups/GroupTree.css
index 0b8b66b1928..ecee1015d44 100644
--- a/src/main/java/org/jabref/gui/groups/GroupTree.css
+++ b/src/main/java/org/jabref/gui/groups/GroupTree.css
@@ -20,7 +20,7 @@
 .numberColumn > .hits {
     -fx-font-size: 85%;
     -fx-background-color: -jr-group-hits-bg;
-    -fx-padding: 0.1em 0.4em 0.1em 0.4em;
+    -fx-padding: 0.4em 0.4em 0.4em 0.4em;
     -fx-background-insets: 0;
     -fx-background-radius: 0.8em;
 }

From 031e9624c8e575816ca2a7c00c5d012c001be6d7 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Thu, 14 Mar 2019 21:15:12 +0100
Subject: [PATCH 117/184] Add changelog entry for #4520

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 28d10b93720..efb09d26162 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -48,6 +48,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
 - We added an option in the preference dialog box that allows user to choose behavior after dragging and dropping files in Entry Editor. [#4356](https://github.com/JabRef/jabref/issues/4356)
 - We added the ability to have an export preference where previously "File"-->"Export"/"Export selected entries" would not save the user's preference[#4495](https://github.com/JabRef/jabref/issues/4495)
+- We optimized the code responsible for connecting to an external database, which should lead to huge improvements in performance.
 - For automatically created groups, added ability to filter groups by entry type. [#4539](https://github.com/JabRef/jabref/issues/4539)
 - We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added the ability change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)

From 46d2c7dc2c0a584168840550808e4b2fc86754c6 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 15 Mar 2019 09:51:58 +0100
Subject: [PATCH 118/184] Improve Remote messaging (#4760)

Fixes #4023 and should fix #4481.
---
 src/main/java/org/jabref/JabRefMain.java                  | 2 ++
 .../java/org/jabref/gui/remote/JabRefMessageHandler.java  | 4 ----
 .../java/org/jabref/logic/remote/client/RemoteClient.java | 8 +++++---
 .../jabref/logic/remote/server/RemoteListenerServer.java  | 4 ++--
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/main/java/org/jabref/JabRefMain.java b/src/main/java/org/jabref/JabRefMain.java
index 249c97f8251..66e624a002d 100644
--- a/src/main/java/org/jabref/JabRefMain.java
+++ b/src/main/java/org/jabref/JabRefMain.java
@@ -141,6 +141,8 @@ private static boolean handleMultipleAppInstances(String[] args) {
                     // So we assume it's all taken care of, and quit.
                     LOGGER.info(Localization.lang("Arguments passed on to running JabRef instance. Shutting down."));
                     return false;
+                } else {
+                    LOGGER.warn("Could not communicate with other running JabRef instance.");
                 }
             } else {
                 // We are alone, so we start the server
diff --git a/src/main/java/org/jabref/gui/remote/JabRefMessageHandler.java b/src/main/java/org/jabref/gui/remote/JabRefMessageHandler.java
index 8033c9343d9..9ddc9d5d96e 100644
--- a/src/main/java/org/jabref/gui/remote/JabRefMessageHandler.java
+++ b/src/main/java/org/jabref/gui/remote/JabRefMessageHandler.java
@@ -1,6 +1,5 @@
 package org.jabref.gui.remote;
 
-import java.util.Arrays;
 import java.util.List;
 
 import javafx.application.Platform;
@@ -15,9 +14,6 @@ public class JabRefMessageHandler implements MessageHandler {
     @Override
     public void handleCommandLineArguments(String[] message) {
         ArgumentProcessor argumentProcessor = new ArgumentProcessor(message, ArgumentProcessor.Mode.REMOTE_START);
-        if (!(argumentProcessor.hasParserResults())) {
-            throw new IllegalStateException("Could not start JabRef with arguments " + Arrays.toString(message));
-        }
 
         List<ParserResult> loaded = argumentProcessor.getParserResults();
         for (int i = 0; i < loaded.size(); i++) {
diff --git a/src/main/java/org/jabref/logic/remote/client/RemoteClient.java b/src/main/java/org/jabref/logic/remote/client/RemoteClient.java
index 5fc416da214..6942a902522 100644
--- a/src/main/java/org/jabref/logic/remote/client/RemoteClient.java
+++ b/src/main/java/org/jabref/logic/remote/client/RemoteClient.java
@@ -1,6 +1,7 @@
 package org.jabref.logic.remote.client;
 
 import java.io.IOException;
+import java.net.InetSocketAddress;
 import java.net.Socket;
 
 import javafx.util.Pair;
@@ -17,8 +18,8 @@ public class RemoteClient {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(RemoteClient.class);
 
-    private static final int TIMEOUT = 2000;
-    private int port;
+    private static final int TIMEOUT = 200;
+    private final int port;
 
     public RemoteClient(int port) {
         this.port = port;
@@ -61,8 +62,9 @@ public boolean sendCommandLineArguments(String[] args) {
     }
 
     private Protocol openNewConnection() throws IOException {
-        Socket socket = new Socket(RemotePreferences.getIpAddress(), port);
+        Socket socket = new Socket();
         socket.setSoTimeout(TIMEOUT);
+        socket.connect(new InetSocketAddress(RemotePreferences.getIpAddress(), port), TIMEOUT);
         return new Protocol(socket);
     }
 }
diff --git a/src/main/java/org/jabref/logic/remote/server/RemoteListenerServer.java b/src/main/java/org/jabref/logic/remote/server/RemoteListenerServer.java
index d87fa2d5b33..b0a4c6ebc29 100644
--- a/src/main/java/org/jabref/logic/remote/server/RemoteListenerServer.java
+++ b/src/main/java/org/jabref/logic/remote/server/RemoteListenerServer.java
@@ -19,7 +19,7 @@ public class RemoteListenerServer implements Runnable {
 
     private static final int BACKLOG = 1;
 
-    private static final int ONE_SECOND_TIMEOUT = 1000;
+    private static final int TIMEOUT = 1000;
 
     private final MessageHandler messageHandler;
     private final ServerSocket serverSocket;
@@ -35,7 +35,7 @@ public void run() {
         try {
             while (!Thread.interrupted()) {
                 try (Socket socket = serverSocket.accept()) {
-                    socket.setSoTimeout(ONE_SECOND_TIMEOUT);
+                    socket.setSoTimeout(TIMEOUT);
 
                     try (Protocol protocol = new Protocol(socket)) {
                         Pair<RemoteMessage, Object> input = protocol.receiveMessage();

From 7ed15bc4a257bc724c5d4f1cf7d872fad7cb07e7 Mon Sep 17 00:00:00 2001
From: Samiya Caur <36728314+samiyac@users.noreply.github.com>
Date: Fri, 15 Mar 2019 17:14:49 +0530
Subject: [PATCH 119/184] Enable import button only if entry selected (#4761)

---
 CHANGELOG.md                                                | 1 +
 .../java/org/jabref/gui/importer/ImportEntriesDialog.java   | 6 ++++++
 2 files changed, 7 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index efb09d26162..9e14888432a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -58,6 +58,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We grouped the toolbar icons and changed the Open Library and Copy icons. [#4584](https://github.com/JabRef/jabref/issues/4584) 
 - We added a browse button next to the path text field for aux-based groups. [#4586](https://github.com/JabRef/jabref/issues/4586)
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
+- We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
 - We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
 
 ### Fixed
diff --git a/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java b/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java
index bc72cb28fcb..ae5352deade 100644
--- a/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java
+++ b/src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java
@@ -5,6 +5,8 @@
 import javax.inject.Inject;
 import javax.swing.undo.UndoManager;
 
+import javafx.beans.binding.Bindings;
+import javafx.beans.binding.BooleanBinding;
 import javafx.css.PseudoClass;
 import javafx.fxml.FXML;
 import javafx.scene.Node;
@@ -61,6 +63,10 @@ public ImportEntriesDialog(BibDatabaseContext database, BackgroundTask<List<BibE
                   .load()
                   .setAsDialogPane(this);
 
+        BooleanBinding booleanBind = Bindings.isEmpty(entriesListView.getCheckModel().getCheckedItems());
+        Button btn = (Button) this.getDialogPane().lookupButton(importButton);
+        btn.disableProperty().bind(booleanBind);
+
         setResultConverter(button -> {
             if (button == importButton) {
                 viewModel.importEntries(entriesListView.getCheckModel().getCheckedItems());

From cd979c5b68ea0d08ab707b69f7ac105d47af566c Mon Sep 17 00:00:00 2001
From: Yash  Kothari <yashkothari199767@gmail.com>
Date: Sat, 16 Mar 2019 04:44:36 +0530
Subject: [PATCH 120/184] Feature: implement search filter in show preferences
 (#4759)

* Feature: implement search filter in show preferences

Add a search box in show preferences window to allow users to filter
preference options.

Resolves #1019

* Add Locale.ROOT when converting to lower case

* Fixed indentation for fxml

* Added Locale.ROOT when converting to lower case

* Using FilteredList to filter options on search

* set the count label text, which was accidently removed

* Moved checkbox to the top

* Bind count label to table size property
---
 .../preferences/PreferencesFilterDialog.fxml  | 17 ++++++++++++----
 .../preferences/PreferencesFilterDialog.java  | 20 +++++++++++++++++--
 2 files changed, 31 insertions(+), 6 deletions(-)

diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesFilterDialog.fxml b/src/main/java/org/jabref/gui/preferences/PreferencesFilterDialog.fxml
index 399e2c9fc27..e69a587836e 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesFilterDialog.fxml
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesFilterDialog.fxml
@@ -7,21 +7,30 @@
 <?import javafx.scene.control.Label?>
 <?import javafx.scene.control.TableColumn?>
 <?import javafx.scene.control.TableView?>
+<?import javafx.scene.control.TextField?>
 <?import javafx.scene.layout.BorderPane?>
 <?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
 <DialogPane xmlns:fx="http://javafx.com/fxml/1" prefHeight="600.0" prefWidth="950.0"
             xmlns="http://javafx.com/javafx/8.0.121" fx:controller="org.jabref.gui.preferences.PreferencesFilterDialog">
 
     <content>
         <BorderPane>
             <bottom>
-                <HBox>
-                    <CheckBox fx:id="showOnlyDeviatingPreferenceOptions"
-                              text="%Show only preferences deviating from their default value"/>
-                    <HBox HBox.hgrow="ALWAYS"/>
+                <HBox alignment="BOTTOM_RIGHT">
                     <Label fx:id="count"/>
                 </HBox>
             </bottom>
+            <top>
+                <HBox spacing="20">
+                    <TextField fx:id="searchField" promptText="%Search"/>
+                    <VBox alignment="CENTER">
+                        <CheckBox fx:id="showOnlyDeviatingPreferenceOptions"
+                            text="%Show only preferences deviating from their default value" alignment="bottom_right"/>
+                    </VBox>
+                    <HBox HBox.hgrow="ALWAYS"/>
+                </HBox>
+            </top>
             <center>
                 <TableView fx:id="table">
                     <columns>
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesFilterDialog.java b/src/main/java/org/jabref/gui/preferences/PreferencesFilterDialog.java
index 09d01ec3510..54b5e34c1f3 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesFilterDialog.java
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesFilterDialog.java
@@ -1,16 +1,20 @@
 package org.jabref.gui.preferences;
 
+import java.util.Locale;
 import java.util.Objects;
 
+import javafx.beans.binding.Bindings;
 import javafx.beans.property.ReadOnlyObjectWrapper;
 import javafx.beans.property.ReadOnlyStringWrapper;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
+import javafx.collections.transformation.FilteredList;
 import javafx.fxml.FXML;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.Label;
 import javafx.scene.control.TableColumn;
 import javafx.scene.control.TableView;
+import javafx.scene.control.TextField;
 
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.logic.l10n.Localization;
@@ -22,6 +26,7 @@ public class PreferencesFilterDialog extends BaseDialog<Void> {
 
     private final JabRefPreferencesFilter preferencesFilter;
     private final ObservableList<JabRefPreferencesFilter.PreferenceOption> preferenceOptions;
+    private final FilteredList<JabRefPreferencesFilter.PreferenceOption> filteredOptions;
 
     @FXML private TableView<JabRefPreferencesFilter.PreferenceOption> table;
     @FXML private TableColumn<JabRefPreferencesFilter.PreferenceOption, JabRefPreferencesFilter.PreferenceType> columnType;
@@ -30,10 +35,12 @@ public class PreferencesFilterDialog extends BaseDialog<Void> {
     @FXML private TableColumn<JabRefPreferencesFilter.PreferenceOption, Object> columnDefaultValue;
     @FXML private CheckBox showOnlyDeviatingPreferenceOptions;
     @FXML private Label count;
+    @FXML private TextField searchField;
 
     public PreferencesFilterDialog(JabRefPreferencesFilter preferencesFilter) {
         this.preferencesFilter = Objects.requireNonNull(preferencesFilter);
         this.preferenceOptions = FXCollections.observableArrayList();
+        this.filteredOptions = new FilteredList<>(this.preferenceOptions);
 
         ViewLoader.view(this)
                   .load()
@@ -45,11 +52,20 @@ public PreferencesFilterDialog(JabRefPreferencesFilter preferencesFilter) {
     @FXML
     private void initialize() {
         showOnlyDeviatingPreferenceOptions.setOnAction(event -> updateModel());
+        filteredOptions.predicateProperty().bind(Bindings.createObjectBinding(() -> {
+            String searchText = searchField.getText();
+            if ((searchText == null) || searchText.isEmpty()) {
+                return null;
+            }
+            String lowerCaseSearchText = searchText.toLowerCase(Locale.ROOT);
+            return (option) -> option.getKey().toLowerCase(Locale.ROOT).contains(lowerCaseSearchText);
+        }, searchField.textProperty()));
         columnType.setCellValueFactory(data -> new ReadOnlyObjectWrapper<>(data.getValue().getType()));
         columnKey.setCellValueFactory(data -> new ReadOnlyStringWrapper(data.getValue().getKey()));
         columnValue.setCellValueFactory(data -> new ReadOnlyObjectWrapper<>(data.getValue().getValue()));
         columnDefaultValue.setCellValueFactory(data -> new ReadOnlyObjectWrapper<>(data.getValue().getDefaultValue().orElse("")));
-        table.setItems(preferenceOptions);
+        table.setItems(filteredOptions);
+        count.textProperty().bind(Bindings.size(table.getItems()).asString("(%d)"));
         updateModel();
     }
 
@@ -59,6 +75,6 @@ private void updateModel() {
         } else {
             preferenceOptions.setAll(preferencesFilter.getPreferenceOptions());
         }
-        count.setText(String.format("(%d)", preferenceOptions.size()));
     }
+
 }

From d7dd41b0022978b9db958505cf6031768cf2cd8c Mon Sep 17 00:00:00 2001
From: Ronak Lakhotia <ronak.lakhotia999@gmail.com>
Date: Sat, 16 Mar 2019 18:57:02 +0800
Subject: [PATCH 121/184] [#4306] Disable renaming (#4727)

* Disable renaming
* Fix issues


Co-authored-by: Patrick Lin <patrick.lin.007@hotmail.com>
---
 .../gui/fieldeditors/LinkedFileViewModel.java | 33 +++++++++++++++++++
 .../gui/fieldeditors/LinkedFilesEditor.java   |  6 ++--
 .../org/jabref/model/util/OptionalUtil.java   | 13 ++++++++
 3 files changed, 49 insertions(+), 3 deletions(-)

diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
index 3ef40844f14..68da8aec6f5 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
@@ -9,6 +9,7 @@
 import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
+import java.util.function.BiPredicate;
 
 import javax.xml.transform.TransformerException;
 
@@ -44,6 +45,7 @@
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.metadata.FilePreferences;
 import org.jabref.model.strings.StringUtil;
+import org.jabref.model.util.OptionalUtil;
 import org.jabref.preferences.JabRefPreferences;
 
 import org.slf4j.Logger;
@@ -267,6 +269,37 @@ public void moveToDefaultDirectory() {
         }
     }
 
+    /**
+     * Gets the filename for the current linked file and compares it to the new suggested filename.
+     * @return true if the suggested filename is same as current filename.
+     */
+    public boolean isGeneratedNameSameAsOriginal() {
+        Path file = Paths.get(this.linkedFile.getLink());
+        String currentFileName = file.getFileName().toString();
+        String suggestedFileName = this.linkedFileHandler.getSuggestedFileName();
+
+        return currentFileName.equals(suggestedFileName);
+    }
+
+    /**
+     * Compares suggested filepath of current linkedFile with existing filepath.
+     * @return true if suggested filepath is same as existing filepath.
+     */
+    public boolean isGeneratedPathSameAsOriginal() {
+        Optional<Path> newDir = databaseContext.getFirstExistingFileDir(filePreferences);
+
+        Optional<Path> currentDir = linkedFile.findIn(databaseContext, filePreferences);
+
+        BiPredicate<Path, Path> equality = (fileA, fileB) -> {
+            try {
+                return Files.isSameFile(fileA, fileB);
+            } catch (IOException e) {
+                return false;
+            }
+        };
+        return OptionalUtil.equals(newDir, currentDir, equality);
+    }
+
     public void moveToDefaultDirectoryAndRename() {
         moveToDefaultDirectory();
         rename();
diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java
index b782ae80c61..a2f1f168fce 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java
@@ -220,15 +220,15 @@ private ContextMenu createContextMenuForFile(LinkedFileViewModel linkedFile) {
 
         MenuItem renameFile = new MenuItem(Localization.lang("Rename file"));
         renameFile.setOnAction(event -> linkedFile.rename());
-        renameFile.setDisable(linkedFile.getFile().isOnlineLink());
+        renameFile.setDisable(linkedFile.getFile().isOnlineLink() || linkedFile.isGeneratedNameSameAsOriginal());
 
         MenuItem moveFile = new MenuItem(Localization.lang("Move file to file directory"));
         moveFile.setOnAction(event -> linkedFile.moveToDefaultDirectory());
-        moveFile.setDisable(linkedFile.getFile().isOnlineLink());
+        moveFile.setDisable(linkedFile.getFile().isOnlineLink() || linkedFile.isGeneratedPathSameAsOriginal());
 
         MenuItem renameAndMoveFile = new MenuItem(Localization.lang("Move file to file directory and rename file"));
         renameAndMoveFile.setOnAction(event -> linkedFile.moveToDefaultDirectoryAndRename());
-        renameAndMoveFile.setDisable(linkedFile.getFile().isOnlineLink());
+        renameAndMoveFile.setDisable(linkedFile.getFile().isOnlineLink() || linkedFile.isGeneratedPathSameAsOriginal());
 
         MenuItem deleteFile = new MenuItem(Localization.lang("Permanently delete local file"));
         deleteFile.setOnAction(event -> viewModel.deleteFile(linkedFile));
diff --git a/src/main/java/org/jabref/model/util/OptionalUtil.java b/src/main/java/org/jabref/model/util/OptionalUtil.java
index 6d127c4e5ce..90290f597b2 100644
--- a/src/main/java/org/jabref/model/util/OptionalUtil.java
+++ b/src/main/java/org/jabref/model/util/OptionalUtil.java
@@ -5,6 +5,7 @@
 import java.util.List;
 import java.util.Optional;
 import java.util.function.BiFunction;
+import java.util.function.BiPredicate;
 import java.util.function.Function;
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
@@ -20,6 +21,18 @@ public static <T> List<T> toList(Optional<T> value) {
         }
     }
 
+    public static <T, U> boolean equals(Optional<T> left, Optional<U> right, BiPredicate<T, U> equality) {
+        if (!left.isPresent()) {
+            return !right.isPresent();
+        } else {
+            if (right.isPresent()) {
+                return equality.test(left.get(), right.get());
+            } else {
+                return false;
+            }
+        }
+    }
+
     /**
      * No longer needed in Java 9 where {@code Optional<T>.stream()} is added.
      */

From 65245999ba988d81e1c1e39e738445f2dbcf4eaf Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 08:32:21 +0100
Subject: [PATCH 122/184] Bump mockito-core from 2.25.0 to 2.25.1 (#4771)

Bumps [mockito-core](https://github.com/mockito/mockito) from 2.25.0 to 2.25.1.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v2.25.0...v2.25.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 0a45aab3885..599dd191bfe 100644
--- a/build.gradle
+++ b/build.gradle
@@ -167,7 +167,7 @@ dependencies {
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
-    testCompile 'org.mockito:mockito-core:2.25.0'
+    testCompile 'org.mockito:mockito-core:2.25.1'
     testCompile 'com.github.tomakehurst:wiremock:2.21.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'

From d64494e517893e71e2f1cdafa9ed826c0c1935b9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 08:32:44 +0100
Subject: [PATCH 123/184] Bump junit-vintage-engine from 5.4.0 to 5.4.1 (#4772)

Bumps [junit-vintage-engine](https://github.com/junit-team/junit5) from 5.4.0 to 5.4.1.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/compare/r5.4.0...r5.4.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 599dd191bfe..c329ea2d3c5 100644
--- a/build.gradle
+++ b/build.gradle
@@ -162,7 +162,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.4.0'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.0'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'

From 8a1fbe1ee6f1ed6aa47ebe989081fd7e3825ecb8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 08:34:05 +0100
Subject: [PATCH 124/184] Bump archunit-junit5-api from 0.9.3 to 0.10.1 (#4773)

Bumps [archunit-junit5-api](https://github.com/TNG/ArchUnit) from 0.9.3 to 0.10.1.
- [Release notes](https://github.com/TNG/ArchUnit/releases)
- [Commits](https://github.com/TNG/ArchUnit/compare/v0.9.3...v0.10.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index c329ea2d3c5..9b75a95267f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -173,7 +173,7 @@ dependencies {
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
     testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.3'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.3'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.1'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 

From 52696f04b518f4093fea32aff0c2f80b540dab67 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 10:50:00 +0100
Subject: [PATCH 125/184] Bump wiremock from 2.21.0 to 2.22.0 (#4776)

Bumps [wiremock](https://github.com/tomakehurst/wiremock) from 2.21.0 to 2.22.0.
- [Release notes](https://github.com/tomakehurst/wiremock/releases)
- [Changelog](https://github.com/tomakehurst/wiremock/blob/master/release-settings.gradle)
- [Commits](https://github.com/tomakehurst/wiremock/compare/2.21.0...2.22.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9b75a95267f..0b8f14c6198 100644
--- a/build.gradle
+++ b/build.gradle
@@ -168,7 +168,7 @@ dependencies {
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
     testCompile 'org.mockito:mockito-core:2.25.1'
-    testCompile 'com.github.tomakehurst:wiremock:2.21.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.22.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'

From 39f7690c2c3ec76a9747b2e65e77d31d1c741dba Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 10:50:18 +0100
Subject: [PATCH 126/184] Bump junit-jupiter from 5.4.0 to 5.4.1 (#4775)

Bumps [junit-jupiter](https://github.com/junit-team/junit5) from 5.4.0 to 5.4.1.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/compare/r5.4.0...r5.4.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 0b8f14c6198..1bee7bc1732 100644
--- a/build.gradle
+++ b/build.gradle
@@ -161,7 +161,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.1'
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.0'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.1'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
 

From 2512657ea02908057787dfb124ed0bcb84df07e9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 10:50:38 +0100
Subject: [PATCH 127/184] Bump junit-platform-launcher from 1.4.0 to 1.4.1
 (#4774)

Bumps [junit-platform-launcher](https://github.com/junit-team/junit5) from 1.4.0 to 1.4.1.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/commits)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 1bee7bc1732..70d2bc30c2b 100644
--- a/build.gradle
+++ b/build.gradle
@@ -163,7 +163,7 @@ dependencies {
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.4.1'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.4.1'
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'

From 2b791c306070f08e31b5218b4de1f818fb25a49e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 10:51:02 +0100
Subject: [PATCH 128/184] Bump archunit-junit5-engine from 0.9.3 to 0.10.1
 (#4777)

Bumps [archunit-junit5-engine](https://github.com/TNG/ArchUnit) from 0.9.3 to 0.10.1.
- [Release notes](https://github.com/TNG/ArchUnit/releases)
- [Commits](https://github.com/TNG/ArchUnit/compare/v0.9.3...v0.10.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 70d2bc30c2b..9673626d496 100644
--- a/build.gradle
+++ b/build.gradle
@@ -172,7 +172,7 @@ dependencies {
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.3'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.1'
     testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.1'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"

From 90376f40fe0acc9b4b85c5574292e3997d3975f5 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 19 Mar 2019 23:29:48 +0100
Subject: [PATCH 129/184] Fix opening of entry editor (#4784)

Fixes #4762. The problem was that the NotificationPane was hiding the entry editor/preview.
---
 src/main/java/org/jabref/gui/BasePanel.java | 40 ++++++---------------
 1 file changed, 11 insertions(+), 29 deletions(-)

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index ea88315f304..96d68e870dd 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -25,7 +25,6 @@
 import javafx.scene.Node;
 import javafx.scene.control.ScrollPane;
 import javafx.scene.control.SplitPane;
-import javafx.scene.layout.AnchorPane;
 import javafx.scene.layout.StackPane;
 
 import org.jabref.Globals;
@@ -191,7 +190,7 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         if (file.isPresent()) {
             // Register so we get notifications about outside changes to the file.
             changeMonitor = Optional.of(new DatabaseChangeMonitor(bibDatabaseContext, Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR));
-            changePane = new DatabaseChangePane(mainTable.getPane(), bibDatabaseContext, changeMonitor.get());
+            changePane = new DatabaseChangePane(splitPane, bibDatabaseContext, changeMonitor.get());
             getChildren().add(changePane);
         } else {
             if (bibDatabaseContext.getDatabase().hasEntries()) {
@@ -394,7 +393,7 @@ private void setupActions() {
                                                                          .withPreviewPanelEnabled(enabled)
                                                                          .build();
             Globals.prefs.storePreviewPreferences(newPreviewPreferences);
-            DefaultTaskExecutor.runInJavaFXThread(() -> setPreviewActiveBasePanels(enabled));
+            setPreviewActive(enabled);
         });
 
         actions.put(Actions.NEXT_PREVIEW_STYLE, this::nextPreviewStyle);
@@ -776,13 +775,9 @@ public void setupMainPanel() {
         createMainTable();
 
         ScrollPane pane = mainTable.getPane();
-        AnchorPane anchorPane = new AnchorPane(pane);
-        AnchorPane.setBottomAnchor(pane, 0.0);
-        AnchorPane.setTopAnchor(pane, 0.0);
-        AnchorPane.setLeftAnchor(pane, 0.0);
-        AnchorPane.setRightAnchor(pane, 0.0);
-        splitPane.getItems().add(anchorPane);
-        this.getChildren().setAll(splitPane);
+        pane.setFitToHeight(true);
+        pane.setFitToWidth(true);
+        splitPane.getItems().add(pane);
 
         // Set up name autocompleter for search:
         instantiateSearchAutoCompleter();
@@ -845,17 +840,13 @@ public EntryEditor getEntryEditor() {
      * @param entry The entry to edit.
      */
     public void showAndEdit(BibEntry entry) {
-        DefaultTaskExecutor.runInJavaFXThread(() -> {
+        showBottomPane(BasePanelMode.SHOWING_EDITOR);
 
-            showBottomPane(BasePanelMode.SHOWING_EDITOR);
-
-            if (entry != getShowing()) {
-                entryEditor.setEntry(entry);
-                showing = entry;
-            }
-            entryEditor.requestFocus();
-
-        });
+        if (entry != getShowing()) {
+            entryEditor.setEntry(entry);
+            showing = entry;
+        }
+        entryEditor.requestFocus();
     }
 
     private void showBottomPane(BasePanelMode newMode) {
@@ -1150,15 +1141,6 @@ public String formatOutputMessage(String start, int count) {
         return String.format("%s %d %s.", start, count, (count > 1 ? Localization.lang("entries") : Localization.lang("entry")));
     }
 
-    /**
-     * Set the preview active state for all BasePanel instances.
-     */
-    private void setPreviewActiveBasePanels(boolean enabled) {
-        for (int i = 0; i < frame.getTabbedPane().getTabs().size(); i++) {
-            frame.getBasePanelAt(i).setPreviewActive(enabled);
-        }
-    }
-
     private void setPreviewActive(boolean enabled) {
         if (enabled) {
             showPreview();

From 6c61664a8f715e4011064ddca5cb0ace0b803131 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Wed, 20 Mar 2019 20:48:13 +0100
Subject: [PATCH 130/184] Fix NPE in Duplicate Resolver Dialog (#4791)

* Fix NPE in Duplicate Resolver Dialog


Fixes #4785

* Fix NPE in review dialog

Fixes #4786
---
 src/main/java/org/jabref/gui/DuplicateResolverDialog.java      | 2 +-
 src/main/java/org/jabref/gui/PreviewPanel.java                 | 2 +-
 .../java/org/jabref/gui/collab/EntryAddChangeViewModel.java    | 2 +-
 src/main/java/org/jabref/gui/search/SearchResultFrame.java     | 3 ++-
 4 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
index 858a7c7e7f2..fa1b2b92b96 100644
--- a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
+++ b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
@@ -39,8 +39,8 @@ public enum DuplicateResolverResult {
 
     public DuplicateResolverDialog(BibEntry one, BibEntry two, DuplicateResolverType type, BibDatabaseContext database) {
         this.setTitle(Localization.lang("Possible duplicate entries"));
-        init(one, two, type);
         this.database = database;
+        init(one, two, type);
     }
 
     private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
diff --git a/src/main/java/org/jabref/gui/PreviewPanel.java b/src/main/java/org/jabref/gui/PreviewPanel.java
index 796fafdd016..ff26ee6765b 100644
--- a/src/main/java/org/jabref/gui/PreviewPanel.java
+++ b/src/main/java/org/jabref/gui/PreviewPanel.java
@@ -84,7 +84,7 @@ public class PreviewPanel extends ScrollPane implements SearchQueryHighlightList
 
     /**
      * @param panel           (may be null) Only set this if the preview is associated to the main window.
-     * @param databaseContext Used for resolving pdf directories for links. Must not be null.
+     * @param databaseContext Used for resolving pdf directories for links. Must not be null, just pass a new empty BibDatabaseContext()
      */
     public PreviewPanel(BasePanel panel, BibDatabaseContext databaseContext, KeyBindingRepository keyBindingRepository, PreviewPreferences preferences, DialogService dialogService, ExternalFileTypes externalFileTypes) {
         this.databaseContext = Objects.requireNonNull(databaseContext);
diff --git a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
index 8284f544cab..c5849decfef 100644
--- a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
@@ -29,7 +29,7 @@ public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
 
     @Override
     public Node description() {
-        PreviewPanel previewPanel = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
         previewPanel.setEntry(diskEntry);
         return previewPanel;
     }
diff --git a/src/main/java/org/jabref/gui/search/SearchResultFrame.java b/src/main/java/org/jabref/gui/search/SearchResultFrame.java
index 9977866efad..376de69855e 100644
--- a/src/main/java/org/jabref/gui/search/SearchResultFrame.java
+++ b/src/main/java/org/jabref/gui/search/SearchResultFrame.java
@@ -55,6 +55,7 @@
 import org.jabref.logic.bibtex.comparator.FieldComparator;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.search.SearchQuery;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.FieldProperty;
@@ -122,7 +123,7 @@ private void init(String title) {
         searchResultFrame.setTitle(title);
         searchResultFrame.setIconImages(IconTheme.getLogoSet());
 
-        preview = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), frame.getDialogService(), ExternalFileTypes.getInstance());
+        preview = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), frame.getDialogService(), ExternalFileTypes.getInstance());
 
         sortedEntries = new SortedList<>(entries, new EntryComparator(false, true, FieldName.AUTHOR));
         model = (DefaultEventTableModel<BibEntry>) GlazedListsSwing.eventTableModelWithThreadProxyList(sortedEntries,

From 29e9d4971954a80510134800499fd65563e3b280 Mon Sep 17 00:00:00 2001
From: samiyac <samiya17094@iiitd.ac.in>
Date: Fri, 22 Mar 2019 01:57:11 +0530
Subject: [PATCH 131/184] Shortens text fields in Required Fields Tab

---
 src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java  | 2 +-
 src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java b/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
index bbd23b29d97..26f22eb2b6f 100644
--- a/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
@@ -103,7 +103,7 @@ private void setupPanel(BibEntry entry, boolean compressed, SuggestionProviders
         }
 
         ColumnConstraints columnExpand = new ColumnConstraints();
-        columnExpand.setHgrow(Priority.ALWAYS);
+        columnExpand.setPercentWidth(60);
 
         ColumnConstraints columnDoNotContract = new ColumnConstraints();
         columnDoNotContract.setMinWidth(Region.USE_PREF_SIZE);
diff --git a/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml b/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
index 99d6d3f7601..32160f0c544 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
+++ b/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
@@ -6,5 +6,5 @@
 <fx:root xmlns:fx="http://javafx.com/fxml/1" type="HBox" xmlns="http://javafx.com/javafx/8.0.112"
          fx:controller="org.jabref.gui.fieldeditors.BibtexKeyEditor">
     <EditorTextField fx:id="textField"/>
-    <Button fx:id="generateCiteKeyButton" styleClass="icon-button"/>
+    <Button fx:id="generateCiteKeyButton" text="Generate" styleClass="icon-button"/>
 </fx:root>

From 48ed0bae4c59b370bfb1be01328f99c06c141f5b Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 25 Mar 2019 17:36:02 +0100
Subject: [PATCH 132/184] fix npe

---
 .../java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
index 22f4c9a80b9..e4b658036a0 100644
--- a/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
@@ -46,7 +46,7 @@ public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
 
     @Override
     public Node description() {
-        PreviewPanel previewPanel = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
         previewPanel.setEntry(memEntry);
         return previewPanel;
     }

From e14b567425cdd2a49efcf56b0e4eafd0b96f1c1a Mon Sep 17 00:00:00 2001
From: Matthias Geiger <matthias.geiger@uni-bamberg.de>
Date: Mon, 25 Mar 2019 17:54:03 +0100
Subject: [PATCH 133/184] Followup of #4784 - fixes remaining issues of #4762
 (#4806)

* followup of #4784 - fixes remaining issues of #4762

* use Path instead of File

Co-authored-by: matthiasgeiger <matthias.geiger@uni-bamberg.de>
---
 src/main/java/org/jabref/gui/BasePanel.java   | 41 ++++++++++---------
 .../gui/exporter/SaveDatabaseAction.java      |  2 +-
 2 files changed, 23 insertions(+), 20 deletions(-)

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index 96d68e870dd..b64b181f60a 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -1,6 +1,5 @@
 package org.jabref.gui;
 
-import java.io.File;
 import java.io.IOException;
 import java.io.StringReader;
 import java.lang.reflect.InvocationTargetException;
@@ -115,7 +114,6 @@ public class BasePanel extends StackPane {
 
     private final BibDatabaseContext bibDatabaseContext;
     private final MainTableDataModel tableModel;
-    private final DatabaseChangePane changePane;
 
     private final CitationStyleCache citationStyleCache;
     private final FileAnnotationCache annotationCache;
@@ -138,6 +136,7 @@ public class BasePanel extends StackPane {
     // As most enums, this must not be null
     private BasePanelMode mode = BasePanelMode.SHOWING_NOTHING;
     private SplitPane splitPane;
+    private DatabaseChangePane changePane;
     private boolean saving;
 
     // AutoCompleter used in the search bar
@@ -186,22 +185,6 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         // ensure that all entry changes mark the panel as changed
         this.bibDatabaseContext.getDatabase().registerListener(this);
 
-        Optional<File> file = bibDatabaseContext.getDatabaseFile();
-        if (file.isPresent()) {
-            // Register so we get notifications about outside changes to the file.
-            changeMonitor = Optional.of(new DatabaseChangeMonitor(bibDatabaseContext, Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR));
-            changePane = new DatabaseChangePane(splitPane, bibDatabaseContext, changeMonitor.get());
-            getChildren().add(changePane);
-        } else {
-            if (bibDatabaseContext.getDatabase().hasEntries()) {
-                // if the database is not empty and no file is assigned,
-                // the database came from an import and has to be treated somehow
-                // -> mark as changed
-                this.baseChanged = true;
-            }
-            changePane = null;
-        }
-
         this.getDatabase().registerListener(new UpdateTimestampListener(Globals.prefs));
 
         this.entryEditor = new EntryEditor(this, preferences.getEntryEditorPreferences(), Globals.getFileUpdateMonitor(), dialogService, externalFileTypes, Globals.TASK_EXECUTOR);
@@ -790,6 +773,22 @@ public void setupMainPanel() {
         dividerPositionSubscription = EasyBind.monadic(Bindings.valueAt(splitPane.getDividers(), 0))
                                               .flatMap(SplitPane.Divider::positionProperty)
                                               .subscribe((observable, oldValue, newValue) -> saveDividerLocation(newValue));
+
+        // Add changePane in case a file is present - otherwise just add the splitPane to the panel
+        Optional<Path> file = bibDatabaseContext.getDatabasePath();
+        if (file.isPresent()) {
+            // create changeMonitor and changePane so we get notifications about outside changes to the file.
+            resetChangeMonitorAndChangePane();
+        } else {
+            if (bibDatabaseContext.getDatabase().hasEntries()) {
+                // if the database is not empty and no file is assigned,
+                // the database came from an import and has to be treated somehow
+                // -> mark as changed
+                this.baseChanged = true;
+            }
+            changePane = null;
+            getChildren().add(splitPane);
+        }
     }
 
     /**
@@ -1182,9 +1181,13 @@ public FileAnnotationCache getAnnotationCache() {
         return annotationCache;
     }
 
-    public void resetChangeMonitor() {
+    public void resetChangeMonitorAndChangePane() {
         changeMonitor.ifPresent(DatabaseChangeMonitor::unregister);
         changeMonitor = Optional.of(new DatabaseChangeMonitor(bibDatabaseContext, Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR));
+
+        changePane = new DatabaseChangePane(splitPane, bibDatabaseContext, changeMonitor.get());
+
+        this.getChildren().setAll(changePane);
     }
 
     public void updateTimeStamp() {
diff --git a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
index f1bfe5c0739..b743b7fa199 100644
--- a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
@@ -211,7 +211,7 @@ public void saveAs(Path file) {
         save();
 
         // Reinstall AutosaveManager and BackupManager
-        panel.resetChangeMonitor();
+        panel.resetChangeMonitorAndChangePane();
         if (readyForAutosave(context)) {
             AutosaveManager autosaver = AutosaveManager.start(context);
             autosaver.registerListener(new AutosaveUIManager(panel));

From 8e6b1772ef9f3486e6fe1d459d1b77f78018f335 Mon Sep 17 00:00:00 2001
From: Tim Kilian <mail@timkilian.pl>
Date: Tue, 26 Mar 2019 16:14:40 +0100
Subject: [PATCH 134/184] Fix do not clear wanted special characters (#4770)

---
 CHANGELOG.md                                              | 2 +-
 .../jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java | 6 ++++--
 .../logic/bibtexkeypattern/BibtexKeyGeneratorTest.java    | 8 ++++++++
 3 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9e14888432a..1450b5b5201 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -99,7 +99,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
-
+- We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
 
 
 
diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
index 6e10ac5ff8f..6309b297168 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
@@ -133,6 +133,9 @@ public String generateKey(BibEntry entry) {
                         label = applyModifiers(label, parts, 1);
                     }
 
+                    // Remove all illegal characters from the label.
+                    label = cleanKey(label, bibtexKeyPatternPreferences.isEnforceLegalKey());
+
                     stringBuilder.append(label);
 
                 } else {
@@ -143,8 +146,7 @@ public String generateKey(BibEntry entry) {
             LOGGER.warn("Cannot make label", e);
         }
 
-        // Remove all illegal characters from the key.
-        key = cleanKey(stringBuilder.toString(), bibtexKeyPatternPreferences.isEnforceLegalKey());
+        key = stringBuilder.toString();
 
         // Remove Regular Expressions while generating Keys
         String regex = bibtexKeyPatternPreferences.getKeyPatternRegex();
diff --git a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
index 3857cfb6c8b..ad6e2d86e1c 100644
--- a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
+++ b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
@@ -1073,4 +1073,12 @@ public void generateKeyWithYearAuthUpperTitleSentenceCaseModifier() throws Excep
         assertEquals("NewtonMaxwellEtAl_2019_TheInterestingTitleLongerThanThreeWords", BibtexKeyGenerator.generateKey(entry, "[authors2]_[year]_[title:capitalize]"));
     }
 
+    @Test
+    public void generateKeyWithMinusInCitationStyleOutsideAField() throws Exception {
+        BibEntry entry = new BibEntry();
+        entry.setField("author", AUTHOR_STRING_FIRSTNAME_FULL_LASTNAME_FULL_COUNT_1);
+        entry.setField("year", "2019");
+
+        assertEquals("Newton-2019", BibtexKeyGenerator.generateKey(entry, "[auth]-[year]"));
+    }
 }

From 83c8022697bef2756d238ad401adc6697ada467f Mon Sep 17 00:00:00 2001
From: Yash  Kothari <yashkothari199767@gmail.com>
Date: Tue, 26 Mar 2019 21:16:14 +0530
Subject: [PATCH 135/184] Fix closing of library not handling backup and
 autosave manager shutdown (#4794)

---
 src/main/java/org/jabref/gui/JabRefFrame.java | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index ff496a25e09..1cf05c35116 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -1154,6 +1154,10 @@ public void addTab(BasePanel basePanel, boolean raisePanel) {
             // add tab
             Tab newTab = new Tab(basePanel.getTabTitle(), basePanel);
             tabbedPane.getTabs().add(newTab);
+            newTab.setOnCloseRequest(event -> {
+                closeTab((BasePanel) newTab.getContent());
+                event.consume();
+            });
 
             // update all tab titles
             updateAllTabTitles();
@@ -1340,6 +1344,8 @@ private void closeTab(BasePanel panel) {
         if (panel.isModified() && (context.getLocation() == DatabaseLocation.LOCAL)) {
             if (confirmClose(panel)) {
                 removeTab(panel);
+            } else {
+                return;
             }
         } else if (context.getLocation() == DatabaseLocation.SHARED) {
             context.convertToLocalDatabase();

From 44163bfe151a6a09b8f1b355698a1c550a41ec16 Mon Sep 17 00:00:00 2001
From: Johannes Manner <johannes.manner@web.de>
Date: Wed, 27 Mar 2019 15:37:11 +0100
Subject: [PATCH 136/184] Change latex command handling only for XML Chars
 (#4379)

* Change latex command handling only for XML Chars

* Added Test for DocbookExporter

* Hopefully fixed travis error and added changelog entry

* Update DocbookExporterTest.java

* Resolve jupiter problem

* Update DocbookExporterTest.java
---
 CHANGELOG.md                                  |  1 +
 .../jabref/logic/layout/format/XMLChars.java  |  8 +-
 .../logic/exporter/DocbookExporterTest.java   | 74 +++++++++++++++++++
 3 files changed, 82 insertions(+), 1 deletion(-)
 create mode 100644 src/test/java/org/jabref/logic/exporter/DocbookExporterTest.java

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1450b5b5201..d5983623107 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We changed the latex command removal for docbook exporter. [#3838](https://github.com/JabRef/jabref/issues/3838)
 - We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
   - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
   - DOI/URL: General -> Optional
diff --git a/src/main/java/org/jabref/logic/layout/format/XMLChars.java b/src/main/java/org/jabref/logic/layout/format/XMLChars.java
index 59c98142969..4a3ada367a7 100644
--- a/src/main/java/org/jabref/logic/layout/format/XMLChars.java
+++ b/src/main/java/org/jabref/logic/layout/format/XMLChars.java
@@ -30,7 +30,8 @@ public String format(String fieldText) {
             return fieldText;
         }
 
-        String formattedFieldText = firstFormat(fieldText);
+        String latexCommandFree = removeLatexCommands(fieldText);
+        String formattedFieldText = firstFormat(latexCommandFree);
 
         for (Map.Entry<String, String> entry : XML_CHARS.entrySet()) {
             String s = entry.getKey();
@@ -42,6 +43,11 @@ public String format(String fieldText) {
         return restFormat(formattedFieldText);
     }
 
+    private String removeLatexCommands(String fieldText) {
+        LatexToUnicodeFormatter latexToUnicode = new LatexToUnicodeFormatter();
+        return latexToUnicode.format(fieldText);
+    }
+
     private static String firstFormat(String s) {
         return s.replaceAll("&|\\\\&", "&#x0026;").replace("--", "&#x2013;");
     }
diff --git a/src/test/java/org/jabref/logic/exporter/DocbookExporterTest.java b/src/test/java/org/jabref/logic/exporter/DocbookExporterTest.java
new file mode 100644
index 00000000000..a10a91ec6ff
--- /dev/null
+++ b/src/test/java/org/jabref/logic/exporter/DocbookExporterTest.java
@@ -0,0 +1,74 @@
+package org.jabref.logic.exporter;
+
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.jabref.logic.layout.LayoutFormatterPreferences;
+import org.jabref.logic.xmp.XmpPreferences;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import org.mockito.Answers;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.Mockito.mock;
+
+public class DocbookExporterTest {
+
+    public BibDatabaseContext databaseContext = new BibDatabaseContext();;
+    public Charset charset = StandardCharsets.UTF_8;
+
+    private Exporter exportFormat;
+
+    @BeforeEach
+    public void setUp() {
+        List<TemplateExporter> customFormats = new ArrayList<>();
+        LayoutFormatterPreferences layoutPreferences = mock(LayoutFormatterPreferences.class, Answers.RETURNS_DEEP_STUBS);
+        SavePreferences savePreferences = mock(SavePreferences.class);
+        XmpPreferences xmpPreferences = mock(XmpPreferences.class);
+        ExporterFactory exporterFactory = ExporterFactory.create(customFormats, layoutPreferences, savePreferences, xmpPreferences);
+
+        exportFormat = exporterFactory.getExporterByName("docbook4").get();
+    }
+
+    @Test
+    public void testCorruptedTitleBraces(@TempDir Path testFolder) throws Exception {
+        Path tmpFile = testFolder.resolve("testBraces");
+
+        BibEntry entry = new BibEntry();
+        entry.setField("title", "Peptidomics of the larval {\\protect{{D}rosophila melanogaster}} central nervous system.");
+
+        List<BibEntry> entries = Arrays.asList(entry);
+
+        exportFormat.export(databaseContext, tmpFile, charset, entries);
+
+        List<String> lines = Files.readAllLines(tmpFile);
+        assertEquals(20, lines.size());
+        assertEquals("   <citetitle pubwork=\"article\">Peptidomics of the larval Drosophila melanogaster central nervous system.</citetitle>", lines.get(9));
+    }
+
+    @Test
+    public void testCorruptedTitleUnicode(@TempDir Path testFolder) throws Exception {
+        Path tmpFile = testFolder.resolve("testBraces");
+
+        BibEntry entry = new BibEntry();
+        entry.setField("title", "Insect neuropeptide bursicon homodimers induce innate immune and stress genes during molting by activating the {NF}-$\\kappa$B transcription factor Relish.");
+
+        List<BibEntry> entries = Arrays.asList(entry);
+
+        exportFormat.export(databaseContext, tmpFile, charset, entries);
+
+        List<String> lines = Files.readAllLines(tmpFile);
+        assertEquals(20, lines.size());
+        assertEquals("   <citetitle pubwork=\"article\">Insect neuropeptide bursicon homodimers induce innate immune and stress genes during molting by activating the NF&#45;&#954;B transcription factor Relish.</citetitle>", lines.get(9));
+    }
+
+}

From ef5710c464612fc363f5e2f20b96b21463473236 Mon Sep 17 00:00:00 2001
From: Manuel <WtfJoke@users.noreply.github.com>
Date: Wed, 27 Mar 2019 18:58:45 +0100
Subject: [PATCH 137/184] Searchable/Filterable preferences (#4415)

* add search box to preferences

* replace deprecated method call

* Fix codestyle/checkstyle

* Add Preferences Search Handler

still work in progress
mapping search to preference and start searching it
still needs a way to filter the found items

* Remove unused variable

* Add a list of filtered preftabs instead of filtered preftabnames

* :tada: Add the actual filtering of the elements

* Favor SimpleListProperty over SimpleObjectProperty

* Fix Imports

also be explicit about method visibility

* Add filtering of labels

* Remove some unneeded member variables

* extract filterBy methods

* Fix Type of ListProperty

* Remove todo

Verified this is not the case: label names dont contain tab names

* Reformat code

* Favor regular List over ObservableList

* Use existing translated text for prompt

* Revert: Favor regular List over ObservableList

because build (guiTest) fails

* Favor regular List over ObservableList

is not the cause of the build failure

* Adding search highlight while filtering

* Replacing map by multimaps and changing the mapping relation

* Fixing checkstyle error

* Added Locale.ROOT when converting to lower case

* Removed redundant comments

* Removed LabeledWrapper inner class and refactored PreferencesSearchHandler

* Fixed checkstyle error

* add bidiretional binding to searchProperty

* Added change listener on searchBox and removed search text property

Co-authored-by: Yash Kothari <yashkothari199767@gmail.com>
---
 .../gui/preferences/PreferencesDialog.css     |  4 +
 .../gui/preferences/PreferencesDialog.java    | 21 +++-
 .../preferences/PreferencesSearchHandler.java | 98 +++++++++++++++++++
 3 files changed, 119 insertions(+), 4 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/preferences/PreferencesSearchHandler.java

diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css
index f79bfba706e..8407e1276de 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css
@@ -12,3 +12,7 @@
 .preferencePaneContainer {
     -fx-padding: 0em 1em 0em 3em;
 }
+
+*:search-highlight {
+	-fx-background-color: -jr-light-red;
+}
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
index e966cd2eb66..a64fa630780 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
@@ -1,6 +1,7 @@
 package org.jabref.gui.preferences;
 
 import java.util.List;
+import java.util.Locale;
 import java.util.prefs.BackingStoreException;
 
 import javafx.collections.FXCollections;
@@ -12,6 +13,7 @@
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.ListView;
 import javafx.scene.control.ScrollPane;
+import javafx.scene.control.TextField;
 import javafx.scene.control.Tooltip;
 import javafx.scene.layout.BorderPane;
 import javafx.scene.layout.Priority;
@@ -127,6 +129,15 @@ private void construct() {
                                                 .withText(PrefsTab::getTabName)
                                                 .install(tabsList);
 
+        TextField searchBox = new TextField();
+        searchBox.setPromptText(Localization.lang("Search"));
+
+        PreferencesSearchHandler searchHandler = new PreferencesSearchHandler(preferenceTabs);
+        tabsList.itemsProperty().bindBidirectional(searchHandler.filteredPreferenceTabsProperty());
+        searchBox.textProperty().addListener((observable, previousText, newText) -> {
+            searchHandler.filterTabs(newText.toLowerCase(Locale.ROOT));
+        });
+
         VBox buttonContainer = new VBox();
         buttonContainer.setAlignment(Pos.BOTTOM_LEFT);
         buttonContainer.setSpacing(3.0);
@@ -155,9 +166,11 @@ private void construct() {
         VBox.setVgrow(tabsList, Priority.ALWAYS);
         VBox.setVgrow(spacer, Priority.SOMETIMES);
         vBox.getChildren().addAll(
-                                  tabsList,
-                                  spacer,
-                                  buttonContainer);
+                searchBox,
+                tabsList,
+                spacer,
+                buttonContainer
+        );
 
         container.setLeft(vBox);
 
@@ -230,7 +243,7 @@ private void storeAllSettings() {
 
         GUIGlobals.updateEntryEditorColors();
         frame.setupAllTables();
-        frame.output(Localization.lang("Preferences recorded."));
+        dialogService.notify(Localization.lang("Preferences recorded."));
     }
 
     public void setValues() {
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesSearchHandler.java b/src/main/java/org/jabref/gui/preferences/PreferencesSearchHandler.java
new file mode 100644
index 00000000000..4478d88f75e
--- /dev/null
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesSearchHandler.java
@@ -0,0 +1,98 @@
+package org.jabref.gui.preferences;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Locale;
+
+import javafx.beans.property.ListProperty;
+import javafx.beans.property.SimpleListProperty;
+import javafx.collections.FXCollections;
+import javafx.css.PseudoClass;
+import javafx.scene.Node;
+import javafx.scene.Parent;
+import javafx.scene.control.Labeled;
+
+import com.google.common.collect.ArrayListMultimap;
+
+class PreferencesSearchHandler {
+
+    private static PseudoClass labelHighlight = PseudoClass.getPseudoClass("search-highlight");
+    private final List<PrefsTab> preferenceTabs;
+    private final ListProperty<PrefsTab> filteredPreferenceTabs;
+    private final ArrayListMultimap<PrefsTab, Labeled> preferenceTabsLabelNames;
+    private final ArrayList<Labeled> highlightedLabels = new ArrayList<>();
+
+    PreferencesSearchHandler(List<PrefsTab> preferenceTabs) {
+        this.preferenceTabs = preferenceTabs;
+        this.preferenceTabsLabelNames = getPrefsTabLabelMap();
+        this.filteredPreferenceTabs = new SimpleListProperty<>(FXCollections.observableArrayList(preferenceTabs));
+    }
+
+    public void filterTabs(String text) {
+        clearHighlights();
+        if (text.isEmpty()) {
+            clearSearch();
+            return;
+        }
+
+        filteredPreferenceTabs.clear();
+        for (PrefsTab tab : preferenceTabsLabelNames.keySet()) {
+            boolean tabContainsLabel = false;
+            for (Labeled labeled : preferenceTabsLabelNames.get(tab)) {
+                if (labelContainsText(labeled, text)) {
+                    tabContainsLabel = true;
+                    highlightLabel(labeled);
+                }
+            }
+            boolean tabNameIsMatchedByQuery = tab.getTabName().toLowerCase(Locale.ROOT).contains(text);
+            if (tabContainsLabel || tabNameIsMatchedByQuery) {
+                filteredPreferenceTabs.add(tab);
+            }
+        }
+    }
+
+    private boolean labelContainsText(Labeled labeled, String text) {
+        return labeled.getText().toLowerCase(Locale.ROOT).contains(text);
+    }
+
+    private void highlightLabel(Labeled labeled) {
+        labeled.pseudoClassStateChanged(labelHighlight, true);
+        highlightedLabels.add(labeled);
+    }
+
+    private void clearHighlights() {
+        highlightedLabels.forEach(labeled -> labeled.pseudoClassStateChanged(labelHighlight, false));
+    }
+
+    private void clearSearch() {
+        filteredPreferenceTabs.setAll(preferenceTabs);
+    }
+
+    /*
+     * Traverse all nodes of a PrefsTab and return a
+     * mapping from PrefsTab to all its Labeled type nodes.
+     */
+    private ArrayListMultimap<PrefsTab, Labeled> getPrefsTabLabelMap() {
+        ArrayListMultimap<PrefsTab, Labeled> prefsTabLabelMap = ArrayListMultimap.create();
+        for (PrefsTab prefsTab : preferenceTabs) {
+            Node builder = prefsTab.getBuilder();
+            if (builder instanceof Parent) {
+                Parent parentBuilder = (Parent) builder;
+                for (Node child : parentBuilder.getChildrenUnmodifiable()) {
+                    if (child instanceof Labeled) {
+                        Labeled labeled = (Labeled) child;
+                        if (!labeled.getText().isEmpty()) {
+                            prefsTabLabelMap.put(prefsTab, labeled);
+                        }
+                    }
+                }
+            }
+        }
+        return prefsTabLabelMap;
+    }
+
+    protected ListProperty<PrefsTab> filteredPreferenceTabsProperty() {
+        return filteredPreferenceTabs;
+    }
+
+}

From ce7293dc4ea0ba8cb56deff62419ac6fe0ea11fe Mon Sep 17 00:00:00 2001
From: Samiya Caur <36728314+samiyac@users.noreply.github.com>
Date: Wed, 27 Mar 2019 23:40:39 +0530
Subject: [PATCH 138/184] Item Count in a group updated correctly (#4807)

* Item Count in a group updated correctly

* Added comments

* changes
---
 src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java b/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java
index c31c9ce6dd9..cb17247dd0c 100644
--- a/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java
+++ b/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java
@@ -55,6 +55,7 @@ public class GroupNodeViewModel {
     private final BooleanBinding allSelectedEntriesMatched;
     private final TaskExecutor taskExecutor;
     private final CustomLocalDragboard localDragBoard;
+    private final ObservableList<BibEntry> entriesList;
 
     public GroupNodeViewModel(BibDatabaseContext databaseContext, StateManager stateManager, TaskExecutor taskExecutor, GroupTreeNode groupNode, CustomLocalDragboard localDragBoard) {
         this.databaseContext = Objects.requireNonNull(databaseContext);
@@ -84,7 +85,9 @@ public GroupNodeViewModel(BibDatabaseContext databaseContext, StateManager state
         expandedProperty.addListener((observable, oldValue, newValue) -> groupNode.getGroup().setExpanded(newValue));
 
         // Register listener
-        databaseContext.getDatabase().getEntries().addListener(this::onDatabaseChanged);
+        // The wrapper created by the FXCollections will set a weak listener on the wrapped list. This weak listener gets garbage collected. Hence, we need to maintain a reference to this list.
+        entriesList = databaseContext.getDatabase().getEntries();
+        entriesList.addListener(this::onDatabaseChanged);
 
         ObservableList<Boolean> selectedEntriesMatchStatus = EasyBind.map(stateManager.getSelectedEntries(), groupNode::matches);
         anySelectedEntriesMatched = BindingsHelper.any(selectedEntriesMatchStatus, matched -> matched);

From 133fbaa376e779ab515f763f7a6986a0ba4f37ce Mon Sep 17 00:00:00 2001
From: Yash  Kothari <yashkothari199767@gmail.com>
Date: Thu, 28 Mar 2019 13:34:47 +0530
Subject: [PATCH 139/184] Fix removing entries when source-code-field is out of
 focus (#4769)

Fixes #4764
---
 .../org/jabref/gui/entryeditor/SourceTab.java | 28 +++++++++----------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
index 89f97ffbf2e..2752103316d 100644
--- a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
@@ -145,7 +145,7 @@ protected void bindToEntry(BibEntry entry) {
         // and update source code for every change of entry field values
         BindingsHelper.bindContentBidirectional(entry.getFieldsObservable(), codeArea.focusedProperty(), onFocus -> {
             if (!onFocus) {
-                storeSource(codeArea.textProperty().getValue());
+                storeSource(entry, codeArea.textProperty().getValue());
             }
         }, fields -> {
             DefaultTaskExecutor.runAndWaitInJavaFXThread(() -> {
@@ -163,8 +163,8 @@ protected void bindToEntry(BibEntry entry) {
 
     }
 
-    private void storeSource(String text) {
-        if ((currentEntry == null) || text.isEmpty()) {
+    private void storeSource(BibEntry outOfFocusEntry, String text) {
+        if ((outOfFocusEntry == null) || text.isEmpty()) {
             return;
         }
 
@@ -197,42 +197,42 @@ private void storeSource(String text) {
             String newKey = newEntry.getCiteKeyOptional().orElse(null);
 
             if (newKey != null) {
-                currentEntry.setCiteKey(newKey);
+                outOfFocusEntry.setCiteKey(newKey);
             } else {
-                currentEntry.clearCiteKey();
+                outOfFocusEntry.clearCiteKey();
             }
 
             // First, remove fields that the user has removed.
-            for (Map.Entry<String, String> field : currentEntry.getFieldMap().entrySet()) {
+            for (Map.Entry<String, String> field : outOfFocusEntry.getFieldMap().entrySet()) {
                 String fieldName = field.getKey();
                 String fieldValue = field.getValue();
 
                 if (InternalBibtexFields.isDisplayableField(fieldName) && !newEntry.hasField(fieldName)) {
                     compound.addEdit(
-                            new UndoableFieldChange(currentEntry, fieldName, fieldValue, null));
-                    currentEntry.clearField(fieldName);
+                                     new UndoableFieldChange(outOfFocusEntry, fieldName, fieldValue, null));
+                    outOfFocusEntry.clearField(fieldName);
                 }
             }
 
             // Then set all fields that have been set by the user.
             for (Map.Entry<String, String> field : newEntry.getFieldMap().entrySet()) {
                 String fieldName = field.getKey();
-                String oldValue = currentEntry.getField(fieldName).orElse(null);
+                String oldValue = outOfFocusEntry.getField(fieldName).orElse(null);
                 String newValue = field.getValue();
                 if (!Objects.equals(oldValue, newValue)) {
                     // Test if the field is legally set.
                     new LatexFieldFormatter(fieldFormatterPreferences)
                             .format(newValue, fieldName);
 
-                    compound.addEdit(new UndoableFieldChange(currentEntry, fieldName, oldValue, newValue));
-                    currentEntry.setField(fieldName, newValue);
+                    compound.addEdit(new UndoableFieldChange(outOfFocusEntry, fieldName, oldValue, newValue));
+                    outOfFocusEntry.setField(fieldName, newValue);
                 }
             }
 
             // See if the user has changed the entry type:
-            if (!Objects.equals(newEntry.getType(), currentEntry.getType())) {
-                compound.addEdit(new UndoableChangeType(currentEntry, currentEntry.getType(), newEntry.getType()));
-                currentEntry.setType(newEntry.getType());
+            if (!Objects.equals(newEntry.getType(), outOfFocusEntry.getType())) {
+                compound.addEdit(new UndoableChangeType(outOfFocusEntry, outOfFocusEntry.getType(), newEntry.getType()));
+                outOfFocusEntry.setType(newEntry.getType());
             }
             compound.end();
             undoManager.addEdit(compound);

From a9115a256107620fcfbb7c087f1e89e14a632b0d Mon Sep 17 00:00:00 2001
From: Robin <robin.lichtenthaeler@web.de>
Date: Thu, 28 Mar 2019 12:07:14 +0100
Subject: [PATCH 140/184] put renaming of file entries in JavaFX thread for
 cleanup (#4818)

---
 src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java b/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
index 4016081e60b..72912ed73de 100644
--- a/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
+++ b/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
@@ -7,6 +7,7 @@
 import java.util.Objects;
 import java.util.Optional;
 
+import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.externalfiles.LinkedFileHandler;
 import org.jabref.model.FieldChange;
 import org.jabref.model.cleanup.CleanupJob;
@@ -54,8 +55,8 @@ public List<FieldChange> cleanup(BibEntry entry) {
         }
 
         if (changed) {
-            Optional<FieldChange> changes = entry.setFiles(files);
-            return OptionalUtil.toList(changes);
+            Optional<FieldChange> fileFieldChanged = DefaultTaskExecutor.runInJavaFXThread(() -> entry.setFiles(files));
+            return OptionalUtil.toList(fileFieldChanged);
         }
 
         return Collections.emptyList();

From a731679333d3c8b91a3a24c69b6a7bd9151639e2 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Thu, 28 Mar 2019 18:48:08 +0100
Subject: [PATCH 141/184] Remove unused swing code (#4787)

