Merge remote-tracking branch 'upstream/main'

* upstream/main:
  AtomicFileOutputStream does not overwrite file if exception occurred during write (#9067)
  Observable Preferences L (GrobidPreferences) (#9065)

CHANGELOG.md

@@ -29,6 +29,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - The [HtmlToLaTeXFormatter](https://docs.jabref.org/finding-sorting-and-cleaning-entries/saveactions#html-to-latex) keeps single `<` characters.
 - We fixed a performance regression when opening large libraries [#9041](https://github.com/JabRef/jabref/issues/9041)
 - We fixed a bug where spaces are trimmed when highlighting differences in the Entries merge dialog. [koppor#371](https://github.com/koppor/jabref/issues/371)
+- We fixed several bugs regarding the manual and the autosave of library files that sometimes lead to exceptions or data loss. [#8448](https://github.com/JabRef/jabref/issues/8484), [#8746](https://github.com/JabRef/jabref/issues/8746), [#6684](https://github.com/JabRef/jabref/issues/6684), [#6644](https://github.com/JabRef/jabref/issues/6644), [#6102](https://github.com/JabRef/jabref/issues/6102), [#6002](https://github.com/JabRef/jabref/issues/6000)
+- We fixed an issue where applied save actions on saving the library file would lead to the dialog "The libary has been modified by another program" popping up [#4877](https://github.com/JabRef/jabref/issues/4877)
 
 ### Removed
 

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

@@ -162,10 +162,12 @@ private static void applyPreferences(PreferencesService preferences) {
         Globals.journalAbbreviationRepository = JournalAbbreviationLoader.loadRepository(preferences.getJournalAbbreviationPreferences());
 
         // Build list of Import and Export formats
-        Globals.IMPORT_FORMAT_READER.resetImportFormats(preferences.getImporterPreferences(),
+        Globals.IMPORT_FORMAT_READER.resetImportFormats(
+                preferences.getImporterPreferences(),
                 preferences.getImportFormatPreferences(),
-                preferences.getXmpPreferences(), Globals.getFileUpdateMonitor());
-        Globals.entryTypesManager.addCustomOrModifiedTypes(preferences.getBibEntryTypes(BibDatabaseMode.BIBTEX),
+                Globals.getFileUpdateMonitor());
+        Globals.entryTypesManager.addCustomOrModifiedTypes(
+                preferences.getBibEntryTypes(BibDatabaseMode.BIBTEX),
                 preferences.getBibEntryTypes(BibDatabaseMode.BIBLATEX));
         Globals.exportFactory = ExporterFactory.create(
                 preferences.getCustomExportFormats(Globals.journalAbbreviationRepository),

src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractorViewModel.java

@@ -64,7 +64,7 @@ public StringProperty inputTextProperty() {
     }
 
     public void startParsing() {
-        if (preferencesService.getImporterPreferences().isGrobidEnabled()) {
+        if (preferencesService.getGrobidPreferences().isGrobidEnabled()) {
             parseUsingGrobid();
         } else {
             parseUsingBibtexExtractor();
@@ -78,7 +78,7 @@ private void parseUsingBibtexExtractor() {
     }
 
     private void parseUsingGrobid() {
-        GrobidCitationFetcher grobidCitationFetcher = new GrobidCitationFetcher(preferencesService.getImporterPreferences(), preferencesService.getImportFormatPreferences());
+        GrobidCitationFetcher grobidCitationFetcher = new GrobidCitationFetcher(preferencesService.getGrobidPreferences(), preferencesService.getImportFormatPreferences());
         BackgroundTask.wrap(() -> grobidCitationFetcher.performSearch(inputTextProperty.getValue()))
                       .onRunning(() -> dialogService.notify(Localization.lang("Your text is being parsed...")))
                       .onFailure((e) -> {

