Merge branch 'main' into fix-pdf-url-paste

Author: Kaan0029

.github/workflows/on-pr-closed.yml

@@ -83,10 +83,13 @@ jobs:
           default-column: "Free to take"
           issue-number: ${{ steps.get_issue_number.outputs.ticketNumber }}
           skip-if-not-in-project: true
-  close_issue_on_pr_merge:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Closes issues related to a merged pull request.
-        uses: ldez/[email protected]
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Comment on issue
+        uses: thollander/actions-comment-pull-request@v3
+        with:
+          pr-number: ${{ steps.get_issue_number.outputs.ticketNumber }}
+          message: |
+            Closed by ${{ github.event.pull_request.html_url }}
+
+            Please head to <https://builds.jabref.org/main> to try it out.
+
+            For any feedback, add a comment to the pull request at ${{ github.event.pull_request.html_url }}.

.github/workflows/unassign-issues.yml

@@ -12,7 +12,7 @@ jobs:
     permissions:
       issues: write
     outputs:
-      unassigned_issues: ${{ steps.unassign.outputs.unassigned_issues }}
+      unassigned_issues: ${{ steps.unassign.outputs.unassigned_issues || '[]' }}
     steps:
       - name: Unassign stale assignments
         id: unassign

CHANGELOG.md

@@ -26,6 +26,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a feature for enabling drag-and-drop of files into groups  [#12540](https://github.com/JabRef/jabref/issues/12540)
 - We added support for reordering keywords via drag and drop, automatic alphabetical ordering, and improved pasting and editing functionalities in the keyword editor. [#10984](https://github.com/JabRef/jabref/issues/10984)
 - We added a new functionality where author names having multiple spaces in-between will be considered as separate user block as it does for " and ". [#12701](https://github.com/JabRef/jabref/issues/12701)
+- We added an option to choose whether to open the file explorer in the files directory or in the last opened directory when attaching files. [#12554](https://github.com/JabRef/jabref/issues/12554)
 - We enhanced support for parsing XMP metadata from PDF files. [#12829](https://github.com/JabRef/jabref/issues/12829)
 - We added a "Preview" header in the JStyles tab in the "Select style" dialog, to make it consistent with the CSL styles tab. [#12838](https://github.com/JabRef/jabref/pull/12838)
 - We added automatic PubMed URL insertion when importing from PubMed if no URL is present. [#12832](https://github.com/JabRef/jabref/issues/12832/)
@@ -104,6 +105,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the tooltip only displayed the first linked file when hovering. [#12470](https://github.com/JabRef/jabref/issues/12470)
 - We fixed an issue where some texts in the "Citation Information" tab and the "Preferences" dialog could not be translated. [#12883](https://github.com/JabRef/jabref/pull/12883)
 - We fixed an issue where pasting a PDF URL into the main table caused an import error instead of creating a new entry. [#12911](https://github.com/JabRef/jabref/pull/12911)
+- We fixed an issue where libraries would sometimes be hidden when closing tabs with the Welcome tab open. [#12894](https://github.com/JabRef/jabref/issues/12894)
 
 ### Removed
 

docs/Gemfile

@@ -7,6 +7,12 @@ gem 'jekyll-figure'
 
 gem "just-the-docs", "0.10.0"
 
+# "required" by just-the-docs
+gem 'jekyll-seo-tag'
+gem 'jekyll-github-metadata'
+gem 'jekyll-include-cache'
+gem 'jekyll-sitemap'
+
 gem "jekyll-remote-theme"
 
 # Added, because defualt layout with path "**/*.md" does not work at Jekyll
@@ -20,3 +26,4 @@ gem 'jekyll-titles-from-headings'
 
