Adds a dynamic group mirroring the file system (#10930)

CHANGELOG.md

@@ -24,6 +24,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added the possibility to configure the email provided to unpaywall. [#14340](https://github.com/JabRef/jabref/pull/14340)
 - We added a "Regenerate" button for the AI chat allowing the user to make the language model reformulate its response to the previous prompt. [#12191](https://github.com/JabRef/jabref/issues/12191)
 - We added support for transliteration of fields to English and automatic transliteration of generated citation key. [#11377](https://github.com/JabRef/jabref/issues/11377)
+- We added groups that mirror the local file directory structure. [#10930](https://github.com/JabRef/jabref/issues/10930)
 
 ### Changed
 

jabgui/src/main/java/org/jabref/cli/CliImportHelper.java

@@ -12,6 +12,7 @@
 import org.jabref.logic.net.URLDownload;
 import org.jabref.logic.os.OS;
 import org.jabref.logic.preferences.CliPreferences;
+import org.jabref.model.util.DummyDirectoryUpdateMonitor;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
 import org.slf4j.Logger;
@@ -71,7 +72,8 @@ public static Optional<ParserResult> importFile(Path file,
                     cliPreferences.getImporterPreferences(),
                     cliPreferences.getImportFormatPreferences(),
                     cliPreferences.getCitationKeyPatternPreferences(),
-                    new DummyFileUpdateMonitor()
+                    new DummyFileUpdateMonitor(),
+                    new DummyDirectoryUpdateMonitor()
             );
 
             if (!porcelain) {

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

@@ -28,6 +28,7 @@
 import org.jabref.gui.remote.CLIMessageHandler;
 import org.jabref.gui.theme.ThemeManager;
 import org.jabref.gui.undo.CountingUndoManager;
+import org.jabref.gui.util.DefaultDirectoryUpdateMonitor;
 import org.jabref.gui.util.DefaultFileUpdateMonitor;
 import org.jabref.gui.util.DirectoryMonitor;
 import org.jabref.gui.util.UiTaskExecutor;
@@ -54,6 +55,7 @@
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.logic.util.strings.StringUtil;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.util.DirectoryUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
 
 import com.airhacks.afterburner.injection.Injector;
@@ -78,6 +80,7 @@ public class JabRefGUI extends Application {
     private static SearchCitationsRelationsService citationsAndRelationsSearchService;
 
     private static FileUpdateMonitor fileUpdateMonitor;
+    private static DirectoryUpdateMonitor directoryUpdateMonitor;
     private static StateManager stateManager;
     private static ThemeManager themeManager;
     private static CountingUndoManager countingUndoManager;
@@ -111,6 +114,7 @@ public void start(Stage stage) {
                     mainStage,
                     dialogService,
                     fileUpdateMonitor,
+                    directoryUpdateMonitor,
                     preferences,
                     aiService,
                     stateManager,
@@ -131,6 +135,13 @@ public void start(Stage stage) {
                                 "with this session."));
             }
 
+            if (!directoryUpdateMonitor.isActive()) {
+                dialogService.showErrorDialogAndWait(
+                        Localization.lang("Unable to monitor directory changes. Please close directories " +
+                                "and processes and restart. You may encounter errors if you continue " +
+                                "with this session."));
+            }
+
             BuildInfo buildInfo = Injector.instantiateModelOrService(BuildInfo.class);
             EasyBind.subscribe(preferences.getInternalPreferences().versionCheckEnabledProperty(), enabled -> {
                 if (enabled) {
@@ -207,6 +218,11 @@ public void initialize() {
         JabRefGUI.dialogService = new JabRefDialogService(mainStage);
         Injector.setModelOrService(DialogService.class, dialogService);
 
+        DefaultDirectoryUpdateMonitor directoryUpdateMonitor = new DefaultDirectoryUpdateMonitor(preferences, fileUpdateMonitor, countingUndoManager, stateManager, dialogService, taskExecutor);
+        JabRefGUI.directoryUpdateMonitor = directoryUpdateMonitor;
+        HeadlessExecutorService.INSTANCE.executeInterruptableTask(directoryUpdateMonitor, "DirectoryUpdateMonitor");
+        Injector.setModelOrService(DirectoryUpdateMonitor.class, directoryUpdateMonitor);
+
         JabRefGUI.clipBoardManager = new ClipBoardManager();
         Injector.setModelOrService(ClipBoardManager.class, clipBoardManager);
 
@@ -512,6 +528,12 @@ public void stop() {
                 LOGGER.trace("FileUpdateMonitor shut down");
             });
 
