Merge remote-tracking branch 'upstream/main' into followUpCitativKnow…

…ledgeItems * upstream/main: Fixed table update in eft preferences (#9051) Keep EOL setting at backups (#9048) ExternalFileTypes singleton refactor (#9044) Fix dead link (#9047) Fix performance regresssion (#9045) # Conflicts: # CHANGELOG.md
JabRef · Aug 12, 2022 · 86d70b5 · 86d70b5
2 parents 5d978f3 + 0b58079
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ### Fixed
 
 - 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)
 
 ### Removed
 

diff --git a/docs/decisions/0001-use-crowdin-for-translations.md b/docs/decisions/0001-use-crowdin-for-translations.md
@@ -13,7 +13,7 @@ The JabRef UI is offered in multiple languages. It should be easy for translator
 * Use [Crowdin](http://crowdin.com/)
 * Use [popeye](https://github.com/JabRef/popeye)
 * Use [Lingohub](https://lingohub.com/)
-* Keep current GitHub flow. See the [Step-by-step guide](https://docs.jabref.org/faq/how-to-translate-the-ui).
+* Keep current GitHub flow. See the [Step-by-step guide](https://docs.jabref.org/contributing/how-to-translate-the-ui).
 
 ## Decision Outcome
 

diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -15,7 +15,6 @@
 
 import org.jabref.gui.Globals;
 import org.jabref.gui.externalfiles.AutoSetFileLinksUtil;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.logic.JabRefException;
 import org.jabref.logic.bibtex.FieldWriterPreferences;
@@ -640,8 +639,7 @@ private void automaticallySetFileLinks(List<ParserResult> loaded) {
             AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(
                     parserResult.getDatabaseContext(),
                     preferencesService.getFilePreferences(),
-                    preferencesService.getAutoLinkPreferences(),
-                    ExternalFileTypes.getInstance());
+                    preferencesService.getAutoLinkPreferences());
             util.linkAssociatedFiles(database.getEntries(), new NamedCompound(""));
         }
     }

diff --git a/src/main/java/org/jabref/gui/EntryTypeViewModel.java b/src/main/java/org/jabref/gui/EntryTypeViewModel.java
@@ -15,7 +15,6 @@
 import javafx.concurrent.Worker;
 
 import org.jabref.gui.externalfiles.ImportHandler;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.importer.NewEntryAction;
 import org.jabref.logic.importer.FetcherClientException;
 import org.jabref.logic.importer.FetcherException;
@@ -169,7 +168,6 @@ public void runFetcherWorker() {
 
                 ImportHandler handler = new ImportHandler(
                         libraryTab.getBibDatabaseContext(),
-                        ExternalFileTypes.getInstance(),
                         preferencesService,
                         Globals.getFileUpdateMonitor(),
                         libraryTab.getUndoManager(),

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -81,7 +81,6 @@
 import org.jabref.gui.externalfiles.AutoLinkFilesAction;
 import org.jabref.gui.externalfiles.DownloadFullTextAction;
 import org.jabref.gui.externalfiles.FindUnlinkedFilesAction;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.help.AboutAction;
 import org.jabref.gui.help.ErrorConsoleAction;
 import org.jabref.gui.help.HelpAction;
@@ -1143,7 +1142,7 @@ private void trackOpenNewDatabase(LibraryTab libraryTab) {
     public LibraryTab addTab(BibDatabaseContext databaseContext, boolean raisePanel) {
         Objects.requireNonNull(databaseContext);
 
-        LibraryTab libraryTab = new LibraryTab(this, prefs, stateManager, themeManager, databaseContext, ExternalFileTypes.getInstance(), importFormatReader);
+        LibraryTab libraryTab = new LibraryTab(this, prefs, stateManager, themeManager, databaseContext, importFormatReader);
         addTab(libraryTab, raisePanel);
         return libraryTab;
     }