src/main/java/org/jabref/gui/bibtexextractor/ExtractBibtexAction.java

@@ -24,7 +24,7 @@ public ExtractBibtexAction(DialogService dialogService, PreferencesService prefe
     @Override
     public void execute() {
         DialogService dialogService = Injector.instantiateModelOrService(DialogService.class);
-        GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferencesService.getImporterPreferences());
+        GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferencesService.getGrobidPreferences());
         dialogService.showCustomDialogAndWait(new ExtractBibtexDialog());
     }
 }

src/main/java/org/jabref/gui/collab/DatabaseChangeMonitor.java

@@ -58,7 +58,7 @@ public DatabaseChangeMonitor(BibDatabaseContext database,
             try {
                 fileMonitor.addListenerForFile(path, this);
             } catch (IOException e) {
-                LOGGER.error("Error while trying to monitor " + path, e);
+                LOGGER.error("Error while trying to monitor {}", path, e);
             }
         });
 
@@ -75,16 +75,18 @@ public DatabaseChangeMonitor(BibDatabaseContext database,
 
     @Override
     public void fileUpdated() {
-        // File on disk has changed, thus look for notable changes and notify listeners in case there are such changes
-        ChangeScanner scanner = new ChangeScanner(database, dialogService, preferencesService, stateManager, themeManager);
-        BackgroundTask.wrap(scanner::scanForChanges)
-                      .onSuccess(changes -> {
-                          if (!changes.isEmpty()) {
-                              listeners.forEach(listener -> listener.databaseChanged(changes));
-                          }
-                      })
-                      .onFailure(e -> LOGGER.error("Error while watching for changes", e))
-                      .executeWith(taskExecutor);
+        synchronized (database) {
+            // File on disk has changed, thus look for notable changes and notify listeners in case there are such changes
+            ChangeScanner scanner = new ChangeScanner(database, dialogService, preferencesService, stateManager, themeManager);
+            BackgroundTask.wrap(scanner::scanForChanges)
+                          .onSuccess(changes -> {
+                              if (!changes.isEmpty()) {
+                                  listeners.forEach(listener -> listener.databaseChanged(changes));
+                              }
+                          })
+                          .onFailure(e -> LOGGER.error("Error while watching for changes", e))
+                          .executeWith(taskExecutor);
+        }
     }
 
     public void addListener(DatabaseChangeListener listener) {

src/main/java/org/jabref/gui/dialogs/AutosaveUiManager.java

@@ -16,16 +16,16 @@
 public class AutosaveUiManager {
     private static final Logger LOGGER = LoggerFactory.getLogger(AutosaveUiManager.class);
 
-    private final LibraryTab libraryTab;
+    private SaveDatabaseAction saveDatabaseAction;
 
     public AutosaveUiManager(LibraryTab libraryTab) {
-        this.libraryTab = libraryTab;
+        this.saveDatabaseAction = new SaveDatabaseAction(libraryTab, Globals.prefs, Globals.entryTypesManager);
     }
 
     @Subscribe
     public void listen(AutosaveEvent event) {
         try {
-            new SaveDatabaseAction(libraryTab, Globals.prefs, Globals.entryTypesManager).save(SaveDatabaseAction.SaveDatabaseMode.SILENT);
+            this.saveDatabaseAction.save(SaveDatabaseAction.SaveDatabaseMode.SILENT);
         } catch (Throwable e) {
             LOGGER.error("Problem occurred while saving.", e);
         }

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

@@ -378,10 +378,9 @@ private void setupToolBar() {
             if (fetcher instanceof PdfMergeMetadataImporter.EntryBasedFetcherWrapper) {
                 // Handle Grobid Opt-In in case of the PdfMergeMetadataImporter
                 fetcherMenuItem.setOnAction(event -> {
-                    GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferencesService.getImporterPreferences());
+                    GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferencesService.getGrobidPreferences());
                     PdfMergeMetadataImporter.EntryBasedFetcherWrapper pdfMergeMetadataImporter =
                             new PdfMergeMetadataImporter.EntryBasedFetcherWrapper(
-                                    preferencesService.getImporterPreferences(),
                                     preferencesService.getImportFormatPreferences(),
                                     preferencesService.getFilePreferences(),
                                     databaseContext);

src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java

@@ -192,13 +192,21 @@ private boolean save(Path targetPath, SaveDatabaseMode mode) {
             dialogService.notify(String.format("%s...", Localization.lang("Saving library")));
         }
 
