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

* upstream/master:
  Fix NPE and not on FX Thread in PreviewPrefs Tabs (#4624)
  Fix preview style configuration (#4613)
  Bump wiremock from 2.20.0 to 2.21.0 (#4623)
  snap: disable tests build, add removable media and specify architectures (#4619)
  Bump checkstyle from 8.16 to 8.17 (#4620)
  Fix preferences path: use _JAVA_OPTIONS
  Try to fix not on FX thread for search and autocomplete (#4618)
  Update snapcraft.yaml Move to snap folder
  Convert DuplicateResolverDialog to javafx (#4601)
  Fix for BibTex source tab parsing issue if field contains {} (#4581)
  Convert OO/LO SidePanel to javafx (#4341)
  Convert "Customize importer" dialog to JavaFX (#4608)
  Convert "From Aux file" dialog to JavaFX (#4607)
  Convert "Show preferences" dialog to JavaFX (#4605)
  Fix not on FX thread exception
  Force javafx to run thread (#4604)
  Convert new version dialog to JavaFX (#4602)
  Add a variable to track the change in preview style (#4587)
  Solution for submitting dialog with Ctrl + Enter (#4496) (#4592)
  Bump mysql-connector-java from 8.0.13 to 8.0.14 (#4599)

# Conflicts:
#	src/main/resources/l10n/JabRef_en.properties

.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/
@@ -23,18 +31,6 @@ 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 ###

CHANGELOG.md

@@ -50,6 +50,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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 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)
 
 
 

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:8.0.13'
+    compile 'mysql:mysql-connector-java:8.0.14'
 
     compile 'org.postgresql:postgresql:42.2.5'
 
@@ -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'
@@ -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 {

buildres/snapcraft/jabref.desktop → 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;

snap/snapcraft.yaml

@@ -0,0 +1,41 @@
+name: jabref
+version: "git"
+version-script: cat build.gradle | grep "^version =" | cut -d'"' -f2
+#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: "-Duser.home=$SNAP_USER_DATA"
+    plugs:
+      - desktop
+      - desktop-legacy
+      - wayland
+      - unity7
+      - 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, -xtest]
+    gradle-output-dir: 'build/releases'
+    after: [desktop-gtk2]

src/main/java/org/jabref/FallbackExceptionHandler.java

@@ -1,5 +1,7 @@
 package org.jabref;
 
+import org.jabref.gui.util.DefaultTaskExecutor;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -17,9 +19,11 @@ public static void installExceptionHandler() {
     @Override
     public void uncaughtException(Thread thread, Throwable exception) {
         LOGGER.error("Uncaught exception occurred in " + thread, exception);
-        JabRefGUI.getMainFrame()
-                 .getDialogService()
-                 .showErrorDialogAndWait(
-                                         exception.getLocalizedMessage(), exception);
+
+        DefaultTaskExecutor.runInJavaFXThread(() ->
+                JabRefGUI.getMainFrame()
+                         .getDialogService()
+                         .showErrorDialogAndWait("Uncaught exception occurred in " + thread, exception)
+        );
     }
 }

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

@@ -1345,39 +1345,41 @@ public void listen(EntryRemovedEvent entryRemovedEvent) {
     /**
      * Ensures that the search auto completer is up to date when entries are changed AKA Let the auto completer, if any,
      * harvest words from the entry
+     * Actual methods for autocomplete indexing  must run in javafx thread
      */
     private class SearchAutoCompleteListener {
 
         @Subscribe
         public void listen(EntryAddedEvent addedEntryEvent) {
-            searchAutoCompleter.indexEntry(addedEntryEvent.getBibEntry());
+            DefaultTaskExecutor.runInJavaFXThread(() -> searchAutoCompleter.indexEntry(addedEntryEvent.getBibEntry()));
         }
 
         @Subscribe
         public void listen(EntryChangedEvent entryChangedEvent) {
-            searchAutoCompleter.indexEntry(entryChangedEvent.getBibEntry());
+            DefaultTaskExecutor.runInJavaFXThread(() -> searchAutoCompleter.indexEntry(entryChangedEvent.getBibEntry()));
         }
     }
 
     /**
      * Ensures that the results of the current search are updated when a new entry is inserted into the database
+     * Actual methods for performing search must run in javafx thread
      */
     private class SearchListener {
 
         @Subscribe
         public void listen(EntryAddedEvent addedEntryEvent) {
-            frame.getGlobalSearchBar().performSearch();
+            DefaultTaskExecutor.runInJavaFXThread(() -> frame.getGlobalSearchBar().performSearch());
         }
 
         @Subscribe
         public void listen(EntryChangedEvent entryChangedEvent) {
-            frame.getGlobalSearchBar().performSearch();
+            DefaultTaskExecutor.runInJavaFXThread(() -> frame.getGlobalSearchBar().performSearch());
         }
 
         @Subscribe
         public void listen(EntryRemovedEvent removedEntryEvent) {
             // IMO only used to update the status (found X entries)
-            frame.getGlobalSearchBar().performSearch();
+            DefaultTaskExecutor.runInJavaFXThread(() -> frame.getGlobalSearchBar().performSearch());
         }
     }
 

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

@@ -1,5 +1,6 @@
 package org.jabref.gui;
 
+import java.io.IOException;
 import java.nio.file.Path;
 import java.util.Collection;
 import java.util.List;
@@ -139,7 +140,7 @@ default void showErrorDialogAndWait(Exception exception) {
      * @return true if the use clicked "YES" otherwise false
      */
     boolean showConfirmationDialogWithOptOutAndWait(String title, String content,
-            String optOutMessage, Consumer<Boolean> optOutAction);
+                                                    String optOutMessage, Consumer<Boolean> optOutAction);
 
     /**
      * Create and display a new confirmation dialog.
@@ -151,8 +152,8 @@ boolean showConfirmationDialogWithOptOutAndWait(String title, String content,
      * @return true if the use clicked "YES" otherwise false
      */
     boolean showConfirmationDialogWithOptOutAndWait(String title, String content,
-            String okButtonLabel, String cancelButtonLabel,
-            String optOutMessage, Consumer<Boolean> optOutAction);
+                                                    String okButtonLabel, String cancelButtonLabel,
+                                                    String optOutMessage, Consumer<Boolean> optOutAction);
 
     /**
      * This will create and display a new dialog of the specified
@@ -162,7 +163,7 @@ boolean showConfirmationDialogWithOptOutAndWait(String title, String content,
      * @return Optional with the pressed Button as ButtonType
      */
     Optional<ButtonType> showCustomButtonDialogAndWait(Alert.AlertType type, String title, String content,
-            ButtonType... buttonTypes);
+                                                       ButtonType... buttonTypes);
 
     /**
      * This will create and display a new dialog showing a custom {@link DialogPane}
@@ -247,4 +248,12 @@ Optional<ButtonType> showCustomButtonDialogAndWait(Alert.AlertType type, String
      */
     boolean showPrintDialog(PrinterJob job);
 
+    /**
+     * Shows a new dialog that list all files contained in the given archive and which lets the user select one of these
+     * files. The method doesn't return until the displayed open dialog is dismissed. The return value specifies the
+     * file chosen by the user or an empty {@link Optional} if no selection has been made.
+     *
+     * @return the selected file or an empty {@link Optional} if no file has been selected
+     */
+    Optional<Path> showFileOpenFromArchiveDialog(Path archivePath) throws IOException;
 }