* Remove unused swing code

* Implement feedback and fix tests
---
 src/main/java/org/jabref/JabRefGUI.java       |  23 +-
 src/main/java/org/jabref/gui/BasePanel.java   |  34 --
 .../jabref/gui/DuplicateResolverDialog.java   |   2 +-
 src/main/java/org/jabref/gui/GUIGlobals.java  |   8 -
 .../gui/JEditorPaneWithHighlighting.java      |  57 ---
 src/main/java/org/jabref/gui/JabRefFrame.java |  26 --
 .../jabref/gui/actions/ChangeTypeAction.java  |  52 ---
 .../jabref/gui/actions/CopyDoiUrlAction.java  |  18 +-
 .../gui/actions/MnemonicAwareAction.java      |  44 --
 .../jabref/gui/actions/StandardActions.java   |   5 +
 .../BibtexKeyPatternPanel.java                |  18 +-
 .../gui/cleanup/CleanupActionsListModel.java  |  81 ----
 .../CustomizeGeneralFieldsDialogView.java     |   6 +-
 .../jabref/gui/entryeditor/EntryEditor.java   |   2 +-
 .../externalfiles/DownloadExternalFile.java   | 345 ----------------
 .../JTextAreaWithHighlighting.java            | 173 --------
 .../gui/fieldeditors/LinkedFileViewModel.java |  10 +-
 .../fieldeditors/contextmenu/EditorMenus.java |  11 +-
 .../ConfirmCloseFileListEntryEditor.java      |  14 -
 .../gui/filelist/FileListEntryEditor.java     | 386 ------------------
 .../gui/groups/GroupTreeCellRenderer.java     | 114 ------
 .../java/org/jabref/gui/help/HelpAction.java  |  58 +--
 .../gui/importer/fetcher/WebSearchPane.java   |   3 +-
 .../org/jabref/gui/keyboard/KeyBinder.java    |  29 --
 .../org/jabref/gui/maintable/MainTable.java   |  14 +-
 .../jabref/gui/maintable/RightClickMenu.java  |   4 +-
 .../jabref/gui/menus/ChangeEntryTypeMenu.java |  91 +----
 .../gui/openoffice/OpenOfficePanel.java       |   4 +-
 .../jabref/gui/preferences/AdvancedTab.java   |   2 +-
 .../org/jabref/gui/preferences/FileTab.java   |   5 +-
 .../jabref/gui/preferences/GeneralTab.java    |   4 +-
 .../gui/preferences/NameFormatterTab.java     |   3 +-
 .../gui/preferences/TableColumnsTab.java      |  57 +--
 .../org/jabref/gui/util/ControlHelper.java    |  10 -
 .../gui/util/component/CheckBoxMessage.java   |  37 --
 .../component/JTextAreaWithPlaceholder.java   |  90 ----
 .../component/JTextFieldWithPlaceholder.java  |  91 -----
 .../java/org/jabref/gui/worker/CallBack.java  |  11 -
 .../java/org/jabref/logic/net/URLUtil.java    |  57 ++-
 src/main/resources/l10n/JabRef_en.properties  |  10 -
 .../cleanup/CleanupActionsListModelTest.java  |  94 -----
 41 files changed, 147 insertions(+), 1956 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/JEditorPaneWithHighlighting.java
 delete mode 100644 src/main/java/org/jabref/gui/actions/ChangeTypeAction.java
 delete mode 100644 src/main/java/org/jabref/gui/actions/MnemonicAwareAction.java
 delete mode 100644 src/main/java/org/jabref/gui/cleanup/CleanupActionsListModel.java
 delete mode 100644 src/main/java/org/jabref/gui/externalfiles/DownloadExternalFile.java
 delete mode 100644 src/main/java/org/jabref/gui/fieldeditors/JTextAreaWithHighlighting.java
 delete mode 100644 src/main/java/org/jabref/gui/filelist/ConfirmCloseFileListEntryEditor.java
 delete mode 100644 src/main/java/org/jabref/gui/filelist/FileListEntryEditor.java
 delete mode 100644 src/main/java/org/jabref/gui/groups/GroupTreeCellRenderer.java
 delete mode 100644 src/main/java/org/jabref/gui/keyboard/KeyBinder.java
 delete mode 100644 src/main/java/org/jabref/gui/util/component/CheckBoxMessage.java
 delete mode 100644 src/main/java/org/jabref/gui/util/component/JTextAreaWithPlaceholder.java
 delete mode 100644 src/main/java/org/jabref/gui/util/component/JTextFieldWithPlaceholder.java
 delete mode 100644 src/main/java/org/jabref/gui/worker/CallBack.java
 delete mode 100644 src/test/java/org/jabref/cleanup/CleanupActionsListModelTest.java

diff --git a/src/main/java/org/jabref/JabRefGUI.java b/src/main/java/org/jabref/JabRefGUI.java
index 57214d9ef9f..203dcf03386 100644
--- a/src/main/java/org/jabref/JabRefGUI.java
+++ b/src/main/java/org/jabref/JabRefGUI.java
@@ -65,17 +65,7 @@ public JabRefGUI(Stage mainStage, List<ParserResult> argsDatabases, boolean isBl
     }
 
     private void openWindow(Stage mainStage) {
-        // Set antialiasing on everywhere. This only works in JRE >= 1.5.
-        // Or... it doesn't work, period.
-        // TODO test and maybe remove this! I found this commented out with no additional info ( payload@lavabit.com )
-        // Enabled since JabRef 2.11 beta 4
-        System.setProperty("swing.aatext", "true");
-        // Default is "on".
-        // "lcd" instead of "on" because of http://wiki.netbeans.org/FaqFontRendering and http://docs.oracle.com/javase/6/docs/technotes/guides/2d/flags.html#aaFonts
-        System.setProperty("awt.useSystemAAFontSettings", "lcd");
-
-        // look and feel. This MUST be the first thing to do before loading any Swing-specific code!
-        setLookAndFeel();
+        applyFontRenderingTweak();
 
         // If the option is enabled, open the last edited libraries, if any.
         if (!isBlank && Globals.prefs.getBoolean(JabRefPreferences.OPEN_LAST_EDITED)) {
@@ -242,9 +232,9 @@ private boolean isLoaded(File fileToOpen) {
         return false;
     }
 
-    private void setLookAndFeel() {
-        // On Linux, Java FX fonts look blurry per default. This can be improved by using a non-default rendering
-        // setting. See https://github.com/woky/javafx-hates-linux
+    private void applyFontRenderingTweak() {
+        // On Linux, Java FX fonts look blurry per default. This can be improved by using a non-default rendering setting.
+        // See https://github.com/woky/javafx-hates-linux
         if (Globals.prefs.getBoolean(JabRefPreferences.FX_FONT_RENDERING_TWEAK)) {
             System.setProperty("prism.text", "t2k");
             System.setProperty("prism.lcdtext", "true");
@@ -254,9 +244,4 @@ private void setLookAndFeel() {
     public static JabRefFrame getMainFrame() {
         return mainFrame;
     }
-
-    // Only used for testing, other than that do NOT set the mainFrame...
-    public static void setMainFrame(JabRefFrame mainFrame) {
-        JabRefGUI.mainFrame = mainFrame;
-    }
 }
diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index b64b181f60a..2ccfcdcc927 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -63,7 +63,6 @@
 import org.jabref.gui.specialfields.SpecialFieldViewModel;
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableChangeType;
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.gui.undo.UndoableInsertEntry;
 import org.jabref.gui.undo.UndoableRemoveEntry;
@@ -1011,39 +1010,6 @@ public BibDatabase getDatabase() {
         return bibDatabaseContext.getDatabase();
     }
 
-    public void changeTypeOfSelectedEntries(String newType) {
-        List<BibEntry> bes = mainTable.getSelectedEntries();
-        changeType(bes, newType);
-    }
-
-    private void changeType(List<BibEntry> entries, String newType) {
-        if ((entries == null) || (entries.isEmpty())) {
-            LOGGER.error("At least one entry must be selected to be able to change the type.");
-            return;
-        }
-
-        if (entries.size() > 1) {
-            boolean proceed = dialogService.showConfirmationDialogAndWait(Localization.lang("Change entry type"), Localization.lang("Multiple entries selected. Do you want to change the type of all these to '%0'?"));
-            if (!proceed) {
-                return;
-            }
-        }
-
-        NamedCompound compound = new NamedCompound(Localization.lang("Change entry type"));
-        for (BibEntry entry : entries) {
-            compound.addEdit(new UndoableChangeType(entry, entry.getType(), newType));
-            DefaultTaskExecutor.runInJavaFXThread(() -> {
-                entry.setType(newType);
-            });
-        }
-
-        output(formatOutputMessage(Localization.lang("Changed type to '%0' for", newType), entries.size()));
-        compound.end();
-        getUndoManager().addEdit(compound);
-        markBaseChanged();
-        updateEntryEditorIfShowing();
-    }
-
     public boolean showDeleteConfirmationDialog(int numberOfEntries) {
         if (Globals.prefs.getBoolean(JabRefPreferences.CONFIRM_DELETE)) {
             String title = Localization.lang("Delete entry");
diff --git a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
index fa1b2b92b96..a56da356f6f 100644
--- a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
+++ b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
@@ -116,7 +116,7 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
 
         getDialogPane().setContent(borderPane);
         Button helpButton = (Button) this.getDialogPane().lookupButton(help);
-        helpButton.setOnAction(evt -> helpCommand.getCommand().execute());
+        helpButton.setOnAction(evt -> helpCommand.execute());
     }
 
     public BibEntry getMergedEntry() {
diff --git a/src/main/java/org/jabref/gui/GUIGlobals.java b/src/main/java/org/jabref/gui/GUIGlobals.java
index e1f145054ff..12d55f69bbe 100644
--- a/src/main/java/org/jabref/gui/GUIGlobals.java
+++ b/src/main/java/org/jabref/gui/GUIGlobals.java
@@ -10,9 +10,6 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.preferences.JabRefPreferences;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /**
  * Static variables for graphics files and keyboard shortcuts.
  */
@@ -32,11 +29,6 @@ public class GUIGlobals {
 
     public static final String UNTITLED_TITLE = Localization.lang("untitled");
 
-    //	Colors.
-    public static final Color ENTRY_EDITOR_LABEL_COLOR = new Color(100, 100, 150); // Empty field, blue.
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(GUIGlobals.class);
-
     private GUIGlobals() {
     }
 
diff --git a/src/main/java/org/jabref/gui/JEditorPaneWithHighlighting.java b/src/main/java/org/jabref/gui/JEditorPaneWithHighlighting.java
deleted file mode 100644
index 71235c5d08e..00000000000
--- a/src/main/java/org/jabref/gui/JEditorPaneWithHighlighting.java
+++ /dev/null
@@ -1,57 +0,0 @@
-package org.jabref.gui;
-
-import java.util.Optional;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.swing.JEditorPane;
-import javax.swing.text.BadLocationException;
-import javax.swing.text.DefaultHighlighter;
-import javax.swing.text.Document;
-import javax.swing.text.Highlighter;
-import javax.swing.text.LayeredHighlighter.LayerPainter;
-
-import org.jabref.gui.fieldeditors.JTextAreaWithHighlighting;
-import org.jabref.logic.search.SearchQueryHighlightListener;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class JEditorPaneWithHighlighting extends JEditorPane implements SearchQueryHighlightListener {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(JTextAreaWithHighlighting.class);
-
-    public void highlightPattern(Optional<Pattern> highlightPattern) {
-        Highlighter highlighter = getHighlighter();
-        highlighter.removeAllHighlights();
-
-        if ((highlightPattern == null) || !highlightPattern.isPresent()) {
-            return;
-        }
-
-        String text = getDocumentText();
-
-        Matcher matcher = highlightPattern.get().matcher(text);
-        LayerPainter painter = DefaultHighlighter.DefaultPainter;
-        while (matcher.find()) {
-            try {
-                highlighter.addHighlight(matcher.start(), matcher.end(), painter);
-            } catch (BadLocationException ble) {
-                // should not occur if matcher works right
-                LOGGER.warn("Highlighting not possible, bad location", ble);
-            }
-        }
-    }
-
-    private String getDocumentText() {
-        Document doc = getDocument();
-        String text;
-        try {
-            text = doc.getText(0, doc.getLength());
-        } catch (Exception e) {
-            LOGGER.error("Error while getting document text");
-            text = "";
-        }
-        return text;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 1cf05c35116..838f5d459f0 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -550,32 +550,6 @@ public void changed(ObservableValue<? extends Boolean> observable, Boolean oldVa
         });
 
         setCenter(splitPane);
-
-        /*
-        GridBagLayout gbl = new GridBagLayout();
-        GridBagConstraints con = new GridBagConstraints();
-        con.fill = GridBagConstraints.BOTH;
-        con.anchor = GridBagConstraints.WEST;
-        JPanel status = new JPanel();
-        status.setLayout(gbl);
-        con.weighty = 0;
-        con.weightx = 0;
-        con.gridwidth = 1;
-        con.insets = new Insets(0, 2, 0, 0);
-        gbl.setConstraints(statusLabel, con);
-        status.add(statusLabel);
-        con.weightx = 1;
-        con.insets = new Insets(0, 4, 0, 0);
-        con.gridwidth = 1;
-        gbl.setConstraints(statusLine, con);
-        status.add(statusLine);
-        con.weightx = 0;
-        con.gridwidth = GridBagConstraints.REMAINDER;
-        con.insets = new Insets(2, 4, 2, 2);
-        gbl.setConstraints(progressBar, con);
-        status.add(progressBar);
-        statusLabel.setForeground(GUIGlobals.ENTRY_EDITOR_LABEL_COLOR.darker());
-        */
     }
 
     private void setDividerPosition() {
diff --git a/src/main/java/org/jabref/gui/actions/ChangeTypeAction.java b/src/main/java/org/jabref/gui/actions/ChangeTypeAction.java
deleted file mode 100644
index b7b907a662c..00000000000
--- a/src/main/java/org/jabref/gui/actions/ChangeTypeAction.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package org.jabref.gui.actions;
-
-import java.awt.event.ActionEvent;
-import java.util.Collections;
-import java.util.List;
-
-import javax.swing.AbstractAction;
-import javax.swing.undo.UndoManager;
-
-import javafx.scene.control.MenuItem;
-
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableChangeType;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.EntryType;
-
-public class ChangeTypeAction extends AbstractAction {
-
-    private final String type;
-    private final BasePanel panel;
-
-    public ChangeTypeAction(EntryType type, BasePanel bp) {
-        super(type.getName());
-        this.type = type.getName();
-        panel = bp;
-    }
-
-    @Override
-    public void actionPerformed(ActionEvent evt) {
-        panel.changeTypeOfSelectedEntries(type);
-    }
-
-    public static MenuItem as(EntryType type, BibEntry entry, UndoManager undoManager) {
-        return as(type, Collections.singletonList(entry), undoManager);
-    }
-
-    public static MenuItem as(EntryType type, List<BibEntry> entries, UndoManager undoManager) {
-        MenuItem menuItem = new MenuItem(type.getName());
-        menuItem.setOnAction(event -> {
-            NamedCompound compound = new NamedCompound(Localization.lang("Change entry type"));
-            for (BibEntry entry : entries) {
-                entry.setType(type)
-                        .ifPresent(change -> compound.addEdit(new UndoableChangeType(change)));
-            }
-
-            undoManager.addEdit(compound);
-        });
-        return menuItem;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java b/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
index aa8ee344abe..51adf9ba8b3 100644
--- a/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
+++ b/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
@@ -1,10 +1,7 @@
 package org.jabref.gui.actions;
 
-import java.awt.event.ActionEvent;
 import java.util.Optional;
 
-import javax.swing.AbstractAction;
-
 import javafx.scene.control.TextArea;
 
 import org.jabref.Globals;
@@ -15,24 +12,17 @@
 /**
  * Copies the doi url to the clipboard
  */
-public class CopyDoiUrlAction extends AbstractAction {
-
-    private TextArea component = null;
-    private String identifier;
+public class CopyDoiUrlAction extends SimpleCommand {
 
-    public CopyDoiUrlAction(String identifier) {
-        super(Localization.lang("Copy DOI url"));
-        this.identifier = identifier;
-    }
+    private TextArea component;
 
     public CopyDoiUrlAction(TextArea component) {
-        this(component.getText());
         this.component = component;
     }
 
     @Override
-    public void actionPerformed(ActionEvent e) {
-        identifier = component == null ? identifier : component.getText();
+    public void execute() {
+        String identifier = component.getText();
 
         Optional<String> urlOptional = DOI.parse(identifier).map(DOI::getURIAsASCIIString);
         if (urlOptional.isPresent()) {
diff --git a/src/main/java/org/jabref/gui/actions/MnemonicAwareAction.java b/src/main/java/org/jabref/gui/actions/MnemonicAwareAction.java
deleted file mode 100644
index b1bfa9f87d5..00000000000
--- a/src/main/java/org/jabref/gui/actions/MnemonicAwareAction.java
+++ /dev/null
@@ -1,44 +0,0 @@
-package org.jabref.gui.actions;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.Icon;
-
-import org.jabref.gui.icon.IconTheme;
-
-/**
- * This class extends {@link AbstractAction} with the ability to set
- * the mnemonic key based on a '&' character inserted in front of
- * the desired mnemonic letter. This is done by setting the action's
- * name using putValue(NAME, actionname).
- * This facilitates localized mnemonics.
- */
-public abstract class MnemonicAwareAction extends AbstractAction {
-
-    public MnemonicAwareAction() { }
-
-    public MnemonicAwareAction(Icon icon) {
-        if (icon instanceof IconTheme.FontBasedIcon) {
-            putValue(Action.SMALL_ICON, ((IconTheme.FontBasedIcon) icon).createSmallIcon());
-            putValue(Action.LARGE_ICON_KEY, icon);
-        } else {
-            putValue(Action.SMALL_ICON, icon);
-        }
-    }
-
-    @Override
-    public void putValue(String key, Object value) {
-        if (key.equals(Action.NAME)) {
-            String name = value.toString();
-            int i = name.indexOf('&');
-            if (i >= 0) {
-                char mnemonic = Character.toUpperCase(name.charAt(i + 1));
-                putValue(Action.MNEMONIC_KEY, (int) mnemonic);
-                value = name.substring(0, i) + name.substring(i + 1);
-            } else {
-                value = name;
-            }
-        }
-        super.putValue(key, value);
-    }
-}
diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
index 6e7493f32d7..2c91ff5c4b5 100644
--- a/src/main/java/org/jabref/gui/actions/StandardActions.java
+++ b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -91,6 +91,7 @@ public enum StandardActions implements Action {
     OPEN_FILE(Localization.lang("Open file"), Localization.lang("Open file"), IconTheme.JabRefIcons.FILE, KeyBinding.OPEN_FILE),
     OPEN_CONSOLE(Localization.lang("Open terminal here"), Localization.lang("Open terminal here"), IconTheme.JabRefIcons.CONSOLE, KeyBinding.OPEN_CONSOLE),
     COPY_LINKED_FILES(Localization.lang("Copy linked files to folder...")),
+    COPY_DOI(Localization.lang("Copy DOI url")),
     ABBREVIATE(Localization.lang("Abbreviate journal names")),
     ABBREVIATE_ISO("ISO", Localization.lang("Abbreviate journal names of the selected entries (ISO abbreviation)"), KeyBinding.ABBREVIATE),
     ABBREVIATE_MEDLINE("MEDLINE", Localization.lang("Abbreviate journal names of the selected entries (MEDLINE abbreviation)")),
@@ -138,6 +139,10 @@ public enum StandardActions implements Action {
     SET_FILE_LINKS(Localization.lang("Automatically set file links"), KeyBinding.AUTOMATICALLY_LINK_FILES),
 
     HELP(Localization.lang("Online help"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
+    HELP_KEY_PATTERNS(Localization.lang("Help on key patterns"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
+    HELP_REGEX_SEARCH(Localization.lang("Help on regular expression search"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
+    HELP_NAME_FORMATTER(Localization.lang("Help on Name Formatting"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
+    HELP_SPECIAL_FIELDS(Localization.lang("Help on special fields"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
     WEB_MENU(Localization.lang("JabRef resources")),
     OPEN_WEBPAGE(Localization.lang("Website"), Localization.lang("Opens JabRef's website")),
     OPEN_FACEBOOK("Facebook", Localization.lang("Opens JabRef's Facebook page"), IconTheme.JabRefIcons.FACEBOOK),
diff --git a/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java b/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
index e3796c623ee..e1e81d2bc03 100644
--- a/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
+++ b/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
@@ -1,7 +1,5 @@
 package org.jabref.gui.bibtexkeypattern;
 
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
 import java.util.HashMap;
 import java.util.Locale;
 import java.util.Map;
@@ -30,15 +28,9 @@
 
 public class BibtexKeyPatternPanel extends Pane {
 
-    // used by both BibtexKeyPatternPanel and TabLabelPAttern
-    protected final GridBagLayout gbl = new GridBagLayout();
-    protected final GridBagConstraints con = new GridBagConstraints();
-
     // default pattern
     protected final TextField defaultPat = new TextField();
 
-    private final int COLUMNS = 2;
-
     // one field for each type
     private final Map<String, TextField> textFields = new HashMap<>();
     private final BasePanel panel;
@@ -64,7 +56,8 @@ private void buildGUI() {
         int rowIndex = 1;
         int columnIndex = 0;
         // The header - can be removed
-        for (int i = 0; i < COLUMNS; i++) {
+        int columnsNumber = 2;
+        for (int i = 0; i < columnsNumber; i++) {
             Label label = new Label(Localization.lang("Entry type"));
             Label keyPattern = new Label(Localization.lang("Key pattern"));
             gridPane.add(label, ++columnIndex, rowIndex);
@@ -93,7 +86,7 @@ private void buildGUI() {
 
             textFields.put(type.getName().toLowerCase(Locale.ROOT), textField);
 
-            if (columnIndex == (COLUMNS - 1)) {
+            if (columnIndex == (columnsNumber - 1)) {
                 columnIndex = 0;
                 rowIndex++;
             } else {
@@ -104,7 +97,7 @@ private void buildGUI() {
         rowIndex++;
 
         ActionFactory factory = new ActionFactory(Globals.prefs.getKeyBindingRepository());
-        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on key patterns"), HelpFile.BIBTEX_KEY_PATTERN).getCommand());
+        Button help = factory.createIconButton(StandardActions.HELP_KEY_PATTERNS, new HelpAction(HelpFile.BIBTEX_KEY_PATTERN));
         gridPane.add(help, 1, rowIndex);
 
         Button btnDefaultAll1 = new Button(Localization.lang("Reset all"));
@@ -138,8 +131,7 @@ private void fillPatternUsingPanelData(AbstractBibtexKeyPattern keypatterns) {
     }
 
     protected GlobalBibtexKeyPattern getKeyPatternAsGlobalBibtexKeyPattern() {
-        GlobalBibtexKeyPattern res = GlobalBibtexKeyPattern.fromPattern(
-                                                                        JabRefPreferences.getInstance().get(JabRefPreferences.DEFAULT_BIBTEX_KEY_PATTERN));
+        GlobalBibtexKeyPattern res = GlobalBibtexKeyPattern.fromPattern(Globals.prefs.get(JabRefPreferences.DEFAULT_BIBTEX_KEY_PATTERN));
         fillPatternUsingPanelData(res);
         return res;
     }
diff --git a/src/main/java/org/jabref/gui/cleanup/CleanupActionsListModel.java b/src/main/java/org/jabref/gui/cleanup/CleanupActionsListModel.java
deleted file mode 100644
index f7bf8a5e463..00000000000
--- a/src/main/java/org/jabref/gui/cleanup/CleanupActionsListModel.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package org.jabref.gui.cleanup;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-
-import javax.swing.ListModel;
-import javax.swing.event.ListDataEvent;
-import javax.swing.event.ListDataListener;
-
-import org.jabref.model.cleanup.FieldFormatterCleanup;
-import org.jabref.model.cleanup.FieldFormatterCleanups;
-
-public class CleanupActionsListModel implements ListModel<FieldFormatterCleanup> {
-
-    private List<FieldFormatterCleanup> cleanupActions;
-    private final List<ListDataListener> listeners = new ArrayList<>();
-
-
-    public CleanupActionsListModel(List<FieldFormatterCleanup> cleanupAction) {
-        Objects.requireNonNull(cleanupAction);
-        this.cleanupActions = cleanupAction;
-
-    }
-
-    public void addCleanupAction(FieldFormatterCleanup action) {
-        if (!cleanupActions.contains(action)) {
-            cleanupActions.add(action);
-            for (ListDataListener listener : listeners) {
-                listener.intervalAdded(new ListDataEvent(action, ListDataEvent.INTERVAL_ADDED, cleanupActions.size(),
-                        cleanupActions.size()));
-            }
-        }
-    }
-
-    /**
-     * Removes the action at the specified index from the list.
-     * Removal is only done when index {@code >=0} and index {@code<=} list size
-     * @param index The index to remove
-     */
-    public void removeAtIndex(int index) {
-
-        if ((index >= 0) && (index < cleanupActions.size())) {
-            FieldFormatterCleanup action = cleanupActions.remove(index);
-            for (ListDataListener listener : listeners) {
-                listener.intervalRemoved(new ListDataEvent(action, ListDataEvent.INTERVAL_REMOVED, index, index));
-            }
-        }
-    }
-
-    public List<FieldFormatterCleanup> getAllActions() {
-        return cleanupActions;
-    }
-
-    @Override
-    public int getSize() {
-        return cleanupActions.size();
-    }
-
-    @Override
-    public FieldFormatterCleanup getElementAt(int index) {
-        return cleanupActions.get(index);
-    }
-
-    @Override
-    public void addListDataListener(ListDataListener l) {
-        listeners.add(l);
-    }
-
-    @Override
-    public void removeListDataListener(ListDataListener l) {
-        listeners.remove(l);
-    }
-
-    public void reset(FieldFormatterCleanups defaultFormatters) {
-        cleanupActions = new ArrayList<>(defaultFormatters.getConfiguredActions());
-        for (ListDataListener listener : listeners) {
-            listener.contentsChanged(new ListDataEvent(this, ListDataEvent.CONTENTS_CHANGED, 0, cleanupActions.size()));
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/gui/customizefields/CustomizeGeneralFieldsDialogView.java b/src/main/java/org/jabref/gui/customizefields/CustomizeGeneralFieldsDialogView.java
index a36f44bb86d..e2e6fe781fb 100644
--- a/src/main/java/org/jabref/gui/customizefields/CustomizeGeneralFieldsDialogView.java
+++ b/src/main/java/org/jabref/gui/customizefields/CustomizeGeneralFieldsDialogView.java
@@ -36,11 +36,7 @@ public CustomizeGeneralFieldsDialogView() {
                   .load()
                   .setAsDialogPane(this);
 
-        HelpAction helpCommand = new HelpAction(HelpFile.GENERAL_FIELDS);
-        //HelpAction is written with Swing, not JavaFX, so runCommand() cannot be used normally.  Here I am reaching into
-        //the command and running execute.  When HelpAction is converted to JavaFX,
-        //the following will need to be changed.
-        ControlHelper.setAction(helpButton, getDialogPane(), event -> helpCommand.getCommand().execute());
+        ControlHelper.setAction(helpButton, getDialogPane(), event -> new HelpAction(HelpFile.GENERAL_FIELDS).execute());
         ControlHelper.setAction(resetButton, getDialogPane(), event -> resetFields());
         ControlHelper.setAction(okButton, getDialogPane(), event -> saveFieldsAndCloseDialog());
 
diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
index 450da9e98d9..4ebdb2b1b72 100644
--- a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
+++ b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -376,7 +376,7 @@ private void setupToolBar() {
         typeLabel.setText(typedEntry.getTypeForDisplay());
 
         // Add type change menu
-        ContextMenu typeMenu = new ChangeEntryTypeMenu(preferences.getKeyBindings()).getChangeEntryTypePopupMenu(entry, databaseContext, undoManager);
+        ContextMenu typeMenu = new ChangeEntryTypeMenu().getChangeEntryTypePopupMenu(entry, databaseContext, undoManager);
         typeLabel.setOnMouseClicked(event -> typeMenu.show(typeLabel, Side.RIGHT, 0, 0));
         typeChangeButton.setOnMouseClicked(event -> typeMenu.show(typeChangeButton, Side.RIGHT, 0, 0));
         // Add menu for fetching bibliographic information
diff --git a/src/main/java/org/jabref/gui/externalfiles/DownloadExternalFile.java b/src/main/java/org/jabref/gui/externalfiles/DownloadExternalFile.java
deleted file mode 100644
index b4e1ad794db..00000000000
--- a/src/main/java/org/jabref/gui/externalfiles/DownloadExternalFile.java
+++ /dev/null
@@ -1,345 +0,0 @@
-package org.jabref.gui.externalfiles;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.List;
-import java.util.Optional;
-
-import javax.swing.SwingUtilities;
-
-import org.jabref.Globals;
-import org.jabref.JabRefExecutorService;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.filelist.FileListEntryEditor;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.net.URLDownload;
-import org.jabref.logic.util.OS;
-import org.jabref.logic.util.io.FileUtil;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.LinkedFile;
-import org.jabref.preferences.JabRefPreferences;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * This class handles the download of an external file. Typically called when the user clicks
- * the "Download" button in a FileListEditor shown in an EntryEditor.
- * <p/>
- * The FileListEditor constructs the DownloadExternalFile instance, then calls the download()
- * method passing a reference to itself as a callback. The download() method asks for the URL,
- * then starts the download. When the download is completed, it calls the downloadCompleted()
- * method on the callback FileListEditor, which then needs to take care of linking to the file.
- * The local filename is passed as an argument to the downloadCompleted() method.
- * <p/>
- * If the download is canceled, or failed, the user is informed. The callback is never called.
- */
-public class DownloadExternalFile {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(DownloadExternalFile.class);
-
-    private final BibDatabaseContext databaseContext;
-    private final BibEntry entry;
-    private final DialogService dialogService;
-
-    private FileListEntryEditor editor;
-    private boolean downloadFinished;
-    private boolean dontShowDialog;
-
-    public DownloadExternalFile(DialogService dialogService, BibDatabaseContext databaseContext, BibEntry entry) {
-        this.dialogService = dialogService;
-        this.databaseContext = databaseContext;
-        this.entry = entry;
-    }
-
-    /**
-     * Look for the last '.' in the link, and return the following characters.
-     * This gives the extension for most reasonably named links.
-     *
-     * @param link The link
-     * @return The suffix, excluding the dot (e.g. "pdf")
-     */
-    public static String getSuffix(final String link) {
-        String strippedLink = link;
-        try {
-            // Try to strip the query string, if any, to get the correct suffix:
-            URL url = new URL(link);
-            if ((url.getQuery() != null) && (url.getQuery().length() < (link.length() - 1))) {
-                strippedLink = link.substring(0, link.length() - url.getQuery().length() - 1);
-            }
-        } catch (MalformedURLException e) {
-            // Don't report this error, since this getting the suffix is a non-critical
-            // operation, and this error will be triggered and reported elsewhere.
-        }
-        // First see if the stripped link gives a reasonable suffix:
-        String suffix;
-        int strippedLinkIndex = strippedLink.lastIndexOf('.');
-        if ((strippedLinkIndex <= 0) || (strippedLinkIndex == (strippedLink.length() - 1))) {
-            suffix = null;
-        } else {
-            suffix = strippedLink.substring(strippedLinkIndex + 1);
-        }
-        if (!ExternalFileTypes.getInstance().isExternalFileTypeByExt(suffix)) {
-            // If the suffix doesn't seem to give any reasonable file type, try
-            // with the non-stripped link:
-            int index = link.lastIndexOf('.');
-            if ((index <= 0) || (index == (link.length() - 1))) {
-                // No occurrence, or at the end
-                // Check if there are path separators in the suffix - if so, it is definitely
-                // not a proper suffix, so we should give up:
-                if (strippedLink.substring(strippedLinkIndex + 1).indexOf('/') >= 1) {
-                    return "";
-                } else {
-                    return suffix; // return the first one we found, anyway.
-                }
-            } else {
-                // Check if there are path separators in the suffix - if so, it is definitely
-                // not a proper suffix, so we should give up:
-                if (link.substring(index + 1).indexOf('/') >= 1) {
-                    return "";
-                } else {
-                    return link.substring(index + 1);
-                }
-            }
-        } else {
-            return suffix;
-        }
-    }
-
-    /**
-     * Start a download.
-     *
-     * @param callback The object to which the filename should be reported when download
-     *                 is complete.
-     */
-    public void download(final DownloadCallback callback) throws IOException {
-        dontShowDialog = false;
-
-        Optional<String> res = dialogService.showInputDialogAndWait(Localization.lang("Download file"), Localization.lang("Enter URL to download"));
-
-        if (res.isPresent()) {
-            URL url;
-            try {
-                url = new URL(res.get());
-            } catch (MalformedURLException ex1) {
-                dialogService.showErrorDialogAndWait(Localization.lang("Download file"),
-                        Localization.lang("Invalid URL"));
-
-                return;
-            }
-            download(url, callback);
-        }
-    }
-
-    public void download(URL url, final DownloadCallback callback) throws IOException {
-        // TODO: what if this takes long time?
-        // TODO: stop editor dialog if this results in an error?
-        String mimeType = new URLDownload(url).getMimeType();
-        download(url, mimeType, callback);
-    }
-
-    private Optional<ExternalFileType> getExternalFileType(String mimeType) {
-        Optional<ExternalFileType> suggestedType = Optional.empty();
-        if (mimeType != null) {
-            LOGGER.debug("MIME Type suggested: " + mimeType);
-            suggestedType = ExternalFileTypes.getInstance().getExternalFileTypeByMimeType(mimeType);
-        }
-        return suggestedType;
-    }
-
-    /**
-     * Start a download.
-     *
-     * @param callback The object to which the filename should be reported when download
-     *                 is complete.
-     */
-    public void download(URL url, String mimeType, final DownloadCallback callback) throws IOException {
-        Optional<ExternalFileType> fileType = getExternalFileType(mimeType);
-
-        // First of all, start the download itself in the background to a temporary file:
-        final Path tempFile = Files.createTempFile("jabref_download", "tmp");
-        tempFile.toFile().deleteOnExit();
-
-        final URLDownload fileDownload = new URLDownload(url);
-
-        JabRefExecutorService.INSTANCE.execute(() -> {
-            try {
-                fileDownload.toFile(tempFile);
-            } catch (IOException e) {
-                dontShowDialog = true;
-                if ((editor != null) && editor.isVisible()) {
-                    editor.setVisible(false, false);
-                }
-
-                LOGGER.info("Error while downloading " + "'" + url + "'", e);
-
-                dialogService.showErrorDialogAndWait(Localization.lang("Download file"), Localization.lang("Invalid URL") + ": " + e.getMessage());
-
-                return;
-            }
-            // Download finished: call the method that stops the progress bar etc.:
-            SwingUtilities.invokeLater(DownloadExternalFile.this::downloadFinished);
-        });
-
-        // Then, while the download is proceeding, let the user choose the details of the file:
-        String suffix;
-        if (fileType.isPresent()) {
-            suffix = fileType.get().getExtension();
-        } else {
-            // If we did not find a file type from the MIME type, try based on extension:
-            suffix = getSuffix(url.toString());
-            if (suffix == null) {
-                suffix = "";
-            }
-            fileType = ExternalFileTypes.getInstance().getExternalFileTypeByExt(suffix);
-        }
-        String suggestedName = getSuggestedFileName(suffix);
-        List<String> fDirectory = databaseContext.getFileDirectories(Globals.prefs.getFilePreferences());
-        String directory;
-        if (fDirectory.isEmpty()) {
-            directory = null;
-        } else {
-            directory = fDirectory.get(0);
-        }
-        final String suggestDir = directory == null ? System.getProperty("user.home") : directory;
-        File file = new File(new File(suggestDir), suggestedName);
-        LinkedFile fileListEntry = new LinkedFile("", file.getCanonicalPath(), fileType.map(ExternalFileType::getName).orElse(""));
-        editor = new FileListEntryEditor(fileListEntry, true, false, databaseContext, true);
-        editor.getProgressBar().setIndeterminate(true);
-        editor.setOkEnabled(false);
-        editor.setExternalConfirm(closeEntry -> {
-            File f = directory == null ? new File(closeEntry.getLink()) : expandFilename(directory, closeEntry.getLink());
-            if (f.isDirectory()) {
-                dialogService.showErrorDialogAndWait(Localization.lang("Download file"),
-                        Localization.lang("Target file cannot be a directory."));
-
-                return false;
-            }
-            if (f.exists()) {
-                return dialogService.showConfirmationDialogAndWait(Localization.lang("Download file"),
-                        Localization.lang("'%0' exists. Overwrite file?", f.getName()), Localization.lang("Overwrite file"),
-                        Localization.lang("Cancel"));
-
-            } else {
-                return true;
-            }
-        });
-        if (dontShowDialog) {
-            return;
-        } else {
-            editor.setVisible(true, false);
-        }
-        // Editor closed. Go on:
-        if (editor.okPressed()) {
-            File toFile = directory == null ? new File(fileListEntry.getLink()) : expandFilename(directory,
-                    fileListEntry.getLink());
-            String dirPrefix;
-            if (directory == null) {
-                dirPrefix = null;
-            } else {
-                if (directory.endsWith(OS.FILE_SEPARATOR)) {
-                    dirPrefix = directory;
-                } else {
-                    dirPrefix = directory + OS.FILE_SEPARATOR;
-                }
-            }
-
-            boolean success = FileUtil.copyFile(tempFile, Paths.get(toFile.toURI()), true);
-            if (!success) {
-                // OOps, the file exists!
-                LOGGER.error("File already exists! DownloadExternalFile.download()");
-            }
-
-            // If the local file is in or below the main file directory, change the
-            // path to relative:
-            if ((dirPrefix != null) && fileListEntry.getLink().startsWith(directory)
-                    && (fileListEntry.getLink().length() > dirPrefix.length())) {
-                fileListEntry = new LinkedFile(fileListEntry.getDescription(),
-                        fileListEntry.getLink().substring(dirPrefix.length()), fileListEntry.getFileType());
-            }
-            callback.downloadComplete(fileListEntry);
-
-            if (!Files.deleteIfExists(tempFile)) {
-                LOGGER.info("Cannot delete temporary file");
-            }
-        } else {
-            // Canceled. Just delete the temp file:
-            if (downloadFinished && !Files.deleteIfExists(tempFile)) {
-                LOGGER.info("Cannot delete temporary file");
-            }
-        }
-    }
-
-    /**
-     * Construct a File object pointing to the file linked, whether the link is
-     * absolute or relative to the main directory.
-     *
-     * @param directory The main directory.
-     * @param link      The absolute or relative link.
-     * @return The expanded File.
-     */
-    private File expandFilename(String directory, String link) {
-        File toFile = new File(link);
-        // If this is a relative link, we should perhaps append the directory:
-        String dirPrefix = directory + OS.FILE_SEPARATOR;
-        if (!toFile.isAbsolute()) {
-            toFile = new File(dirPrefix + link);
-        }
-        return toFile;
-    }
-
-    /**
-     * This is called by the download thread when download is completed.
-     */
-    private void downloadFinished() {
-        downloadFinished = true;
-        editor.getProgressBar().setVisible(false);
-        editor.getProgressBarLabel().setVisible(false);
-        editor.setOkEnabled(true);
-        editor.getProgressBar().setValue(editor.getProgressBar().getMaximum());
-    }
-
-    private String getSuggestedFileName(String suffix) {
-        String plannedName = FileUtil.createFileNameFromPattern(databaseContext.getDatabase(), entry,
-                Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN));
-
-        if (!suffix.isEmpty()) {
-            plannedName += "." + suffix;
-        }
-
-        /*
-        * [ 1548875 ] download pdf produces unsupported filename
-        *
-        * http://sourceforge.net/tracker/index.php?func=detail&aid=1548875&group_id=92314&atid=600306
-        * FIXME: rework this! just allow alphanumeric stuff or so?
-        * https://msdn.microsoft.com/en-us/library/windows/desktop/aa365247(v=vs.85).aspx#naming_conventions
-        * http://superuser.com/questions/358855/what-characters-are-safe-in-cross-platform-file-names-for-linux-windows-and-os
-        * https://support.apple.com/en-us/HT202808
-        */
-        if (OS.WINDOWS) {
-            plannedName = plannedName.replaceAll("\\?|\\*|\\<|\\>|\\||\\\"|\\:|\\.$|\\[|\\]", "");
-        } else if (OS.OS_X) {
-            plannedName = plannedName.replace(":", "");
-        }
-
-        return plannedName;
-    }
-
-    /**
-     * Callback interface that users of this class must implement in order to receive
-     * notification when download is complete.
-     */
-    @FunctionalInterface
-    public interface DownloadCallback {
-
-        void downloadComplete(LinkedFile file);
-    }
-}
diff --git a/src/main/java/org/jabref/gui/fieldeditors/JTextAreaWithHighlighting.java b/src/main/java/org/jabref/gui/fieldeditors/JTextAreaWithHighlighting.java
deleted file mode 100644
index 05bb4c791b4..00000000000
--- a/src/main/java/org/jabref/gui/fieldeditors/JTextAreaWithHighlighting.java
+++ /dev/null
@@ -1,173 +0,0 @@
-package org.jabref.gui.fieldeditors;
-
-import java.awt.event.ActionEvent;
-import java.util.Optional;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.swing.AbstractAction;
-import javax.swing.KeyStroke;
-import javax.swing.text.BadLocationException;
-import javax.swing.text.DefaultHighlighter;
-import javax.swing.text.Document;
-import javax.swing.text.Highlighter;
-import javax.swing.text.Keymap;
-import javax.swing.undo.CannotRedoException;
-import javax.swing.undo.CannotUndoException;
-import javax.swing.undo.UndoManager;
-
-import org.jabref.Globals;
-import org.jabref.gui.actions.Actions;
-import org.jabref.gui.util.component.JTextAreaWithPlaceholder;
-import org.jabref.logic.search.SearchQueryHighlightListener;
-import org.jabref.preferences.JabRefPreferences;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class JTextAreaWithHighlighting extends JTextAreaWithPlaceholder implements SearchQueryHighlightListener {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(JTextAreaWithHighlighting.class);
-
-    private Optional<Pattern> highlightPattern = Optional.empty();
-
-    private UndoManager undo;
-
-    public JTextAreaWithHighlighting() {
-        this("");
-    }
-
-    public JTextAreaWithHighlighting(String text) {
-        this(text, "");
-    }
-
-    /**
-     * Creates a text area with the ability to highlight parts of the content.
-     * It also defines a placeholder which will be displayed the content is empty.
-     *
-     * @param text
-     * @param placeholder
-     */
-    public JTextAreaWithHighlighting(String text, String placeholder) {
-        super(text, placeholder);
-        setupUndoRedo();
-        setupPasteListener();
-    }
-
-    private void setupPasteListener() {
-        // Bind paste command to KeyBinds.PASTE
-        getInputMap().put(Globals.getKeyPrefs().getKey(org.jabref.gui.keyboard.KeyBinding.PASTE), Actions.PASTE);
-    }
-
-    private void setupUndoRedo() {
-        undo = new UndoManager();
-        Document doc = getDocument();
-
-        // Listen for undo and redo events
-        doc.addUndoableEditListener(evt -> undo.addEdit(evt.getEdit()));
-
-        // Create an undo action and add it to the text component
-        getActionMap().put("Undo", new AbstractAction("Undo") {
-
-            @Override
-            public void actionPerformed(ActionEvent evt) {
-                try {
-                    if (undo.canUndo()) {
-                        undo.undo();
-                    }
-                } catch (CannotUndoException ignored) {
-                    // Ignored
-                }
-            }
-        });
-
-        // Bind the undo action to ctl-Z
-        getInputMap().put(Globals.getKeyPrefs().getKey(org.jabref.gui.keyboard.KeyBinding.UNDO), "Undo");
-
-        // Create a redo action and add it to the text component
-        getActionMap().put("Redo", new AbstractAction(Actions.REDO.name()) {
-
-            @Override
-            public void actionPerformed(ActionEvent evt) {
-                try {
-                    if (undo.canRedo()) {
-                        undo.redo();
-                    }
-                } catch (CannotRedoException ignored) {
-                    // Ignored
-                }
-            }
-        });
-
-        // Bind the redo action to ctrl-Y
-        boolean bind = true;
-        KeyStroke redoKey = Globals.getKeyPrefs().getKey(org.jabref.gui.keyboard.KeyBinding.REDO);
-        if (Globals.prefs.getBoolean(JabRefPreferences.EDITOR_EMACS_KEYBINDINGS)) {
-            // If emacs is enabled, check if we have a conflict at keys
-            // If yes, do not bind
-            // Typically, we have: CTRL+y is "yank" in emacs and REDO in 'normal' settings
-            // The Emacs key bindings are stored in the keymap, not in the input map.
-            Keymap keymap = getKeymap();
-            KeyStroke[] keys = keymap.getBoundKeyStrokes();
-            int i = 0;
-            while ((i < keys.length) && !keys[i].equals(redoKey)) {
-                i++;
-            }
-            if (i < keys.length) {
-                // conflict found -> do not bind
-                bind = false;
-            }
-        }
-        if (bind) {
-            getInputMap().put(redoKey, "Redo");
-        }
-    }
-
-    /**
-     * Highlight words in the Textarea
-     *
-     * @param words to highlight
-     */
-    private void highLight() {
-        // highlight all characters that appear in charsToHighlight
-        Highlighter highlighter = getHighlighter();
-        highlighter.removeAllHighlights();
-
-        if ((highlightPattern == null) || !highlightPattern.isPresent()) {
-            return;
-        }
-        String content = getText();
-        if (content.isEmpty()) {
-            return;
-        }
-
-        highlightPattern.ifPresent(pattern -> {
-            Matcher matcher = pattern.matcher(content);
-            while (matcher.find()) {
-                try {
-                    highlighter.addHighlight(matcher.start(), matcher.end(), DefaultHighlighter.DefaultPainter);
-                } catch (BadLocationException ble) {
-                    // should not occur if matcher works right
-                    LOGGER.warn("Highlighting not possible, bad location", ble);
-                }
-            }
-        });
-
-    }
-
-    @Override
-    public void setText(String text) {
-        super.setText(text);
-        highLight();
-        if (undo != null) {
-            undo.discardAllEdits();
-        }
-    }
-
-    @Override
-    public void highlightPattern(Optional<Pattern> highlightPattern) {
-        this.highlightPattern = highlightPattern;
-        highLight();
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
index 68da8aec6f5..c4f11bb73b3 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
@@ -26,7 +26,6 @@
 import org.jabref.gui.AbstractViewModel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.desktop.JabRefDesktop;
-import org.jabref.gui.externalfiles.DownloadExternalFile;
 import org.jabref.gui.externalfiles.FileDownloadTask;
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
@@ -38,6 +37,7 @@
 import org.jabref.logic.externalfiles.LinkedFileHandler;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.URLDownload;
+import org.jabref.logic.net.URLUtil;
 import org.jabref.logic.xmp.XmpPreferences;
 import org.jabref.logic.xmp.XmpUtilWriter;
 import org.jabref.model.database.BibDatabaseContext;
@@ -439,12 +439,8 @@ private Optional<ExternalFileType> inferFileTypeFromMimeType(URLDownload urlDown
     }
 
     private Optional<ExternalFileType> inferFileTypeFromURL(String url) {
-        String extension = DownloadExternalFile.getSuffix(url);
-        if (extension != null) {
-            return ExternalFileTypes.getInstance().getExternalFileTypeByExt(extension);
-        } else {
-            return Optional.empty();
-        }
+        return URLUtil.getSuffix(url)
+                      .flatMap(extension -> ExternalFileTypes.getInstance().getExternalFileTypeByExt(extension));
     }
 
     public LinkedFile getFile() {
diff --git a/src/main/java/org/jabref/gui/fieldeditors/contextmenu/EditorMenus.java b/src/main/java/org/jabref/gui/fieldeditors/contextmenu/EditorMenus.java
index 575403025f0..baaabbe8f93 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/contextmenu/EditorMenus.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/contextmenu/EditorMenus.java
@@ -4,9 +4,6 @@
 import java.util.List;
 import java.util.function.Supplier;
 
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-
 import javafx.scene.control.CustomMenuItem;
 import javafx.scene.control.Label;
 import javafx.scene.control.MenuItem;
@@ -15,7 +12,10 @@
 import javafx.scene.control.TextInputControl;
 import javafx.scene.control.Tooltip;
 
+import org.jabref.Globals;
+import org.jabref.gui.actions.ActionFactory;
 import org.jabref.gui.actions.CopyDoiUrlAction;
+import org.jabref.gui.actions.StandardActions;
 import org.jabref.logic.formatter.bibtexfields.CleanupURLFormatter;
 import org.jabref.logic.formatter.bibtexfields.NormalizeNamesFormatter;
 import org.jabref.logic.l10n.Localization;
@@ -74,9 +74,8 @@ public static Supplier<List<MenuItem>> getNameMenu(final TextInputControl textIn
      */
     public static Supplier<List<MenuItem>> getDOIMenu(TextArea textArea) {
         return () -> {
-            AbstractAction copyDoiUrlAction = new CopyDoiUrlAction(textArea);
-            MenuItem copyDoiUrlMenuItem = new MenuItem((String) copyDoiUrlAction.getValue(Action.NAME));
-            copyDoiUrlMenuItem.setOnAction(event -> copyDoiUrlAction.actionPerformed(null));
+            ActionFactory factory = new ActionFactory(Globals.getKeyPrefs());
+            MenuItem copyDoiUrlMenuItem = factory.createMenuItem(StandardActions.COPY_DOI, new CopyDoiUrlAction(textArea));
 
             List<MenuItem> menuItems = new ArrayList<>();
             menuItems.add(copyDoiUrlMenuItem);
diff --git a/src/main/java/org/jabref/gui/filelist/ConfirmCloseFileListEntryEditor.java b/src/main/java/org/jabref/gui/filelist/ConfirmCloseFileListEntryEditor.java
deleted file mode 100644
index 92e92a8eaa9..00000000000
--- a/src/main/java/org/jabref/gui/filelist/ConfirmCloseFileListEntryEditor.java
+++ /dev/null
@@ -1,14 +0,0 @@
-package org.jabref.gui.filelist;
-
-import org.jabref.model.entry.LinkedFile;
-
-/**
- * An implementation of this interface is called to confirm whether a FileListEntryEditor
- * is ready to close when Ok is pressed, or whether there is a problem that needs to be
- * resolved first.
- */
-@FunctionalInterface
-public interface ConfirmCloseFileListEntryEditor {
-
-    boolean confirmClose(LinkedFile entry);
-}
diff --git a/src/main/java/org/jabref/gui/filelist/FileListEntryEditor.java b/src/main/java/org/jabref/gui/filelist/FileListEntryEditor.java
deleted file mode 100644
index fc590f146e2..00000000000
--- a/src/main/java/org/jabref/gui/filelist/FileListEntryEditor.java
+++ /dev/null
@@ -1,386 +0,0 @@
-package org.jabref.gui.filelist;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.Collection;
-import java.util.List;
-import java.util.Optional;
-import java.util.regex.Pattern;
-
-import javax.swing.AbstractAction;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.DefaultComboBoxModel;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JProgressBar;
-import javax.swing.JTextField;
-import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
-import javax.swing.event.DocumentEvent;
-import javax.swing.event.DocumentListener;
-
-import org.jabref.Globals;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.desktop.JabRefDesktop;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.externalfiletype.UnknownExternalFileType;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.gui.util.FileDialogConfiguration;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.io.FileUtil;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.LinkedFile;
-import org.jabref.model.util.FileHelper;
-import org.jabref.preferences.JabRefPreferences;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import com.jgoodies.forms.builder.FormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * This class produces a dialog box for editing a single file link from a Bibtex entry.
- *
- * The information to be edited includes the file description, the link itself and the
- * file type. The dialog also includes convenience buttons for quick linking.
- *
- * For use when downloading files, this class also offers a progress bar and a "Downloading..."
- * label that can be hidden when the download is complete.
- * @deprecated Use {@link LinkedFileEditDialogView}
- */
-@Deprecated
-public class FileListEntryEditor {
-
-    private static final Pattern REMOTE_LINK_PATTERN = Pattern.compile("[a-z]+://.*");
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(FileListEntryEditor.class);
-    private final JTextField link = new JTextField();
-    private final JTextField description = new JTextField();
-    private final JButton ok = new JButton(Localization.lang("OK"));
-    private final JComboBox<ExternalFileType> types;
-    private final JProgressBar prog = new JProgressBar(SwingConstants.HORIZONTAL);
-    private final JLabel downloadLabel = new JLabel(Localization.lang("Downloading..."));
-    private JDialog dialog;
-    //Do not make this variable final, as then the lambda action listener will fail on compile
-    private JabRefFrame frame;
-    private boolean showSaveDialog;
-    private ConfirmCloseFileListEntryEditor externalConfirm;
-    private LinkedFile entry;
-    //Do not make this variable final, as then the lambda action listener will fail on compiöe
-    private BibDatabaseContext databaseContext;
-    private final ActionListener browsePressed = e -> {
-        String fileText = link.getText().trim();
-        Optional<Path> file = FileHelper.expandFilename(this.databaseContext, fileText,
-                Globals.prefs.getFilePreferences());
-
-        Path workingDir = file.orElse(Paths.get(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)));
-        String fileName = Paths.get(fileText).getFileName().toString();
-
-        FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                .withInitialDirectory(workingDir)
-                .withInitialFileName(fileName).build();
-
-        Optional<Path> path;
-        if (showSaveDialog) {
-            path = DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().showFileSaveDialog(fileDialogConfiguration));
-        } else {
-            path = DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().showFileOpenDialog(fileDialogConfiguration));
-        }
-
-        path.ifPresent(newFile -> {
-            // Store the directory for next time:
-            Globals.prefs.put(JabRefPreferences.WORKING_DIRECTORY, newFile.toString());
-
-            // If the file is below the file directory, make the path relative:
-            List<Path> fileDirectories = this.databaseContext
-                    .getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
-            newFile = FileUtil.relativize(newFile, fileDirectories);
-
-            link.setText(newFile.toString());
-            link.requestFocus();
-        });
-    };
-    private boolean okPressed;
-
-    private boolean okDisabledExternally;
-    private boolean openBrowseWhenShown;
-
-    private boolean dontOpenBrowseUntilDisposed;
-
-    public FileListEntryEditor(LinkedFile entry, boolean showProgressBar, boolean showOpenButton, BibDatabaseContext databaseContext, boolean showSaveDialog) {
-        this(entry, showProgressBar, showOpenButton, databaseContext);
-        this.showSaveDialog = showSaveDialog;
-    }
-
-    public FileListEntryEditor(LinkedFile entry, boolean showProgressBar, boolean showOpenButton, BibDatabaseContext databaseContext) {
-        this.entry = entry;
-        this.databaseContext = databaseContext;
-
-        ActionListener okAction = e -> {
-            // If OK button is disabled, ignore this event:
-            if (!ok.isEnabled()) {
-                return;
-            }
-            // If necessary, ask the external confirm object whether we are ready to close.
-            if (externalConfirm != null) {
-                // Construct an updated FileListEntry:
-                storeSettings(entry);
-                if (!externalConfirm.confirmClose(entry)) {
-                    return;
-                }
-            }
-            dialog.dispose();
-            storeSettings(FileListEntryEditor.this.entry);
-            okPressed = true;
-        };
-        types = new JComboBox<>();
-        types.addItemListener(itemEvent -> {
-            if (!okDisabledExternally) {
-                ok.setEnabled(types.getSelectedItem() != null);
-            }
-        });
-
-        FormLayout fileDialog = new FormLayout(
-                "left:pref, 4dlu, fill:400dlu, 4dlu, fill:pref, 4dlu, fill:pref",
-                "p, 8dlu, p, 8dlu, p");
-        FormBuilder builder = FormBuilder.create().layout(fileDialog);
-        builder.add(Localization.lang("Link")).xy(1, 1);
-        builder.add(link).xy(3, 1);
-
-        final JButton browseBut = new JButton(Localization.lang("Browse"));
-        browseBut.addActionListener(browsePressed);
-        builder.add(browseBut).xy(5, 1);
-        JButton open = new JButton(Localization.lang("Open"));
-        if (showOpenButton) {
-            builder.add(open).xy(7, 1);
-        }
-        builder.add(Localization.lang("Description")).xy(1, 3);
-        builder.add(description).xyw(3, 3, 5);
-        builder.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-        builder.add(Localization.lang("File type")).xy(1, 5);
-        builder.add(types).xyw(3, 5, 5);
-        if (showProgressBar) {
-            builder.appendRows("2dlu, p");
-            builder.add(downloadLabel).xy(1, 7);
-            builder.add(prog).xyw(3, 7, 3);
-        }
-
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        bb.addRelatedGap();
-        bb.addButton(ok);
-        JButton cancel = new JButton(Localization.lang("Cancel"));
-        bb.addButton(cancel);
-        bb.addGlue();
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        ok.addActionListener(okAction);
-        // Add OK action to the two text fields to simplify entering:
-        link.addActionListener(okAction);
-        description.addActionListener(okAction);
-
-        open.addActionListener(e -> openFile());
-
-        AbstractAction cancelAction = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                dialog.dispose();
-            }
-        };
-        cancel.addActionListener(cancelAction);
-
-        // Key bindings:
-        ActionMap am = builder.getPanel().getActionMap();
-        InputMap im = builder.getPanel().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", cancelAction);
-
-        link.getDocument().addDocumentListener(new DocumentListener() {
-
-            @Override
-            public void insertUpdate(DocumentEvent documentEvent) {
-                checkExtension();
-            }
-
-            @Override
-            public void removeUpdate(DocumentEvent documentEvent) {
-                // Do nothing
-            }
-
-            @Override
-            public void changedUpdate(DocumentEvent documentEvent) {
-                checkExtension();
-            }
-
-        });
-
-        dialog = new JDialog();
-        dialog.setTitle(Localization.lang("Select files"));
-        dialog.setModal(true);
-        dialog.getContentPane().add(builder.getPanel(), BorderLayout.CENTER);
-        dialog.getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-        dialog.pack();
-        dialog.addWindowListener(new WindowAdapter() {
-
-            @Override
-            public void windowActivated(WindowEvent event) {
-                if (openBrowseWhenShown && !dontOpenBrowseUntilDisposed) {
-                    dontOpenBrowseUntilDisposed = true;
-                    SwingUtilities.invokeLater(() -> browsePressed.actionPerformed(new ActionEvent(browseBut, 0, "")));
-                }
-            }
-
-            @Override
-            public void windowClosed(WindowEvent event) {
-                dontOpenBrowseUntilDisposed = false;
-            }
-        });
-        setValues(entry);
-    }
-
-    private void checkExtension() {
-        if ((types.getSelectedIndex() == -1) && (!link.getText().trim().isEmpty())) {
-
-            // Check if this looks like a remote link:
-            if (FileListEntryEditor.REMOTE_LINK_PATTERN.matcher(link.getText()).matches()) {
-                Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByExt("html");
-                if (type.isPresent()) {
-                    types.setSelectedItem(type.get());
-                    return;
-                }
-            }
-
-            // Try to guess the file type:
-            String theLink = link.getText().trim();
-            ExternalFileTypes.getInstance().getExternalFileTypeForName(theLink).ifPresent(types::setSelectedItem);
-        }
-    }
-
-    private void openFile() {
-        ExternalFileType type = (ExternalFileType) types.getSelectedItem();
-        if (type != null) {
-            try {
-                JabRefDesktop.openExternalFileAnyFormat(databaseContext, link.getText(), Optional.of(type));
-            } catch (IOException e) {
-                LOGGER.error("File could not be opened", e);
-            }
-        }
-    }
-
-    public void setExternalConfirm(ConfirmCloseFileListEntryEditor eC) {
-        this.externalConfirm = eC;
-    }
-
-    public void setOkEnabled(boolean enabled) {
-        okDisabledExternally = !enabled;
-        ok.setEnabled(enabled);
-    }
-
-    public JProgressBar getProgressBar() {
-        return prog;
-    }
-
-    public JLabel getProgressBarLabel() {
-        return downloadLabel;
-    }
-
-    public void setEntry(LinkedFile entry) {
-        this.entry = entry;
-        setValues(entry);
-    }
-
-    public void setVisible(boolean visible, boolean openBrowse) {
-        openBrowseWhenShown = openBrowse && Globals.prefs.getBoolean(JabRefPreferences.ALLOW_FILE_AUTO_OPEN_BROWSE);
-        if (visible) {
-            okPressed = false;
-        }
-        String title;
-        if (showSaveDialog) {
-            title = Localization.lang("Save file");
-        } else {
-            title = Localization.lang("Select files");
-        }
-        dialog.setTitle(title);
-        dialog.setVisible(visible);
-    }
-
-    public boolean isVisible() {
-        return (dialog != null) && dialog.isVisible();
-    }
-
-    private void setValues(LinkedFile entry) {
-        description.setText(entry.getDescription());
-        link.setText(entry.getLink());
-
-        Collection<ExternalFileType> list = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
-
-        types.setModel(new DefaultComboBoxModel<>(list.toArray(new ExternalFileType[list.size()])));
-        types.setSelectedIndex(-1);
-        // See what is a reasonable selection for the type combobox:
-        Optional<ExternalFileType> fileType = ExternalFileTypes.getInstance().fromLinkedFile(entry, false);
-        if (fileType.isPresent() && !(fileType.get() instanceof UnknownExternalFileType)) {
-            types.setSelectedItem(fileType.get());
-        } else if ((entry.getLink() != null) && (!entry.getLink().isEmpty())) {
-            checkExtension();
-        }
-    }
-
-    private void storeSettings(LinkedFile listEntry) {
-        String descriptionText = this.description.getText().trim();
-        String fileLink = "";
-        // See if we should trim the file link to be relative to the file directory:
-        try {
-            List<String> dirs = databaseContext.getFileDirectories(Globals.prefs.getFilePreferences());
-            if (dirs.isEmpty()) {
-                fileLink = this.link.getText().trim();
-            } else {
-                boolean found = false;
-                for (String dir : dirs) {
-                    String canPath = (new File(dir)).getCanonicalPath();
-                    File fl = new File(this.link.getText().trim());
-                    if (fl.isAbsolute()) {
-                        String flPath = fl.getCanonicalPath();
-                        if ((flPath.length() > canPath.length()) && (flPath.startsWith(canPath))) {
-                            fileLink = fl.getCanonicalPath().substring(canPath.length() + 1);
-                            found = true;
-                            break;
-                        }
-                    }
-                }
-                if (!found) {
-                    fileLink = this.link.getText().trim();
-                }
-            }
-        } catch (IOException ex) {
-            // Don't think this should happen, but set the file link directly as a fallback:
-            fileLink = this.link.getText().trim();
-        }
-
-        ExternalFileType type = (ExternalFileType) types.getSelectedItem();
-
-        listEntry.setDescription(descriptionText);
-        listEntry.setFileType(type.getName());
-        listEntry.setLink(fileLink);
-    }
-
-    public boolean okPressed() {
-        return okPressed;
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/groups/GroupTreeCellRenderer.java b/src/main/java/org/jabref/gui/groups/GroupTreeCellRenderer.java
deleted file mode 100644
index 4b128b2593d..00000000000
--- a/src/main/java/org/jabref/gui/groups/GroupTreeCellRenderer.java
+++ /dev/null
@@ -1,114 +0,0 @@
-package org.jabref.gui.groups;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-
-import javax.swing.BorderFactory;
-import javax.swing.JLabel;
-import javax.swing.JTree;
-import javax.swing.border.Border;
-import javax.swing.tree.DefaultTreeCellRenderer;
-
-import org.jabref.model.groups.GroupTreeNode;
-
-/**
- * Renders a GroupTreeNode using its group's getName() method, rather that its toString() method.
- */
-public class GroupTreeCellRenderer extends DefaultTreeCellRenderer {
-
-    /** The cell over which the user is currently dragging */
-    private Object highlight1Cell;
-    private List<GroupTreeNode> overlappingGroups = new ArrayList<>();
-    private List<GroupTreeNode> matchingGroups = new ArrayList<>();
-    private Object highlightBorderCell;
-
-    @Override
-    public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf,
-            int row, boolean tmpHasFocus) {
-        // show as selected
-        selected = (Objects.equals(highlight1Cell, value)) || sel;
-        Component c = super.getTreeCellRendererComponent(tree, value, selected, expanded, leaf, row, tmpHasFocus);
-        // this is sometimes called from deep within somewhere, with a dummy
-        // value (probably for layout etc.), so we've got to check here!
-        if (!(value instanceof GroupTreeNodeViewModel)) {
-            return c;
-        }
-        if (!(c instanceof JLabel)) {
-            return c; // sanity check
-        }
-
-        GroupTreeNodeViewModel viewModel = (GroupTreeNodeViewModel) value;
-        JLabel label = (JLabel) c;
-
-        Border border;
-        if (Objects.equals(highlightBorderCell, value)) {
-            border = BorderFactory.createLineBorder(Color.BLACK);
-        } else {
-            border = BorderFactory.createEmptyBorder();
-        }
-        if (label.getBorder() != border) {
-            label.setBorder(border);
-        }
-
-        Boolean red = printInRed(viewModel) && !selected; // do not print currently selected node in red
-        Boolean underlined = printUnderlined(viewModel);
-        StringBuilder sb = new StringBuilder(60);
-        sb.append("<html>");
-        if (red) {
-            sb.append("<font color=\"#FF0000\">");
-        }
-        if (underlined) {
-            sb.append("<u>");
-        }
-        if (viewModel.printInItalics()) {
-            sb.append("<i>");
-        }
-        sb.append(viewModel.getName());
-        if (viewModel.printInItalics()) {
-            sb.append("</i>");
-        }
-        if (underlined) {
-            sb.append("</u>");
-        }
-        if (red) {
-            sb.append("</font>");
-        }
-        sb.append("</html>");
-
-        String text = sb.toString();
-        if (!label.getText().equals(text)) {
-            label.setText(text);
-        }
-        label.setToolTipText(viewModel.getDescription());
-
-        return c;
-    }
-
-    private boolean printInRed(GroupTreeNodeViewModel viewModel) {
-        if (viewModel.isAllEntriesGroup()) {
-            // Do not print all entries group in red
-            return false;
-        }
-
-        return overlappingGroups.contains(viewModel.getNode());
-    }
-
-    private boolean printUnderlined(GroupTreeNodeViewModel viewModel) {
-        if (viewModel.isAllEntriesGroup()) {
-            // Do not underline all entries group
-            return false;
-        }
-        return matchingGroups.contains(viewModel.getNode());
-    }
-
-    /**
-     * Highlights the specified cells (by drawing a border around it), or disables highlight if highlightBorderCell ==
-     * null.
-     */
-    public void setHighlightBorderCell(Object highlightBorderCell) {
-        this.highlightBorderCell = highlightBorderCell;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/help/HelpAction.java b/src/main/java/org/jabref/gui/help/HelpAction.java
index d18d3f0b34b..603e055abaf 100644
--- a/src/main/java/org/jabref/gui/help/HelpAction.java
+++ b/src/main/java/org/jabref/gui/help/HelpAction.java
@@ -1,68 +1,39 @@
 package org.jabref.gui.help;
 