-        libraryTab.setSaving(true);
+        synchronized (libraryTab) {
+            if (libraryTab.isSaving()) {
+                // if another thread is saving, we do not need to save
+                return true;
+            }
+            libraryTab.setSaving(true);
+        }
+
         try {
             Charset encoding = libraryTab.getBibDatabaseContext()
                                          .getMetaData()
                                          .getEncoding()
                                          .orElse(StandardCharsets.UTF_8);
-            // Make sure to remember which encoding we used.
+
+            // Make sure to remember which encoding we used
             libraryTab.getBibDatabaseContext().getMetaData().setEncoding(encoding, ChangePropagation.DO_NOT_POST_EVENT);
 
             // Save the database
@@ -227,28 +235,29 @@ private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding,
         SavePreferences savePreferences = this.preferences.getSavePreferences()
                                                       .withSaveType(saveType);
         BibDatabaseContext bibDatabaseContext = libraryTab.getBibDatabaseContext();
-        try (AtomicFileWriter fileWriter = new AtomicFileWriter(file, encoding, savePreferences.shouldMakeBackup())) {
-            BibWriter bibWriter = new BibWriter(fileWriter, bibDatabaseContext.getDatabase().getNewLineSeparator());
-            BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(bibWriter, generalPreferences, savePreferences, entryTypesManager);
-
-            if (selectedOnly) {
-                databaseWriter.savePartOfDatabase(bibDatabaseContext, libraryTab.getSelectedEntries());
-            } else {
-                databaseWriter.saveDatabase(bibDatabaseContext);
-            }
+        synchronized (bibDatabaseContext) {
+            try (AtomicFileWriter fileWriter = new AtomicFileWriter(file, encoding, savePreferences.shouldMakeBackup())) {
+                BibWriter bibWriter = new BibWriter(fileWriter, bibDatabaseContext.getDatabase().getNewLineSeparator());
+                BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(bibWriter, generalPreferences, savePreferences, entryTypesManager);
+
+                if (selectedOnly) {
+                    databaseWriter.savePartOfDatabase(bibDatabaseContext, libraryTab.getSelectedEntries());
+                } else {
+                    databaseWriter.saveDatabase(bibDatabaseContext);
+                }
 
-            libraryTab.registerUndoableChanges(databaseWriter.getSaveActionsFieldChanges());
+                libraryTab.registerUndoableChanges(databaseWriter.getSaveActionsFieldChanges());
 
-            if (fileWriter.hasEncodingProblems()) {
-                saveWithDifferentEncoding(file, selectedOnly, encoding, fileWriter.getEncodingProblems(), saveType);
+                if (fileWriter.hasEncodingProblems()) {
+                    saveWithDifferentEncoding(file, selectedOnly, encoding, fileWriter.getEncodingProblems(), saveType);
+                }
+            } catch (UnsupportedCharsetException ex) {
+                throw new SaveException(Localization.lang("Character encoding '%0' is not supported.", encoding.displayName()), ex);
+            } catch (IOException ex) {
+                throw new SaveException("Problems saving: " + ex, ex);
             }
-        } catch (UnsupportedCharsetException ex) {
-            throw new SaveException(Localization.lang("Character encoding '%0' is not supported.", encoding.displayName()), ex);
-        } catch (IOException ex) {
-            throw new SaveException("Problems saving: " + ex, ex);
+            return true;
         }
-
-        return true;
     }
 
     private void saveWithDifferentEncoding(Path file, boolean selectedOnly, Charset encoding, Set<Character> encodingProblems, SavePreferences.DatabaseSaveType saveType) throws SaveException {

