Merge branch 'main' into fix-for-JabRef#10935

Author: Anirudhxx

.github/workflows/deployment-arm64.yml

@@ -66,12 +66,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.11.0
+        uses: gittools/actions/gitversion/setup@v0.13.2
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.11.0
+        uses: gittools/actions/gitversion/execute@v0.13.2
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

.github/workflows/deployment-jdk-ea.yml

@@ -82,18 +82,17 @@ jobs:
           show-progress: 'false'
       - name: Install pigz and cache (linux)
         if: (matrix.os == 'ubuntu-latest') || (matrix.os == 'buildjet-4vcpu-ubuntu-2204-arm')
-        # 1.3.1 works, 1.4.1 does not (https://github.com/awalsh128/cache-apt-pkgs-action/issues/126)
-        uses: koppor/cache-apt-pkgs-action@add-arm64-support
+        uses: awalsh128/cache-apt-pkgs-action@master
         with:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.11.0
+        uses: gittools/actions/gitversion/setup@v0.13.2
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.11.0
+        uses: gittools/actions/gitversion/execute@v0.13.2
       - name: 'Set up JDK ${{ matrix.jdk }}'
         uses: oracle-actions/setup-java@v1
         with:

.github/workflows/deployment.yml

@@ -79,12 +79,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.11.0
+        uses: gittools/actions/gitversion/setup@v0.13.2
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.11.0
+        uses: gittools/actions/gitversion/execute@v0.13.2
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We converted the "Custom API key" list to a table to be more accessible. [#10926](https://github.com/JabRef/jabref/issues/10926)
 - We added a "refresh" button for the LaTeX citations tab in the entry editor. [#10584](https://github.com/JabRef/jabref/issues/10584)
 - We added the possibility to show the BibTeX source in the [web search](https://docs.jabref.org/collect/import-using-online-bibliographic-database) import screen. [#560](https://github.com/koppor/jabref/issues/560)
 - We added a fetcher for [ISIDORE](https://isidore.science/), simply paste in the link into the text field or the last 6 digits in the link that identify that paper. [#10423](https://github.com/JabRef/jabref/issues/10423)
@@ -24,6 +25,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added the possibility to redownload files that had been present but are no longer in the specified location. [#10848](https://github.com/JabRef/jabref/issues/10848)
 - We added the citation key pattern `[camelN]`. Equivalent to the first N words of the `[camel]` pattern.
 - We added ability to export in CFF (Citation File Format) [#10661](https://github.com/JabRef/jabref/issues/10661).
+- We added ability to push entries to TeXworks. [#3197](https://github.com/JabRef/jabref/issues/3197)
+- We added the ability to zoom in and out in the document viewer using <kbd>Ctrl</kbd> + <kbd>Scroll</kbd>. [#10964](https://github.com/JabRef/jabref/pull/10964)
 
 ### Changed
 
@@ -38,6 +41,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We made the command "Push to TexShop" more robust to allow cite commands with a character before the first slash. [forum#2699](https://discourse.jabref.org/t/push-to-texshop-mac/2699/17?u=siedlerchr)
 - We only show the notification "Saving library..." if the library contains more than 2000 entries. [#9803](https://github.com/JabRef/jabref/issues/9803)
 - We enhanced the dialog for adding new fields in the content selector with a selection box containing a list of standard fields. [#10912](https://github.com/JabRef/jabref/pull/10912)
+- Keywords filed are now displayed as tags. [#10910](https://github.com/JabRef/jabref/pull/10910)
 
 ### Fixed
 
@@ -52,6 +56,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the CrossRef field did not work if autocompletion was disabled [#8145](https://github.com/JabRef/jabref/issues/8145)
 - We fixed an issue where exporting`@electronic` and `@online` entry types to the Office XMl would duplicate the field `title`  [#10807](https://github.com/JabRef/jabref/issues/10807)
 - We fixed an issue where the `CommentsTab` was not properly formatted when the `defaultOwner` contained capital or special letters. [#10870](https://github.com/JabRef/jabref/issues/10870)
+- We fixed an issue where the `File -> Close library` menu item was not disabled when no library was open. [#10948](https://github.com/JabRef/jabref/issues/10948)
+- We fixed an issue where the Document Viewer would show the PDF in only half the window when maximized. [#10934](https://github.com/JabRef/jabref/issues/10934)
 