-import java.awt.event.ActionEvent;
 import java.util.HashSet;
 import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import javax.swing.Action;
-import javax.swing.Icon;
-import javax.swing.KeyStroke;
-
 import org.jabref.Globals;
-import org.jabref.gui.actions.MnemonicAwareAction;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.desktop.JabRefDesktop;
-import org.jabref.gui.icon.IconTheme;
 import org.jabref.logic.help.HelpFile;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.preferences.JabRefPreferences;
 
 /**
  * This Action keeps a reference to a URL. When activated, it shows the help
  * Dialog unless it is already visible, and shows the URL in it.
  */
-public class HelpAction extends MnemonicAwareAction {
+public class HelpAction extends SimpleCommand {
 
     /**
      * New languages of the help have to be added here
      */
-    private static final Set<String> AVAIABLE_LANG_FILES = Stream.of("en", "de", "fr", "in", "ja")
-            .collect(Collectors.toCollection(HashSet::new));
+    private static final Set<String> AVAILABLE_LANG_FILES = Stream.of("en", "de", "fr", "in", "ja")
+                                                                  .collect(Collectors.toCollection(HashSet::new));
 
     private HelpFile helpPage;
 
-
-    public HelpAction(String title, String tooltip, HelpFile helpPage, KeyStroke key) {
-        this(title, tooltip, helpPage, IconTheme.JabRefIcons.HELP.getSmallIcon());
-        putValue(Action.ACCELERATOR_KEY, key);
-    }
-
-    private HelpAction(String title, String tooltip, HelpFile helpPage, Icon icon) {
-        super(icon);
-        this.helpPage = helpPage;
-        putValue(Action.NAME, title);
-        putValue(Action.SHORT_DESCRIPTION, tooltip);
-    }
-
-    public HelpAction(String tooltip, HelpFile helpPage) {
-        this(Localization.lang("Help"), tooltip, helpPage, IconTheme.JabRefIcons.HELP.getSmallIcon());
-    }
-
-    public HelpAction(HelpFile helpPage, Icon icon) {
-        this(Localization.lang("Help"), Localization.lang("Help"), helpPage, icon);
-    }
-
     public HelpAction(HelpFile helpPage) {
-        this(Localization.lang("Help"), Localization.lang("Help"), helpPage, IconTheme.JabRefIcons.HELP.getSmallIcon());
+        this.helpPage = helpPage;
     }
 
     public static void openHelpPage(HelpFile helpPage) {
         String lang = Globals.prefs.get(JabRefPreferences.LANGUAGE);
         StringBuilder sb = new StringBuilder("https://help.jabref.org/");
 
-        if (AVAIABLE_LANG_FILES.contains(lang)) {
+        if (AVAILABLE_LANG_FILES.contains(lang)) {
             sb.append(lang);
             sb.append("/");
         } else {
@@ -72,15 +43,6 @@ public static void openHelpPage(HelpFile helpPage) {
         JabRefDesktop.openBrowserShowPopup(sb.toString());
     }
 
-    public void setHelpFile(HelpFile urlPart) {
-        this.helpPage = urlPart;
-    }
-
-    @Override
-    public void actionPerformed(ActionEvent e) {
-        openHelpPage(helpPage);
-    }
-
     public static SimpleCommand getMainHelpPageCommand() {
         return new SimpleCommand() {
             @Override
@@ -90,12 +52,8 @@ public void execute() {
         };
     }
 
-    public SimpleCommand getCommand() {
-        return new SimpleCommand() {
-            @Override
-            public void execute() {
-                openHelpPage(helpPage);
-            }
-        };
+    @Override
+    public void execute() {
+        openHelpPage(helpPage);
     }
 }
diff --git a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java
index 30ee0635043..b3851939465 100644
--- a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java
+++ b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java
@@ -59,8 +59,7 @@ protected Node createContentPane() {
         ActionFactory factory = new ActionFactory(preferences.getKeyBindingRepository());
         EasyBind.subscribe(viewModel.selectedFetcherProperty(), fetcher -> {
             if ((fetcher != null) && fetcher.getHelpPage().isPresent()) {
-                HelpAction helpCommand = new HelpAction(fetcher.getHelpPage().get());
-                Button helpButton = factory.createIconButton(StandardActions.HELP, helpCommand.getCommand());
+                Button helpButton = factory.createIconButton(StandardActions.HELP, new HelpAction(fetcher.getHelpPage().get()));
                 helpButtonContainer.getChildren().setAll(helpButton);
             } else {
                 helpButtonContainer.getChildren().clear();
diff --git a/src/main/java/org/jabref/gui/keyboard/KeyBinder.java b/src/main/java/org/jabref/gui/keyboard/KeyBinder.java
deleted file mode 100644
index 1944bd038cd..00000000000
--- a/src/main/java/org/jabref/gui/keyboard/KeyBinder.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package org.jabref.gui.keyboard;
-
-import javax.swing.Action;
-import javax.swing.ActionMap;
-import javax.swing.InputMap;
-import javax.swing.JComponent;
-import javax.swing.JRootPane;
-
-import org.jabref.Globals;
-
-public class KeyBinder {
-
-    private KeyBinder() {
-    }
-
-    /**
-     * Binds ESC-Key to cancel button
-     *
-     * @param rootPane     the pane to bind the action to. Typically, this variable is retrieved by this.getRootPane();
-     * @param cancelAction the action to bind
-     */
-    public static void bindCloseDialogKeyToCancelAction(JRootPane rootPane, Action cancelAction) {
-        InputMap im = rootPane.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        ActionMap am = rootPane.getActionMap();
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", cancelAction);
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/maintable/MainTable.java b/src/main/java/org/jabref/gui/maintable/MainTable.java
index d852104c1fd..892116fb337 100644
--- a/src/main/java/org/jabref/gui/maintable/MainTable.java
+++ b/src/main/java/org/jabref/gui/maintable/MainTable.java
@@ -83,17 +83,17 @@ public MainTable(MainTableDataModel model, JabRefFrame frame,
         this.getColumns().addAll(new MainTableColumnFactory(database, preferences.getColumnPreferences(), externalFileTypes, panel.getUndoManager(), frame.getDialogService()).createColumns());
 
         new ViewModelTableRowFactory<BibEntryTableViewModel>()
-                                                              .withOnMouseClickedEvent((entry, event) -> {
+                .withOnMouseClickedEvent((entry, event) -> {
                                                                   if (event.getClickCount() == 2) {
                                                                       panel.showAndEdit(entry.getEntry());
                                                                   }
                                                               })
-                                                              .withContextMenu(entry -> RightClickMenu.create(entry, keyBindingRepository, panel, Globals.getKeyPrefs(), frame.getDialogService()))
-                                                              .setOnDragDetected(this::handleOnDragDetected)
-                                                              .setOnDragDropped(this::handleOnDragDropped)
-                                                              .setOnDragOver(this::handleOnDragOver)
-                                                              .setOnMouseDragEntered(this::handleOnDragEntered)
-                                                              .install(this);
+                .withContextMenu(entry -> RightClickMenu.create(entry, keyBindingRepository, panel, frame.getDialogService()))
+                .setOnDragDetected(this::handleOnDragDetected)
+                .setOnDragDropped(this::handleOnDragDropped)
+                .setOnDragOver(this::handleOnDragOver)
+                .setOnMouseDragEntered(this::handleOnDragEntered)
+                .install(this);
 
         /*for (Entry<String, SortType> entries : preferences.getColumnPreferences().getSortTypesForColumns().entrySet()) {
             Optional<TableColumn<BibEntryTableViewModel, ?>> column = this.getColumns().stream().filter(col -> entries.getKey().equals(col.getText())).findFirst();
diff --git a/src/main/java/org/jabref/gui/maintable/RightClickMenu.java b/src/main/java/org/jabref/gui/maintable/RightClickMenu.java
index 3070a50a2b7..66b1c5c3765 100644
--- a/src/main/java/org/jabref/gui/maintable/RightClickMenu.java
+++ b/src/main/java/org/jabref/gui/maintable/RightClickMenu.java
@@ -29,7 +29,7 @@
 
 public class RightClickMenu {
 
-    public static ContextMenu create(BibEntryTableViewModel entry, KeyBindingRepository keyBindingRepository, BasePanel panel, KeyBindingRepository keyBindings, DialogService dialogService) {
+    public static ContextMenu create(BibEntryTableViewModel entry, KeyBindingRepository keyBindingRepository, BasePanel panel, DialogService dialogService) {
         ContextMenu contextMenu = new ContextMenu();
         ActionFactory factory = new ActionFactory(keyBindingRepository);
 
@@ -79,7 +79,7 @@ public static ContextMenu create(BibEntryTableViewModel entry, KeyBindingReposit
 
         contextMenu.getItems().add(new SeparatorMenuItem());
 
-        contextMenu.getItems().add(new ChangeEntryTypeMenu(keyBindings).getChangeEntryTypeMenu(entry.getEntry(), panel.getBibDatabaseContext(), panel.getUndoManager()));
+        contextMenu.getItems().add(new ChangeEntryTypeMenu().getChangeEntryTypeMenu(entry.getEntry(), panel.getBibDatabaseContext(), panel.getUndoManager()));
         contextMenu.getItems().add(factory.createMenuItem(StandardActions.MERGE_WITH_FETCHED_ENTRY, getFetchEntryData(panel)));
         contextMenu.getItems().add(factory.createMenuItem(StandardActions.ATTACH_FILE, new AttachFileAction(panel, dialogService)));
         contextMenu.getItems().add(factory.createMenuItem(StandardActions.MERGE_ENTRIES, mergeEntries(panel)));
diff --git a/src/main/java/org/jabref/gui/menus/ChangeEntryTypeMenu.java b/src/main/java/org/jabref/gui/menus/ChangeEntryTypeMenu.java
index f65f4517030..eb7ca539262 100644
--- a/src/main/java/org/jabref/gui/menus/ChangeEntryTypeMenu.java
+++ b/src/main/java/org/jabref/gui/menus/ChangeEntryTypeMenu.java
@@ -1,14 +1,8 @@
 package org.jabref.gui.menus;
 
-import java.awt.Font;
 import java.util.Collection;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.KeyStroke;
 import javax.swing.undo.UndoManager;
 
 import javafx.collections.ObservableList;
@@ -17,11 +11,9 @@
 import javafx.scene.control.MenuItem;
 import javafx.scene.control.SeparatorMenuItem;
 
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.actions.ChangeTypeAction;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.undo.CountingUndoManager;
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.gui.undo.UndoableChangeType;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.EntryTypes;
 import org.jabref.model.database.BibDatabaseContext;
@@ -32,23 +24,20 @@
 import org.jabref.model.entry.IEEETranEntryTypes;
 
 public class ChangeEntryTypeMenu {
-    public final Map<String, KeyStroke> entryShortCuts = new HashMap<>();
-
-    public ChangeEntryTypeMenu(KeyBindingRepository keyBindings) {
-        entryShortCuts.put(BibtexEntryTypes.ARTICLE.getName(), keyBindings.getKey(KeyBinding.NEW_ARTICLE));
-        entryShortCuts.put(BibtexEntryTypes.BOOK.getName(), keyBindings.getKey(KeyBinding.NEW_BOOK));
-        entryShortCuts.put(BibtexEntryTypes.PHDTHESIS.getName(), keyBindings.getKey(KeyBinding.NEW_PHDTHESIS));
-        entryShortCuts.put(BibtexEntryTypes.INBOOK.getName(), keyBindings.getKey(KeyBinding.NEW_MASTERSTHESIS));
-        entryShortCuts.put(BibtexEntryTypes.INBOOK.getName(), keyBindings.getKey(KeyBinding.NEW_INBOOK));
-        entryShortCuts.put(BibtexEntryTypes.PROCEEDINGS.getName(), keyBindings.getKey(KeyBinding.NEW_PROCEEDINGS));
-        entryShortCuts.put(BibtexEntryTypes.UNPUBLISHED.getName(), keyBindings.getKey(KeyBinding.NEW_UNPUBLISHED));
-        entryShortCuts.put(BibtexEntryTypes.TECHREPORT.getName(), keyBindings.getKey(KeyBinding.NEW_TECHREPORT));
+
+    public ChangeEntryTypeMenu() {
+
     }
 
-    public JMenu getChangeEntryTypeMenu(BasePanel panel) {
-        JMenu menu = new JMenu(Localization.lang("Change entry type"));
-        populateChangeEntryTypeMenu(menu, panel);
-        return menu;
+    public static MenuItem createMenuItem(EntryType type, BibEntry entry, UndoManager undoManager) {
+        MenuItem menuItem = new MenuItem(type.getName());
+        menuItem.setOnAction(event -> {
+            NamedCompound compound = new NamedCompound(Localization.lang("Change entry type"));
+            entry.setType(type)
+                 .ifPresent(change -> compound.addEdit(new UndoableChangeType(change)));
+            undoManager.addEdit(compound);
+        });
+        return menuItem;
     }
 
     public ContextMenu getChangeEntryTypePopupMenu(BibEntry entry, BibDatabaseContext bibDatabaseContext, CountingUndoManager undoManager) {
@@ -95,61 +84,11 @@ private void populateSubMenu(ObservableList<MenuItem> items, String text, List<E
 
     private void populate(ObservableList<MenuItem> items, Collection<EntryType> types, BibEntry entry, UndoManager undoManager) {
         for (EntryType type : types) {
-            items.add(ChangeTypeAction.as(type, entry, undoManager));
+            items.add(createMenuItem(type, entry, undoManager));
         }
     }
 
     private void populate(Menu menu, Collection<EntryType> types, BibEntry entry, UndoManager undoManager) {
         populate(menu.getItems(), types, entry, undoManager);
     }
-
-    /**
-     * Remove all types from the menu. Then cycle through all available
-     * types, and add them.
-     */
-    private void populateChangeEntryTypeMenu(JMenu menu, BasePanel panel) {
-        menu.removeAll();
-
-        // biblatex?
-        if (panel.getBibDatabaseContext().isBiblatexMode()) {
-            for (EntryType type : EntryTypes.getAllValues(BibDatabaseMode.BIBLATEX)) {
-                menu.add(new ChangeTypeAction(type, panel));
-            }
-
-            List<EntryType> customTypes = EntryTypes.getAllCustomTypes(BibDatabaseMode.BIBLATEX);
-            if (!customTypes.isEmpty()) {
-                menu.addSeparator();
-                // custom types
-                createEntryTypeSection(panel, menu, "Custom Entries", customTypes);
-            }
-        } else {
-            // Bibtex
-            createEntryTypeSection(panel, menu, "BibTeX Entries", BibtexEntryTypes.ALL);
-            menu.addSeparator();
-            // ieeetran
-            createEntryTypeSection(panel, menu, "IEEETran Entries", IEEETranEntryTypes.ALL);
-
-            List<EntryType> customTypes = EntryTypes.getAllCustomTypes(BibDatabaseMode.BIBTEX);
-            if (!customTypes.isEmpty()) {
-                menu.addSeparator();
-                // custom types
-                createEntryTypeSection(panel, menu, "Custom Entries", customTypes);
-            }
-        }
-    }
-
-    private void createEntryTypeSection(BasePanel panel, JMenu menu, String title, List<? extends EntryType> types) {
-        // bibtex
-        JMenuItem header = new JMenuItem(title);
-        Font font = new Font(menu.getFont().getName(), Font.ITALIC, menu.getFont().getSize());
-        header.setFont(font);
-        header.setEnabled(false);
-        if (!types.isEmpty()) {
-            menu.add(header);
-        }
-
-        for (EntryType type : types) {
-            menu.add(new ChangeTypeAction(type, panel));
-        }
-    }
 }
diff --git a/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java b/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
index 7d2c1c20e70..c56e7606c29 100644
--- a/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
+++ b/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
@@ -117,9 +117,7 @@ public OpenOfficePanel(JabRefFrame frame, JabRefPreferences jabRefPreferences, O
         manualConnect.setTooltip(new Tooltip(Localization.lang("Manual connect")));
         manualConnect.setMaxWidth(Double.MAX_VALUE);
 
-        HelpAction helpCommand = new HelpAction(HelpFile.OPENOFFICE_LIBREOFFICE);
-
-        help = factory.createIconButton(StandardActions.HELP, helpCommand.getCommand());
+        help = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.OPENOFFICE_LIBREOFFICE));
         help.setMaxWidth(Double.MAX_VALUE);
 
         selectDocument = new Button();
diff --git a/src/main/java/org/jabref/gui/preferences/AdvancedTab.java b/src/main/java/org/jabref/gui/preferences/AdvancedTab.java
index 4a8dbf0a075..03f67d319cb 100644
--- a/src/main/java/org/jabref/gui/preferences/AdvancedTab.java
+++ b/src/main/java/org/jabref/gui/preferences/AdvancedTab.java
@@ -80,7 +80,7 @@ public AdvancedTab(DialogService dialogService, JabRefPreferences prefs) {
         p.getChildren().add(remoteServerPort);
 
         ActionFactory factory = new ActionFactory(preferences.getKeyBindingRepository());
-        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.REMOTE).getCommand());
+        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.REMOTE));
         help.setMaxWidth(Double.MAX_VALUE);
         p.getChildren().add(help);
 
diff --git a/src/main/java/org/jabref/gui/preferences/FileTab.java b/src/main/java/org/jabref/gui/preferences/FileTab.java
index 4067cf08751..060afb272cd 100644
--- a/src/main/java/org/jabref/gui/preferences/FileTab.java
+++ b/src/main/java/org/jabref/gui/preferences/FileTab.java
@@ -143,8 +143,7 @@ public FileTab(DialogService dialogService, JabRefPreferences prefs) {
         matchExactKeyOnly.setToggleGroup(autolinkGroup);
         useRegExpComboBox.setToggleGroup(autolinkGroup);
 
-        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on regular expression search"),
-                                                                                    HelpFile.REGEX_SEARCH).getCommand());
+        Button help = factory.createIconButton(StandardActions.HELP_REGEX_SEARCH, new HelpAction(HelpFile.REGEX_SEARCH));
         builder.add(help, 3, 16);
         builder.add(runAutoFileSearch, 1, 17);
         builder.add(allowFileAutoOpenBrowse, 1, 18);
@@ -157,7 +156,7 @@ public FileTab(DialogService dialogService, JabRefPreferences prefs) {
         builder.add(autosave, 1, 20);
         builder.add(localAutoSave, 1, 21);
 
-        Button helpAutosave = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.AUTOSAVE).getCommand());
+        Button helpAutosave = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.AUTOSAVE));
         builder.add(helpAutosave, 2, 21);
     }
 
diff --git a/src/main/java/org/jabref/gui/preferences/GeneralTab.java b/src/main/java/org/jabref/gui/preferences/GeneralTab.java
index c7f3759755d..4dacdd38e8a 100644
--- a/src/main/java/org/jabref/gui/preferences/GeneralTab.java
+++ b/src/main/java/org/jabref/gui/preferences/GeneralTab.java
@@ -95,7 +95,7 @@ public GeneralTab(DialogService dialogService, JabRefPreferences prefs) {
         builder.add(defOwnerField, 2, 10);
         builder.add(overwriteOwner, 3, 10);
 
-        Button helpOwner = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.OWNER).getCommand());
+        Button helpOwner = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.OWNER));
         builder.add(helpOwner, 4, 10);
 
         builder.add(useTimeStamp, 1, 13);
@@ -105,7 +105,7 @@ public GeneralTab(DialogService dialogService, JabRefPreferences prefs) {
         builder.add(fieldName, 3, 13);
         builder.add(timeStampField, 4, 13);
 
-        Button helpTimestamp = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.TIMESTAMP).getCommand());
+        Button helpTimestamp = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.TIMESTAMP));
         builder.add(helpTimestamp, 6, 13);
 
         builder.add(updateTimeStamp, 1, 14);
diff --git a/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java b/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java
index da1f649fb2c..bfc0de4fbfd 100644
--- a/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java
+++ b/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java
@@ -151,8 +151,7 @@ public NameFormatterTab(JabRefPreferences prefs) {
             }
         });
 
-        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on Name Formatting"),
-                                                                                    HelpFile.CUSTOM_EXPORTS_NAME_FORMATTER).getCommand());
+        Button help = factory.createIconButton(StandardActions.HELP_NAME_FORMATTER, new HelpAction(HelpFile.CUSTOM_EXPORTS_NAME_FORMATTER));
         HBox toolbar = new HBox();
         toolbar.getChildren().addAll(addName, addLast, add, delete, help);
         tabPanel.setBottom(toolbar);
diff --git a/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java b/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
index fe9dd582df7..38c252b642c 100644
--- a/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
@@ -1,15 +1,11 @@
 package org.jabref.gui.preferences;
 
-import java.awt.event.ActionEvent;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Locale;
 
-import javax.swing.AbstractAction;
-
 import javafx.beans.property.SimpleDoubleProperty;
 import javafx.beans.property.SimpleStringProperty;
 import javafx.collections.FXCollections;
@@ -50,7 +46,7 @@ class TableColumnsTab extends Pane implements PrefsTab {
 
     private final JabRefPreferences prefs;
     private boolean tableChanged;
-    private final TableView colSetup;
+    private final TableView<TableRow> colSetup;
     private final JabRefFrame frame;
 
     private final CheckBox urlColumn;
@@ -229,8 +225,7 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
 
         ActionFactory factory = new ActionFactory(prefs.getKeyBindingRepository());
 
-        Button helpButton = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on special fields"),
-                                                                                          HelpFile.SPECIAL_FIELDS).getCommand());
+        Button helpButton = factory.createIconButton(StandardActions.HELP_SPECIAL_FIELDS, new HelpAction(HelpFile.SPECIAL_FIELDS));
 
         rankingColumn = new CheckBox(Localization.lang("Show rank"));
         qualityColumn = new CheckBox(Localization.lang("Show quality"));
@@ -299,7 +294,7 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
         builder.add(tabPanel, 1, 5);
         Button buttonOrder = new Button("Update to current column order");
         buttonOrder.setPrefSize(300, 30);
-        buttonOrder.setOnAction(e -> new UpdateOrderAction());
+        buttonOrder.setOnAction(e -> updateOrderAction());
         builder.add(buttonOrder, 1, 7);
     }
 
@@ -517,23 +512,16 @@ public void storeSettings() {
 
     }
 
-    class UpdateOrderAction extends AbstractAction {
-
-        public UpdateOrderAction() {
-            super(Localization.lang("Update to current column order"));
+    private void updateOrderAction() {
+        BasePanel panel = frame.getCurrentBasePanel();
+        if (panel == null) {
+            return;
         }
+        // idea: sort elements according to value stored in hash, keep
+        // everything not inside hash/mainTable as it was
+        final HashMap<String, Integer> map = new HashMap<>();
 
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            BasePanel panel = frame.getCurrentBasePanel();
-            if (panel == null) {
-                return;
-            }
-            // idea: sort elements according to value stored in hash, keep
-            // everything not inside hash/mainTable as it was
-            final HashMap<String, Integer> map = new HashMap<>();
-
-            // first element (#) not inside data
+        // first element (#) not inside data
             /*
             for (TableColumn<BibEntry, ?> column : panel.getMainTable().getColumns()) {
                 String name = column.getText();
@@ -542,19 +530,18 @@ public void actionPerformed(ActionEvent e) {
                 }
             }
             */
-            Collections.sort(data, (o1, o2) -> {
-                Integer n1 = map.get(o1.getName());
-                Integer n2 = map.get(o2.getName());
-                if ((n1 == null) || (n2 == null)) {
-                    return 0;
-                }
-                return n1.compareTo(n2);
-            });
+        data.sort((o1, o2) -> {
+            Integer n1 = map.get(o1.getName());
+            Integer n2 = map.get(o2.getName());
+            if ((n1 == null) || (n2 == null)) {
+                return 0;
+            }
+            return n1.compareTo(n2);
+        });
 
-            colSetup.setItems(data);
-            colSetup.refresh();
-            tableChanged = true;
-        }
+        colSetup.setItems(data);
+        colSetup.refresh();
+        tableChanged = true;
     }
 
     @Override
diff --git a/src/main/java/org/jabref/gui/util/ControlHelper.java b/src/main/java/org/jabref/gui/util/ControlHelper.java
index b5d139b338a..ca9b703880a 100644
--- a/src/main/java/org/jabref/gui/util/ControlHelper.java
+++ b/src/main/java/org/jabref/gui/util/ControlHelper.java
@@ -3,9 +3,6 @@
 import java.util.function.Consumer;
 import java.util.function.UnaryOperator;
 
-import javax.swing.JComponent;
-
-import javafx.embed.swing.SwingNode;
 import javafx.event.ActionEvent;
 import javafx.event.Event;
 import javafx.scene.Parent;
@@ -24,13 +21,6 @@ public static void setAction(ButtonType buttonType, DialogPane dialogPane, Consu
         }));
     }
 
-    public static void setSwingContent(DialogPane dialogPane, JComponent content) {
-        SwingNode node = new SwingNode();
-        node.setContent(content);
-        node.setVisible(true);
-        dialogPane.setContent(node);
-    }
-
     public static boolean childIsFocused(Parent node) {
         return node.isFocused() || node.getChildrenUnmodifiable().stream().anyMatch(child -> {
             if (child instanceof Parent) {
diff --git a/src/main/java/org/jabref/gui/util/component/CheckBoxMessage.java b/src/main/java/org/jabref/gui/util/component/CheckBoxMessage.java
deleted file mode 100644
index 99aa890ca7d..00000000000
--- a/src/main/java/org/jabref/gui/util/component/CheckBoxMessage.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package org.jabref.gui.util.component;
-
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-
-import javax.swing.JCheckBox;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.SwingConstants;
-
-public class CheckBoxMessage extends JPanel {
-
-    private final JCheckBox cb;
-
-
-    public CheckBoxMessage(String message, String cbText, boolean defaultValue) {
-        cb = new JCheckBox(cbText, defaultValue);
-        GridBagLayout gbl = new GridBagLayout();
-        setLayout(gbl);
-        GridBagConstraints con = new GridBagConstraints();
-        con.gridwidth = GridBagConstraints.REMAINDER;
-
-        JLabel lab = new JLabel(message + '\n');
-        cb.setHorizontalAlignment(SwingConstants.LEFT);
-        gbl.setConstraints(lab, con);
-        add(lab);
-        con.anchor = GridBagConstraints.WEST;
-        con.insets = new Insets(10, 0, 0, 0);
-        gbl.setConstraints(cb, con);
-        add(cb);
-    }
-
-    public boolean isSelected() {
-        return cb.isSelected();
-    }
-}
diff --git a/src/main/java/org/jabref/gui/util/component/JTextAreaWithPlaceholder.java b/src/main/java/org/jabref/gui/util/component/JTextAreaWithPlaceholder.java
deleted file mode 100644
index 0c0c0b06acb..00000000000
--- a/src/main/java/org/jabref/gui/util/component/JTextAreaWithPlaceholder.java
+++ /dev/null
@@ -1,90 +0,0 @@
-package org.jabref.gui.util.component;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-
-import javax.swing.JTextArea;
-import javax.swing.UIManager;
-
-/**
- * A text area which displays a predefined text the same way as {@link JTextFieldWithPlaceholder} does.
- */
-public class JTextAreaWithPlaceholder extends JTextArea implements KeyListener {
-
-    private final String textWhenNotFocused;
-
-    public JTextAreaWithPlaceholder() {
-        this("");
-    }
-
-    /**
-     * Additionally to {@link JTextAreaWithPlaceholder#JTextAreaWithPlaceholder(String)}
-     * this also sets the initial text of the text field component.
-     *
-     * @param content as the text of the textfield
-     * @param placeholder as the placeholder of the textfield
-     */
-    public JTextAreaWithPlaceholder(String content, String placeholder) {
-        this(placeholder);
-        setText(content);
-    }
-
-    /**
-     * This will create a {@link JTextArea} with a placeholder text. The placeholder
-     * will always be displayed if the text of the {@link JTextArea} is empty.
-     *
-     * @param placeholder as the placeholder of the textarea
-     */
-    public JTextAreaWithPlaceholder(String placeholder) {
-        super();
-        this.setEditable(true);
-        this.setText("");
-        this.textWhenNotFocused = placeholder;
-    }
-
-    @Override
-    protected void paintComponent(Graphics graphics) {
-        super.paintComponent(graphics);
-
-        if (this.getText().isEmpty()) {
-            Font prev = graphics.getFont();
-            Color prevColor = graphics.getColor();
-            graphics.setColor(UIManager.getColor("textInactiveText"));
-            int textHeight = graphics.getFontMetrics().getHeight();
-            int x = this.getInsets().left;
-            Graphics2D g2d = (Graphics2D) graphics;
-            RenderingHints hints = g2d.getRenderingHints();
-            g2d.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
-            g2d.drawString(textWhenNotFocused, x, textHeight + this.getInsets().top);
-            g2d.setRenderingHints(hints);
-            graphics.setFont(prev);
-            graphics.setColor(prevColor);
-        }
-    }
-
-    @Override
-    public void keyTyped(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-
-    @Override
-    public void keyPressed(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-
-    @Override
-    public void keyReleased(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/gui/util/component/JTextFieldWithPlaceholder.java b/src/main/java/org/jabref/gui/util/component/JTextFieldWithPlaceholder.java
deleted file mode 100644
index b676b20adb4..00000000000
--- a/src/main/java/org/jabref/gui/util/component/JTextFieldWithPlaceholder.java
+++ /dev/null
@@ -1,91 +0,0 @@
-package org.jabref.gui.util.component;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-
-import javax.swing.JTextField;
-import javax.swing.UIManager;
-
-/**
- * A text field which displays a predefined text (e.g. "Search") if the text field is empty.
- * This is similar to a html5 input element with a defined placeholder attribute.
- * Implementation based on https://gmigdos.wordpress.com/2010/03/30/java-a-custom-jtextfield-for-searching/
- */
-public class JTextFieldWithPlaceholder extends JTextField implements KeyListener {
-
-    private final String textWhenNotFocused;
-
-    /**
-     * Additionally to {@link JTextFieldWithPlaceholder#JTextFieldWithPlaceholder(String)}
-     * this also sets the initial text of the text field component.
-     *
-     * @param content as the text of the textfield
-     * @param placeholder as the placeholder of the textfield
-     */
-    public JTextFieldWithPlaceholder(String content, String placeholder) {
-        this(placeholder);
-        setText(content);
-    }
-
-    /**
-     * This will create a {@link JTextField} with a placeholder text. The placeholder
-     * will always be displayed if the text of the {@link JTextField} is empty.
-     *
-     * @param placeholder as the placeholder of the textfield
-     */
-    public JTextFieldWithPlaceholder(String placeholder) {
-        super();
-        this.setEditable(true);
-        this.setText("");
-        this.textWhenNotFocused = placeholder;
-    }
-
-    @Override
-    protected void paintComponent(Graphics graphics) {
-        super.paintComponent(graphics);
-
-        if (this.getText().isEmpty()) {
-            int height = this.getHeight();
-            Font prev = graphics.getFont();
-            Color prevColor = graphics.getColor();
-            graphics.setColor(UIManager.getColor("textInactiveText"));
-            int textHeight = graphics.getFontMetrics().getHeight();
-            int textBottom = (((height - textHeight) / 2) + textHeight) - 4;
-            int x = this.getInsets().left;
-            Graphics2D g2d = (Graphics2D) graphics;
-            RenderingHints hints = g2d.getRenderingHints();
-            g2d.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
-            g2d.drawString(textWhenNotFocused, x, textBottom);
-            g2d.setRenderingHints(hints);
-            graphics.setFont(prev);
-            graphics.setColor(prevColor);
-        }
-    }
-
-    @Override
-    public void keyTyped(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-
-    @Override
-    public void keyPressed(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-
-    @Override
-    public void keyReleased(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/worker/CallBack.java b/src/main/java/org/jabref/gui/worker/CallBack.java
deleted file mode 100644
index 4fa4c6eb60e..00000000000
--- a/src/main/java/org/jabref/gui/worker/CallBack.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package org.jabref.gui.worker;
-
-/**
- * Represents a task that is to be executed on the GUI thread
- */
-@FunctionalInterface
-public interface CallBack {
-
-    void update();
-
-}
diff --git a/src/main/java/org/jabref/logic/net/URLUtil.java b/src/main/java/org/jabref/logic/net/URLUtil.java
index 05644fd4a18..e927d6933ff 100644
--- a/src/main/java/org/jabref/logic/net/URLUtil.java
+++ b/src/main/java/org/jabref/logic/net/URLUtil.java
@@ -6,7 +6,9 @@
 import java.net.URLDecoder;
 import java.nio.charset.StandardCharsets;
 import java.util.Objects;
+import java.util.Optional;
 
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.model.strings.StringUtil;
 
 import org.apache.http.client.utils.URIBuilder;
@@ -52,7 +54,7 @@ public static String cleanGoogleSearchURL(String url) {
             for (String pair: pairs) {
                 // "clean" url is decoded value of "url" parameter
                 if (pair.startsWith("url=")) {
-                    String value = pair.substring(pair.indexOf('=') + 1, pair.length());
+                    String value = pair.substring(pair.indexOf('=') + 1);
 
                     String decode = URLDecoder.decode(value, StandardCharsets.UTF_8.name());
                     // url?
@@ -102,4 +104,57 @@ private static String appendSegmentToPath(String path, String segment) {
         return path + "/" + segment;
     }
 
+    /**
+     * Look for the last '.' in the link, and return the following characters.
+     * This gives the extension for most reasonably named links.
+     *
+     * @param link The link
+     * @return The suffix, excluding the dot (e.g. "pdf")
+     */
+    public static Optional<String> getSuffix(final String link) {
+        String strippedLink = link;
+        try {
+            // Try to strip the query string, if any, to get the correct suffix:
+            URL url = new URL(link);
+            if ((url.getQuery() != null) && (url.getQuery().length() < (link.length() - 1))) {
+                strippedLink = link.substring(0, link.length() - url.getQuery().length() - 1);
+            }
+        } catch (MalformedURLException e) {
+            // Don't report this error, since this getting the suffix is a non-critical
+            // operation, and this error will be triggered and reported elsewhere.
+        }
+        // First see if the stripped link gives a reasonable suffix:
+        String suffix;
+        int strippedLinkIndex = strippedLink.lastIndexOf('.');
+        if ((strippedLinkIndex <= 0) || (strippedLinkIndex == (strippedLink.length() - 1))) {
+            suffix = null;
+        } else {
+            suffix = strippedLink.substring(strippedLinkIndex + 1);
+        }
+        if (!ExternalFileTypes.getInstance().isExternalFileTypeByExt(suffix)) {
+            // If the suffix doesn't seem to give any reasonable file type, try
+            // with the non-stripped link:
+            int index = link.lastIndexOf('.');
+            if ((index <= 0) || (index == (link.length() - 1))) {
+                // No occurrence, or at the end
+                // Check if there are path separators in the suffix - if so, it is definitely
+                // not a proper suffix, so we should give up:
+                if (strippedLink.substring(strippedLinkIndex + 1).indexOf('/') >= 1) {
+                    return Optional.empty();
+                } else {
+                    return Optional.of(suffix); // return the first one we found, anyway.
+                }
+            } else {
+                // Check if there are path separators in the suffix - if so, it is definitely
+                // not a proper suffix, so we should give up:
+                if (link.substring(index + 1).indexOf('/') >= 1) {
+                    return Optional.empty();
+                } else {
+                    return Optional.of(link.substring(index + 1));
+                }
+            }
+        } else {
+            return Optional.ofNullable(suffix);
+        }
+    }
 }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 6f889dd0133..c553d2896fa 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -280,9 +280,6 @@ Donate\ to\ JabRef=Donate to JabRef
 Down=Down
 
 Download\ file=Download file
-
-Downloading...=Downloading...
-
 duplicate\ removal=duplicate removal
 
 Duplicate\ string\ name=Duplicate string name
@@ -300,7 +297,6 @@ Each\ line\ must\ be\ of\ the\ following\ form=Each line must be of the followin
 Edit=Edit
 
 Edit\ entry=Edit entry
-Save\ file=Save file
 Edit\ file\ type=Edit file type
 
 Edit\ group=Edit group
@@ -390,7 +386,6 @@ File\ directory\ is\ not\ set\ or\ does\ not\ exist\!=File directory is not set
 File\ exists=File exists
 
 File\ not\ found=File not found
-File\ type=File type
 filename=filename
 
 Files\ opened=Files opened
@@ -927,8 +922,6 @@ Sublibrary\ from\ AUX=Sublibrary from AUX
 Switches\ between\ full\ and\ abbreviated\ journal\ name\ if\ the\ journal\ name\ is\ known.=Switches between full and abbreviated journal name if the journal name is known.
 
 Tabname=Tabname
-Target\ file\ cannot\ be\ a\ directory.=Target file cannot be a directory.
-
 Tertiary\ sort\ criterion=Tertiary sort criterion
 
 Test=Test
@@ -1097,7 +1090,6 @@ Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ %1.=Line %0: Found corrupted BibTeX k
 Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ %1\ (contains\ whitespaces).=Line %0: Found corrupted BibTeX key %1 (contains whitespaces).
 Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ %1\ (comma\ missing).=Line %0: Found corrupted BibTeX key %1 (comma missing).
 No\ full\ text\ document\ found=No full text document found
-Update\ to\ current\ column\ order=Update to current column order
 Download\ from\ URL=Download from URL
 Rename\ field=Rename field
 Append\ field=Append field
@@ -1451,8 +1443,6 @@ Could\ not\ connect\ to\ %0=Could not connect to %0
 Warning\:\ %0\ out\ of\ %1\ entries\ have\ undefined\ title.=Warning: %0 out of %1 entries have undefined title.
 Warning\:\ %0\ out\ of\ %1\ entries\ have\ undefined\ BibTeX\ key.=Warning: %0 out of %1 entries have undefined BibTeX key.
 Added\ new\ '%0'\ entry.=Added new '%0' entry.
-Multiple\ entries\ selected.\ Do\ you\ want\ to\ change\ the\ type\ of\ all\ these\ to\ '%0'?=Multiple entries selected. Do you want to change the type of all these to '%0'?
-Changed\ type\ to\ '%0'\ for=Changed type to '%0' for
 Really\ delete\ the\ selected\ entry?=Really delete the selected entry?
 Really\ delete\ the\ %0\ selected\ entries?=Really delete the %0 selected entries?
 Keep\ merged\ entry\ only=Keep merged entry only
diff --git a/src/test/java/org/jabref/cleanup/CleanupActionsListModelTest.java b/src/test/java/org/jabref/cleanup/CleanupActionsListModelTest.java
deleted file mode 100644
index b44b0c572aa..00000000000
--- a/src/test/java/org/jabref/cleanup/CleanupActionsListModelTest.java
+++ /dev/null
@@ -1,94 +0,0 @@
-package org.jabref.cleanup;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-
-import javax.swing.event.ListDataEvent;
-import javax.swing.event.ListDataListener;
-
-import org.jabref.gui.cleanup.CleanupActionsListModel;
-import org.jabref.logic.cleanup.Cleanups;
-import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
-import org.jabref.model.cleanup.FieldFormatterCleanup;
-import org.jabref.model.cleanup.FieldFormatterCleanups;
-
-import org.junit.jupiter.api.Test;
-import org.mockito.ArgumentCaptor;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.verify;
-import static org.mockito.Mockito.verifyZeroInteractions;
-import static org.mockito.Mockito.when;
-
-public class CleanupActionsListModelTest {
-
-    @Test
-    public void resetFiresItemsChanged() throws Exception {
-        CleanupActionsListModel model = new CleanupActionsListModel(Collections.emptyList());
-        ListDataListener listener = mock(ListDataListener.class);
-        model.addListDataListener(listener);
-        FieldFormatterCleanups defaultFormatters = mock(FieldFormatterCleanups.class);
-
-        model.reset(defaultFormatters);
-
-        ArgumentCaptor<ListDataEvent> argument = ArgumentCaptor.forClass(ListDataEvent.class);
-        verify(listener).contentsChanged(argument.capture());
-        assertEquals(ListDataEvent.CONTENTS_CHANGED, argument.getValue().getType());
-    }
-
-    @Test
-    public void resetSetsFormattersToPassedList() throws Exception {
-        CleanupActionsListModel model = new CleanupActionsListModel(Collections.emptyList());
-        FieldFormatterCleanups defaultFormatters = mock(FieldFormatterCleanups.class);
-        List<FieldFormatterCleanup> formatters = Arrays.asList(new FieldFormatterCleanup("test", new ClearFormatter()));
-        when(defaultFormatters.getConfiguredActions()).thenReturn(formatters);
-
-        model.reset(defaultFormatters);
-
-        assertEquals(formatters, model.getAllActions());
-    }
-
-    public List<FieldFormatterCleanup> getDefaultFieldFormatterCleanups() {
-        FieldFormatterCleanups formatters = Cleanups.DEFAULT_SAVE_ACTIONS;
-        //new ArrayList because configured actions is an unmodifiable collection
-        return new ArrayList<>(formatters.getConfiguredActions());
-    }
-
-    @Test
-    public void removedAtIndexOkay() {
-
-        CleanupActionsListModel model = new CleanupActionsListModel(getDefaultFieldFormatterCleanups());
-        ListDataListener listener = mock(ListDataListener.class);
-        model.addListDataListener(listener);
-        model.removeAtIndex(0);
-
-        ArgumentCaptor<ListDataEvent> argument = ArgumentCaptor.forClass(ListDataEvent.class);
-        verify(listener).intervalRemoved(argument.capture());
-        assertEquals(ListDataEvent.INTERVAL_REMOVED, argument.getValue().getType());
-    }
-
-    @Test
-    public void removedAtIndexMinus1DoesNothing() {
-
-        CleanupActionsListModel model = new CleanupActionsListModel(getDefaultFieldFormatterCleanups());
-        ListDataListener listener = mock(ListDataListener.class);
-        model.addListDataListener(listener);
-        model.removeAtIndex(-1);
-
-        verifyZeroInteractions(listener);
-    }
-
-    @Test
-    public void removedAtIndexgreaterListSizeDoesNothing() {
-
-        CleanupActionsListModel model = new CleanupActionsListModel(getDefaultFieldFormatterCleanups());
-        ListDataListener listener = mock(ListDataListener.class);
-        model.addListDataListener(listener);
-        model.removeAtIndex((getDefaultFieldFormatterCleanups().size() + 1));
-
-        verifyZeroInteractions(listener);
-    }
-}

From 2c327259a45e744c7ad9a46ae35af3145940a830 Mon Sep 17 00:00:00 2001
From: Johannes Manner <johannes.manner@web.de>
Date: Fri, 29 Mar 2019 13:21:28 +0100
Subject: [PATCH 142/184] =?UTF-8?q?Moved=20cleanup=20out=20of=20background?=
 =?UTF-8?q?=20thread=20to=20stick=20with=20the=20architecture=E2=80=A6=20(?=
 =?UTF-8?q?#4823)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Moved cleanup out of background thread to stick with the architecture tests

* remove unused imports

* Had to split the URLUtil since another logic class used URLUtil functionality

* fixed checkstyle

* Update DOAJFetcher.java

* checkstyle III
---
 .../org/jabref/gui/actions/CleanupAction.java |  6 ++--
 .../gui/fieldeditors/LinkedFileViewModel.java |  1 -
 .../net => gui/fieldeditors}/URLUtil.java     | 29 +-----------------
 .../gui/fieldeditors/UrlEditorViewModel.java  |  1 -
 .../logic/cleanup/RenamePdfCleanup.java       |  5 ++--
 .../logic/importer/fetcher/DOAJFetcher.java   | 28 +++++++++++++++--
 .../importer/fetcher/DOAJFetcherTest.java     | 29 ++++++++++++++++++
 .../org/jabref/logic/net/URLUtilTest.java     | 30 ++-----------------
 8 files changed, 62 insertions(+), 67 deletions(-)
 rename src/main/java/org/jabref/{logic/net => gui/fieldeditors}/URLUtil.java (85%)

diff --git a/src/main/java/org/jabref/gui/actions/CleanupAction.java b/src/main/java/org/jabref/gui/actions/CleanupAction.java
index 648af8313b7..f2251d45616 100644
--- a/src/main/java/org/jabref/gui/actions/CleanupAction.java
+++ b/src/main/java/org/jabref/gui/actions/CleanupAction.java
@@ -9,7 +9,6 @@
 import org.jabref.gui.cleanup.CleanupDialog;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.gui.util.BackgroundTask;
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.cleanup.CleanupWorker;
 import org.jabref.logic.l10n.Localization;
@@ -59,9 +58,8 @@ public void action() {
 
             preferences.setCleanupPreset(chosenPreset.get());
 
-            BackgroundTask.wrap(() -> cleanup(chosenPreset.get()))
-                          .onSuccess(result -> showResults())
-                          .executeWith(Globals.TASK_EXECUTOR);
+            this.cleanup(chosenPreset.get());
+            this.showResults();
         }
     }
 
diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
index c4f11bb73b3..d902b93a233 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
@@ -37,7 +37,6 @@
 import org.jabref.logic.externalfiles.LinkedFileHandler;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.URLDownload;
-import org.jabref.logic.net.URLUtil;
 import org.jabref.logic.xmp.XmpPreferences;
 import org.jabref.logic.xmp.XmpUtilWriter;
 import org.jabref.model.database.BibDatabaseContext;
diff --git a/src/main/java/org/jabref/logic/net/URLUtil.java b/src/main/java/org/jabref/gui/fieldeditors/URLUtil.java
similarity index 85%
rename from src/main/java/org/jabref/logic/net/URLUtil.java
rename to src/main/java/org/jabref/gui/fieldeditors/URLUtil.java
index e927d6933ff..5ab4a3b8e87 100644
--- a/src/main/java/org/jabref/logic/net/URLUtil.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/URLUtil.java
@@ -1,4 +1,4 @@
-package org.jabref.logic.net;
+package org.jabref.gui.fieldeditors;
 
 import java.io.UnsupportedEncodingException;
 import java.net.MalformedURLException;
@@ -9,9 +9,6 @@
 import java.util.Optional;
 
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.model.strings.StringUtil;
-
-import org.apache.http.client.utils.URIBuilder;
 
 public class URLUtil {
     private static final String URL_EXP = "^(https?|ftp)://.+";
@@ -80,30 +77,6 @@ public static boolean isURL(String url) {
         return url.contains("://");
     }
 
-    /**
-     * @implNote slightly altered version based on https://gist.github.com/enginer/230e2dc2f1d213a825d5
-     */
-    public static URIBuilder addPath(URIBuilder base, String subPath) {
-        if (StringUtil.isBlank(subPath) || "/".equals(subPath)) {
-            return base;
-        } else {
-            base.setPath(appendSegmentToPath(base.getPath(), subPath));
-            return base;
-        }
-    }
-
-    private static String appendSegmentToPath(String path, String segment) {
-        if (StringUtil.isBlank(path)) {
-            path = "/";
-        }
-
-        if (path.charAt(path.length() - 1) == '/' || segment.startsWith("/")) {
-            return path + segment;
-        }
-
-        return path + "/" + segment;
-    }
-
     /**
      * Look for the last '.' in the link, and return the following characters.
      * This gives the extension for most reasonably named links.
diff --git a/src/main/java/org/jabref/gui/fieldeditors/UrlEditorViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/UrlEditorViewModel.java
index f370a1a89ad..e6b785b488a 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/UrlEditorViewModel.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/UrlEditorViewModel.java
@@ -10,7 +10,6 @@
 import org.jabref.gui.desktop.JabRefDesktop;
 import org.jabref.logic.integrity.FieldCheckers;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.net.URLUtil;
 import org.jabref.model.strings.StringUtil;
 
 import org.fxmisc.easybind.EasyBind;
diff --git a/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java b/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
index 72912ed73de..4016081e60b 100644
--- a/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
+++ b/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
@@ -7,7 +7,6 @@
 import java.util.Objects;
 import java.util.Optional;
 
-import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.externalfiles.LinkedFileHandler;
 import org.jabref.model.FieldChange;
 import org.jabref.model.cleanup.CleanupJob;
@@ -55,8 +54,8 @@ public List<FieldChange> cleanup(BibEntry entry) {
         }
 
         if (changed) {
-            Optional<FieldChange> fileFieldChanged = DefaultTaskExecutor.runInJavaFXThread(() -> entry.setFiles(files));
-            return OptionalUtil.toList(fileFieldChanged);
+            Optional<FieldChange> changes = entry.setFiles(files);
+            return OptionalUtil.toList(changes);
         }
 
         return Collections.emptyList();
diff --git a/src/main/java/org/jabref/logic/importer/fetcher/DOAJFetcher.java b/src/main/java/org/jabref/logic/importer/fetcher/DOAJFetcher.java
index 67bc0dc97ac..40b617a2301 100644
--- a/src/main/java/org/jabref/logic/importer/fetcher/DOAJFetcher.java
+++ b/src/main/java/org/jabref/logic/importer/fetcher/DOAJFetcher.java
@@ -16,10 +16,10 @@
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.Parser;
 import org.jabref.logic.importer.SearchBasedParserFetcher;
-import org.jabref.logic.net.URLUtil;
 import org.jabref.logic.util.OS;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
+import org.jabref.model.strings.StringUtil;
 
 import org.apache.http.client.utils.URIBuilder;
 import org.json.JSONArray;
@@ -165,12 +165,36 @@ public Optional<HelpFile> getHelpPage() {
     @Override
     public URL getURLForQuery(String query) throws URISyntaxException, MalformedURLException, FetcherException {
         URIBuilder uriBuilder = new URIBuilder(SEARCH_URL);
-        URLUtil.addPath(uriBuilder, query);
+        DOAJFetcher.addPath(uriBuilder, query);
         uriBuilder.addParameter("pageSize", "30"); // Number of results
         //uriBuilder.addParameter("page", "1"); // Page (not needed so far)
         return uriBuilder.build().toURL();
     }
 
+    /**
+     * @implNote slightly altered version based on https://gist.github.com/enginer/230e2dc2f1d213a825d5
+     */
+    public static URIBuilder addPath(URIBuilder base, String subPath) {
+        if (StringUtil.isBlank(subPath) || "/".equals(subPath)) {
+            return base;
+        } else {
+            base.setPath(appendSegmentToPath(base.getPath(), subPath));
+            return base;
+        }
+    }
+
+    private static String appendSegmentToPath(String path, String segment) {
+        if (StringUtil.isBlank(path)) {
+            path = "/";
+        }
+
+        if (path.charAt(path.length() - 1) == '/' || segment.startsWith("/")) {
+            return path + segment;
+        }
+
+        return path + "/" + segment;
+    }
+
     @Override
     public Parser getParser() {
         return inputStream -> {
diff --git a/src/test/java/org/jabref/logic/importer/fetcher/DOAJFetcherTest.java b/src/test/java/org/jabref/logic/importer/fetcher/DOAJFetcherTest.java
index 77a0a20b925..f49b0e21d17 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/DOAJFetcherTest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/DOAJFetcherTest.java
@@ -9,6 +9,7 @@
 import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.testutils.category.FetcherTest;
 
+import org.apache.http.client.utils.URIBuilder;
 import org.json.JSONObject;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -73,4 +74,32 @@ void testBibJSONConverter() {
     public void searchByEmptyQuery() throws Exception {
         assertEquals(Collections.emptyList(), fetcher.performSearch(""));
     }
+
+    @Test
+    void appendSingleWord() throws Exception {
+        URIBuilder builder = new URIBuilder("http://example.com/test");
+        DOAJFetcher.addPath(builder, "/example");
+        assertEquals("http://example.com/test/example", builder.build().toASCIIString());
+    }
+
+    @Test
+    void appendSingleWordWithSlash() throws Exception {
+        URIBuilder builder = new URIBuilder("http://example.com/test");
+        DOAJFetcher.addPath(builder, "/example");
+        assertEquals("http://example.com/test/example", builder.build().toASCIIString());
+    }
+
+    @Test
+    void appendSlash() throws Exception {
+        URIBuilder builder = new URIBuilder("http://example.com/test");
+        DOAJFetcher.addPath(builder, "/");
+        assertEquals("http://example.com/test", builder.build().toASCIIString());
+    }
+
+    @Test
+    void appendTwoWords() throws Exception {
+        URIBuilder builder = new URIBuilder("http://example.com/test");
+        DOAJFetcher.addPath(builder, "example two");
+        assertEquals("http://example.com/test/example%20two", builder.build().toASCIIString());
+    }
 }
diff --git a/src/test/java/org/jabref/logic/net/URLUtilTest.java b/src/test/java/org/jabref/logic/net/URLUtilTest.java
index 01f181eb465..6a6cfc12972 100644
--- a/src/test/java/org/jabref/logic/net/URLUtilTest.java
+++ b/src/test/java/org/jabref/logic/net/URLUtilTest.java
@@ -1,6 +1,7 @@
 package org.jabref.logic.net;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.jabref.gui.fieldeditors.URLUtil;
+
 import org.junit.jupiter.api.Test;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -73,31 +74,4 @@ void isURLshouldRejectInvalidURL() {
         assertFalse(URLUtil.isURL("google.com"));
     }
 
-    @Test
-    void appendSingleWord() throws Exception {
-        URIBuilder builder = new URIBuilder("http://example.com/test");
-        URLUtil.addPath(builder, "/example");
-        assertEquals("http://example.com/test/example", builder.build().toASCIIString());
-    }
-
-    @Test
-    void appendSingleWordWithSlash() throws Exception {
-        URIBuilder builder = new URIBuilder("http://example.com/test");
-        URLUtil.addPath(builder, "/example");
-        assertEquals("http://example.com/test/example", builder.build().toASCIIString());
-    }
-
-    @Test
-    void appendSlash() throws Exception {
-        URIBuilder builder = new URIBuilder("http://example.com/test");
-        URLUtil.addPath(builder, "/");
-        assertEquals("http://example.com/test", builder.build().toASCIIString());
-    }
-
-    @Test
-    void appendTwoWords() throws Exception {
-        URIBuilder builder = new URIBuilder("http://example.com/test");
-        URLUtil.addPath(builder, "example two");
-        assertEquals("http://example.com/test/example%20two", builder.build().toASCIIString());
-    }
 }

From ee0f42c02bf69f03015d654c7f3cb5f1cc976a83 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Fri, 29 Mar 2019 15:04:38 +0100
Subject: [PATCH 143/184] Fix overwriting of date in RIS import (#4821)

* Fix overwriting of date in RIS import

Now the first valid year is taken into account
Adjusted the tests to reflect the new behvaiour

* add changelog
---
 CHANGELOG.md                                  |  1 +
 .../importer/fileformat/RisImporter.java      | 28 +++++++++++++----
 .../importer/fileformat/RisImporterTest3.bib  |  1 -
 .../importer/fileformat/RisImporterTest6.bib  |  1 -
 .../fileformat/RisImporterTest8_date.bib      | 15 ++++++++++
 .../fileformat/RisImporterTest8_date.ris      | 30 +++++++++++++++++++
 6 files changed, 68 insertions(+), 8 deletions(-)
 create mode 100644 src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.bib
 create mode 100644 src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.ris

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d5983623107..a64512c0723 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -101,6 +101,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
 - We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
+- We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 
 
 
diff --git a/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java
index d778dd3d357..3adfa827d19 100644
--- a/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java
+++ b/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java
@@ -2,6 +2,9 @@
 
 import java.io.BufferedReader;
 import java.io.IOException;
+import java.time.Year;
+import java.time.format.DateTimeFormatter;
+import java.time.format.DateTimeParseException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -23,6 +26,7 @@
 public class RisImporter extends Importer {
 
     private static final Pattern RECOGNIZED_FORMAT_PATTERN = Pattern.compile("TY  - .*");
+    private static DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy");
 
     @Override
     public String getName() {
@@ -53,10 +57,12 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
         String linesAsString = reader.lines().reduce((line, nextline) -> line + "\n" + nextline).orElse("");
 
         String[] entries = linesAsString.replace("\u2013", "-").replace("\u2014", "--").replace("\u2015", "--")
-                .split("ER  -.*\\n");
+                                        .split("ER  -.*\\n");
 
         for (String entry1 : entries) {
 
+            boolean foundDate = false;
+
             String type = "";
             String author = "";
             String editor = "";
@@ -74,7 +80,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                 while (!done && (j < (lines.length - 1))) {
                     if ((lines[j + 1].length() >= 6) && !"  - ".equals(lines[j + 1].substring(2, 6))) {
                         if ((current.length() > 0) && !Character.isWhitespace(current.charAt(current.length() - 1))
-                                && !Character.isWhitespace(lines[j + 1].charAt(0))) {
+                            && !Character.isWhitespace(lines[j + 1].charAt(0))) {
                             current.append(' ');
                         }
                         current.append(lines[j + 1]);
@@ -123,7 +129,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                         fields.put(FieldName.TITLE, fields.get(FieldName.TITLE).replaceAll("\\s+", " ")); // Normalize whitespaces
                     } else if ("BT".equals(tag)) {
                         fields.put(FieldName.BOOKTITLE, value);
-                    } else if (("T2".equals(tag) || "J2".equals(tag) || "JA".equals(tag)) && (fields.get(FieldName.JOURNAL) == null || "".equals(fields.get(FieldName.JOURNAL)))) {
+                    } else if (("T2".equals(tag) || "J2".equals(tag) || "JA".equals(tag)) && ((fields.get(FieldName.JOURNAL) == null) || "".equals(fields.get(FieldName.JOURNAL)))) {
                         //if there is no journal title, then put second title as journal title
                         fields.put(FieldName.JOURNAL, value);
                     } else if ("JO".equals(tag) || "J1".equals(tag) || "JF".equals(tag)) {
@@ -187,8 +193,18 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                         }
                     } else if ("UR".equals(tag) || "L2".equals(tag) || "LK".equals(tag)) {
                         fields.put(FieldName.URL, value);
-                    } else if (("Y1".equals(tag) || "Y2".equals(tag) || "PY".equals(tag) || "DA".equals(tag)) && (value.length() >= 4)) {
-                        fields.put(FieldName.YEAR, value.substring(0, 4));
+                    } else if (!foundDate && (("Y1".equals(tag) || "Y2".equals(tag) || "PY".equals(tag) || "DA".equals(tag)) && (value.length() >= 4))) {
+                        String year = value.substring(0, 4);
+
+                        try {
+                            Year.parse(year, formatter);
+                            //if the year is parsebale we have found our date
+                            fields.put(FieldName.YEAR, value.substring(0, 4));
+                            foundDate = true;
+                        } catch (DateTimeParseException ex) {
+                            //We can't parse the year, we ignore it
+                        }
+
                         String[] parts = value.split("/");
                         if ((parts.length > 1) && !parts[1].isEmpty()) {
                             try {
@@ -210,7 +226,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                             comment = comment + OS.NEWLINE;
                         }
                         comment = comment + value;
-                    }  else if ("M3".equals(tag) || "DO".equals(tag)) {
+                    } else if ("M3".equals(tag) || "DO".equals(tag)) {
                         addDoi(fields, value);
                     } else if ("C3".equals(tag)) {
                         fields.put(FieldName.EVENTTITLE, value);
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest3.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest3.bib
index 13eb9b9a606..9bd2b47b290 100644
--- a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest3.bib
+++ b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest3.bib
@@ -4,7 +4,6 @@ @incollection{
   doi = {10.1201/b19107-2},
   issn = {978-1-4822-5326-9},
   journal = {Dermoscopy Image Analysis},
-  month = {#nov#},
   number = {0},
   pages = {1-22},
   publisher = {CRC Press},
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib
index e94772ff175..12a03af5704 100644
--- a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib
+++ b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib
@@ -4,7 +4,6 @@ @article{
   database = {PMC},
   issn = {1537-744X},
   journal = {The Scientific World Journal},
-  month = {#mar#},
   number = {PMC3654245},
   pages = {219840},
   publisher = {Hindawi Publishing Corporation},
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.bib
new file mode 100644
index 00000000000..8c200fa3c7a
--- /dev/null
+++ b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.bib
@@ -0,0 +1,15 @@
+@article{,
+  author = {Valle-Delgado, J. J. and Molina-Bolívar, J. A. and Galisteo-González, F. and Gálvez-Ruiz, M. J. and Feiler, A. and Rutland, M. W.},
+  comment = {doi: 10.1063/1.1954747},
+  doi = {10.1063/1.1954747},
+  issn = {0021-9606},
+  journal = {J. Chem. Phys.},
+  month = {#jul#},
+  number = {3},
+  pages = {034708},
+  publisher = {American Institute of Physics},
+  title = {Hydration forces between silica surfaces: Experimental data and predictions from different theories},
+  url = {https://doi.org/10.1063/1.1954747},
+  volume = {123},
+  year = {2005}
+}
\ No newline at end of file
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.ris b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.ris
new file mode 100644
index 00000000000..2ba45d82897
--- /dev/null
+++ b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.ris
@@ -0,0 +1,30 @@
+
+
+
+
+
+TY  - JOUR
+T1  - Hydration forces between silica surfaces: Experimental data and predictions from different theories
+AU  - Valle-Delgado,J. J. 
+AU  - Molina-Bolívar,J. A. 
+AU  - Galisteo-González,F. 
+AU  - Gálvez-Ruiz,M. J. 
+AU  - Feiler,A. 
+AU  - Rutland,M. W. 
+Y1  - 2005/07/15
+PY  - 2005
+DA  - 2005/07/15
+N1  - doi: 10.1063/1.1954747
+DO  - 10.1063/1.1954747
+T2  - The Journal of Chemical Physics
+JF  - The Journal of Chemical Physics
+JO  - J. Chem. Phys.
+SP  - 034708
+VL  - 123
+IS  - 3
+PB  - American Institute of Physics
+SN  - 0021-9606
+M3  - doi: 10.1063/1.1954747
+UR  - https://doi.org/10.1063/1.1954747
+Y2  - 2019/03/28
+ER  - 

From 3f48bf094ae29e46a58d62608fd8ecb2cdf7a11f Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 29 Mar 2019 15:45:03 +0100
Subject: [PATCH 144/184] Update BibtexKeyEditor.fxml

---
 src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml b/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
index 32160f0c544..7feb0fe3335 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
+++ b/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
@@ -6,5 +6,5 @@
 <fx:root xmlns:fx="http://javafx.com/fxml/1" type="HBox" xmlns="http://javafx.com/javafx/8.0.112"
          fx:controller="org.jabref.gui.fieldeditors.BibtexKeyEditor">
     <EditorTextField fx:id="textField"/>
-    <Button fx:id="generateCiteKeyButton" text="Generate" styleClass="icon-button"/>
+    <Button fx:id="generateCiteKeyButton" text="%Generate" styleClass="icon-button"/>
 </fx:root>