+            executor.submit(() -> {
+                LOGGER.trace("Shutting down directoryUpdateMonitor");
+                directoryUpdateMonitor.shutdown();
+                LOGGER.trace("DirectoryUpdateMonitor shut down");
+            });
+
             executor.submit(() -> {
                 LOGGER.trace("Shutting down directoryMonitor");
                 DirectoryMonitor directoryMonitor = Injector.instantiateModelOrService(DirectoryMonitor.class);

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

@@ -89,8 +89,10 @@
 import org.jabref.model.entry.event.EntriesEventSource;
 import org.jabref.model.entry.event.FieldChangedEvent;
 import org.jabref.model.entry.field.FieldFactory;
+import org.jabref.model.groups.DirectoryGroup;
 import org.jabref.model.groups.GroupTreeNode;
 import org.jabref.model.search.query.SearchQuery;
+import org.jabref.model.util.DirectoryUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
 
 import com.airhacks.afterburner.injection.Injector;
@@ -113,6 +115,7 @@ public class LibraryTab extends Tab implements CommandSelectionTab {
     private final DialogService dialogService;
     private final GuiPreferences preferences;
     private final FileUpdateMonitor fileUpdateMonitor;
+    private final DirectoryUpdateMonitor directoryUpdateMonitor;
     private final StateManager stateManager;
     private final BibEntryTypesManager entryTypesManager;
     private final BooleanProperty changedProperty = new SimpleBooleanProperty(false);
@@ -179,6 +182,7 @@ private LibraryTab(@NonNull BibDatabaseContext bibDatabaseContext,
                        @NonNull GuiPreferences preferences,
                        @NonNull StateManager stateManager,
                        FileUpdateMonitor fileUpdateMonitor,
+                       DirectoryUpdateMonitor directoryUpdateMonitor,
                        BibEntryTypesManager entryTypesManager,
                        CountingUndoManager undoManager,
                        ClipBoardManager clipBoardManager,
@@ -192,6 +196,7 @@ private LibraryTab(@NonNull BibDatabaseContext bibDatabaseContext,
         this.stateManager = stateManager;
         assert bibDatabaseContext.getDatabasePath().isEmpty() || fileUpdateMonitor != null;
         this.fileUpdateMonitor = fileUpdateMonitor;
+        this.directoryUpdateMonitor = directoryUpdateMonitor;
         this.entryTypesManager = entryTypesManager;
         this.clipBoardManager = clipBoardManager;
         this.taskExecutor = taskExecutor;
@@ -231,6 +236,7 @@ private void initializeComponentsAndListeners(boolean isDummyContext) {
                 bibDatabaseContext,
                 preferences,
                 fileUpdateMonitor,
+                directoryUpdateMonitor,
                 undoManager,
                 stateManager,
                 dialogService,
@@ -311,7 +317,19 @@ private void onDatabaseLoadingSucceed(ParserResult result) {
             this.markBaseChanged();
         }
 
-        setDatabaseContext(result.getDatabaseContext());
+        BibDatabaseContext newDatabase = result.getDatabaseContext();
+        setDatabaseContext(newDatabase);
+
+        // Update the database stored in Directory Groups
+        newDatabase.getMetaData().getGroups().ifPresent(groupTree -> {
+            groupTree.findChildrenSatisfying(groupTreeNode -> groupTreeNode.getGroup() instanceof DirectoryGroup)
+                     .forEach(groupTreeNode -> {
+                         if (groupTreeNode.getGroup() instanceof DirectoryGroup directoryGroup) {
+                             directoryGroup.setBibDatabaseContext(newDatabase);
+                         }
+                     });
+        });
+
         // Notify listeners that the auto-completer may have changed
         if (autoCompleterChangedListener != null) {
             autoCompleterChangedListener.run();
@@ -1033,6 +1051,7 @@ public static LibraryTab createLibraryTab(BackgroundTask<ParserResult> dataLoadi
                                               StateManager stateManager,
                                               LibraryTabContainer tabContainer,
                                               FileUpdateMonitor fileUpdateMonitor,
+                                              DirectoryUpdateMonitor directoryUpdateMonitor,
                                               BibEntryTypesManager entryTypesManager,
                                               CountingUndoManager undoManager,
                                               ClipBoardManager clipBoardManager,
@@ -1048,6 +1067,7 @@ public static LibraryTab createLibraryTab(BackgroundTask<ParserResult> dataLoadi
                 preferences,
                 stateManager,
                 fileUpdateMonitor,
+                directoryUpdateMonitor,
                 entryTypesManager,
                 undoManager,
                 clipBoardManager,
@@ -1070,6 +1090,7 @@ public static LibraryTab createLibraryTab(@NonNull BibDatabaseContext databaseCo
                                               GuiPreferences preferences,
                                               StateManager stateManager,
                                               FileUpdateMonitor fileUpdateMonitor,
+                                              DirectoryUpdateMonitor directoryUpdateMonitor,
                                               BibEntryTypesManager entryTypesManager,
                                               UndoManager undoManager,
                                               ClipBoardManager clipBoardManager,
@@ -1082,6 +1103,7 @@ public static LibraryTab createLibraryTab(@NonNull BibDatabaseContext databaseCo
                 preferences,
                 stateManager,
                 fileUpdateMonitor,
+                directoryUpdateMonitor,
                 entryTypesManager,
                 (CountingUndoManager) undoManager,
                 clipBoardManager,

