Fix moving of file into library (#12001)

* Fix comments * Improve comment * Fix variable name * Add list of entries to ImportFilesResultItemViewModel If any error, no double entries in result set * Fix support to move files into library * Handle existing files in the case of "Copy" * Add link to PR * Fix mocking for CitationsRelationTabViewModelTest * Use Files.isSameFile * Clean filenames at "getValidFileName" * Add JavaDoc comment * Rewrite LinkedFileHandler to do the renaming, too * Remove unused method * Introduce DragDrop.handleDropOfFiles (to avoid code duplication) * Group file related methods together (in BibEntry) * Remove unused methods * Refine CHANGELOG.md * Avoid double-addition when linking files * Fix condition * Fix flag * Add notification also on move/copy if file exists * Fix checkstyle error * Streamline code * Fix target directory creation * Fix compilation, and remove Index Manager from ImportHandler * Remove IndexManager from EntryEditor * Update CommentsTabTest.java --------- Co-authored-by: Loay Ghreeb <loayahmed655@gmail.com>
JabRef · Oct 23, 2024 · 650d4a2 · 650d4a2
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,6 +33,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a different background color to the search bar to indicate when the search syntax is wrong. [#11658](https://github.com/JabRef/jabref/pull/11658)
 - We added a setting which always adds the literal "Cited on pages" text before each JStyle citation. [#11691](https://github.com/JabRef/jabref/pull/11732)
 - We added a new plain citation parser that uses LLMs. [#11825](https://github.com/JabRef/jabref/issues/11825)
+- We added support for modifier keys when dropping a file on an entry in the main table. [#12001](https://github.com/JabRef/jabref/pull/12001)
 - We added an importer for SSRN URLs. [#12021](https://github.com/JabRef/jabref/pull/12021)
 - We added a compare button to the duplicates in the citation relations tab to open the "Possible duplicate entries" window. [#11192](https://github.com/JabRef/jabref/issues/11192)
 - We added automatic browser extension install on Windows for Chrome and Edge. [#6076](https://github.com/JabRef/jabref/issues/6076)
@@ -48,6 +49,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - JabRef respects the [configuration for storing files relative to the .bib file](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#directories-for-files) in more cases. [#11492](https://github.com/JabRef/jabref/pull/11492)
 - JabRef does not show finished background tasks in the status bar popup. [#11821](https://github.com/JabRef/jabref/pull/11821)
 - We enhanced the indexing speed. [#11502](https://github.com/JabRef/jabref/pull/11502)
+- When dropping a file into the main table, after copy or move, the file is now put in the [configured directory and renamed according to the configured patterns](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#filename-format-and-file-directory-pattern). [#12001](https://github.com/JabRef/jabref/pull/12001)
 - ⚠️ Renamed command line parameters `embeddBibfileInPdf` to `embedBibFileInPdf`, `writeMetadatatoPdf` to `writeMetadataToPdf`, and `writeXMPtoPdf` to `writeXmpToPdf`. [#11575](https://github.com/JabRef/jabref/pull/11575)
 - The browse button for a Custom theme now opens in the directory of the current used CSS file. [#11597](https://github.com/JabRef/jabref/pull/11597)
 - The browse button for a Custom exporter now opens in the directory of the current used exporter file. [#11717](https://github.com/JabRef/jabref/pull/11717)

diff --git a/src/main/java/org/jabref/gui/entryeditor/CommentsTab.java b/src/main/java/org/jabref/gui/entryeditor/CommentsTab.java
@@ -29,7 +29,6 @@
 import org.jabref.gui.util.OptionalObjectProperty;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.search.IndexManager;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -56,7 +55,6 @@ public CommentsTab(GuiPreferences preferences,
                        ThemeManager themeManager,
                        TaskExecutor taskExecutor,
                        JournalAbbreviationRepository journalAbbreviationRepository,
-                       IndexManager indexManager,
                        OptionalObjectProperty<SearchQuery> searchQueryProperty) {
         super(
                 false,
@@ -70,7 +68,6 @@ public CommentsTab(GuiPreferences preferences,
                 themeManager,
                 taskExecutor,
                 journalAbbreviationRepository,
-                indexManager,
                 searchQueryProperty
         );
         this.defaultOwner = preferences.getOwnerPreferences().getDefaultOwner().toLowerCase(Locale.ROOT).replaceAll("[^a-z0-9]", "-");