From 60148642e4c727198414e12d9a2f4d1a57c753af Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 29 Mar 2019 22:00:26 +0100
Subject: [PATCH 145/184] Remove "plain text import" feature (#4717)

---
 src/main/java/org/jabref/gui/JabRefFrame.java |   2 -
 .../actions/NewEntryFromPlainTextAction.java  |  54 --
 .../plaintextimport/TagToMarkedTextStore.java |  81 --
 .../gui/plaintextimport/TextInputDialog.java  | 735 ------------------
 src/main/resources/l10n/JabRef_en.properties  |  32 -
 5 files changed, 904 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/actions/NewEntryFromPlainTextAction.java
 delete mode 100644 src/main/java/org/jabref/gui/plaintextimport/TagToMarkedTextStore.java
 delete mode 100644 src/main/java/org/jabref/gui/plaintextimport/TextInputDialog.java

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 838f5d459f0..06ab62cb461 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -71,7 +71,6 @@
 import org.jabref.gui.actions.ManageJournalsAction;
 import org.jabref.gui.actions.NewDatabaseAction;
 import org.jabref.gui.actions.NewEntryAction;
-import org.jabref.gui.actions.NewEntryFromPlainTextAction;
 import org.jabref.gui.actions.NewSubLibraryAction;
 import org.jabref.gui.actions.OldDatabaseCommandWrapper;
 import org.jabref.gui.actions.OpenBrowserAction;
@@ -795,7 +794,6 @@ private MenuBar createMenu() {
         //@formatter:off
         library.getItems().addAll(
                 factory.createMenuItem(StandardActions.NEW_ENTRY, new NewEntryAction(this, dialogService, Globals.prefs)),
-                factory.createMenuItem(StandardActions.NEW_ENTRY_FROM_PLAINTEX, new NewEntryFromPlainTextAction(this, Globals.prefs.getUpdateFieldPreferences(), dialogService, Globals.prefs)),
                 factory.createMenuItem(StandardActions.DELETE_ENTRY, new OldDatabaseCommandWrapper(Actions.DELETE, this, Globals.stateManager)),
 
                 new SeparatorMenuItem(),
diff --git a/src/main/java/org/jabref/gui/actions/NewEntryFromPlainTextAction.java b/src/main/java/org/jabref/gui/actions/NewEntryFromPlainTextAction.java
deleted file mode 100644
index b4c3faa9a2b..00000000000
--- a/src/main/java/org/jabref/gui/actions/NewEntryFromPlainTextAction.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package org.jabref.gui.actions;
-
-import org.jabref.gui.DialogService;
-import org.jabref.gui.EntryTypeView;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.plaintextimport.TextInputDialog;
-import org.jabref.logic.util.UpdateField;
-import org.jabref.logic.util.UpdateFieldPreferences;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.EntryType;
-import org.jabref.preferences.JabRefPreferences;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class NewEntryFromPlainTextAction extends SimpleCommand {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(NewEntryFromPlainTextAction.class);
-
-    private final UpdateFieldPreferences prefs;
-    private final JabRefFrame jabRefFrame;
-    private final DialogService dialogService;
-    private final JabRefPreferences preferences;
-
-    public NewEntryFromPlainTextAction(JabRefFrame jabRefFrame, UpdateFieldPreferences prefs, DialogService dialogService, JabRefPreferences preferences) {
-        this.jabRefFrame = jabRefFrame;
-        this.prefs = prefs;
-        this.dialogService = dialogService;
-        this.preferences = preferences;
-
-    }
-
-    @Override
-    public void execute() {
-        if (jabRefFrame.getBasePanelCount() <= 0) {
-            LOGGER.error("Action 'New entry' must be disabled when no database is open.");
-            return;
-        }
-
-        EntryTypeView typeChoiceDialog = new EntryTypeView(jabRefFrame.getCurrentBasePanel(), dialogService, preferences);
-        EntryType selectedType = typeChoiceDialog.showAndWait().orElse(null);
-        if (selectedType == null) {
-            return;
-        }
-        BibEntry bibEntry = new BibEntry(selectedType);
-
-        TextInputDialog tidialog = new TextInputDialog(jabRefFrame, bibEntry);
-        tidialog.setVisible(true);
-        if (tidialog.okPressed()) {
-            UpdateField.setAutomaticFields(bibEntry, false, false, prefs);
-            jabRefFrame.getCurrentBasePanel().insertEntry(bibEntry);
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/gui/plaintextimport/TagToMarkedTextStore.java b/src/main/java/org/jabref/gui/plaintextimport/TagToMarkedTextStore.java
deleted file mode 100644
index 9b191abdd1e..00000000000
--- a/src/main/java/org/jabref/gui/plaintextimport/TagToMarkedTextStore.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package org.jabref.gui.plaintextimport;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.swing.text.StyledDocument;
-
-/**
- * Save the textposition for tags in a recent TextInputDialog context
- */
-public class TagToMarkedTextStore {
-
-    private final Map<String, List<TMarkedStoreItem>> tagMap;
-
-    public TagToMarkedTextStore() {
-        tagMap = new HashMap<>();
-    }
-
-    /** appends a selection property for tag */
-    public void appendPosition(String tag, int start, int end) {
-        List<TMarkedStoreItem> ll = tagMap.get(tag);
-        if (ll == null) {
-            ll = new ArrayList<>();
-            tagMap.put(tag, ll);
-        }
-
-        ll.add(new TMarkedStoreItem(start, end));
-    }
-
-    /** insert selection properties for tag, old entries were deleted */
-    public void insertPosition(String tag, int start, int end) {
-        List<TMarkedStoreItem> ll = tagMap.get(tag);
-
-        if (ll == null) {
-            ll = new ArrayList<>();
-            tagMap.put(tag, ll);
-        } else {
-            ll.clear();
-        }
-
-        ll.add(new TMarkedStoreItem(start, end));
-    }
-
-    /** set the Style for the tag if an entry is available */
-    public void setStyleForTag(String tag, String style, StyledDocument doc) {
-        List<TMarkedStoreItem> ll = tagMap.get(tag);
-
-        if (ll != null) {
-            // iterate over all saved selections
-            for (TMarkedStoreItem item : ll) {
-                if (item != null) {
-                    doc.setCharacterAttributes(item.getStart(), item.getLength(), doc.getStyle(style), true);
-                }
-            }
-        }
-    }
-
-    private static class TMarkedStoreItem {
-
-        private final int start;
-        private final int end;
-
-
-        public TMarkedStoreItem(int start, int end) {
-            this.start = start;
-            this.end = end;
-        }
-
-        public int getStart() {
-            return start;
-        }
-
-        public int getLength() {
-            return end - start;
-        }
-
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/plaintextimport/TextInputDialog.java b/src/main/java/org/jabref/gui/plaintextimport/TextInputDialog.java
deleted file mode 100644
index f2aee0e94fa..00000000000
--- a/src/main/java/org/jabref/gui/plaintextimport/TextInputDialog.java
+++ /dev/null
@@ -1,735 +0,0 @@
-package org.jabref.gui.plaintextimport;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.GridLayout;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringWriter;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-import java.util.Optional;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.ButtonGroup;
-import javax.swing.DefaultListCellRenderer;
-import javax.swing.Icon;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JLabel;
-import javax.swing.JList;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButton;
-import javax.swing.JScrollPane;
-import javax.swing.JTabbedPane;
-import javax.swing.JTextArea;
-import javax.swing.JTextPane;
-import javax.swing.JToolBar;
-import javax.swing.ListSelectionModel;
-import javax.swing.ScrollPaneConstants;
-import javax.swing.border.TitledBorder;
-import javax.swing.event.ListSelectionEvent;
-import javax.swing.event.ListSelectionListener;
-import javax.swing.text.BadLocationException;
-import javax.swing.text.EditorKit;
-import javax.swing.text.Style;
-import javax.swing.text.StyleConstants;
-import javax.swing.text.StyleContext;
-import javax.swing.text.StyledDocument;
-
-import org.jabref.Globals;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.JabRefDialog;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.OSXCompatibleToolbar;
-import org.jabref.gui.icon.IconTheme;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.gui.util.FileDialogConfiguration;
-import org.jabref.gui.util.component.OverlayPanel;
-import org.jabref.logic.bibtex.BibEntryWriter;
-import org.jabref.logic.bibtex.LatexFieldFormatter;
-import org.jabref.logic.importer.ParserResult;
-import org.jabref.logic.importer.fileformat.FreeCiteImporter;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.OS;
-import org.jabref.logic.util.StandardFileType;
-import org.jabref.logic.util.UpdateField;
-import org.jabref.model.EntryTypes;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.EntryType;
-import org.jabref.model.entry.FieldName;
-import org.jabref.model.entry.FieldProperty;
-import org.jabref.model.entry.InternalBibtexFields;
-import org.jabref.preferences.JabRefPreferences;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * import from plain text => simple mark/copy/paste into bibtex entry
- * <p>
- * TODO
- * - change colors and fonts
- * - delete selected text
- * - make textarea editable
- * - create several bibtex entries in dialog
- * - if the dialog works with an existing entry (right click menu item), the cancel option doesn't work well
- */
-public class TextInputDialog extends JabRefDialog {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(TextInputDialog.class);
-
-    private final JButton okButton = new JButton(Localization.lang("Accept"));
-    private final JButton cancelButton = new JButton(Localization.lang("Cancel"));
-    private final JButton insertButton = new JButton(Localization.lang("Insert"));
-    private final JButton parseWithFreeCiteButton = new JButton(Localization.lang("Parse with FreeCite"));
-    private final JPanel panel1 = new JPanel();
-    private final JPanel buttons = new JPanel();
-    private final JPanel rawPanel = new JPanel();
-    private final JPanel sourcePanel = new JPanel();
-    private JList<String> fieldList;
-    private final JRadioButton override = new JRadioButton(Localization.lang("Override"));
-    private final JRadioButton append = new JRadioButton(Localization.lang("Append"));
-    private final JToolBar toolBar = new OSXCompatibleToolbar();
-
-    private final List<String> allFields = new ArrayList<>();
-    private final List<String> requiredFields = new ArrayList<>();
-    private final List<String> optionalFields = new ArrayList<>();
-
-    private final BibEntry entry;
-
-    private final JPopupMenu inputMenu = new JPopupMenu();
-    private StyledDocument document; // content from inputPane
-    private final JTextPane textPane = new JTextPane();
-    private final JTextArea sourcePreview = new JTextArea();
-
-    private final TagToMarkedTextStore markedTextStore;
-
-    private final JabRefFrame frame;
-
-    private boolean okPressed;
-
-
-    public TextInputDialog(JabRefFrame frame, BibEntry bibEntry) {
-        super(true, TextInputDialog.class);
-
-        this.frame = Objects.requireNonNull(frame);
-
-        entry = Objects.requireNonNull(bibEntry);
-        markedTextStore = new TagToMarkedTextStore();
-
-        jbInit();
-        pack();
-        updateSourceView();
-    }
-
-    private void jbInit() {
-        getContentPane().setLayout(new BorderLayout());
-        StringBuilder typeStr = new StringBuilder("Plain text import");
-        if (entry.getType() != null) {
-            typeStr.append(' ').append(Localization.lang("for")).append(' ').append(entry.getType());
-        }
-
-        this.setTitle(typeStr.toString());
-        getContentPane().add(panel1, BorderLayout.CENTER);
-
-        initRawPanel();
-        initButtonPanel();
-        initSourcePanel();
-
-        JTabbedPane tabbed = new JTabbedPane();
-
-        tabbed.add(rawPanel, Localization.lang("Raw source"));
-        tabbed.add(sourcePanel, Localization.lang("%0 source", frame.getCurrentBasePanel().getBibDatabaseContext().getMode().getFormattedName()));
-
-        // Panel Layout
-        panel1.setLayout(new BorderLayout());
-        panel1.add(tabbed, BorderLayout.CENTER);
-        panel1.add(buttons, BorderLayout.SOUTH);
-
-        // Key bindings:
-        ActionMap am = buttons.getActionMap();
-        InputMap im = buttons.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                dispose();
-            }
-        });
-    }
-
-    // Panel with text import functionality
-    private void initRawPanel() {
-        rawPanel.setLayout(new BorderLayout());
-
-        // Textarea
-        textPane.setEditable(false);
-
-        document = textPane.getStyledDocument();
-        addStylesToDocument();
-
-        try {
-            document.insertString(0, "", document.getStyle("regular"));
-        } catch (BadLocationException ex) {
-            LOGGER.warn("Problem setting style", ex);
-
-        }
-
-        OverlayPanel testPanel = new OverlayPanel(textPane, Localization.lang("paste text here"));
-
-        testPanel.setPreferredSize(new Dimension(450, 255));
-        testPanel.setMaximumSize(new Dimension(450, Integer.MAX_VALUE));
-
-        // Setup fields (required to be done before setting up popup menu)
-        fieldList = new JList<>(getAllFields());
-        fieldList.setCellRenderer(new SimpleCellRenderer(fieldList.getFont()));
-        ListSelectionModel listSelectionModel = fieldList.getSelectionModel();
-        listSelectionModel.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        listSelectionModel.addListSelectionListener(new FieldListSelectionHandler());
-        fieldList.addMouseListener(new FieldListMouseListener());
-
-        // After the call to getAllFields
-        initPopupMenuAndToolbar();
-
-        //Add listener to components that can bring up popup menus.
-        MouseListener popupListener = new PopupListener(inputMenu);
-        textPane.addMouseListener(popupListener);
-        testPanel.addMouseListener(popupListener);
-
-        JPanel leftPanel = new JPanel(new BorderLayout());
-
-        leftPanel.add(toolBar, BorderLayout.NORTH);
-        leftPanel.add(testPanel, BorderLayout.CENTER);
-
-        JPanel inputPanel = setUpFieldListPanel();
-
-        // parse with FreeCite button
-        parseWithFreeCiteButton.addActionListener(event -> {
-            if (parseWithFreeCiteAndAddEntries()) {
-                okPressed = false; // we do not want to have the super method to handle our entries, we do it on our own
-                dispose();
-            }
-        });
-
-        rawPanel.add(leftPanel, BorderLayout.CENTER);
-        rawPanel.add(inputPanel, BorderLayout.EAST);
-
-        JLabel desc = new JLabel("<html><h3>" + Localization.lang("Plain text import") + "</h3><p>"
-                + Localization.lang("This is a simple copy and paste dialog. First load or paste some text into "
-                + "the text input area.<br>After that, you can mark text and assign it to a BibTeX field.")
-                + "</p></html>");
-        desc.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        rawPanel.add(desc, BorderLayout.SOUTH);
-    }
-
-    private JPanel setUpFieldListPanel() {
-        JPanel inputPanel = new JPanel();
-
-        // Panel Layout
-        GridBagLayout gbl = new GridBagLayout();
-        GridBagConstraints con = new GridBagConstraints();
-        con.weightx = 0;
-        con.insets = new Insets(5, 5, 0, 5);
-        con.fill = GridBagConstraints.HORIZONTAL;
-
-        inputPanel.setLayout(gbl);
-
-        // Border
-        TitledBorder titledBorder1 = new TitledBorder(BorderFactory.createLineBorder(new Color(153, 153, 153), 2),
-                Localization.lang("Work options"));
-        inputPanel.setBorder(titledBorder1);
-        inputPanel.setMinimumSize(new Dimension(10, 10));
-
-        JScrollPane fieldScroller = new JScrollPane(fieldList);
-        fieldScroller.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED);
-
-        // insert buttons
-        insertButton.addActionListener(event -> insertTextForTag(override.isSelected()));
-
-        // Radio buttons
-        append.setToolTipText(Localization.lang("Append the selected text to BibTeX field"));
-        append.setMnemonic(KeyEvent.VK_A);
-        append.setSelected(true);
-
-        override.setToolTipText(Localization.lang("Override the BibTeX field by the selected text"));
-        override.setMnemonic(KeyEvent.VK_O);
-        override.setSelected(false);
-
-        //Group the radio buttons.
-        ButtonGroup group = new ButtonGroup();
-        group.add(append);
-        group.add(override);
-
-        JPanel radioPanel = new JPanel(new GridLayout(0, 1));
-        radioPanel.add(append);
-        radioPanel.add(override);
-
-        // insert sub components
-        JLabel label1 = new JLabel(Localization.lang("Available BibTeX fields"));
-        con.gridwidth = GridBagConstraints.REMAINDER;
-        gbl.setConstraints(label1, con);
-        inputPanel.add(label1);
-
-        con.gridwidth = GridBagConstraints.REMAINDER;
-        con.gridheight = 8;
-        con.weighty = 1;
-        con.fill = GridBagConstraints.BOTH;
-        gbl.setConstraints(fieldScroller, con);
-        inputPanel.add(fieldScroller);
-
-        con.fill = GridBagConstraints.HORIZONTAL;
-        con.weighty = 0;
-        con.gridwidth = 2;
-        gbl.setConstraints(radioPanel, con);
-        inputPanel.add(radioPanel);
-
-        con.gridwidth = GridBagConstraints.REMAINDER;
-        gbl.setConstraints(insertButton, con);
-        inputPanel.add(insertButton);
-        return inputPanel;
-    }
-
-    private void initPopupMenuAndToolbar() {
-        // copy/paste Menu
-        PasteAction pasteAction = new PasteAction();
-        ClearAction clearAction = new ClearAction();
-        JMenuItem pasteMI = new JMenuItem(pasteAction);
-
-        inputMenu.add(clearAction);
-        inputMenu.addSeparator();
-        inputMenu.add(pasteMI);
-        inputMenu.addSeparator();
-
-        // Right-click append/override
-        JMenu appendMenu = new JMenu(Localization.lang("Append"));
-        appendMenu.setToolTipText(Localization.lang("Append the selected text to BibTeX field"));
-        JMenu overrideMenu = new JMenu(Localization.lang("Override"));
-        overrideMenu.setToolTipText(Localization.lang("Override the BibTeX field by the selected text"));
-        for (String field : allFields) {
-            appendMenu.add(new JMenuItem(new MenuTextForTagAction(field, false)));
-            overrideMenu.add(new JMenuItem(new MenuTextForTagAction(field, true)));
-        }
-
-        inputMenu.add(appendMenu);
-        inputMenu.add(overrideMenu);
-
-        // Toolbar
-
-        toolBar.add(clearAction);
-        toolBar.setBorderPainted(false);
-        toolBar.addSeparator();
-        toolBar.add(pasteAction);
-        toolBar.add(new LoadAction());
-    }
-
-    private void initButtonPanel() {
-        okButton.addActionListener(event -> {
-            okPressed = true;
-            dispose();
-        });
-        cancelButton.addActionListener(event -> dispose());
-
-        ButtonBarBuilder bb = new ButtonBarBuilder(buttons);
-        buttons.setBorder(BorderFactory.createEmptyBorder(2, 2, 2, 2));
-        bb.addGlue();
-        bb.addButton(okButton);
-        bb.addButton(parseWithFreeCiteButton);
-        bb.addButton(cancelButton);
-        bb.addGlue();
-    }
-
-    // Panel with BibTeX source code
-    private void initSourcePanel() {
-        sourcePreview.setEditable(false);
-        sourcePreview.setFont(new Font("Monospaced", Font.PLAIN, Globals.prefs.getInt(JabRefPreferences.FONT_SIZE)));
-        JScrollPane paneScrollPane = new JScrollPane(sourcePreview);
-        paneScrollPane.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
-        paneScrollPane.setPreferredSize(new Dimension(500, 255));
-        paneScrollPane.setMinimumSize(new Dimension(10, 10));
-
-        sourcePanel.setLayout(new BorderLayout());
-        sourcePanel.add(paneScrollPane, BorderLayout.CENTER);
-    }
-
-    private void addStylesToDocument() {
-        //Initialize some styles.
-        Style defaultStyle = StyleContext.getDefaultStyleContext().getStyle(StyleContext.DEFAULT_STYLE);
-
-        Style regularStyle = document.addStyle("regular", defaultStyle);
-        StyleConstants.setFontFamily(defaultStyle, "SansSerif");
-        StyleConstants.setFontSize(defaultStyle, Globals.prefs.getInt(JabRefPreferences.FONT_SIZE));
-
-        Style s = document.addStyle("used", regularStyle);
-        StyleConstants.setBold(s, true);
-        StyleConstants.setForeground(s, Color.blue);
-
-        s = document.addStyle("marked", regularStyle);
-        StyleConstants.setBold(s, true);
-        StyleConstants.setForeground(s, Color.red);
-    }
-
-    private void insertTextForTag(boolean overrideField) {
-        String fieldName = fieldList.getSelectedValue();
-        if (fieldName != null) {
-            String txt = textPane.getSelectedText();
-
-            if (txt != null) {
-                int selectionStart = textPane.getSelectionStart();
-                int selectionEnd = textPane.getSelectionEnd();
-
-                // unselect text
-                textPane.setSelectionEnd(selectionStart);
-
-                // mark the selected text as "used"
-                document.setCharacterAttributes(selectionStart, selectionEnd - selectionStart,
-                        document.getStyle("marked"), true);
-
-                // override an existing entry
-                if (overrideField) {
-                    entry.setField(fieldName, txt);
-                    // erase old text selection
-                    markedTextStore.setStyleForTag(fieldName, "regular", document); // delete all previous styles
-                    markedTextStore.insertPosition(fieldName, selectionStart, selectionEnd); // insert new selection style
-                } else {
-                    // memorize the selection for text highlighting
-                    markedTextStore.appendPosition(fieldName, selectionStart, selectionEnd);
-
-                    // get old text from BibTeX tag
-                    Optional<String> old = entry.getField(fieldName);
-
-                    // merge old and selected text
-                    if (old.isPresent()) {
-                        // insert a new name with an additional "and"
-                        if (InternalBibtexFields.getFieldProperties(fieldName).contains(FieldProperty.PERSON_NAMES)) {
-                            entry.setField(fieldName, old.get() + " and " + txt);
-                        } else if (FieldName.KEYWORDS.equals(fieldName)) {
-                            // Add keyword
-                            entry.addKeyword(txt, Globals.prefs.getKeywordDelimiter());
-                        } else {
-                            entry.setField(fieldName, old.get() + txt);
-                        }
-                    } else {
-                        // "null"+"txt" Strings forbidden
-                        entry.setField(fieldName, txt);
-                    }
-                }
-                // make the new data in BibTeX source code visible
-                updateSourceView();
-            }
-        }
-    }
-
-    public boolean okPressed() {
-        return okPressed;
-    }
-
-    /**
-     * tries to parse the pasted reference with freecite
-     *
-     * @return true if successful, false otherwise
-     */
-    private boolean parseWithFreeCiteAndAddEntries() {
-        FreeCiteImporter fimp = new FreeCiteImporter(Globals.prefs.getImportFormatPreferences());
-        String text = textPane.getText();
-
-        // we have to remove line breaks (but keep empty lines)
-        // otherwise, the result is broken
-        text = text.replace(OS.NEWLINE.concat(OS.NEWLINE), "##NEWLINE##");
-        // possible URL line breaks are removed completely.
-        text = text.replace("/".concat(OS.NEWLINE), "/");
-        text = text.replace(OS.NEWLINE, " ");
-        text = text.replace("##NEWLINE##", OS.NEWLINE);
-
-        ParserResult importerResult = fimp.importEntries(text);
-        if (importerResult.hasWarnings()) {
-            frame.showMessage(importerResult.getErrorMessage());
-        }
-        List<BibEntry> importedEntries = importerResult.getDatabase().getEntries();
-        if (importedEntries.isEmpty()) {
-            return false;
-        } else {
-            UpdateField.setAutomaticFields(importedEntries, false, false, Globals.prefs.getUpdateFieldPreferences());
-
-            importedEntries.forEach(entry -> frame.getCurrentBasePanel().insertEntry(entry));
-            return true;
-        }
-    }
-
-    // update the bibtex source view and available List
-    private void updateSourceView() {
-        StringWriter sw = new StringWriter(200);
-        try {
-            new BibEntryWriter(new LatexFieldFormatter(Globals.prefs.getLatexFieldFormatterPreferences()),
-                    false).write(entry, sw, frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
-            sourcePreview.setText(sw.getBuffer().toString());
-        } catch (IOException ex) {
-            LOGGER.error("Error in entry" + ": " + ex.getMessage(), ex);
-        }
-
-        fieldList.clearSelection();
-    }
-
-    private String[] getAllFields() {
-        Optional<EntryType> type = EntryTypes.getType(entry.getType(),
-                frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
-        if (type.isPresent()) {
-            allFields.addAll(type.get().getAllFields());
-            requiredFields.addAll(type.get().getRequiredFieldsFlat());
-            optionalFields.addAll(type.get().getPrimaryOptionalFields());
-        }
-        for (String field : InternalBibtexFields.getAllPublicFieldNames()) {
-            if (!allFields.contains(field)) {
-                allFields.add(field);
-            }
-        }
-        return allFields.toArray(new String[allFields.size()]);
-    }
-
-    private class PasteAction extends BasicAction {
-
-        public PasteAction() {
-            super(Localization.lang("Paste"), Localization.lang("Paste from clipboard"),
-                    IconTheme.JabRefIcons.PASTE.getIcon());
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            String data = Globals.clipboardManager.getContents();
-            int selStart = textPane.getSelectionStart();
-            int selEnd = textPane.getSelectionEnd();
-            if ((selEnd - selStart) > 0) {
-                textPane.replaceSelection("");
-            }
-            int cPos = textPane.getCaretPosition();
-            try {
-                document.insertString(cPos, data, document.getStyle("regular"));
-            } catch (BadLocationException ex) {
-                LOGGER.warn("Could not paste text", ex);
-            }
-        }
-    }
-
-    private class LoadAction extends BasicAction {
-
-        public LoadAction() {
-            super(Localization.lang("Open"), Localization.lang("Open file"), IconTheme.JabRefIcons.OPEN.getIcon());
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            try {
-                FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                        .addExtensionFilter(Localization.lang("Plain text"), StandardFileType.TXT)
-                        .withDefaultExtension(Localization.lang("Plain text"), StandardFileType.TXT)
-                        .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)).build();
-                DialogService ds = frame.getDialogService();
-
-                Optional<Path> path = DefaultTaskExecutor
-                        .runInJavaFXThread(() -> ds.showFileOpenDialog(fileDialogConfiguration));
-
-                if (path.isPresent()) {
-                    Path file = path.get();
-                    document.remove(0, document.getLength());
-                    EditorKit eKit = textPane.getEditorKit();
-                    if (eKit != null) {
-                        try (InputStream fis = Files.newInputStream(file)) {
-                            eKit.read(fis, document, 0);
-                            document.setLogicalStyle(0, document.getStyle("regular"));
-                        }
-                    }
-                }
-            } catch (BadLocationException | IOException ex) {
-                LOGGER.warn("Problem reading or inserting file", ex);
-            }
-        }
-    }
-
-    private class ClearAction extends BasicAction {
-
-        public ClearAction() {
-            super(Localization.lang("Clear"), Localization.lang("Clear inputarea"), IconTheme.JabRefIcons.NEW.getIcon());
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            textPane.setText("");
-        }
-    }
-
-    class FieldListSelectionHandler implements ListSelectionListener {
-
-        private int lastIndex = -1;
-
-        @Override
-        public void valueChanged(ListSelectionEvent e) {
-            ListSelectionModel lsm = (ListSelectionModel) e.getSource();
-
-            int index = lsm.getAnchorSelectionIndex();
-            if (index != lastIndex) {
-                boolean isAdjusting = e.getValueIsAdjusting();
-
-                if (!isAdjusting) {
-                    if (lastIndex > -1) {
-                        String tag1 = fieldList.getModel().getElementAt(lastIndex);
-                        markedTextStore.setStyleForTag(tag1, "used", document);
-                    }
-
-                    String tag2 = fieldList.getModel().getElementAt(index);
-                    markedTextStore.setStyleForTag(tag2, "marked", document);
-
-                    lastIndex = index;
-                }
-            }
-        }
-    }
-
-    // simple JList Renderer
-    // based on : Advanced JList Programming at developers.sun.com
-    private class SimpleCellRenderer extends DefaultListCellRenderer {
-
-        private final Font baseFont;
-        private final Font usedFont;
-        private final Icon okIcon = IconTheme.JabRefIcons.PLAIN_TEXT_IMPORT_DONE.getSmallIcon();
-        private final Icon needIcon = IconTheme.JabRefIcons.PLAIN_TEXT_IMPORT_TODO.getSmallIcon();
-        private final Color requiredColor = new Color(230, 235, 255);
-        private final Color optionalColor = new Color(230, 255, 230);
-
-
-        public SimpleCellRenderer(Font normFont) {
-            baseFont = normFont;
-            usedFont = baseFont.deriveFont(Font.ITALIC);
-        }
-
-        /* This is the only method defined by ListCellRenderer.  We just
-         * reconfigure the Jlabel each time we're called.
-         */
-        @Override
-        public Component getListCellRendererComponent(JList<?> list, Object value, // value to display
-                                                      int index, // cell index
-                                                      boolean iss, // is the cell selected
-                                                      boolean chf) // the list and the cell have the focus
-        {
-            /* The DefaultListCellRenderer class will take care of
-             * the JLabels text property, it's foreground and background
-             * colors, and so on.
-             */
-            super.getListCellRendererComponent(list, value, index, iss, chf);
-
-            /* We additionally set the JLabels icon property here.
-             */
-            String s = value.toString();
-            if (entry.hasField(s)) {
-                this.setForeground(Color.gray);
-                this.setFont(usedFont);
-                this.setIcon(okIcon);
-                this.setToolTipText(Localization.lang("Filled"));
-            } else {
-                this.setIcon(needIcon);
-                this.setToolTipText(Localization.lang("Field is missing"));
-            }
-            if (requiredFields.contains(s)) {
-                this.setBackground(requiredColor);
-            } else if (optionalFields.contains(s)) {
-                this.setBackground(optionalColor);
-            }
-            return this;
-        }
-    }
-
-    private class FieldListMouseListener extends MouseAdapter {
-
-        @Override
-        public void mouseClicked(MouseEvent e) {
-            if (e.getClickCount() == 2) {
-                insertTextForTag(override.isSelected());
-            }
-        }
-    }
-
-    private class MenuTextForTagAction extends AbstractAction {
-
-        private final String field;
-        private final Boolean overrideField;
-
-
-        public MenuTextForTagAction(String field, Boolean overrideField) {
-            super(field);
-            this.field = field;
-            this.overrideField = overrideField;
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            // To enable correct marking of used values
-            fieldList.setSelectedValue(field, false);
-            insertTextForTag(overrideField);
-        }
-    }
-}
-
-class PopupListener extends MouseAdapter {
-
-    private final JPopupMenu popMenu;
-
-
-    public PopupListener(JPopupMenu menu) {
-        popMenu = menu;
-    }
-
-    @Override
-    public void mousePressed(MouseEvent e) {
-        maybeShowPopup(e);
-    }
-
-    @Override
-    public void mouseReleased(MouseEvent e) {
-        maybeShowPopup(e);
-    }
-
-    private void maybeShowPopup(MouseEvent e) {
-        if (e.isPopupTrigger()) {
-            popMenu.show(e.getComponent(), e.getX(), e.getY());
-        }
-    }
-}
-
-abstract class BasicAction extends AbstractAction {
-
-    public BasicAction(String text, String description, Icon icon) {
-        super(text, icon);
-        putValue(Action.SHORT_DESCRIPTION, description);
-    }
-
-    public BasicAction(String text) {
-        super(text);
-    }
-
-    @Override
-    public abstract void actionPerformed(ActionEvent e);
-}
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index c553d2896fa..3a6655432a7 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -61,12 +61,10 @@ any\ field\ that\ matches\ the\ regular\ expression\ <b>%0</b>=any field that ma
 
 Appearance=Appearance
 
-Append=Append
 Append\ contents\ from\ a\ BibTeX\ library\ into\ the\ currently\ viewed\ library=Append contents from a BibTeX library into the currently viewed library
 
 Append\ library=Append library
 
-Append\ the\ selected\ text\ to\ BibTeX\ field=Append the selected text to BibTeX field
 Application=Application
 
 Apply=Apply
@@ -93,8 +91,6 @@ AUX\ file\ import=AUX file import
 
 Available\ export\ formats=Available export formats
 
-Available\ BibTeX\ fields=Available BibTeX fields
-
 Available\ import\ formats=Available import formats
 
 Backup\ old\ file\ when\ saving=Backup old file when saving
@@ -401,9 +397,6 @@ First\ select\ the\ entries\ you\ want\ keys\ to\ be\ generated\ for.=First sele
 Fit\ table\ horizontally\ on\ screen=Fit table horizontally on screen
 
 Float=Float
-
-for=for
-
 Format\:\ Tab\:field;field;...\ (e.g.\ General\:url;pdf;note...)=Format\: Tab\:field;field;... (e.g. General\:url;pdf;note...)
 
 Format\ of\ author\ and\ editor\ names=Format of author and editor names
@@ -501,13 +494,7 @@ Importing\ in\ unknown\ format=Importing in unknown format
 Include\ subgroups\:\ When\ selected,\ view\ entries\ contained\ in\ this\ group\ or\ its\ subgroups=Include subgroups: When selected, view entries contained in this group or its subgroups
 
 Independent\ group\:\ When\ selected,\ view\ only\ this\ group's\ entries=Independent group: When selected, view only this group's entries
-
-Work\ options=Work options
-
 I\ Agree=I Agree
-
-Insert=Insert
-
 Insert\ rows=Insert rows
 
 Intersection=Intersection
@@ -663,13 +650,7 @@ or=or
 
 Output\ or\ export\ file=Output or export file
 
-Override=Override
-
 Override\ default\ file\ directories=Override default file directories
-
-Override\ the\ BibTeX\ field\ by\ the\ selected\ text=Override the BibTeX field by the selected text
-
-
 Overwrite=Overwrite
 
 Overwrite\ keys=Overwrite keys
@@ -682,7 +663,6 @@ Paste=Paste
 paste\ entries=paste entries
 
 paste\ entry=paste entry
-Paste\ from\ clipboard=Paste from clipboard
 
 Pasted=Pasted
 
@@ -694,8 +674,6 @@ PDF\ does\ not\ exist=PDF does not exist
 
 File\ has\ no\ attached\ annotations=File has no attached annotations
 
-Plain\ text\ import=Plain text import
-
 Please\ enter\ a\ name\ for\ the\ group.=Please enter a name for the group.
 
 Please\ enter\ a\ search\ term.\ For\ example,\ to\ search\ all\ fields\ for\ <b>Smith</b>,\ enter\:<p><tt>smith</tt><p>To\ search\ the\ field\ <b>Author</b>\ for\ <b>Smith</b>\ and\ the\ field\ <b>Title</b>\ for\ <b>electrical</b>,\ enter\:<p><tt>author\=smith\ and\ title\=electrical</tt>=Please enter a search term. For example, to search all fields for <b>Smith</b>, enter:<p><tt>smith</tt><p>To search the field <b>Author</b> for <b>Smith</b> and the field <b>Title</b> for <b>electrical</b>, enter:<p><tt>author=smith and title=electrical</tt>
@@ -735,8 +713,6 @@ Pushed\ citations\ to\ %0=Pushed citations to %0
 
 Quit\ JabRef=Quit JabRef
 
-Raw\ source=Raw source
-
 Redo=Redo
 
 Refine\ supergroup\:\ When\ selected,\ view\ entries\ contained\ in\ both\ this\ group\ and\ its\ supergroup=Refine supergroup: When selected, view entries contained in both this group and its supergroup
@@ -925,9 +901,6 @@ Tabname=Tabname
 Tertiary\ sort\ criterion=Tertiary sort criterion
 
 Test=Test
-
-paste\ text\ here=paste text here
-
 The\ chosen\ date\ format\ for\ new\ entries\ is\ not\ valid=The chosen date format for new entries is not valid
 
 The\ chosen\ encoding\ '%0'\ could\ not\ encode\ the\ following\ characters\:=The chosen encoding '%0' could not encode the following characters:
@@ -1112,7 +1085,6 @@ Export\ entries\ in\ their\ original\ order=Export entries in their original ord
 Error\ opening\ file\ '%0'.=Error opening file '%0'.
 
 Formatter\ not\ found\:\ %0=Formatter not found: %0
-Clear\ inputarea=Clear inputarea
 
 Could\ not\ save,\ file\ locked\ by\ another\ JabRef\ instance.=Could not save, file locked by another JabRef instance.
 Current\ tmp\ value=Current tmp value
@@ -1226,7 +1198,6 @@ Use\ the\ BIB\ file\ location\ as\ primary\ file\ directory=Use the BIB file loc
 Could\ not\ run\ the\ gnuclient/emacsclient\ program.\ Make\ sure\ you\ have\ the\ emacsclient/gnuclient\ program\ installed\ and\ available\ in\ the\ PATH.=Could not run the gnuclient/emacsclient program. Make sure you have the emacsclient/gnuclient program installed and available in the PATH.
 You\ must\ select\ either\ a\ valid\ style\ file,\ or\ use\ one\ of\ the\ default\ styles.=You must select either a valid style file, or use one of the default styles.
 
-This\ is\ a\ simple\ copy\ and\ paste\ dialog.\ First\ load\ or\ paste\ some\ text\ into\ the\ text\ input\ area.<br>After\ that,\ you\ can\ mark\ text\ and\ assign\ it\ to\ a\ BibTeX\ field.=This is a simple copy and paste dialog. First load or paste some text into the text input area.<br>After that, you can mark text and assign it to a BibTeX field.
 This\ feature\ generates\ a\ new\ library\ based\ on\ which\ entries\ are\ needed\ in\ an\ existing\ LaTeX\ document.=This feature generates a new library based on which entries are needed in an existing LaTeX document.
 
 First\ select\ entries\ to\ clean\ up.=First select entries to clean up.
@@ -1278,7 +1249,6 @@ Select\ directory=Select directory
 Select\ files=Select files
 BibTeX\ entry\ creation=BibTeX entry creation
 Unable\ to\ connect\ to\ FreeCite\ online\ service.=Unable to connect to FreeCite online service.
-Parse\ with\ FreeCite=Parse with FreeCite
 BibTeX\ key\ patterns=BibTeX key patterns
 Changed\ special\ field\ settings=Changed special field settings
 Clear\ priority=Clear priority
@@ -1466,8 +1436,6 @@ unexpected\ opening\ curly\ bracket=unexpected opening curly bracket
 capital\ letters\ are\ not\ masked\ using\ curly\ brackets\ {}=capital letters are not masked using curly brackets {}
 should\ contain\ a\ four\ digit\ number=should contain a four digit number
 should\ contain\ a\ valid\ page\ number\ range=should contain a valid page number range
-Filled=Filled
-Field\ is\ missing=Field is missing
 Search\ %0=Search %0
 
 Search\ results\ in\ all\ libraries\ for\ %0=Search results in all libraries for %0

From 91d779ad9385f1132a929c9bab6ce73b49ea4f98 Mon Sep 17 00:00:00 2001
From: Samiya Caur <36728314+samiyac@users.noreply.github.com>
Date: Sat, 30 Mar 2019 02:43:04 +0530
Subject: [PATCH 146/184] Relativizes paths to aux files (#4792)

* Relativizes paths to aux files

* relativize code shifted to FileHelper

* changes

* Shortens text fields in Required Fields Tab

* Removing irrelevant changes

* Implemented requested changes

* Implemented changes

* Delete irrelevant code
---
 .../org/jabref/gui/groups/GroupDialog.java    | 24 +++++++++-
 .../LibraryPropertiesDialog.fxml              | 10 ++--
 .../LibraryPropertiesDialogView.java          | 17 ++++++-
 .../LibraryPropertiesDialogViewModel.java     | 19 ++++++++
 .../logic/exporter/MetaDataSerializer.java    |  2 +
 .../logic/importer/util/GroupsParser.java     | 13 +++---
 .../logic/importer/util/MetaDataParser.java   | 10 +++-
 .../model/database/BibDatabaseContext.java    |  2 +-
 .../org/jabref/model/groups/TexGroup.java     | 46 ++++++++++++++++---
 .../org/jabref/model/metadata/MetaData.java   | 25 +++++++++-
 .../org/jabref/model/util/FileHelper.java     | 13 ++++++
 src/main/resources/l10n/JabRef_en.properties  |  1 +
 .../exporter/BibtexDatabaseWriterTest.java    |  3 +-
 .../logic/exporter/GroupSerializerTest.java   |  3 +-
 .../importer/fileformat/BibtexParserTest.java |  4 +-
 .../logic/importer/util/GroupsParserTest.java | 25 +++++-----
 .../org/jabref/model/groups/TexGroupTest.java | 24 +++++++++-
 17 files changed, 202 insertions(+), 39 deletions(-)

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
index 94c9f519fa7..2285db635ac 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDialog.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -1,8 +1,10 @@
 package org.jabref.gui.groups;
 
 import java.io.IOException;
+import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Optional;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
@@ -45,6 +47,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.search.SearchQuery;
 import org.jabref.logic.util.StandardFileType;
+import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.Keyword;
@@ -58,6 +61,7 @@
 import org.jabref.model.groups.SearchGroup;
 import org.jabref.model.groups.TexGroup;
 import org.jabref.model.groups.WordKeywordGroup;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.preferences.JabRefPreferences;
 
@@ -90,6 +94,7 @@ class GroupDialog extends BaseDialog<AbstractGroup> {
     private final RadioButton unionButton = new RadioButton(Localization.lang("Include subgroups: When selected, view entries contained in this group or its subgroups"));
     private final DialogService dialogService;
     private final JabRefPreferences prefs;
+    private final BasePanel basePanel;
 
     // for KeywordGroup
     private final TextField keywordGroupSearchTerm = new TextField();
@@ -144,6 +149,7 @@ public GroupDialog(DialogService dialogService, BasePanel basePanel, JabRefPrefe
 
         this.dialogService = dialogService;
         this.prefs = prefs;
+        this.basePanel = basePanel;
 
         // set default values (overwritten if editedGroup != null)
         keywordGroupSearchField.setText(prefs.get(JabRefPreferences.GROUPS_DEFAULT_FIELD));
@@ -330,7 +336,7 @@ groupName, getContext(),
                         }
                     } else if (texRadioButton.isSelected()) {
                         resultingGroup = new TexGroup(groupName, getContext(),
-                                Paths.get(texGroupFilePath.getText().trim()), new DefaultAuxParser(new BibDatabase()), Globals.getFileUpdateMonitor());
+                                                      Paths.get(texGroupFilePath.getText().trim()), new DefaultAuxParser(new BibDatabase()), Globals.getFileUpdateMonitor(), basePanel.getBibDatabaseContext().getMetaData());
                     }
 
                     resultingGroup.setColor(colorField.getValue());
@@ -610,7 +616,21 @@ private void openBrowseDialog() {
             .addExtensionFilter(StandardFileType.AUX)
             .withDefaultExtension(StandardFileType.AUX)
             .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)).build();
-        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> texGroupFilePath.setText(file.toAbsolutePath().toString()));
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> texGroupFilePath.setText(relativize(file.toAbsolutePath()).toString()));
+    }
+
+    private Path relativize(Path path) {
+        List<Path> fileDirectories = getFileDirectoriesAsPaths();
+        return FileUtil.relativize(path, fileDirectories);
+    }
+
+    private List<Path> getFileDirectoriesAsPaths() {
+        List<Path> fileDirs = new ArrayList<>();
+        MetaData metaData = basePanel.getBibDatabaseContext().getMetaData();
+        metaData.getLaTexFileDirectory(prefs.getFilePreferences().getUser())
+                .ifPresent(laTexFileDirectory -> fileDirs.add(laTexFileDirectory));
+
+        return fileDirs;
     }
 
     private String fromTextFlowToHTMLString(TextFlow textFlow) {
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
index 126d9e959b6..2cb00861431 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
@@ -26,6 +26,7 @@
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
                         <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="SOMETIMES" />
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="ALWAYS" />
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="ALWAYS" />
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
                         <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="ALWAYS" />
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
@@ -40,10 +41,13 @@
                         <Label text="%User-specific file directory" GridPane.rowIndex="3" />
                         <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
                         <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
+                        <Label text="%LaTex file directory" GridPane.rowIndex="4" />
+                        <TextField fx:id="laTexFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="4" />
+                        <Button fx:id="browseLatexFileDir" mnemonicParsing="false" onAction="#browseLaTexFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="4" />
                         <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Override default file directories" GridPane.columnSpan="3" GridPane.rowIndex="1" />
-                        <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Library protection" GridPane.columnSpan="3" GridPane.rowIndex="4" />
-                        <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." GridPane.columnSpan="3" GridPane.rowIndex="5" />
-                        <Label styleClass="sectionHeader" text="%Export sort order" GridPane.rowIndex="6" />
+                        <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Library protection" GridPane.columnSpan="3" GridPane.rowIndex="5" />
+                        <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." GridPane.columnSpan="3" GridPane.rowIndex="6" />
+                        <Label styleClass="sectionHeader" text="%Export sort order" GridPane.rowIndex="7" />
                     </children>
                 </GridPane>
             </children>
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
index 8ed238faf8a..58002962d84 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
@@ -1,6 +1,7 @@
 package org.jabref.gui.libraryproperties;
 
 import java.nio.charset.Charset;
+import java.nio.file.Paths;
 import java.util.Optional;
 
 import javax.inject.Inject;
@@ -36,6 +37,7 @@ public class LibraryPropertiesDialogView extends BaseDialog<Void> {
     @FXML private Button browseGeneralFileDir;
     @FXML private TextField userSpecificFileDirectory;
     @FXML private Button browseUserSpefiicFileDir;
+    @FXML private TextField laTexFileDirectory;
     @FXML private CheckBox protect;
     @Inject private PreferencesService preferencesService;
 
@@ -70,6 +72,7 @@ private void initialize() {
 
         generalFileDirectory.textProperty().bindBidirectional(viewModel.generalFileDirectoryPropertyProperty());
         userSpecificFileDirectory.textProperty().bindBidirectional(viewModel.userSpecificFileDirectoryProperty());
+        laTexFileDirectory.textProperty().bindBidirectional(viewModel.LaTexFileDirectoryProperty());
 
         encoding.itemsProperty().bind(viewModel.encodingsProperty());
         encoding.valueProperty().bindBidirectional(viewModel.selectedEncodingProperty());
@@ -112,6 +115,11 @@ public void browseUserSpecificFileDirectory(ActionEvent event) {
         viewModel.browseUserDir();
     }
 
+    @FXML
+    void browseLaTexFileDirectory(ActionEvent event) {
+        viewModel.browseLaTexDir();
+    }
+
     private void storeSettings() {
         //FIXME: Move to viewModel until fieldFormatterCleanupsPanel is property implemented
         MetaData metaData = panel.getBibDatabaseContext().getMetaData();
@@ -134,6 +142,13 @@ private void storeSettings() {
             metaData.setUserFileDirectory(preferencesService.getUser(), text);
         }
 
+        text = viewModel.LaTexFileDirectoryProperty().getValue();
+        if (text.isEmpty()) {
+            metaData.clearLaTexFileDirectory(preferencesService.getUser());
+        } else {
+            metaData.setLaTexFileDirectory(preferencesService.getUser(), Paths.get(text));
+        }
+
         if (viewModel.libraryProtectedProperty().getValue()) {
             metaData.markAsProtected();
         } else {
@@ -165,7 +180,7 @@ private void storeSettings() {
 
         boolean changed = saveOrderConfigChanged || encodingChanged
                           || viewModel.generalFileDirChanged() || viewModel.userFileDirChanged()
-                          || viewModel.protectedValueChanged() || saveActionsChanged;
+                          || viewModel.protectedValueChanged() || saveActionsChanged || viewModel.LaTexFileDirChanged();
         // ... if so, mark base changed. Prevent the Undo button from removing
         // change marking:
         if (changed) {
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
index 05f3982d7e0..e7791d7a534 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
@@ -1,6 +1,7 @@
 package org.jabref.gui.libraryproperties;
 
 import java.nio.charset.Charset;
+import java.nio.file.Path;
 import java.util.Optional;
 
 import javafx.beans.property.BooleanProperty;
@@ -25,6 +26,7 @@ public class LibraryPropertiesDialogViewModel {
 
     private final StringProperty generalFileDirectoryProperty = new SimpleStringProperty("");
     private final StringProperty userSpecificFileDirectoryProperty = new SimpleStringProperty("");
+    private final StringProperty laTexFileDirectoryProperty = new SimpleStringProperty("");
     private final ListProperty<Charset> encodingsProperty = new SimpleListProperty<>(FXCollections.observableArrayList(Encodings.getCharsets()));
     private final ObjectProperty<Charset> selectedEncodingPropety = new SimpleObjectProperty<>(Encodings.getCharsets().get(0));
     private final BooleanProperty libraryProtectedProperty = new SimpleBooleanProperty();
@@ -36,6 +38,7 @@ public class LibraryPropertiesDialogViewModel {
 
     private final String oldUserSpecificFileDir;
     private final String oldGeneralFileDir;
+    private final String oldLaTexFileDir;
     private final boolean oldLibraryProtected;
 
     public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogService, PreferencesService preferencesService) {
@@ -59,8 +62,11 @@ public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogSer
         Optional<String> fileDI = metaData.getUserFileDirectory(preferencesService.getUser());
         fileDI.ifPresent(userSpecificFileDirectoryProperty::setValue);
 
+        metaData.getLaTexFileDirectory(preferencesService.getUser()).map(Path::toString).ifPresent(laTexFileDirectoryProperty::setValue);
+
         oldUserSpecificFileDir = generalFileDirectoryProperty.getValue();
         oldGeneralFileDir = userSpecificFileDirectoryProperty.getValue();
+        oldLaTexFileDir = laTexFileDirectoryProperty.getValue();
 
         libraryProtectedProperty.setValue(metaData.isProtected());
         oldLibraryProtected = libraryProtectedProperty.getValue();
@@ -74,6 +80,10 @@ public StringProperty userSpecificFileDirectoryProperty() {
         return this.userSpecificFileDirectoryProperty;
     }
 
+    public StringProperty LaTexFileDirectoryProperty() {
+        return this.laTexFileDirectoryProperty;
+    }
+
     public ListProperty<Charset> encodingsProperty() {
         return this.encodingsProperty;
     }
@@ -90,6 +100,10 @@ public void browseUserDir() {
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> userSpecificFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
     }
 
+    public void browseLaTexDir() {
+        dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> laTexFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
+    }
+
     public BooleanProperty libraryProtectedProperty() {
         return this.libraryProtectedProperty;
     }
@@ -102,6 +116,10 @@ public boolean userFileDirChanged() {
         return !oldUserSpecificFileDir.equals(userSpecificFileDirectoryProperty.getValue());
     }
 
+    public boolean LaTexFileDirChanged() {
+        return !oldLaTexFileDir.equals(laTexFileDirectoryProperty.getValue());
+    }
+
     public boolean protectedValueChanged() {
         return !oldLibraryProtected == libraryProtectedProperty.getValue();
     }
@@ -113,4 +131,5 @@ public BooleanProperty encodingDisableProperty() {
     public BooleanProperty protectDisableProperty() {
         return protectDisableProperty;
     }
+
 }
diff --git a/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java b/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
index 92944665575..b75253685d4 100644
--- a/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
+++ b/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
@@ -43,6 +43,8 @@ public static Map<String, String> getSerializedStringMap(MetaData metaData,
                 path -> stringyMetaData.put(MetaData.FILE_DIRECTORY, Collections.singletonList(path.trim())));
         metaData.getUserFileDirectories().forEach((user, path) -> stringyMetaData
                 .put(MetaData.FILE_DIRECTORY + '-' + user, Collections.singletonList(path.trim())));
+        metaData.getLaTexFileDirectories().forEach((user, path) -> stringyMetaData
+                .put(MetaData.FILE_DIRECTORY + "Latex-" + user, Collections.singletonList(path.toString().trim())));
 
         for (ContentSelector selector: metaData.getContentSelectorList()) {
                 stringyMetaData.put(MetaData.SELECTOR_META_PREFIX + selector.getFieldName(), selector.getValues());
diff --git a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
index ca04fafd0ca..4c9365b0dd8 100644
--- a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
+++ b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
@@ -24,6 +24,7 @@
 import org.jabref.model.groups.SearchGroup;
 import org.jabref.model.groups.TexGroup;
 import org.jabref.model.groups.WordKeywordGroup;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -35,7 +36,7 @@ public class GroupsParser {
     private GroupsParser() {
     }
 
-    public static GroupTreeNode importGroups(List<String> orderedData, Character keywordSeparator, FileUpdateMonitor fileMonitor)
+    public static GroupTreeNode importGroups(List<String> orderedData, Character keywordSeparator, FileUpdateMonitor fileMonitor, MetaData metaData)
             throws ParseException {
         try {
             GroupTreeNode cursor = null;
@@ -52,7 +53,7 @@ public static GroupTreeNode importGroups(List<String> orderedData, Character key
                     throw new ParseException("Expected \"" + string + "\" to contain whitespace");
                 }
                 int level = Integer.parseInt(string.substring(0, spaceIndex));
-                AbstractGroup group = GroupsParser.fromString(string.substring(spaceIndex + 1), keywordSeparator, fileMonitor);
+                AbstractGroup group = GroupsParser.fromString(string.substring(spaceIndex + 1), keywordSeparator, fileMonitor, metaData);
                 GroupTreeNode newNode = GroupTreeNode.fromGroup(group);
                 if (cursor == null) {
                     // create new root
@@ -84,7 +85,7 @@ public static GroupTreeNode importGroups(List<String> orderedData, Character key
      * @throws ParseException If an error occurred and a group could not be created,
      *                        e.g. due to a malformed regular expression.
      */
-    public static AbstractGroup fromString(String s, Character keywordSeparator, FileUpdateMonitor fileMonitor)
+    public static AbstractGroup fromString(String s, Character keywordSeparator, FileUpdateMonitor fileMonitor, MetaData metaData)
             throws ParseException {
         if (s.startsWith(MetadataSerializationConfiguration.KEYWORD_GROUP_ID)) {
             return keywordGroupFromString(s, keywordSeparator);
@@ -108,13 +109,13 @@ public static AbstractGroup fromString(String s, Character keywordSeparator, Fil
             return automaticKeywordGroupFromString(s);
         }
         if (s.startsWith(MetadataSerializationConfiguration.TEX_GROUP_ID)) {
-            return texGroupFromString(s, fileMonitor);
+            return texGroupFromString(s, fileMonitor, metaData);
         }
 
         throw new ParseException("Unknown group: " + s);
     }
 
-    private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor fileMonitor) throws ParseException {
+    private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor fileMonitor, MetaData metaData) throws ParseException {
         QuotedStringTokenizer tok = new QuotedStringTokenizer(string.substring(MetadataSerializationConfiguration.TEX_GROUP_ID
                 .length()), MetadataSerializationConfiguration.GROUP_UNIT_SEPARATOR, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
 
@@ -122,7 +123,7 @@ private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor
         GroupHierarchyType context = GroupHierarchyType.getByNumberOrDefault(Integer.parseInt(tok.nextToken()));
         try {
             Path path = Paths.get(tok.nextToken());
-            TexGroup newGroup = new TexGroup(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor);
+            TexGroup newGroup = new TexGroup(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
             addGroupDetails(tok, newGroup);
             return newGroup;
         } catch (InvalidPathException | IOException ex) {
diff --git a/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java b/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
index ecd8e4ba4cf..1c3a9b211c5 100644
--- a/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
+++ b/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
@@ -3,6 +3,8 @@
 import java.io.IOException;
 import java.io.Reader;
 import java.io.StringReader;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -60,12 +62,18 @@ public MetaData parse(MetaData metaData, Map<String, String> data, Character key
             } else if (entry.getKey().startsWith(MetaData.SELECTOR_META_PREFIX)) {
                 metaData.addContentSelector(ContentSelectors.parse(entry.getKey().substring(MetaData.SELECTOR_META_PREFIX.length()), StringUtil.unquote(entry.getValue(), MetaData.ESCAPE_CHARACTER)));
                 continue;
+            } else if (entry.getKey().startsWith(MetaData.FILE_DIRECTORY + "Latex-")) {
+                // The user name comes directly after "FILE_DIRECTORYLatex-"
+                String user = entry.getKey().substring(MetaData.FILE_DIRECTORY.length() + 6);
+                Path path = Paths.get(getSingleItem(value)).normalize();
+                metaData.setLaTexFileDirectory(user, path);
+                continue;
             }
 
             switch (entry.getKey()) {
                 case MetaData.GROUPSTREE:
                 case MetaData.GROUPSTREE_LEGACY:
-                    metaData.setGroups(GroupsParser.importGroups(value, keywordSeparator, fileMonitor));
+                    metaData.setGroups(GroupsParser.importGroups(value, keywordSeparator, fileMonitor, metaData));
                     break;
                 case MetaData.SAVE_ACTIONS:
                     metaData.setSaveActions(Cleanups.parse(value));
diff --git a/src/main/java/org/jabref/model/database/BibDatabaseContext.java b/src/main/java/org/jabref/model/database/BibDatabaseContext.java
index adabb5805ed..3acdf7b484e 100644
--- a/src/main/java/org/jabref/model/database/BibDatabaseContext.java
+++ b/src/main/java/org/jabref/model/database/BibDatabaseContext.java
@@ -185,7 +185,7 @@ public Optional<Path> getFirstExistingFileDir(FilePreferences preferences) {
      * metadata can specify a general directory and/or a user-specific directory or the preferences can specify one. <p>
      * The settings are prioritized in the following order and the first defined setting is used:
      * <ol>
-     *     <li>metdata</li>
+     *     <li>metadata</li>
      *     <li>user-specific directory</li>
      *     <li>preferences directory</li>
      *     <li>BIB file directory</li>
diff --git a/src/main/java/org/jabref/model/groups/TexGroup.java b/src/main/java/org/jabref/model/groups/TexGroup.java
index 92a47028eae..ab350c486d5 100644
--- a/src/main/java/org/jabref/model/groups/TexGroup.java
+++ b/src/main/java/org/jabref/model/groups/TexGroup.java
@@ -1,13 +1,18 @@
 package org.jabref.model.groups;
 
 import java.io.IOException;
+import java.net.InetAddress;
 import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Objects;
 import java.util.Set;
 
 import org.jabref.model.auxparser.AuxParser;
 import org.jabref.model.auxparser.AuxParserResult;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.metadata.MetaData;
+import org.jabref.model.util.FileHelper;
 import org.jabref.model.util.FileUpdateListener;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -22,13 +27,21 @@ public class TexGroup extends AbstractGroup implements FileUpdateListener {
     private Set<String> keysUsedInAux = null;
     private final FileUpdateMonitor fileMonitor;
     private AuxParser auxParser;
+    private final MetaData metaData;
+    private String user;
 
-    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor) throws IOException {
+    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData, String user) throws IOException {
         super(name, context);
-        this.filePath = Objects.requireNonNull(filePath);
+        this.metaData = metaData;
+        this.user = user;
+        this.filePath = expandPath(Objects.requireNonNull(filePath));
         this.auxParser = auxParser;
         this.fileMonitor = fileMonitor;
-        fileMonitor.addListenerForFile(filePath, this);
+        fileMonitor.addListenerForFile(this.filePath, this);
+    }
+
+    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+        this(name, context, filePath, auxParser, fileMonitor, metaData, System.getProperty("user.name") + '-' + InetAddress.getLocalHost().getHostName());
     }
 
     @Override
@@ -49,7 +62,7 @@ public boolean isDynamic() {
     @Override
     public AbstractGroup deepCopy() {
         try {
-            return new TexGroup(name.getValue(), context, filePath, auxParser, fileMonitor);
+            return new TexGroup(name.getValue(), context, filePath, auxParser, fileMonitor, metaData);
         } catch (IOException ex) {
             // This should never happen because we were able to monitor the file just fine until now
             LOGGER.error("Problem creating copy of group", ex);
@@ -62,7 +75,7 @@ public boolean equals(Object o) {
         if (this == o) {
             return true;
         }
-        if (o == null || getClass() != o.getClass()) {
+        if ((o == null) || (getClass() != o.getClass())) {
             return false;
         }
         if (!super.equals(o)) {
@@ -75,7 +88,7 @@ public boolean equals(Object o) {
     @Override
     public String toString() {
         return "TexGroup{" +
-                "filePath=" + filePath +
+               "filePath=" + filePath +
                 ", keysUsedInAux=" + keysUsedInAux +
                 ", auxParser=" + auxParser +
                 ", fileMonitor=" + fileMonitor +
@@ -88,7 +101,7 @@ public int hashCode() {
     }
 
     public Path getFilePath() {
-        return filePath;
+        return relativize(filePath);
     }
 
     @Override
@@ -96,4 +109,23 @@ public void fileUpdated() {
         // Reset previous parse result
         keysUsedInAux = null;
     }
+
+    private Path relativize(Path path) {
+        List<Path> fileDirectories = getFileDirectoriesAsPaths();
+        return FileHelper.relativize(path, fileDirectories);
+    }
+
+    private Path expandPath(Path path) {
+        List<Path> fileDirectories = getFileDirectoriesAsPaths();
+        return FileHelper.expandFilenameAsPath(path.toString(), fileDirectories).orElse(path);
+    }
+
+    private List<Path> getFileDirectoriesAsPaths() {
+        List<Path> fileDirs = new ArrayList<>();
+
+        metaData.getLaTexFileDirectory(user)
+                .ifPresent(laTexFileDirectory -> fileDirs.add(laTexFileDirectory));
+
+        return fileDirs;
+    }
 }
diff --git a/src/main/java/org/jabref/model/metadata/MetaData.java b/src/main/java/org/jabref/model/metadata/MetaData.java
index 94b105eadac..7fc52e99842 100644
--- a/src/main/java/org/jabref/model/metadata/MetaData.java
+++ b/src/main/java/org/jabref/model/metadata/MetaData.java
@@ -1,6 +1,7 @@
 package org.jabref.model.metadata;
 
 import java.nio.charset.Charset;
+import java.nio.file.Path;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -42,6 +43,7 @@ public class MetaData {
     private final EventBus eventBus = new EventBus();
     private final Map<String, String> citeKeyPatterns = new HashMap<>(); // <BibType, Pattern>
     private final Map<String, String> userFileDirectory = new HashMap<>(); // <User, FilePath>
+    private final Map<String, Path> laTexFileDirectory = new HashMap<>(); // <User, FilePath>
     private GroupTreeNode groupsRoot;
     private Charset encoding;
     private SaveOrderConfig saveOrderConfig;
@@ -50,8 +52,8 @@ public class MetaData {
     private BibDatabaseMode mode;
     private boolean isProtected;
     private String defaultFileDirectory;
-    private ContentSelectors contentSelectors = new ContentSelectors();
-    private Map<String, List<String>> unkownMetaData = new HashMap<>();
+    private final ContentSelectors contentSelectors = new ContentSelectors();
+    private final Map<String, List<String>> unkownMetaData = new HashMap<>();
     private boolean isEventPropagationEnabled = true;
 
     /**
@@ -209,6 +211,20 @@ public void clearUserFileDirectory(String user) {
         postChange();
     }
 
+    public Optional<Path> getLaTexFileDirectory(String user) {
+        return Optional.ofNullable(laTexFileDirectory.get(user));
+    }
+
+    public void setLaTexFileDirectory(String user, Path path) {
+        laTexFileDirectory.put(Objects.requireNonNull(user), Objects.requireNonNull(path));
+        postChange();
+    }
+
+    public void clearLaTexFileDirectory(String user) {
+        laTexFileDirectory.remove(user);
+        postChange();
+    }
+
     public void markAsNotProtected() {
         isProtected = false;
         postChange();
@@ -285,6 +301,10 @@ public Map<String, String> getUserFileDirectories() {
         return Collections.unmodifiableMap(userFileDirectory);
     }
 
