Support customized entry types in BibliographyConsistencyCheck

jabgui/src/main/java/org/jabref/Launcher.java

@@ -27,6 +27,7 @@
 import org.jabref.logic.util.BuildInfo;
 import org.jabref.logic.util.Directories;
 import org.jabref.migrations.PreferencesMigrations;
+import org.jabref.model.entry.BibEntryTypesManager;
 
 import com.airhacks.afterburner.injection.Injector;
 import org.slf4j.Logger;
@@ -56,6 +57,7 @@ public static void main(String[] args) {
         Injector.setModelOrService(BuildInfo.class, new BuildInfo());
 
         final JabRefGuiPreferences preferences = JabRefGuiPreferences.getInstance();
+        final BibEntryTypesManager bibEntryTypesManager = new BibEntryTypesManager();
 
         ArgumentProcessor argumentProcessor = new ArgumentProcessor(
                 args,
@@ -87,7 +89,7 @@ public static void main(String[] args) {
             systemExit();
         }
 
-        PreferencesMigrations.runMigrations(preferences);
+        PreferencesMigrations.runMigrations(preferences, bibEntryTypesManager);
 
         PostgreServer postgreServer = new PostgreServer();
         Injector.setModelOrService(PostgreServer.class, postgreServer);

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

@@ -43,6 +43,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.ProxyRegisterer;
 import org.jabref.logic.os.OS;
+import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.logic.remote.RemotePreferences;
 import org.jabref.logic.remote.server.RemoteListenerServerManager;
@@ -71,6 +72,7 @@ public class JabRefGUI extends Application {
 
     private static List<UiCommand> uiCommands;
     private static GuiPreferences preferences;
+    private static CliPreferences cliPreferences;
 
     // AI Service handles chat messages etc. Therefore, it is tightly coupled to the GUI.
     private static AiService aiService;
@@ -85,6 +87,8 @@ public class JabRefGUI extends Application {
     private static ClipBoardManager clipBoardManager;
     private static DialogService dialogService;
     private static JabRefFrame mainFrame;
+
+    private static BibEntryTypesManager bibEntryTypesManager;
     private static GitHandlerRegistry gitHandlerRegistry;
 
     private static RemoteListenerServerManager remoteListenerServerManager;
@@ -116,13 +120,14 @@ public void start(Stage stage) {
                 dialogService,
                 fileUpdateMonitor,
                 preferences,
+                cliPreferences,
+                gitHandlerRegistry,
                 aiService,
                 stateManager,
                 countingUndoManager,
                 Injector.instantiateModelOrService(BibEntryTypesManager.class),
                 clipBoardManager,
-                taskExecutor,
-                gitHandlerRegistry);
+                taskExecutor);
 
         openWindow();
 
@@ -163,7 +168,8 @@ public void initialize() {
         gitHandlerRegistry = new GitHandlerRegistry();
         Injector.setModelOrService(GitHandlerRegistry.class, gitHandlerRegistry);
 
-        BibEntryTypesManager entryTypesManager = preferences.getCustomEntryTypesRepository();
+        BibEntryTypesManager entryTypesManager = preferences.getCustomEntryTypesRepository(bibEntryTypesManager);
+
         JournalAbbreviationRepository journalAbbreviationRepository = JournalAbbreviationLoader.loadRepository(preferences.getJournalAbbreviationPreferences());
         Injector.setModelOrService(BibEntryTypesManager.class, entryTypesManager);
         Injector.setModelOrService(JournalAbbreviationRepository.class, journalAbbreviationRepository);

jabgui/src/main/java/org/jabref/gui/consistency/ConsistencyCheckAction.java

@@ -13,6 +13,7 @@
 import org.jabref.gui.preferences.GuiPreferences;
 import org.jabref.gui.util.UiTaskExecutor;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.logic.quality.consistency.BibliographyConsistencyCheck;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntryTypesManager;
@@ -29,19 +30,22 @@ public class ConsistencyCheckAction extends SimpleCommand {
     private final DialogService dialogService;
     private final StateManager stateManager;
     private final GuiPreferences preferences;
+    private final CliPreferences cliPreferences;
     private final BibEntryTypesManager entryTypesManager;
     private final UiTaskExecutor taskExecutor;
 
