Support customized entry types in BibliographyConsistencyCheck

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

@@ -116,13 +116,13 @@ public void start(Stage stage) {
                 dialogService,
                 fileUpdateMonitor,
                 preferences,
+                gitHandlerRegistry,
                 aiService,
                 stateManager,
                 countingUndoManager,
                 Injector.instantiateModelOrService(BibEntryTypesManager.class),
                 clipBoardManager,
-                taskExecutor,
-                gitHandlerRegistry);
+                taskExecutor);
 
         openWindow();
 
@@ -164,6 +164,7 @@ public void initialize() {
         Injector.setModelOrService(GitHandlerRegistry.class, gitHandlerRegistry);
 
         BibEntryTypesManager entryTypesManager = preferences.getCustomEntryTypesRepository();
+
         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

@@ -62,7 +62,7 @@ public BibliographyConsistencyCheck.Result call() {
 
                 BibDatabaseContext bibContext = databaseContext.get();
 
-                BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
+                BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck(preferences, entryTypesManager);
                 return consistencyCheck.check(bibContext, (count, total) ->
                         UiTaskExecutor.runInJavaFXThread(() -> {
                             updateProgress(count, total);

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

@@ -58,6 +58,7 @@
 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;
@@ -100,11 +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;
@@ -123,24 +124,24 @@ public JabRefFrame(Stage mainStage,
                        DialogService dialogService,
                        FileUpdateMonitor fileUpdateMonitor,
                        GuiPreferences preferences,
+                       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.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");
 

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

@@ -50,13 +50,14 @@ private PreferencesMigrations() {
      */
     public static void runMigrations(JabRefGuiPreferences preferences) {
         Preferences mainPrefsNode = Preferences.userRoot().node("/org/jabref");
+        BibEntryTypesManager bibEntryTypesManager = preferences.getCustomEntryTypesRepository();
 
         upgradePrefsToOrgJabRef(mainPrefsNode);
         upgradeSortOrder(preferences);
         upgradeFaultyEncodingStrings(preferences);
         upgradeLabelPatternToCitationKeyPattern(preferences, mainPrefsNode);
         upgradeImportFileAndDirePatterns(preferences, mainPrefsNode);
-        upgradeStoredBibEntryTypes(preferences, mainPrefsNode, preferences.getCustomEntryTypesRepository());
+        upgradeStoredBibEntryTypes(preferences, mainPrefsNode, 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;
@@ -64,7 +66,7 @@ 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

@@ -37,6 +37,7 @@
 @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;
@@ -93,7 +94,7 @@ 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"),

jablib/src/main/java/org/jabref/logic/exporter/ExporterFactory.java

@@ -13,6 +13,7 @@
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.logic.xmp.XmpPreferences;
 import org.jabref.model.database.BibDatabaseMode;
+import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.metadata.SelfContainedSaveOrder;
 
 public class ExporterFactory {
@@ -30,6 +31,7 @@ public static ExporterFactory create(CliPreferences preferences) {
         XmpPreferences xmpPreferences = preferences.getXmpPreferences();
         FieldPreferences fieldPreferences = preferences.getFieldPreferences();
         BibDatabaseMode bibDatabaseMode = preferences.getLibraryPreferences().getDefaultBibDatabaseMode();
+        BibEntryTypesManager bibEntryTypesManager = new BibEntryTypesManager();
 
         List<Exporter> exporters = new ArrayList<>();
 
@@ -59,7 +61,7 @@ public static ExporterFactory create(CliPreferences preferences) {
         exporters.add(new ModsExporter());
         exporters.add(new XmpExporter(xmpPreferences));
         exporters.add(new XmpPdfExporter(xmpPreferences));
-        exporters.add(new EmbeddedBibFilePdfExporter(bibDatabaseMode, preferences.getCustomEntryTypesRepository(), fieldPreferences));
+        exporters.add(new EmbeddedBibFilePdfExporter(bibDatabaseMode, preferences.getCustomEntryTypesRepository(bibEntryTypesManager), fieldPreferences));
         exporters.add(new CffExporter());
         exporters.add(new EndnoteXmlExporter(preferences.getBibEntryPreferences()));
 

jablib/src/main/java/org/jabref/logic/preferences/CliPreferences.java

@@ -69,6 +69,8 @@ public interface CliPreferences {
      */
     SelfContainedSaveConfiguration getSelfContainedExportConfiguration();
 
+    BibEntryTypesManager getCustomEntryTypesRepository(BibEntryTypesManager bibEntryTypesManager);
+
     BibEntryTypesManager getCustomEntryTypesRepository();
 
     void storeCustomEntryTypesRepository(BibEntryTypesManager entryTypesManager);

jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java

@@ -1219,15 +1219,20 @@ public JournalAbbreviationPreferences getJournalAbbreviationPreferences() {
     //*************************************************************************************************************
     // CustomEntryTypes
     //*************************************************************************************************************
-
-    @Override
     public BibEntryTypesManager getCustomEntryTypesRepository() {
         BibEntryTypesManager bibEntryTypesManager = new BibEntryTypesManager();
         EnumSet.allOf(BibDatabaseMode.class).forEach(mode ->
                 bibEntryTypesManager.addCustomOrModifiedTypes(getBibEntryTypes(mode), mode));
         return bibEntryTypesManager;
     }
 