diff --git a/src/main/java/org/jabref/gui/entryeditor/DeprecatedFieldsTab.java b/src/main/java/org/jabref/gui/entryeditor/DeprecatedFieldsTab.java
@@ -19,7 +19,6 @@
 import org.jabref.gui.util.OptionalObjectProperty;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.search.IndexManager;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -47,9 +46,8 @@ public DeprecatedFieldsTab(BibDatabaseContext databaseContext,
                                BibEntryTypesManager entryTypesManager,
                                TaskExecutor taskExecutor,
                                JournalAbbreviationRepository journalAbbreviationRepository,
-                               IndexManager indexManager,
                                OptionalObjectProperty<SearchQuery> searchQueryProperty) {
-        super(false, databaseContext, suggestionProviders, undoManager, undoAction, redoAction, dialogService, preferences, themeManager, taskExecutor, journalAbbreviationRepository, indexManager, searchQueryProperty);
+        super(false, databaseContext, suggestionProviders, undoManager, undoAction, redoAction, dialogService, preferences, themeManager, taskExecutor, journalAbbreviationRepository, searchQueryProperty);
         this.entryTypesManager = entryTypesManager;
 
         setText(Localization.lang("Deprecated fields"));

diff --git a/src/main/java/org/jabref/gui/entryeditor/DetailOptionalFieldsTab.java b/src/main/java/org/jabref/gui/entryeditor/DetailOptionalFieldsTab.java
@@ -11,7 +11,6 @@
 import org.jabref.gui.util.OptionalObjectProperty;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.search.IndexManager;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntryTypesManager;
@@ -32,7 +31,6 @@ public DetailOptionalFieldsTab(BibDatabaseContext databaseContext,
                                    BibEntryTypesManager entryTypesManager,
                                    TaskExecutor taskExecutor,
                                    JournalAbbreviationRepository journalAbbreviationRepository,
-                                   IndexManager indexManager,
                                    OptionalObjectProperty<SearchQuery> searchQueryProperty) {
         super(
                 Localization.lang("Optional fields 2"),
@@ -48,7 +46,6 @@ public DetailOptionalFieldsTab(BibDatabaseContext databaseContext,
                 entryTypesManager,
                 taskExecutor,
                 journalAbbreviationRepository,
-                indexManager,
                 searchQueryProperty
         );
     }

diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -47,6 +47,7 @@
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.gui.undo.RedoAction;
 import org.jabref.gui.undo.UndoAction;
+import org.jabref.gui.util.DragDrop;
 import org.jabref.gui.util.UiTaskExecutor;
 import org.jabref.logic.ai.AiService;
 import org.jabref.logic.bibtex.TypedBibEntry;
@@ -171,21 +172,11 @@ private void setupDragAndDrop(LibraryTab libraryTab) {
             boolean success = false;
 
             if (event.getDragboard().hasContent(DataFormat.FILES)) {
-                List<Path> draggedFiles = event.getDragboard().getFiles().stream().map(File::toPath).collect(Collectors.toList());
-                switch (event.getTransferMode()) {
-                    case COPY -> {
-                        LOGGER.debug("Mode COPY");
-                        fileLinker.copyFilesToFileDirAndAddToEntry(entry, draggedFiles, libraryTab.getIndexManager());
-                    }
-                    case MOVE -> {
-                        LOGGER.debug("Mode MOVE");
-                        fileLinker.moveFilesToFileDirRenameAndAddToEntry(entry, draggedFiles, libraryTab.getIndexManager());
-                    }
-                    case LINK -> {
-                        LOGGER.debug("Mode LINK");
-                        fileLinker.addFilesToEntry(entry, draggedFiles);
-                    }
-                }
+                TransferMode transferMode = event.getTransferMode();
+                List<Path> files = event.getDragboard().getFiles().stream().map(File::toPath).collect(Collectors.toList());
+                // Modifiers do not work on macOS: https://bugs.openjdk.org/browse/JDK-8264172
+                // Similar code as org.jabref.gui.externalfiles.ImportHandler.importFilesInBackground
+                DragDrop.handleDropOfFiles(files, transferMode, fileLinker, entry);
                 success = true;
             }
 
