Merge remote-tracking branch 'upstream/main' into a1-bs

.github/workflows/check-outdated-dependencies.yml

@@ -12,9 +12,10 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
+          distribution: 'adopt'
       - name: Look for outdated dependencies
         run: ./gradlew -q checkOutdatedDependencies
       - name: Report issues

.github/workflows/deployment.yml

@@ -42,7 +42,7 @@ jobs:
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.8.0
+        uses: styfle/cancel-workflow-action@0.9.0
         with:
           access_token: ${{ github.token }}
       - name: Fetch all history for all tags and branches
@@ -57,14 +57,16 @@ jobs:
         id: gitversion
         uses: gittools/actions/gitversion/[email protected]
       - name: Set up JDK 15 for linux and mac
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 15
+          distribution: 'adopt'
         if: matrix.os != 'windows-latest'
       - name: Set up JDK 14 for windows
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
+          distribution: 'adopt'
         if: matrix.os == 'windows-latest'
       - name: Restore gradle cache
         uses: actions/cache@master

.github/workflows/refresh-journal-lists.yml

@@ -16,7 +16,7 @@ jobs:
           persist-credentials: false
           fetch-depth: 0
       - name: Set up JDK
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
       - uses: actions/cache@v1

.github/workflows/tests-fetchers.yml

@@ -34,9 +34,10 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
+          distribution: 'adopt'
       - uses: actions/cache@v1
         name: Restore gradle cache
         with:

.github/workflows/tests.yml

@@ -18,15 +18,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.8.0
+        uses: styfle/cancel-workflow-action@0.9.0
         with:
           access_token: ${{ github.token }}
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
+          distribution: 'adopt'
       - uses: actions/cache@v1
         name: Restore gradle cache
         with:
@@ -60,9 +61,10 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
+          distribution: 'adopt'
       - uses: actions/cache@v1
         name: Restore gradle cache
         with:
@@ -104,9 +106,10 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
+          distribution: 'adopt'
       - uses: actions/cache@v1
         name: Restore gradle cache
         with:
@@ -150,9 +153,10 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
+          distribution: 'adopt'
       - uses: actions/cache@v1
         name: Restore gradle cache
         with:
@@ -200,9 +204,10 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
+          distribution: 'adopt'
       - uses: actions/cache@v1
         name: Restore gradle cache
         with:

.markdownlint.yml

@@ -18,4 +18,4 @@ MD031: false
 
 MD033:
   # we have <a> tags with ids and superscript
-  allowed_elements: ['a', 'sup']
+  allowed_elements: ['a', 'kbd', 'sup']

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+- We added a progress counter to the title bar in Possible Duplicates dialog window. [#7366](https://github.com/JabRef/jabref/issues/7366)
 - We added new "Customization" tab to the preferences which includes option to choose a custom address for DOI access. [#7337](https://github.com/JabRef/jabref/issues/7337)
 - We added zbmath to the public databases from which the bibliographic information of an existing entry can be updated. [#7437](https://github.com/JabRef/jabref/issues/7437)
 - We added the possibility to add a new entry via its zbMath ID (zbMATH can be chosen as ID type in the "Select entry type" window). [#7202](https://github.com/JabRef/jabref/issues/7202)

build.gradle

@@ -204,7 +204,7 @@ dependencies {
     testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.22'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testImplementation 'org.mockito:mockito-core:3.8.0'
+    testImplementation 'org.mockito:mockito-core:3.9.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
     testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.17.0'

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md

@@ -5,7 +5,7 @@ This guide explains how to set up your environment for development of JabRef. It
 ```text
 The most important step is to configure your IDE.
 In case you know how to install JDK15 with JavaFX support and to fork JabRef's code,
-        please scroll down to the IDE setup.
+please scroll down to the IDE setup.
 ```
 
 For a complete step-by-step guide for Linux using IntelliJ IDEA as the IDE, have a look at the following video instructions:
@@ -20,7 +20,7 @@ This section list the prerequisites you need to get started to develop JabRef. A
 
 A working Java \(Develoment Kit\) 15 installation with Java FX support is required. In the command line \(terminal in Linux, cmd in Windows\) run `javac -version` and make sure that the reported version is Java 15 \(e.g `javac 15`\). If `javac` is not found or a wrong version is reported, check your `PATH` environment variable, your `JAVA_HOME` environment variable or install the most recent JDK.
 