src/main/java/org/jabref/gui/externalfiles/ImportHandler.java

@@ -79,10 +79,7 @@ public ImportHandler(BibDatabaseContext database,
         this.importFormatReader = importFormatReader;
 
         this.linker = new ExternalFilesEntryLinker(preferencesService.getFilePreferences(), database);
-        this.contentImporter = new ExternalFilesContentImporter(
-                preferencesService.getGeneralPreferences(),
-                preferencesService.getImporterPreferences(),
-                preferencesService.getImportFormatPreferences());
+        this.contentImporter = new ExternalFilesContentImporter(preferencesService.getImportFormatPreferences());
         this.undoManager = undoManager;
     }
 

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

@@ -548,8 +548,8 @@ public void parsePdfMetadataAndShowMergeDialog() {
             dialog.addSource(Localization.lang("Entry"), entry);
             dialog.addSource(Localization.lang("Verbatim"), wrapImporterToSupplier(new PdfVerbatimBibTextImporter(preferences.getImportFormatPreferences()), filePath));
             dialog.addSource(Localization.lang("Embedded"), wrapImporterToSupplier(new PdfEmbeddedBibFileImporter(preferences.getImportFormatPreferences()), filePath));
-            if (preferences.getImporterPreferences().isGrobidEnabled()) {
-                dialog.addSource("Grobid", wrapImporterToSupplier(new PdfGrobidImporter(preferences.getImporterPreferences(), preferences.getImportFormatPreferences()), filePath));
+            if (preferences.getGrobidPreferences().isGrobidEnabled()) {
+                dialog.addSource("Grobid", wrapImporterToSupplier(new PdfGrobidImporter(preferences.getImportFormatPreferences()), filePath));
             }
             dialog.addSource(Localization.lang("XMP metadata"), wrapImporterToSupplier(new PdfXmpImporter(preferences.getXmpPreferences()), filePath));
             dialog.addSource(Localization.lang("Content"), wrapImporterToSupplier(new PdfContentImporter(preferences.getImportFormatPreferences()), filePath));

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

@@ -190,7 +190,7 @@ private Node createFileDisplay(LinkedFileViewModel linkedFile) {
         parsePdfMetadata.setTooltip(new Tooltip(Localization.lang("Parse Metadata from PDF.")));
         parsePdfMetadata.visibleProperty().bind(linkedFile.isOfflinePdfProperty());
         parsePdfMetadata.setOnAction(event -> {
-            GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferencesService.getImporterPreferences());
+            GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferencesService.getGrobidPreferences());
             linkedFile.parsePdfMetadataAndShowMergeDialog();
         });
         parsePdfMetadata.getStyleClass().setAll("icon-button");

src/main/java/org/jabref/gui/importer/GrobidOptInDialogHelper.java

@@ -1,7 +1,7 @@
 package org.jabref.gui.importer;
 
 import org.jabref.gui.DialogService;
-import org.jabref.logic.importer.ImporterPreferences;
+import org.jabref.logic.importer.fetcher.GrobidPreferences;
 import org.jabref.logic.l10n.Localization;
 
 /**
@@ -18,7 +18,7 @@ public class GrobidOptInDialogHelper {
      * @param dialogService the DialogService to use
      * @return if the user enabled Grobid, either in the past or after being asked by the dialog.
      */
-    public static boolean showAndWaitIfUserIsUndecided(DialogService dialogService, ImporterPreferences preferences) {
+    public static boolean showAndWaitIfUserIsUndecided(DialogService dialogService, GrobidPreferences preferences) {
         if (preferences.isGrobidEnabled()) {
             return true;
         }

