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

* upstream/master: (30 commits)
  Bump applicationinsights-core from 2.3.0 to 2.3.1 (#4656)
  Bump applicationinsights-logging-log4j2 from 2.3.0 to 2.3.1 (#4657)
  Bump bcprov-jdk15on from 1.60 to 1.61 (#4653)
  Bump log4j-jcl from 2.11.1 to 2.11.2 (#4646)
  Bump log4j-api from 2.11.1 to 2.11.2 (#4650)
  Bump assertj-swing-junit from 3.8.0 to 3.9.2 (#4647)
  Bump log4j-jul from 2.11.1 to 2.11.2 (#4648)
  Bump log4j-slf4j18-impl from 2.11.1 to 2.11.2 (#4649)
  Bump log4j-core from 2.11.1 to 2.11.2 (#4651)
  Remove old code for PDF import (#4634)
  Reorder conditional checks
  Automatically created groups with Field to group by as entrytype (#4539) (#4555)
  Fix for issue 4641: Remove usage of TempDirectory extension from junit-pioneer (#4644)
  Edit localization file
  Add Integrity check for books with edition reported as 1
  Use 'junit-jupiter' aggregator module (#4640)
  Bump junit-jupiter-params from 5.3.2 to 5.4.0 (#4638)
  Bump junit-vintage-engine from 5.3.2 to 5.4.0 (#4637)
  Bump junit-platform-launcher from 1.3.2 to 1.4.0 (#4636)
  Bump junit-jupiter-api from 5.3.2 to 5.4.0 (#4639)
  ...

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

Author: Siedlerchr

.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

@@ -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)

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'
 
@@ -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'
 
@@ -147,32 +147,29 @@ 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-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-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'
+    compile 'org.apache.logging.log4j:log4j-core:2.11.2'
 
     compile 'de.undercouch:citeproc-java:1.0.1'
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
     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-core', version: '2.3.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
-    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.vintage:junit-vintage-engine:5.3.2'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.3.2'
+    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'
 
-    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 'com.github.tomakehurst:wiremock:2.20.0'
-    testCompile 'org.assertj:assertj-swing-junit:3.8.0'
+    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:3.9.2'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
@@ -181,7 +178,7 @@ 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 {
@@ -192,9 +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 ->

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;

buildres/snapcraft/JabRef-icon-256.png snap/gui/jabref.png

@@ -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]

snap/snapcraft.yaml

@@ -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) {

snapcraft.yaml

@@ -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);
 

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

@@ -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>

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

@@ -923,7 +923,7 @@ 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(),
 
@@ -939,8 +939,7 @@ private MenuBar createMenu() {
 
                 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_CITE_KEY_PATTERNS, new BibtexKeyPatternAction(this)));
 
         help.getItems().addAll(
                 factory.createMenuItem(StandardActions.HELP, HelpAction.getMainHelpPageCommand()),