@@ -276,21 +267,21 @@ private void navigateToNextEntry() {
     private List<EntryEditorTab> createTabs() {
         List<EntryEditorTab> tabs = new LinkedList<>();
 
-        tabs.add(new PreviewTab(databaseContext, dialogService, preferences, themeManager, taskExecutor, libraryTab.getIndexManager(), libraryTab.searchQueryProperty()));
+        tabs.add(new PreviewTab(databaseContext, dialogService, preferences, themeManager, taskExecutor, libraryTab.searchQueryProperty()));
 
         // Required, optional (important+detail), deprecated, and "other" fields
-        tabs.add(new RequiredFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, bibEntryTypesManager, taskExecutor, journalAbbreviationRepository, libraryTab.getIndexManager(), libraryTab.searchQueryProperty()));
-        tabs.add(new ImportantOptionalFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, bibEntryTypesManager, taskExecutor, journalAbbreviationRepository, libraryTab.getIndexManager(), libraryTab.searchQueryProperty()));
-        tabs.add(new DetailOptionalFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, bibEntryTypesManager, taskExecutor, journalAbbreviationRepository, libraryTab.getIndexManager(), libraryTab.searchQueryProperty()));
-        tabs.add(new DeprecatedFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, bibEntryTypesManager, taskExecutor, journalAbbreviationRepository, libraryTab.getIndexManager(), libraryTab.searchQueryProperty()));
-        tabs.add(new OtherFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, bibEntryTypesManager, taskExecutor, journalAbbreviationRepository, libraryTab.getIndexManager(), libraryTab.searchQueryProperty()));
+        tabs.add(new RequiredFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, bibEntryTypesManager, taskExecutor, journalAbbreviationRepository, libraryTab.searchQueryProperty()));
+        tabs.add(new ImportantOptionalFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, bibEntryTypesManager, taskExecutor, journalAbbreviationRepository, libraryTab.searchQueryProperty()));
+        tabs.add(new DetailOptionalFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, bibEntryTypesManager, taskExecutor, journalAbbreviationRepository, libraryTab.searchQueryProperty()));
+        tabs.add(new DeprecatedFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, bibEntryTypesManager, taskExecutor, journalAbbreviationRepository, libraryTab.searchQueryProperty()));
+        tabs.add(new OtherFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, bibEntryTypesManager, taskExecutor, journalAbbreviationRepository, libraryTab.searchQueryProperty()));
 
         // Comment Tab: Tab for general and user-specific comments
-        tabs.add(new CommentsTab(preferences, databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, themeManager, taskExecutor, journalAbbreviationRepository, libraryTab.getIndexManager(), libraryTab.searchQueryProperty()));
+        tabs.add(new CommentsTab(preferences, databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, themeManager, taskExecutor, journalAbbreviationRepository, libraryTab.searchQueryProperty()));
 
         Map<String, Set<Field>> entryEditorTabList = getAdditionalUserConfiguredTabs();
         for (Map.Entry<String, Set<Field>> tab : entryEditorTabList.entrySet()) {
-            tabs.add(new UserDefinedFieldsTab(tab.getKey(), tab.getValue(), databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, taskExecutor, journalAbbreviationRepository, libraryTab.getIndexManager(), libraryTab.searchQueryProperty()));
+            tabs.add(new UserDefinedFieldsTab(tab.getKey(), tab.getValue(), databaseContext, libraryTab.getSuggestionProviders(), undoManager, undoAction, redoAction, dialogService, preferences, themeManager, taskExecutor, journalAbbreviationRepository, libraryTab.searchQueryProperty()));
         }
 
         tabs.add(new MathSciNetTab());