 ### Removed
 

build.gradle

@@ -9,7 +9,7 @@ plugins {
 
     id 'me.champeau.jmh' version '0.7.2'
 
-    id 'org.javamodularity.moduleplugin' version '1.8.13'
+    id 'org.javamodularity.moduleplugin' version '1.8.14'
 
     id 'org.openjfx.javafxplugin' version '0.1.0'
 
@@ -27,7 +27,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.8.2'
+    id 'org.openrewrite.rewrite' version '6.8.4'
 }
 
 // Enable following for debugging
@@ -177,7 +177,7 @@ dependencies {
     implementation('com.tobiasdiez:easybind:2.2.1-SNAPSHOT')
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.0.3') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.2.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude group: 'org.apache.logging.log4j'
     }
@@ -246,7 +246,7 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'
 
-    testImplementation 'org.mockito:mockito-core:5.10.0'
+    testImplementation 'org.mockito:mockito-core:5.11.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.1'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.1'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.2.1'
@@ -260,7 +260,7 @@ dependencies {
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.6.4"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.7.1"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

rewrite.yml

@@ -94,8 +94,6 @@ recipeList:
   #  - org.openrewrite.staticanalysis.UseAsBuilder
   # "Upgrades" too much, deletes fields
   #  - org.openrewrite.staticanalysis.UseCollectionInterfaces
-  # Does not work at TreeNode
-  #  - org.openrewrite.staticanalysis.UseDiamondOperator
   # States that it gains performance, but the code is more unreable
   #  - org.openrewrite.staticanalysis.UseForEachRemoveInsteadOfSetRemoveAll
   # We voted against it
@@ -189,6 +187,7 @@ recipeList:
   - org.openrewrite.staticanalysis.TypecastParenPad
   - org.openrewrite.staticanalysis.UnwrapRepeatableAnnotations
   - org.openrewrite.staticanalysis.UpperCaseLiteralSuffixes
+  - org.openrewrite.staticanalysis.UseDiamondOperator
 #  - org.openrewrite.staticanalysis.UseJavaStyleArrayDeclarations
   - org.openrewrite.staticanalysis.UseLambdaForFunctionalInterface
 #  - org.openrewrite.staticanalysis.UseListSort

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

@@ -638,7 +638,7 @@ private ContextMenu createTabContextMenuFor(LibraryTab tab, KeyBindingRepository
                 factory.createMenuItem(StandardActions.OPEN_DATABASE_FOLDER, new OpenDatabaseFolder(tab::getBibDatabaseContext)),
                 factory.createMenuItem(StandardActions.OPEN_CONSOLE, new OpenConsoleAction(tab::getBibDatabaseContext, stateManager, prefs, dialogService)),
                 new SeparatorMenuItem(),
-                factory.createMenuItem(StandardActions.CLOSE_LIBRARY, new CloseDatabaseAction(this, tab)),
+                factory.createMenuItem(StandardActions.CLOSE_LIBRARY, new CloseDatabaseAction(this, tab, stateManager)),
                 factory.createMenuItem(StandardActions.CLOSE_OTHER_LIBRARIES, new CloseOthersDatabaseAction(tab)),
                 factory.createMenuItem(StandardActions.CLOSE_ALL_LIBRARIES, new CloseAllDatabaseAction()));
 
@@ -1059,22 +1059,27 @@ static protected class CloseDatabaseAction extends SimpleCommand {
         private final LibraryTabContainer tabContainer;
         private final LibraryTab libraryTab;
 
-        public CloseDatabaseAction(LibraryTabContainer tabContainer, LibraryTab libraryTab) {
+        public CloseDatabaseAction(LibraryTabContainer tabContainer, LibraryTab libraryTab, StateManager stateManager) {
             this.tabContainer = tabContainer;
             this.libraryTab = libraryTab;
+            this.executable.bind(ActionHelper.needsDatabase(stateManager));
         }
 
         /**
          * Using this constructor will result in executing the command on the currently open library tab
          */
-        public CloseDatabaseAction(LibraryTabContainer tabContainer) {
-            this(tabContainer, null);
+        public CloseDatabaseAction(LibraryTabContainer tabContainer, StateManager stateManager) {
+            this(tabContainer, null, stateManager);
         }
 
