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

* upstream/master:
  Update Libraries (#4366)
  ArXiv fetcher support http url (#4367)
  Fix issue 3861 : XMP Dialog, Add new Groups dialog, Append Library dialog to javafx (#4264)
  fix IndexOutOfBoundsException when saving preferences
  group RadioButtons in ExportSortingPrefsTab to prevent the selection of multiple or no order types
  Convert Part of the Issue#3861 Quality->Cleanup entries (#4268)
  UPDATE gradle to 4.10.2 (#4358)
  Completed General Fields Customizer conversion to JavaFX (#4346)
  Fix JavaFX thread exception when fetching new infos (#4354)
  Auto trim url field (#4355)
  Fix freezes in entry editor (#4351)

# Conflicts:
#	src/main/java/org/jabref/preferences/PreferencesService.java

CHANGELOG.md

@@ -11,6 +11,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We updated the dialog for setting up general fields.
+- URL field formatting is updated. All whitespace chars, located at the beginning/ending of the url, are trimmed automatically
 - We changed the behavior of the field formatting dialog such that the `bibtexkey` is not changed when formatting all fields or all text fields.
 - We added a "Move file to file directory and rename file" option for simultaneously moving and renaming of document file. [#4166](https://github.com/JabRef/jabref/issues/4166)
 - Use integrated graphics card instead of discrete on macOS [#4070](https://github.com/JabRef/jabref/issues/4070)
@@ -69,6 +71,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where files added via the "Attach file" contextmenu of an entry were not made relative. [#4201](https://github.com/JabRef/jabref/issues/4201) and [#4241](https://github.com/JabRef/jabref/issues/4241)
 - We fixed an issue where author list parser can't generate bibtex for Chinese author. [#4169](https://github.com/JabRef/jabref/issues/4169)
 - We fixed an issue where the list of XMP Exclusion fields in the preferences was not be saved [#4072](https://github.com/JabRef/jabref/issues/4072)
+- We fixed an issue where the ArXiv Fetcher did not support HTTP URLs [#4367](https://github.com/JabRef/jabref/pull/4367)
 
 
 

build.gradle

@@ -17,11 +17,11 @@ buildscript {
 plugins {
     id 'com.gradle.build-scan' version '1.16'
     id 'com.install4j.gradle' version '7.0.7'
-    id 'com.github.johnrengelman.shadow' version '2.0.4'
+    id 'com.github.johnrengelman.shadow' version '4.0.0'
     id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
     id "com.simonharrer.modernizer" version '1.6.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.7'
-    id 'net.ltgt.errorprone' version '0.0.16'
+    id 'net.ltgt.errorprone' version '0.6'
     id 'com.github.ben-manes.versions' version '0.20.0'
 }
 
@@ -65,7 +65,7 @@ sourceSets {
             srcDirs = ["src/main/java", "src/main/resources"]
         }
     }
-    test{
+    test {
         java {
             srcDirs = ["src/test/java"]
         }
@@ -96,9 +96,9 @@ dependencies {
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.11'
-    compile 'org.apache.pdfbox:fontbox:2.0.11'
-    compile 'org.apache.pdfbox:xmpbox:2.0.11'
+    compile 'org.apache.pdfbox:pdfbox:2.0.12'
+    compile 'org.apache.pdfbox:fontbox:2.0.12'
+    compile 'org.apache.pdfbox:xmpbox:2.0.12'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     compile 'org.bouncycastle:bcprov-jdk15on:1.60'
@@ -158,21 +158,21 @@ dependencies {
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
-    errorprone 'com.google.errorprone:error_prone_core:2.3.1'
+    errorproneJavac 'com.google.errorprone:javac:1.8.0-u20'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.1.2'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.1.2'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.2.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.2.0'
 
