Merge remote-tracking branch 'origin/main' into LSP-add-features

Author: palukku

CHANGELOG.md

@@ -12,6 +12,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 ### Added
 
 - We added the option to enable the language server in the preferences. [#13697](https://github.com/JabRef/jabref/pull/13697)
+- We introduced an option in Preferences under (under Linked files -> Linked file name conventions) to automatically rename linked files when an entry data changes. [#11316](https://github.com/JabRef/jabref/issues/11316)
 - We added tooltips (on hover) for 'Library-specific file directory', 'User-specific file directory' and 'LaTeX file directory' fields of the library properties window. [#12269](https://github.com/JabRef/jabref/issues/12269)
 - A space is now added by default after citations inserted via the Libre/OpenOffice integration. [#13559](https://github.com/JabRef/jabref/issues/13559)
 - We added the option to configure 'Add space after citation' in Libre/OpenOffice panel settings. [#13559](https://github.com/JabRef/jabref/issues/13559)
@@ -78,12 +79,14 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We introduced walkthrough functionality [#12664](https://github.com/JabRef/jabref/issues/12664)
 - The Welcome tab now has a responsive layout. [#12664](https://github.com/JabRef/jabref/issues/12664)
 - We introduced a donation prompt in the Welcome tab. [#12664](https://github.com/JabRef/jabref/issues/12664)
+- We changed to syntax for the websearch to the one of the main search bar. [#13607](https://github.com/JabRef/jabref/issues/13607)
 
 ### Fixed
 
 - We fixed an issue where "Specify Bib(La)TeX" tab was not focused when Bib(La)TeX was in the clipboard [#13597](https://github.com/JabRef/jabref/issues/13597)
 - We fixed an issue whereby the 'About' dialog was not honouring the user's configured font preferences. [#13558](https://github.com/JabRef/jabref/issues/13558)
 - We fixed an issue where the Pagetotal column was sorting the values alphabetically instead of numerically. [#12533](https://github.com/JabRef/jabref/issues/12533)
+- We fixed an issue where URLs starting with "www." (without a protocol) in file fields caused an `IllegalArgumentException: URI is not absolute` error. [#12186](https://github.com/JabRef/jabref/issues/12186)
 - We fixed the dark mode of the BibTeX Source dialog in the Citation Relations tab. [#13599](https://github.com/JabRef/jabref/issues/13599)
 - We fixed an issue where the LibreOffice integration did not support citation keys containing Unicode characters. [#13301](https://github.com/JabRef/jabref/issues/13301)
 - We fixed an issue where the "Search ShortScience" action did not convert LaTeX-formatted titles to Unicode. [#13418](https://github.com/JabRef/jabref/issues/13418)

jabgui/src/main/java/org/jabref/gui/LibraryTab.java

@@ -43,6 +43,7 @@
 import org.jabref.gui.collab.DatabaseChangeMonitor;
 import org.jabref.gui.dialogs.AutosaveUiManager;
 import org.jabref.gui.exporter.SaveDatabaseAction;
+import org.jabref.gui.externalfiles.AutoRenameFileOnEntryChange;
 import org.jabref.gui.externalfiles.ImportHandler;
 import org.jabref.gui.fieldeditors.LinkedFileViewModel;
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
@@ -128,6 +129,7 @@ public class LibraryTab extends Tab implements CommandSelectionTab {
     private FileAnnotationCache annotationCache;
     private MainTable mainTable;
     private DatabaseNotification databaseNotificationPane;
+    private AutoRenameFileOnEntryChange autoRenameFileOnEntryChange;
 
     // Indicates whether the tab is loading data using a dataloading task
     // The constructors take care to the right true/false assignment during start.
@@ -244,6 +246,9 @@ private void initializeComponentsAndListeners(boolean isDummyContext) {
 
         this.getDatabase().registerListener(new UpdateTimestampListener(preferences));
 
+        autoRenameFileOnEntryChange = new AutoRenameFileOnEntryChange(bibDatabaseContext, preferences.getFilePreferences());
+        coarseChangeFilter.registerListener(autoRenameFileOnEntryChange);
+
         aiService.setupDatabase(bibDatabaseContext);
 
         Platform.runLater(() -> {
@@ -717,6 +722,10 @@ private void onClosed(Event event) {
             tableModel.unbind();
         }
 
+        if (autoRenameFileOnEntryChange != null) {
+            coarseChangeFilter.unregisterListener(autoRenameFileOnEntryChange);
+        }
+
         // clean up the groups map
         stateManager.clearSelectedGroups(bibDatabaseContext);
     }

jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java

@@ -0,0 +1,44 @@
+package org.jabref.gui.externalfiles;
+
+import org.jabref.logic.FilePreferences;
+import org.jabref.logic.cleanup.RenamePdfCleanup;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.event.FieldChangedEvent;
+import org.jabref.model.entry.field.StandardField;
+
+import com.google.common.eventbus.Subscribe;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class AutoRenameFileOnEntryChange {
+    private static final Logger LOGGER = LoggerFactory.getLogger(AutoRenameFileOnEntryChange.class);
+
+    private final FilePreferences filePreferences;
+    private final RenamePdfCleanup renamePdfCleanup;
+
+    public AutoRenameFileOnEntryChange(BibDatabaseContext bibDatabaseContext, FilePreferences filePreferences) {
+        this.filePreferences = filePreferences;
+        renamePdfCleanup = new RenamePdfCleanup(false, () -> bibDatabaseContext, filePreferences);
+    }
+
+    @Subscribe
+    public void listen(FieldChangedEvent event) {
+        if (!filePreferences.shouldAutoRenameFilesOnChange()
+                || filePreferences.getFileNamePattern().isEmpty()
+                || filePreferences.getFileNamePattern() == null) {
+            return;
+        }
+
+        if (event.getField().equals(StandardField.FILE)) {
+            return;
+        }
+
+        BibEntry entry = event.getBibEntry();
+        LOGGER.debug("Field changed for entry {}: {}", entry.getCitationKey().orElse("defaultCitationKey"), event.getField().getName());
+        if (entry.getFiles().isEmpty()) {
+            return;
+        }
+        renamePdfCleanup.cleanup(entry);
+    }
+}

jabgui/src/main/java/org/jabref/gui/preferences/linkedfiles/LinkedFilesTab.java

@@ -36,6 +36,7 @@ public class LinkedFilesTab extends AbstractPreferenceTabView<LinkedFilesTabView
     @FXML private TextField autolinkRegexKey;
 
     @FXML private CheckBox fulltextIndex;
+    @FXML private CheckBox autoRenameFilesOnChange;
 
     @FXML private ComboBox<String> fileNamePattern;
     @FXML private TextField fileDirectoryPattern;
@@ -73,6 +74,7 @@ public void initialize() {
         autolinkRegexKey.textProperty().bindBidirectional(viewModel.autolinkRegexKeyProperty());
         autolinkRegexKey.disableProperty().bind(autolinkUseRegex.selectedProperty().not());
         fulltextIndex.selectedProperty().bindBidirectional(viewModel.fulltextIndexProperty());
+        autoRenameFilesOnChange.selectedProperty().bindBidirectional(viewModel.autoRenameFilesOnChangeProperty());
         fileNamePattern.valueProperty().bindBidirectional(viewModel.fileNamePatternProperty());
         fileNamePattern.itemsProperty().bind(viewModel.defaultFileNamePatternsProperty());
         fileDirectoryPattern.textProperty().bindBidirectional(viewModel.fileDirectoryPatternProperty());

jabgui/src/main/java/org/jabref/gui/preferences/linkedfiles/LinkedFilesTabViewModel.java

@@ -37,6 +37,7 @@ public class LinkedFilesTabViewModel implements PreferenceTabViewModel {
     private final ListProperty<String> defaultFileNamePatternsProperty =
             new SimpleListProperty<>(FXCollections.observableArrayList(FilePreferences.DEFAULT_FILENAME_PATTERNS));
     private final BooleanProperty fulltextIndex = new SimpleBooleanProperty();
+    private final BooleanProperty autoRenameFilesOnChangeProperty = new SimpleBooleanProperty();
     private final StringProperty fileNamePatternProperty = new SimpleStringProperty();
     private final StringProperty fileDirectoryPatternProperty = new SimpleStringProperty();
     private final BooleanProperty confirmLinkedFileDeleteProperty = new SimpleBooleanProperty();
@@ -82,6 +83,7 @@ public void setValues() {
         useMainFileDirectoryProperty.setValue(!filePreferences.shouldStoreFilesRelativeToBibFile());
         useBibLocationAsPrimaryProperty.setValue(filePreferences.shouldStoreFilesRelativeToBibFile());
         fulltextIndex.setValue(filePreferences.shouldFulltextIndexLinkedFiles());
+        autoRenameFilesOnChangeProperty.setValue(filePreferences.shouldAutoRenameFilesOnChange());
         fileNamePatternProperty.setValue(filePreferences.getFileNamePattern());
         fileDirectoryPatternProperty.setValue(filePreferences.getFileDirectoryPattern());
         confirmLinkedFileDeleteProperty.setValue(filePreferences.confirmDeleteLinkedFile());
@@ -104,6 +106,7 @@ public void storeSettings() {
         // External files preferences / Attached files preferences / File preferences
         filePreferences.setMainFileDirectory(mainFileDirectoryProperty.getValue());
         filePreferences.setStoreFilesRelativeToBibFile(useBibLocationAsPrimaryProperty.getValue());
+        filePreferences.setAutoRenameFilesOnChange(autoRenameFilesOnChangeProperty.getValue());
         filePreferences.setFileNamePattern(fileNamePatternProperty.getValue());
         filePreferences.setFileDirectoryPattern(fileDirectoryPatternProperty.getValue());
         filePreferences.setFulltextIndexLinkedFiles(fulltextIndex.getValue());
@@ -179,6 +182,10 @@ public ListProperty<String> defaultFileNamePatternsProperty() {
         return defaultFileNamePatternsProperty;
     }
 
+    public BooleanProperty autoRenameFilesOnChangeProperty() {
+        return autoRenameFilesOnChangeProperty;
+    }
+
     public StringProperty fileNamePatternProperty() {
         return fileNamePatternProperty;
     }

jabgui/src/main/java/org/jabref/gui/walkthrough/WalkthroughAction.java

@@ -314,7 +314,7 @@ private Walkthrough createGroupWalkthrough() {
                 new WindowEffect(HighlightEffect.PING),
                 new WindowEffect(mainResolver, HighlightEffect.FULL_SCREEN_DARKEN)
         );
-        String groupName = Localization.lang("Research Papers");
+        String groupName = Localization.lang("Research");
         String addGroup = Localization.lang("Add group");
         String addSelectedEntries = Localization.lang("Add selected entries to this group");
 

jabgui/src/main/java/org/jabref/gui/walkthrough/WalkthroughOverlay.java

@@ -35,8 +35,8 @@ public class WalkthroughOverlay {
     private final Map<Window, WindowOverlay> overlays = new HashMap<>();
     private final Stage stage;
     private final Walkthrough walkthrough;
-    private final WalkthroughHighlighter walkthroughHighlighter;
-    private final WalkthroughReverter walkthroughReverter;
+    private final WalkthroughHighlighter highlighter;
+    private final WalkthroughReverter reverter;
     private final SideEffectExecutor sideEffectExecutor;
 
     private @Nullable WalkthroughScroller scroller;
@@ -48,10 +48,10 @@ public class WalkthroughOverlay {
     public WalkthroughOverlay(Stage stage, Walkthrough walkthrough) {
         this.stage = stage;
         this.walkthrough = walkthrough;
-        this.walkthroughHighlighter = new WalkthroughHighlighter();
+        this.highlighter = new WalkthroughHighlighter();
+        this.highlighter.setOnBackgroundClick(this::showQuitConfirmationAndQuit);
         this.sideEffectExecutor = new SideEffectExecutor();
-        this.walkthroughReverter = new WalkthroughReverter(walkthrough, stage, sideEffectExecutor);
-        this.walkthroughHighlighter.setOnBackgroundClick(this::showQuitConfirmationAndQuit);
+        this.reverter = new WalkthroughReverter(walkthrough, stage, sideEffectExecutor);
     }
 
     public void show(@NonNull WalkthroughStep step) {
@@ -67,7 +67,7 @@ case SideEffect(String title, WalkthroughSideEffect sideEffect) -> {
                 } else {
                     LOGGER.error("Failed to execute side effect: {}", sideEffect.description());
                     LOGGER.warn("Side effect failed for step: {}", title);
-                    revertToPreviousStep();
+                    reverter.findAndUndo();
                 }
             }
             case VisibleComponent component -> {
@@ -83,8 +83,8 @@ case SideEffect(String title, WalkthroughSideEffect sideEffect) -> {
 
     public void detachAll() {
         cleanUp();
-        walkthroughReverter.revertAll();
-        walkthroughHighlighter.detachAll();
+        reverter.revertAll();
+        highlighter.detachAll();
         overlays.values().forEach(WindowOverlay::detach);
         overlays.clear();
     }
@@ -114,7 +114,7 @@ private void handleResolutionResult(WalkthroughResult result) {
             displayWalkthroughStep(result);
         } else {
             LOGGER.error("Failed to resolve node for step '{}'. Reverting.", walkthrough.getCurrentStep().title());
-            revertToPreviousStep();
+            reverter.findAndUndo();
         }
         resolver = null;
     }
@@ -134,7 +134,7 @@ private void displayWalkthroughStep(WalkthroughResult result) {
             this.scroller = new WalkthroughScroller(resolvedNode);
         }
 
-        walkthroughHighlighter.applyHighlight(
+        highlighter.applyHighlight(
                 component.highlight().orElse(null),
                 resolvedWindow.getScene(),
                 resolvedNode);
@@ -146,11 +146,7 @@ private void displayWalkthroughStep(WalkthroughResult result) {
             case PanelStep panel -> overlay.showPanel(panel, resolvedNode, this::prepareForNavigation);
         }
 
-        walkthroughReverter.attach(resolvedWindow, resolvedNode);
-    }
-
-    private void revertToPreviousStep() {
-        walkthroughReverter.findAndUndo();
+        reverter.attach(resolvedWindow, resolvedNode);
     }
 
     private void cleanUp() {
@@ -160,7 +156,7 @@ private void cleanUp() {
             resolver = null;
         }
 
-        walkthroughReverter.detach();
+        reverter.detach();
         if (scroller != null) {
             scroller.cleanup();
             scroller = null;
@@ -189,7 +185,7 @@ private void cleanUp() {
     ///
     /// So the current hack is we will hide [WindowOverlay] so that they won't get hacked restored.
     private void prepareForNavigation() {
-        walkthroughReverter.detach();
+        reverter.detach();
         hide();
     }
 }

jabgui/src/main/java/org/jabref/gui/walkthrough/WalkthroughRenderer.java

@@ -41,11 +41,11 @@ public Node render(TooltipStep step, Walkthrough walkthrough, Runnable beforeNav
         titleContainer.getChildren().add(titleFlow);
 
         VBox contentContainer = createContent(step, walkthrough, beforeNavigate);
-        contentContainer.getStyleClass().add("walkthrough-tooltip-content");
+        contentContainer.getStyleClass().add("walkthrough-content");
         VBox.setVgrow(contentContainer, Priority.ALWAYS);
 
         HBox actionsContainer = createActions(step, walkthrough, beforeNavigate);
-        actionsContainer.getStyleClass().add("walkthrough-tooltip-actions");
+        actionsContainer.getStyleClass().add("walkthrough-actions");
 
         step.maxHeight().ifPresent(tooltip::setMaxHeight);
         step.maxWidth().ifPresent(tooltip::setMaxWidth);

jabgui/src/main/java/org/jabref/gui/walkthrough/WindowOverlay.java

@@ -267,7 +267,8 @@ public void detach() {
     private PopOver createPopover(TooltipStep step, Runnable beforeNavigate) {
         Node content = renderer.render(step, walkthrough, beforeNavigate);
         PopOver popover = new PopOver();
-        popover.getScene().getStylesheets().setAll(window.getScene().getStylesheets());
+        popover.getStyleClass().add("walkthrough-tooltip");
+        popover.getScene().getStylesheets().setAll(window.getScene().getStylesheets()); // NOTE: Hack because ThemeManager cannot consistently apply themes
         popover.setContentNode(content);
         popover.setDetachable(false);
         popover.setCloseButtonEnabled(false);