jabgui/src/main/java/org/jabref/gui/collab/ChangeScanner.java

@@ -9,6 +9,7 @@
 import org.jabref.logic.importer.OpenDatabase;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.util.DummyDirectoryUpdateMonitor;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
 import org.slf4j.Logger;
@@ -39,7 +40,7 @@ public List<DatabaseChange> scanForChanges() {
             // Parse the modified file
             // Important: apply all post-load actions
             ImportFormatPreferences importFormatPreferences = preferences.getImportFormatPreferences();
-            ParserResult result = OpenDatabase.loadDatabase(database.getDatabasePath().get(), importFormatPreferences, new DummyFileUpdateMonitor());
+            ParserResult result = OpenDatabase.loadDatabase(database.getDatabasePath().get(), importFormatPreferences, new DummyFileUpdateMonitor(), new DummyDirectoryUpdateMonitor());
             BibDatabaseContext databaseOnDisk = result.getDatabaseContext();
 
             return DatabaseChangeList.compareAndGetChanges(database, databaseOnDisk, databaseChangeResolverFactory);

jabgui/src/main/java/org/jabref/gui/dialogs/BackupUIManager.java

@@ -29,6 +29,8 @@
 import org.jabref.logic.util.BackupFileType;
 import org.jabref.logic.util.io.BackupFileUtil;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.util.DirectoryUpdateMonitor;
+import org.jabref.model.util.DummyDirectoryUpdateMonitor;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -48,6 +50,7 @@ public static Optional<ParserResult> showRestoreBackupDialog(DialogService dialo
                                                                  Path originalPath,
                                                                  GuiPreferences preferences,
                                                                  FileUpdateMonitor fileUpdateMonitor,
+                                                                 DirectoryUpdateMonitor directoryUpdateMonitor,
                                                                  UndoManager undoManager,
                                                                  StateManager stateManager) {
         Optional<ButtonType> actionOpt = showBackupResolverDialog(
@@ -60,7 +63,7 @@ public static Optional<ParserResult> showRestoreBackupDialog(DialogService dialo
                 BackupManager.restoreBackup(originalPath, preferences.getFilePreferences().getBackupDirectory());
                 return Optional.empty();
             } else if (action == BackupResolverDialog.REVIEW_BACKUP) {
-                return showReviewBackupDialog(dialogService, originalPath, preferences, fileUpdateMonitor, undoManager, stateManager);
+                return showReviewBackupDialog(dialogService, originalPath, preferences, fileUpdateMonitor, directoryUpdateMonitor, undoManager, stateManager);
             }
             return Optional.empty();
         });
@@ -79,18 +82,19 @@ private static Optional<ParserResult> showReviewBackupDialog(
             Path originalPath,
             GuiPreferences preferences,
             FileUpdateMonitor fileUpdateMonitor,
+            DirectoryUpdateMonitor directoryUpdateMonitor,
             UndoManager undoManager,
             StateManager stateManager) {
         try {
             ImportFormatPreferences importFormatPreferences = preferences.getImportFormatPreferences();
 
             // The database of the originalParserResult will be modified
-            ParserResult originalParserResult = OpenDatabase.loadDatabase(originalPath, importFormatPreferences, fileUpdateMonitor);
+            ParserResult originalParserResult = OpenDatabase.loadDatabase(originalPath, importFormatPreferences, fileUpdateMonitor, directoryUpdateMonitor);
             // This will be modified by using the `DatabaseChangesResolverDialog`.
             BibDatabaseContext originalDatabase = originalParserResult.getDatabaseContext();
 