diff --git a/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java b/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
@@ -36,7 +36,6 @@
 import org.jabref.gui.undo.UndoAction;
 import org.jabref.gui.util.OptionalObjectProperty;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
-import org.jabref.logic.search.IndexManager;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -64,7 +63,6 @@ abstract class FieldsEditorTab extends EntryEditorTab implements OffersPreview {
     private final JournalAbbreviationRepository journalAbbreviationRepository;
     private PreviewPanel previewPanel;
     private final UndoManager undoManager;
-    private final IndexManager indexManager;
     private final OptionalObjectProperty<SearchQuery> searchQueryProperty;
     private Collection<Field> fields = new ArrayList<>();
     @SuppressWarnings("FieldCanBeLocal")
@@ -81,7 +79,6 @@ public FieldsEditorTab(boolean compressed,
                            ThemeManager themeManager,
                            TaskExecutor taskExecutor,
                            JournalAbbreviationRepository journalAbbreviationRepository,
-                           IndexManager indexManager,
                            OptionalObjectProperty<SearchQuery> searchQueryProperty) {
         this.isCompressed = compressed;
         this.databaseContext = Objects.requireNonNull(databaseContext);
@@ -94,7 +91,6 @@ public FieldsEditorTab(boolean compressed,
         this.themeManager = themeManager;
         this.taskExecutor = Objects.requireNonNull(taskExecutor);
         this.journalAbbreviationRepository = Objects.requireNonNull(journalAbbreviationRepository);
-        this.indexManager = indexManager;
         this.searchQueryProperty = searchQueryProperty;
     }
 
@@ -265,7 +261,6 @@ private void initPanel() {
                     preferences,
                     themeManager,
                     taskExecutor,
-                    indexManager,
                     searchQueryProperty);
             EasyBind.subscribe(preferences.getPreviewPreferences().showPreviewAsExtraTabProperty(), show -> {
                 if (show) {

diff --git a/src/main/java/org/jabref/gui/entryeditor/ImportantOptionalFieldsTab.java b/src/main/java/org/jabref/gui/entryeditor/ImportantOptionalFieldsTab.java
@@ -11,7 +11,6 @@
 import org.jabref.gui.util.OptionalObjectProperty;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.search.IndexManager;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntryTypesManager;
@@ -32,7 +31,6 @@ public ImportantOptionalFieldsTab(BibDatabaseContext databaseContext,
                                       BibEntryTypesManager entryTypesManager,
                                       TaskExecutor taskExecutor,
                                       JournalAbbreviationRepository journalAbbreviationRepository,
-                                      IndexManager indexManager,
                                       OptionalObjectProperty<SearchQuery> searchQueryProperty) {
         super(
                 Localization.lang("Optional fields"),
@@ -48,7 +46,6 @@ public ImportantOptionalFieldsTab(BibDatabaseContext databaseContext,
                 entryTypesManager,
                 taskExecutor,
                 journalAbbreviationRepository,
-                indexManager,
                 searchQueryProperty
         );
     }

diff --git a/src/main/java/org/jabref/gui/entryeditor/OptionalFieldsTabBase.java b/src/main/java/org/jabref/gui/entryeditor/OptionalFieldsTabBase.java
@@ -18,7 +18,6 @@
 import org.jabref.gui.util.OptionalObjectProperty;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.search.IndexManager;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -45,7 +44,6 @@ public OptionalFieldsTabBase(String title,
                                  BibEntryTypesManager entryTypesManager,
                                  TaskExecutor taskExecutor,
                                  JournalAbbreviationRepository journalAbbreviationRepository,
-                                 IndexManager indexManager,
                                  OptionalObjectProperty<SearchQuery> searchQueryProperty) {
         super(true,
                 databaseContext,
@@ -58,7 +56,6 @@ public OptionalFieldsTabBase(String title,
                 themeManager,
                 taskExecutor,
                 journalAbbreviationRepository,
-                indexManager,
                 searchQueryProperty);
         this.entryTypesManager = entryTypesManager;
         this.isImportantOptionalFields = isImportantOptionalFields;

diff --git a/src/main/java/org/jabref/gui/entryeditor/OtherFieldsTab.java b/src/main/java/org/jabref/gui/entryeditor/OtherFieldsTab.java
@@ -22,7 +22,6 @@
 import org.jabref.gui.util.OptionalObjectProperty;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.search.IndexManager;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -52,7 +51,6 @@ public OtherFieldsTab(BibDatabaseContext databaseContext,
                           BibEntryTypesManager entryTypesManager,
                           TaskExecutor taskExecutor,
                           JournalAbbreviationRepository journalAbbreviationRepository,
-                          IndexManager indexManager,
                           OptionalObjectProperty<SearchQuery> searchQueryProperty) {
         super(false,
                 databaseContext,
@@ -65,7 +63,6 @@ public OtherFieldsTab(BibDatabaseContext databaseContext,
                 themeManager,
                 taskExecutor,
                 journalAbbreviationRepository,
-                indexManager,
                 searchQueryProperty);
 
         this.entryTypesManager = entryTypesManager;