-[JavaFX is not part of the default JDK any more](https://www.reddit.com/r/java/comments/82qm9x/javafx_will_be_removed_from_the_java_jdk_in_jdk_11/), it needs to be installed separately if not using a special JDK. ~~We recommend to setup the full Liberica JDK including JavaFX. You can get it from~~ [~~https://bell-sw.com/pages/downloads/?version=java-15&package=jdk-full~~](https://bell-sw.com/pages/downloads/?version=java-15&package=jdk-full)~~. On Windows, you can execute `choco install libericajdkfull` \(requires~~ [~~installation of chocolatey - a package manager for Windows~~](https://chocolatey.org/install)~~\).~~ \(Liberica JDK 15 does not include the Java compiler properly any more\)
+[JavaFX is not part of the default JDK any more](https://www.reddit.com/r/java/comments/82qm9x/javafx_will_be_removed_from_the_java_jdk_in_jdk_11/), it needs to be installed separately if not using a special JDK.
 
 Download and install the JDK from [https://jdk.java.net/](https://jdk.java.net/). Afterwards, download the "jmods" JavaFX 15 zip archive from [https://gluonhq.com/products/javafx/](https://gluonhq.com/products/javafx/) and put the `.jmod` files into `C:\Program Files\OpenJDK\jdk-15\jmods`.
 
@@ -92,7 +92,7 @@ This section explains how you get the JabRef code onto your machine in a form al
 
 ## Configure your IDE
 
-These steps are very important. They allow you to focus on the content and ensure that the code formatting always goes well. Did you know that [IntelliJ allows for reformatting selected code](https://www.jetbrains.com/help/idea/reformat-and-rearrange-code.html#reformat_code) if you press Ctrl+Alt+L?
+These steps are very important. They allow you to focus on the content and ensure that the code formatting always goes well. Did you know that [IntelliJ allows for reformatting selected code](https://www.jetbrains.com/help/idea/reformat-and-rearrange-code.html#reformat_code) if you press <kbd>Ctrl</kbd> + <kbd>Alt</kbd> + <kbd>L</kbd>?
 
 ### Configuration of IntelliJ IDEA
 

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

@@ -11,6 +11,10 @@
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.atomic.AtomicInteger;
 
+import javafx.beans.binding.Bindings;
+import javafx.beans.property.SimpleIntegerProperty;
+import javafx.beans.property.SimpleStringProperty;
+
 import org.jabref.gui.DialogService;
 import org.jabref.gui.Globals;
 import org.jabref.gui.JabRefExecutorService;
@@ -41,6 +45,9 @@ public class DuplicateSearch extends SimpleCommand {
     private final AtomicBoolean libraryAnalyzed = new AtomicBoolean();
     private final AtomicBoolean autoRemoveExactDuplicates = new AtomicBoolean();
     private final AtomicInteger duplicateCount = new AtomicInteger();
+    private final SimpleStringProperty duplicateCountObservable = new SimpleStringProperty();
+    private final SimpleStringProperty duplicateTotal = new SimpleStringProperty();
+    private final SimpleIntegerProperty duplicateProgress = new SimpleIntegerProperty(0);
     private final DialogService dialogService;
     private final StateManager stateManager;
 