         @Override
         public void execute() {
             Platform.runLater(() -> {
                 if (libraryTab == null) {
+                    if (tabContainer.getCurrentLibraryTab() == null) {
+                        LOGGER.error("No library tab to close");
+                        return;
+                    }
                     tabContainer.closeCurrentTab();
                 } else {
                     tabContainer.closeTab(libraryTab);

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

@@ -137,7 +137,7 @@ private void createMenu() {
                 factory.createMenuItem(StandardActions.SAVE_LIBRARY, new SaveAction(SaveAction.SaveMethod.SAVE, frame::getCurrentLibraryTab, dialogService, preferencesService, stateManager)),
                 factory.createMenuItem(StandardActions.SAVE_LIBRARY_AS, new SaveAction(SaveAction.SaveMethod.SAVE_AS, frame::getCurrentLibraryTab, dialogService, preferencesService, stateManager)),
                 factory.createMenuItem(StandardActions.SAVE_ALL, new SaveAllAction(frame::getLibraryTabs, preferencesService, dialogService)),
-                factory.createMenuItem(StandardActions.CLOSE_LIBRARY, new JabRefFrame.CloseDatabaseAction(frame)),
+                factory.createMenuItem(StandardActions.CLOSE_LIBRARY, new JabRefFrame.CloseDatabaseAction(frame, stateManager)),
 
                 new SeparatorMenuItem(),
 

src/main/java/org/jabref/gui/documentviewer/DocumentViewerControl.java

@@ -14,6 +14,7 @@
 import javafx.scene.control.ProgressIndicator;
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
+import javafx.scene.input.ScrollEvent;
 import javafx.scene.layout.StackPane;
 import javafx.scene.shape.Rectangle;
 import javafx.util.Duration;
@@ -76,6 +77,16 @@ public void show(DocumentViewModel document) {
         flow.estimatedScrollYProperty().addListener((observable, oldValue, newValue) -> scrollY.setValue(newValue));
         scrollY.addListener((observable, oldValue, newValue) -> flow.estimatedScrollYProperty().setValue((double) newValue));
         flow.totalLengthEstimateProperty().addListener((observable, oldValue, newValue) -> scrollYMax.setValue(newValue));
+        flow.addEventFilter(ScrollEvent.SCROLL, (ScrollEvent event) -> {
+            if (event.isControlDown()) {
+                event.consume();
+                if (event.getDeltaY() > 0) {
+                    changePageWidth(100);
+                } else {
+                    changePageWidth(-100);
+                }
+            }
+        });
     }
 
     private void updateCurrentPage(ObservableList<DocumentViewerPage> visiblePages) {
@@ -128,7 +139,16 @@ private void updateSizeOfDisplayedPages() {
 
     public void changePageWidth(int delta) {
         // Assuming the current page is A4 (or has same aspect ratio)
-        setPageWidth(desiredPageDimension.getWidth(Math.sqrt(2)) + delta);
+        int newWidth = desiredPageDimension.getWidth(Math.sqrt(2)) + delta;
+        // Limit zoom out to ~1 page due to occasional display errors when zooming out further
+        int minWidth = (int) (flow.getHeight() / 2 * Math.sqrt(2));
+        if (newWidth < minWidth) {
+            if (newWidth - delta == minWidth) {  // Attempting to zoom out when already at minWidth
+                return;
+            }
+            newWidth = minWidth;
+        }
+        setPageWidth(newWidth);
     }
 
     /**

src/main/java/org/jabref/gui/documentviewer/DocumentViewerView.java

@@ -47,7 +47,7 @@ public DocumentViewerView() {
 
         ViewLoader.view(this)
                   .load()
-                  .setAsContent(this.getDialogPane());
+                  .setAsDialogPane(this);
 
         // Remove button bar at bottom, but add close button to keep the dialog closable by clicking the "x" window symbol
         getDialogPane().getButtonTypes().add(ButtonType.CLOSE);

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/BibEntryRelationsRepository.java

@@ -6,7 +6,12 @@
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.model.entry.BibEntry;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 public class BibEntryRelationsRepository {
+    private static final Logger LOGGER = LoggerFactory.getLogger(BibEntryRelationsRepository.class);
+
     private final SemanticScholarFetcher fetcher;
     private final BibEntryRelationsCache cache;
 