diff --git a/src/main/java/org/jabref/gui/LibraryTab.java b/src/main/java/org/jabref/gui/LibraryTab.java
@@ -29,7 +29,6 @@
 import org.jabref.gui.collab.DatabaseChangeMonitor;
 import org.jabref.gui.dialogs.AutosaveUiManager;
 import org.jabref.gui.entryeditor.EntryEditor;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.gui.maintable.MainTable;
 import org.jabref.gui.maintable.MainTableDataModel;
@@ -84,7 +83,6 @@ public class LibraryTab extends Tab {
     private static final Logger LOGGER = LoggerFactory.getLogger(LibraryTab.class);
     private final JabRefFrame frame;
     private final CountingUndoManager undoManager;
-    private final ExternalFileTypes externalFileTypes;
     private final DialogService dialogService;
     private final PreferencesService preferencesService;
     private final StateManager stateManager;
@@ -122,11 +120,9 @@ public LibraryTab(JabRefFrame frame,
                       StateManager stateManager,
                       ThemeManager themeManager,
                       BibDatabaseContext bibDatabaseContext,
-                      ExternalFileTypes externalFileTypes,
                       ImportFormatReader importFormatReader) {
         this.frame = Objects.requireNonNull(frame);
         this.bibDatabaseContext = Objects.requireNonNull(bibDatabaseContext);
-        this.externalFileTypes = Objects.requireNonNull(externalFileTypes);
         this.undoManager = frame.getUndoManager();
         this.dialogService = frame.getDialogService();
         this.preferencesService = Objects.requireNonNull(preferencesService);
@@ -156,7 +152,7 @@ public LibraryTab(JabRefFrame frame,
 
         this.getDatabase().registerListener(new UpdateTimestampListener(preferencesService));
 
-        this.entryEditor = new EntryEditor(this, externalFileTypes);
+        this.entryEditor = new EntryEditor(this);
 
         // set LibraryTab ID for drag'n'drop
         // ID content doesn't matter, we only need different tabs to have different ID
@@ -257,7 +253,7 @@ public void feedData(BibDatabaseContext bibDatabaseContext) {
 
         this.getDatabase().registerListener(new UpdateTimestampListener(preferencesService));
 
-        this.entryEditor = new EntryEditor(this, externalFileTypes);
+        this.entryEditor = new EntryEditor(this);
 
         Platform.runLater(() -> {
             EasyBind.subscribe(changedProperty, this::updateTabTitle);
@@ -488,7 +484,6 @@ private void createMainTable() {
                 preferencesService,
                 dialogService,
                 stateManager,
-                externalFileTypes,
                 Globals.getKeyPrefs(),
                 Globals.getClipboardManager(),
                 Globals.IMPORT_FORMAT_READER);
@@ -808,7 +803,7 @@ public LibraryTab createLibraryTab(JabRefFrame frame, PreferencesService prefere
             BibDatabaseContext context = new BibDatabaseContext();
             context.setDatabasePath(file);
 
-            LibraryTab newTab = new LibraryTab(frame, preferencesService, stateManager, themeManager, context, ExternalFileTypes.getInstance(), importFormatReader);
+            LibraryTab newTab = new LibraryTab(frame, preferencesService, stateManager, themeManager, context, importFormatReader);
             newTab.setDataLoadingTask(dataLoadingTask);
 
             dataLoadingTask.onRunning(newTab::onDatabaseLoadingStarted)

diff --git a/src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractorViewModel.java b/src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractorViewModel.java
@@ -13,7 +13,6 @@
 import org.jabref.gui.Globals;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.externalfiles.ImportHandler;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.importer.FetcherException;
@@ -52,7 +51,6 @@ public BibtexExtractorViewModel(BibDatabaseContext bibdatabaseContext,
         this.taskExecutor = taskExecutor;
         this.importHandler = new ImportHandler(
                 bibdatabaseContext,
-                ExternalFileTypes.getInstance(),
                 preferencesService,
                 fileUpdateMonitor,
                 undoManager,

diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -219,7 +219,7 @@ public static void openFolderAndSelectFile(Path fileLink, PreferencesService pre
      * @param url the URL to open
      */
     public static void openBrowser(String url) throws IOException {
-        Optional<ExternalFileType> fileType = ExternalFileTypes.getInstance().getExternalFileTypeByExt("html");
+        Optional<ExternalFileType> fileType = ExternalFileTypes.getExternalFileTypeByExt("html", Globals.prefs.getFilePreferences());
         openExternalFilePlatformIndependent(fileType, url);
     }
 

diff --git a/src/main/java/org/jabref/gui/desktop/os/Linux.java b/src/main/java/org/jabref/gui/desktop/os/Linux.java
@@ -12,6 +12,7 @@
 
 import org.jabref.architecture.AllowedToUseAwt;
 import org.jabref.gui.DialogService;
+import org.jabref.gui.Globals;
 import org.jabref.gui.JabRefExecutorService;
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
@@ -48,7 +49,7 @@ private void nativeOpenFile(String filePath) {
 
     @Override
     public void openFile(String filePath, String fileType) throws IOException {
-        Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByExt(fileType);
+        Optional<ExternalFileType> type = ExternalFileTypes.getExternalFileTypeByExt(fileType, Globals.prefs.getFilePreferences());
         String viewer;
 
         if (type.isPresent() && !type.get().getOpenWithApplication().isEmpty()) {

diff --git a/src/main/java/org/jabref/gui/desktop/os/OSX.java b/src/main/java/org/jabref/gui/desktop/os/OSX.java
@@ -6,6 +6,7 @@
 
 import org.jabref.architecture.AllowedToUseAwt;
 import org.jabref.gui.DialogService;
+import org.jabref.gui.Globals;
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 
@@ -14,7 +15,7 @@ public class OSX implements NativeDesktop {
 