+    public Map<String, Path> getLaTexFileDirectories() {
+        return Collections.unmodifiableMap(laTexFileDirectory);
+    }
+
     public Map<String, List<String>> getUnknownMetaData() {
         return Collections.unmodifiableMap(unkownMetaData);
     }
@@ -310,6 +330,7 @@ public boolean equals(Object o) {
                 && Objects.equals(saveOrderConfig, metaData.saveOrderConfig)
                 && Objects.equals(citeKeyPatterns, metaData.citeKeyPatterns)
                 && Objects.equals(userFileDirectory, metaData.userFileDirectory)
+               && Objects.equals(laTexFileDirectory, metaData.laTexFileDirectory)
                 && Objects.equals(defaultCiteKeyPattern, metaData.defaultCiteKeyPattern)
                 && Objects.equals(saveActions, metaData.saveActions) && (mode == metaData.mode)
                 && Objects.equals(defaultFileDirectory, metaData.defaultFileDirectory)
diff --git a/src/main/java/org/jabref/model/util/FileHelper.java b/src/main/java/org/jabref/model/util/FileHelper.java
index e86e4686429..b2864ff5811 100644
--- a/src/main/java/org/jabref/model/util/FileHelper.java
+++ b/src/main/java/org/jabref/model/util/FileHelper.java
@@ -175,4 +175,17 @@ private static boolean isUrl(String url) {
             return false;
         }
     }
+
+    public static Path relativize(Path path, List<Path> fileDirectories) {
+        if (!path.isAbsolute()) {
+            return path;
+        }
+
+        for (Path directory : fileDirectories) {
+            if (path.startsWith(directory)) {
+                return directory.relativize(path);
+            }
+        }
+        return path;
+    }
 }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 3a6655432a7..0258d204ee7 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1118,6 +1118,7 @@ Ensure\ unique\ keys\ using\ letters\ (b,\ c,\ ...)=Ensure unique keys using let
 
 General\ file\ directory=General file directory
 User-specific\ file\ directory=User-specific file directory
+LaTex\ file\ directory=LaTex file directory
 Search\ failed\:\ illegal\ search\ expression=Search failed: illegal search expression
 Show\ ArXiv\ column=Show ArXiv column
 
diff --git a/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java b/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java
index a7f2ef36a4c..c0d3994dbfc 100644
--- a/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java
+++ b/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java
@@ -485,12 +485,13 @@ void writeProtectedFlag() throws Exception {
     void writeFileDirectories() throws Exception {
         metaData.setDefaultFileDirectory("\\Literature\\");
         metaData.setUserFileDirectory("defaultOwner-user", "D:\\Documents");
+        metaData.setLaTexFileDirectory("defaultOwner-user", Paths.get("D:\\Latex"));
 
         databaseWriter.savePartOfDatabase(bibtexContext, Collections.emptyList());
 
         assertEquals(OS.NEWLINE + "@Comment{jabref-meta: fileDirectory:\\\\Literature\\\\;}" + OS.NEWLINE +
                 OS.NEWLINE + "@Comment{jabref-meta: fileDirectory-defaultOwner-user:D:\\\\Documents;}"
-                + OS.NEWLINE, stringWriter.toString());
+                     + OS.NEWLINE + OS.NEWLINE + "@Comment{jabref-meta: fileDirectoryLatex-defaultOwner-user:D:\\\\Latex;}" + OS.NEWLINE, stringWriter.toString());
     }
 
     @Test
diff --git a/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java b/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
index b1560a3aa65..b8625babeb4 100644
--- a/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
+++ b/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
@@ -22,6 +22,7 @@
 import org.jabref.model.groups.SearchGroup;
 import org.jabref.model.groups.TexGroup;
 import org.jabref.model.groups.WordKeywordGroup;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
 import org.junit.jupiter.api.BeforeEach;
@@ -115,7 +116,7 @@ public void serializeSingleAutomaticPersonGroup() {
 
     @Test
     public void serializeSingleTexGroup() throws Exception {
-        TexGroup group = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor());
+        TexGroup group = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), new MetaData());
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 TexGroup:myTexGroup;0;path/To/File;1;;;;"), serialization);
     }
diff --git a/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java b/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
index 116cfd198aa..04fca15aff8 100644
--- a/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
+++ b/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
@@ -1474,10 +1474,12 @@ void parseDoesNotRecognizeDatabaseIDasUserComment() throws Exception {
     void integrationTestFileDirectories() throws IOException {
         ParserResult result = parser.parse(
                 new StringReader("@comment{jabref-meta: fileDirectory:\\\\Literature\\\\;}"
-                        + "@comment{jabref-meta: fileDirectory-defaultOwner-user:D:\\\\Documents;}"));
+                        + "@comment{jabref-meta: fileDirectory-defaultOwner-user:D:\\\\Documents;}"
+                         + "@comment{jabref-meta: fileDirectoryLatex-defaultOwner-user:D:\\\\Latex;}"));
 
         assertEquals("\\Literature\\", result.getMetaData().getDefaultFileDirectory().get());
         assertEquals("D:\\Documents", result.getMetaData().getUserFileDirectory("defaultOwner-user").get());
+        assertEquals("D:\\Latex", result.getMetaData().getLaTexFileDirectory("defaultOwner-user").get().toString());
     }
 
     @Test
diff --git a/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java b/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
index 765f93ddcfe..080b2594e69 100644
--- a/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
+++ b/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
@@ -17,6 +17,7 @@
 import org.jabref.model.groups.GroupHierarchyType;
 import org.jabref.model.groups.GroupTreeNode;
 import org.jabref.model.groups.TexGroup;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -28,17 +29,19 @@
 
 public class GroupsParserTest {
     private FileUpdateMonitor fileMonitor;
+    private MetaData metaData;
 
     @BeforeEach
     public void setUp() throws Exception {
         fileMonitor = new DummyFileUpdateMonitor();
+        metaData = new MetaData();
     }
 
     @Test
     // For https://github.com/JabRef/jabref/issues/1681
     public void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exception {
         ExplicitGroup expected = new ExplicitGroup("B{\\\"{o}}hmer", GroupHierarchyType.INDEPENDENT, ',');
-        AbstractGroup parsed = GroupsParser.fromString("ExplicitGroup:B{\\\\\"{o}}hmer;0;", ',', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("ExplicitGroup:B{\\\\\"{o}}hmer;0;", ',', fileMonitor, metaData);
 
         assertEquals(expected, parsed);
     }
@@ -46,20 +49,20 @@ public void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exc
     @Test
     public void keywordDelimiterThatNeedsToBeEscaped() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("group1", GroupHierarchyType.INDEPENDENT, "keywords", ';', '>');
-        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;\\;;>;1;;;;;", ';', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;\\;;>;1;;;;;", ';', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
     public void hierarchicalDelimiterThatNeedsToBeEscaped() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("group1", GroupHierarchyType.INDEPENDENT, "keywords", ',', ';');
-        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;,;\\;;1;;;;;", ';', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;,;\\;;1;;;;;", ';', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
     public void fromStringThrowsParseExceptionForNotEscapedGroupName() throws Exception {
-        assertThrows(ParseException.class, () -> GroupsParser.fromString("ExplicitGroup:slit\\\\;0\\;mertsch_slit2_2007\\;;", ',', fileMonitor));
+        assertThrows(ParseException.class, () -> GroupsParser.fromString("ExplicitGroup:slit\\\\;0\\;mertsch_slit2_2007\\;;", ',', fileMonitor, metaData));
     }
 
     @Test
@@ -85,7 +88,7 @@ public void testImportSubGroups() throws Exception {
         AbstractGroup thirdSubGrpLvl1 = new ExplicitGroup("3", GroupHierarchyType.INDEPENDENT, ',');
         rootNode.addSubgroup(thirdSubGrpLvl1);
 
-        GroupTreeNode parsedNode = GroupsParser.importGroups(orderedData, ',', fileMonitor);
+        GroupTreeNode parsedNode = GroupsParser.importGroups(orderedData, ',', fileMonitor, metaData);
         assertEquals(rootNode.getChildren(), parsedNode.getChildren());
     }
 
@@ -96,7 +99,7 @@ public void fromStringParsesExplicitGroupWithIconAndDescription() throws Excepti
         expected.setExpanded(true);
         expected.setColor(Color.ALICEBLUE);
         expected.setDescription("test description");
-        AbstractGroup parsed = GroupsParser.fromString("StaticGroup:myExplicitGroup;0;1;0xf0f8ffff;test icon;test description;", ',', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("StaticGroup:myExplicitGroup;0;1;0xf0f8ffff;test icon;test description;", ',', fileMonitor, metaData);
 
         assertEquals(expected, parsed);
     }
@@ -104,26 +107,26 @@ public void fromStringParsesExplicitGroupWithIconAndDescription() throws Excepti
     @Test
     public void fromStringParsesAutomaticKeywordGroup() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "keywords", ',', '>');
-        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:myAutomaticGroup;0;keywords;,;>;1;;;;", ',', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:myAutomaticGroup;0;keywords;,;>;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
     public void fromStringParsesAutomaticPersonGroup() throws Exception {
         AutomaticPersonsGroup expected = new AutomaticPersonsGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "authors");
-        AbstractGroup parsed = GroupsParser.fromString("AutomaticPersonsGroup:myAutomaticGroup;0;authors;1;;;;", ',', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("AutomaticPersonsGroup:myAutomaticGroup;0;authors;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
     public void fromStringParsesTexGroup() throws Exception {
-        TexGroup expected = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), fileMonitor);
-        AbstractGroup parsed = GroupsParser.fromString("TexGroup:myTexGroup;0;path/To/File;1;;;;", ',', fileMonitor);
+        TexGroup expected = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+        AbstractGroup parsed = GroupsParser.fromString("TexGroup:myTexGroup;0;path/To/File;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
     public void fromStringUnknownGroupThrowsException() throws Exception {
-        assertThrows(ParseException.class, () -> GroupsParser.fromString("0 UnknownGroup:myUnknownGroup;0;;1;;;;", ',', fileMonitor));
+        assertThrows(ParseException.class, () -> GroupsParser.fromString("0 UnknownGroup:myUnknownGroup;0;;1;;;;", ',', fileMonitor, metaData));
     }
 }
diff --git a/src/test/java/org/jabref/model/groups/TexGroupTest.java b/src/test/java/org/jabref/model/groups/TexGroupTest.java
index 3d869bee22f..e2408b08308 100644
--- a/src/test/java/org/jabref/model/groups/TexGroupTest.java
+++ b/src/test/java/org/jabref/model/groups/TexGroupTest.java
@@ -6,19 +6,29 @@
 import org.jabref.logic.auxparser.DefaultAuxParser;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
+import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class TexGroupTest {
 
+    private MetaData metaData;
+
+    @BeforeEach
+    public void setUp() throws Exception {
+        metaData = new MetaData();
+    }
+
     @Test
     public void containsReturnsTrueForEntryInAux() throws Exception {
         Path auxFile = Paths.get(TexGroupTest.class.getResource("paper.aux").toURI());
-        TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor());
+        TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), metaData);
         BibEntry inAux = new BibEntry();
         inAux.setCiteKey("Darwin1888");
 
@@ -28,10 +38,20 @@ public void containsReturnsTrueForEntryInAux() throws Exception {
     @Test
     public void containsReturnsTrueForEntryNotInAux() throws Exception {
         Path auxFile = Paths.get(TexGroupTest.class.getResource("paper.aux").toURI());
-        TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor());
+        TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), metaData);
         BibEntry notInAux = new BibEntry();
         notInAux.setCiteKey("NotInAux2017");
 
         assertFalse(group.contains(notInAux));
     }
+
+    @Test
+    public void getFilePathReturnsRelativePath() throws Exception {
+        Path auxFile = Paths.get(TexGroupTest.class.getResource("paper.aux").toURI());
+        String user = "Darwin";
+        metaData.setLaTexFileDirectory(user, auxFile.getParent());
+        TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), metaData, user);
+
+        assertEquals("paper.aux", group.getFilePath().toString());
+    }
 }

From 40600b35420e688ee5d5758224717b484ad34f84 Mon Sep 17 00:00:00 2001
From: Yash  Kothari <yashkothari199767@gmail.com>
Date: Sat, 30 Mar 2019 14:35:56 +0530
Subject: [PATCH 147/184] Select the first tab which matches the search query
 in preferences (#4825)

window

After every search clear the selection of tabs and select the first
tab in the tabsList.

Fixes #4824
---
 .../java/org/jabref/gui/preferences/PreferencesDialog.java    | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
index a64fa630780..437d26cbdf1 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
@@ -122,6 +122,8 @@ private void construct() {
                 ScrollPane preferencePaneContainer = new ScrollPane(tab.getBuilder());
                 preferencePaneContainer.getStyleClass().add("preferencePaneContainer");
                 container.setCenter(preferencePaneContainer);
+            } else {
+                container.setCenter(null);
             }
         });
         tabsList.getSelectionModel().selectFirst();
@@ -136,6 +138,8 @@ private void construct() {
         tabsList.itemsProperty().bindBidirectional(searchHandler.filteredPreferenceTabsProperty());
         searchBox.textProperty().addListener((observable, previousText, newText) -> {
             searchHandler.filterTabs(newText.toLowerCase(Locale.ROOT));
+            tabsList.getSelectionModel().clearSelection();
+            tabsList.getSelectionModel().selectFirst();
         });
 
         VBox buttonContainer = new VBox();

From df04e02255ce07175b878eed25df3947085c1566 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 1 Apr 2019 08:23:25 +0200
Subject: [PATCH 148/184] Bump checkstyle from 8.18 to 8.19 (#4834)

Bumps [checkstyle](https://github.com/checkstyle/checkstyle) from 8.18 to 8.19.
- [Release notes](https://github.com/checkstyle/checkstyle/releases)
- [Commits](https://github.com/checkstyle/checkstyle/compare/checkstyle-8.18...checkstyle-8.19)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9673626d496..a40b34db6e9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -177,7 +177,7 @@ dependencies {
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.18'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.19'
 }
 
 jacoco {

From f51b97291a8bdabba6c1fabb75a4afc6f55c919a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 1 Apr 2019 08:26:19 +0200
Subject: [PATCH 149/184] Bump archunit-junit5-engine from 0.10.1 to 0.10.2
 (#4832)

Bumps [archunit-junit5-engine](https://github.com/TNG/ArchUnit) from 0.10.1 to 0.10.2.
- [Release notes](https://github.com/TNG/ArchUnit/releases)
- [Commits](https://github.com/TNG/ArchUnit/compare/v0.10.1...0.10.2)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index a40b34db6e9..a693f117e9e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -172,7 +172,7 @@ dependencies {
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.1'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.2'
     testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.1'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"

From 85e684b5e6c04c8f47834b3c0a960a9c53d00a3c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 1 Apr 2019 08:47:11 +0200
Subject: [PATCH 150/184] Bump archunit-junit5-api from 0.10.1 to 0.10.2
 (#4833)

Bumps [archunit-junit5-api](https://github.com/TNG/ArchUnit) from 0.10.1 to 0.10.2.
- [Release notes](https://github.com/TNG/ArchUnit/releases)
- [Commits](https://github.com/TNG/ArchUnit/compare/v0.10.1...0.10.2)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index a693f117e9e..261a39e8223 100644
--- a/build.gradle
+++ b/build.gradle
@@ -173,7 +173,7 @@ dependencies {
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
     testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.2'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.1'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.2'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 

From 05eaa64f409a722e54be102d869d09956f436063 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Mon, 1 Apr 2019 13:09:07 +0200
Subject: [PATCH 151/184] Convert AutoLinkFilesAction to JavaFX (#4822)

* Convert AutoLinkFilesAction to JavaFX

Fixes #4819.

* Convert a few more dialogs to JavaFX
---
 src/main/java/org/jabref/JabRefMain.java      |  12 +-
 .../org/jabref/cli/ArgumentProcessor.java     |   7 +-
 src/main/java/org/jabref/gui/JabRefFrame.java |  24 +--
 .../gui/actions/AutoLinkFilesAction.java      |  52 ------
 .../externalfiles/AutoLinkFilesAction.java    |  68 +++++++
 .../externalfiles/AutoSetFileLinksUtil.java   |  66 +++++--
 .../gui/externalfiles/AutoSetLinks.java       | 172 ------------------
 .../importer/ParserResultWarningDialog.java   |  17 +-
 .../actions/MergeReviewIntoCommentAction.java |   2 +-
 ...geReviewIntoCommentConfirmationDialog.java |  28 ++-
 .../gui/mergeentries/FetchAndMergeEntry.java  |   2 +-
 11 files changed, 153 insertions(+), 297 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/actions/AutoLinkFilesAction.java
 create mode 100644 src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java
 delete mode 100644 src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java

diff --git a/src/main/java/org/jabref/JabRefMain.java b/src/main/java/org/jabref/JabRefMain.java
index 66e624a002d..7c6f3d78f49 100644
--- a/src/main/java/org/jabref/JabRefMain.java
+++ b/src/main/java/org/jabref/JabRefMain.java
@@ -2,14 +2,13 @@
 
 import java.net.Authenticator;
 
-import javax.swing.JFrame;
-import javax.swing.JOptionPane;
-
 import javafx.application.Application;
 import javafx.application.Platform;
+import javafx.scene.control.Alert;
 import javafx.stage.Stage;
 
 import org.jabref.cli.ArgumentProcessor;
+import org.jabref.gui.FXDialog;
 import org.jabref.gui.remote.JabRefMessageHandler;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.l10n.Localization;
@@ -119,9 +118,10 @@ private static void ensureCorrectJavaVersion() {
                 versionError.append("\n");
                 versionError.append(Localization.lang("Note that currently, JabRef does not run with Java 9."));
             }
-            final JFrame frame = new JFrame();
-            JOptionPane.showMessageDialog(null, versionError, Localization.lang("Error"), JOptionPane.ERROR_MESSAGE);
-            frame.dispose();
+
+            FXDialog alert = new FXDialog(Alert.AlertType.ERROR, Localization.lang("Error"), true);
+            alert.setHeaderText(null);
+            alert.setContentText(versionError.toString());
 
             // We exit on Java 9 error since this will definitely not work
             if (java9Fail) {
diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
index f97a582daab..56a4de65bde 100644
--- a/src/main/java/org/jabref/cli/ArgumentProcessor.java
+++ b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -13,7 +13,9 @@
 
 import org.jabref.Globals;
 import org.jabref.JabRefException;
-import org.jabref.gui.externalfiles.AutoSetLinks;
+import org.jabref.gui.externalfiles.AutoSetFileLinksUtil;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.undo.NamedCompound;
 import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
 import org.jabref.logic.exporter.AtomicFileWriter;
 import org.jabref.logic.exporter.BibDatabaseWriter;
@@ -496,7 +498,8 @@ private void automaticallySetFileLinks(List<ParserResult> loaded) {
         for (ParserResult parserResult : loaded) {
             BibDatabase database = parserResult.getDatabase();
             LOGGER.info(Localization.lang("Automatically setting file links"));
-            AutoSetLinks.autoSetLinks(database.getEntries(), parserResult.getDatabaseContext());
+            AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(parserResult.getDatabaseContext(), Globals.prefs.getFilePreferences(), Globals.prefs.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
+            util.linkAssociatedFiles(database.getEntries(), new NamedCompound(""));
         }
     }
 
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 06ab62cb461..939a1aeb689 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -56,7 +56,6 @@
 import org.jabref.JabRefExecutorService;
 import org.jabref.gui.actions.ActionFactory;
 import org.jabref.gui.actions.Actions;
-import org.jabref.gui.actions.AutoLinkFilesAction;
 import org.jabref.gui.actions.BibtexKeyPatternAction;
 import org.jabref.gui.actions.ConnectToSharedDatabaseCommand;
 import org.jabref.gui.actions.CopyFilesAction;
@@ -87,6 +86,7 @@
 import org.jabref.gui.exporter.ExportToClipboardAction;
 import org.jabref.gui.exporter.SaveAllAction;
 import org.jabref.gui.exporter.SaveDatabaseAction;
+import org.jabref.gui.externalfiles.AutoLinkFilesAction;
 import org.jabref.gui.externalfiles.FindUnlinkedFilesAction;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.help.AboutAction;
@@ -112,7 +112,6 @@
 import org.jabref.logic.autosaveandbackup.BackupManager;
 import org.jabref.logic.importer.IdFetcher;
 import org.jabref.logic.importer.OpenDatabase;
-import org.jabref.logic.importer.OutputPrinter;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.l10n.Localization;
@@ -147,7 +146,7 @@
 /**
  * The main window of the application.
  */
-public class JabRefFrame extends BorderPane implements OutputPrinter {
+public class JabRefFrame extends BorderPane {
 
     // Frame titles.
     public static final String FRAME_TITLE = "JabRef";
@@ -819,7 +818,7 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction())
+                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs))
         );
 
         PushToApplicationButton pushToExternal = new PushToApplicationButton(this, pushApplications.getApplications());
@@ -1249,17 +1248,6 @@ private boolean isExistURLorDOI(List<BibEntry> selectEntryList) {
         return false;
     }
 
-    @Override
-    public void showMessage(String message, String title, int msgType) {
-        JOptionPane.showMessageDialog(null, message, title, msgType);
-    }
-
-    @Override
-    public void setStatus(String s) {
-        output(s);
-    }
-
-    @Override
     public void showMessage(String message) {
         JOptionPane.showMessageDialog(null, message);
     }
@@ -1438,7 +1426,7 @@ private void setDefaultTableFontSize() {
         for (BasePanel basePanel : getBasePanelList()) {
             basePanel.updateTableFont();
         }
-        setStatus(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
+        dialogService.notify(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
     }
 
     private void increaseTableFontSize() {
@@ -1446,7 +1434,7 @@ private void increaseTableFontSize() {
         for (BasePanel basePanel : getBasePanelList()) {
             basePanel.updateTableFont();
         }
-        setStatus(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
+        dialogService.notify(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
     }
 
     private void decreaseTableFontSize() {
@@ -1458,7 +1446,7 @@ private void decreaseTableFontSize() {
         for (BasePanel basePanel : getBasePanelList()) {
             basePanel.updateTableFont();
         }
-        setStatus(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
+        dialogService.notify(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
     }
 
     private class CloseDatabaseAction extends SimpleCommand {
diff --git a/src/main/java/org/jabref/gui/actions/AutoLinkFilesAction.java b/src/main/java/org/jabref/gui/actions/AutoLinkFilesAction.java
deleted file mode 100644
index 7b77c9f59b4..00000000000
--- a/src/main/java/org/jabref/gui/actions/AutoLinkFilesAction.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package org.jabref.gui.actions;
-
-import java.util.List;
-
-import javax.swing.JDialog;
-import javax.swing.JFrame;
-
-import org.jabref.JabRefExecutorService;
-import org.jabref.JabRefGUI;
-import org.jabref.gui.externalfiles.AutoSetLinks;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.entry.BibEntry;
-
-/**
- * This Action may only be used in a menu or button.
- * Never in the entry editor. FileListEditor and EntryEditor have other ways to update the file links
- */
-public class AutoLinkFilesAction extends SimpleCommand {
-
-    public AutoLinkFilesAction() {
-
-    }
-
-    @Override
-    public void execute() {
-        List<BibEntry> entries = JabRefGUI.getMainFrame().getCurrentBasePanel().getSelectedEntries();
-        if (entries.isEmpty()) {
-            JabRefGUI.getMainFrame().getCurrentBasePanel()
-                    .output(Localization.lang("This operation requires one or more entries to be selected."));
-            return;
-        }
-        JDialog diag = new JDialog((JFrame) null, true);
-        final NamedCompound nc = new NamedCompound(Localization.lang("Automatically set file links"));
-        Runnable runnable = AutoSetLinks.autoSetLinks(entries, nc, null,
-                JabRefGUI.getMainFrame().getCurrentBasePanel().getBibDatabaseContext(), e -> {
-                    if (e.getID() > 0) {
-                        // entry has been updated in Util.autoSetLinks, only treat nc and status message
-                        if (nc.hasEdits()) {
-                            nc.end();
-                            JabRefGUI.getMainFrame().getCurrentBasePanel().getUndoManager().addEdit(nc);
-                            JabRefGUI.getMainFrame().getCurrentBasePanel().markBaseChanged();
-                        }
-                        JabRefGUI.getMainFrame().output(Localization.lang("Finished automatically setting external links."));
-                    } else {
-                        JabRefGUI.getMainFrame().output(Localization.lang("Finished automatically setting external links.") + " "
-                                + Localization.lang("No files found."));
-                    }
-                } , diag);
-        JabRefExecutorService.INSTANCE.execute(runnable);
-    }
-}
diff --git a/src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java b/src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java
new file mode 100644
index 00000000000..967243e840b
--- /dev/null
+++ b/src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java
@@ -0,0 +1,68 @@
+package org.jabref.gui.externalfiles;
+
+import java.util.List;
+
+import javafx.concurrent.Task;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.preferences.JabRefPreferences;
+
+/**
+ * This Action may only be used in a menu or button.
+ * Never in the entry editor. FileListEditor and EntryEditor have other ways to update the file links
+ */
+public class AutoLinkFilesAction extends SimpleCommand {
+
+    private final DialogService dialogService;
+    private final JabRefFrame frame;
+    private final JabRefPreferences preferences;
+
+    public AutoLinkFilesAction(JabRefFrame frame, JabRefPreferences preferences) {
+        this.frame = frame;
+        this.dialogService = frame.getDialogService();
+        this.preferences = preferences;
+    }
+
+    @Override
+    public void execute() {
+        List<BibEntry> entries = frame.getCurrentBasePanel().getSelectedEntries();
+        if (entries.isEmpty()) {
+            dialogService.notify(Localization.lang("This operation requires one or more entries to be selected."));
+            return;
+        }
+
+        final NamedCompound nc = new NamedCompound(Localization.lang("Automatically set file links"));
+        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(frame.getCurrentBasePanel().getBibDatabaseContext(), preferences.getFilePreferences(), preferences.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
+        Task<List<BibEntry>> linkFilesTask = new Task<List<BibEntry>>() {
+            @Override
+            protected List<BibEntry> call() {
+                return util.linkAssociatedFiles(entries, nc);
+            }
+
+            @Override
+            protected void succeeded() {
+                if (!getValue().isEmpty()) {
+                    if (nc.hasEdits()) {
+                        nc.end();
+                        frame.getCurrentBasePanel().getUndoManager().addEdit(nc);
+                    }
+                    dialogService.notify(Localization.lang("Finished automatically setting external links."));
+                } else {
+                    dialogService.notify(Localization.lang("Finished automatically setting external links.") + " " + Localization.lang("No files found."));
+                }
+            }
+        };
+
+        dialogService.showProgressDialogAndWait(
+                Localization.lang("Automatically setting file links"),
+                Localization.lang("Searching for files"),
+                linkFilesTask
+        );
+    }
+}
diff --git a/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java b/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java
index f1f07088a16..284eba0f689 100644
--- a/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java
+++ b/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java
@@ -11,12 +11,17 @@
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.externalfiletype.UnknownExternalFileType;
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.gui.undo.UndoableFieldChange;
+import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.util.io.AutoLinkPreferences;
 import org.jabref.logic.util.io.FileFinder;
 import org.jabref.logic.util.io.FileFinders;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.FieldName;
+import org.jabref.model.entry.FileFieldWriter;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.metadata.FilePreferences;
 import org.jabref.model.util.FileHelper;
@@ -26,7 +31,7 @@
 
 public class AutoSetFileLinksUtil {
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(AutoSetLinks.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(AutoSetFileLinksUtil.class);
     private List<Path> directories;
     private AutoLinkPreferences autoLinkPreferences;
     private ExternalFileTypes externalFileTypes;
@@ -35,12 +40,44 @@ public AutoSetFileLinksUtil(BibDatabaseContext databaseContext, FilePreferences
         this(databaseContext.getFileDirectoriesAsPaths(filePreferences), autoLinkPreferences, externalFileTypes);
     }
 
-    public AutoSetFileLinksUtil(List<Path> directories, AutoLinkPreferences autoLinkPreferences, ExternalFileTypes externalFileTypes) {
+    private AutoSetFileLinksUtil(List<Path> directories, AutoLinkPreferences autoLinkPreferences, ExternalFileTypes externalFileTypes) {
         this.directories = directories;
         this.autoLinkPreferences = autoLinkPreferences;
         this.externalFileTypes = externalFileTypes;
     }
 
+    public List<BibEntry> linkAssociatedFiles(List<BibEntry> entries, NamedCompound ce) {
+        List<BibEntry> changedEntries = new ArrayList<>();
+        for (BibEntry entry : entries) {
+
+            List<LinkedFile> linkedFiles = new ArrayList<>();
+            try {
+                linkedFiles = findAssociatedNotLinkedFiles(entry);
+            } catch (IOException e) {
+                LOGGER.error("Problem finding files", e);
+            }
+
+            if (ce != null) {
+                for (LinkedFile linkedFile : linkedFiles) {
+                    // store undo information
+                    String newVal = FileFieldWriter.getStringRepresentation(linkedFile);
+
+                    String oldVal = entry.getField(FieldName.FILE).orElse(null);
+
+                    UndoableFieldChange fieldChange = new UndoableFieldChange(entry, FieldName.FILE, oldVal, newVal);
+                    ce.addEdit(fieldChange);
+
+                    DefaultTaskExecutor.runInJavaFXThread(() -> {
+                        entry.addFile(linkedFile);
+                    });
+                }
+
+                changedEntries.add(entry);
+            }
+        }
+        return changedEntries;
+    }
+
     public List<LinkedFile> findAssociatedNotLinkedFiles(BibEntry entry) throws IOException {
         List<LinkedFile> linkedFiles = new ArrayList<>();
 
@@ -53,22 +90,23 @@ public List<LinkedFile> findAssociatedNotLinkedFiles(BibEntry entry) throws IOEx
         // Collect the found files that are not yet linked
         for (Path foundFile : result) {
             boolean fileAlreadyLinked = entry.getFiles().stream()
-                    .map(file -> file.findIn(directories))
-                    .anyMatch(file -> {
-                        try {
-                            return file.isPresent() && Files.isSameFile(file.get(), foundFile);
-                        } catch (IOException e) {
-                            LOGGER.error("Problem with isSameFile", e);
-                        }
-                        return false;
-                    });
+                                             .map(file -> file.findIn(directories))
+                                             .anyMatch(file -> {
+                                                 try {
+                                                     return file.isPresent() && Files.isSameFile(file.get(), foundFile);
+                                                 } catch (IOException e) {
+                                                     LOGGER.error("Problem with isSameFile", e);
+                                                 }
+                                                 return false;
+                                             });
+
             if (!fileAlreadyLinked) {
                 Optional<ExternalFileType> type = FileHelper.getFileExtension(foundFile)
-                        .map(externalFileTypes::getExternalFileTypeByExt)
-                        .orElse(Optional.of(new UnknownExternalFileType("")));
+                                                            .map(externalFileTypes::getExternalFileTypeByExt)
+                                                            .orElse(Optional.of(new UnknownExternalFileType("")));
 
                 String strType = type.isPresent() ? type.get().getName() : "";
-                String relativeFilePath = FileUtil.relativize(foundFile, directories).toString();
+                Path relativeFilePath = FileUtil.relativize(foundFile, directories);
                 LinkedFile linkedFile = new LinkedFile("", relativeFilePath, strType);
                 linkedFiles.add(linkedFile);
             }
diff --git a/src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java b/src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java
deleted file mode 100644
index d874493a98d..00000000000
--- a/src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java
+++ /dev/null
@@ -1,172 +0,0 @@
-package org.jabref.gui.externalfiles;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-import java.util.Set;
-
-import javax.swing.BorderFactory;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JProgressBar;
-import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
-
-import org.jabref.Globals;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FieldName;
-import org.jabref.model.entry.FileFieldWriter;
-import org.jabref.model.entry.LinkedFile;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class AutoSetLinks {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(AutoSetLinks.class);
-
-    private AutoSetLinks() {
-    }
-
-    /**
-     * Shortcut method if links are set without using the GUI
-     *
-     * @param entries  the entries for which links should be set
-     * @param databaseContext the database for which links are set
-     */
-    public static void autoSetLinks(List<BibEntry> entries, BibDatabaseContext databaseContext) {
-        autoSetLinks(entries, null, null, databaseContext, null, null);
-    }
-
-    /**
-     * Automatically add links for this set of entries, based on the globally stored list of external file types. The
-     * entries are modified, and corresponding UndoEdit elements added to the NamedCompound given as argument.
-     * Furthermore, all entries which are modified are added to the Set of entries given as an argument.
-     * <p>
-     * The entries' bibtex keys must have been set - entries lacking key are ignored. The operation is done in a new
-     * thread, which is returned for the caller to wait for if needed.
-     *
-     * @param entries          A collection of BibEntry objects to find links for.
-     * @param ce               A NamedCompound to add UndoEdit elements to.
-     * @param changedEntries   MODIFIED, optional. A Set of BibEntry objects to which all modified entries is added.
-
-     * @param databaseContext  The database providing the relevant file directory, if any.
-     * @param callback         An ActionListener that is notified (on the event dispatch thread) when the search is finished.
-     *                         The ActionEvent has id=0 if no new links were added, and id=1 if one or more links were added. This
-     *                         parameter can be null, which means that no callback will be notified.
-     * @param diag             An instantiated modal JDialog which will be used to display the progress of the automatically setting. This
-     *                         parameter can be null, which means that no progress update will be shown.
-     * @return the thread performing the automatically setting
-     */
-    public static Runnable autoSetLinks(final List<BibEntry> entries, final NamedCompound ce,
-            final Set<BibEntry> changedEntries,
-            final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
-        final Collection<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
-        if (diag != null) {
-            final JProgressBar prog = new JProgressBar(SwingConstants.HORIZONTAL, 0, types.size() - 1);
-            final JLabel label = new JLabel(Localization.lang("Searching for files"));
-            prog.setIndeterminate(true);
-            prog.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-            diag.setTitle(Localization.lang("Automatically setting file links"));
-            diag.getContentPane().add(prog, BorderLayout.CENTER);
-            diag.getContentPane().add(label, BorderLayout.SOUTH);
-
-            diag.pack();
-            diag.setLocationRelativeTo(diag.getParent());
-        }
-
-        Runnable r = () -> {
-            boolean foundAny = false;
-            AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, Globals.prefs.getFilePreferences(), Globals.prefs.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
-
-            for (BibEntry entry : entries) {
-
-                List<LinkedFile> linkedFiles = new ArrayList<>();
-                try {
-                    linkedFiles = util.findAssociatedNotLinkedFiles(entry);
-                } catch (IOException e) {
-                    LOGGER.error("Problem finding files", e);
-                }
-
-                if (ce != null) {
-                    for (LinkedFile linkedFile : linkedFiles) {
-                        // store undo information
-                        String newVal = FileFieldWriter.getStringRepresentation(linkedFile);
-
-                        String oldVal = entry.getField(FieldName.FILE).orElse(null);
-
-                        UndoableFieldChange fieldChange = new UndoableFieldChange(entry, FieldName.FILE, oldVal, newVal);
-                        ce.addEdit(fieldChange);
-
-                        DefaultTaskExecutor.runInJavaFXThread(() -> {
-                            entry.addFile(linkedFile);
-                        });
-                        foundAny = true;
-                    }
-
-                    if (changedEntries != null) {
-                        changedEntries.add(entry);
-                    }
-                }
-
-            }
-
-            final int id = foundAny ? 1 : 0;
-            SwingUtilities.invokeLater(() -> {
-
-                if (diag != null) {
-                    diag.dispose();
-                }
-                if (callback != null) {
-                    callback.actionPerformed(new ActionEvent(AutoSetLinks.class, id, ""));
-                }
-
-            });
-
-        };
-
-        SwingUtilities.invokeLater(() -> {
-            // show dialog which will be hidden when the task is done
-            if (diag != null) {
-                diag.setVisible(true);
-            }
-        });
-
-        return r;
-    }
-
-    /**
-     * Automatically add links for this entry to the table model given as an argument, based on the globally stored list
-     * of external file types. The entry itself is not modified. The entry's bibtex key must have been set.
-     *
-     * @param entry            The BibEntry to find links for.
-
-     * @param databaseContext  The database providing the relevant file directory, if any.
-     * @param callback         An ActionListener that is notified (on the event dispatch thread) when the search is finished.
-     *                         The ActionEvent has id=0 if no new links were added, and id=1 if one or more links were added. This
-     *                         parameter can be null, which means that no callback will be notified. The passed ActionEvent is
-     *                         constructed with (this, id, ""), where id is 1 if something has been done and 0 if nothing has been
-     *                         done.
-     * @param diag             An instantiated modal JDialog which will be used to display the progress of the automatically setting. This
-     *                         parameter can be null, which means that no progress update will be shown.
-     * @return the runnable able to perform the automatically setting
-     */
-    public static Runnable autoSetLinks(final BibEntry entry,
-            final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
-        return autoSetLinks(Collections.singletonList(entry), null, null, databaseContext, callback,
-                diag);
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/importer/ParserResultWarningDialog.java b/src/main/java/org/jabref/gui/importer/ParserResultWarningDialog.java
index 45dbf2fc9e7..827f88f51de 100644
--- a/src/main/java/org/jabref/gui/importer/ParserResultWarningDialog.java
+++ b/src/main/java/org/jabref/gui/importer/ParserResultWarningDialog.java
@@ -1,13 +1,8 @@
 package org.jabref.gui.importer;
 
-import java.awt.Dimension;
 import java.util.List;
 import java.util.Objects;
 
-import javax.swing.JOptionPane;
-import javax.swing.JScrollPane;
-import javax.swing.JTextArea;
-
 import org.jabref.gui.JabRefFrame;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
@@ -71,17 +66,7 @@ public static void showParserResultWarningDialog(final ParserResult parserResult
             dialogTitle = Localization.lang("Warnings") + " (" + parserResult.getFile().get().getName() + ")";
         }
 
-        // Create JTextArea with JScrollPane
-        final JTextArea textArea = new JTextArea(dialogContent.toString());
-        final JScrollPane scrollPane = new JScrollPane(textArea) {
-
-            @Override
-            public Dimension getPreferredSize() {
-                return new Dimension(800, Math.min(Math.max(100, warnings.size() * 15), 400)); // Guess a suitable height between 100 and 400
-            }
-        };
-
         // Show dialog
-        JOptionPane.showMessageDialog(null, scrollPane, dialogTitle, JOptionPane.WARNING_MESSAGE);
+        jabRefFrame.getDialogService().showWarningDialogAndWait(dialogTitle, dialogContent.toString());
     }
 }
diff --git a/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentAction.java b/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentAction.java
index 2a76c406f62..3196f1c46aa 100644
--- a/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentAction.java
+++ b/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentAction.java
@@ -20,7 +20,7 @@ public void performAction(BasePanel basePanel, ParserResult parserResult) {
 
         migration.performMigration(parserResult);
         List<BibEntry> conflicts = MergeReviewIntoCommentMigration.collectConflicts(parserResult);
-        if (!conflicts.isEmpty() && new MergeReviewIntoCommentConfirmationDialog(basePanel).askUserForMerge(conflicts)) {
+        if (!conflicts.isEmpty() && new MergeReviewIntoCommentConfirmationDialog(basePanel.frame().getDialogService()).askUserForMerge(conflicts)) {
             migration.performConflictingMigration(parserResult);
         }
     }
diff --git a/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentConfirmationDialog.java b/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentConfirmationDialog.java
index 2f789560771..74889ba5462 100644
--- a/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentConfirmationDialog.java
+++ b/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentConfirmationDialog.java
@@ -4,18 +4,16 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import javax.swing.JOptionPane;
-
-import org.jabref.gui.BasePanel;
+import org.jabref.gui.DialogService;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 
 public class MergeReviewIntoCommentConfirmationDialog {
 
-    private final BasePanel panel;
+    private final DialogService dialogService;
 
-    public MergeReviewIntoCommentConfirmationDialog(BasePanel panel) {
-        this.panel = panel;
+    public MergeReviewIntoCommentConfirmationDialog(DialogService dialogService) {
+        this.dialogService = dialogService;
     }
 
     public boolean askUserForMerge(List<BibEntry> conflicts) {
@@ -25,15 +23,15 @@ public boolean askUserForMerge(List<BibEntry> conflicts) {
                 .map(Optional::get)
                 .collect(Collectors.joining(",\n"));
 
-        String[] options = {Localization.lang("Merge fields")};
-        int answer = JOptionPane.showOptionDialog(
-                null,
-                bibKeys + " " +
-                        Localization.lang("has/have both a 'Comment' and a 'Review' field.") + "\n" +
-                        Localization.lang("Since the 'Review' field was deprecated in JabRef 4.2, these two fields are about to be merged into the 'Comment' field.") + "\n" +
-                        Localization.lang("The conflicting fields of these entries will be merged into the 'Comment' field."),
-                Localization.lang("Review Field Migration"), JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE, null, options, options[0]);
+        String content = bibKeys + " " +
+                Localization.lang("has/have both a 'Comment' and a 'Review' field.") + "\n" +
+                Localization.lang("Since the 'Review' field was deprecated in JabRef 4.2, these two fields are about to be merged into the 'Comment' field.") + "\n" +
+                Localization.lang("The conflicting fields of these entries will be merged into the 'Comment' field.");
 
-        return 0 == answer;
+        return dialogService.showConfirmationDialogAndWait(
+                Localization.lang("Review Field Migration"),
+                content,
+                Localization.lang("Merge fields")
+        );
     }
 }
diff --git a/src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java b/src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java
index cd7be54acc3..ff87b3ddf2c 100644
--- a/src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java
+++ b/src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java
@@ -65,7 +65,7 @@ public void fetchAndMerge(BibEntry entry, List<String> fields) {
                                       if (fetchedEntry.isPresent()) {
                                           showMergeDialog(entry, fetchedEntry.get(), fetcher.get());
                                       } else {
-                                          panel.frame().setStatus(Localization.lang("Cannot get info based on given %0: %1", type, fieldContent.get()));
+                                          dialogService.notify(Localization.lang("Cannot get info based on given %0: %1", type, fieldContent.get()));
                                       }
                                   })
                                   .onFailure(exception -> {

From 1c1a6a42ca7fbd77905d6e06819bd6209d4aa7ee Mon Sep 17 00:00:00 2001
From: Johannes Manner <johannes.manner@web.de>
Date: Tue, 2 Apr 2019 22:45:03 +0200
Subject: [PATCH 152/184] All buttons in custom dialogs react on enter (#4835)

---
 src/main/java/org/jabref/gui/util/BaseDialog.java | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/main/java/org/jabref/gui/util/BaseDialog.java b/src/main/java/org/jabref/gui/util/BaseDialog.java
index 6cf9a1faf5b..921be10e748 100644
--- a/src/main/java/org/jabref/gui/util/BaseDialog.java
+++ b/src/main/java/org/jabref/gui/util/BaseDialog.java
@@ -6,6 +6,7 @@
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.Dialog;
 import javafx.scene.image.Image;
+import javafx.scene.input.KeyCode;
 import javafx.stage.Stage;
 
 import org.jabref.Globals;
@@ -23,6 +24,14 @@ protected BaseDialog() {
             } else if (keyBindingRepository.checkKeyCombinationEquality(KeyBinding.DEFAULT_DIALOG_ACTION, event)) {
                 getDefaultButton().ifPresent(Button::fire);
             }
+
+            // all buttons in base dialogs react on enter
+            if (event.getCode() == KeyCode.ENTER) {
+                if (event.getTarget() instanceof Button) {
+                    ((Button) event.getTarget()).fire();
+                    event.consume();
+                }
+            }
         });
 
         setDialogIcon(IconTheme.getJabRefImageFX());

From 3ed41efdcbe741793329a2954cea01a8c4934ceb Mon Sep 17 00:00:00 2001
From: Johannes Manner <johannes.manner@web.de>
Date: Tue, 2 Apr 2019 23:12:16 +0200
Subject: [PATCH 153/184] Adds a delay to the group expansion (#4838)

* Adds a delay to the group expansion

* Also collapses the item after 1 second

* Renamed handler class and method signature
---
 .../org/jabref/gui/groups/GroupTreeView.java  | 29 ++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/groups/GroupTreeView.java b/src/main/java/org/jabref/gui/groups/GroupTreeView.java
index 4dbbf152859..abc6e9fb460 100644
--- a/src/main/java/org/jabref/gui/groups/GroupTreeView.java
+++ b/src/main/java/org/jabref/gui/groups/GroupTreeView.java
@@ -71,6 +71,8 @@ public class GroupTreeView {
     private GroupTreeViewModel viewModel;
     private CustomLocalDragboard localDragboard;
 
+    private DragExpansionHandler dragExpansionHandler;
+
     private static void removePseudoClasses(TreeTableRow<GroupNodeViewModel> row, PseudoClass... pseudoClasses) {
         for (PseudoClass pseudoClass : pseudoClasses) {
             row.pseudoClassStateChanged(pseudoClass, false);
@@ -84,6 +86,7 @@ public void initialize() {
 
         // Set-up groups tree
         groupTree.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
+        dragExpansionHandler = new DragExpansionHandler();
 
         // Set-up bindings
         Consumer<ObservableList<GroupNodeViewModel>> updateSelectedGroups =
@@ -220,7 +223,7 @@ public void initialize() {
                     event.acceptTransferModes(TransferMode.MOVE, TransferMode.LINK);
 
                     //expand node and all children on drag over
-                    row.getTreeItem().setExpanded(true);
+                    dragExpansionHandler.expandGroup(row.getTreeItem());
 
                     removePseudoClasses(row, dragOverBottom, dragOverCenter, dragOverTop);
                     switch (getDroppingMouseLocation(row, event)) {
@@ -399,4 +402,28 @@ private DroppingMouseLocation getDroppingMouseLocation(TreeTableRow<GroupNodeVie
             return DroppingMouseLocation.CENTER;
         }
     }
+
+    private class DragExpansionHandler {
+        private static final long DRAG_TIME_BEFORE_EXPANDING_MS = 1000;
+        private TreeItem<GroupNodeViewModel> draggedItem;
+        private long dragStarted;
+
+        public void expandGroup(TreeItem<GroupNodeViewModel> treeItem) {
+            if (!treeItem.equals(draggedItem)) {
+                this.draggedItem = treeItem;
+                this.dragStarted = System.currentTimeMillis();
+                this.draggedItem.setExpanded(this.draggedItem.isExpanded());
+                return;
+            }
+
+            if (System.currentTimeMillis() - this.dragStarted > DRAG_TIME_BEFORE_EXPANDING_MS) {
+                // expand or collapse the tree item and reset the time
+                this.dragStarted = System.currentTimeMillis();
+                this.draggedItem.setExpanded(!this.draggedItem.isExpanded());
+            } else {
+                // leave the expansion state of the tree item as it is
+                this.draggedItem.setExpanded(this.draggedItem.isExpanded());
+            }
+        }
+    }
 }

From 54892f2ed6e2af249da48e367ceed116c4eeb728 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 2 Apr 2019 23:18:31 +0200
Subject: [PATCH 154/184] Remove global search feature (#4694)

* Remove global search feature

* Remove unused code
---
 CHANGELOG.md                                  |   2 +-
 src/main/java/org/jabref/gui/JabRefFrame.java |  17 +-
 .../java/org/jabref/gui/icon/IconTheme.java   |   2 -
 .../org/jabref/gui/keyboard/KeyBinding.java   |   1 -
 .../jabref/gui/search/GlobalSearchBar.java    | 124 +---
 .../jabref/gui/search/GlobalSearchWorker.java |  68 --
 .../jabref/gui/search/SearchResultFrame.java  | 650 ------------------
 .../jabref/preferences/SearchPreferences.java |  11 -
 src/main/resources/l10n/JabRef_en.properties  |   7 -
 9 files changed, 10 insertions(+), 872 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/search/GlobalSearchWorker.java
 delete mode 100644 src/main/java/org/jabref/gui/search/SearchResultFrame.java

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a64512c0723..564d782c9da 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -109,6 +109,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ### Removed
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.
 - The number column was removed.
+- We removed the global search feature.
 - We removed the coloring of cells in the maintable according to whether the field is optional/required.
 - We removed the feature to find and resolve duplicate BibTeX keys (as this use case is already covered by the integrity check).
 - We removed a few commands from the right-click menu that are not needed often and thus don't need to be placed that prominently:
@@ -146,7 +147,6 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 
-
 
 
 ## Older versions
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 939a1aeb689..d32b48dd30f 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -130,7 +130,6 @@
 import org.jabref.model.entry.specialfields.SpecialField;
 import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.LastFocusedTabPreferences;
-import org.jabref.preferences.SearchPreferences;
 
 import com.google.common.eventbus.Subscribe;
 import com.jfoenix.controls.JFXSnackbar;
@@ -270,16 +269,14 @@ private void init() {
             // Poor-mans binding to global state
             // We need to invoke this in the JavaFX thread as all the listeners sit there
             Platform.runLater(() -> Globals.stateManager.activeDatabaseProperty().setValue(Optional.of(currentBasePanel.getBibDatabaseContext())));
-            if (new SearchPreferences(Globals.prefs).isGlobalSearch()) {
-                globalSearchBar.performSearch();
-            } else {
-                String content = "";
-                Optional<SearchQuery> currentSearchQuery = currentBasePanel.getCurrentSearchQuery();
-                if (currentSearchQuery.isPresent()) {
-                    content = currentSearchQuery.get().getQuery();
-                }
-                globalSearchBar.setSearchTerm(content);
+
+            // Update search query
+            String content = "";
+            Optional<SearchQuery> currentSearchQuery = currentBasePanel.getCurrentSearchQuery();
+            if (currentSearchQuery.isPresent()) {
+                content = currentSearchQuery.get().getQuery();
             }
+            globalSearchBar.setSearchTerm(content);
 
             currentBasePanel.getPreviewPanel().updateLayout(Globals.prefs.getPreviewPreferences());
 
diff --git a/src/main/java/org/jabref/gui/icon/IconTheme.java b/src/main/java/org/jabref/gui/icon/IconTheme.java
index fbb97842ecf..e24a8e5d80a 100644
--- a/src/main/java/org/jabref/gui/icon/IconTheme.java
+++ b/src/main/java/org/jabref/gui/icon/IconTheme.java
@@ -283,7 +283,6 @@ public enum JabRefIcons implements JabRefIcon {
         SUCCESS(MaterialDesignIcon.CHECK_CIRCLE),
         WARNING(MaterialDesignIcon.ALERT),
         ERROR(MaterialDesignIcon.ALERT_CIRCLE),
-        OPEN_IN_NEW_WINDOW(MaterialDesignIcon.OPEN_IN_NEW), /*css: open-in-new */
         CASE_SENSITIVE(MaterialDesignIcon.ALPHABETICAL), /* css: mdi-alphabetical */
         REG_EX(MaterialDesignIcon.REGEX), /*css: mdi-regex */
         CONSOLE(MaterialDesignIcon.CONSOLE), /*css: console */
@@ -291,7 +290,6 @@ public enum JabRefIcons implements JabRefIcon {
         FACEBOOK(MaterialDesignIcon.FACEBOOK), /* css: facebook */
         TWITTER(MaterialDesignIcon.TWITTER), /* css: twitter */
         BLOG(MaterialDesignIcon.RSS), /* css: rss */
-        GLOBAL_SEARCH(MaterialDesignIcon.EARTH), /* css: earth */
         DATE_PICKER(MaterialDesignIcon.CALENDAR), /* css: calendar */
         DEFAULT_GROUP_ICON_COLORED(MaterialDesignIcon.PLAY),
         DEFAULT_GROUP_ICON(MaterialDesignIcon.LABEL_OUTLINE),
diff --git a/src/main/java/org/jabref/gui/keyboard/KeyBinding.java b/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
index b1b2cbbb4b5..43c55b7d444 100644
--- a/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
+++ b/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
@@ -40,7 +40,6 @@ public enum KeyBinding {
     FILE_LIST_EDITOR_MOVE_ENTRY_UP("File list editor, move entry up", Localization.lang("File list editor, move entry up"), "ctrl+UP", KeyBindingCategory.VIEW),
     FIND_UNLINKED_FILES("Find unlinked files", Localization.lang("Find unlinked files"), "shift+F7", KeyBindingCategory.QUALITY),
     FOCUS_ENTRY_TABLE("Focus entry table", Localization.lang("Focus entry table"), "alt+1", KeyBindingCategory.VIEW),
-    GLOBAL_SEARCH("Search globally", Localization.lang("Search globally"), "ctrl+shift+F", KeyBindingCategory.SEARCH),
     HELP("Help", Localization.lang("Help"), "F1", KeyBindingCategory.FILE),
     IMPORT_INTO_CURRENT_DATABASE("Import into current library", Localization.lang("Import into current library"), "ctrl+I", KeyBindingCategory.FILE),
     IMPORT_INTO_NEW_DATABASE("Import into new library", Localization.lang("Import into new library"), "ctrl+alt+I", KeyBindingCategory.FILE),
diff --git a/src/main/java/org/jabref/gui/search/GlobalSearchBar.java b/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
index 3f18ba400c6..8426b3fb290 100644
--- a/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
+++ b/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
@@ -1,7 +1,6 @@
 package org.jabref.gui.search;
 
 import java.lang.reflect.Field;
-import java.nio.file.Path;
 import java.util.Objects;
 import java.util.Optional;
 
@@ -11,14 +10,12 @@
 import javafx.beans.binding.Bindings;
 import javafx.css.PseudoClass;
 import javafx.event.Event;
-import javafx.geometry.Orientation;
 import javafx.geometry.Pos;
 import javafx.scene.Node;
 import javafx.scene.control.Button;
 import javafx.scene.control.ContentDisplay;
 import javafx.scene.control.Label;
 import javafx.scene.control.ListView;
-import javafx.scene.control.Separator;
 import javafx.scene.control.Skin;
 import javafx.scene.control.TextField;
 import javafx.scene.control.ToggleButton;
@@ -35,7 +32,6 @@
 
 import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
-import org.jabref.gui.GUIGlobals;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.autocompleter.AppendPersonNamesStrategy;
 import org.jabref.gui.autocompleter.AutoCompleteFirstNameMode;
@@ -74,23 +70,13 @@ public class GlobalSearchBar extends HBox {
     private final TextField searchField = SearchTextField.create();
     private final ToggleButton caseSensitive;
     private final ToggleButton regularExp;
-    private final ToggleButton globalSearch;
     private final Button searchModeButton = new Button();
     private final Label currentResults = new Label("");
     private final SearchQueryHighlightObservable searchQueryHighlightObservable = new SearchQueryHighlightObservable();
-    private final Button openCurrentResultsInDialog = IconTheme.JabRefIcons.OPEN_IN_NEW_WINDOW.asButton();
     private SearchWorker searchWorker;
-    private GlobalSearchWorker globalSearchWorker;
-
-    private SearchResultFrame searchResultFrame;
 
     private SearchDisplayMode searchDisplayMode;
 
-    /**
-     * if this flag is set the searchbar won't be selected after the next search
-     */
-    private boolean dontSelectSearchBar;
-
     public GlobalSearchBar(JabRefFrame frame) {
         super();
         this.frame = Objects.requireNonNull(frame);
@@ -100,22 +86,11 @@ public GlobalSearchBar(JabRefFrame frame) {
         // fits the standard "found x entries"-message thus hinders the searchbar to jump around while searching if the frame width is too small
         currentResults.setPrefWidth(150);
 
-        globalSearch = IconTheme.JabRefIcons.GLOBAL_SEARCH.asToggleButton();
-        globalSearch.setSelected(searchPreferences.isGlobalSearch());
-        globalSearch.setTooltip(new Tooltip(Localization.lang("Search in all open libraries")));
-
-
         KeyBindingRepository keyBindingRepository = Globals.getKeyPrefs();
         searchField.addEventFilter(KeyEvent.KEY_PRESSED, event -> {
             Optional<KeyBinding> keyBinding = keyBindingRepository.mapToKeyBinding(event);
             if (keyBinding.isPresent()) {
-                if (keyBinding.get().equals(KeyBinding.GLOBAL_SEARCH)) {
-                    globalSearch.setSelected(true);
-                    searchPreferences.setGlobalSearch(globalSearch.isSelected());
-                    updateOpenCurrentResultsTooltip(globalSearch.isSelected());
-                    focus();
-                    event.consume();
-                } else if (keyBinding.get().equals(KeyBinding.CLOSE)) {
+                if (keyBinding.get().equals(KeyBinding.CLOSE)) {
                     // Clear search and select first entry, if available
                     clearSearch();
                     frame.getCurrentBasePanel().getMainTable().getSelectionModel().selectFirst();
@@ -124,22 +99,6 @@ public GlobalSearchBar(JabRefFrame frame) {
             }
         });
 
-        globalSearch.setOnAction(event -> {
-            searchPreferences.setGlobalSearch(globalSearch.isSelected());
-            updateOpenCurrentResultsTooltip(globalSearch.isSelected());
-        });
-
-        //openCurrentResultsInDialog.setDisabledIcon(IconTheme.JabRefIcons.OPEN_IN_NEW_WINDOW.disabled().getSmallIcon());
-        openCurrentResultsInDialog.setOnAction(event -> {
-            if (globalSearch.isSelected()) {
-                performGlobalSearch();
-            } else {
-                openLocalFindingsInExternalPanel();
-            }
-        });
-        openCurrentResultsInDialog.setDisable(true);
-        updateOpenCurrentResultsTooltip(globalSearch.isSelected());
-
         regularExp = IconTheme.JabRefIcons.REG_EX.asToggleButton();
         regularExp.setSelected(searchPreferences.isRegularExpression());
         regularExp.setTooltip(new Tooltip(Localization.lang("regular expression")));
@@ -193,64 +152,6 @@ public GlobalSearchBar(JabRefFrame frame) {
         this.setAlignment(Pos.CENTER_LEFT);
     }
 
-    private void performGlobalSearch() {
-        BasePanel currentBasePanel = frame.getCurrentBasePanel();
-        if ((currentBasePanel == null) || validateSearchResultFrame(true)) {
-            return;
-        }
-
-        if (globalSearchWorker != null) {
-            globalSearchWorker.cancel(true);
-        }
-
-        if (searchField.getText().isEmpty()) {
-            focus();
-            return;
-        }
-
-        globalSearchWorker = new GlobalSearchWorker(currentBasePanel.frame(), getSearchQuery());
-        globalSearchWorker.execute();
-    }
-
-    private void openLocalFindingsInExternalPanel() {
-        BasePanel currentBasePanel = frame.getCurrentBasePanel();
-        if ((currentBasePanel == null) || validateSearchResultFrame(false)) {
-            return;
-        }
-
-        if (searchField.getText().isEmpty()) {
-            focus();
-            return;
-        }
-
-        SearchResultFrame searchDialog = new SearchResultFrame(
-                currentBasePanel.frame(),
-                Localization.lang("Search results in library %0 for %1",
-                        currentBasePanel.getBibDatabaseContext()
-                                        .getDatabasePath()
-                                        .map(Path::getFileName)
-                                        .map(Path::toString)
-                                        .orElse(GUIGlobals.UNTITLED_TITLE),
-                        this.getSearchQuery().localize()), getSearchQuery(), false);
-        searchDialog.addEntries(currentBasePanel.getDatabase().getEntries(), currentBasePanel);
-        searchDialog.selectFirstEntry();
-        searchDialog.setVisible(true);
-    }
-
-    private boolean validateSearchResultFrame(boolean globalSearch) {
-        if (searchResultFrame != null) {
-            if ((searchResultFrame.isGlobalSearch() == globalSearch) && isStillValidQuery(searchResultFrame.getSearchQuery())) {
-                searchResultFrame.focus();
-                return true;
-            } else {
-                searchResultFrame.dispose();
-                return false;
-            }
-        }
-
-        return false;
-    }
-
     private void toggleSearchModeAndSearch() {
         int nextSearchMode = (searchDisplayMode.ordinal() + 1) % SearchDisplayMode.values().length;
         searchDisplayMode = SearchDisplayMode.values()[nextSearchMode];
@@ -288,7 +189,6 @@ private void clearSearch() {
         currentResults.setText("");
         searchField.setText("");
         searchQueryHighlightObservable.reset();
-        openCurrentResultsInDialog.setDisable(true);
 
         Globals.stateManager.clearSearchQuery();
     }
@@ -331,7 +231,6 @@ private void informUserAboutInvalidSearchQuery() {
 
         String illegalSearch = Localization.lang("Search failed: illegal search expression");
         currentResults.setText(illegalSearch);
-        openCurrentResultsInDialog.setDisable(true);
     }
 
     public void setAutoCompleter(AutoCompleteSuggestionProvider<Author> searchCompleter) {
@@ -364,12 +263,6 @@ public SearchQueryHighlightObservable getSearchQueryHighlightObservable() {
         return searchQueryHighlightObservable;
     }
 
-    public boolean isStillValidQuery(SearchQuery query) {
-        return query.getQuery().equals(this.searchField.getText())
-                && (query.isRegularExpression() == regularExp.isSelected())
-                && (query.isCaseSensitive() == caseSensitive.isSelected());
-    }
-
     private SearchQuery getSearchQuery() {
         SearchQuery searchQuery = new SearchQuery(this.searchField.getText(), this.caseSensitive.isSelected(), this.regularExp.isSelected());
         this.frame.getCurrentBasePanel().setCurrentSearchQuery(searchQuery);
@@ -396,11 +289,6 @@ public void updateResults(int matched, TextFlow description, boolean grammarBase
         tooltip.setGraphic(description);
         tooltip.setMaxHeight(10);
         searchField.setTooltip(tooltip);
-        openCurrentResultsInDialog.setDisable(false);
-    }
-
-    public void setSearchResultFrame(SearchResultFrame searchResultFrame) {
-        this.searchResultFrame = searchResultFrame;
     }
 
     public void setSearchTerm(String searchTerm) {
@@ -411,14 +299,6 @@ public void setSearchTerm(String searchTerm) {
         DefaultTaskExecutor.runInJavaFXThread(() -> searchField.setText(searchTerm));
     }
 
-    private void updateOpenCurrentResultsTooltip(boolean globalSearchEnabled) {
-        if (globalSearchEnabled) {
-            openCurrentResultsInDialog.setTooltip(new Tooltip(Localization.lang("Show global search results in a window")));
-        } else {
-            openCurrentResultsInDialog.setTooltip(new Tooltip(Localization.lang("Show search results in a window")));
-        }
-    }
-
     private class SearchPopupSkin<T> implements Skin<AutoCompletePopup<T>> {
 
         private final AutoCompletePopup<T> control;
@@ -436,7 +316,7 @@ public SearchPopupSkin(AutoCompletePopup<T> control) {
             this.suggestionList.maxWidthProperty().bind(control.maxWidthProperty());
             this.suggestionList.minWidthProperty().bind(control.minWidthProperty());
 
