Merge remote-tracking branch 'upstream/master' into fixlookupfulltext

* upstream/master: (27 commits) remove wrong dependencies add missing dependencies Fix exception when adding field formatter in 'Cleanup entries' dialog Disables the preview cycling Removed unused method (#5219) Switch from tika-parsers to tika-core (#5217) Fix for issue 4629 (#5150) fix l10n, again fix l10n Fix checkstyle Removed old entrypreview and corresponding actions Prototype Add minor improvements and remove unused code Update CHANGELOG.md Update to current entry types and reformat code Convert Integer type to primitive Fix localization keys fix checkstyle again fix checkstyle erros Bibtexextractor ...
JabRef · Aug 25, 2019 · 1846b24 · 1846b24
2 parents d2c4724 + 06f1049
commit 1846b24
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diff --git a/AUTHORS b/AUTHORS
@@ -210,3 +210,4 @@ Yang Zongze
 Yara Grassi Gouffon
 Yifan Peng
 Zhang Liang
+Nikita Borovikov
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -70,6 +70,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
 - We added an option on the Linked File Viewer to rename the attached file of an entry directly on the JabRef. [#4844](https://github.com/JabRef/jabref/issues/4844)
 - We added an option in the preference dialog box that allows user to enable helpful tooltips.[#3599](https://github.com/JabRef/jabref/issues/3599)
+- We added a tool for extracting BibTeX entries from plain text. [#5206](https://github.com/JabRef/jabref/pull/5206)
 - We moved the dropdown menu for selecting the push-application from the toolbar into the external application preferences. [#674](https://github.com/JabRef/jabref/issues/674)
 - We removed the alphabetical ordering of the custom tabs and updated the error message when trying to create a general field with a name containing an illegal character. [#5019](https://github.com/JabRef/jabref/issues/5019)
 - We added a context menu to the bib(la)tex-source-editor to copy'n'paste. [#5007](https://github.com/JabRef/jabref/pull/5007)

diff --git a/build.gradle b/build.gradle
@@ -94,7 +94,7 @@ dependencies {
     compile 'org.apache.pdfbox:fontbox:2.0.16'
     compile 'org.apache.pdfbox:xmpbox:2.0.16'
 
-    compile group: 'org.apache.tika', name: 'tika-parsers', version: '1.22'
+    compile group: 'org.apache.tika', name: 'tika-core', version: '1.22'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     compile 'org.bouncycastle:bcprov-jdk15on:1.62'
@@ -121,6 +121,7 @@ dependencies {
 
     compile 'com.google.guava:guava:28.0-jre'
 
+
     // JavaFX stuff
     compile 'de.jensd:fontawesomefx-commons:8.15'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'

diff --git a/docs/adr/0005-fully-support-utf8-only-for-latex-files.md b/docs/adr/0005-fully-support-utf8-only-for-latex-files.md
@@ -0,0 +1,44 @@
+# Fully Support UTF-8 Only For LaTeX Files
+
+## Context and Problem Statement
+
+The feature [search for citations](https://github.com/JabRef/help.jabref.org/issues/210) displays the content of LaTeX files.
+The LaTeX files are text files and might be encoded arbitrarily.
+
+## Considered Options
+
+* Support UTF-8 encoding only
+* Support ASCII encoding only
+* Support (nearly) all encodings
+
+## Decision Outcome
+
+Chosen option: "Support UTF-8 encoding only", because comes out best (see below).
+
+### Positive Consequences
+
+* All content of LaTeX files are displayed in JabRef
+
+### Negative Consequences
+
+* When a LaTeX files is encoded in another encoding, the user might see strange characters in JabRef
+
+## Pros and Cons of the Options
+
+### Support UTF-8 encoding only
+
+* Good, because covers most tex file encodings
+* Good, because easy to implement
+* Bad, because does not support encodings used before around 2010
+
+### Support ASCII encoding only
+
+* Good, because easy to implement
+* Bad, because does not support any encoding at all
+
+### Support (nearly) all encodings
+
+* Good, because easy to implement
+* Bad, because it relies on Apache Tika's `CharsetDetector`, which resides in `tika-parsers`.
+  This causes issues during compilation (see https://github.com/JabRef/jabref/pull/3421#issuecomment-524532832).
+  Example: `error: module java.xml.bind reads package javax.activation from both java.activation and jakarta.activation`.
diff --git a/docs/adr/index.md b/docs/adr/index.md
@@ -9,6 +9,7 @@ This log lists the architectural decisions for JabRef.
 - [ADR-0002](0002-use-slf4j-for-logging.md) - Use slf4j together with log4j2 for logging
 - [ADR-0003](0003-use-gradle-as-build-tool.md) - Use Gradle as build tool
 - [ADR-0004](0004-use-mariadb-connector.md) - Use MariaDB Connector
+- [ADR-0005](0005-fully-support-utf8-only-for-latex-files.md) - Fully Support UTF-8 Only For LaTeX Files
 