     @Override
     public void openFile(String filePath, String fileType) throws IOException {
-        Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByExt(fileType);
+        Optional<ExternalFileType> type = ExternalFileTypes.getExternalFileTypeByExt(fileType, Globals.prefs.getFilePreferences());
         if (type.isPresent() && !type.get().getOpenWithApplication().isEmpty()) {
             openFileWithApplication(filePath, type.get().getOpenWithApplication());
         } else {

diff --git a/src/main/java/org/jabref/gui/desktop/os/Windows.java b/src/main/java/org/jabref/gui/desktop/os/Windows.java
@@ -7,6 +7,7 @@
 import java.util.Optional;
 
 import org.jabref.gui.DialogService;
+import org.jabref.gui.Globals;
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 
@@ -15,7 +16,7 @@ public class Windows implements NativeDesktop {
 
     @Override
     public void openFile(String filePath, String fileType) throws IOException {
-        Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByExt(fileType);
+        Optional<ExternalFileType> type = ExternalFileTypes.getExternalFileTypeByExt(fileType, Globals.prefs.getFilePreferences());
 
         if (type.isPresent() && !type.get().getOpenWithApplication().isEmpty()) {
             openFileWithApplication(filePath, type.get().getOpenWithApplication());

diff --git a/src/main/java/org/jabref/gui/entryeditor/DeprecatedFieldsTab.java b/src/main/java/org/jabref/gui/entryeditor/DeprecatedFieldsTab.java
@@ -12,7 +12,6 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.autocompleter.SuggestionProviders;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.theme.ThemeManager;
 import org.jabref.gui.util.TaskExecutor;
@@ -39,10 +38,9 @@ public DeprecatedFieldsTab(BibDatabaseContext databaseContext,
                                ThemeManager themeManager,
                                IndexingTaskManager indexingTaskManager,
                                BibEntryTypesManager entryTypesManager,
-                               ExternalFileTypes externalFileTypes,
                                TaskExecutor taskExecutor,
                                JournalAbbreviationRepository journalAbbreviationRepository) {
-        super(false, databaseContext, suggestionProviders, undoManager, dialogService, preferences, stateManager, themeManager, externalFileTypes, taskExecutor, journalAbbreviationRepository, indexingTaskManager);
+        super(false, databaseContext, suggestionProviders, undoManager, dialogService, preferences, stateManager, themeManager, taskExecutor, journalAbbreviationRepository, indexingTaskManager);
         this.entryTypesManager = entryTypesManager;
 
         setText(Localization.lang("Deprecated fields"));

diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -34,7 +34,6 @@
 import org.jabref.gui.entryeditor.fileannotationtab.FileAnnotationTab;
 import org.jabref.gui.entryeditor.fileannotationtab.FulltextSearchResultsTab;
 import org.jabref.gui.externalfiles.ExternalFilesEntryLinker;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.help.HelpAction;
 import org.jabref.gui.importer.GrobidOptInDialogHelper;
 import org.jabref.gui.keyboard.KeyBinding;
@@ -113,7 +112,7 @@ public class EntryEditor extends BorderPane {
 
     private final List<EntryEditorTab> entryEditorTabs = new LinkedList<>();
 
-    public EntryEditor(LibraryTab libraryTab, ExternalFileTypes externalFileTypes) {
+    public EntryEditor(LibraryTab libraryTab) {
         this.libraryTab = libraryTab;
         this.databaseContext = libraryTab.getBibDatabaseContext();
 
@@ -122,8 +121,7 @@ public EntryEditor(LibraryTab libraryTab, ExternalFileTypes externalFileTypes) {
                   .load();
 
         this.entryEditorPreferences = preferencesService.getEntryEditorPreferences();
-        this.fileLinker = new ExternalFilesEntryLinker(externalFileTypes, preferencesService.getFilePreferences(),
-                databaseContext);
+        this.fileLinker = new ExternalFilesEntryLinker(preferencesService.getFilePreferences(), databaseContext);
 
         EasyBind.subscribe(tabbed.getSelectionModel().selectedItemProperty(), tab -> {
             EntryEditorTab activeTab = (EntryEditorTab) tab;
@@ -242,22 +240,22 @@ private void navigateToNextEntry() {
 
     private List<EntryEditorTab> createTabs() {
         // Preview tab
-        entryEditorTabs.add(new PreviewTab(databaseContext, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), ExternalFileTypes.getInstance()));
+        entryEditorTabs.add(new PreviewTab(databaseContext, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager()));
 
         // Required fields
-        entryEditorTabs.add(new RequiredFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, ExternalFileTypes.getInstance(), taskExecutor, journalAbbreviationRepository));
+        entryEditorTabs.add(new RequiredFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, taskExecutor, journalAbbreviationRepository));
 
         // Optional fields
-        entryEditorTabs.add(new OptionalFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, ExternalFileTypes.getInstance(), taskExecutor, journalAbbreviationRepository));
-        entryEditorTabs.add(new OptionalFields2Tab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, ExternalFileTypes.getInstance(), taskExecutor, journalAbbreviationRepository));
-        entryEditorTabs.add(new DeprecatedFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, ExternalFileTypes.getInstance(), taskExecutor, journalAbbreviationRepository));
+        entryEditorTabs.add(new OptionalFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, taskExecutor, journalAbbreviationRepository));
+        entryEditorTabs.add(new OptionalFields2Tab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, taskExecutor, journalAbbreviationRepository));
+        entryEditorTabs.add(new DeprecatedFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, taskExecutor, journalAbbreviationRepository));
 
         // Other fields
-        entryEditorTabs.add(new OtherFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, ExternalFileTypes.getInstance(), taskExecutor, journalAbbreviationRepository));
+        entryEditorTabs.add(new OtherFieldsTab(databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, taskExecutor, journalAbbreviationRepository));
 
         // General fields from preferences
         for (Map.Entry<String, Set<Field>> tab : entryEditorPreferences.getEntryEditorTabList().entrySet()) {
-            entryEditorTabs.add(new UserDefinedFieldsTab(tab.getKey(), tab.getValue(), databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), bibEntryTypesManager, ExternalFileTypes.getInstance(), taskExecutor, journalAbbreviationRepository));
+            entryEditorTabs.add(new UserDefinedFieldsTab(tab.getKey(), tab.getValue(), databaseContext, libraryTab.getSuggestionProviders(), undoManager, dialogService, preferencesService, stateManager, themeManager, libraryTab.getIndexingTaskManager(), taskExecutor, journalAbbreviationRepository));
         }
 
         // Special tabs

diff --git a/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java b/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
@@ -26,7 +26,6 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.autocompleter.SuggestionProviders;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.fieldeditors.FieldEditorFX;
 import org.jabref.gui.fieldeditors.FieldEditors;
 import org.jabref.gui.fieldeditors.FieldNameLabel;
@@ -53,7 +52,6 @@ abstract class FieldsEditorTab extends EntryEditorTab {
     private final DialogService dialogService;
     private final PreferencesService preferences;
     private final ThemeManager themeManager;
-    private final ExternalFileTypes externalFileTypes;
     private final TaskExecutor taskExecutor;
     private final JournalAbbreviationRepository journalAbbreviationRepository;
     private final StateManager stateManager;
@@ -71,7 +69,6 @@ public FieldsEditorTab(boolean compressed,
                            PreferencesService preferences,
                            StateManager stateManager,
                            ThemeManager themeManager,
-                           ExternalFileTypes externalFileTypes,
                            TaskExecutor taskExecutor,
                            JournalAbbreviationRepository journalAbbreviationRepository,
                            IndexingTaskManager indexingTaskManager) {
@@ -82,7 +79,6 @@ public FieldsEditorTab(boolean compressed,
         this.dialogService = Objects.requireNonNull(dialogService);
         this.preferences = Objects.requireNonNull(preferences);
         this.themeManager = themeManager;
-        this.externalFileTypes = Objects.requireNonNull(externalFileTypes);
         this.taskExecutor = Objects.requireNonNull(taskExecutor);
         this.journalAbbreviationRepository = Objects.requireNonNull(journalAbbreviationRepository);
         this.stateManager = stateManager;
@@ -246,7 +242,7 @@ private void initPanel() {
             scrollPane.setFitToHeight(true);
 
             SplitPane container = new SplitPane(scrollPane);
-            previewPanel = new PreviewPanel(databaseContext, dialogService, externalFileTypes, preferences.getKeyBindingRepository(), preferences, stateManager, themeManager, indexingTaskManager);
+            previewPanel = new PreviewPanel(databaseContext, dialogService, preferences.getKeyBindingRepository(), preferences, stateManager, themeManager, indexingTaskManager);
             EasyBind.subscribe(preferences.getPreviewPreferences().showPreviewAsExtraTabProperty(), show -> {
                 if (show) {
                     container.getItems().remove(previewPanel);