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.3.1'
     testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.1'
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.3.1'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.1'
     testCompile 'org.junit.platform:junit-platform-launcher:1.3.1'
-    testCompile 'org.junit-pioneer:junit-pioneer:0.1.2'
+    testCompile 'org.junit-pioneer:junit-pioneer:0.2.1'
     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:2.22.0'
-    testCompile 'com.github.tomakehurst:wiremock:2.18.0'
+    testCompile 'org.mockito:mockito-core:2.23.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.19.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
@@ -181,7 +181,7 @@ dependencies {
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.12'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.13'
 }
 
 jacoco {
@@ -199,7 +199,7 @@ dependencyUpdates.revision = 'integration'
 dependencyUpdates.resolutionStrategy = {
     componentSelection { rules ->
         rules.all { ComponentSelection selection ->
-            if ( selection.candidate.module!="javax.inject"  && selection.candidate.version ==~ /[0-9].*SNAPSHOT/ ) {
+            if (selection.candidate.version ==~ /[0-9].*SNAPSHOT/) {
                 selection.reject("Ignore SNAPSHOT releases")
             }
         }
@@ -209,20 +209,36 @@ dependencyUpdates.resolutionStrategy = {
             }
         }
         rules.withModule("com.github.tomtung:latex2unicode_2.12") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /0.2.2/) { // Reject version higher than 2.0.2
+            if (selection.candidate.version ==~ /0.2.[3,4]/) {
+                // Reject version higher than 2.0.2. see https://github.com/JabRef/jabref/pull/3781
                 selection.reject("Cannot be updated to 0.2.4 until JabRef is prepared for it")
             }
         }
+        rules.withModule("com.github.johnrengelman.shadow:com.github.johnrengelman.shadow.gradle.plugin") { ComponentSelection selection ->
+            if (selection.candidate.version == /4.0.1/) {
+                selection.reject("Version 4.0.1 breaks the release process.")
+            }
+        }
         rules.withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
             if (selection.candidate.version ==~ /2.*/) {
                 selection.reject("Cannot be upgraded to version 2")
             }
         }
-         rules.withModule("com.jfoenix:jfoenix") { ComponentSelection selection ->
+        rules.withModule("com.jfoenix:jfoenix") { 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")
             }
         }
+        rules.withModule("com.google.errorprone:javac") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /1.9.*/ || selection.candidate.version ==~ /9.*/) {
+                selection.reject("Cannot be updated to 9.*.* until Jabref works with Java 9")
+            }
+        }
+        rules.withModule("com.sun.xml.bind:jaxb-xjc") { ComponentSelection selection ->
+            if (!(selection.candidate.version ==~ /2.2.4.*/) || selection.candidate.version ==~ /2.[3-9].*/) {
+                selection.reject("Cannot be updated to 2.2.5 or higher.")
+            }
+        }
     }
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.10.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.10.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

src/main/java/org/jabref/JabRefGUI.java

@@ -29,6 +29,7 @@
 import org.jabref.model.database.shared.DatabaseNotSupportedException;
 import org.jabref.preferences.JabRefPreferences;
 
+import impl.org.controlsfx.skin.DecorationPane;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -143,7 +144,12 @@ private void openWindow(Stage mainStage) {
             mainStage.setHeight(Globals.prefs.getDouble(JabRefPreferences.SIZE_Y));
         }
 
-        Scene scene = new Scene(JabRefGUI.mainFrame, 800, 800);
+        // We create a decoration pane ourselves for performance reasons
+        // (otherwise it has to be injected later, leading to a complete redraw/relayout of the complete scene)
+        DecorationPane root = new DecorationPane();
+        root.getChildren().add(JabRefGUI.mainFrame);
+
+        Scene scene = new Scene(root, 800, 800);
         Globals.getThemeLoader().installBaseCss(scene, Globals.prefs);
         mainStage.setTitle(JabRefFrame.FRAME_TITLE);
         mainStage.getIcons().addAll(IconTheme.getLogoSetFX());

src/main/java/org/jabref/gui/BasePanel.java

@@ -44,6 +44,7 @@
 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;
 import org.jabref.gui.exporter.SaveDatabaseAction;
 import org.jabref.gui.externalfiles.FindFullTextAction;
@@ -203,7 +204,7 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
 
         this.getDatabase().registerListener(new UpdateTimestampListener(Globals.prefs));
 
-        this.entryEditor = new EntryEditor(this, preferences.getEntryEditorPreferences(), Globals.getFileUpdateMonitor(), dialogService, externalFileTypes);
+        this.entryEditor = new EntryEditor(this, preferences.getEntryEditorPreferences(), Globals.getFileUpdateMonitor(), dialogService, externalFileTypes, Globals.TASK_EXECUTOR);
 
         this.preview = new PreviewPanel(this, getBibDatabaseContext(), preferences.getKeyBindings(), preferences.getPreviewPreferences(), dialogService, externalFileTypes);
         frame().getGlobalSearchBar().getSearchQueryHighlightObservable().addSearchListener(preview);