@@ -67,6 +74,8 @@ public void execute() {
             return;
         }
 
+        duplicateCountObservable.addListener((obj, oldValue, newValue) -> DefaultTaskExecutor.runAndWaitInJavaFXThread(() -> duplicateTotal.set(newValue)));
+
         JabRefExecutorService.INSTANCE.executeInterruptableTask(() -> searchPossibleDuplicates(entries, database.getMode()), "DuplicateSearcher");
         BackgroundTask.wrap(this::verifyDuplicates)
                       .onSuccess(this::handleDuplicates)
@@ -85,7 +94,7 @@ private void searchPossibleDuplicates(List<BibEntry> entries, BibDatabaseMode da
 
                 if (new DuplicateCheck(Globals.entryTypesManager).isDuplicate(first, second, databaseMode)) {
                     duplicates.add(Arrays.asList(first, second));
-                    duplicateCount.getAndIncrement();
+                    duplicateCountObservable.set(String.valueOf(duplicateCount.incrementAndGet()));
                 }
             }
         }
@@ -96,6 +105,8 @@ private DuplicateSearchResult verifyDuplicates() {
         DuplicateSearchResult result = new DuplicateSearchResult();
 
         while (!libraryAnalyzed.get() || !duplicates.isEmpty()) {
+            duplicateProgress.set(duplicateProgress.getValue() + 1);
+
             List<BibEntry> dups;
             try {
                 // poll with timeout in case the library is not analyzed completely, but contains no more duplicates
@@ -133,6 +144,8 @@ private DuplicateSearchResult verifyDuplicates() {
     private void askResolveStrategy(DuplicateSearchResult result, BibEntry first, BibEntry second, DuplicateResolverType resolverType) {
         DuplicateResolverDialog dialog = new DuplicateResolverDialog(first, second, resolverType, frame.getCurrentLibraryTab().getBibDatabaseContext(), stateManager);
 
+        dialog.titleProperty().bind(Bindings.concat(dialog.getTitle()).concat(" (").concat(duplicateProgress.getValue()).concat("/").concat(duplicateTotal).concat(")"));
+
         DuplicateResolverResult resolverResult = dialogService.showCustomDialogAndWait(dialog)
                                                               .orElse(DuplicateResolverResult.BREAK);
 
@@ -172,6 +185,8 @@ private void handleDuplicates(DuplicateSearchResult result) {
             libraryTab.markBaseChanged();
         }
 
+        duplicateProgress.set(0);
+
         dialogService.notify(Localization.lang("Duplicates found") + ": " + duplicateCount.get() + ' '
                 + Localization.lang("pairs processed") + ": " + result.getDuplicateCount());
         compoundEdit.end();

src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java

@@ -149,7 +149,11 @@ private void setupValidation() {
                     }
                     return true;
                 },
-                ValidationMessage.error(Localization.lang("There exists already a group with the same name.")));
+                ValidationMessage.warning(
+                    Localization.lang("There exists already a group with the same name.") + "\n" +
+                    Localization.lang("If you use it, it will inherit all entries from this other group.")
+                )
+        );
 
         keywordRegexValidator = new FunctionBasedValidator<>(
                 keywordGroupSearchTermProperty,
@@ -234,8 +238,6 @@ private void setupValidation() {
                 },
                 ValidationMessage.error(Localization.lang("Please provide a valid aux file.")));
 
-        validator.addValidators(nameValidator, sameNameValidator);
-
         typeSearchProperty.addListener((obs, _oldValue, isSelected) -> {
             if (isSelected) {
                 validator.addValidators(searchRegexValidator, searchSearchTermEmptyValidator);

src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java

@@ -195,6 +195,16 @@ public void editGroup(GroupNodeViewModel oldGroup) {
                 boolean removePreviousAssignments = (oldGroup.getGroupNode().getGroup() instanceof ExplicitGroup)
                         && (group instanceof ExplicitGroup);
 