 <!-- adrlogstop -->
 

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
@@ -53,7 +53,6 @@
 import org.jabref.gui.mergeentries.MergeEntriesAction;
 import org.jabref.gui.mergeentries.MergeWithFetchedEntryAction;
 import org.jabref.gui.preview.CitationStyleToClipboardWorker;
-import org.jabref.gui.preview.PreviewPanel;
 import org.jabref.gui.specialfields.SpecialFieldDatabaseChangeListener;
 import org.jabref.gui.specialfields.SpecialFieldValueViewModel;
 import org.jabref.gui.specialfields.SpecialFieldViewModel;
@@ -122,7 +121,6 @@ public class BasePanel extends StackPane {
     // Keeps track of the string dialog if it is open.
     private final Map<Actions, BaseAction> actions = new HashMap<>();
     private final SidePaneManager sidePaneManager;
-    private final PreviewPanel preview;
     private final BasePanelPreferences preferences;
     private final ExternalFileTypes externalFileTypes;
 
@@ -179,8 +177,6 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         this.getDatabase().registerListener(new UpdateTimestampListener(Globals.prefs));
 
         this.entryEditor = new EntryEditor(this, externalFileTypes);
-
-        this.preview = new PreviewPanel(getBibDatabaseContext(), this, dialogService, externalFileTypes, Globals.getKeyPrefs(), preferences.getPreviewPreferences());
     }
 
     @Subscribe
@@ -263,8 +259,6 @@ private void setupActions() {
         // The action for copying selected entries.
         actions.put(Actions.COPY, this::copy);
 
-        actions.put(Actions.PRINT_PREVIEW, new PrintPreviewAction());
-
         actions.put(Actions.CUT, this::cut);
 
         actions.put(Actions.DELETE, () -> delete(false));
@@ -358,19 +352,6 @@ private void setupActions() {
                     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();
-            Globals.prefs.storePreviewPreferences(newPreviewPreferences);
-            setPreviewActive(enabled);
-        });
-
-        actions.put(Actions.NEXT_PREVIEW_STYLE, this::nextPreviewStyle);
-        actions.put(Actions.PREVIOUS_PREVIEW_STYLE, this::previousPreviewStyle);
-
         actions.put(Actions.SEND_AS_EMAIL, new SendAsEMailAction(frame));
 
         actions.put(Actions.WRITE_XMP, new WriteXMPAction(this)::execute);
@@ -679,7 +660,6 @@ private void createMainTable() {
                                                          .stream()
                                                          .findFirst()
                                                          .ifPresent(entry -> {
-                                                             preview.setEntry(entry);
                                                              entryEditor.setEntry(entry);
                                                          }));
 
@@ -816,9 +796,7 @@ private void instantiateSearchAutoCompleter() {
     }
 
     private void adjustSplitter() {
-        if (mode == BasePanelMode.SHOWING_PREVIEW) {
-            splitPane.setDividerPositions(Globals.prefs.getPreviewPreferences().getPreviewPanelDividerPosition().doubleValue());
-        } else if (mode == BasePanelMode.SHOWING_EDITOR) {
+        if (mode == BasePanelMode.SHOWING_EDITOR) {
             splitPane.setDividerPositions(preferences.getEntryEditorDividerPosition());
         }
     }
@@ -844,17 +822,11 @@ public void showAndEdit(BibEntry entry) {
     }
 
     private void showBottomPane(BasePanelMode newMode) {
-        Node pane;
-        switch (newMode) {
-            case SHOWING_PREVIEW:
-                pane = preview;
-                break;
-            case SHOWING_EDITOR:
-                pane = entryEditor;
-                break;
-            default:
-                throw new UnsupportedOperationException("new mode not recognized: " + newMode.name());
+        if (newMode != BasePanelMode.SHOWING_EDITOR) {
+            throw new UnsupportedOperationException("new mode not recognized: " + newMode.name());
         }
+        Node pane = entryEditor;
+
         if (splitPane.getItems().size() == 2) {
             splitPane.getItems().set(1, pane);
         } else {
@@ -870,23 +842,6 @@ private void showAndEdit() {
         }
     }
 