-            ToolBar toolBar = new ToolBar(openCurrentResultsInDialog, new Separator(Orientation.VERTICAL), globalSearch, regularExp, caseSensitive, searchModeButton);
+            ToolBar toolBar = new ToolBar(regularExp, caseSensitive, searchModeButton);
 
             this.container = new BorderPane();
             this.container.setCenter(suggestionList);
diff --git a/src/main/java/org/jabref/gui/search/GlobalSearchWorker.java b/src/main/java/org/jabref/gui/search/GlobalSearchWorker.java
deleted file mode 100644
index bdbd6fe4bba..00000000000
--- a/src/main/java/org/jabref/gui/search/GlobalSearchWorker.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package org.jabref.gui.search;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.concurrent.ExecutionException;
-import java.util.stream.Collectors;
-
-import javax.swing.SwingWorker;
-
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.search.SearchQuery;
-import org.jabref.model.entry.BibEntry;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-class GlobalSearchWorker extends SwingWorker<Map<BasePanel, List<BibEntry>>, Void> {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(GlobalSearchWorker.class);
-
-    private final JabRefFrame frame;
-    private final SearchQuery searchQuery;
-    private final SearchResultFrame dialog;
-
-    public GlobalSearchWorker(JabRefFrame frame, SearchQuery query) {
-        this.frame = Objects.requireNonNull(frame);
-        this.searchQuery = Objects.requireNonNull(query);
-
-        dialog = new SearchResultFrame(frame,
-                Localization.lang("Search results in all libraries for %0",
-                        this.searchQuery.localize()),
-                searchQuery, true);
-        frame.getGlobalSearchBar().setSearchResultFrame(dialog);
-    }
-
-    @Override
-    protected Map<BasePanel, List<BibEntry>> doInBackground() throws Exception {
-        Map<BasePanel, List<BibEntry>> matches = new HashMap<>();
-        for (BasePanel basePanel : frame.getBasePanelList()) {
-            matches.put(basePanel, basePanel.getDatabase().getEntries().parallelStream()
-                    .filter(searchQuery::isMatch)
-                    .collect(Collectors.toList()));
-        }
-        return matches;
-    }
-
-    @Override
-    protected void done() {
-        if (isCancelled()) {
-            return;
-        }
-
-        try {
-            for (Map.Entry<BasePanel, List<BibEntry>> match : get().entrySet()) {
-                dialog.addEntries(match.getValue(), match.getKey());
-            }
-            dialog.selectFirstEntry();
-            dialog.setVisible(true);
-        } catch (InterruptedException | ExecutionException e) {
-            LOGGER.error("something went wrong during the search", e);
-        }
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/search/SearchResultFrame.java b/src/main/java/org/jabref/gui/search/SearchResultFrame.java
deleted file mode 100644
index 376de69855e..00000000000
--- a/src/main/java/org/jabref/gui/search/SearchResultFrame.java
+++ /dev/null
@@ -1,650 +0,0 @@
-package org.jabref.gui.search;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ComponentAdapter;
-import java.awt.event.ComponentEvent;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.IOException;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.Optional;
-
-import javax.swing.AbstractAction;
-import javax.swing.ActionMap;
-import javax.swing.InputMap;
-import javax.swing.JComponent;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JPopupMenu;
-import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
-import javax.swing.JTable;
-import javax.swing.KeyStroke;
-import javax.swing.table.TableColumnModel;
-
-import javafx.embed.swing.JFXPanel;
-import javafx.scene.Scene;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.GUIGlobals;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.PreviewPanel;
-import org.jabref.gui.customjfx.CustomJFXPanel;
-import org.jabref.gui.desktop.JabRefDesktop;
-import org.jabref.gui.externalfiletype.ExternalFileMenuItem;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.filelist.FileListEntry;
-import org.jabref.gui.filelist.FileListTableModel;
-import org.jabref.gui.icon.IconTheme;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.maintable.MainTableNameFormatter;
-import org.jabref.gui.renderer.GeneralRenderer;
-import org.jabref.gui.util.comparator.IconComparator;
-import org.jabref.logic.bibtex.comparator.EntryComparator;
-import org.jabref.logic.bibtex.comparator.FieldComparator;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.search.SearchQuery;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FieldName;
-import org.jabref.model.entry.FieldProperty;
-import org.jabref.model.entry.InternalBibtexFields;
-import org.jabref.model.strings.StringUtil;
-import org.jabref.preferences.SearchPreferences;
-
-import ca.odell.glazedlists.BasicEventList;
-import ca.odell.glazedlists.EventList;
-import ca.odell.glazedlists.SortedList;
-import ca.odell.glazedlists.event.ListEvent;
-import ca.odell.glazedlists.event.ListEventListener;
-import ca.odell.glazedlists.gui.AbstractTableComparatorChooser;
-import ca.odell.glazedlists.gui.AdvancedTableFormat;
-import ca.odell.glazedlists.swing.DefaultEventSelectionModel;
-import ca.odell.glazedlists.swing.DefaultEventTableModel;
-import ca.odell.glazedlists.swing.GlazedListsSwing;
-import ca.odell.glazedlists.swing.TableComparatorChooser;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * Dialog to display search results, potentially from more than one BasePanel, with
- * possibility to preview and to locate each entry in the main window.
- */
-public class SearchResultFrame {
-
-    private static final String[] FIELDS = new String[] {FieldName.AUTHOR, FieldName.TITLE, FieldName.YEAR, FieldName.JOURNAL};
-    private static final int DATABASE_COL = 0;
-    private static final int FILE_COL = 1;
-    private static final int URL_COL = 2;
-    private static final int PAD = 3;
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(SearchResultFrame.class);
-
-    private final JabRefFrame frame;
-    private JFrame searchResultFrame;
-    private final JLabel fileLabel = new JLabel(IconTheme.JabRefIcons.FILE.getSmallIcon());
-    private final JLabel urlLabel = new JLabel(IconTheme.JabRefIcons.WWW.getSmallIcon());
-
-    private final JSplitPane contentPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
-
-    private final EventList<BibEntry> entries = new BasicEventList<>();
-
-    private final Map<BibEntry, BasePanel> entryHome = new HashMap<>();
-    private DefaultEventTableModel<BibEntry> model;
-
-    private SortedList<BibEntry> sortedEntries;
-    private JTable entryTable;
-    private PreviewPanel preview;
-
-    private final SearchQuery searchQuery;
-    private final boolean globalSearch;
-
-    public SearchResultFrame(JabRefFrame frame, String title, SearchQuery searchQuery, boolean globalSearch) {
-        this.frame = Objects.requireNonNull(frame);
-        this.searchQuery = searchQuery;
-        this.globalSearch = globalSearch;
-        frame.getGlobalSearchBar().setSearchResultFrame(this);
-        init(Objects.requireNonNull(title));
-    }
-
-    private void init(String title) {
-        searchResultFrame = new JFrame();
-        searchResultFrame.setTitle(title);
-        searchResultFrame.setIconImages(IconTheme.getLogoSet());
-
-        preview = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), frame.getDialogService(), ExternalFileTypes.getInstance());
-
-        sortedEntries = new SortedList<>(entries, new EntryComparator(false, true, FieldName.AUTHOR));
-        model = (DefaultEventTableModel<BibEntry>) GlazedListsSwing.eventTableModelWithThreadProxyList(sortedEntries,
-                                                                                                       new EntryTableFormat());
-        entryTable = new JTable(model);
-
-        GeneralRenderer renderer = new GeneralRenderer(Color.white);
-        entryTable.setDefaultRenderer(JLabel.class, renderer);
-        entryTable.setDefaultRenderer(String.class, renderer);
-        setWidths();
-        TableComparatorChooser<BibEntry> tableSorter = TableComparatorChooser.install(entryTable, sortedEntries,
-                                                                                      AbstractTableComparatorChooser.MULTIPLE_COLUMN_KEYBOARD);
-        setupComparatorChooser(tableSorter);
-        JScrollPane sp = new JScrollPane(entryTable);
-
-        final DefaultEventSelectionModel<BibEntry> selectionModel = (DefaultEventSelectionModel<BibEntry>) GlazedListsSwing
-                                                                                                                           .eventSelectionModelWithThreadProxyList(sortedEntries);
-        entryTable.setSelectionModel(selectionModel);
-        selectionModel.getSelected().addListEventListener(new EntrySelectionListener());
-        entryTable.addMouseListener(new TableClickListener());
-
-        contentPane.setTopComponent(sp);
-
-        JFXPanel container = CustomJFXPanel.wrap(new Scene(preview));
-        contentPane.setBottomComponent(container);
-
-        // Key bindings:
-        AbstractAction closeAction = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                dispose();
-            }
-        };
-
-        ActionMap actionMap = contentPane.getActionMap();
-        InputMap inputMap = contentPane.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        inputMap.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        inputMap.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE_DATABASE), "close");
-        actionMap.put("close", closeAction);
-
-        actionMap = entryTable.getActionMap();
-        inputMap = entryTable.getInputMap();
-        //Override 'selectNextColumnCell' and 'selectPreviousColumnCell' to move rows instead of cells on TAB
-        actionMap.put("selectNextColumnCell", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                selectNextEntry();
-            }
-        });
-        actionMap.put("selectPreviousColumnCell", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                selectPreviousEntry();
-            }
-        });
-        actionMap.put("selectNextRow", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                selectNextEntry();
-            }
-        });
-        actionMap.put("selectPreviousRow", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                selectPreviousEntry();
-            }
-        });
-
-        String selectFirst = "selectFirst";
-        inputMap.put(Globals.getKeyPrefs().getKey(KeyBinding.SELECT_FIRST_ENTRY), selectFirst);
-        actionMap.put(selectFirst, new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent event) {
-                selectFirstEntry();
-            }
-        });
-
-        String selectLast = "selectLast";
-        inputMap.put(Globals.getKeyPrefs().getKey(KeyBinding.SELECT_LAST_ENTRY), selectLast);
-        actionMap.put(selectLast, new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent event) {
-                selectLastEntry();
-            }
-        });
-
-        actionMap.put("copy", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                if (!selectionModel.getSelected().isEmpty()) {
-                    List<BibEntry> bes = selectionModel.getSelected();
-                    try {
-                        Globals.clipboardManager.setContent(bes);
-                    } catch (IOException e1) {
-                        LOGGER.error("Error while serializing entries for clipboard", e1);
-                    }
-                    frame.output(Localization.lang("Copied") + ' ' + (bes.size() > 1 ? bes.size() + " "
-                            + Localization.lang("entries")
-                            : "1 " + Localization.lang("entry") + '.'));
-                }
-            }
-        });
-
-        // override standard enter-action; enter opens the selected entry
-        entryTable.getInputMap(JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT).put(KeyStroke.getKeyStroke(KeyEvent.VK_ENTER, 0), "Enter");
-        actionMap.put("Enter", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent ae) {
-                BibEntry entry = sortedEntries.get(entryTable.getSelectedRow());
-                selectEntryInBasePanel(entry);
-            }
-        });
-
-        searchResultFrame.addWindowListener(new WindowAdapter() {
-
-            @Override
-            public void windowOpened(WindowEvent e) {
-                contentPane.setDividerLocation(0.5f);
-            }
-
-            @Override
-            public void windowClosing(WindowEvent event) {
-                dispose();
-            }
-        });
-
-        searchResultFrame.getContentPane().add(contentPane, BorderLayout.CENTER);
-
-        // Remember and default to last size:
-        SearchPreferences searchPreferences = new SearchPreferences(Globals.prefs);
-        searchResultFrame.setSize(searchPreferences.getSeachDialogWidth(), searchPreferences.getSeachDialogHeight());
-        searchResultFrame.setLocation(searchPreferences.getSearchDialogPosX(), searchPreferences.getSearchDialogPosY());
-
-        searchResultFrame.addComponentListener(new ComponentAdapter() {
-
-            @Override
-            public void componentResized(ComponentEvent e) {
-                new SearchPreferences(Globals.prefs)
-                        .setSearchDialogWidth(searchResultFrame.getSize().width)
-                        .setSearchDialogHeight(searchResultFrame.getSize().height);
-            }
-
-            @Override
-            public void componentMoved(ComponentEvent e) {
-                new SearchPreferences(Globals.prefs)
-                                                    .setSearchDialogPosX(searchResultFrame.getLocation().x)
-                                                    .setSearchDialogPosY(searchResultFrame.getLocation().y);
-            }
-        });
-    }
-
-    /**
-     * Control the visibility of the dialog.
-     * @param visible true to show dialog, false to hide.
-     */
-    public void setVisible(boolean visible) {
-        searchResultFrame.setVisible(visible);
-    }
-
-    public void selectFirstEntry() {
-        selectEntry(0);
-    }
-
-    public void selectLastEntry() {
-        selectEntry(entryTable.getRowCount() - 1);
-    }
-
-    public void selectPreviousEntry() {
-        selectEntry(((entryTable.getSelectedRow() - 1) + entryTable.getRowCount()) % entryTable.getRowCount());
-    }
-
-    public void selectNextEntry() {
-        selectEntry((entryTable.getSelectedRow() + 1) % entryTable.getRowCount());
-    }
-
-    public void selectEntry(int index) {
-        if ((index >= 0) && (index < entryTable.getRowCount())) {
-            entryTable.changeSelection(index, 0, false, false);
-        } else {
-            contentPane.setDividerLocation(1.0f);
-        }
-    }
-
-    /**
-     * Set up the comparators for each column, so the user can modify sort order
-     * by clicking the column labels.
-     * @param comparatorChooser The comparator chooser controlling the sort order.
-     */
-    private void setupComparatorChooser(TableComparatorChooser<BibEntry> comparatorChooser) {
-        List<Comparator> comparators;
-        // Icon columns:
-        for (int i = 0; i < PAD; i++) {
-            comparators = comparatorChooser.getComparatorsForColumn(i);
-            comparators.clear();
-            if (i == FILE_COL) {
-                comparators.add(new IconComparator(Collections.singletonList(FieldName.FILE)));
-            } else if (i == URL_COL) {
-                comparators.add(new IconComparator(Collections.singletonList(FieldName.URL)));
-            } else if (i == DATABASE_COL) {
-                comparators.add((entry1, entry2) -> {
-                    String databaseTitle1 = entryHome.get(entry1).getTabTitle();
-                    String databaseTitle2 = entryHome.get(entry2).getTabTitle();
-                    return databaseTitle1.compareTo(databaseTitle2);
-                });
-            }
-
-        }
-        // Remaining columns:
-        for (int i = PAD; i < (PAD + FIELDS.length); i++) {
-            comparators = comparatorChooser.getComparatorsForColumn(i);
-            comparators.clear();
-            comparators.add(new FieldComparator(FIELDS[i - PAD]));
-        }
-
-        sortedEntries.getReadWriteLock().writeLock().lock();
-        comparatorChooser.appendComparator(PAD, 0, false);
-        sortedEntries.getReadWriteLock().writeLock().unlock();
-
-    }
-
-    /**
-     * Set column widths according to which field is shown, and lock icon columns
-     * to a suitable width.
-     */
-    private void setWidths() {
-        TableColumnModel cm = entryTable.getColumnModel();
-        for (int i = 0; i < (PAD + FIELDS.length); i++) {
-            switch (i) {
-                case FILE_COL:
-                case URL_COL:
-                    cm.getColumn(i).setPreferredWidth(GUIGlobals.WIDTH_ICON_COL);
-                    cm.getColumn(i).setMinWidth(GUIGlobals.WIDTH_ICON_COL);
-                    cm.getColumn(i).setMaxWidth(GUIGlobals.WIDTH_ICON_COL);
-                    break;
-                case DATABASE_COL: {
-                    Double width = InternalBibtexFields.getFieldLength(FieldName.AUTHOR);
-                    cm.getColumn(i).setPreferredWidth(width.intValue());
-                    break;
-                }
-                default: {
-                    Double width = InternalBibtexFields.getFieldLength(FIELDS[i - PAD]);
-                    cm.getColumn(i).setPreferredWidth(width.intValue());
-                    break;
-                }
-            }
-        }
-    }
-
-    /**
-     * Add a list of entries to the table.
-     * @param newEntries The list of entries.
-     * @param panel A reference to the BasePanel where the entries belong.
-     */
-    public void addEntries(List<BibEntry> newEntries, BasePanel panel) {
-        for (BibEntry entry : newEntries) {
-            addEntry(entry, panel);
-        }
-    }
-
-    /**
-     * Add a single entry to the table.
-     * @param entry The entry to add.
-     * @param panel A reference to the BasePanel where the entry belongs.
-     */
-    private void addEntry(BibEntry entry, BasePanel panel) {
-        entries.add(entry);
-        entryHome.put(entry, panel);
-
-        if ((preview.getEntry() == null) || !preview.getBasePanel().isPresent()) {
-            preview.setEntry(entry);
-            preview.setBasePanel(panel);
-            preview.setDatabaseContext(panel.getBibDatabaseContext());
-        }
-    }
-
-    private void selectEntryInBasePanel(BibEntry entry) {
-        BasePanel basePanel = entryHome.get(entry);
-        frame.showBasePanel(basePanel);
-        basePanel.requestFocus();
-        basePanel.clearAndSelect(entry);
-    }
-
-    public void dispose() {
-        frame.getGlobalSearchBar().setSearchResultFrame(null);
-        searchResultFrame.dispose();
-        frame.getGlobalSearchBar().focus();
-    }
-
-    public void focus() {
-        entryTable.requestFocus();
-    }
-
-    public SearchQuery getSearchQuery() {
-        return searchQuery;
-    }
-
-    public boolean isGlobalSearch() {
-        return globalSearch;
-    }
-
-    /**
-     * Mouse listener for the entry table. Processes icon clicks to open external
-     * files or urls, as well as the opening of the context menu.
-     */
-    class TableClickListener extends MouseAdapter {
-
-        @Override
-        public void mouseReleased(MouseEvent e) {
-            if (e.isPopupTrigger()) {
-                processPopupTrigger(e);
-            }
-        }
-
-        @Override
-        public void mousePressed(MouseEvent e) {
-            if (e.isPopupTrigger()) {
-                processPopupTrigger(e);
-                return;
-            }
-
-            // First find the row on which the user has clicked.
-            final int row = entryTable.rowAtPoint(e.getPoint());
-
-            // A double click on an entry should highlight the entry in its BasePanel:
-            if (e.getClickCount() == 2) {
-                selectEntryInBasePanel(model.getElementAt(row));
-            }
-        }
-
-        @Override
-        public void mouseClicked(MouseEvent e) {
-            if (e.isPopupTrigger()) {
-                processPopupTrigger(e);
-                return;
-            }
-            //if (e.)
-            final int col = entryTable.columnAtPoint(e.getPoint());
-            final int row = entryTable.rowAtPoint(e.getPoint());
-            if (col < PAD) {
-                BibEntry entry = sortedEntries.get(row);
-                BasePanel p = entryHome.get(entry);
-                switch (col) {
-                case FILE_COL:
-                    if (entry.hasField(FieldName.FILE)) {
-                        FileListTableModel tableModel = new FileListTableModel();
-                        entry.getField(FieldName.FILE).ifPresent(tableModel::setContent);
-                        if (tableModel.getRowCount() == 0) {
-                            return;
-                        }
-                        FileListEntry fl = tableModel.getEntry(0);
-                            (new ExternalFileMenuItem(frame, "", fl.getLink(), null,
-                                p.getBibDatabaseContext(), fl.getType())).actionPerformed(null);
-                    }
-                    break;
-                case URL_COL:
-                    entry.getField(FieldName.URL).ifPresent(link -> { try {
-                        JabRefDesktop.openExternalViewer(p.getBibDatabaseContext(), link, FieldName.URL);
-                    } catch (IOException ex) {
-                            LOGGER.warn("Could not open viewer", ex);
-                        }
-                    });
-                    break;
-                default:
-                    break;
-                }
-            }
-        }
-
-        /**
-         * If the user has signalled the opening of a context menu, the event
-         * gets redirected to this method. Here we open a file link menu if the
-         * user is pointing at a file link icon. Otherwise a general context
-         * menu should be shown.
-         * @param e The triggering mouse event.
-         */
-        public void processPopupTrigger(MouseEvent e) {
-            BibEntry entry = sortedEntries.get(entryTable.rowAtPoint(e.getPoint()));
-            BasePanel p = entryHome.get(entry);
-            int col = entryTable.columnAtPoint(e.getPoint());
-            JPopupMenu menu = new JPopupMenu();
-            int count = 0;
-
-            if (col == FILE_COL) {
-                // We use a FileListTableModel to parse the field content:
-                FileListTableModel fileList = new FileListTableModel();
-                entry.getField(FieldName.FILE).ifPresent(fileList::setContent);
-                // If there are one or more links, open the first one:
-                for (int i = 0; i < fileList.getRowCount(); i++) {
-                    FileListEntry flEntry = fileList.getEntry(i);
-                    String description = flEntry.getDescription();
-                    if ((description == null) || (description.trim().isEmpty())) {
-                        description = flEntry.getLink();
-                    }
-                    menu.add(new ExternalFileMenuItem(p.frame(), description, flEntry.getLink(),
-                                                      flEntry.getType().get().getIcon().getSmallIcon(), p.getBibDatabaseContext(), flEntry.getType()));
-                    count++;
-                }
-
-            }
-
-            if (count > 0) {
-                menu.show(entryTable, e.getX(), e.getY());
-            }
-        }
-    }
-
-    /**
-     * The listener for the Glazed list monitoring the current selection.
-     * When selection changes, we need to update the preview panel.
-     */
-    private class EntrySelectionListener implements ListEventListener<BibEntry> {
-
-        @Override
-        public void listChanged(ListEvent<BibEntry> listEvent) {
-            if (listEvent.getSourceList().size() == 1) {
-                BibEntry entry = listEvent.getSourceList().get(0);
-                // Find out which BasePanel the selected entry belongs to:
-                BasePanel basePanel = entryHome.get(entry);
-                // Update the preview's database context:
-                preview.setDatabaseContext(basePanel.getBibDatabaseContext());
-                // Update the preview's entry:
-                preview.setEntry(entry);
-                preview.setBasePanel(entryHome.get(entry));
-                preview.setDatabaseContext(entryHome.get(entry).getBibDatabaseContext());
-                contentPane.setDividerLocation(0.5f);
-            }
-        }
-    }
-
-    /**
-     * TableFormat for the table shown in the dialog. Handles the display of entry
-     * fields and icons for linked files and urls.
-     */
-    private class EntryTableFormat implements AdvancedTableFormat<BibEntry> {
-
-        @Override
-        public int getColumnCount() {
-            return PAD + FIELDS.length;
-        }
-
-        @Override
-        public String getColumnName(int column) {
-            if (column >= PAD) {
-                return StringUtil.capitalizeFirst(FIELDS[column - PAD]);
-            } else if (column == DATABASE_COL) {
-                return Localization.lang("Library");
-            } else {
-                return "";
-            }
-        }
-
-        @Override
-        public Object getColumnValue(BibEntry entry, int column) {
-            if (column < PAD) {
-                switch (column) {
-                    case DATABASE_COL:
-                        return entryHome.get(entry).getTabTitle();
-                    case FILE_COL:
-                        if (entry.hasField(FieldName.FILE)) {
-                            FileListTableModel tmpModel = new FileListTableModel();
-                            entry.getField(FieldName.FILE).ifPresent(tmpModel::setContent);
-                            fileLabel.setToolTipText(tmpModel.getToolTipHTMLRepresentation());
-                            if (tmpModel.getRowCount() > 0) {
-                                if (tmpModel.getEntry(0).getType().isPresent()) {
-                                    fileLabel.setIcon(tmpModel.getEntry(0).getType().get().getIcon().getSmallIcon());
-                                } else {
-                                    fileLabel.setIcon(IconTheme.JabRefIcons.FILE.getSmallIcon());
-                                }
-                            }
-                            return fileLabel;
-                        } else {
-                            return null;
-                        }
-                    case URL_COL: {
-                        Optional<String> urlField = entry.getField(FieldName.URL);
-                        if (urlField.isPresent()) {
-                            urlLabel.setToolTipText(urlField.get());
-                            return urlLabel;
-                        }
-                        return null;
-                    }
-                    default:
-                        return null;
-                }
-            } else {
-                String field = FIELDS[column - PAD];
-                String fieldContent = entry.getLatexFreeField(field).orElse("");
-
-                if (InternalBibtexFields.getFieldProperties(field).contains(FieldProperty.PERSON_NAMES)) {
-                    // For name fields, tap into a MainTableFormat instance and use
-                    // the same name formatting as is used in the entry table:
-                    return MainTableNameFormatter.formatName(fieldContent);
-                }
-                return fieldContent;
-            }
-        }
-
-        @Override
-        public Class<?> getColumnClass(int i) {
-            switch (i) {
-                case FILE_COL:
-                case URL_COL:
-                    return JLabel.class;
-                default:
-                    return String.class;
-            }
-        }
-
-        @Override
-        public Comparator<?> getColumnComparator(int i) {
-            return null;
-        }
-    }
-
-}
diff --git a/src/main/java/org/jabref/preferences/SearchPreferences.java b/src/main/java/org/jabref/preferences/SearchPreferences.java
index 53452b5d639..78c1ba8aff8 100644
--- a/src/main/java/org/jabref/preferences/SearchPreferences.java
+++ b/src/main/java/org/jabref/preferences/SearchPreferences.java
@@ -7,7 +7,6 @@
 
 public class SearchPreferences {
 
-    private static final String SEARCH_GLOBAL = "searchGlobal";
     private static final String SEARCH_DISPLAY_MODE = "searchDisplayMode";
     private static final String SEARCH_CASE_SENSITIVE = "caseSensitiveSearch";
     private static final String SEARCH_REG_EXP = "regExpSearch";
@@ -25,7 +24,6 @@ public SearchPreferences(JabRefPreferences preferences) {
     }
 
     public static void putDefaults(Map<String, Object> defaults) {
-        defaults.put(SEARCH_GLOBAL, Boolean.FALSE);
         defaults.put(SEARCH_DISPLAY_MODE, SearchDisplayMode.FILTER.toString());
         defaults.put(SEARCH_CASE_SENSITIVE, Boolean.FALSE);
         defaults.put(SEARCH_REG_EXP, Boolean.FALSE);
@@ -36,15 +34,6 @@ public static void putDefaults(Map<String, Object> defaults) {
         defaults.put(SEARCH_DIALOG_POS_Y, 0);
     }
 
-    public boolean isGlobalSearch() {
-        return preferences.getBoolean(SEARCH_GLOBAL);
-    }
-
-    public SearchPreferences setGlobalSearch(boolean isGlobalSearch) {
-        preferences.putBoolean(SEARCH_GLOBAL, isGlobalSearch);
-        return this;
-    }
-
     public SearchDisplayMode getSearchMode() {
         try {
             return SearchDisplayMode.valueOf(preferences.get(SEARCH_DISPLAY_MODE));
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 0258d204ee7..7893e31e5d1 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1039,9 +1039,6 @@ Could\ not\ find\ file\ '%0'.=Could not find file '%0'.
 Number\ of\ entries\ successfully\ imported=Number of entries successfully imported
 Error\ while\ fetching\ from\ %0=Error while fetching from %0
 
-Show\ search\ results\ in\ a\ window=Show search results in a window
-Show\ global\ search\ results\ in\ a\ window=Show global search results in a window
-Search\ in\ all\ open\ libraries=Search in all open libraries
 Refuse\ to\ save\ the\ library\ before\ external\ changes\ have\ been\ reviewed.=Refuse to save the library before external changes have been reviewed.
 Library\ protection=Library protection
 Unable\ to\ save\ library=Unable to save library
@@ -1438,10 +1435,6 @@ capital\ letters\ are\ not\ masked\ using\ curly\ brackets\ {}=capital letters a
 should\ contain\ a\ four\ digit\ number=should contain a four digit number
 should\ contain\ a\ valid\ page\ number\ range=should contain a valid page number range
 Search\ %0=Search %0
-
-Search\ results\ in\ all\ libraries\ for\ %0=Search results in all libraries for %0
-Search\ results\ in\ library\ %0\ for\ %1=Search results in library %0 for %1
-Search\ globally=Search globally
 No\ results\ found.=No results found.
 Found\ %0\ results.=Found %0 results.
 plain\ text=plain text

From 47772fd8ceffbe8eefac78bf680032cdf0bd72bc Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 2 Apr 2019 23:33:56 +0200
Subject: [PATCH 155/184] Fix parser exception when loading tex-groups with
 non-existing file (#4839)

* Fix #4735. Catch file not found exception and handle non existing aux files gracefully.

* Fix build

* Fix checkstyle
---
 CHANGELOG.md                                  |  1 +
 .../org/jabref/gui/groups/GroupDialog.java    |  4 +--
 .../logic/auxparser/DefaultAuxParser.java     |  2 +-
 .../logic/importer/util/GroupsParser.java     | 19 +++++++++--
 .../org/jabref/model/groups/TexGroup.java     | 17 +++++++---
 .../logic/exporter/GroupSerializerTest.java   | 32 +++++++++----------
 .../logic/importer/util/GroupsParserTest.java | 26 +++++++--------
 7 files changed, 62 insertions(+), 39 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 564d782c9da..60394941469 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -74,6 +74,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where selecting a group messed up the focus of the main table / entry editor. https://github.com/JabRef/jabref/issues/3367
 - We fixed an issue where composite author names were sorted incorrectly. https://github.com/JabRef/jabref/issues/2828
 - We fixed an issue where commands followed by `-` didn't work. [#3805](https://github.com/JabRef/jabref/issues/3805)
+- We fixed an issue where a non-existing aux file in a group made it impossible to open the library. [#4735](https://github.com/JabRef/jabref/issues/4735)
 - We fixed an issue where some journal names were wrongly marked as abbreviated. [#4115](https://github.com/JabRef/jabref/issues/4115)
 - We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
 - We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
index 2285db635ac..b40755e97e4 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDialog.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -335,7 +335,7 @@ groupName, getContext(),
                                     autoGroupPersonsField.getText().trim());
                         }
                     } else if (texRadioButton.isSelected()) {
-                        resultingGroup = new TexGroup(groupName, getContext(),
+                        resultingGroup = TexGroup.create(groupName, getContext(),
                                                       Paths.get(texGroupFilePath.getText().trim()), new DefaultAuxParser(new BibDatabase()), Globals.getFileUpdateMonitor(), basePanel.getBibDatabaseContext().getMetaData());
                     }
 
@@ -466,7 +466,7 @@ private VBox createOptionsTexGroup() {
         texGroupBrowseButton.setOnAction((ActionEvent e) -> openBrowseDialog());
         texGroupHBox.getChildren().add(texGroupFilePath);
         texGroupHBox.getChildren().add(texGroupBrowseButton);
-        texGroupHBox.setHgrow(texGroupFilePath, Priority.ALWAYS);
+        HBox.setHgrow(texGroupFilePath, Priority.ALWAYS);
         texPanel.getChildren().add(texGroupHBox);
         return texPanel;
     }
diff --git a/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java b/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java
index f8579ac68b9..054230c730b 100644
--- a/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java
+++ b/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java
@@ -77,7 +77,7 @@ private AuxParserResult parseAuxFile(Path auxFile) {
                     matchNestedAux(auxFile, result, fileList, line);
                 }
             } catch (FileNotFoundException e) {
-                LOGGER.info("Cannot locate input file", e);
+                LOGGER.warn("Cannot locate input file", e);
             } catch (IOException e) {
                 LOGGER.warn("Problem opening file", e);
             }
diff --git a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
index 4c9365b0dd8..f7f8dc27cdb 100644
--- a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
+++ b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
@@ -28,11 +28,15 @@
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileUpdateMonitor;
 
+import org.slf4j.LoggerFactory;
+
 /**
  * Converts string representation of groups to a parsed {@link GroupTreeNode}.
  */
 public class GroupsParser {
 
+    private static final org.slf4j.Logger LOGGER = LoggerFactory.getLogger(GroupsParser.class);
+
     private GroupsParser() {
     }
 
@@ -123,9 +127,18 @@ private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor
         GroupHierarchyType context = GroupHierarchyType.getByNumberOrDefault(Integer.parseInt(tok.nextToken()));
         try {
             Path path = Paths.get(tok.nextToken());
-            TexGroup newGroup = new TexGroup(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
-            addGroupDetails(tok, newGroup);
-            return newGroup;
+            try {
+                TexGroup newGroup = TexGroup.create(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+                addGroupDetails(tok, newGroup);
+                return newGroup;
+            } catch (IOException ex) {
+                // Problem accessing file -> create without file monitoring
+                LOGGER.warn("Could not access file " + path + ". The group " + name + " will not reflect changes to the aux file.", ex);
+
+                TexGroup newGroup = TexGroup.createWithoutFileMonitoring(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+                addGroupDetails(tok, newGroup);
+                return newGroup;
+            }
         } catch (InvalidPathException | IOException ex) {
             throw new ParseException(ex);
         }
diff --git a/src/main/java/org/jabref/model/groups/TexGroup.java b/src/main/java/org/jabref/model/groups/TexGroup.java
index ab350c486d5..b56e92dafff 100644
--- a/src/main/java/org/jabref/model/groups/TexGroup.java
+++ b/src/main/java/org/jabref/model/groups/TexGroup.java
@@ -30,20 +30,29 @@ public class TexGroup extends AbstractGroup implements FileUpdateListener {
     private final MetaData metaData;
     private String user;
 
-    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData, String user) throws IOException {
+    TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData, String user) {
         super(name, context);
         this.metaData = metaData;
         this.user = user;
         this.filePath = expandPath(Objects.requireNonNull(filePath));
         this.auxParser = auxParser;
         this.fileMonitor = fileMonitor;
-        fileMonitor.addListenerForFile(this.filePath, this);
     }
 
-    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+    TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
         this(name, context, filePath, auxParser, fileMonitor, metaData, System.getProperty("user.name") + '-' + InetAddress.getLocalHost().getHostName());
     }
 
+    public static TexGroup create(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+        TexGroup group = new TexGroup(name, context, filePath, auxParser, fileMonitor, metaData);
+        fileMonitor.addListenerForFile(filePath, group);
+        return group;
+    }
+
+    public static TexGroup createWithoutFileMonitoring(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+        return new TexGroup(name, context, filePath, auxParser, fileMonitor, metaData);
+    }
+    
     @Override
     public boolean contains(BibEntry entry) {
         if (keysUsedInAux == null) {
@@ -124,7 +133,7 @@ private List<Path> getFileDirectoriesAsPaths() {
         List<Path> fileDirs = new ArrayList<>();
 
         metaData.getLaTexFileDirectory(user)
-                .ifPresent(laTexFileDirectory -> fileDirs.add(laTexFileDirectory));
+                .ifPresent(fileDirs::add);
 
         return fileDirs;
     }
diff --git a/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java b/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
index b8625babeb4..26c7c61b0f2 100644
--- a/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
+++ b/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
@@ -30,31 +30,31 @@
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
-public class GroupSerializerTest {
+class GroupSerializerTest {
 
     private GroupSerializer groupSerializer;
 
     @BeforeEach
-    public void setUp() throws Exception {
+    void setUp() throws Exception {
         groupSerializer = new GroupSerializer();
     }
 
     @Test
-    public void serializeSingleAllEntriesGroup() {
+    void serializeSingleAllEntriesGroup() {
         AllEntriesGroup group = new AllEntriesGroup("");
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 AllEntriesGroup:"), serialization);
     }
 
     @Test
-    public void serializeSingleExplicitGroup() {
+    void serializeSingleExplicitGroup() {
         ExplicitGroup group = new ExplicitGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, ',');
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 StaticGroup:myExplicitGroup;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleExplicitGroupWithIconAndDescription() {
+    void serializeSingleExplicitGroupWithIconAndDescription() {
         ExplicitGroup group = new ExplicitGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, ',');
         group.setIconName("test icon");
         group.setExpanded(true);
@@ -66,63 +66,63 @@ public void serializeSingleExplicitGroupWithIconAndDescription() {
 
     @Test
     // For https://github.com/JabRef/jabref/issues/1681
-    public void serializeSingleExplicitGroupWithEscapedSlash() {
+    void serializeSingleExplicitGroupWithEscapedSlash() {
         ExplicitGroup group = new ExplicitGroup("B{\\\"{o}}hmer", GroupHierarchyType.INDEPENDENT, ',');
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 StaticGroup:B{\\\\\"{o}}hmer;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleSimpleKeywordGroup() {
+    void serializeSingleSimpleKeywordGroup() {
         WordKeywordGroup group = new WordKeywordGroup("name", GroupHierarchyType.INDEPENDENT, "keywords", "test", false, ',', false);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 KeywordGroup:name;0;keywords;test;0;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleRegexKeywordGroup() {
+    void serializeSingleRegexKeywordGroup() {
         KeywordGroup group = new RegexKeywordGroup("myExplicitGroup", GroupHierarchyType.REFINING, "author", "asdf", false);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 KeywordGroup:myExplicitGroup;1;author;asdf;0;1;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleSearchGroup() {
+    void serializeSingleSearchGroup() {
         SearchGroup group = new SearchGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, "author=harrer", true, true);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 SearchGroup:myExplicitGroup;0;author=harrer;1;1;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleSearchGroupWithRegex() {
+    void serializeSingleSearchGroupWithRegex() {
         SearchGroup group = new SearchGroup("myExplicitGroup", GroupHierarchyType.INCLUDING, "author=\"harrer\"", true, false);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 SearchGroup:myExplicitGroup;2;author=\"harrer\";1;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleAutomaticKeywordGroup() {
+    void serializeSingleAutomaticKeywordGroup() {
         AutomaticGroup group = new AutomaticKeywordGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "keywords", ',', '>');
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 AutomaticKeywordGroup:myAutomaticGroup;0;keywords;,;>;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleAutomaticPersonGroup() {
+    void serializeSingleAutomaticPersonGroup() {
         AutomaticPersonsGroup group = new AutomaticPersonsGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "authors");
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 AutomaticPersonsGroup:myAutomaticGroup;0;authors;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleTexGroup() throws Exception {
-        TexGroup group = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), new MetaData());
+    void serializeSingleTexGroup() throws Exception {
+        TexGroup group = TexGroup.createWithoutFileMonitoring("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), new MetaData());
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 TexGroup:myTexGroup;0;path/To/File;1;;;;"), serialization);
     }
 
     @Test
-    public void getTreeAsStringInSimpleTree() throws Exception {
+    void getTreeAsStringInSimpleTree() throws Exception {
         GroupTreeNode root = GroupTreeNodeTest.getRoot();
         GroupTreeNodeTest.getNodeInSimpleTree(root);
 
@@ -136,7 +136,7 @@ public void getTreeAsStringInSimpleTree() throws Exception {
     }
 
     @Test
-    public void getTreeAsStringInComplexTree() throws Exception {
+    void getTreeAsStringInComplexTree() throws Exception {
         GroupTreeNode root = GroupTreeNodeTest.getRoot();
         GroupTreeNodeTest.getNodeInComplexTree(root);
 
diff --git a/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java b/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
index 080b2594e69..640644dec0d 100644
--- a/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
+++ b/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
@@ -27,19 +27,19 @@
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
-public class GroupsParserTest {
+class GroupsParserTest {
     private FileUpdateMonitor fileMonitor;
     private MetaData metaData;
 
     @BeforeEach
-    public void setUp() throws Exception {
+    void setUp() throws Exception {
         fileMonitor = new DummyFileUpdateMonitor();
         metaData = new MetaData();
     }
 
     @Test
     // For https://github.com/JabRef/jabref/issues/1681
-    public void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exception {
+    void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exception {
         ExplicitGroup expected = new ExplicitGroup("B{\\\"{o}}hmer", GroupHierarchyType.INDEPENDENT, ',');
         AbstractGroup parsed = GroupsParser.fromString("ExplicitGroup:B{\\\\\"{o}}hmer;0;", ',', fileMonitor, metaData);
 
@@ -47,26 +47,26 @@ public void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exc
     }
 
     @Test
-    public void keywordDelimiterThatNeedsToBeEscaped() throws Exception {
+    void keywordDelimiterThatNeedsToBeEscaped() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("group1", GroupHierarchyType.INDEPENDENT, "keywords", ';', '>');
         AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;\\;;>;1;;;;;", ';', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void hierarchicalDelimiterThatNeedsToBeEscaped() throws Exception {
+    void hierarchicalDelimiterThatNeedsToBeEscaped() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("group1", GroupHierarchyType.INDEPENDENT, "keywords", ',', ';');
         AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;,;\\;;1;;;;;", ';', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringThrowsParseExceptionForNotEscapedGroupName() throws Exception {
+    void fromStringThrowsParseExceptionForNotEscapedGroupName() throws Exception {
         assertThrows(ParseException.class, () -> GroupsParser.fromString("ExplicitGroup:slit\\\\;0\\;mertsch_slit2_2007\\;;", ',', fileMonitor, metaData));
     }
 
     @Test
-    public void testImportSubGroups() throws Exception {
+    void testImportSubGroups() throws Exception {
 
         List<String> orderedData = Arrays.asList("0 AllEntriesGroup:", "1 ExplicitGroup:1;0;",
                 "2 ExplicitGroup:2;0;", "0 ExplicitGroup:3;0;");
@@ -93,7 +93,7 @@ public void testImportSubGroups() throws Exception {
     }
 
     @Test
-    public void fromStringParsesExplicitGroupWithIconAndDescription() throws Exception {
+    void fromStringParsesExplicitGroupWithIconAndDescription() throws Exception {
         ExplicitGroup expected = new ExplicitGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, ',');
         expected.setIconName("test icon");
         expected.setExpanded(true);
@@ -105,28 +105,28 @@ public void fromStringParsesExplicitGroupWithIconAndDescription() throws Excepti
     }
 
     @Test
-    public void fromStringParsesAutomaticKeywordGroup() throws Exception {
+    void fromStringParsesAutomaticKeywordGroup() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "keywords", ',', '>');
         AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:myAutomaticGroup;0;keywords;,;>;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringParsesAutomaticPersonGroup() throws Exception {
+    void fromStringParsesAutomaticPersonGroup() throws Exception {
         AutomaticPersonsGroup expected = new AutomaticPersonsGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "authors");
         AbstractGroup parsed = GroupsParser.fromString("AutomaticPersonsGroup:myAutomaticGroup;0;authors;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringParsesTexGroup() throws Exception {
-        TexGroup expected = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+    void fromStringParsesTexGroup() throws Exception {
+        TexGroup expected = TexGroup.createWithoutFileMonitoring("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
         AbstractGroup parsed = GroupsParser.fromString("TexGroup:myTexGroup;0;path/To/File;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringUnknownGroupThrowsException() throws Exception {
+    void fromStringUnknownGroupThrowsException() throws Exception {
         assertThrows(ParseException.class, () -> GroupsParser.fromString("0 UnknownGroup:myUnknownGroup;0;;1;;;;", ',', fileMonitor, metaData));
     }
 }

From a273eb1fa13317d4091a767849c40e9495de2b7e Mon Sep 17 00:00:00 2001
From: Robin <robin.lichtenthaeler@web.de>
Date: Wed, 3 Apr 2019 11:19:03 +0200
Subject: [PATCH 156/184] Enhanced message log (#4815)

* refactored JabRefFrame.output and FXDialogService.notify to only use FXDialogService.notify

* added logging to notifications and fixed problem with logger in JabRefGUI

* moved copying of logevents to GuiAppender

* directly use dialogService in BasePanel

* changed constructor to avoid NPE

* refactored code so that DialogService.notify does not need DefaultTaskExecutor.runInJavaFXThread

* replaced old swing dialog

* replaced another swing dialog
---
 src/main/java/org/jabref/gui/BasePanel.java   | 23 +++++----
 .../java/org/jabref/gui/FXDialogService.java  | 21 ++++++++-
 src/main/java/org/jabref/gui/JabRefFrame.java | 23 ++-------
 .../org/jabref/gui/actions/CleanupAction.java |  4 +-
 .../actions/CopyBibTeXKeyAndLinkAction.java   |  6 +--
 .../jabref/gui/actions/CopyDoiUrlAction.java  |  4 +-
 .../gui/actions/GenerateBibtexKeyAction.java  |  4 +-
 .../gui/actions/LookupIdentifierAction.java   | 13 +++--
 .../jabref/gui/actions/NewDatabaseAction.java |  2 +-
 .../jabref/gui/actions/WriteXMPAction.java    |  4 +-
 .../org/jabref/gui/desktop/JabRefDesktop.java | 20 +++-----
 .../jabref/gui/exporter/ExportCommand.java    |  4 +-
 .../gui/exporter/ExportToClipboardAction.java |  4 +-
 .../gui/exporter/SaveDatabaseAction.java      |  6 +--
 .../gui/externalfiles/FindFullTextAction.java | 27 ++++-------
 .../ExternalFileMenuItem.java                 |  4 +-
 .../jabref/gui/filelist/AttachFileAction.java |  2 +-
 .../org/jabref/gui/importer/ImportAction.java |  5 +-
 .../actions/AppendDatabaseAction.java         | 47 +++++++++----------
 .../importer/actions/OpenDatabaseAction.java  |  8 ++--
 .../fetcher/WebSearchPaneViewModel.java       |  4 +-
 .../jabref/gui/journals/AbbreviateAction.java |  3 +-
 .../gui/journals/UnabbreviateAction.java      |  3 +-
 .../org/jabref/gui/logging/GuiAppender.java   |  6 ++-
 .../gui/shared/SharedDatabaseUIManager.java   | 11 ++---
 .../gui/specialfields/SpecialFieldAction.java |  2 +-
 .../jabref/gui/worker/SendAsEMailAction.java  |  4 +-
 .../org/jabref/logic/logging/LogMessages.java |  6 +--
 28 files changed, 126 insertions(+), 144 deletions(-)

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index 2ccfcdcc927..c6501ec7da9 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -250,7 +250,7 @@ public JabRefFrame frame() {
     }
 
     public void output(String s) {
-        frame.output(s);
+        dialogService.notify(s);
     }
 
     private void setupActions() {
@@ -441,7 +441,7 @@ private void delete(boolean cut, List<BibEntry> entries) {
         getUndoManager().addEdit(compound);
 
         markBaseChanged();
-        frame.output(formatOutputMessage(cut ? Localization.lang("Cut") : Localization.lang("Deleted"), entries.size()));
+        this.output(formatOutputMessage(cut ? Localization.lang("Cut") : Localization.lang("Deleted"), entries.size()));
 
         // prevent the main table from loosing focus
         mainTable.requestFocus();
@@ -569,13 +569,12 @@ private void copyKeyAndTitle() {
     }
 
     private void openExternalFile() {
+        final List<BibEntry> selectedEntries = mainTable.getSelectedEntries();
+        if (selectedEntries.size() != 1) {
+            output(Localization.lang("This operation requires exactly one item to be selected."));
+            return;
+        }
         JabRefExecutorService.INSTANCE.execute(() -> {
-            final List<BibEntry> selectedEntries = mainTable.getSelectedEntries();
-            if (selectedEntries.size() != 1) {
-                output(Localization.lang("This operation requires exactly one item to be selected."));
-                return;
-            }
-
             final BibEntry entry = selectedEntries.get(0);
             if (!entry.hasField(FieldName.FILE)) {
                 // no bibtex field
@@ -1292,10 +1291,10 @@ public void action() {
             try {
                 getUndoManager().undo();
                 markBaseChanged();
-                frame.output(Localization.lang("Undo"));
+                output(Localization.lang("Undo"));
             } catch (CannotUndoException ex) {
                 LOGGER.warn("Nothing to undo", ex);
-                frame.output(Localization.lang("Nothing to undo") + '.');
+                output(Localization.lang("Nothing to undo") + '.');
             }
 
             markChangedOrUnChanged();
@@ -1363,9 +1362,9 @@ public void action() {
             try {
                 getUndoManager().redo();
                 markBaseChanged();
-                frame.output(Localization.lang("Redo"));
+                output(Localization.lang("Redo"));
             } catch (CannotRedoException ex) {
-                frame.output(Localization.lang("Nothing to redo") + '.');
+                output(Localization.lang("Nothing to redo") + '.');
             }
 
             markChangedOrUnChanged();
diff --git a/src/main/java/org/jabref/gui/FXDialogService.java b/src/main/java/org/jabref/gui/FXDialogService.java
index f3edaba275a..2fe537a30a1 100644
--- a/src/main/java/org/jabref/gui/FXDialogService.java
+++ b/src/main/java/org/jabref/gui/FXDialogService.java
@@ -24,21 +24,27 @@
 import javafx.scene.control.ChoiceDialog;
 import javafx.scene.control.DialogPane;
 import javafx.scene.control.TextInputDialog;
+import javafx.scene.layout.Pane;
 import javafx.scene.layout.Region;
 import javafx.stage.DirectoryChooser;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 import javafx.stage.Window;
+import javafx.util.Duration;
 
-import org.jabref.JabRefGUI;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.gui.util.ZipFileChooser;
 import org.jabref.logic.l10n.Localization;
 
+import com.jfoenix.controls.JFXSnackbar;
+import com.jfoenix.controls.JFXSnackbar.SnackbarEvent;
+import com.jfoenix.controls.JFXSnackbarLayout;
 import org.controlsfx.dialog.ExceptionDialog;
 import org.controlsfx.dialog.ProgressDialog;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * This class provides methods to create default
@@ -51,7 +57,11 @@
  */
 public class FXDialogService implements DialogService {
 
+    private static final Duration TOAST_MESSAGE_DISPLAY_TIME = Duration.millis(3000);
+    private static final Logger LOGGER = LoggerFactory.getLogger(FXDialogService.class);
+
     private final Window mainWindow;
+    private final JFXSnackbar statusLine;
 
     /**
      * @deprecated try not to initialize a new dialog service but reuse the one constructed in {@link org.jabref.gui.JabRefFrame}.
@@ -63,6 +73,12 @@ public FXDialogService() {
 
     public FXDialogService(Window mainWindow) {
         this.mainWindow = mainWindow;
+        this.statusLine = new JFXSnackbar();
+    }
+
+    public FXDialogService(Window mainWindow, Pane mainPane) {
+        this.mainWindow = mainWindow;
+        this.statusLine = new JFXSnackbar(mainPane);
     }
 
     private static FXDialog createDialog(AlertType type, String title, String content) {
@@ -253,7 +269,8 @@ public <V> void showProgressDialogAndWait(String title, String content, Task<V>
 
     @Override
     public void notify(String message) {
-        JabRefGUI.getMainFrame().output(message);
+        LOGGER.info(message);
+        statusLine.fireEvent(new SnackbarEvent(new JFXSnackbarLayout(message), TOAST_MESSAGE_DISPLAY_TIME, null));
     }
 
     @Override
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index d32b48dd30f..71e75d1c54d 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -50,7 +50,6 @@
 import javafx.scene.layout.Pane;
 import javafx.scene.layout.Priority;
 import javafx.stage.Stage;
-import javafx.util.Duration;
 
 import org.jabref.Globals;
 import org.jabref.JabRefExecutorService;
@@ -132,9 +131,6 @@
 import org.jabref.preferences.LastFocusedTabPreferences;
 
 import com.google.common.eventbus.Subscribe;
-import com.jfoenix.controls.JFXSnackbar;
-import com.jfoenix.controls.JFXSnackbar.SnackbarEvent;
-import com.jfoenix.controls.JFXSnackbarLayout;
 import org.eclipse.fx.ui.controls.tabpane.DndTabPane;
 import org.eclipse.fx.ui.controls.tabpane.DndTabPaneFactory;
 import org.fxmisc.easybind.EasyBind;
@@ -151,12 +147,11 @@ public class JabRefFrame extends BorderPane {
     public static final String FRAME_TITLE = "JabRef";
 
     private static final Logger LOGGER = LoggerFactory.getLogger(JabRefFrame.class);
-    private static final Duration TOAST_MESSAGE_DISPLAY_TIME = Duration.millis(3000);
 
     private final SplitPane splitPane = new SplitPane();
     private final JabRefPreferences prefs = Globals.prefs;
     private final GlobalSearchBar globalSearchBar = new GlobalSearchBar(this);
-    private final JFXSnackbar statusLine = new JFXSnackbar(this);
+
     private final ProgressBar progressBar = new ProgressBar();
     private final FileHistoryMenu fileHistory = new FileHistoryMenu(prefs, this);
 
@@ -182,7 +177,7 @@ public class JabRefFrame extends BorderPane {
 
     public JabRefFrame(Stage mainStage) {
         this.mainStage = mainStage;
-        this.dialogService = new FXDialogService(mainStage);
+        this.dialogService = new FXDialogService(mainStage, this);
         init();
     }
 
@@ -962,16 +957,6 @@ public void addParserResult(ParserResult pr, boolean focusPanel) {
         }
     }
 
-    /**
-     * Displays the given message at the bottom of the main frame
-     *
-     * @deprecated use {@link DialogService#notify(String)} instead. However, do not remove this method, it's called from the dialogService
-     */
-    @Deprecated
-    public void output(final String message) {
-        DefaultTaskExecutor.runInJavaFXThread(() -> statusLine.fireEvent(new SnackbarEvent(new JFXSnackbarLayout(message), TOAST_MESSAGE_DISPLAY_TIME, null)));
-    }
-
     private void initActions() {
         /*
         openDatabaseOnlyActions.clear();
@@ -1279,7 +1264,7 @@ private boolean confirmClose(BasePanel panel) {
                     return true;
                 }
                 // The action was either canceled or unsuccessful.
-                output(Localization.lang("Unable to save library"));
+                dialogService.notify(Localization.lang("Unable to save library"));
             } catch (Throwable ex) {
                 LOGGER.error("A problem occurred when trying to save the file", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("Save library"), Localization.lang("Could not save file."), ex);
@@ -1321,7 +1306,7 @@ private void removeTab(BasePanel panel) {
             panel.cleanUp();
             tabbedPane.getTabs().remove(getTab(panel));
             setWindowTitle();
-            output(Localization.lang("Closed library") + '.');
+            dialogService.notify(Localization.lang("Closed library") + '.');
             // update tab titles
             updateAllTabTitles();
         });
diff --git a/src/main/java/org/jabref/gui/actions/CleanupAction.java b/src/main/java/org/jabref/gui/actions/CleanupAction.java
index f2251d45616..d79a8a62c4f 100644
--- a/src/main/java/org/jabref/gui/actions/CleanupAction.java
+++ b/src/main/java/org/jabref/gui/actions/CleanupAction.java
@@ -71,7 +71,7 @@ public void init() {
             isCanceled = true;
             return;
         }
-        panel.output(Localization.lang("Doing a cleanup for %0 entries...",
+        dialogService.notify(Localization.lang("Doing a cleanup for %0 entries...",
                 Integer.toString(panel.getSelectedEntries().size())));
     }
 
@@ -115,7 +115,7 @@ private void showResults() {
                 message = Localization.lang("%0 entries needed a clean up", Integer.toString(modifiedEntriesCount));
                 break;
         }
-        panel.output(message);
+        dialogService.notify(message);
     }
 
     private void cleanup(CleanupPreset cleanupPreset) {
diff --git a/src/main/java/org/jabref/gui/actions/CopyBibTeXKeyAndLinkAction.java b/src/main/java/org/jabref/gui/actions/CopyBibTeXKeyAndLinkAction.java
index 6f55af1e27b..49c8a5f46ec 100644
--- a/src/main/java/org/jabref/gui/actions/CopyBibTeXKeyAndLinkAction.java
+++ b/src/main/java/org/jabref/gui/actions/CopyBibTeXKeyAndLinkAction.java
@@ -36,7 +36,7 @@ public void action() throws Exception {
             List<BibEntry> entriesWithKey = entries.stream().filter(BibEntry::hasCiteKey).collect(Collectors.toList());
 
             if (entriesWithKey.isEmpty()) {
-                JabRefGUI.getMainFrame().output(Localization.lang("None of the selected entries have BibTeX keys."));
+                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("None of the selected entries have BibTeX keys."));
                 return;
             }
 
@@ -53,9 +53,9 @@ public void action() throws Exception {
             int toCopy = entries.size();
             if (copied == toCopy) {
                 // All entries had keys.
-                JabRefGUI.getMainFrame().output((entries.size() > 1 ? Localization.lang("Copied keys") : Localization.lang("Copied key")) + '.');
+                JabRefGUI.getMainFrame().getDialogService().notify((entries.size() > 1 ? Localization.lang("Copied keys") : Localization.lang("Copied key")) + '.');
             } else {
-                JabRefGUI.getMainFrame().output(Localization.lang("Warning: %0 out of %1 entries have undefined BibTeX key.",
+                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Warning: %0 out of %1 entries have undefined BibTeX key.",
                         Long.toString(toCopy - copied), Integer.toString(toCopy)));
             }
         }
diff --git a/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java b/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
index 51adf9ba8b3..e541cd58d5a 100644
--- a/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
+++ b/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
@@ -27,9 +27,9 @@ public void execute() {
         Optional<String> urlOptional = DOI.parse(identifier).map(DOI::getURIAsASCIIString);
         if (urlOptional.isPresent()) {
             Globals.clipboardManager.setContent(urlOptional.get());
-            JabRefGUI.getMainFrame().output(Localization.lang("The link has been copied to the clipboard."));
+            JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("The link has been copied to the clipboard."));
         } else {
-            JabRefGUI.getMainFrame().output(Localization.lang("Invalid DOI: '%0'.", identifier));
+            JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Invalid DOI: '%0'.", identifier));
         }
     }
 }
diff --git a/src/main/java/org/jabref/gui/actions/GenerateBibtexKeyAction.java b/src/main/java/org/jabref/gui/actions/GenerateBibtexKeyAction.java
index 90b61800215..744db49711c 100644
--- a/src/main/java/org/jabref/gui/actions/GenerateBibtexKeyAction.java
+++ b/src/main/java/org/jabref/gui/actions/GenerateBibtexKeyAction.java
@@ -33,7 +33,7 @@ public void init() {
                                                    Localization.lang("First select the entries you want keys to be generated for."));
             return;
         }
-        basePanel.output(formatOutputMessage(Localization.lang("Generating BibTeX key for"), entries.size()));
+        dialogService.notify(formatOutputMessage(Localization.lang("Generating BibTeX key for"), entries.size()));
     }
 
     public static boolean confirmOverwriteKeys(DialogService dialogService) {
@@ -87,7 +87,7 @@ private void generateKeys() {
         }
 
         basePanel.markBaseChanged();
-        basePanel.output(formatOutputMessage(Localization.lang("Generated BibTeX key for"), entries.size()));
+        dialogService.notify(formatOutputMessage(Localization.lang("Generated BibTeX key for"), entries.size()));
     }
 
     private String formatOutputMessage(String start, int count) {
diff --git a/src/main/java/org/jabref/gui/actions/LookupIdentifierAction.java b/src/main/java/org/jabref/gui/actions/LookupIdentifierAction.java
index f1f6e6f0846..a2d6c7372d9 100644
--- a/src/main/java/org/jabref/gui/actions/LookupIdentifierAction.java
+++ b/src/main/java/org/jabref/gui/actions/LookupIdentifierAction.java
@@ -12,6 +12,7 @@
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdFetcher;
 import org.jabref.logic.l10n.Localization;
@@ -39,7 +40,7 @@ public LookupIdentifierAction(JabRefFrame frame, IdFetcher<T> fetcher) {
     public void execute() {
         try {
             BackgroundTask.wrap(this::lookupIdentifiers)
-                          .onSuccess(frame::output)
+                          .onSuccess(frame.getDialogService()::notify)
                           .executeWith(Globals.TASK_EXECUTOR);
         } catch (Exception e) {
             LOGGER.error("Problem running ID Worker", e);
@@ -84,8 +85,9 @@ private String lookupIdentifiers() {
         int foundCount = 0;
         for (BibEntry bibEntry : bibEntries) {
             count++;
-            frame.output(Localization.lang("Looking up %0... - entry %1 out of %2 - found %3",
-                    fetcher.getIdentifierName(), Integer.toString(count), totalCount, Integer.toString(foundCount)));
+            final String statusMessage = Localization.lang("Looking up %0... - entry %1 out of %2 - found %3",
+                    fetcher.getIdentifierName(), Integer.toString(count), totalCount, Integer.toString(foundCount));
+            DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().notify(statusMessage));
             Optional<T> identifier = Optional.empty();
             try {
                 identifier = fetcher.findIdentifier(bibEntry);
@@ -97,8 +99,9 @@ private String lookupIdentifiers() {
                 if (fieldChange.isPresent()) {
                     namedCompound.addEdit(new UndoableFieldChange(fieldChange.get()));
                     foundCount++;
-                    frame.output(Localization.lang("Looking up %0... - entry %1 out of %2 - found %3",
-                            Integer.toString(count), totalCount, Integer.toString(foundCount)));
+                    final String nextStatusMessage = Localization.lang("Looking up %0... - entry %1 out of %2 - found %3",
+                            fetcher.getIdentifierName(), Integer.toString(count), totalCount, Integer.toString(foundCount));
+                    DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().notify(nextStatusMessage));
                 }
             }
         }
diff --git a/src/main/java/org/jabref/gui/actions/NewDatabaseAction.java b/src/main/java/org/jabref/gui/actions/NewDatabaseAction.java
index 90b2f8ced30..e00604e3a1b 100644
--- a/src/main/java/org/jabref/gui/actions/NewDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/actions/NewDatabaseAction.java
@@ -24,6 +24,6 @@ public void execute() {
         BibDatabaseContext bibDatabaseContext = new BibDatabaseContext(new Defaults(BibDatabaseMode.BIBTEX));
         bibDatabaseContext.setMode(mode);
         jabRefFrame.addTab(bibDatabaseContext, true);
-        jabRefFrame.output(Localization.lang("New %0 library created.", mode.getFormattedName()));
+        jabRefFrame.getDialogService().notify(Localization.lang("New %0 library created.", mode.getFormattedName()));
     }
 }
diff --git a/src/main/java/org/jabref/gui/actions/WriteXMPAction.java b/src/main/java/org/jabref/gui/actions/WriteXMPAction.java
index de4face8b53..67a1217a113 100644
--- a/src/main/java/org/jabref/gui/actions/WriteXMPAction.java
+++ b/src/main/java/org/jabref/gui/actions/WriteXMPAction.java
@@ -92,7 +92,7 @@ public void init() {
         }
         optionsDialog.open();
 
-        basePanel.output(Localization.lang("Writing XMP-metadata..."));
+        dialogService.notify(Localization.lang("Writing XMP-metadata..."));
     }
 
     private void writeXMP() {
@@ -162,7 +162,7 @@ private void writeXMP() {
             return;
         }
 
-        basePanel.output(Localization.lang("Finished writing XMP for %0 file (%1 skipped, %2 errors).",
+        dialogService.notify(Localization.lang("Finished writing XMP for %0 file (%1 skipped, %2 errors).",
                 String.valueOf(entriesChanged), String.valueOf(skipped), String.valueOf(errors)));
     }
 
diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
index aa7f9dd22fc..fbd9478789b 100644
--- a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
+++ b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -10,8 +10,6 @@
 import java.util.Optional;
 import java.util.regex.Pattern;
 
-import javax.swing.JOptionPane;
-
 import org.jabref.Globals;
 import org.jabref.JabRefGUI;
 import org.jabref.gui.desktop.os.DefaultDesktop;
@@ -201,12 +199,8 @@ public static void openBrowserShowPopup(String url) {
             String couldNotOpenBrowser = Localization.lang("Could not open browser.");
             String openManually = Localization.lang("Please open %0 manually.", url);
             String copiedToClipboard = Localization.lang("The link has been copied to the clipboard.");
-            JabRefGUI.getMainFrame().output(couldNotOpenBrowser);
-            JOptionPane.showMessageDialog(null,
-                                          couldNotOpenBrowser + "\n" + openManually + "\n" +
-                                                copiedToClipboard,
-                                          couldNotOpenBrowser,
-                                          JOptionPane.ERROR_MESSAGE);
+            JabRefGUI.getMainFrame().getDialogService().notify(couldNotOpenBrowser);
+            JabRefGUI.getMainFrame().getDialogService().showErrorDialogAndWait(couldNotOpenBrowser, couldNotOpenBrowser + "\n" + openManually + "\n" + copiedToClipboard);
         }
     }
 
@@ -239,7 +233,7 @@ public static void openConsole(File file) throws IOException {
                 // replace the placeholder if used
                 String commandLoggingText = command.replace("%DIR", absolutePath);
 
-                JabRefGUI.getMainFrame().output(Localization.lang("Executing command \"%0\"...", commandLoggingText));
+                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", commandLoggingText));
                 LOGGER.info("Executing command \"" + commandLoggingText + "\"...");
 
                 try {
@@ -247,11 +241,9 @@ public static void openConsole(File file) throws IOException {
                 } catch (IOException exception) {
                     LOGGER.error("Open console", exception);
 