+                int groupsWithSameName = 0;
+                Optional<GroupTreeNode> databaseRootGroup = currentDatabase.get().getMetaData().getGroups();
+                if (databaseRootGroup.isPresent()) {
+                    String name = oldGroup.getGroupNode().getGroup().getName();
+                    groupsWithSameName = databaseRootGroup.get().findChildrenSatisfying(g -> g.getName().equals(name)).size();
+                }
+                if (groupsWithSameName >= 2) {
+                    removePreviousAssignments = false;
+                }
+
                 oldGroup.getGroupNode().setGroup(
                         group,
                         keepPreviousAssignments,
@@ -236,6 +246,9 @@ public void removeSubgroups(GroupNodeViewModel group) {
             /// TODO: Add undo
             // final UndoableModifySubtree undo = new UndoableModifySubtree(getGroupTreeRoot(), node, "Remove subgroups");
             // panel.getUndoManager().addEdit(undo);
+            for (GroupNodeViewModel child : group.getChildren()) {
+                removeGroupsAndSubGroupsFromEntries(child);
+            }
             group.getGroupNode().removeAllChildren();
             dialogService.notify(Localization.lang("Removed all subgroups of group \"%0\".", group.getDisplayName()));
             writeGroupChangesToMetaData();
@@ -290,8 +303,16 @@ void removeGroupsAndSubGroupsFromEntries(GroupNodeViewModel group) {
 
         // only remove explicit groups from the entries, keyword groups should not be deleted
         if (group.getGroupNode().getGroup() instanceof ExplicitGroup) {
-            List<BibEntry> entriesInGroup = group.getGroupNode().getEntriesInGroup(this.currentDatabase.get().getEntries());
-            group.getGroupNode().removeEntriesFromGroup(entriesInGroup);
+            int groupsWithSameName = 0;
+            String name = group.getGroupNode().getGroup().getName();
+            Optional<GroupTreeNode> rootGroup = currentDatabase.get().getMetaData().getGroups();
+            if (rootGroup.isPresent()) {
+                groupsWithSameName = rootGroup.get().findChildrenSatisfying(g -> g.getName().equals(name)).size();
+            }
+            if (groupsWithSameName < 2) {
+                List<BibEntry> entriesInGroup = group.getGroupNode().getEntriesInGroup(this.currentDatabase.get().getEntries());
+                group.getGroupNode().removeEntriesFromGroup(entriesInGroup);
+            }
         }
     }
 

src/main/resources/l10n/JabRef_de.properties

@@ -1757,6 +1757,7 @@ Delete\ '%0'=Lösche Datei '%0'
 Delete\ from\ disk=Auf der Festplatte löschen
 Remove\ from\ entry=Vom Eintrag entfernen
 There\ exists\ already\ a\ group\ with\ the\ same\ name.=Es existiert bereits eine Gruppe mit demselben Namen.
+If\ you\ use\ it,\ it\ will\ inherit\ all\ entries\ from\ this\ other\ group.=Wenn Sie diese Name benutzen, wird die neue Gruppe dieselbe Einträge beinhalten wie die bereits vorhandene Gruppe.
 
 Copy\ linked\ file=Verlinkte Datei kopieren
 Copy\ linked\ file\ to\ folder...=Verlinkte Datei in den Ordner kopieren...

src/main/resources/l10n/JabRef_en.properties

@@ -1737,6 +1737,7 @@ Delete\ '%0'=Delete '%0'
 Delete\ from\ disk=Delete from disk
 Remove\ from\ entry=Remove from entry
 There\ exists\ already\ a\ group\ with\ the\ same\ name.=There exists already a group with the same name.
+If\ you\ use\ it,\ it\ will\ inherit\ all\ entries\ from\ this\ other\ group.=If you use it, it will inherit all entries from this other group.
 
 Copy\ linked\ file=Copy linked file
 Copy\ linked\ file\ to\ folder...=Copy linked file to folder...

src/main/resources/l10n/JabRef_ru.properties

@@ -1752,6 +1752,7 @@ Delete\ '%0'=Удалить '%0'
 Delete\ from\ disk=Удалить с диска
 Remove\ from\ entry=Удалить из записи
 There\ exists\ already\ a\ group\ with\ the\ same\ name.=Группа с таким именем уже существует.
+If\ you\ use\ it,\ it\ will\ inherit\ all\ entries\ from\ this\ other\ group.=Если Вы используете это имя, новая группа будет содержать те же записи, что и уже существующая.
 
 Copy\ linked\ file=Копировать связанный файл
 Copy\ linked\ file\ to\ folder...=Копировать прикрепленный файл в папку...