-    /**
-     * Sets the given preview panel as the bottom component in the split panel. Updates the mode to SHOWING_PREVIEW.
-     *
-     * @param entry The entry to show in the preview.
-     */
-    private void showPreview(BibEntry entry) {
-        showBottomPane(BasePanelMode.SHOWING_PREVIEW);
-
-        preview.setEntry(entry);
-    }
-
-    private void showPreview() {
-        if (!mainTable.getSelectedEntries().isEmpty()) {
-            showPreview(mainTable.getSelectedEntries().get(0));
-        }
-    }
-
     public void nextPreviewStyle() {
         cyclePreview(Globals.prefs.getPreviewPreferences().getPreviewCyclePosition() + 1);
     }
@@ -901,16 +856,15 @@ private void cyclePreview(int newPosition) {
                                                              .withPreviewCyclePosition(newPosition)
                                                              .build();
         Globals.prefs.storePreviewPreferences(previewPreferences);
-
-        preview.updateLayout(previewPreferences);
+        entryEditor.updatePreviewInTabs(previewPreferences);
     }
 
     /**
      * Removes the bottom component.
      */
     public void closeBottomPane() {
         mode = BasePanelMode.SHOWING_NOTHING;
-        splitPane.getItems().removeAll(entryEditor, preview);
+        splitPane.getItems().remove(entryEditor);
     }
 
     /**
@@ -932,23 +886,17 @@ public void selectNextEntry() {
     /**
      * This method is called from an EntryEditor when it should be closed. We relay to the selection listener, which
      * takes care of the rest.
-     *
-     * @param editor The entry editor to close.
      */
-    public void entryEditorClosing(EntryEditor editor) {
-        if (Globals.prefs.getPreviewPreferences().isPreviewPanelEnabled()) {
-            showPreview(editor.getEntry());
-        } else {
-            closeBottomPane();
-        }
+    public void entryEditorClosing() {
+        closeBottomPane();
         mainTable.requestFocus();
     }
 
     /**
-     * Closes the entry editor or preview panel if it is showing the given entry.
+     * Closes the entry editor if it is showing the given entry.
      */
-    public void ensureNotShowingBottomPanel(BibEntry entry) {
-        if (((mode == BasePanelMode.SHOWING_EDITOR) && (entryEditor.getEntry() == entry)) || ((mode == BasePanelMode.SHOWING_PREVIEW))) {
+    private void ensureNotShowingBottomPanel(BibEntry entry) {
+        if (((mode == BasePanelMode.SHOWING_EDITOR) && (entryEditor.getEntry() == entry))) {
             closeBottomPane();
         }
     }
@@ -996,7 +944,7 @@ public BibDatabase getDatabase() {
         return bibDatabaseContext.getDatabase();
     }
 
-    public boolean showDeleteConfirmationDialog(int numberOfEntries) {
+    private boolean showDeleteConfirmationDialog(int numberOfEntries) {
         if (Globals.prefs.getBoolean(JabRefPreferences.CONFIRM_DELETE)) {
             String title = Localization.lang("Delete entry");
             String message = Localization.lang("Really delete the selected entry?");
@@ -1029,13 +977,7 @@ private void saveDividerLocation(Number position) {
             return;
         }
 
-        if (mode == BasePanelMode.SHOWING_PREVIEW) {
-            PreviewPreferences previewPreferences = Globals.prefs.getPreviewPreferences()
-                                                                 .getBuilder()
-                                                                 .withPreviewPanelDividerPosition(position)
-                                                                 .build();
-            Globals.prefs.storePreviewPreferences(previewPreferences);
-        } else if (mode == BasePanelMode.SHOWING_EDITOR) {
+        if (mode == BasePanelMode.SHOWING_EDITOR) {
             preferences.setEntryEditorDividerPosition(position.doubleValue());
         }
     }
@@ -1093,14 +1035,6 @@ public String formatOutputMessage(String start, int count) {
         return String.format("%s %d %s.", start, count, (count > 1 ? Localization.lang("entries") : Localization.lang("entry")));
     }
 
-    private void setPreviewActive(boolean enabled) {
-        if (enabled) {
-            showPreview();
-        } else {
-            preview.close();
-        }
-    }
-
     public CountingUndoManager getUndoManager() {
         return undoManager;
     }
@@ -1353,13 +1287,4 @@ public void action() {
             markChangedOrUnChanged();
         }
     }
-
-    private class PrintPreviewAction implements BaseAction {
-
-        @Override
-        public void action() {
-            showPreview();
-            preview.print();
-        }
-    }
 }
diff --git a/src/main/java/org/jabref/gui/BasePanelMode.java b/src/main/java/org/jabref/gui/BasePanelMode.java
@@ -6,7 +6,6 @@
 