     public ConsistencyCheckAction(Supplier<LibraryTab> tabSupplier,
                                   DialogService dialogService,
                                   StateManager stateManager,
                                   GuiPreferences preferences,
+                                  CliPreferences cliPreferences,
                                   BibEntryTypesManager entryTypesManager,
                                   UiTaskExecutor taskExecutor) {
         this.tabSupplier = tabSupplier;
         this.dialogService = dialogService;
         this.stateManager = stateManager;
         this.preferences = preferences;
+        this.cliPreferences = cliPreferences;
         this.entryTypesManager = entryTypesManager;
         this.taskExecutor = taskExecutor;
 
@@ -62,7 +66,7 @@ public BibliographyConsistencyCheck.Result call() {
 
                 BibDatabaseContext bibContext = databaseContext.get();
 
-                BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
+                BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck(cliPreferences, entryTypesManager);
                 return consistencyCheck.check(bibContext, (count, total) ->
                         UiTaskExecutor.runInJavaFXThread(() -> {
                             updateProgress(count, total);

jabgui/src/main/java/org/jabref/gui/frame/JabRefFrame.java

@@ -57,6 +57,7 @@
 import org.jabref.logic.ai.AiService;
 import org.jabref.logic.git.util.GitHandlerRegistry;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
+import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.logic.util.BuildInfo;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
@@ -88,6 +89,7 @@ private enum PanelMode { MAIN_TABLE, MAIN_TABLE_AND_ENTRY_EDITOR }
     private static final Logger LOGGER = LoggerFactory.getLogger(JabRefFrame.class);
 
     private final GuiPreferences preferences;
+    private final CliPreferences cliPreferences;
     private final AiService aiService;
     private final GlobalSearchBar globalSearchBar;
 
@@ -99,11 +101,11 @@ private enum PanelMode { MAIN_TABLE, MAIN_TABLE_AND_ENTRY_EDITOR }
     private final StateManager stateManager;
     private final CountingUndoManager undoManager;
     private final DialogService dialogService;
+    private final GitHandlerRegistry gitHandlerRegistry;
     private final FileUpdateMonitor fileUpdateMonitor;
     private final BibEntryTypesManager entryTypesManager;
     private final ClipBoardManager clipBoardManager;
     private final TaskExecutor taskExecutor;
-    private final GitHandlerRegistry gitHandlerRegistry;
 
     private final JabRefFrameViewModel viewModel;
     private final GuiPushToApplicationCommand pushToApplicationCommand;
@@ -122,24 +124,26 @@ public JabRefFrame(Stage mainStage,
                        DialogService dialogService,
                        FileUpdateMonitor fileUpdateMonitor,
                        GuiPreferences preferences,
+                       CliPreferences cliPreferences,
+                       GitHandlerRegistry gitHandlerRegistry,
                        AiService aiService,
                        StateManager stateManager,
                        CountingUndoManager undoManager,
                        BibEntryTypesManager entryTypesManager,
                        ClipBoardManager clipBoardManager,
-                       TaskExecutor taskExecutor,
-                       GitHandlerRegistry gitHandlerRegistry) {
+                       TaskExecutor taskExecutor) {
         this.mainStage = mainStage;
         this.dialogService = dialogService;
         this.fileUpdateMonitor = fileUpdateMonitor;
         this.preferences = preferences;
+        this.cliPreferences = cliPreferences;
+        this.gitHandlerRegistry = gitHandlerRegistry;
         this.aiService = aiService;
         this.stateManager = stateManager;
         this.undoManager = undoManager;
         this.entryTypesManager = entryTypesManager;
         this.clipBoardManager = clipBoardManager;
         this.taskExecutor = taskExecutor;
-        this.gitHandlerRegistry = gitHandlerRegistry;
 
         setId("frame");
 