src/main/java/org/jabref/gui/importer/ImportAction.java

@@ -121,17 +121,25 @@ private List<ImportFormatReader.UnknownFormatImport> doImport(List<Path> files)
                 if (importer.isEmpty()) {
                     // Unknown format:
                     DefaultTaskExecutor.runAndWaitInJavaFXThread(() -> {
-                        if (fileIsPdf(filename) && GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(frame.getDialogService(), prefs.getImporterPreferences())) {
-                            Globals.IMPORT_FORMAT_READER.resetImportFormats(prefs.getImporterPreferences(), prefs.getImportFormatPreferences(), prefs.getXmpPreferences(), Globals.getFileUpdateMonitor());
+                        if (fileIsPdf(filename) && GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(frame.getDialogService(), prefs.getGrobidPreferences())) {
+                            Globals.IMPORT_FORMAT_READER.resetImportFormats(
+                                    prefs.getImporterPreferences(),
+                                    prefs.getImportFormatPreferences(),
+                                    Globals.getFileUpdateMonitor());
                         }
                         frame.getDialogService().notify(Localization.lang("Importing in unknown format") + "...");
                     });
                     // This import method never throws an IOException:
                     imports.add(Globals.IMPORT_FORMAT_READER.importUnknownFormat(filename, Globals.getFileUpdateMonitor()));
                 } else {
                     DefaultTaskExecutor.runAndWaitInJavaFXThread(() -> {
-                        if ((importer.get() instanceof PdfGrobidImporter) || ((importer.get() instanceof PdfMergeMetadataImporter) && GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(frame.getDialogService(), prefs.getImporterPreferences()))) {
-                                Globals.IMPORT_FORMAT_READER.resetImportFormats(prefs.getImporterPreferences(), prefs.getImportFormatPreferences(), prefs.getXmpPreferences(), Globals.getFileUpdateMonitor());
+                        if ((importer.get() instanceof PdfGrobidImporter) || (
+                                (importer.get() instanceof PdfMergeMetadataImporter)
+                                && GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(frame.getDialogService(), prefs.getGrobidPreferences()))) {
+                                Globals.IMPORT_FORMAT_READER.resetImportFormats(
+                                        prefs.getImporterPreferences(),
+                                        prefs.getImportFormatPreferences(),
+                                        Globals.getFileUpdateMonitor());
                         }
                         frame.getDialogService().notify(Localization.lang("Importing in %0 format", importer.get().getName()) + "...");
                     });

src/main/java/org/jabref/gui/preferences/customimporter/CustomImporterTabViewModel.java

@@ -42,21 +42,21 @@ public CustomImporterTabViewModel(PreferencesService preferences, DialogService
 
     @Override
     public void setValues() {
-        Set<CustomImporter> importersLogic = preferences.getCustomImportFormats();
+        Set<CustomImporter> importersLogic = preferences.getImporterPreferences().getCustomImportList();
         for (CustomImporter importer : importersLogic) {
             importers.add(new ImporterViewModel(importer));
         }
     }
 
     @Override
     public void storeSettings() {
-        preferences.storeCustomImportFormats(importers.stream()
-                                                      .map(ImporterViewModel::getLogic)
-                                                      .collect(Collectors.toSet()));
+        preferences.getImporterPreferences().getCustomImportList().clear();
+        preferences.getImporterPreferences().getCustomImportList().addAll(importers.stream()
+                                                                                   .map(ImporterViewModel::getLogic)
+                                                                                   .collect(Collectors.toSet()));
         Globals.IMPORT_FORMAT_READER.resetImportFormats(
                 preferences.getImporterPreferences(),
                 preferences.getImportFormatPreferences(),
-                preferences.getXmpPreferences(),
                 Globals.getFileUpdateMonitor());
     }
 

src/main/java/org/jabref/gui/preferences/importexport/ImportExportTab.java

@@ -46,7 +46,7 @@ public String getTabName() {
     }
 
     public void initialize() {
-        this.viewModel = new ImportExportTabViewModel(preferencesService, preferencesService.getDOIPreferences(), dialogService, preferencesService.getImportExportPreferences());
+        this.viewModel = new ImportExportTabViewModel(preferencesService, dialogService);
 
         useCustomDOI.selectedProperty().bindBidirectional(viewModel.useCustomDOIProperty());
         useCustomDOIName.textProperty().bindBidirectional(viewModel.useCustomDOINameProperty());