 public enum BasePanelMode {
     SHOWING_NOTHING,
-    SHOWING_PREVIEW,
     SHOWING_EDITOR,
     WILL_SHOW_EDITOR
 }
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -52,6 +52,7 @@
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.auximport.NewSubLibraryAction;
+import org.jabref.gui.bibtexextractor.ExtractBibtexAction;
 import org.jabref.gui.bibtexkeypattern.BibtexKeyPatternAction;
 import org.jabref.gui.contentselector.ManageContentSelectorAction;
 import org.jabref.gui.copyfiles.CopyFilesAction;
@@ -772,6 +773,7 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.FIND_UNLINKED_FILES, new FindUnlinkedFilesAction(this, stateManager)),
                 factory.createMenuItem(StandardActions.WRITE_XMP, new OldDatabaseCommandWrapper(Actions.WRITE_XMP, this, stateManager)),
                 factory.createMenuItem(StandardActions.COPY_LINKED_FILES, new CopyFilesAction(stateManager, this.getDialogService())),
+                factory.createMenuItem(StandardActions.EXTRACT_BIBTEX, new ExtractBibtexAction(stateManager)),
 
                 new SeparatorMenuItem(),
 
@@ -806,7 +808,6 @@ private MenuBar createMenu() {
 
                     new SeparatorMenuItem(),
 
-                    factory.createCheckMenuItem(StandardActions.TOGGLE_PREVIEW, new OldDatabaseCommandWrapper(Actions.TOGGLE_PREVIEW, this, stateManager), Globals.prefs.getPreviewPreferences().isPreviewPanelEnabled()),
                     factory.createMenuItem(StandardActions.NEXT_PREVIEW_STYLE, new OldDatabaseCommandWrapper(Actions.NEXT_PREVIEW_STYLE, this, stateManager)),
                     factory.createMenuItem(StandardActions.PREVIOUS_PREVIEW_STYLE, new OldDatabaseCommandWrapper(Actions.PREVIOUS_PREVIEW_STYLE, this, stateManager)),
 
@@ -1225,6 +1226,11 @@ public EditAction(Actions command) {
             this.command = command;
         }
 
+        @Override
+        public String toString() {
+            return this.command.toString();
+        }
+
         @Override
         public void execute() {
             Node focusOwner = mainStage.getScene().getFocusOwner();

diff --git a/src/main/java/org/jabref/gui/actions/ActionFactory.java b/src/main/java/org/jabref/gui/actions/ActionFactory.java
@@ -74,7 +74,7 @@ private static Label getAssociatedNode(MenuItem menuItem) {
     }
 
     public MenuItem configureMenuItem(Action action, Command command, MenuItem menuItem) {
-        ActionUtils.configureMenuItem(new JabRefAction(action, command, keyBindingRepository), menuItem);
+        ActionUtils.configureMenuItem(new JabRefAction(action, command, keyBindingRepository, Sources.FromMenu), menuItem);
         setGraphic(menuItem, action);
 
         // Show tooltips
@@ -105,7 +105,7 @@ public MenuItem createMenuItem(Action action, Command command) {
     }
 
     public CheckMenuItem createCheckMenuItem(Action action, Command command, boolean selected) {
-        CheckMenuItem checkMenuItem = ActionUtils.createCheckMenuItem(new JabRefAction(action, command, keyBindingRepository));
+        CheckMenuItem checkMenuItem = ActionUtils.createCheckMenuItem(new JabRefAction(action, command, keyBindingRepository, Sources.FromMenu));
         checkMenuItem.setSelected(selected);
         setGraphic(checkMenuItem, action);
 
@@ -127,7 +127,7 @@ public Menu createSubMenu(Action action, MenuItem... children) {
     }
 
     public Button createIconButton(Action action, Command command) {
-        Button button = ActionUtils.createButton(new JabRefAction(action, command, keyBindingRepository), ActionUtils.ActionTextBehavior.HIDE);
+        Button button = ActionUtils.createButton(new JabRefAction(action, command, keyBindingRepository, Sources.FromButton), ActionUtils.ActionTextBehavior.HIDE);
 
         button.getStyleClass().setAll("icon-button");
 
@@ -140,7 +140,7 @@ public Button createIconButton(Action action, Command command) {
 
     public ButtonBase configureIconButton(Action action, Command command, ButtonBase button) {
         ActionUtils.configureButton(
-                new JabRefAction(action, command, keyBindingRepository),
+                                    new JabRefAction(action, command, keyBindingRepository, Sources.FromButton),
                 button,
                 ActionUtils.ActionTextBehavior.HIDE);
 

diff --git a/src/main/java/org/jabref/gui/actions/Actions.java b/src/main/java/org/jabref/gui/actions/Actions.java
@@ -49,7 +49,6 @@ public enum Actions {
     SELECT_ALL,
     SEND_AS_EMAIL,
     TOGGLE_GROUPS,
-    TOGGLE_PREVIEW,
     UNABBREVIATE,
     UNDO,
     WRITE_XMP,