+    @Override
+    public BibEntryTypesManager getCustomEntryTypesRepository(BibEntryTypesManager bibEntryTypesManager) {
+        EnumSet.allOf(BibDatabaseMode.class).forEach(mode ->
+                bibEntryTypesManager.addCustomOrModifiedTypes(getBibEntryTypes(mode), mode));
+        return bibEntryTypesManager;
+    }
+
     private List<BibEntryType> getBibEntryTypes(BibDatabaseMode bibDatabaseMode) {
         List<BibEntryType> storedEntryTypes = new ArrayList<>();
         Preferences prefsNode = getPrefsNodeForCustomizedEntryTypes(bibDatabaseMode);

jablib/src/main/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheck.java

@@ -1,7 +1,6 @@
 package org.jabref.logic.quality.consistency;
 
 import java.util.Collection;
-import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
@@ -17,16 +16,14 @@
 import org.jabref.logic.bibtex.comparator.BibEntryByFieldsComparator;
 import org.jabref.logic.bibtex.comparator.FieldComparatorStack;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryType;
+import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.InternalField;
 import org.jabref.model.entry.field.SpecialField;
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.field.UserSpecificCommentField;
-import org.jabref.model.entry.types.BiblatexEntryTypeDefinitions;
-import org.jabref.model.entry.types.BibtexEntryTypeDefinitions;
 import org.jabref.model.entry.types.EntryType;
 
 import com.google.common.annotations.VisibleForTesting;
@@ -55,6 +52,12 @@ public class BibliographyConsistencyCheck {
             StandardField.MODIFICATIONDATE
     );
 
+    private final BibEntryTypesManager bibEntryTypesManager;
+
+    public BibliographyConsistencyCheck(org.jabref.logic.preferences.CliPreferences cliPreferences, BibEntryTypesManager bibEntryTypesManager) {
+        this.bibEntryTypesManager = cliPreferences.getCustomEntryTypesRepository(bibEntryTypesManager);
+    }
+
     private static Set<Field> filterExcludedFields(Collection<Field> fields) {
         return fields.stream()
                      .filter(field -> !EXPLICITLY_EXCLUDED_FIELDS.contains(field))
@@ -73,11 +76,17 @@ private static Set<Field> filterExcludedFields(Collection<Field> fields) {
     @VisibleForTesting
     List<BibEntry> filterAndSortEntriesWithFieldDifferences(Set<BibEntry> entries, Set<Field> differingFields, Set<Field> requiredFields) {
         return entries.stream()
-                      .filter(entry ->
-                              // This removes entries that have all differing fields set (could be confusing to the user)
-                              !Collections.disjoint(entry.getFields(), differingFields)
-                                      // This ensures that all entries with missing required fields are included
-                                      || !entry.getFields().containsAll(requiredFields))
+                      .filter(entry -> {
+                          // Include entries that are missing any required fields
+                          boolean missingRequiredField = requiredFields.stream().anyMatch(field -> !entry.hasField(field));
+
+                          // Include entries that have any of the differing fields
+                          boolean hasDifferingField = differingFields.stream().anyMatch(entry::hasField);
+
+                          // Include all entries when there are differing fields (to show inconsistencies)
+                          // OR when missing required fields
+                          return !differingFields.isEmpty() || missingRequiredField;
+                      })
                       .sorted(new FieldComparatorStack<>(List.of(
                               new BibEntryByCitationKeyComparator(),
                               new BibEntryByFieldsComparator()
@@ -112,12 +121,10 @@ public Result check(BibDatabaseContext bibContext, BiConsumer<Integer, Integer>
 
         collectEntriesIntoMaps(bibContext, entryTypeToFieldsInAnyEntryMap, entryTypeToFieldsInAllEntriesMap, entryTypeToEntriesMap);
 
-        List<BibEntryType> entryTypeDefinitions;
-        if (bibContext.getMode() == BibDatabaseMode.BIBLATEX) {
-            entryTypeDefinitions = BiblatexEntryTypeDefinitions.ALL;
-        } else {
-            entryTypeDefinitions = BibtexEntryTypeDefinitions.ALL;
-        }
+        List<BibEntryType> entryTypeDefinitions = bibEntryTypesManager
+                .getAllTypes(bibContext.getMode())
+                .stream()
+                .toList();
 
         // Use LinkedHashMap to preserve the order of Bib(tex|latex)EntryTypeDefinitions.ALL
         Map<EntryType, EntryTypeResult> resultMap = new LinkedHashMap<>();
@@ -161,7 +168,6 @@ public Result check(BibDatabaseContext bibContext, BiConsumer<Integer, Integer>
     }
 
     private static void collectEntriesIntoMaps(BibDatabaseContext bibContext, Map<EntryType, Set<Field>> entryTypeToFieldsInAnyEntryMap, Map<EntryType, Set<Field>> entryTypeToFieldsInAllEntriesMap, Map<EntryType, Set<BibEntry>> entryTypeToEntriesMap) {
-        BibDatabaseMode mode = bibContext.getMode();
         List<BibEntry> entries = bibContext.getEntries();
 
         for (BibEntry entry : entries) {