@@ -25,7 +30,13 @@ public List<BibEntry> getCitations(BibEntry entry) {
 
     public List<BibEntry> getReferences(BibEntry entry) {
         if (needToRefreshReferences(entry)) {
-            List<BibEntry> references = fetcher.searchCiting(entry);
+            List<BibEntry> references;
+            try {
+                references = fetcher.searchCiting(entry);
+            } catch (FetcherException e) {
+                LOGGER.error("Error while fetching references", e);
+                references = List.of();
+            }
             cache.cacheOrMergeReferences(entry, references);
         }
 
@@ -37,7 +48,7 @@ public void forceRefreshCitations(BibEntry entry) {
             List<BibEntry> citations = fetcher.searchCitedBy(entry);
             cache.cacheOrMergeCitations(entry, citations);
         } catch (FetcherException e) {
-            throw new RuntimeException(e);
+            LOGGER.error("Error while fetching citations", e);
         }
     }
 
@@ -50,7 +61,13 @@ public boolean needToRefreshReferences(BibEntry entry) {
     }
 
     public void forceRefreshReferences(BibEntry entry) {
-        List<BibEntry> references = fetcher.searchCiting(entry);
+        List<BibEntry> references;
+        try {
+            references = fetcher.searchCiting(entry);
+        } catch (FetcherException e) {
+            LOGGER.error("Error while fetching references", e);
+            references = List.of();
+        }
         cache.cacheOrMergeReferences(entry, references);
     }
 }

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/semanticscholar/SemanticScholarFetcher.java

@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.net.URI;
 import java.net.URL;
-import java.util.ArrayList;
 import java.util.List;
 
 import org.jabref.logic.importer.FetcherException;
@@ -50,15 +49,14 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
                                         .stream().filter(citationDataItem -> citationDataItem.getCitingPaper() != null)
                                         .map(citationDataItem -> citationDataItem.getCitingPaper().toBibEntry()).toList();
             } catch (IOException e) {
-                throw new RuntimeException(e);
+                throw new FetcherException("Could not fetch", e);
             }
         }
-
-        return new ArrayList<>();
+        return List.of();
     }
 
     @Override
-    public List<BibEntry> searchCiting(BibEntry entry) {
+    public List<BibEntry> searchCiting(BibEntry entry) throws FetcherException {
         if (entry.getDOI().isPresent()) {
             StringBuilder urlBuilder = new StringBuilder(SEMANTIC_SCHOLAR_API)
                     .append("paper/")
@@ -82,11 +80,10 @@ public List<BibEntry> searchCiting(BibEntry entry) {
                                          .filter(citationDataItem -> citationDataItem.getCitedPaper() != null)
                                          .map(referenceDataItem -> referenceDataItem.getCitedPaper().toBibEntry()).toList();
             } catch (IOException e) {
-                throw new RuntimeException(e);
+                throw new FetcherException("Could not fetch", e);
             }
         }
-
-        return new ArrayList<>();
+        return List.of();
     }
 
     @Override

src/main/java/org/jabref/gui/fieldeditors/FieldEditors.java

@@ -96,7 +96,7 @@ public static FieldEditorFX getForField(final Field field,
         } else if (fieldProperties.contains(FieldProperty.PERSON_NAMES)) {
             return new PersonsEditor(field, suggestionProvider, preferences, fieldCheckers, isMultiLine, undoManager);
         } else if (StandardField.KEYWORDS == field) {
-            return new KeywordsEditor(field, suggestionProvider, fieldCheckers, preferences, undoManager);
+            return new KeywordsEditor(field, suggestionProvider, fieldCheckers);
         } else if (field == InternalField.KEY_FIELD) {
             return new CitationKeyEditor(field, suggestionProvider, fieldCheckers, databaseContext);
         } else if (fieldProperties.contains(FieldProperty.MARKDOWN)) {

src/main/java/org/jabref/gui/fieldeditors/KeywordsEditor.fxml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.layout.HBox?>
+<?import com.dlsc.gemsfx.TagsField?>
+<fx:root xmlns:fx="http://javafx.com/fxml/1" type="HBox" xmlns="http://javafx.com/javafx/8.0.112"
+         fx:controller="org.jabref.gui.fieldeditors.KeywordsEditor" >
+    <TagsField fx:id="keywordTagsField" HBox.hgrow="ALWAYS"/>
+</fx:root>