             Path backupPath = BackupFileUtil.getPathOfLatestExistingBackupFile(originalPath, BackupFileType.BACKUP, preferences.getFilePreferences().getBackupDirectory()).orElseThrow();
-            BibDatabaseContext backupDatabase = OpenDatabase.loadDatabase(backupPath, importFormatPreferences, new DummyFileUpdateMonitor()).getDatabaseContext();
+            BibDatabaseContext backupDatabase = OpenDatabase.loadDatabase(backupPath, importFormatPreferences, new DummyFileUpdateMonitor(), new DummyDirectoryUpdateMonitor()).getDatabaseContext();
 
             DatabaseChangeResolverFactory changeResolverFactory = new DatabaseChangeResolverFactory(dialogService, originalDatabase, preferences);
 
@@ -119,7 +123,7 @@ private static Optional<ParserResult> showReviewBackupDialog(
                 }
 
                 // In case not all changes are resolved, start from scratch
-                return showRestoreBackupDialog(dialogService, originalPath, preferences, fileUpdateMonitor, undoManager, stateManager);
+                return showRestoreBackupDialog(dialogService, originalPath, preferences, fileUpdateMonitor, directoryUpdateMonitor, undoManager, stateManager);
             });
         } catch (IOException e) {
             LOGGER.error("Error while loading backup or current database", e);

jabgui/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -69,6 +69,7 @@
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.entry.EntryConverter;
 import org.jabref.model.entry.field.Field;
+import org.jabref.model.util.DirectoryUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
 
 import com.airhacks.afterburner.views.ViewLoader;
@@ -114,6 +115,7 @@ public class EntryEditor extends BorderPane implements PreviewControls, AdaptVis
     @Inject private StateManager stateManager;
     @Inject private ThemeManager themeManager;
     @Inject private FileUpdateMonitor fileMonitor;
+    @Inject private DirectoryUpdateMonitor directoryUpdateMonitor;
     @Inject private DirectoryMonitor directoryMonitor;
     @Inject private CountingUndoManager undoManager;
     @Inject private BibEntryTypesManager bibEntryTypesManager;
@@ -342,6 +344,7 @@ private List<EntryEditorTab> createTabs() {
                 undoManager,
                 stateManager,
                 fileMonitor,
+                directoryUpdateMonitor,
                 preferences,
                 taskExecutor,
                 bibEntryTypesManager,
@@ -353,6 +356,7 @@ private List<EntryEditorTab> createTabs() {
                 preferences.getFieldPreferences(),
                 preferences.getImportFormatPreferences(),
                 fileMonitor,
+                directoryUpdateMonitor,
                 dialogService,
                 bibEntryTypesManager,
                 keyBindingRepository,

jabgui/src/main/java/org/jabref/gui/entryeditor/SourceTab.java

@@ -51,6 +51,7 @@
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.search.query.SearchQuery;
+import org.jabref.model.util.DirectoryUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.model.util.Range;
 
@@ -74,6 +75,7 @@ public class SourceTab extends EntryEditorTab {
     private final ObservableRuleBasedValidator sourceValidator = new ObservableRuleBasedValidator();
     private final ImportFormatPreferences importFormatPreferences;
     private final FileUpdateMonitor fileMonitor;
+    private final DirectoryUpdateMonitor directoryUpdateMonitor;
     private final DialogService dialogService;
     private final BibEntryTypesManager entryTypesManager;
     private final KeyBindingRepository keyBindingRepository;
@@ -86,6 +88,7 @@ public SourceTab(CountingUndoManager undoManager,
                      FieldPreferences fieldPreferences,
                      ImportFormatPreferences importFormatPreferences,
                      FileUpdateMonitor fileMonitor,
+                     DirectoryUpdateMonitor directoryUpdateMonitor,
                      DialogService dialogService,
                      BibEntryTypesManager entryTypesManager,
                      KeyBindingRepository keyBindingRepository,
@@ -96,6 +99,7 @@ public SourceTab(CountingUndoManager undoManager,
         this.fieldPreferences = fieldPreferences;
         this.importFormatPreferences = importFormatPreferences;
         this.fileMonitor = fileMonitor;
+        this.directoryUpdateMonitor = directoryUpdateMonitor;
         this.dialogService = dialogService;
         this.entryTypesManager = entryTypesManager;
         this.keyBindingRepository = keyBindingRepository;
@@ -287,7 +291,7 @@ private void storeSource(BibEntry outOfFocusEntry, String text) {
             return;
         }
 
-        BibtexParser bibtexParser = new BibtexParser(importFormatPreferences, fileMonitor);
+        BibtexParser bibtexParser = new BibtexParser(importFormatPreferences, fileMonitor, directoryUpdateMonitor);
         try {
             ParserResult parserResult = bibtexParser.parse(Reader.of(text));
             BibDatabase database = parserResult.getDatabase();