-                    JOptionPane.showMessageDialog(null,
-                                                  Localization.lang("Error occured while executing the command \"%0\".", commandLoggingText),
-                                                  Localization.lang("Open console") + " - " + Localization.lang("Error"),
-                                                  JOptionPane.ERROR_MESSAGE);
-                    JabRefGUI.getMainFrame().output(null);
+                    JabRefGUI.getMainFrame().getDialogService().showErrorDialogAndWait(
+                            Localization.lang("Open console") + " - " + Localization.lang("Error",
+                            Localization.lang("Error occured while executing the command \"%0\".", commandLoggingText)));
                 }
             }
         }
diff --git a/src/main/java/org/jabref/gui/exporter/ExportCommand.java b/src/main/java/org/jabref/gui/exporter/ExportCommand.java
index 36bb095a027..77b3a8430de 100644
--- a/src/main/java/org/jabref/gui/exporter/ExportCommand.java
+++ b/src/main/java/org/jabref/gui/exporter/ExportCommand.java
@@ -113,14 +113,14 @@ private void export(Path file, FileChooser.ExtensionFilter selectedExtensionFilt
                             finEntries);
                     return null; // can not use BackgroundTask.wrap(Runnable) because Runnable.run() can't throw Exceptions
                 })
-                .onSuccess(x -> frame.output(Localization.lang("%0 export successful", format.getName())))
+                .onSuccess(x -> frame.getDialogService().notify(Localization.lang("%0 export successful", format.getName())))
                 .onFailure(this::handleError)
                 .executeWith(Globals.TASK_EXECUTOR);
     }
 
     private void handleError(Exception ex) {
         LOGGER.warn("Problem exporting", ex);
-        frame.output(Localization.lang("Could not save file."));
+        frame.getDialogService().notify(Localization.lang("Could not save file."));
         // Need to warn the user that saving failed!
         frame.getDialogService().showErrorDialogAndWait(Localization.lang("Save library"), Localization.lang("Could not save file."), ex);
     }
diff --git a/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java b/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
index 2148a0146c0..122b5baf610 100644
--- a/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
+++ b/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
@@ -53,7 +53,7 @@ public void execute() {
         }
 
         if (panel.getSelectedEntries().isEmpty()) {
-            panel.output(Localization.lang("This operation requires one or more entries to be selected."));
+            dialogService.notify(Localization.lang("This operation requires one or more entries to be selected."));
             return;
         }
 
@@ -123,7 +123,7 @@ private void setContentToClipboard(String content) {
         clipboardContent.putRtf(content);
         Globals.clipboardManager.setContent(clipboardContent);
 
-        panel.output(Localization.lang("Entries exported to clipboard") + ": " + entries.size());
+        dialogService.notify(Localization.lang("Entries exported to clipboard") + ": " + entries.size());
 
     }
 
diff --git a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
index b743b7fa199..db4a591b1ec 100644
--- a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
@@ -140,7 +140,7 @@ private boolean doSave() {
                 // Reset title of tab
                 frame.setTabTitle(panel, panel.getTabTitle(),
                                   panel.getBibDatabaseContext().getDatabaseFile().get().getAbsolutePath());
-                frame.output(Localization.lang("Saved library") + " '"
+                frame.getDialogService().notify(Localization.lang("Saved library") + " '"
                              + panel.getBibDatabaseContext().getDatabaseFile().get().getPath() + "'.");
                 frame.setWindowTitle();
                 frame.updateAllTabTitles();
@@ -158,7 +158,7 @@ private boolean doSave() {
 
     public boolean save() {
         if (panel.getBibDatabaseContext().getDatabasePath().isPresent()) {
-            panel.frame().output(Localization.lang("Saving library") + "...");
+            panel.frame().getDialogService().notify(Localization.lang("Saving library") + "...");
             panel.setSaving(true);
             return doSave();
         } else {
@@ -240,7 +240,7 @@ public void saveSelectedAsPlain() {
             try {
                 saveDatabase(path, true, prefs.getDefaultEncoding(), SavePreferences.DatabaseSaveType.PLAIN_BIBTEX);
                 frame.getFileHistory().newFile(path);
-                frame.output(Localization.lang("Saved selected to '%0'.", path.toString()));
+                frame.getDialogService().notify(Localization.lang("Saved selected to '%0'.", path.toString()));
             } catch (SaveException ex) {
                 LOGGER.error("A problem occurred when trying to save the file", ex);
                 frame.getDialogService().showErrorDialogAndWait(Localization.lang("Save library"), Localization.lang("Could not save file."), ex);
diff --git a/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java b/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
index 3874a503d16..adb6affcc4c 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
@@ -2,8 +2,6 @@
 
 import java.net.URL;
 import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 import java.util.concurrent.ConcurrentHashMap;
@@ -42,12 +40,6 @@ public FindFullTextAction(BasePanel basePanel) {
 
     @Override
     public void execute() {
-        BackgroundTask.wrap(this::findFullTexts)
-                      .onSuccess(this::downloadFullTexts)
-                      .executeWith(Globals.TASK_EXECUTOR);
-    }
-
-    private Map<Optional<URL>, BibEntry> findFullTexts() {
         if (!basePanel.getSelectedEntries().isEmpty()) {
             basePanel.output(Localization.lang("Looking for full text document..."));
         } else {
@@ -68,21 +60,24 @@ private Map<Optional<URL>, BibEntry> findFullTexts() {
 
             if (!confirmDownload) {
                 basePanel.output(Localization.lang("Operation canceled."));
-                return null;
+                return;
             }
         }
+        BackgroundTask.wrap(this::findFullTexts)
+                      .onSuccess(this::downloadFullTexts)
+                      .executeWith(Globals.TASK_EXECUTOR);
+    }
 
+    private Map<Optional<URL>, BibEntry> findFullTexts() {
         Map<Optional<URL>, BibEntry> downloads = new ConcurrentHashMap<>();
         for (BibEntry entry : basePanel.getSelectedEntries()) {
             FulltextFetchers fetchers = new FulltextFetchers(Globals.prefs.getImportFormatPreferences());
             downloads.put(fetchers.findFullTextPDF(entry), entry);
         }
-
         return downloads;
     }
 
     private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
-        List<Optional<URL>> finishedTasks = new ArrayList<>();
         for (Map.Entry<Optional<URL>, BibEntry> download : downloads.entrySet()) {
             BibEntry entry = download.getValue();
             Optional<URL> result = download.getKey();
@@ -94,20 +89,15 @@ private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
                     dialogService.showErrorDialogAndWait(Localization.lang("Directory not found"),
                             Localization.lang("Main file directory not set!") + " " + Localization.lang("Preferences")
                                     + " -> " + Localization.lang("File"));
-
                     return;
                 }
-
-                //Download full text
+                //Download and link full text
                 addLinkedFileFromURL(result.get(), entry);
+
             } else {
                 dialogService.notify(Localization.lang("No full text document found for entry %0.",
                         entry.getCiteKeyOptional().orElse(Localization.lang("undefined"))));
             }
-            finishedTasks.add(result);
-        }
-        for (Optional<URL> result : finishedTasks) {
-            downloads.remove(result);
         }
     }
 
@@ -119,7 +109,6 @@ private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
      * @param entry the entry "value"
      */
     private void addLinkedFileFromURL(URL url, BibEntry entry) {
-
         LinkedFile newLinkedFile = new LinkedFile(url, "");
 
         if (!entry.getFiles().contains(newLinkedFile)) {
diff --git a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileMenuItem.java b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileMenuItem.java
index a2ebcb02dae..e204ca6b761 100644
--- a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileMenuItem.java
+++ b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileMenuItem.java
@@ -58,12 +58,12 @@ public void actionPerformed(ActionEvent e) {
         boolean success = openLink();
         if (!success) {
             List<Path> searchedDirs = databaseContext.getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
-            frame.output(Localization.lang("Unable to open %0", link) + " " + Arrays.toString(searchedDirs.toArray()));
+            frame.getDialogService().notify(Localization.lang("Unable to open %0", link) + " " + Arrays.toString(searchedDirs.toArray()));
         }
     }
 
     private boolean openLink() {
-        frame.output(Localization.lang("External viewer called") + ".");
+        frame.getDialogService().notify(Localization.lang("External viewer called") + ".");
         try {
             Optional<ExternalFileType> type = fileType;
             if (!this.fileType.isPresent()) {
diff --git a/src/main/java/org/jabref/gui/filelist/AttachFileAction.java b/src/main/java/org/jabref/gui/filelist/AttachFileAction.java
index c36318ea60e..8ff43c37060 100644
--- a/src/main/java/org/jabref/gui/filelist/AttachFileAction.java
+++ b/src/main/java/org/jabref/gui/filelist/AttachFileAction.java
@@ -28,7 +28,7 @@ public AttachFileAction(BasePanel panel, DialogService dialogService) {
     @Override
     public void execute() {
         if (panel.getSelectedEntries().size() != 1) {
-            panel.output(Localization.lang("This operation requires exactly one item to be selected."));
+            dialogService.notify(Localization.lang("This operation requires exactly one item to be selected."));
             return;
         }
         BibEntry entry = panel.getSelectedEntries().get(0);
diff --git a/src/main/java/org/jabref/gui/importer/ImportAction.java b/src/main/java/org/jabref/gui/importer/ImportAction.java
index 99fa2b36f33..7a945fef1f8 100644
--- a/src/main/java/org/jabref/gui/importer/ImportAction.java
+++ b/src/main/java/org/jabref/gui/importer/ImportAction.java
@@ -15,6 +15,7 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.importer.ImportException;
 import org.jabref.logic.importer.ImportFormatReader;
@@ -95,11 +96,11 @@ private List<ImportFormatReader.UnknownFormatImport> doImport(List<Path> files)
             try {
                 if (!importer.isPresent()) {
                     // Unknown format:
-                    frame.output(Localization.lang("Importing in unknown format") + "...");
+                    DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().notify(Localization.lang("Importing in unknown format") + "..."));
                     // This import method never throws an IOException:
                     imports.add(Globals.IMPORT_FORMAT_READER.importUnknownFormat(filename, Globals.getFileUpdateMonitor()));
                 } else {
-                    frame.output(Localization.lang("Importing in %0 format", importer.get().getName()) + "...");
+                    DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().notify(Localization.lang("Importing in %0 format", importer.get().getName()) + "..."));
                     // Specific importer:
                     ParserResult pr = importer.get().importDatabase(filename, Globals.prefs.getDefaultEncoding());
                     imports.add(new ImportFormatReader.UnknownFormatImport(importer.get().getName(), pr));
diff --git a/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java b/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java
index 5231d0edede..a5f190f5de5 100644
--- a/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java
@@ -9,7 +9,6 @@
 import javax.swing.undo.CompoundEdit;
 
 import org.jabref.Globals;
-import org.jabref.JabRefExecutorService;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
@@ -18,6 +17,7 @@
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableInsertEntry;
 import org.jabref.gui.undo.UndoableInsertString;
+import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.importer.OpenDatabase;
 import org.jabref.logic.importer.ParserResult;
@@ -159,32 +159,31 @@ public void action() {
             }
             filesToOpen.addAll(chosen);
 
-            // Run the actual open in a thread to prevent the program locking until the file is loaded.
-            JabRefExecutorService.INSTANCE.execute(
-                    () -> openIt(dialog.importEntries(), dialog.importStrings(), dialog.importGroups(), dialog.importSelectorWords()));
-        }
-    }
+            if (filesToOpen.isEmpty()) {
+                return;
+            }
 
-    private void openIt(boolean importEntries, boolean importStrings, boolean importGroups,
-                        boolean importSelectorWords) {
-        if (filesToOpen.isEmpty()) {
-            return;
-        }
-        for (Path file : filesToOpen) {
-            try {
-                Globals.prefs.put(JabRefPreferences.WORKING_DIRECTORY, file.getParent().toString());
-                // Should this be done _after_ we know it was successfully opened?
-                ParserResult parserResult = OpenDatabase.loadDatabase(file.toFile(),
-                        Globals.prefs.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
-                AppendDatabaseAction.mergeFromBibtex(panel, parserResult, importEntries, importStrings, importGroups,
-                        importSelectorWords);
-                panel.output(Localization.lang("Imported from library") + " '" + file + "'");
-            } catch (IOException | KeyCollisionException ex) {
-                LOGGER.warn("Could not open database", ex);
-
-                dialogService.showErrorDialogAndWait(Localization.lang("Open library"), ex);
+            for (Path file : filesToOpen) {
+                // Run the actual open in a thread to prevent the program locking until the file is loaded.
+                BackgroundTask.wrap(() -> openIt(file, dialog.importEntries(), dialog.importStrings(), dialog.importGroups(), dialog.importSelectorWords()))
+                              .onSuccess(fileName -> dialogService.notify(Localization.lang("Imported from library") + " '" + fileName + "'"))
+                              .onFailure(exception -> {
+                                  LOGGER.warn("Could not open database", exception);
+                                  dialogService.showErrorDialogAndWait(Localization.lang("Open library"), exception);})
+                              .executeWith(Globals.TASK_EXECUTOR);;
             }
         }
     }
 
+    private String openIt(Path file, boolean importEntries, boolean importStrings, boolean importGroups,
+                        boolean importSelectorWords) throws IOException, KeyCollisionException {
+            Globals.prefs.put(JabRefPreferences.WORKING_DIRECTORY, file.getParent().toString());
+            // Should this be done _after_ we know it was successfully opened?
+            ParserResult parserResult = OpenDatabase.loadDatabase(file.toFile(),
+                    Globals.prefs.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
+            AppendDatabaseAction.mergeFromBibtex(panel, parserResult, importEntries, importStrings, importGroups,
+                    importSelectorWords);
+            return file.toString();
+    }
+
 }
diff --git a/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java b/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
index 67bd022cbc0..b8be7090041 100644
--- a/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
@@ -174,12 +174,12 @@ public void openFiles(List<Path> filesToOpen, boolean raisePanel) {
         // If no files are remaining to open, this could mean that a file was
         // already open. If so, we may have to raise the correct tab:
         else if (toRaise != null) {
-            frame.output(Localization.lang("File '%0' is already open.",
+            frame.getDialogService().notify(Localization.lang("File '%0' is already open.",
                     toRaise.getBibDatabaseContext().getDatabaseFile().get().getPath()));
             frame.showBasePanel(toRaise);
         }
 
-        frame.output(Localization.lang("Files opened") + ": " + (filesToOpen.size()));
+        frame.getDialogService().notify(Localization.lang("Files opened") + ": " + (filesToOpen.size()));
     }
 
     /**
@@ -190,7 +190,7 @@ private void openTheFile(Path file, boolean raisePanel) {
         if (Files.exists(file)) {
             Path fileToLoad = file.toAbsolutePath();
 
-            frame.output(Localization.lang("Opening") + ": '" + file + "'");
+            frame.getDialogService().notify(Localization.lang("Opening") + ": '" + file + "'");
 
             Globals.prefs.put(JabRefPreferences.WORKING_DIRECTORY, fileToLoad.getParent().toString());
 
@@ -239,7 +239,7 @@ private BasePanel addNewDatabase(ParserResult result, final Path file, boolean r
         }
 
         if (Objects.nonNull(file)) {
-            frame.output(Localization.lang("Opened library") + " '" + file.toString() + "' "
+            frame.getDialogService().notify(Localization.lang("Opened library") + " '" + file.toString() + "' "
                     + Localization.lang("with")
                     + " "
                     + database.getEntryCount() + " " + Localization.lang("entries") + ".");
diff --git a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java
index 77354393115..dba5c3352da 100644
--- a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java
+++ b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java
@@ -84,12 +84,12 @@ public StringProperty queryProperty() {
 
     public void search() {
         if (StringUtil.isBlank(getQuery())) {
-            frame.output(Localization.lang("Please enter a search string"));
+            frame.getDialogService().notify(Localization.lang("Please enter a search string"));
             return;
         }
 
         if (frame.getCurrentBasePanel() == null) {
-            frame.output(Localization.lang("Please open or start a new library before searching"));
+            frame.getDialogService().notify(Localization.lang("Please open or start a new library before searching"));
             return;
         }
 
diff --git a/src/main/java/org/jabref/gui/journals/AbbreviateAction.java b/src/main/java/org/jabref/gui/journals/AbbreviateAction.java
index 283905fb435..734074c74fe 100644
--- a/src/main/java/org/jabref/gui/journals/AbbreviateAction.java
+++ b/src/main/java/org/jabref/gui/journals/AbbreviateAction.java
@@ -37,6 +37,7 @@ public AbbreviateAction(BasePanel panel, boolean iso) {
 
     @Override
     public void action() {
+        panel.output(Localization.lang("Abbreviating..."));
         BackgroundTask.wrap(this::abbreviate)
                       .onSuccess(panel::output)
                       .executeWith(Globals.TASK_EXECUTOR);
@@ -44,8 +45,6 @@ public void action() {
     }
 
     private String abbreviate() {
-        panel.output(Localization.lang("Abbreviating..."));
-
         List<BibEntry> entries = panel.getSelectedEntries();
         UndoableAbbreviator undoableAbbreviator = new UndoableAbbreviator(
                 Globals.journalAbbreviationLoader.getRepository(Globals.prefs.getJournalAbbreviationPreferences()),
diff --git a/src/main/java/org/jabref/gui/journals/UnabbreviateAction.java b/src/main/java/org/jabref/gui/journals/UnabbreviateAction.java
index 770c996856a..7980beabdc0 100644
--- a/src/main/java/org/jabref/gui/journals/UnabbreviateAction.java
+++ b/src/main/java/org/jabref/gui/journals/UnabbreviateAction.java
@@ -24,14 +24,13 @@ public UnabbreviateAction(BasePanel panel) {
 
     @Override
     public void action() {
+        panel.output(Localization.lang("Unabbreviating..."));
         BackgroundTask.wrap(this::unabbreviate)
                       .onSuccess(panel::output)
                       .executeWith(Globals.TASK_EXECUTOR);
     }
 
     private String unabbreviate() {
-        panel.output(Localization.lang("Unabbreviating..."));
-
         List<BibEntry> entries = panel.getSelectedEntries(); // never null
 
         UndoableUnabbreviator undoableAbbreviator = new UndoableUnabbreviator(Globals.journalAbbreviationLoader
diff --git a/src/main/java/org/jabref/gui/logging/GuiAppender.java b/src/main/java/org/jabref/gui/logging/GuiAppender.java
index d6a6f25ebd6..4d5956b94c5 100644
--- a/src/main/java/org/jabref/gui/logging/GuiAppender.java
+++ b/src/main/java/org/jabref/gui/logging/GuiAppender.java
@@ -13,6 +13,7 @@
 import org.apache.logging.log4j.core.config.plugins.PluginAttribute;
 import org.apache.logging.log4j.core.config.plugins.PluginElement;
 import org.apache.logging.log4j.core.config.plugins.PluginFactory;
+import org.apache.logging.log4j.core.impl.MutableLogEvent;
 import org.apache.logging.log4j.core.layout.PatternLayout;
 
 @Plugin(name = "GuiAppender", category = "Core", elementType = "appender", printObject = true)
@@ -44,6 +45,9 @@ public static GuiAppender createAppender(@PluginAttribute("name") String name,
      */
     @Override
     public void append(LogEvent event) {
-        DefaultTaskExecutor.runInJavaFXThread(() -> LogMessages.getInstance().add(event));
+        // We need to make a copy as instances of LogEvent are reused by log4j
+        MutableLogEvent copy = new MutableLogEvent();
+        copy.initFrom(event);
+        DefaultTaskExecutor.runInJavaFXThread(() -> LogMessages.getInstance().add(copy));
     }
 }
diff --git a/src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java b/src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java
index 219c157fc53..94bc02ddc5b 100644
--- a/src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java
+++ b/src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java
@@ -48,7 +48,7 @@ public SharedDatabaseUIManager(JabRefFrame jabRefFrame) {
     @Subscribe
     public void listen(ConnectionLostEvent connectionLostEvent) {
 
-        jabRefFrame.output(Localization.lang("Connection lost."));
+        jabRefFrame.getDialogService().notify(Localization.lang("Connection lost."));
 
         ButtonType reconnect = new ButtonType(Localization.lang("Reconnect"), ButtonData.YES);
         ButtonType workOffline = new ButtonType(Localization.lang("Work offline"), ButtonData.NO);
@@ -69,7 +69,7 @@ public void listen(ConnectionLostEvent connectionLostEvent) {
             } else if (answer.get().equals(workOffline)) {
                 connectionLostEvent.getBibDatabaseContext().convertToLocalDatabase();
                 jabRefFrame.refreshTitleAndTabs();
-                jabRefFrame.output(Localization.lang("Working offline."));
+                jabRefFrame.getDialogService().notify(Localization.lang("Working offline."));
             }
         } else {
             jabRefFrame.closeCurrentTab();
@@ -79,7 +79,7 @@ public void listen(ConnectionLostEvent connectionLostEvent) {
     @Subscribe
     public void listen(UpdateRefusedEvent updateRefusedEvent) {
 
-        jabRefFrame.output(Localization.lang("Update refused."));
+        jabRefFrame.getDialogService().notify(Localization.lang("Update refused."));
 
         new MergeSharedEntryDialog(jabRefFrame, dbmsSynchronizer, updateRefusedEvent.getLocalBibEntry(),
                                    updateRefusedEvent.getSharedBibEntry(),
@@ -107,7 +107,6 @@ public void listen(SharedEntryNotPresentEvent event) {
      * Opens a new shared database tab with the given {@link DBMSConnectionProperties}.
      *
      * @param dbmsConnectionProperties Connection data
-     * @param raiseTab If <code>true</code> the new tab gets selected.
      * @return BasePanel which also used by {@link SaveDatabaseAction}
      */
     public BasePanel openNewSharedDatabaseTab(DBMSConnectionProperties dbmsConnectionProperties)
@@ -121,7 +120,7 @@ public BasePanel openNewSharedDatabaseTab(DBMSConnectionProperties dbmsConnectio
         dbmsSynchronizer = bibDatabaseContext.getDBMSSynchronizer();
         dbmsSynchronizer.openSharedDatabase(new DBMSConnection(dbmsConnectionProperties));
         dbmsSynchronizer.registerListener(this);
-        jabRefFrame.output(Localization.lang("Connection to %0 server established.", dbmsConnectionProperties.getType().toString()));
+        jabRefFrame.getDialogService().notify(Localization.lang("Connection to %0 server established.", dbmsConnectionProperties.getType().toString()));
         return jabRefFrame.addTab(bibDatabaseContext, true);
     }
 
@@ -150,6 +149,6 @@ public void openSharedDatabaseFromParserResult(ParserResult parserResult)
         dbmsSynchronizer.openSharedDatabase(new DBMSConnection(dbmsConnectionProperties));
         dbmsSynchronizer.registerListener(this);
         parserResult.setDatabaseContext(bibDatabaseContext);
-        jabRefFrame.output(Localization.lang("Connection to %0 server established.", dbmsConnectionProperties.getType().toString()));
+        jabRefFrame.getDialogService().notify(Localization.lang("Connection to %0 server established.", dbmsConnectionProperties.getType().toString()));
     }
 }
diff --git a/src/main/java/org/jabref/gui/specialfields/SpecialFieldAction.java b/src/main/java/org/jabref/gui/specialfields/SpecialFieldAction.java
index 7c5f1f0e217..db486945462 100644
--- a/src/main/java/org/jabref/gui/specialfields/SpecialFieldAction.java
+++ b/src/main/java/org/jabref/gui/specialfields/SpecialFieldAction.java
@@ -70,7 +70,7 @@ public void action() {
                 } else {
                     outText = getTextDone(specialField, value, Integer.toString(bes.size()));
                 }
-                frame.output(outText);
+                frame.getDialogService().notify(outText);
             } else {
                 // if user does not change anything with his action, we do not do anything either
                 // even no output message
diff --git a/src/main/java/org/jabref/gui/worker/SendAsEMailAction.java b/src/main/java/org/jabref/gui/worker/SendAsEMailAction.java
index 51b85ba2784..ee8b7eace9a 100644
--- a/src/main/java/org/jabref/gui/worker/SendAsEMailAction.java
+++ b/src/main/java/org/jabref/gui/worker/SendAsEMailAction.java
@@ -46,11 +46,11 @@ public SendAsEMailAction(JabRefFrame frame) {
     @Override
     public void action() {
         BackgroundTask.wrap(this::sendEmail)
-                      .onSuccess(frame::output)
+                      .onSuccess(frame.getDialogService()::notify)
                       .onFailure(e -> {
                           String message = Localization.lang("Error creating email");
                           LOGGER.warn(message, e);
-                          frame.output(message);
+                          frame.getDialogService().notify(message);
                       })
                       .executeWith(Globals.TASK_EXECUTOR);
     }
diff --git a/src/main/java/org/jabref/logic/logging/LogMessages.java b/src/main/java/org/jabref/logic/logging/LogMessages.java
index 06f10f1c3eb..053252b6e1f 100644
--- a/src/main/java/org/jabref/logic/logging/LogMessages.java
+++ b/src/main/java/org/jabref/logic/logging/LogMessages.java
@@ -4,7 +4,6 @@
 import javafx.collections.ObservableList;
 
 import org.apache.logging.log4j.core.LogEvent;
-import org.apache.logging.log4j.core.impl.MutableLogEvent;
 
 /**
  * This class is used for storing and archiving all message output of JabRef as log events.
@@ -28,10 +27,7 @@ public ObservableList<LogEvent> getMessages() {
     }
 
     public void add(LogEvent event) {
-        // We need to make a copy as instances of LogEvent are reused by log4j
-        MutableLogEvent copy = new MutableLogEvent();
-        copy.initFrom(event);
-        messages.add(copy);
+        messages.add(event);
     }
 
     public void clear() {

From 8095f46a6e21fa98c7445f2a77f707a679a41a3c Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Thu, 4 Apr 2019 12:48:59 +0200
Subject: [PATCH 157/184] Fix custom name formatters (#4848)

Fixes #3531.
---
 CHANGELOG.md                                  |  1 +
 .../org/jabref/logic/layout/LayoutEntry.java  | 30 ++++++-------------
 .../logic/layout/format/NameFormatter.java    |  1 -
 .../layout/format/NotFoundFormatter.java      |  2 --
 .../org/jabref/logic/layout/LayoutTest.java   | 16 +++++++++-
 5 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 60394941469..4ba983b0641 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -88,6 +88,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the default icon of a group was not colored correctly.
 - We fixed an issue where the first field in entry editor was not focused when adding a new entry. [#4024](https://github.com/JabRef/jabref/issues/4024)
 - We reworked the "Edit file" dialog to make it resizeable and improved the workflow for adding and editing files https://github.com/JabRef/jabref/issues/2970
+- We fixed an issue where custom name formatters were no longer found correctly. [#3531](https://github.com/JabRef/jabref/issues/3531)
 - We fixed an issue where the month was not shown in the preview https://github.com/JabRef/jabref/issues/3239.
 - Rewritten logic to detect a second jabref instance. [#4023](https://github.com/JabRef/jabref/issues/4023)
 - We fixed an issue where the "Convert to BibTeX-Cleanup" moved the content of the `file` field to the `pdf` field [#4120](https://github.com/JabRef/jabref/issues/4120)
diff --git a/src/main/java/org/jabref/logic/layout/LayoutEntry.java b/src/main/java/org/jabref/logic/layout/LayoutEntry.java
index 18927ef8cf5..cae756e3a22 100644
--- a/src/main/java/org/jabref/logic/layout/LayoutEntry.java
+++ b/src/main/java/org/jabref/logic/layout/LayoutEntry.java
@@ -391,8 +391,7 @@ private void doOptionField(String s) {
         }
     }
 
-    private LayoutFormatter getLayoutFormatterByName(String name) throws Exception {
-
+    private LayoutFormatter getLayoutFormatterByName(String name) {
         switch (name) {
             case "HTMLToLatexFormatter": // For backward compatibility
             case "HtmlToLatex":
@@ -481,8 +480,7 @@ private LayoutFormatter getLayoutFormatterByName(String name) throws Exception {
             case "Iso690NamesAuthors":
                 return new Iso690NamesAuthors();
             case "JournalAbbreviator":
-                return new JournalAbbreviator(prefs.getJournalAbbreviationLoader(),
-                        prefs.getJournalAbbreviationPreferences());
+                return new JournalAbbreviator(prefs.getJournalAbbreviationLoader(), prefs.getJournalAbbreviationPreferences());
             case "LastPage":
                 return new LastPage();
             case "FormatChars": // For backward compatibility
@@ -535,7 +533,7 @@ private LayoutFormatter getLayoutFormatterByName(String name) throws Exception {
             case "WrapFileLinks":
                 return new WrapFileLinks(prefs.getFileLinkPreferences());
             default:
-                return new NotFoundFormatter(name);
+                return null;
         }
     }
 
@@ -544,19 +542,13 @@ private LayoutFormatter getLayoutFormatterByName(String name) throws Exception {
      * string (in order of appearance).
      */
     private List<LayoutFormatter> getOptionalLayout(String formatterName) {
-
         List<List<String>> formatterStrings = parseMethodsCalls(formatterName);
-
         List<LayoutFormatter> results = new ArrayList<>(formatterStrings.size());
-
         Map<String, String> userNameFormatter = NameFormatter.getNameFormatters(prefs.getNameFormatterPreferences());
-
         for (List<String> strings : formatterStrings) {
-
             String nameFormatterName = strings.get(0).trim();
 
             // Check if this is a name formatter defined by this export filter:
-
             Optional<String> contents = prefs.getCustomExportNameFormatter(nameFormatterName);
             if (contents.isPresent()) {
                 NameFormatter nf = new NameFormatter();
@@ -566,22 +558,18 @@ private List<LayoutFormatter> getOptionalLayout(String formatterName) {
             }
 
             // Try to load from formatters in formatter folder
-            try {
-                LayoutFormatter f = getLayoutFormatterByName(nameFormatterName);
-                // If this formatter accepts an argument, check if we have one, and
-                // set it if so:
-                if ((f instanceof ParamLayoutFormatter) && (strings.size() >= 2)) {
-                    ((ParamLayoutFormatter) f).setArgument(strings.get(1));
+            LayoutFormatter formatter = getLayoutFormatterByName(nameFormatterName);
+            if (formatter != null) {
+                // If this formatter accepts an argument, check if we have one, and set it if so
+                if ((formatter instanceof ParamLayoutFormatter) && (strings.size() >= 2)) {
+                    ((ParamLayoutFormatter) formatter).setArgument(strings.get(1));
                 }
-                results.add(f);
+                results.add(formatter);
                 continue;
-            } catch (Exception ex) {
-                LOGGER.info("Problem with formatter", ex);
             }
 
             // Then check whether this is a user defined formatter
             String formatterParameter = userNameFormatter.get(nameFormatterName);
-
             if (formatterParameter != null) {
                 NameFormatter nf = new NameFormatter();
                 nf.setParameter(formatterParameter);
diff --git a/src/main/java/org/jabref/logic/layout/format/NameFormatter.java b/src/main/java/org/jabref/logic/layout/format/NameFormatter.java
index 8c70fad7ea2..e8830ad1c5b 100644
--- a/src/main/java/org/jabref/logic/layout/format/NameFormatter.java
+++ b/src/main/java/org/jabref/logic/layout/format/NameFormatter.java
@@ -124,7 +124,6 @@ private static String format(String toFormat, AuthorList al, String[] formats) {
     }
 
     public String format(String toFormat, String inParameters) {
-
         AuthorList al = AuthorList.parse(toFormat);
         String parameters;
 
diff --git a/src/main/java/org/jabref/logic/layout/format/NotFoundFormatter.java b/src/main/java/org/jabref/logic/layout/format/NotFoundFormatter.java
index 80596b88dcf..e53b71296d9 100644
--- a/src/main/java/org/jabref/logic/layout/format/NotFoundFormatter.java
+++ b/src/main/java/org/jabref/logic/layout/format/NotFoundFormatter.java
@@ -11,9 +11,7 @@ public class NotFoundFormatter implements LayoutFormatter {
 
     private final String notFound;
 
-
     public NotFoundFormatter(String notFound) {
-
         this.notFound = notFound;
     }
 
diff --git a/src/test/java/org/jabref/logic/layout/LayoutTest.java b/src/test/java/org/jabref/logic/layout/LayoutTest.java
index 06ec187f56b..34e04b157e3 100644
--- a/src/test/java/org/jabref/logic/layout/LayoutTest.java
+++ b/src/test/java/org/jabref/logic/layout/LayoutTest.java
@@ -6,6 +6,7 @@
 import java.util.Collections;
 
 import org.jabref.logic.layout.format.FileLinkPreferences;
+import org.jabref.logic.layout.format.NameFormatterPreferences;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.CustomEntryType;
@@ -98,8 +99,10 @@ void HTMLCharsWithDotlessIAndTiled() throws IOException {
                 layoutText);
     }
 
+    /**
+     * Test for http://discourse.jabref.org/t/the-wrapfilelinks-formatter/172 (the example in the help files)
+     */
     @Test
-        // Test for http://discourse.jabref.org/t/the-wrapfilelinks-formatter/172 (the example in the help files)
     void wrapFileLinksExpandFile() throws IOException {
         when(layoutFormatterPreferences.getFileLinkPreferences()).thenReturn(
                 new FileLinkPreferences(Collections.emptyList(), Collections.singletonList("src/test/resources/pdfs/")));
@@ -121,4 +124,15 @@ void expandCommandIfTerminatedByMinus() throws IOException {
 
         assertEquals("2-th ed.-", layoutText);
     }
+
+    @Test
+    void customNameFormatter() throws IOException {
+        when(layoutFormatterPreferences.getNameFormatterPreferences()).thenReturn(
+                new NameFormatterPreferences(Collections.singletonList("DCA"), Collections.singletonList("1@*@{ll}@@2@1..1@{ff}{ll}@2..2@ and {ff}{l}@@*@*@more")));
+        BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE).withField("author", "Joe Doe and Mary Jane");
+
+        String layoutText = layout("\\begin{author}\\format[DCA]{\\author}\\end{author}", entry);
+
+        assertEquals("JoeDoe and MaryJ", layoutText);
+    }
 }

From 42d7b63f1de0615db0b2107a5c01f8c8f3666278 Mon Sep 17 00:00:00 2001
From: Atul Kaushik <atul.kaushikim@gmail.com>
Date: Thu, 4 Apr 2019 16:35:24 +0530
Subject: [PATCH 158/184] Improved and Added Documentation (#4803)

---
 src/main/java/org/jabref/JabRefException.java | 2 +-
 src/main/java/org/jabref/JabRefMain.java      | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/jabref/JabRefException.java b/src/main/java/org/jabref/JabRefException.java
index 0c312fc10df..a1dd034d89e 100644
--- a/src/main/java/org/jabref/JabRefException.java
+++ b/src/main/java/org/jabref/JabRefException.java
@@ -33,7 +33,7 @@ public JabRefException(Throwable cause) {
     @Override
     public String getLocalizedMessage() {
         if (localizedMessage == null) {
-            LOGGER.debug("No localized message exception message defined. Falling back to getMessage().");
+            LOGGER.debug("No localized exception message defined. Falling back to getMessage().");
             return getMessage();
         } else {
             return localizedMessage;
diff --git a/src/main/java/org/jabref/JabRefMain.java b/src/main/java/org/jabref/JabRefMain.java
index 7c6f3d78f49..62758e9c9f0 100644
--- a/src/main/java/org/jabref/JabRefMain.java
+++ b/src/main/java/org/jabref/JabRefMain.java
@@ -88,11 +88,11 @@ public void stop() {
     /**
      * Tests if we are running an acceptable Java and terminates JabRef when we are sure the version is not supported.
      * This test uses the requirements for the Java version as specified in <code>gradle.build</code>. It is possible to
-     * define a minimum version including the built number and to indicate whether Java 9 can be use (which it currently
+     * define a minimum version including the built number and to indicate whether Java 9 can be used (which it currently
      * can't). It tries to compare this version number to the version of the currently running JVM. The check is
      * optimistic and will rather return true even if we could not exactly determine the version.
      * <p>
-     * Note: Users with an very old version like 1.6 will not profit from this since class versions are incompatible and
+     * Note: Users with a very old version like 1.6 will not profit from this since class versions are incompatible and
      * JabRef won't even start. Currently, JabRef won't start with Java 9 either, but the warning that it cannot be used
      * with this version is helpful anyway to prevent users to update from an old 1.8 directly to version 9. Additionally,
      * we soon might have a JabRef that does start with Java 9 but is not perfectly compatible. Therefore, we should leave
@@ -163,7 +163,7 @@ private static void applyPreferences(JabRefPreferences preferences) {
         // Read list(s) of journal names and abbreviations
         Globals.journalAbbreviationLoader = new JournalAbbreviationLoader();
 
-        /* Build list of Import and Export formats */
+        // Build list of Import and Export formats
         Globals.IMPORT_FORMAT_READER.resetImportFormats(Globals.prefs.getImportFormatPreferences(),
                                                         Globals.prefs.getXMPPreferences(), Globals.getFileUpdateMonitor());
         EntryTypes.loadCustomEntryTypes(preferences.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
@@ -173,7 +173,7 @@ private static void applyPreferences(JabRefPreferences preferences) {
         // Initialize protected terms loader
         Globals.protectedTermsLoader = new ProtectedTermsLoader(Globals.prefs.getProtectedTermsPreferences());
 
-        // override used newline character with the one stored in the preferences
+        // Override used newline character with the one stored in the preferences
         // The preferences return the system newline character sequence as default
         OS.NEWLINE = Globals.prefs.get(JabRefPreferences.NEWLINE);
     }

From 7db6e7c4d85e075829d7de1a58d585d76d5da303 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2019 08:21:32 +0200
Subject: [PATCH 159/184] Bump mockito-core from 2.25.1 to 2.26.0 (#4849)

Bumps [mockito-core](https://github.com/mockito/mockito) from 2.25.1 to 2.26.0.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v2.25.1...v2.26.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 261a39e8223..c75f020e690 100644
--- a/build.gradle
+++ b/build.gradle
@@ -167,7 +167,7 @@ dependencies {
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
-    testCompile 'org.mockito:mockito-core:2.25.1'
+    testCompile 'org.mockito:mockito-core:2.26.0'
     testCompile 'com.github.tomakehurst:wiremock:2.22.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'

From ca504d90863557350dde381203ff3b79f556f325 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2019 08:22:00 +0200
Subject: [PATCH 160/184] Bump jurt from 5.4.2 to 6.2.2 (#4850)

Bumps jurt from 5.4.2 to 6.2.2.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index c75f020e690..684c9eae541 100644
--- a/build.gradle
+++ b/build.gradle
@@ -107,7 +107,7 @@ dependencies {
     compile 'commons-cli:commons-cli:1.4'
 
     compile "org.libreoffice:juh:5.4.2"
-    compile "org.libreoffice:jurt:5.4.2"
+    compile "org.libreoffice:jurt:6.2.2"
     compile "org.libreoffice:ridl:5.4.2"
     compile "org.libreoffice:unoil:5.4.2"
 

From 99cacc46f9ceb8fafa507ebc9b0efadfdeee4fb0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2019 08:22:22 +0200
Subject: [PATCH 161/184] Bump unoil from 5.4.2 to 6.2.2 (#4852)

Bumps unoil from 5.4.2 to 6.2.2.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 684c9eae541..30b4f47ccdd 100644
--- a/build.gradle
+++ b/build.gradle
@@ -109,7 +109,7 @@ dependencies {
     compile "org.libreoffice:juh:5.4.2"
     compile "org.libreoffice:jurt:6.2.2"
     compile "org.libreoffice:ridl:5.4.2"
-    compile "org.libreoffice:unoil:5.4.2"
+    compile "org.libreoffice:unoil:6.2.2"
 
     compile 'io.github.java-diff-utils:java-diff-utils:4.0'
     compile 'info.debatty:java-string-similarity:1.1.0'

From 44b74ea8b6764cc201af41293609bbec9e2658cd Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2019 14:23:23 +0200
Subject: [PATCH 162/184] Bump ridl from 5.4.2 to 6.2.2 (#4853)

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 30b4f47ccdd..3bd4bc0cd75 100644
--- a/build.gradle
+++ b/build.gradle
@@ -108,7 +108,7 @@ dependencies {
 
     compile "org.libreoffice:juh:5.4.2"
     compile "org.libreoffice:jurt:6.2.2"
-    compile "org.libreoffice:ridl:5.4.2"
+    compile "org.libreoffice:ridl:6.2.2"
     compile "org.libreoffice:unoil:6.2.2"
 
     compile 'io.github.java-diff-utils:java-diff-utils:4.0'

From 7f7d81ab3e79548f3054c9d94af4dff49d21fe39 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2019 14:24:06 +0200
Subject: [PATCH 163/184] Bump juh from 5.4.2 to 6.2.2 (#4851)

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 3bd4bc0cd75..8a6385b8e6e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -106,7 +106,7 @@ dependencies {
 
     compile 'commons-cli:commons-cli:1.4'
 
-    compile "org.libreoffice:juh:5.4.2"
+    compile "org.libreoffice:juh:6.2.2"
     compile "org.libreoffice:jurt:6.2.2"
     compile "org.libreoffice:ridl:6.2.2"
     compile "org.libreoffice:unoil:6.2.2"

From 17bfe91cd5a87f3c0f7299b86686bde0075b2fc4 Mon Sep 17 00:00:00 2001
From: Abraham Polk <abepolk@gmail.com>
Date: Fri, 5 Apr 2019 10:40:30 -0400
Subject: [PATCH 164/184] QuotedStringTokenizer now does not unquote (#4830)

* QuotedStringTokenizer now does not unquote

* Unquote to fix test failures

* Add javadoc to nextToken
---
 .../jabref/logic/importer/util/GroupsParser.java | 16 ++++++++--------
 .../util/strings/QuotedStringTokenizer.java      |  5 +++++
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
index f7f8dc27cdb..dd25ce3dc7a 100644
--- a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
+++ b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
@@ -169,8 +169,8 @@ private static AbstractGroup automaticKeywordGroupFromString(String string) {
         String name = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         GroupHierarchyType context = GroupHierarchyType.getByNumberOrDefault(Integer.parseInt(tok.nextToken()));
         String field = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
-        Character delimiter = tok.nextToken().charAt(0);
-        Character hierarchicalDelimiter = tok.nextToken().charAt(0);
+        Character delimiter = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR).charAt(0);
+        Character hierarchicalDelimiter = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR).charAt(0);
         AutomaticKeywordGroup newGroup = new AutomaticKeywordGroup(name, context, field, delimiter, hierarchicalDelimiter);
         addGroupDetails(tok, newGroup);
         return newGroup;
@@ -212,7 +212,7 @@ private static ExplicitGroup explicitGroupFromString(String input, Character key
         QuotedStringTokenizer tok = new QuotedStringTokenizer(input.substring(MetadataSerializationConfiguration.EXPLICIT_GROUP_ID.length()),
                 MetadataSerializationConfiguration.GROUP_UNIT_SEPARATOR, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
 
-        String name = tok.nextToken();
+        String name = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         try {
             int context = Integer.parseInt(tok.nextToken());
             ExplicitGroup newGroup = new ExplicitGroup(name, GroupHierarchyType.getByNumberOrDefault(context), keywordSeparator);
@@ -230,7 +230,7 @@ private static ExplicitGroup legacyExplicitGroupFromString(String input, Charact
         QuotedStringTokenizer tok = new QuotedStringTokenizer(input.substring(MetadataSerializationConfiguration.LEGACY_EXPLICIT_GROUP_ID.length()),
                 MetadataSerializationConfiguration.GROUP_UNIT_SEPARATOR, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
 
-        String name = tok.nextToken();
+        String name = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         try {
             int context = Integer.parseInt(tok.nextToken());
             ExplicitGroup newGroup = new ExplicitGroup(name, GroupHierarchyType.getByNumberOrDefault(context), keywordSeparator);
@@ -274,15 +274,15 @@ private static AbstractGroup searchGroupFromString(String s) {
         QuotedStringTokenizer tok = new QuotedStringTokenizer(s.substring(MetadataSerializationConfiguration.SEARCH_GROUP_ID.length()),
                 MetadataSerializationConfiguration.GROUP_UNIT_SEPARATOR, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
 
-        String name = tok.nextToken();
+        String name = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         int context = Integer.parseInt(tok.nextToken());
-        String expression = tok.nextToken();
+        String expression = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         boolean caseSensitive = Integer.parseInt(tok.nextToken()) == 1;
         boolean regExp = Integer.parseInt(tok.nextToken()) == 1;
         // version 0 contained 4 additional booleans to specify search
         // fields; these are ignored now, all fields are always searched
-        return new SearchGroup(StringUtil.unquote(name, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR),
-                GroupHierarchyType.getByNumberOrDefault(context), StringUtil.unquote(expression, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR), caseSensitive, regExp
+        return new SearchGroup(name,
+                GroupHierarchyType.getByNumberOrDefault(context), expression, caseSensitive, regExp
         );
     }
 
diff --git a/src/main/java/org/jabref/logic/util/strings/QuotedStringTokenizer.java b/src/main/java/org/jabref/logic/util/strings/QuotedStringTokenizer.java
index 720d6fe12e2..8c27e745dd4 100644
--- a/src/main/java/org/jabref/logic/util/strings/QuotedStringTokenizer.java
+++ b/src/main/java/org/jabref/logic/util/strings/QuotedStringTokenizer.java
@@ -34,6 +34,10 @@ public QuotedStringTokenizer(String content, String delimiters, char quoteCharac
         }
     }
 
+    /**
+     * @return the next token from the content string, ending at the next
+     * unquoted delimiter. Does not unquote the string itself.
+     */
     public String nextToken() {
         char c;
         StringBuilder stringBuilder = new StringBuilder();
@@ -41,6 +45,7 @@ public String nextToken() {
             c = content.charAt(index);
             if (c == quoteChar) { // next is quoted
                 ++index;
+                stringBuilder.append(c);
                 if (index < contentLength) {
                     stringBuilder.append(content.charAt(index));
                     // ignore for delimiter search!

From 38e162df42fddc6b317ea550d538591030b945a9 Mon Sep 17 00:00:00 2001
From: Robin <robin.lichtenthaeler@web.de>
Date: Fri, 5 Apr 2019 19:07:53 +0200
Subject: [PATCH 165/184] removed default constructor of FXDialogService
 (#4847)

* removed default constructor of FXDialogService

* Revert "removed default constructor of FXDialogService"

This reverts commit 4c964ca602a9e4b9081e8273e03277c068da2c4c.

* regained injection and splitted jabrefframe creation and init to hav dialogservice ready

* replaced JabRegGUI.mainFrame with mainFrame
---
 src/main/java/org/jabref/JabRefGUI.java       | 25 ++++++++-----------
 .../java/org/jabref/gui/DefaultInjector.java  |  3 ++-
 .../java/org/jabref/gui/FXDialogService.java  | 13 ----------
 src/main/java/org/jabref/gui/JabRefFrame.java |  3 +--
 .../gui/collab/EntryAddChangeViewModel.java   |  4 +--
 .../collab/EntryDeleteChangeViewModel.java    |  4 +--
 .../ExternalFileTypeEntryEditor.java          |  4 +--
 .../jabref/gui/entryeditor/SourceTabTest.java |  4 +--
 8 files changed, 22 insertions(+), 38 deletions(-)

diff --git a/src/main/java/org/jabref/JabRefGUI.java b/src/main/java/org/jabref/JabRefGUI.java
index 203dcf03386..66fe3694ffa 100644
--- a/src/main/java/org/jabref/JabRefGUI.java
+++ b/src/main/java/org/jabref/JabRefGUI.java
@@ -10,8 +10,6 @@
 import javafx.stage.Stage;
 
 import org.jabref.gui.BasePanel;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.FXDialogService;
 import org.jabref.gui.GUIGlobals;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.dialogs.BackupUIManager;
@@ -43,14 +41,13 @@ public class JabRefGUI {
     private final boolean isBlank;
     private final List<ParserResult> failed = new ArrayList<>();
     private final List<ParserResult> toOpenTab = new ArrayList<>();
-    private final DialogService dialogService;
 
     private final String focusedFile;
 
     public JabRefGUI(Stage mainStage, List<ParserResult> argsDatabases, boolean isBlank) {
         this.bibDatabases = argsDatabases;
         this.isBlank = isBlank;
-        this.dialogService = new FXDialogService(mainStage);
+        mainFrame = new JabRefFrame(mainStage);
 
         // passed file (we take the first one) should be focused
         focusedFile = argsDatabases.stream()
@@ -60,7 +57,7 @@ public JabRefGUI(Stage mainStage, List<ParserResult> argsDatabases, boolean isBl
                                     .orElse(Globals.prefs.get(JabRefPreferences.LAST_FOCUSED));
 
         openWindow(mainStage);
-        new VersionWorker(Globals.BUILD_INFO.getVersion(), Globals.prefs.getVersionPreferences().getIgnoredVersion(), JabRefGUI.getMainFrame().getDialogService(), Globals.TASK_EXECUTOR)
+        new VersionWorker(Globals.BUILD_INFO.getVersion(), Globals.prefs.getVersionPreferences().getIgnoredVersion(), mainFrame.getDialogService(), Globals.TASK_EXECUTOR)
                 .checkForNewVersionAsync(false);
     }
 
@@ -75,7 +72,7 @@ private void openWindow(Stage mainStage) {
         GUIGlobals.init();
 
         LOGGER.debug("Initializing frame");
-        JabRefGUI.mainFrame = new JabRefFrame(mainStage);
+        mainFrame.init();
 
         // Add all bibDatabases databases to the frame:
         boolean first = false;
@@ -99,7 +96,7 @@ private void openWindow(Stage mainStage) {
                         pr.getDatabase().clearSharedDatabaseID();
 
                         LOGGER.error("Connection error", e);
-                        dialogService.showErrorDialogAndWait(
+                        mainFrame.getDialogService().showErrorDialogAndWait(
                                 Localization.lang("Connection error"),
                                 Localization.lang("A local copy will be opened."),
                                 e);
@@ -110,7 +107,7 @@ private void openWindow(Stage mainStage) {
                     // add them to the list
                     toOpenTab.add(pr);
                 } else {
-                    JabRefGUI.getMainFrame().addParserResult(pr, first);
+                    mainFrame.addParserResult(pr, first);
                     first = false;
                 }
             }
@@ -118,7 +115,7 @@ private void openWindow(Stage mainStage) {
 
         // finally add things to the currently opened tab
         for (ParserResult pr : toOpenTab) {
-            JabRefGUI.getMainFrame().addParserResult(pr, first);
+            mainFrame.addParserResult(pr, first);
             first = false;
         }
 
@@ -158,14 +155,14 @@ private void openWindow(Stage mainStage) {
             String message = Localization.lang("Error opening file '%0'.", pr.getFile().get().getName()) + "\n"
                     + pr.getErrorMessage();
 
-            dialogService.showErrorDialogAndWait(Localization.lang("Error opening file"), message);
+            mainFrame.getDialogService().showErrorDialogAndWait(Localization.lang("Error opening file"), message);
 
         }
 
         // Display warnings, if any
         int tabNumber = 0;
         for (ParserResult pr : bibDatabases) {
-            ParserResultWarningDialog.showParserResultWarningDialog(pr, JabRefGUI.getMainFrame(), tabNumber++);
+            ParserResultWarningDialog.showParserResultWarningDialog(pr, mainFrame, tabNumber++);
         }
 
         // After adding the databases, go through each and see if
@@ -177,9 +174,9 @@ private void openWindow(Stage mainStage) {
         // This is because importToOpen might have been used, which adds to
         // loadedDatabases, but not to getBasePanelCount()
 
-        for (int i = 0; (i < bibDatabases.size()) && (i < JabRefGUI.getMainFrame().getBasePanelCount()); i++) {
+        for (int i = 0; (i < bibDatabases.size()) && (i < mainFrame.getBasePanelCount()); i++) {
             ParserResult pr = bibDatabases.get(i);
-            BasePanel panel = JabRefGUI.getMainFrame().getBasePanelAt(i);
+            BasePanel panel = mainFrame.getBasePanelAt(i);
             OpenDatabaseAction.performPostOpenActions(panel, pr);
         }
 
@@ -209,7 +206,7 @@ private void openLastEditedDatabases() {
             }
 
             if (BackupManager.checkForBackupFile(dbFile.toPath())) {
-                BackupUIManager.showRestoreBackupDialog(dialogService, dbFile.toPath());
+                BackupUIManager.showRestoreBackupDialog(mainFrame.getDialogService(), dbFile.toPath());
             }
 
             ParserResult parsedDatabase = OpenDatabase.loadDatabase(fileName,
diff --git a/src/main/java/org/jabref/gui/DefaultInjector.java b/src/main/java/org/jabref/gui/DefaultInjector.java
index ee7c8c05839..ed9963b55c5 100644
--- a/src/main/java/org/jabref/gui/DefaultInjector.java
+++ b/src/main/java/org/jabref/gui/DefaultInjector.java
@@ -5,6 +5,7 @@
 import javax.swing.undo.UndoManager;
 
 import org.jabref.Globals;
+import org.jabref.JabRefGUI;
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
@@ -28,7 +29,7 @@ public class DefaultInjector implements PresenterFactory {
      */
     private static Object createDependency(Class<?> clazz) {
         if (clazz == DialogService.class) {
-            return new FXDialogService();
+            return JabRefGUI.getMainFrame().getDialogService();
         } else if (clazz == TaskExecutor.class) {
             return Globals.TASK_EXECUTOR;
         } else if (clazz == PreferencesService.class) {
diff --git a/src/main/java/org/jabref/gui/FXDialogService.java b/src/main/java/org/jabref/gui/FXDialogService.java
index 2fe537a30a1..579b4de8bdd 100644
--- a/src/main/java/org/jabref/gui/FXDialogService.java
+++ b/src/main/java/org/jabref/gui/FXDialogService.java
@@ -63,19 +63,6 @@ public class FXDialogService implements DialogService {
     private final Window mainWindow;
     private final JFXSnackbar statusLine;
 
-    /**
-     * @deprecated try not to initialize a new dialog service but reuse the one constructed in {@link org.jabref.gui.JabRefFrame}.
-     */
-    @Deprecated
-    public FXDialogService() {
-        this(null);
-    }
-
-    public FXDialogService(Window mainWindow) {
-        this.mainWindow = mainWindow;
-        this.statusLine = new JFXSnackbar();
-    }
-
     public FXDialogService(Window mainWindow, Pane mainPane) {
         this.mainWindow = mainWindow;
         this.statusLine = new JFXSnackbar(mainPane);
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 71e75d1c54d..8ec31a46d11 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -178,7 +178,6 @@ public class JabRefFrame extends BorderPane {
     public JabRefFrame(Stage mainStage) {
         this.mainStage = mainStage;
         this.dialogService = new FXDialogService(mainStage, this);
-        init();
     }
 
     /**
@@ -204,7 +203,7 @@ private static void setEnabled(List<Object> list, boolean enabled) {
         }
     }
 
-    private void init() {
+    public void init() {
         sidePaneManager = new SidePaneManager(Globals.prefs, this);
         sidePane = sidePaneManager.getPane();
 
diff --git a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
index c5849decfef..a84904534bb 100644
--- a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
@@ -3,7 +3,7 @@
 import javafx.scene.Node;
 
 import org.jabref.Globals;
-import org.jabref.gui.FXDialogService;
+import org.jabref.JabRefGUI;
 import org.jabref.gui.PreviewPanel;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
@@ -29,7 +29,7 @@ public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
 
     @Override
     public Node description() {
-        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), JabRefGUI.getMainFrame().getDialogService(), ExternalFileTypes.getInstance());
         previewPanel.setEntry(diskEntry);
         return previewPanel;
     }
diff --git a/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
index e4b658036a0..3efe55cb530 100644
--- a/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
@@ -3,7 +3,7 @@
 import javafx.scene.Node;
 
 import org.jabref.Globals;
-import org.jabref.gui.FXDialogService;
+import org.jabref.JabRefGUI;
 import org.jabref.gui.PreviewPanel;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
@@ -46,7 +46,7 @@ public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
 
     @Override
     public Node description() {
-        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), JabRefGUI.getMainFrame().getDialogService(), ExternalFileTypes.getInstance());
         previewPanel.setEntry(memEntry);
         return previewPanel;
     }
diff --git a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java
index e620e69e84b..676868ac898 100644
--- a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java
+++ b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java
@@ -20,8 +20,8 @@
 import javax.swing.event.DocumentListener;
 
 import org.jabref.Globals;
+import org.jabref.JabRefGUI;
 import org.jabref.gui.DialogService;
-import org.jabref.gui.FXDialogService;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.FileDialogConfiguration;
@@ -62,7 +62,7 @@ public class ExternalFileTypeEntryEditor {
 
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
                 .withInitialDirectory(Paths.get(appDir)).build();
-        DialogService ds = new FXDialogService();
+        DialogService ds = JabRefGUI.getMainFrame().getDialogService();
 
         Optional<Path> path = DefaultTaskExecutor
                 .runInJavaFXThread(() -> ds.showFileOpenDialog(fileDialogConfiguration));
diff --git a/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java b/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java
index 51a27e3b70a..c3f50e3c853 100644
--- a/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java
+++ b/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java
@@ -6,7 +6,7 @@
 import javafx.scene.control.TabPane;
 import javafx.stage.Stage;
 
-import org.jabref.gui.FXDialogService;
+import org.jabref.gui.DialogService;
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.logic.bibtex.LatexFieldFormatterPreferences;
 import org.jabref.logic.importer.ImportFormatPreferences;
@@ -38,7 +38,7 @@ public class SourceTabTest {
     public void onStart(Stage stage) {
         area = new CodeArea();
         area.appendText("some example\n text to go here\n across a couple of \n lines....");
-        sourceTab = new SourceTab(new BibDatabaseContext(), new CountingUndoManager(), new LatexFieldFormatterPreferences(), mock(ImportFormatPreferences.class), new DummyFileUpdateMonitor(), new FXDialogService());
+        sourceTab = new SourceTab(new BibDatabaseContext(), new CountingUndoManager(), new LatexFieldFormatterPreferences(), mock(ImportFormatPreferences.class), new DummyFileUpdateMonitor(), mock(DialogService.class));
         pane = new TabPane(
                 new Tab("main area", area),
                 new Tab("other tab", new Label("some text")),

From 8fb663e477cb357e1faf3491c180982d17451fcb Mon Sep 17 00:00:00 2001
From: Harinda Samarasekara <harindaburndown@gmail.com>
Date: Sun, 7 Apr 2019 20:11:46 +0530
Subject: [PATCH 166/184] Fixed group creation with default settings (#4801)

* Fix for the issue - #4783 Group creation not possible anymore with default settings

* Changed the position of the listeners and onaction replaced with changelistener

* Removed changelog entry

* Fix for issue 4783 - Simplified listeners in to lambdas

* Update GroupDialog.java
---
 src/main/java/org/jabref/gui/groups/GroupDialog.java | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
index b40755e97e4..9fc080c8749 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDialog.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -351,6 +351,10 @@ groupName, getContext(),
             return null;
         });
 
+        nameField.textProperty().addListener((observable, oldValue, newValue) -> updateComponents());
+        keywordGroupSearchTerm.textProperty().addListener((observable, oldValue, newValue) -> updateComponents());
+        searchGroupSearchExpression.textProperty().addListener((observable, oldValue, newValue) -> updateComponents());
+
         EventHandler<ActionEvent> actionHandler = (ActionEvent e) -> updateComponents();
         nameField.setOnAction(actionHandler);
         descriptionField.setOnAction(actionHandler);

From e26d9ab9a7e47b2818c8eafd2e08de5808d6ce98 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Sun, 7 Apr 2019 20:35:26 +0200
Subject: [PATCH 167/184] Add author normalizer for medline import (#4863)

* Add author normalizer for medline import

Author names from medline lack the dot by Abbrevatieed authors
e.g. Lahiru S instead of Lahuri S.