@@ -240,6 +244,7 @@ private void initLayout() {
                 sidePane,
                 pushToApplicationCommand,
                 preferences,
+                cliPreferences,
                 stateManager,
                 fileUpdateMonitor,
                 taskExecutor,

jabgui/src/main/java/org/jabref/gui/frame/MainMenu.java

@@ -88,6 +88,7 @@
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.os.OS;
+import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.entry.field.SpecialField;
@@ -101,6 +102,7 @@ public class MainMenu extends MenuBar {
     private final SidePane sidePane;
     private final GuiPushToApplicationCommand pushToApplicationCommand;
     private final GuiPreferences preferences;
+    private final CliPreferences cliPreferences;
     private final StateManager stateManager;
     private final FileUpdateMonitor fileUpdateMonitor;
     private final TaskExecutor taskExecutor;
@@ -119,6 +121,7 @@ public MainMenu(JabRefFrame frame,
                     SidePane sidePane,
                     GuiPushToApplicationCommand pushToApplicationCommand,
                     GuiPreferences preferences,
+                    CliPreferences cliPreferences,
                     StateManager stateManager,
                     FileUpdateMonitor fileUpdateMonitor,
                     TaskExecutor taskExecutor,
@@ -136,6 +139,7 @@ public MainMenu(JabRefFrame frame,
         this.sidePane = sidePane;
         this.pushToApplicationCommand = pushToApplicationCommand;
         this.preferences = preferences;
+        this.cliPreferences = cliPreferences;
         this.stateManager = stateManager;
         this.fileUpdateMonitor = fileUpdateMonitor;
         this.taskExecutor = taskExecutor;
@@ -274,7 +278,7 @@ private void createMenu() {
                 factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(frame::getCurrentLibraryTab, dialogService, stateManager, preferences, entryTypesManager, taskExecutor)),
                 factory.createMenuItem(StandardActions.MERGE_ENTRIES, new MergeEntriesAction(dialogService, stateManager, undoManager, preferences)),
                 factory.createMenuItem(StandardActions.CHECK_INTEGRITY, new IntegrityCheckAction(frame::getCurrentLibraryTab, preferences, dialogService, stateManager, (UiTaskExecutor) taskExecutor, abbreviationRepository)),
-                factory.createMenuItem(StandardActions.CHECK_CONSISTENCY, new ConsistencyCheckAction(frame::getCurrentLibraryTab, dialogService, stateManager, preferences, entryTypesManager, (UiTaskExecutor) taskExecutor)),
+                factory.createMenuItem(StandardActions.CHECK_CONSISTENCY, new ConsistencyCheckAction(frame::getCurrentLibraryTab, dialogService, stateManager, preferences, cliPreferences, entryTypesManager, (UiTaskExecutor) taskExecutor)),
                 factory.createMenuItem(StandardActions.CLEANUP_ENTRIES, new CleanupAction(frame::getCurrentLibraryTab, preferences, dialogService, stateManager, taskExecutor, undoManager)),
 
                 new SeparatorMenuItem(),

jabgui/src/main/java/org/jabref/gui/preferences/PreferencesDialogView.java

@@ -17,6 +17,7 @@
 import org.jabref.gui.util.ControlHelper;
 import org.jabref.gui.util.ViewModelListCellFactory;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.model.entry.BibEntryTypesManager;
 
 import com.airhacks.afterburner.views.ViewLoader;
 import com.tobiasdiez.easybind.EasyBind;
@@ -39,6 +40,7 @@ public class PreferencesDialogView extends BaseDialog<PreferencesDialogViewModel
 
     @Inject private DialogService dialogService;
     @Inject private GuiPreferences preferences;
+    @Inject private BibEntryTypesManager bibEntryTypesManager;
 
     private PreferencesDialogViewModel viewModel;
     private final Class<? extends PreferencesTab> preferencesTabToSelectClass;
@@ -67,7 +69,7 @@ public PreferencesDialogViewModel getViewModel() {
 
     @FXML
     private void initialize() {
-        viewModel = new PreferencesDialogViewModel(dialogService, preferences);
+        viewModel = new PreferencesDialogViewModel(dialogService, preferences, bibEntryTypesManager);
 
         preferenceTabList.itemsProperty().setValue(viewModel.getPreferenceTabs());
 

jabgui/src/main/java/org/jabref/gui/preferences/PreferencesDialogViewModel.java

@@ -54,10 +54,12 @@ public class PreferencesDialogViewModel extends AbstractViewModel {
     private final DialogService dialogService;
     private final GuiPreferences preferences;
     private final ObservableList<PreferencesTab> preferenceTabs;
+    private final BibEntryTypesManager bibEntryTypesManager;
 
-    public PreferencesDialogViewModel(DialogService dialogService, GuiPreferences preferences) {
+    public PreferencesDialogViewModel(DialogService dialogService, GuiPreferences preferences, BibEntryTypesManager bibEntryTypesManager) {
         this.dialogService = dialogService;
         this.preferences = preferences;
+        this.bibEntryTypesManager = bibEntryTypesManager;
 
         // This enables passing unsaved preference values from the AI tab to the "web search" tab.
         AiTab aiTab = new AiTab();
@@ -190,9 +192,9 @@ public void storeAllSettings() {
                             + Localization.lang("You must restart JabRef for this to come into effect."));
         }
 
-        Injector.setModelOrService(BibEntryTypesManager.class, preferences.getCustomEntryTypesRepository());
+        Injector.setModelOrService(BibEntryTypesManager.class, preferences.getCustomEntryTypesRepository(bibEntryTypesManager));
         dialogService.notify(Localization.lang("Preferences recorded."));
-    }
+    };
 
     /**
      * Inserts the preference values into the Properties of the ViewModel

jabgui/src/main/java/org/jabref/gui/preferences/customentrytypes/CustomEntryTypesTab.java

@@ -57,6 +57,7 @@ public class CustomEntryTypesTab extends AbstractPreferenceTabView<CustomEntryTy
     @FXML private Button addNewFieldButton;
 
     @Inject private StateManager stateManager;
+    @Inject private BibEntryTypesManager bibEntryTypesManager;
 
     private final ControlsFxVisualizer visualizer = new ControlsFxVisualizer();
 
@@ -76,7 +77,7 @@ public String getTabName() {
     public void initialize() {
         BibDatabaseMode mode = stateManager.getActiveDatabase().map(BibDatabaseContext::getMode)
                                            .orElse(preferences.getLibraryPreferences().getDefaultBibDatabaseMode());
-        BibEntryTypesManager entryTypesRepository = preferences.getCustomEntryTypesRepository();
+        BibEntryTypesManager entryTypesRepository = preferences.getCustomEntryTypesRepository(bibEntryTypesManager);
 
         this.viewModel = new CustomEntryTypesTabViewModel(mode, entryTypesRepository, dialogService, preferences);
 

jabgui/src/main/java/org/jabref/migrations/PreferencesMigrations.java

@@ -48,15 +48,15 @@ private PreferencesMigrations() {
     /**
      * Perform checks and changes for users with a preference set from an older JabRef version.
      */
-    public static void runMigrations(JabRefGuiPreferences preferences) {
+    public static void runMigrations(JabRefGuiPreferences preferences, BibEntryTypesManager bibEntryTypesManager) {
         Preferences mainPrefsNode = Preferences.userRoot().node("/org/jabref");
 
         upgradePrefsToOrgJabRef(mainPrefsNode);
         upgradeSortOrder(preferences);
         upgradeFaultyEncodingStrings(preferences);
         upgradeLabelPatternToCitationKeyPattern(preferences, mainPrefsNode);
         upgradeImportFileAndDirePatterns(preferences, mainPrefsNode);
-        upgradeStoredBibEntryTypes(preferences, mainPrefsNode, preferences.getCustomEntryTypesRepository());
+        upgradeStoredBibEntryTypes(preferences, mainPrefsNode, preferences.getCustomEntryTypesRepository(bibEntryTypesManager));
         upgradeKeyBindingsToJavaFX(preferences);
         addCrossRefRelatedFieldsForAutoComplete(preferences);
         upgradePreviewStyle(preferences);

jabkit/src/main/java/org/jabref/JabKit.java

@@ -57,6 +57,7 @@ public class JabKit {
     private static Logger LOGGER;
 
     private static final String JABKIT_BRAND = "JabKit - command line toolkit for JabRef";
+    private static final BibEntryTypesManager bibEntryTypesManager = new BibEntryTypesManager();
 
     public static void main(String[] args) {
         initLogging(args);
@@ -68,7 +69,7 @@ public static void main(String[] args) {
             BuildInfo buildInfo = new BuildInfo();
             Injector.setModelOrService(BuildInfo.class, buildInfo);
 
-            BibEntryTypesManager entryTypesManager = preferences.getCustomEntryTypesRepository();
+            BibEntryTypesManager entryTypesManager = preferences.getCustomEntryTypesRepository(bibEntryTypesManager);
             Injector.setModelOrService(BibEntryTypesManager.class, entryTypesManager);
 
             ArgumentProcessor argumentProcessor = new ArgumentProcessor(preferences, entryTypesManager);

jabkit/src/main/java/org/jabref/cli/CheckConsistency.java

@@ -15,6 +15,7 @@
 import org.jabref.logic.quality.consistency.BibliographyConsistencyCheckResultTxtWriter;
 import org.jabref.logic.quality.consistency.BibliographyConsistencyCheckResultWriter;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntryTypesManager;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -26,6 +27,7 @@
 @Command(name = "check-consistency", description = "Check consistency of the library.")
 class CheckConsistency implements Callable<Integer> {
     private static final Logger LOGGER = LoggerFactory.getLogger(CheckConsistency.class);
+    private static final BibEntryTypesManager bibEntryTypesManager = new BibEntryTypesManager();
 
     @ParentCommand
     private ArgumentProcessor argumentProcessor;
@@ -63,7 +65,7 @@ public Integer call() {
 
         BibDatabaseContext databaseContext = parserResult.get().getDatabaseContext();
 
-        BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
+        BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck(argumentProcessor.cliPreferences, bibEntryTypesManager);
         BibliographyConsistencyCheck.Result result = consistencyCheck.check(databaseContext, (count, total) -> {
             if (!sharedOptions.porcelain) {
                 System.out.println(Localization.lang("Checking consistency for entry type %0 of %1", count + 1, total));

jabkit/src/main/java/org/jabref/cli/PdfUpdate.java

@@ -36,6 +36,7 @@
 @Command(name = "update", description = "Update linked PDFs with XMP and/or embedded BibTeX.")
 class PdfUpdate implements Runnable {
     private static final Logger LOGGER = LoggerFactory.getLogger(PdfUpdate.class);
+    private static final BibEntryTypesManager bibEntryTypesManager = new BibEntryTypesManager();
 
     @ParentCommand
     protected Pdf pdf;
@@ -91,7 +92,7 @@ public void run() {
                 pdf.argumentProcessor.cliPreferences.getXmpPreferences(),
                 pdf.argumentProcessor.cliPreferences.getFilePreferences(),
                 pdf.argumentProcessor.cliPreferences.getLibraryPreferences().getDefaultBibDatabaseMode(),
-                pdf.argumentProcessor.cliPreferences.getCustomEntryTypesRepository(),
+                pdf.argumentProcessor.cliPreferences.getCustomEntryTypesRepository(bibEntryTypesManager),
                 pdf.argumentProcessor.cliPreferences.getFieldPreferences(),
                 Injector.instantiateModelOrService(JournalAbbreviationRepository.class),
                 formats.contains("xmp"),