 # Homepage: https://github.com/benbalter/jekyll-relative-links
 gem 'jekyll-relative-links'
+

docs/_config.yml

@@ -1,6 +1,6 @@
 repository: JabRef/jabref
 title: "Developer Documentation"
-remote_theme: just-the-docs/just-the-docs@v0.5.0
+remote_theme: just-the-docs/just-the-docs@v0.10.0
 color_scheme: light
 
 exclude: [_config.yml, .dockerignore, .gitignore, CNAME, Dockerfile, Gemfile, Gemfile.lock, README.md, mkdocs-custom.css]
@@ -38,6 +38,12 @@ baseurl: ""
 url: ""
 
 plugins:
+  # from https://github.com/just-the-docs/just-the-docs/blob/main/_config.yml
+  - jekyll-seo-tag
+  - jekyll-github-metadata
+  - jekyll-include-cache
+  - jekyll-sitemap
+  # custom additions
   - jekyll-default-layout
   - jekyll-figure
   - jekyll-remote-theme

src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -163,6 +163,7 @@ public enum StandardActions implements Action {
     MOVE_FILE_TO_FOLDER_AND_RENAME(Localization.lang("Move file to file directory and rename file")),
     COPY_FILE_TO_FOLDER(Localization.lang("Copy linked file to folder..."), IconTheme.JabRefIcons.COPY_TO_FOLDER, KeyBinding.COPY),
     REMOVE_LINK(Localization.lang("Remove link"), IconTheme.JabRefIcons.REMOVE_LINK),
+    REMOVE_LINKS(Localization.lang("Remove links"), IconTheme.JabRefIcons.REMOVE_LINK),
     DELETE_FILE(Localization.lang("Permanently delete local file"), IconTheme.JabRefIcons.DELETE_FILE, KeyBinding.DELETE_ENTRY),
 
     HELP(Localization.lang("Online help"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),

src/main/java/org/jabref/gui/consistency/ConsistencyCheckDialog.java

@@ -8,7 +8,6 @@
 import java.util.stream.Collectors;
 
 import javafx.beans.property.ReadOnlyStringWrapper;
-import javafx.collections.ListChangeListener;
 import javafx.collections.transformation.FilteredList;
 import javafx.fxml.FXML;
 import javafx.scene.control.ComboBox;
@@ -25,6 +24,8 @@
 import org.jabref.logic.quality.consistency.BibliographyConsistencyCheck;
 import org.jabref.logic.quality.consistency.ConsistencyMessage;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.field.Field;
+import org.jabref.model.entry.field.FieldFactory;
 import org.jabref.model.entry.field.SpecialField;
 
 import com.airhacks.afterburner.views.ViewLoader;
@@ -62,13 +63,6 @@ public ConsistencyCheckDialog(LibraryTab libraryTab,
                   .setAsDialogPane(this);
     }
 
-    private void onSelectionChanged(ListChangeListener.Change<? extends ConsistencyMessage> change) {
-        if (change.next()) {
-            change.getAddedSubList().stream().findFirst().ifPresent(message ->
-                    libraryTab.showAndEdit(message.bibEntry()));
-        }
-    }
-
     public ConsistencyCheckDialogViewModel getViewModel() {
         return viewModel;
     }
@@ -77,8 +71,6 @@ public ConsistencyCheckDialogViewModel getViewModel() {
     public void initialize() {
         viewModel = new ConsistencyCheckDialogViewModel(dialogService, preferences, entryTypesManager, result);
 
-        tableView.getSelectionModel().getSelectedItems().addListener(this::onSelectionChanged);
-
         entryTypeCombo.getItems().addAll(viewModel.getEntryTypes());
         entryTypeCombo.valueProperty().bindBidirectional(viewModel.selectedEntryTypeProperty());
         EasyBind.listen(entryTypeCombo.getEditor().textProperty(), observable -> entryTypeCombo.commitValue());
@@ -129,6 +121,25 @@ protected void updateItem(String item, boolean empty) {
                                                  setText(item);
                                              }
                                      );
+
+                    this.setOnMouseClicked(event -> {
+                        if (!isEmpty()) {
+                            TableColumn<ConsistencyMessage, String> clickedColumn = getTableColumn();
+
+                            ConsistencyMessage message = getTableRow().getItem();
+                            String cellValue = getTableColumn().getCellObservableValue(getIndex()).getValue();
+                            Field field = FieldFactory.parseField(clickedColumn.getText());
+                            boolean isUnsetField = cellValue.equals(ConsistencySymbol.UNSET_FIELD_AT_ENTRY_TYPE_CELL_ENTRY.getText());
+
+                            if (field.isStandardField()) {
+                                libraryTab.editEntryAndFocusField(message.bibEntry(), field);
+                            } else if (!message.bibEntry().hasField(field) && isUnsetField) {
+                                libraryTab.showAndEdit(message.bibEntry());
+                            } else {
+                                libraryTab.editEntryAndFocusField(message.bibEntry(), field);
+                            }
+                        }
+                    });
                 }
             });
 

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

@@ -19,7 +19,6 @@
 import javafx.scene.control.ProgressBar;
 import javafx.scene.control.ProgressIndicator;
 import javafx.scene.control.SelectionMode;
-import javafx.scene.control.SeparatorMenuItem;
 import javafx.scene.control.Tooltip;
 import javafx.scene.input.ClipboardContent;
 import javafx.scene.input.DragEvent;
@@ -34,25 +33,24 @@
 
 import org.jabref.gui.DialogService;
 import org.jabref.gui.DragAndDropDataFormats;
-import org.jabref.gui.actions.ActionFactory;
-import org.jabref.gui.actions.SimpleCommand;
-import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.autocompleter.SuggestionProvider;
-import org.jabref.gui.copyfiles.CopySingleFileAction;
+import org.jabref.gui.fieldeditors.contextmenu.ContextAction;
+import org.jabref.gui.fieldeditors.contextmenu.ContextMenuFactory;
+import org.jabref.gui.fieldeditors.contextmenu.ContextMenuFactory.MultiContextCommandFactory;
+import org.jabref.gui.fieldeditors.contextmenu.ContextMenuFactory.SingleContextCommandFactory;
+import org.jabref.gui.fieldeditors.contextmenu.MultiContextAction;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.icon.JabRefIconView;
 import org.jabref.gui.importer.GrobidUseDialogHelper;
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.linkedfile.DeleteFileAction;
 import org.jabref.gui.linkedfile.LinkedFileEditDialog;
 import org.jabref.gui.preferences.GuiPreferences;
-import org.jabref.gui.util.BindingsHelper;
 import org.jabref.gui.util.ViewModelListCellFactory;
 import org.jabref.gui.util.uithreadaware.UiThreadObservableList;
 import org.jabref.logic.integrity.FieldCheckers;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -88,6 +86,9 @@ public class LinkedFilesEditor extends HBox implements FieldEditorFX {
     private ObservableOptionalValue<BibEntry> bibEntry = EasyBind.wrapNullable(new SimpleObjectProperty<>());
     private final UiThreadObservableList<LinkedFileViewModel> decoratedModelList;
 
+    private ContextMenu activeContextMenu = null;
+    private ContextMenuFactory contextMenuFactory;
+
     public LinkedFilesEditor(Field field,
                              BibDatabaseContext databaseContext,
                              SuggestionProvider<?> suggestionProvider,
@@ -98,8 +99,8 @@ public LinkedFilesEditor(Field field,
         this.fieldCheckers = fieldCheckers;
 
         ViewLoader.view(this)
-                  .root(this)
-                  .load();
+                .root(this)
+                .load();
 
         decoratedModelList = new UiThreadObservableList<>(viewModel.filesProperty());
         Bindings.bindContentBidirectional(listView.itemsProperty().get(), decoratedModelList);
@@ -120,7 +121,6 @@ private void initialize() {
         new ViewModelListCellFactory<LinkedFileViewModel>()
                 .withStringTooltip(LinkedFileViewModel::getDescriptionAndLink)
                 .withGraphic(this::createFileDisplay)
-                .withContextMenu(this::createContextMenuForFile)
                 .withOnMouseClickedEvent(this::handleItemMouseClick)
                 .setOnDragDetected(this::handleOnDragDetected)
                 .setOnDragDropped(this::handleOnDragDropped)
@@ -302,90 +302,40 @@ private void addFromURL() {
 
     private void handleItemMouseClick(LinkedFileViewModel linkedFile, MouseEvent event) {
         if (event.getButton() == MouseButton.PRIMARY && (event.getClickCount() == 2)) {
-            // Double click -> open
-            linkedFile.open();
+            linkedFile.open(); // Double-click: open file
+        } else if (activeContextMenu != null && event.getButton() == MouseButton.PRIMARY) {
+            activeContextMenu.hide(); // Hide context menu if left-click
+            activeContextMenu = null;
+        } else if (event.getButton() == MouseButton.SECONDARY) {
+            if (activeContextMenu != null) {
+                activeContextMenu.hide(); // Hide any existing context menu
+                activeContextMenu = null;
+            }
+
+            SingleContextCommandFactory contextCommandFactory = (action, file) ->
+                    new ContextAction(action, file, databaseContext, bibEntry, preferences, viewModel);
+
+            MultiContextCommandFactory multiContextCommandFactory = (action, files) ->
+                    new MultiContextAction(action, files, databaseContext, bibEntry, preferences, viewModel);
+
+            contextMenuFactory = new ContextMenuFactory(
+                    dialogService,
+                    preferences,
+                    databaseContext,
+                    bibEntry,
+                    viewModel,
+                    contextCommandFactory,
+                    multiContextCommandFactory
+            );
+
+            ContextMenu contextMenu = contextMenuFactory.createForSelection(listView.getSelectionModel().getSelectedItems());
+            contextMenu.show(listView, event.getScreenX(), event.getScreenY());
+            activeContextMenu = contextMenu;
         }
     }
 
     @Override
     public double getWeight() {
         return 3;
     }
-
-    private ContextMenu createContextMenuForFile(LinkedFileViewModel linkedFile) {
-        ContextMenu menu = new ContextMenu();
-        ActionFactory factory = new ActionFactory();
-
-        menu.getItems().addAll(
-                factory.createMenuItem(StandardActions.EDIT_FILE_LINK, new ContextAction(StandardActions.EDIT_FILE_LINK, linkedFile, preferences)),
-                new SeparatorMenuItem(),
-                factory.createMenuItem(StandardActions.OPEN_FILE, new ContextAction(StandardActions.OPEN_FILE, linkedFile, preferences)),
-                factory.createMenuItem(StandardActions.OPEN_FOLDER, new ContextAction(StandardActions.OPEN_FOLDER, linkedFile, preferences)),
-                new SeparatorMenuItem(),
-                factory.createMenuItem(StandardActions.DOWNLOAD_FILE, new ContextAction(StandardActions.DOWNLOAD_FILE, linkedFile, preferences)),
-                factory.createMenuItem(StandardActions.RENAME_FILE_TO_PATTERN, new ContextAction(StandardActions.RENAME_FILE_TO_PATTERN, linkedFile, preferences)),
-                factory.createMenuItem(StandardActions.RENAME_FILE_TO_NAME, new ContextAction(StandardActions.RENAME_FILE_TO_NAME, linkedFile, preferences)),
-                factory.createMenuItem(StandardActions.MOVE_FILE_TO_FOLDER, new ContextAction(StandardActions.MOVE_FILE_TO_FOLDER, linkedFile, preferences)),
-                factory.createMenuItem(StandardActions.MOVE_FILE_TO_FOLDER_AND_RENAME, new ContextAction(StandardActions.MOVE_FILE_TO_FOLDER_AND_RENAME, linkedFile, preferences)),
-                factory.createMenuItem(StandardActions.COPY_FILE_TO_FOLDER, new CopySingleFileAction(linkedFile.getFile(), dialogService, databaseContext, preferences.getFilePreferences())),
-                factory.createMenuItem(StandardActions.REDOWNLOAD_FILE, new ContextAction(StandardActions.REDOWNLOAD_FILE, linkedFile, preferences)),
-                factory.createMenuItem(StandardActions.REMOVE_LINK, new ContextAction(StandardActions.REMOVE_LINK, linkedFile, preferences)),
-                factory.createMenuItem(StandardActions.DELETE_FILE, new ContextAction(StandardActions.DELETE_FILE, linkedFile, preferences))
-        );
-
-        return menu;
-    }
-
-    private class ContextAction extends SimpleCommand {
-
-        private final StandardActions command;
-        private final LinkedFileViewModel linkedFile;
-
-        public ContextAction(StandardActions command, LinkedFileViewModel linkedFile, CliPreferences preferences) {
-            this.command = command;
-            this.linkedFile = linkedFile;
-
-            this.executable.bind(
-                    switch (command) {
-                        case RENAME_FILE_TO_PATTERN -> Bindings.createBooleanBinding(
-                                () -> !linkedFile.getFile().isOnlineLink()
-                                        && linkedFile.getFile().findIn(databaseContext, preferences.getFilePreferences()).isPresent()
-                                        && !linkedFile.isGeneratedNameSameAsOriginal(),
-                                linkedFile.getFile().linkProperty(), bibEntry.getValue().map(BibEntry::getFieldsObservable).orElse(null));
-                        case MOVE_FILE_TO_FOLDER, MOVE_FILE_TO_FOLDER_AND_RENAME -> Bindings.createBooleanBinding(
-                                () -> !linkedFile.getFile().isOnlineLink()
-                                        && linkedFile.getFile().findIn(databaseContext, preferences.getFilePreferences()).isPresent()
-                                        && !linkedFile.isGeneratedPathSameAsOriginal(),
-                                linkedFile.getFile().linkProperty(), bibEntry.getValue().map(BibEntry::getFieldsObservable).orElse(null));
-                        case DOWNLOAD_FILE -> Bindings.createBooleanBinding(
-                                () -> linkedFile.getFile().isOnlineLink(),
-                                linkedFile.getFile().linkProperty(), bibEntry.getValue().map(BibEntry::getFieldsObservable).orElse(null));
-                        case REDOWNLOAD_FILE -> Bindings.createBooleanBinding(
-                                () -> !linkedFile.getFile().getSourceUrl().isEmpty(),
-                                linkedFile.getFile().sourceUrlProperty(), bibEntry.getValue().map(BibEntry::getFieldsObservable).orElse(null));
-                        case OPEN_FILE, OPEN_FOLDER, RENAME_FILE_TO_NAME, DELETE_FILE -> Bindings.createBooleanBinding(
-                                () -> !linkedFile.getFile().isOnlineLink()
-                                        && linkedFile.getFile().findIn(databaseContext, preferences.getFilePreferences()).isPresent(),
-                                linkedFile.getFile().linkProperty(), bibEntry.getValue().map(BibEntry::getFieldsObservable).orElse(null));
-                        default -> BindingsHelper.constantOf(true);
-                    });
-        }
-
-        @Override
-        public void execute() {
-            switch (command) {
-                case EDIT_FILE_LINK -> linkedFile.edit();
-                case OPEN_FILE -> linkedFile.open();
-                case OPEN_FOLDER -> linkedFile.openFolder();
-                case DOWNLOAD_FILE -> linkedFile.download(true);
-                case REDOWNLOAD_FILE -> linkedFile.redownload();
-                case RENAME_FILE_TO_PATTERN -> linkedFile.renameToSuggestion();
-                case RENAME_FILE_TO_NAME -> linkedFile.askForNameAndRename();
-                case MOVE_FILE_TO_FOLDER -> linkedFile.moveToDefaultDirectory();
-                case MOVE_FILE_TO_FOLDER_AND_RENAME -> linkedFile.moveToDefaultDirectoryAndRename();
-                case DELETE_FILE -> viewModel.deleteFile(linkedFile);
-                case REMOVE_LINK -> viewModel.removeFileLink(linkedFile);
-            }
-        }
-    }
 }