Fix tests
Fixes #4345

* Add changelog entry
---
 CHANGELOG.md                                                | 2 ++
 .../org/jabref/logic/importer/fetcher/MedlineFetcher.java   | 2 ++
 .../jabref/logic/importer/fetcher/MedlineFetcherTest.java   | 6 +++---
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4ba983b0641..2d7c0f75166 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -61,6 +61,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
 - We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
 - We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
+- The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
+
 
 ### Fixed
 - We fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries [#3112](https://github.com/JabRef/jabref/issues/3112)
diff --git a/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java b/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java
index 0b8ace85d7d..7fbe0f809ac 100644
--- a/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java
+++ b/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java
@@ -21,6 +21,7 @@
 
 import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
 import org.jabref.logic.formatter.bibtexfields.NormalizeMonthFormatter;
+import org.jabref.logic.formatter.bibtexfields.NormalizeNamesFormatter;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedParserFetcher;
@@ -153,6 +154,7 @@ public void doPostCleanup(BibEntry entry) {
         new FieldFormatterCleanup("copyright", new ClearFormatter()).cleanup(entry);
 
         new FieldFormatterCleanup(FieldName.MONTH, new NormalizeMonthFormatter()).cleanup(entry);
+        new FieldFormatterCleanup(FieldName.AUTHOR, new NormalizeNamesFormatter()).cleanup(entry);
     }
 
     @Override
diff --git a/src/test/java/org/jabref/logic/importer/fetcher/MedlineFetcherTest.java b/src/test/java/org/jabref/logic/importer/fetcher/MedlineFetcherTest.java
index 54e7ac3944a..bbfa9a6ee8a 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/MedlineFetcherTest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/MedlineFetcherTest.java
@@ -27,7 +27,7 @@ public void setUp() {
 
         entryWijedasa = new BibEntry();
         entryWijedasa.setType(BiblatexEntryTypes.ARTICLE);
-        entryWijedasa.setField("author", "Wijedasa, Lahiru S and Jauhiainen, Jyrki and Könönen, Mari and Lampela, Maija and Vasander, Harri and Leblanc, Marie-Claire and Evers, Stephanie and Smith, Thomas E L and Yule, Catherine M and Varkkey, Helena and Lupascu, Massimo and Parish, Faizal and Singleton, Ian and Clements, Gopalasamy R and Aziz, Sheema Abdul and Harrison, Mark E and Cheyne, Susan and Anshari, Gusti Z and Meijaard, Erik and Goldstein, Jenny E and Waldron, Susan and Hergoualc'h, Kristell and Dommain, Rene and Frolking, Steve and Evans, Christopher D and Posa, Mary Rose C and Glaser, Paul H and Suryadiputra, Nyoman and Lubis, Reza and Santika, Truly and Padfield, Rory and Kurnianto, Sofyan and Hadisiswoyo, Panut and Lim, Teck Wyn and Page, Susan E and Gauci, Vincent and Van Der Meer, Peter J and Buckland, Helen and Garnier, Fabien and Samuel, Marshall K and Choo, Liza Nuriati Lim Kim and O'Reilly, Patrick and Warren, Matthew and Suksuwan, Surin and Sumarga, Elham and Jain, Anuj and Laurance, William F and Couwenberg, John and Joosten, Hans and Vernimmen, Ronald and Hooijer, Aljosja and Malins, Chris and Cochrane, Mark A and Perumal, Balu and Siegert, Florian and Peh, Kelvin S-H and Comeau, Louis-Pierre and Verchot, Louis and Harvey, Charles F and Cobb, Alex and Jaafar, Zeehan and Wösten, Henk and Manuri, Solichin and Müller, Moritz and Giesen, Wim and Phelps, Jacob and Yong, Ding Li and Silvius, Marcel and Wedeux, Béatrice M M and Hoyt, Alison and Osaki, Mitsuru and Hirano, Takashi and Takahashi, Hidenori and Kohyama, Takashi S and Haraguchi, Akira and Nugroho, Nunung P and Coomes, David A and Quoi, Le Phat and Dohong, Alue and Gunawan, Haris and Gaveau, David L A and Langner, Andreas and Lim, Felix K S and Edwards, David P and Giam, Xingli and Van Der Werf, Guido and Carmenta, Rachel and Verwer, Caspar C and Gibson, Luke and Gandois, Laure and Graham, Laura Linda Bozena and Regalino, Jhanson and Wich, Serge A and Rieley, Jack and Kettridge, Nicholas and Brown, Chloe and Pirard, Romain and Moore, Sam and Capilla, B Ripoll and Ballhorn, Uwe and Ho, Hua Chew and Hoscilo, Agata and Lohberger, Sandra and Evans, Theodore A and Yulianti, Nina and Blackham, Grace and Onrizal and Husson, Simon and Murdiyarso, Daniel and Pangala, Sunita and Cole, Lydia E S and Tacconi, Luca and Segah, Hendrik and Tonoto, Prayoto and Lee, Janice S H and Schmilewski, Gerald and Wulffraat, Stephan and Putra, Erianto Indra and Cattau, Megan E and Clymo, R S and Morrison, Ross and Mujahid, Aazani and Miettinen, Jukka and Liew, Soo Chin and Valpola, Samu and Wilson, David and D'Arcy, Laura and Gerding, Michiel and Sundari, Siti and Thornton, Sara A and Kalisz, Barbara and Chapman, Stephen J and Su, Ahmad Suhaizi Mat and Basuki, Imam and Itoh, Masayuki and Traeholt, Carl and Sloan, Sean and Sayok, Alexander K and Andersen, Roxane");
+        entryWijedasa.setField("author", "Wijedasa, Lahiru S. and Jauhiainen, Jyrki and Könönen, Mari and Lampela, Maija and Vasander, Harri and Leblanc, Marie-Claire and Evers, Stephanie and Smith, Thomas E.  L. and Yule, Catherine M. and Varkkey, Helena and Lupascu, Massimo and Parish, Faizal and Singleton, Ian and Clements, Gopalasamy R. and Aziz, Sheema Abdul and Harrison, Mark E. and Cheyne, Susan and Anshari, Gusti Z. and Meijaard, Erik and Goldstein, Jenny E. and Waldron, Susan and Hergoualc'h, Kristell and Dommain, Rene and Frolking, Steve and Evans, Christopher D. and Posa, Mary Rose C. and Glaser, Paul H. and Suryadiputra, Nyoman and Lubis, Reza and Santika, Truly and Padfield, Rory and Kurnianto, Sofyan and Hadisiswoyo, Panut and Lim, Teck Wyn and Page, Susan E. and Gauci, Vincent and Van Der Meer, Peter J. and Buckland, Helen and Garnier, Fabien and Samuel, Marshall K. and Choo, Liza Nuriati Lim Kim and O'Reilly, Patrick and Warren, Matthew and Suksuwan, Surin and Sumarga, Elham and Jain, Anuj and Laurance, William F. and Couwenberg, John and Joosten, Hans and Vernimmen, Ronald and Hooijer, Aljosja and Malins, Chris and Cochrane, Mark A. and Perumal, Balu and Siegert, Florian and Peh, Kelvin S.-H. and Comeau, Louis-Pierre and Verchot, Louis and Harvey, Charles F. and Cobb, Alex and Jaafar, Zeehan and Wösten, Henk and Manuri, Solichin and Müller, Moritz and Giesen, Wim and Phelps, Jacob and Yong, Ding Li and Silvius, Marcel and Wedeux, Béatrice M.  M. and Hoyt, Alison and Osaki, Mitsuru and Hirano, Takashi and Takahashi, Hidenori and Kohyama, Takashi S. and Haraguchi, Akira and Nugroho, Nunung P. and Coomes, David A. and Quoi, Le Phat and Dohong, Alue and Gunawan, Haris and Gaveau, David L.  A. and Langner, Andreas and Lim, Felix K.  S. and Edwards, David P. and Giam, Xingli and Van Der Werf, Guido and Carmenta, Rachel and Verwer, Caspar C. and Gibson, Luke and Gandois, Laure and Graham, Laura Linda Bozena and Regalino, Jhanson and Wich, Serge A. and Rieley, Jack and Kettridge, Nicholas and Brown, Chloe and Pirard, Romain and Moore, Sam and Capilla, B.  Ripoll and Ballhorn, Uwe and Ho, Hua Chew and Hoscilo, Agata and Lohberger, Sandra and Evans, Theodore A. and Yulianti, Nina and Blackham, Grace and Onrizal and Husson, Simon and Murdiyarso, Daniel and Pangala, Sunita and Cole, Lydia E.  S. and Tacconi, Luca and Segah, Hendrik and Tonoto, Prayoto and Lee, Janice S.  H. and Schmilewski, Gerald and Wulffraat, Stephan and Putra, Erianto Indra and Cattau, Megan E. and Clymo, R.  S. and Morrison, Ross and Mujahid, Aazani and Miettinen, Jukka and Liew, Soo Chin and Valpola, Samu and Wilson, David and D'Arcy, Laura and Gerding, Michiel and Sundari, Siti and Thornton, Sara A. and Kalisz, Barbara and Chapman, Stephen J. and Su, Ahmad Suhaizi Mat and Basuki, Imam and Itoh, Masayuki and Traeholt, Carl and Sloan, Sean and Sayok, Alexander K. and Andersen, Roxane");
         entryWijedasa.setField("country", "England");
         entryWijedasa.setField("doi", "10.1111/gcb.13516");
         entryWijedasa.setField("issn", "1365-2486");
@@ -66,7 +66,7 @@ public void setUp() {
         entryEndharti.setField("pmid", "27670445");
         entryEndharti.setField("pubmodel", "Electronic");
         entryEndharti.setField("pubstatus", "epublish");
-        entryEndharti.setField("revised", "2017-02-20");
+        entryEndharti.setField("revised", "2018-11-13");
         entryEndharti.setField("volume", "16");
         entryEndharti.setField("year", "2016");
 
@@ -110,7 +110,7 @@ public void setUp() {
         bibEntrySari.setField("keywords", "Antibodies, Protozoan; Antibodies, Viral, immunology; Coinfection, epidemiology, immunology; Female; HIV Infections, epidemiology; HTLV-I Antibodies, immunology; HTLV-I Infections, epidemiology, immunology; HTLV-II Antibodies, immunology; HTLV-II Infections, epidemiology, immunology; Hepatitis Antibodies, immunology; Hepatitis B Antibodies, immunology; Hepatitis C Antibodies, immunology; Hepatitis Delta Virus, immunology; Hepatitis, Viral, Human, epidemiology, immunology; Humans; Immunoglobulin G, immunology; Immunoglobulin M, immunology; Indonesia, epidemiology; Male; Prisoners; Seroepidemiologic Studies; Toxoplasma, immunology; Toxoplasmosis, epidemiology, immunology");
         bibEntrySari.setField("month", "#nov#");
         bibEntrySari.setField("pubstatus", "ppublish");
-        bibEntrySari.setField("revised", "2016-02-12");
+        bibEntrySari.setField("revised", "2018-12-02");
         bibEntrySari.setField("nlm-id", "0266303");
         bibEntrySari.setField("owner", "NLM");
         bibEntrySari.setField("pages", "977--985");

From ec8ae8401f879ee1443c30e191b234ecc79c47d8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 8 Apr 2019 08:10:33 +0200
Subject: [PATCH 168/184] Bump junit-jupiter from 5.4.1 to 5.4.2 (#4867)

Bumps [junit-jupiter](https://github.com/junit-team/junit5) from 5.4.1 to 5.4.2.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/compare/r5.4.1...r5.4.2)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 8a6385b8e6e..38e6e502cb4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -161,7 +161,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.1'
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.1'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.1'
 

From 3d2d61d0ce3263b257f33d721623b512e748811d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 8 Apr 2019 08:10:58 +0200
Subject: [PATCH 169/184] Bump junit-platform-launcher from 1.4.1 to 1.4.2
 (#4865)

Bumps [junit-platform-launcher](https://github.com/junit-team/junit5) from 1.4.1 to 1.4.2.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/commits)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 38e6e502cb4..8f63f2fdbe1 100644
--- a/build.gradle
+++ b/build.gradle
@@ -163,7 +163,7 @@ dependencies {
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.4.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.4.1'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.4.2'
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'

From 4d3ddf5c6e85fe46563922150203a306781bb7dd Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 8 Apr 2019 11:37:36 +0200
Subject: [PATCH 170/184] Bump junit-vintage-engine from 5.4.1 to 5.4.2 (#4866)

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 8f63f2fdbe1..b20bd600e17 100644
--- a/build.gradle
+++ b/build.gradle
@@ -162,7 +162,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.4.2'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.2'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.2'
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'

From fdb9fa5bcbf96ae30f1467c4a018370373718117 Mon Sep 17 00:00:00 2001
From: Kaique Komata <kaique.komata@usp.br>
Date: Mon, 8 Apr 2019 08:54:55 -0300
Subject: [PATCH 171/184] Fix IllegalArgumentException when ranking entries
 (#4779)

---
 CHANGELOG.md                                           |  1 +
 .../java/org/jabref/gui/actions/StandardActions.java   | 10 +++++-----
 src/main/resources/l10n/JabRef_en.properties           |  5 +++++
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2d7c0f75166..7a941e10ce1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -104,6 +104,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
+- We fixed an issue where ranking an entry would generate an IllegalArgumentException. [#4754](https://github.com/JabRef/jabref/issues/4754)
 - We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
 - We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 
diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
index 2c91ff5c4b5..eb4c6508955 100644
--- a/src/main/java/org/jabref/gui/actions/StandardActions.java
+++ b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -44,11 +44,11 @@ public enum StandardActions implements Action {
     QUALITY_ASSURED(Localization.lang("Toggle quality assured"), IconTheme.JabRefIcons.QUALITY_ASSURED),
     RANKING(Localization.lang("Rank"), IconTheme.JabRefIcons.RANKING),
     CLEAR_RANK(Localization.lang("Clear rank")),
-    RANK_1("", IconTheme.JabRefIcons.RANK1),
-    RANK_2("", IconTheme.JabRefIcons.RANK2),
-    RANK_3("", IconTheme.JabRefIcons.RANK3),
-    RANK_4("", IconTheme.JabRefIcons.RANK4),
-    RANK_5("", IconTheme.JabRefIcons.RANK5),
+    RANK_1(Localization.lang("Set rank to one"), IconTheme.JabRefIcons.RANK1),
+    RANK_2(Localization.lang("Set rank to two"), IconTheme.JabRefIcons.RANK2),
+    RANK_3(Localization.lang("Set rank to three"), IconTheme.JabRefIcons.RANK3),
+    RANK_4(Localization.lang("Set rank to four"), IconTheme.JabRefIcons.RANK4),
+    RANK_5(Localization.lang("Set rank to five"), IconTheme.JabRefIcons.RANK5),
     PRINTED(Localization.lang("Printed"), IconTheme.JabRefIcons.PRINTED),
     TOGGLE_PRINTED(Localization.lang("Toggle print status"), IconTheme.JabRefIcons.PRINTED),
     READ_STATUS(Localization.lang("Read status"), IconTheme.JabRefIcons.READ_STATUS),
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 7893e31e5d1..7398d8fc491 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2081,3 +2081,8 @@ Use\ selected\ document=Use selected document
 Accept\ changes=Accept changes
 Dismiss\ changes=Dismiss changes
 The\ library\ has\ been\ modified\ by\ another\ program.=The library has been modified by another program.
+Set\ rank\ to\ one=Set rank to one
+Set\ rank\ to\ two=Set rank to two
+Set\ rank\ to\ three=Set rank to three
+Set\ rank\ to\ four=Set rank to four
+Set\ rank\ to\ five=Set rank to five

From bb7b7213d7e0339491c066eb457c27b70fad0b16 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Mon, 8 Apr 2019 19:13:51 +0200
Subject: [PATCH 172/184] Remove deprecated awt apple extension (#4860)

---
 lib/AppleJavaExtensions.jar                   | Bin 25467 -> 0 bytes
 src/main/java/org/jabref/gui/JabRefFrame.java |  14 ---
 .../org/jabref/gui/OSXCompatibleToolbar.java  |  39 --------
 src/main/java/osx/macadapter/MacAdapter.java  |  83 ------------------
 4 files changed, 136 deletions(-)
 delete mode 100644 lib/AppleJavaExtensions.jar
 delete mode 100644 src/main/java/org/jabref/gui/OSXCompatibleToolbar.java
 delete mode 100644 src/main/java/osx/macadapter/MacAdapter.java

diff --git a/lib/AppleJavaExtensions.jar b/lib/AppleJavaExtensions.jar
deleted file mode 100644
index 6659a81c69fc189cf966dd79f5824b486c9c0281..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 8ec31a46d11..214530e363e 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -118,7 +118,6 @@
 import org.jabref.logic.undo.AddUndoableActionEvent;
 import org.jabref.logic.undo.UndoChangeEvent;
 import org.jabref.logic.undo.UndoRedoEvent;
-import org.jabref.logic.util.OS;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -136,7 +135,6 @@
 import org.fxmisc.easybind.EasyBind;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import osx.macadapter.MacAdapter;
 
 /**
  * The main window of the application.
@@ -286,18 +284,6 @@ public void init() {
             currentBasePanel.getUndoManager().postUndoRedoEvent();
             currentBasePanel.getMainTable().requestFocus();
         });
-
-        //Note: The registration of Apple event is at the end of initialization, because
-        //if the events happen too early (ie when the window is not initialized yet), the
-        //opened (double-clicked) documents are not displayed.
-        if (OS.OS_X) {
-            try {
-                new MacAdapter().registerMacEvents(this);
-            } catch (Exception e) {
-                LOGGER.error("Could not interface with Mac OS X methods.", e);
-            }
-        }
-
         initShowTrackingNotification();
     }
 
diff --git a/src/main/java/org/jabref/gui/OSXCompatibleToolbar.java b/src/main/java/org/jabref/gui/OSXCompatibleToolbar.java
deleted file mode 100644
index f71c9e72af5..00000000000
--- a/src/main/java/org/jabref/gui/OSXCompatibleToolbar.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package org.jabref.gui;
-
-import java.awt.Component;
-
-import javax.swing.JButton;
-import javax.swing.JToolBar;
-
-import org.jabref.logic.util.OS;
-
-public class OSXCompatibleToolbar extends JToolBar {
-
-    public OSXCompatibleToolbar() {
-    }
-
-    public OSXCompatibleToolbar(int orientation) {
-        super(orientation);
-    }
-
-    public OSXCompatibleToolbar(String name) {
-        super(name);
-    }
-
-    public OSXCompatibleToolbar(String name, int orientation) {
-        super(name, orientation);
-    }
-
-    @Override
-    public Component add(Component a) {
-        if (a instanceof JButton) {
-            JButton button = (JButton) a;
-            if (OS.OS_X) {
-                button.putClientProperty("JButton.buttonType", "toolbar");
-            }
-        }
-
-        return super.add(a);
-    }
-
-}
diff --git a/src/main/java/osx/macadapter/MacAdapter.java b/src/main/java/osx/macadapter/MacAdapter.java
deleted file mode 100644
index 9c7938aa5f6..00000000000
--- a/src/main/java/osx/macadapter/MacAdapter.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package osx.macadapter;
-
-import java.io.File;
-import java.util.List;
-
-import org.jabref.gui.JabRefFrame;
-
-import com.apple.eawt.AboutHandler;
-import com.apple.eawt.AppEvent;
-import com.apple.eawt.AppEvent.AboutEvent;
-import com.apple.eawt.AppEvent.OpenFilesEvent;
-import com.apple.eawt.AppEvent.PreferencesEvent;
-import com.apple.eawt.AppEvent.QuitEvent;
-import com.apple.eawt.AppReOpenedListener;
-import com.apple.eawt.Application;
-import com.apple.eawt.OpenFilesHandler;
-import com.apple.eawt.PreferencesHandler;
-import com.apple.eawt.QuitHandler;
-import com.apple.eawt.QuitResponse;
-
-public class MacAdapter implements PreferencesHandler, AboutHandler, QuitHandler, OpenFilesHandler, AppReOpenedListener {
-
-    private JabRefFrame parentFrame;
-
-    public void registerMacEvents(JabRefFrame inputFrame) {
-        parentFrame = inputFrame;
-        Application.getApplication().setOpenFileHandler(this);
-        Application.getApplication().setAboutHandler(this);
-        Application.getApplication().setPreferencesHandler(this);
-        Application.getApplication().setQuitHandler(this);
-        Application.getApplication().addAppEventListener(this);
-    }
-
-    @Override
-    // The OSXAdapter calls this method when a ".bib" file has been double-clicked from the Finder.
-    public void openFiles(OpenFilesEvent event) {
-        if (parentFrame == null) {
-            return;
-        }
-
-        List<File> files = event.getFiles();
-
-        for (File file : files) {
-            parentFrame.openAction(file.getAbsolutePath());
-        }
-    }
-
-    @Override
-    public void handleQuitRequestWith(QuitEvent evt, QuitResponse resp) {
-        if (parentFrame == null) {
-            return;
-        }
-
-        if (parentFrame.quit()) {
-            resp.performQuit();
-        } else {
-            resp.cancelQuit();
-        }
-    }
-
-    @Override
-    public void handleAbout(AboutEvent arg0) {
-        if (parentFrame == null) {
-            return;
-        }
-
-        parentFrame.about();
-    }
-
-    @Override
-    public void handlePreferences(PreferencesEvent arg0) {
-        if (parentFrame == null) {
-            return;
-        }
-
-        //  parentFrame.showPreferencesDialog();
-    }
-
-    @Override
-    public void appReOpened(AppEvent.AppReOpenedEvent appReOpenedEvent) {
-        parentFrame.setVisible(true);
-    }
-}

From 856c170f2ed4b6eb72907c372e239c32e7fe13f6 Mon Sep 17 00:00:00 2001
From: Ali <alijakparov.kz@gmail.com>
Date: Tue, 9 Apr 2019 09:01:07 +0300
Subject: [PATCH 173/184] #4795 disable menu item if database not connected
 (#4828)

* #4795 disable menu item if database not connected

* resolve merge conflict

* resolve merge conflict

* resolve merge conflicts

* resolve check style

* fix import order

* resolve merge

* delete duplicate code

* change push to application implementation

* fix check style

* delete action

* put deprecated annotation on OldDatabaseCommandWrapper
---
 src/main/java/org/jabref/gui/JabRefFrame.java | 11 +--
 .../actions/OldDatabaseCommandWrapper.java    |  3 +
 .../gui/push/PushToApplicationAction.java     | 68 +++++++++++---
 .../gui/push/PushToApplicationButton.java     | 90 -------------------
 4 files changed, 63 insertions(+), 109 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/push/PushToApplicationButton.java

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 214530e363e..abc4abf83a2 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -100,7 +100,7 @@
 import org.jabref.gui.metadata.BibtexStringEditorAction;
 import org.jabref.gui.metadata.PreambleEditor;
 import org.jabref.gui.protectedterms.ManageProtectedTermsAction;
-import org.jabref.gui.push.PushToApplicationButton;
+import org.jabref.gui.push.PushToApplicationAction;
 import org.jabref.gui.push.PushToApplications;
 import org.jabref.gui.search.GlobalSearchBar;
 import org.jabref.gui.specialfields.SpecialFieldMenuItemFactory;
@@ -559,7 +559,8 @@ private Node createToolbar() {
         leftSide.setMinWidth(100);
         leftSide.prefWidthProperty().bind(sidePane.widthProperty());
         leftSide.maxWidthProperty().bind(sidePane.widthProperty());
-        PushToApplicationButton pushToExternal = new PushToApplicationButton(this, pushApplications.getApplications());
+
+        PushToApplicationAction pushToApplicationAction = new PushToApplicationAction(this, Globals.stateManager);
         HBox rightSide = new HBox(
                 factory.createIconButton(StandardActions.NEW_ARTICLE, new NewEntryAction(this, BiblatexEntryTypes.ARTICLE, dialogService, Globals.prefs)),
                 factory.createIconButton(StandardActions.DELETE_ENTRY, new OldDatabaseCommandWrapper(Actions.DELETE, this, Globals.stateManager)),
@@ -570,7 +571,7 @@ private Node createToolbar() {
                 factory.createIconButton(StandardActions.COPY, new OldDatabaseCommandWrapper(Actions.COPY, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.PASTE, new OldDatabaseCommandWrapper(Actions.PASTE, this, Globals.stateManager)),
                 new Separator(Orientation.VERTICAL),
-                factory.createIconButton(pushToExternal.getMenuAction(), pushToExternal),
+                factory.createIconButton(pushToApplicationAction.getActionInformation(), pushToApplicationAction),
                 factory.createIconButton(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.CLEANUP_ENTRIES, new OldDatabaseCommandWrapper(Actions.CLEANUP, this, Globals.stateManager)),
                 new Separator(Orientation.VERTICAL),
@@ -798,7 +799,7 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs))
         );
 
-        PushToApplicationButton pushToExternal = new PushToApplicationButton(this, pushApplications.getApplications());
+        final PushToApplicationAction pushToApplicationAction = new PushToApplicationAction(this, Globals.stateManager);
         tools.getItems().addAll(
                 factory.createMenuItem(StandardActions.NEW_SUB_LIBRARY_FROM_AUX, new NewSubLibraryAction(this)),
                 factory.createMenuItem(StandardActions.FIND_UNLINKED_FILES, new FindUnlinkedFilesAction(this)),
@@ -815,7 +816,7 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.REPLACE_ALL, new OldDatabaseCommandWrapper(Actions.REPLACE_ALL, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.SEND_AS_EMAIL, new OldDatabaseCommandWrapper(Actions.SEND_AS_EMAIL, this, Globals.stateManager)),
-                factory.createMenuItem(pushToExternal.getMenuAction(), pushToExternal),
+                factory.createMenuItem(pushToApplicationAction.getActionInformation(), pushToApplicationAction),
 
                 factory.createSubMenu(StandardActions.ABBREVIATE,
                         factory.createMenuItem(StandardActions.ABBREVIATE_ISO, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_ISO, this, Globals.stateManager)),
diff --git a/src/main/java/org/jabref/gui/actions/OldDatabaseCommandWrapper.java b/src/main/java/org/jabref/gui/actions/OldDatabaseCommandWrapper.java
index a752da3ce9c..58a702e4190 100644
--- a/src/main/java/org/jabref/gui/actions/OldDatabaseCommandWrapper.java
+++ b/src/main/java/org/jabref/gui/actions/OldDatabaseCommandWrapper.java
@@ -14,7 +14,10 @@
 
 /**
  * A command that is only executable if a database is open.
+ * Deprecated use instead
+ * @see org.jabref.gui.actions.SimpleCommand
  */
+@Deprecated
 public class OldDatabaseCommandWrapper extends CommandBase {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(OldDatabaseCommandWrapper.class);
diff --git a/src/main/java/org/jabref/gui/push/PushToApplicationAction.java b/src/main/java/org/jabref/gui/push/PushToApplicationAction.java
index 468fb8b57dc..e514a8fec55 100644
--- a/src/main/java/org/jabref/gui/push/PushToApplicationAction.java
+++ b/src/main/java/org/jabref/gui/push/PushToApplicationAction.java
@@ -1,39 +1,79 @@
 package org.jabref.gui.push;
 
-import java.awt.event.ActionEvent;
 import java.util.List;
 import java.util.Optional;
 
-import javax.swing.AbstractAction;
-import javax.swing.Action;
 import javax.swing.SwingUtilities;
 
+import org.jabref.Globals;
 import org.jabref.JabRefExecutorService;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.Action;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.icon.JabRefIcon;
+import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.preferences.JabRefPreferences;
+
+import org.fxmisc.easybind.EasyBind;
 
 /**
  * An Action class representing the process of invoking a PushToApplication operation.
  */
-class PushToApplicationAction extends AbstractAction implements Runnable {
+public class PushToApplicationAction extends SimpleCommand implements Runnable {
 
-    private final PushToApplication operation;
-    private final JabRefFrame frame;
+    private PushToApplication operation;
+    private JabRefFrame frame;
     private BasePanel panel;
     private List<BibEntry> entries;
 
-    public PushToApplicationAction(JabRefFrame frame, PushToApplication operation) {
+    public PushToApplicationAction(final JabRefFrame frame, final StateManager stateManager) {
         this.frame = frame;
-        putValue(Action.SMALL_ICON, operation.getIcon());
-        putValue(Action.NAME, operation.getName());
-        putValue(Action.SHORT_DESCRIPTION, operation.getTooltip());
-        this.operation = operation;
+        this.operation = getLastUsedApplication(frame.getPushApplications().getApplications());
+        this.executable.bind(EasyBind.map(stateManager.activeDatabaseProperty(), Optional::isPresent));
+    }
+
+    private PushToApplication getLastUsedApplication(List<PushToApplication> pushActions) {
+        String appSelected = Globals.prefs.get(JabRefPreferences.PUSH_TO_APPLICATION);
+        for (PushToApplication application : pushActions) {
+            if (application.getApplicationName().equals(appSelected)) {
+                return application;
+            }
+        }
+
+        // Nothing found, pick first
+        return pushActions.get(0);
+    }
+
+    public Action getActionInformation() {
+        return new Action() {
+            @Override
+            public Optional<JabRefIcon> getIcon() {
+                return Optional.of(operation.getIcon());
+            }
+
+            @Override
+            public Optional<KeyBinding> getKeyBinding() {
+                return Optional.of(KeyBinding.PUSH_TO_APPLICATION);
+            }
+
+            @Override
+            public String getText() {
+                return Localization.lang("Push entries to external application (%0)", operation.getApplicationName());
+            }
+
+            @Override
+            public String getDescription() {
+                return "";
+            }
+        };
     }
 
     @Override
-    public void actionPerformed(ActionEvent e) {
+    public void execute() {
         panel = frame.getCurrentBasePanel();
 
         // Check if a BasePanel exists:
@@ -44,7 +84,7 @@ public void actionPerformed(ActionEvent e) {
         // Check if any entries are selected:
         entries = panel.getSelectedEntries();
         if (entries.isEmpty()) {
-            frame.getDialogService().showErrorDialogAndWait((String) getValue(Action.NAME),
+            frame.getDialogService().showErrorDialogAndWait(operation.getApplicationName(),
                     Localization.lang("This operation requires one or more entries to be selected."));
 
             return;
@@ -54,7 +94,7 @@ public void actionPerformed(ActionEvent e) {
         if (operation.requiresBibtexKeys()) {
             for (BibEntry entry : entries) {
                 if (!(entry.getCiteKeyOptional().isPresent()) || entry.getCiteKeyOptional().get().trim().isEmpty()) {
-                    frame.getDialogService().showErrorDialogAndWait((String) getValue(Action.NAME),
+                    frame.getDialogService().showErrorDialogAndWait(operation.getApplicationName(),
                             Localization.lang("This operation requires all selected entries to have BibTeX keys defined."));
 
                     return;
diff --git a/src/main/java/org/jabref/gui/push/PushToApplicationButton.java b/src/main/java/org/jabref/gui/push/PushToApplicationButton.java
deleted file mode 100644
index 5ab8fefd4aa..00000000000
--- a/src/main/java/org/jabref/gui/push/PushToApplicationButton.java
+++ /dev/null
@@ -1,90 +0,0 @@
-package org.jabref.gui.push;
-
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
-
-import org.jabref.Globals;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.actions.SimpleCommand;
-import org.jabref.gui.icon.JabRefIcon;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.preferences.JabRefPreferences;
-
-/**
- * Customized UI component for pushing to external applications. Has a selection popup menu to change the selected
- * external application. This class implements the ActionListener interface. When actionPerformed() is invoked, the
- * currently selected PushToApplication is activated. The actionPerformed() method can be called with a null argument.
- */
-public class PushToApplicationButton extends SimpleCommand implements ActionListener {
-
-    private final JabRefFrame frame;
-    private final List<PushToApplication> pushActions;
-    private final PushToApplication toApp;
-    private final Map<PushToApplication, PushToApplicationAction> actions = new HashMap<>();
-
-    public PushToApplicationButton(JabRefFrame frame, List<PushToApplication> pushActions) {
-        this.frame = frame;
-        this.pushActions = pushActions;
-        // Set the last used external application
-        toApp = getLastUsedApplication();
-    }
-
-    private PushToApplication getLastUsedApplication() {
-        String appSelected = Globals.prefs.get(JabRefPreferences.PUSH_TO_APPLICATION);
-        for (PushToApplication application : pushActions) {
-            if (application.getApplicationName().equals(appSelected)) {
-                return application;
-            }
-        }
-
-        // Nothing found, pick first
-        return pushActions.get(0);
-    }
-
-    public org.jabref.gui.actions.Action getMenuAction() {
-        PushToApplication application = getLastUsedApplication();
-
-        return new org.jabref.gui.actions.Action() {
-            @Override
-            public Optional<JabRefIcon> getIcon() {
-                return Optional.of(application.getIcon());
-            }
-
-            @Override
-            public Optional<KeyBinding> getKeyBinding() {
-                return Optional.of(KeyBinding.PUSH_TO_APPLICATION);
-            }
-
-            @Override
-            public String getText() {
-                return Localization.lang("Push entries to external application (%0)", application.getApplicationName());
-            }
-
-            @Override
-            public String getDescription() {
-                return "";
-            }
-        };
-    }
-
-    @Override
-    public void actionPerformed(ActionEvent e) {
-        execute();
-    }
-
-    @Override
-    public void execute() {
-        // Lazy initialization of the push action:
-        PushToApplicationAction action = actions.get(toApp);
-        if (action == null) {
-            action = new PushToApplicationAction(frame, toApp);
-            actions.put(toApp, action);
-        }
-        action.actionPerformed(new ActionEvent(toApp, 0, "push"));
-    }
-}

From 0dd091f31b86b02dd9e44b4ac86aa204d4dec9ef Mon Sep 17 00:00:00 2001
From: Marco Konersmann <marco.konersmann@paluno.uni-due.de>
Date: Tue, 9 Apr 2019 15:36:38 +0200
Subject: [PATCH 174/184] Fix JabRef dying silently without enough inotify
 instances (#4875)

* Logs exceptions in file monitor as errors

An exception in the initialization of DefaultFileUpdateMonitor is now logged as error

* Describes fix for issue #4874
---
 CHANGELOG.md                                                    | 1 +
 src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7a941e10ce1..3ec7d2b519a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -65,6 +65,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 ### Fixed
+- We fixed an issue where JabRef died silently for the user without enough inotify instances [#4874](https://github.com/JabRef/jabref/issues/4847)
 - We fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries [#3112](https://github.com/JabRef/jabref/issues/3112)
 - We fixed an issue where custom exports could not be selected in the 'Export (selected) entries' dialog [#4013](https://github.com/JabRef/jabref/issues/4013)
 - Italic text is now rendered correctly. https://github.com/JabRef/jabref/issues/3356
diff --git a/src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java b/src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java
index 28de7285f3f..bdf0b51e2a6 100644
--- a/src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java
+++ b/src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java
@@ -59,7 +59,7 @@ public void run() {
                 Thread.yield();
             }
         } catch (Throwable e) {
-            LOGGER.debug("FileUpdateMonitor has been interrupted. Terminating...", e);
+            LOGGER.error("FileUpdateMonitor has been interrupted.", e);
         }
     }
 

From e1a01d2a6afd7498e3382f74b172d3b8c5e55293 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Thu, 11 Apr 2019 08:06:54 +0200
Subject: [PATCH 175/184] Bump java-string-similarity from 1.1.0 to 1.2.1
 (#4878)

Bumps [java-string-similarity](https://github.com/tdebatty/java-string-similarity) from 1.1.0 to 1.2.1.
- [Release notes](https://github.com/tdebatty/java-string-similarity/releases)
- [Commits](https://github.com/tdebatty/java-string-similarity/compare/v1.1.0...v1.2.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index b20bd600e17..9b0ba62711c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -112,7 +112,7 @@ dependencies {
     compile "org.libreoffice:unoil:6.2.2"
 
     compile 'io.github.java-diff-utils:java-diff-utils:4.0'
-    compile 'info.debatty:java-string-similarity:1.1.0'
+    compile 'info.debatty:java-string-similarity:1.2.1'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'

From 6e062d9484e31f917c877d9e6fd72e5f62bcb7ff Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Thu, 11 Apr 2019 08:07:28 +0200
Subject: [PATCH 176/184] Bump mockito-core from 2.26.0 to 2.27.0 (#4879)

Bumps [mockito-core](https://github.com/mockito/mockito) from 2.26.0 to 2.27.0.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v2.26.0...v2.27.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9b0ba62711c..5154e337837 100644
--- a/build.gradle
+++ b/build.gradle
@@ -167,7 +167,7 @@ dependencies {
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
-    testCompile 'org.mockito:mockito-core:2.26.0'
+    testCompile 'org.mockito:mockito-core:2.27.0'
     testCompile 'com.github.tomakehurst:wiremock:2.22.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'

From f0e548935fdfe8d4b87e37df0d1eb16b2251500e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Sat, 13 Apr 2019 13:46:44 +0200
Subject: [PATCH 177/184] Bump xmpbox from 2.0.14 to 2.0.15 (#4883)

Bumps xmpbox from 2.0.14 to 2.0.15.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 5154e337837..55b978e8782 100644
--- a/build.gradle
+++ b/build.gradle
@@ -97,7 +97,7 @@ dependencies {
 
     compile 'org.apache.pdfbox:pdfbox:2.0.14'
     compile 'org.apache.pdfbox:fontbox:2.0.14'
-    compile 'org.apache.pdfbox:xmpbox:2.0.14'
+    compile 'org.apache.pdfbox:xmpbox:2.0.15'
 
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'
 

From d68bcb30f14a11dc7c54d965e3195669fdf8944c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Sat, 13 Apr 2019 13:46:58 +0200
Subject: [PATCH 178/184] Bump pdfbox from 2.0.14 to 2.0.15 (#4881)

Bumps pdfbox from 2.0.14 to 2.0.15.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 55b978e8782..8123dcd0a1d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -95,7 +95,7 @@ dependencies {
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.14'
+    compile 'org.apache.pdfbox:pdfbox:2.0.15'
     compile 'org.apache.pdfbox:fontbox:2.0.14'
     compile 'org.apache.pdfbox:xmpbox:2.0.15'
 

From b7989072fd68fe472dd712e18cc72bed69da2247 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Sat, 13 Apr 2019 14:14:07 +0200
Subject: [PATCH 179/184] Bump fontbox from 2.0.14 to 2.0.15 (#4882)

Bumps fontbox from 2.0.14 to 2.0.15.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 8123dcd0a1d..277af5824b9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -96,7 +96,7 @@ dependencies {
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
     compile 'org.apache.pdfbox:pdfbox:2.0.15'
-    compile 'org.apache.pdfbox:fontbox:2.0.14'
+    compile 'org.apache.pdfbox:fontbox:2.0.15'
     compile 'org.apache.pdfbox:xmpbox:2.0.15'
 
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'

From 3d770b858f3a028cdfd9c37aac6c881b0b5fb738 Mon Sep 17 00:00:00 2001
From: Deepak Kumar <deepakkumar24196@gmail.com>
Date: Sat, 13 Apr 2019 21:20:23 +0530
Subject: [PATCH 180/184] Fix right clicking on any entry and selecting "Open
 folder" results in the NullPointer exception (#4797)

* Add an option in preference settings to set what action to be taken by JabRef when user clicks 'open folder' on a entry.

* Fix #4763 and add added required changes in CHANGELOG.md and JabRef_en.properties

* Refactor and Reformat code.

* Fix issue #4802, where option 'open terminal here' with custom command was passing wrong argument

* Fix failure of LocalizationConsistencyTest after code changes.
---
 .mailmap                                      |  3 +-
 CHANGELOG.md                                  |  4 +-
 .../org/jabref/gui/desktop/JabRefDesktop.java | 39 +++++++++++----
 .../java/org/jabref/gui/desktop/os/Linux.java | 19 ++++----
 .../jabref/gui/preferences/ExternalTab.java   | 48 +++++++++++++++++++
 .../jabref/preferences/JabRefPreferences.java |  6 +++
 src/main/resources/l10n/JabRef_en.properties  |  7 ++-
 7 files changed, 105 insertions(+), 21 deletions(-)

diff --git a/.mailmap b/.mailmap
index b8698d75865..3af3033fd28 100644
--- a/.mailmap
+++ b/.mailmap
@@ -142,4 +142,5 @@ Johannes Manner <johannes.manner@web.de>
 Dominik Traczyk <dominik646@gmail.com>
 Cerrianne Santos <cerrianne.santos@gmail.com>
 Stefan Scheffel <st155160@stud.uni-stuttgart.de>
-Stefan Gerzmann <steppery@gmx.de>
\ No newline at end of file
+Stefan Gerzmann <steppery@gmx.de>
+Deepak Kumar <deepakkumar24196@gmail.com>
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3ec7d2b519a..651ab6ab391 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -61,6 +61,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
 - We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
 - We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
+- We added an option in the settings to set the default action in JabRef when right clicking on any entry in any database and selecting "Open folder". [#4763](https://github.com/JabRef/jabref/issues/4763)
 - The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
 
 
@@ -105,13 +106,14 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
+- We fixed an issue where right clicking on any entry in any database and selecting "Open folder" results in the NullPointer exception. [#4763](https://github.com/JabRef/jabref/issues/4763)
+- We fixed an issue where option 'open terminal here' with custom command was passing wrong argument. [#4802](https://github.com/JabRef/jabref/issues/4802)
 - We fixed an issue where ranking an entry would generate an IllegalArgumentException. [#4754](https://github.com/JabRef/jabref/issues/4754)
 - We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
 - We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 
 
 
-
 ### Removed
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.
 - The number column was removed.
diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
index fbd9478789b..befd35ed0af 100644
--- a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
+++ b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -166,7 +166,33 @@ private static void openExternalFilePlatformIndependent(Optional<ExternalFileTyp
      * @throws IOException
      */
     public static void openFolderAndSelectFile(Path fileLink) throws IOException {
-        NATIVE_DESKTOP.openFolderAndSelectFile(fileLink);
+        if (fileLink == null) {
+            return;
+        }
+        boolean usingDefault = Globals.prefs.getBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION);
+
+        if (usingDefault) {
+            NATIVE_DESKTOP.openFolderAndSelectFile(fileLink);
+        } else {
+            String absolutePath = fileLink.toAbsolutePath().getParent().toString();
+            String command = Globals.prefs.get(JabRefPreferences.FILE_BROWSER_COMMAND);
+            if (!command.isEmpty()) {
+                command = command.replaceAll("\\s+", " "); // normalize white spaces
+
+                // replace the placeholder if used
+                command = command.replace("%DIR", absolutePath);
+                String[] subcommands = command.split(" ");
+
+                LOGGER.info("Executing command \"" + command + "\"...");
+
+                try {
+                    new ProcessBuilder(subcommands).start();
+                } catch (IOException exception) {
+                    LOGGER.error("Open File Browser", exception);
+                    JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Error occured while executing the command \"%0\".", command));
+                }
+            }
+        }
     }
 
     /**
@@ -228,22 +254,19 @@ public static void openConsole(File file) throws IOException {
 
             if (!command.isEmpty()) {
                 command = command.replaceAll("\\s+", " "); // normalize white spaces
-                String[] subcommands = command.split(" ");
+                command = command.replace("%DIR", absolutePath); // replace the placeholder if used
 
-                // replace the placeholder if used
-                String commandLoggingText = command.replace("%DIR", absolutePath);
+                String[] subcommands = command.split(" ");
 
+                LOGGER.info("Executing command \"" + command + "\"...");
                 JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", commandLoggingText));
-                LOGGER.info("Executing command \"" + commandLoggingText + "\"...");
 
                 try {
                     new ProcessBuilder(subcommands).start();
                 } catch (IOException exception) {
                     LOGGER.error("Open console", exception);
 
-                    JabRefGUI.getMainFrame().getDialogService().showErrorDialogAndWait(
-                            Localization.lang("Open console") + " - " + Localization.lang("Error",
-                            Localization.lang("Error occured while executing the command \"%0\".", commandLoggingText)));
+                    JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Error occured while executing the command \"%0\".", command));
                 }
             }
         }
diff --git a/src/main/java/org/jabref/gui/desktop/os/Linux.java b/src/main/java/org/jabref/gui/desktop/os/Linux.java
index 4f007e01ce9..dd45135a6b1 100644
--- a/src/main/java/org/jabref/gui/desktop/os/Linux.java
+++ b/src/main/java/org/jabref/gui/desktop/os/Linux.java
@@ -51,18 +51,18 @@ public void openFileWithApplication(String filePath, String application) throws
 
     @Override
     public void openFolderAndSelectFile(Path filePath) throws IOException {
-        String desktopSession = System.getenv("DESKTOP_SESSION").toLowerCase(Locale.ROOT);
+        String desktopSession = System.getenv("DESKTOP_SESSION");
 
-        String cmd;
+        String cmd = "xdg-open " + filePath.toAbsolutePath().getParent().toString(); //default command
 
-        if (desktopSession.contains("gnome")) {
-            cmd = "nautilus" + filePath.toString().replace(" ", "\\ ");
-        } else if (desktopSession.contains("kde")) {
-            cmd = "dolphin --select " + filePath.toString().replace(" ", "\\ ");
-        } else {
-            cmd = "xdg-open " + filePath.toAbsolutePath().getParent().toString();
+        if (desktopSession != null) {
+            desktopSession = desktopSession.toLowerCase(Locale.ROOT);
+            if (desktopSession.contains("gnome")) {
+                cmd = "nautilus" + filePath.toString().replace(" ", "\\ ");
+            } else if (desktopSession.contains("kde")) {
+                cmd = "dolphin --select " + filePath.toString().replace(" ", "\\ ");
+            }
         }
-
         Runtime.getRuntime().exec(cmd);
     }
 
@@ -73,7 +73,6 @@ public void openConsole(String absolutePath) throws IOException {
         BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));
 
         String emulatorName = reader.readLine();
-
         if (emulatorName != null) {
             emulatorName = emulatorName.substring(emulatorName.lastIndexOf(File.separator) + 1);
 
diff --git a/src/main/java/org/jabref/gui/preferences/ExternalTab.java b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
index e872abeadb4..8ce4dced4e7 100644
--- a/src/main/java/org/jabref/gui/preferences/ExternalTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
@@ -20,6 +20,7 @@
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.OS;
+import org.jabref.model.strings.StringUtil;
 import org.jabref.preferences.JabRefPreferences;
 
 class ExternalTab implements PrefsTab {
@@ -38,6 +39,12 @@ class ExternalTab implements PrefsTab {
     private final RadioButton sumatraReader;
     private final TextField adobeAcrobatReaderPath;
     private final TextField sumatraReaderPath;
+
+    private final RadioButton defaultFileBrowser;
+    private final RadioButton executeFileBrowser;
+    private final TextField fileBrowserCommand;
+    private final Button fileBrowserButton;
+
     private final GridPane builder = new GridPane();
     private final DialogService dialogService;
     private final FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder().build();
@@ -59,11 +66,20 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
         sumatraReaderPath = new TextField();
         Button browseSumatraReader = new Button(Localization.lang("Browse"));
 
+        defaultFileBrowser = new RadioButton(Localization.lang("Use default file browser"));
+        executeFileBrowser = new RadioButton(Localization.lang("Execute Command"));
+        fileBrowserCommand = new TextField();
+        fileBrowserButton = new Button(Localization.lang("Browser"));
+
         Label commandDescription = new Label(Localization.lang("Note: Use the placeholder %0 for the location of the opened library file.", "%DIR"));
         defaultConsole.setOnAction(e -> updateExecuteConsoleButtonAndFieldEnabledState());
         executeConsole.setOnAction(e -> updateExecuteConsoleButtonAndFieldEnabledState());
         browseButton.setOnAction(e -> showConsoleChooser());
 
+        fileBrowserButton.disableProperty().bind(executeFileBrowser.selectedProperty().not());
+        fileBrowserCommand.disableProperty().bind(executeFileBrowser.selectedProperty().not());
+        fileBrowserButton.setOnAction(e -> showFileBrowserCommandChooser());
+
         browseAdobeAcrobatReader.setOnAction(e -> showAdobeChooser());
 
         GridPane consoleOptionPanel = new GridPane();
@@ -83,6 +99,17 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
         adobeAcrobatReader.setToggleGroup(pdfReaderGroup);
         pdfOptionPanel.add(browseAdobeAcrobatReader, 3, 1);
 
+        Label fileBrowserCommandDescription = new Label(Localization.lang("Note: Use the placeholder %0 for the location of the opened library file.", "%DIR"));
+        GridPane fileBrowserOptionPanel = new GridPane();
+        final ToggleGroup fileBrowserGroup = new ToggleGroup();
+        defaultFileBrowser.setToggleGroup(fileBrowserGroup);
+        executeFileBrowser.setToggleGroup(fileBrowserGroup);
+        fileBrowserOptionPanel.add(defaultFileBrowser, 1, 1);
+        fileBrowserOptionPanel.add(executeFileBrowser, 1, 2);
+        fileBrowserOptionPanel.add(fileBrowserCommand, 2, 2);
+        fileBrowserOptionPanel.add(fileBrowserButton, 3, 2);
+        fileBrowserOptionPanel.add(fileBrowserCommandDescription, 2, 3);
+
         if (OS.WINDOWS) {
             browseSumatraReader.setOnAction(e -> showSumatraChooser());
             pdfOptionPanel.add(sumatraReader, 1, 2);
@@ -133,6 +160,12 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
 
         builder.add(pdfOptionPanel, 1, 13);
 
+        Label openFileBrowser = new Label(Localization.lang("Open File Browser"));
+        openFileBrowser.getStyleClass().add("sectionHeader");
+        builder.add(openFileBrowser,  1, 14);
+
+        builder.add(fileBrowserOptionPanel, 1, 15);
+
     }
 
     @Override
@@ -165,6 +198,10 @@ public void setValues() {
 
         consoleCommand.setText(Globals.prefs.get(JabRefPreferences.CONSOLE_COMMAND));
 
+        defaultFileBrowser.setSelected(Globals.prefs.getBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION));
+        executeFileBrowser.setSelected(!Globals.prefs.getBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION));
+        fileBrowserCommand.setText(Globals.prefs.get(JabRefPreferences.FILE_BROWSER_COMMAND));
+
         adobeAcrobatReaderPath.setText(Globals.prefs.get(JabRefPreferences.ADOBE_ACROBAT_COMMAND));
         if (OS.WINDOWS) {
             sumatraReaderPath.setText(Globals.prefs.get(JabRefPreferences.SUMATRA_PDF_COMMAND));
@@ -187,6 +224,13 @@ public void storeSettings() {
         prefs.putBoolean(JabRefPreferences.USE_DEFAULT_CONSOLE_APPLICATION, defaultConsole.isSelected());
         prefs.put(JabRefPreferences.CONSOLE_COMMAND, consoleCommand.getText());
         prefs.put(JabRefPreferences.ADOBE_ACROBAT_COMMAND, adobeAcrobatReaderPath.getText());
+
+        prefs.putBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION, defaultFileBrowser.isSelected());
+        if (StringUtil.isNotBlank(fileBrowserCommand.getText())) {
+            prefs.put(JabRefPreferences.FILE_BROWSER_COMMAND, fileBrowserCommand.getText());
+        } else {
+            prefs.putBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION, true); //default if no command specified
+        }
         if (OS.WINDOWS) {
             prefs.put(JabRefPreferences.SUMATRA_PDF_COMMAND, sumatraReaderPath.getText());
         }
@@ -220,6 +264,10 @@ private void showSumatraChooser() {
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> sumatraReaderPath.setText(file.toAbsolutePath().toString()));
     }
 
+    private void showFileBrowserCommandChooser() {
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> fileBrowserCommand.setText(file.toAbsolutePath().toString()));
+    }
+
     private void readerSelected() {
         if (adobeAcrobatReader.isSelected()) {
             prefs.put(JabRefPreferences.USE_PDF_READER, adobeAcrobatReaderPath.getText());
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index 88eae71f20a..92b6fa622a0 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -244,6 +244,9 @@ public class JabRefPreferences implements PreferencesService {
     public static final String ADOBE_ACROBAT_COMMAND = "adobeAcrobatCommand";
     public static final String SUMATRA_PDF_COMMAND = "sumatraCommand";
     public static final String USE_PDF_READER = "usePDFReader";
+    public static final String USE_DEFAULT_FILE_BROWSER_APPLICATION = "userDefaultFileBrowserApplication";
+    public static final String FILE_BROWSER_COMMAND = "fileBrowserCommand";
+
     // Currently, it is not possible to specify defaults for specific entry types
     // When this should be made possible, the code to inspect is org.jabref.gui.preferences.BibtexKeyPatternPrefTab.storeSettings() -> LabelPattern keypatterns = getCiteKeyPattern(); etc
     public static final String DEFAULT_BIBTEX_KEY_PATTERN = "defaultBibtexKeyPattern";
@@ -729,16 +732,19 @@ private JabRefPreferences() {
         defaults.put(USE_UNIT_FORMATTER_ON_SEARCH, Boolean.TRUE);
 
         defaults.put(USE_DEFAULT_CONSOLE_APPLICATION, Boolean.TRUE);
+        defaults.put(USE_DEFAULT_FILE_BROWSER_APPLICATION, Boolean.TRUE);
         if (OS.WINDOWS) {
             defaults.put(CONSOLE_COMMAND, "C:\\Program Files\\ConEmu\\ConEmu64.exe /single /dir \"%DIR\"");
             defaults.put(ADOBE_ACROBAT_COMMAND, "C:\\Program Files (x86)\\Adobe\\Acrobat Reader DC\\Reader");
             defaults.put(SUMATRA_PDF_COMMAND, "C:\\Program Files\\SumatraPDF");
             defaults.put(USE_PDF_READER, ADOBE_ACROBAT_COMMAND);
+            defaults.put(FILE_BROWSER_COMMAND, "explorer.exe /select, \"%DIR\"");
         } else {
             defaults.put(CONSOLE_COMMAND, "");
             defaults.put(ADOBE_ACROBAT_COMMAND, "");
             defaults.put(SUMATRA_PDF_COMMAND, "");
             defaults.put(USE_PDF_READER, "");
+            defaults.put(FILE_BROWSER_COMMAND, "");
         }
 
         //versioncheck defaults
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 7398d8fc491..1d75fc2d918 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1689,7 +1689,6 @@ Open\ console=Open console
 Use\ default\ terminal\ emulator=Use default terminal emulator
 Execute\ command=Execute command
 Note\:\ Use\ the\ placeholder\ %0\ for\ the\ location\ of\ the\ opened\ library\ file.=Note: Use the placeholder %0 for the location of the opened library file.
-Executing\ command\ \"%0\"...=Executing command \"%0\"...
 Error\ occured\ while\ executing\ the\ command\ \"%0\".=Error occured while executing the command \"%0\".
 Reformat\ ISSN=Reformat ISSN
 
@@ -2081,6 +2080,12 @@ Use\ selected\ document=Use selected document
 Accept\ changes=Accept changes
 Dismiss\ changes=Dismiss changes
 The\ library\ has\ been\ modified\ by\ another\ program.=The library has been modified by another program.
+
+Browser=Browser
+Execute\ Command=Execute Command
+Open\ File\ Browser=Open File Browser
+Use\ default\ file\ browser=Use default file browser
+
 Set\ rank\ to\ one=Set rank to one
 Set\ rank\ to\ two=Set rank to two
 Set\ rank\ to\ three=Set rank to three

From 6173de37a3c25d5f880f009fd70b229d84b8b3a4 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sat, 13 Apr 2019 18:12:49 +0200
Subject: [PATCH 181/184] fix compile error

(cherry picked from commit cc7b3a945e546c58aa358fc306111a09f96dbb2c)
---
 src/main/java/org/jabref/gui/desktop/JabRefDesktop.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
index befd35ed0af..40993772e54 100644
--- a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
+++ b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -259,7 +259,7 @@ public static void openConsole(File file) throws IOException {
                 String[] subcommands = command.split(" ");
 
                 LOGGER.info("Executing command \"" + command + "\"...");
-                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", commandLoggingText));
+                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", command));
 
                 try {
                     new ProcessBuilder(subcommands).start();

From 504c0d30cf87106b514e0a204561d19edde322b3 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sat, 13 Apr 2019 18:22:09 +0200
Subject: [PATCH 182/184] fix missing l10n from previous merge

---
 src/main/resources/l10n/JabRef_en.properties | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 1d75fc2d918..41bfe678055 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2091,3 +2091,5 @@ Set\ rank\ to\ two=Set rank to two
 Set\ rank\ to\ three=Set rank to three
 Set\ rank\ to\ four=Set rank to four
 Set\ rank\ to\ five=Set rank to five
+
+Executing\ command\ "%0"...=Executing command "%0"...
\ No newline at end of file

From 793fa88455410e65281acdda37676deb928bbbba Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Sat, 13 Apr 2019 18:33:15 +0200
Subject: [PATCH 183/184] Post change notifications on JavaFX (#4871)

* Post change notifications on JavaFX

Fixes #4817. The problem is that changes in other threads produce a "Not on FX application thread" exception. This is fixed by adding a wrapper around the list of entries. The wrapper only posts changes in the correct thread, without making a copy of the underlying list - so performance shouldn't be affected.

* fix compile error

* fix checkstyle
---
 src/main/java/org/jabref/gui/BasePanel.java   |  2 +-
 .../org/jabref/gui/actions/CleanupAction.java | 11 ++++--
 .../org/jabref/gui/maintable/MainTable.java   |  3 +-
 .../org/jabref/gui/util/BindingsHelper.java   | 35 ++++++++++++-------
 .../org/jabref/gui/util/UiThreadList.java     | 32 +++++++++++++++++
 5 files changed, 66 insertions(+), 17 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/util/UiThreadList.java

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index c6501ec7da9..0fbe1e98e9d 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -255,7 +255,7 @@ public void output(String s) {
 
     private void setupActions() {
         SaveDatabaseAction saveAction = new SaveDatabaseAction(this, Globals.prefs);
-        CleanupAction cleanUpAction = new CleanupAction(this, Globals.prefs);
+        CleanupAction cleanUpAction = new CleanupAction(this, Globals.prefs, Globals.TASK_EXECUTOR);
 
         actions.put(Actions.UNDO, undoAction);
         actions.put(Actions.REDO, redoAction);
diff --git a/src/main/java/org/jabref/gui/actions/CleanupAction.java b/src/main/java/org/jabref/gui/actions/CleanupAction.java
index d79a8a62c4f..4a0f89e8b61 100644
--- a/src/main/java/org/jabref/gui/actions/CleanupAction.java
+++ b/src/main/java/org/jabref/gui/actions/CleanupAction.java
@@ -9,6 +9,8 @@
 import org.jabref.gui.cleanup.CleanupDialog;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
+import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.cleanup.CleanupWorker;
 import org.jabref.logic.l10n.Localization;
@@ -20,15 +22,17 @@ public class CleanupAction implements BaseAction {
 
     private final BasePanel panel;
     private final DialogService dialogService;
+    private final TaskExecutor taskExecutor;
 
     private boolean isCanceled;
     private int modifiedEntriesCount;
     private final JabRefPreferences preferences;
 
-    public CleanupAction(BasePanel panel, JabRefPreferences preferences) {
+    public CleanupAction(BasePanel panel, JabRefPreferences preferences, TaskExecutor taskExecutor) {
         this.panel = panel;
         this.preferences = preferences;
         this.dialogService = panel.frame().getDialogService();
+        this.taskExecutor = taskExecutor;
     }
 
     @Override
@@ -58,8 +62,9 @@ public void action() {
 
             preferences.setCleanupPreset(chosenPreset.get());
 
-            this.cleanup(chosenPreset.get());
-            this.showResults();
+            BackgroundTask.wrap(() -> cleanup(chosenPreset.get()))
+                          .onSuccess(result -> showResults())
+                          .executeWith(taskExecutor);
         }
     }
 
diff --git a/src/main/java/org/jabref/gui/maintable/MainTable.java b/src/main/java/org/jabref/gui/maintable/MainTable.java
index 892116fb337..10c9a278a2b 100644
--- a/src/main/java/org/jabref/gui/maintable/MainTable.java
+++ b/src/main/java/org/jabref/gui/maintable/MainTable.java
@@ -36,6 +36,7 @@
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableInsertEntry;
+import org.jabref.gui.util.BindingsHelper;
 import org.jabref.gui.util.CustomLocalDragboard;
 import org.jabref.gui.util.ViewModelTableRowFactory;
 import org.jabref.logic.l10n.Localization;
@@ -108,7 +109,7 @@ public MainTable(MainTableDataModel model, JabRefFrame frame,
         }
         this.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
 
-        this.setItems(model.getEntriesFilteredAndSorted());
+        this.setItems(BindingsHelper.forUI(model.getEntriesFilteredAndSorted()));
         // Enable sorting
         model.getEntriesFilteredAndSorted().comparatorProperty().bind(this.comparatorProperty());
 
diff --git a/src/main/java/org/jabref/gui/util/BindingsHelper.java b/src/main/java/org/jabref/gui/util/BindingsHelper.java
index af0fafd441b..f53509c3f11 100644
--- a/src/main/java/org/jabref/gui/util/BindingsHelper.java
+++ b/src/main/java/org/jabref/gui/util/BindingsHelper.java
@@ -60,6 +60,7 @@ public static <A, B> MappedList<B, A> mapBacked(ObservableList<A> source, Functi
 
     public static <T, U> ObservableList<U> map(ObservableValue<T> source, Function<T, List<U>> mapper) {
         PreboundBinding<List<U>> binding = new PreboundBinding<List<U>>(source) {
+
             @Override
             protected List<U> computeValue() {
                 return mapper.apply(source.getValue());
@@ -103,10 +104,10 @@ public static <A, B> void bindBidirectional(ObservableValue<A> propertyA, Observ
 
     public static <A, B> void bindContentBidirectional(ObservableList<A> propertyA, ListProperty<B> propertyB, Consumer<ObservableList<B>> updateA, Consumer<List<A>> updateB) {
         bindContentBidirectional(
-                propertyA,
-                (ObservableValue<ObservableList<B>>) propertyB,
-                updateA,
-                updateB);
+                                 propertyA,
+                                 (ObservableValue<ObservableList<B>>) propertyB,
+                                 updateA,
+                                 updateB);
     }
 
     public static <A, B> void bindContentBidirectional(ObservableList<A> propertyA, ObservableValue<B> propertyB, Consumer<B> updateA, Consumer<List<A>> updateB) {
@@ -124,10 +125,10 @@ public static <A, B> void bindContentBidirectional(ListProperty<A> listProperty,
         Consumer<List<A>> updateB = newValueList -> property.setValue(mapToB.apply(newValueList));
 
         bindContentBidirectional(
-                listProperty,
-                property,
-                updateList,
-                updateB);
+                                 listProperty,
+                                 property,
+                                 updateList,
+                                 updateB);
     }
 
     public static <A, V, B> void bindContentBidirectional(ObservableMap<A, V> propertyA, ObservableValue<B> propertyB, Consumer<B> updateA, Consumer<Map<A, V>> updateB) {
@@ -143,14 +144,15 @@ public static <A, V, B> void bindContentBidirectional(ObservableMap<A, V> proper
     public static <A, V, B> void bindContentBidirectional(ObservableMap<A, V> propertyA, Property<B> propertyB, Consumer<B> updateA, Function<Map<A, V>, B> mapToB) {
         Consumer<Map<A, V>> updateB = newValueList -> propertyB.setValue(mapToB.apply(newValueList));
         bindContentBidirectional(
-                propertyA,
-                propertyB,
-                updateA,
-                updateB);
+                                 propertyA,
+                                 propertyB,
+                                 updateA,
+                                 updateB);
     }
 
     public static <T> ObservableValue<T> constantOf(T value) {
         return new ObjectBinding<T>() {
+
             @Override
             protected T computeValue() {
                 return value;
@@ -160,6 +162,7 @@ protected T computeValue() {
 
     public static ObservableValue<Boolean> constantOf(boolean value) {
         return new BooleanBinding() {
+
             @Override
             protected boolean computeValue() {
                 return value;
@@ -169,6 +172,7 @@ protected boolean computeValue() {
 
     public static ObservableValue<? extends String> emptyString() {
         return new StringBinding() {
+
             @Override
             protected String computeValue() {
                 return "";
@@ -176,6 +180,13 @@ protected String computeValue() {
         };
     }
 
+    /**
+     * Returns a wrapper around the given list that posts changes on the JavaFX thread.
+     */
+    public static <T> ObservableList<T> forUI(ObservableList<T> list) {
+        return new UiThreadList<>(list);
+    }
+
     private static class BidirectionalBinding<A, B> {
 
         private final ObservableValue<A> propertyA;
diff --git a/src/main/java/org/jabref/gui/util/UiThreadList.java b/src/main/java/org/jabref/gui/util/UiThreadList.java
new file mode 100644
index 00000000000..a81a7406764
--- /dev/null
+++ b/src/main/java/org/jabref/gui/util/UiThreadList.java
@@ -0,0 +1,32 @@
+package org.jabref.gui.util;
+
+import javafx.application.Platform;
+import javafx.collections.ListChangeListener;
+import javafx.collections.ObservableList;
+import javafx.collections.transformation.TransformationList;
+
+class UiThreadList<T> extends TransformationList<T, T> {
+    public UiThreadList(ObservableList<? extends T> source) {
+        super(source);
+    }
+
+    @Override
+    protected void sourceChanged(ListChangeListener.Change<? extends T> change) {
+        Platform.runLater(() -> fireChange(change));
+    }
+
+    @Override
+    public int getSourceIndex(int index) {
+        return index;
+    }
+
+    @Override
+    public T get(int index) {
+        return getSource().get(index);
+    }
+
+    @Override
+    public int size() {
+        return getSource().size();
+    }
+}

From 7a190c949c8f74324b27828b52771acd5ddd0524 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Sat, 13 Apr 2019 19:08:57 +0200
Subject: [PATCH 184/184] Try to update to gradle 5.0.2 (#4766)

Try to update to gradle 5.3.1
---
 build.gradle                             |  27 ++++++++++-------------
 gradle/wrapper/gradle-wrapper.jar        | Bin 56177 -> 55190 bytes
 gradle/wrapper/gradle-wrapper.properties |   2 +-
 3 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/build.gradle b/build.gradle
index 277af5824b9..9f7a5a4105b 100644
--- a/build.gradle
+++ b/build.gradle
@@ -15,20 +15,18 @@ buildscript {
 }
 
 plugins {
-    id 'com.gradle.build-scan' version '1.16'
-    id 'com.install4j.gradle' version '7.0.9'
-    id 'com.github.johnrengelman.shadow' version '4.0.2'
+    id 'com.gradle.build-scan' version '2.0.2'
+    id 'com.install4j.gradle' version '7.0.10'
+    id 'com.github.johnrengelman.shadow' version '5.0.0'
     id "com.simonharrer.modernizer" version '1.6.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.8'
-    id 'net.ltgt.errorprone' version '0.6.1'
-    id 'com.github.ben-manes.versions' version '0.20.0'
+    id 'net.ltgt.errorprone' version '0.7.1'
+    id 'com.github.ben-manes.versions' version '0.21.0'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
-buildScan {
-    licenseAgreementUrl = 'https://gradle.com/terms-of-service'
-    licenseAgree = 'yes'
-}
+buildScan { termsOfServiceUrl = 'https://gradle.com/terms-of-service'; termsOfServiceAgree = 'yes' }
+
 
 apply plugin: 'java'
 apply plugin: 'application'
@@ -129,9 +127,10 @@ dependencies {
     compile 'com.google.guava:guava:27.1-jre'
 
     // JavaFX stuff
+    compile 'de.jensd:fontawesomefx-commons:8.15'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'de.saxsys:mvvmfx-validation:1.8.0'
-    compile 'de.saxsys:mvvmfx:1.7.0'
+    compile 'de.saxsys:mvvmfx:1.8.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
     compile 'org.fxmisc.richtext:richtextfx:0.9.3'
@@ -196,11 +195,6 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject("Ignore SNAPSHOT releases")
             }
         }
-        rules.withModule("com.gradle.build-scan:com.gradle.build-scan.gradle.plugin") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.*/) {
-                selection.reject("Cannot be upgraded to version 2 until we upgrade to gradle 5")
-            }
-        }
         rules.withModule("org.controlsfx:controlsfx") { ComponentSelection selection ->
             if (selection.candidate.version ==~ /9.*/) { // Reject version 9 or higher
                 selection.reject("Cannot be updated to 9.*.* until Jabref works with Java 9")
@@ -322,11 +316,14 @@ task generateSearchGrammarSource(type: JavaExec) {
 compileJava {
     options.encoding = 'UTF-8'
     options.compilerArgs << "-Xlint:none"
+    //ignore annotation processor from log4j2
+    options.compilerArgs += '-proc:none'
 }
 compileJava.dependsOn "generateSource"
 
 compileTestJava {
     options.encoding = 'UTF-8'
+    options.compilerArgs += '-proc:none'
 }
 
 javadoc {
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index 13536770052936a92b204cc34e72284a03a6903c..87b738cbd051603d91cc39de6cb000dd98fe6b02 100644
GIT binary patch
delta 46897
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diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index e0b3fb8d70b..ea13fdfd192 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.10.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-5.3.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists