Add feature to merge .bib files into current bib

CHANGELOG.md

@@ -36,6 +36,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a new `jabkit` command `pseudonymize` to pseudonymize the library. [#13109](https://github.com/JabRef/jabref/issues/13109)
 - We added functionality to focus running instance when trying to start a second instance. [#13129](https://github.com/JabRef/jabref/issues/13129)
 - We added a new setting in the 'Entry Editor' preferences to hide the 'File Annotations' tab when no annotations are available. [#13143](https://github.com/JabRef/jabref/issues/13143)
+- We added functionality to merge bib files in a given directory to the current bib and added a 'Merge other bib files into current bib' tab in the Preferences menu [#12290](https://github.com/JabRef/jabref/issues/12290)
 - We added support for multi-file import across different formats. [#13269](https://github.com/JabRef/jabref/issues/13269)
 
 ### Changed

jabgui/src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -87,6 +87,7 @@ public enum StandardActions implements Action {
     REPLACE_ALL(Localization.lang("Find and replace"), KeyBinding.REPLACE_STRING),
     MANAGE_KEYWORDS(Localization.lang("Manage keywords")),
     MASS_SET_FIELDS(Localization.lang("Manage field names & content")),
+    MERGE_BIBTEX_FILES_INTO_CURRENT_LIBRARY(Localization.lang("Merge BibTeX files into current library")),
 
     AUTOMATIC_FIELD_EDITOR(Localization.lang("Automatic field editor")),
     TOGGLE_GROUPS(Localization.lang("Groups"), IconTheme.JabRefIcons.TOGGLE_GROUPS, KeyBinding.TOGGLE_GROUPS_INTERFACE),

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

@@ -53,6 +53,7 @@
 import org.jabref.gui.linkedfile.RedownloadMissingFilesAction;
 import org.jabref.gui.maintable.NewLibraryFromPdfActionOffline;
 import org.jabref.gui.maintable.NewLibraryFromPdfActionOnline;
+import org.jabref.gui.mergebibfilesintocurrentbib.MergeBibFilesIntoCurrentBibAction;
 import org.jabref.gui.mergeentries.BatchEntryMergeWithFetchedDataAction;
 import org.jabref.gui.mergeentries.MergeEntriesAction;
 import org.jabref.gui.mergeentries.MergeWithFetchedEntryAction;
@@ -177,6 +178,10 @@ private void createMenu() {
 
                 new SeparatorMenuItem(),
 
+                factory.createMenuItem(StandardActions.MERGE_BIBTEX_FILES_INTO_CURRENT_LIBRARY, new MergeBibFilesIntoCurrentBibAction(dialogService, preferences, stateManager, undoManager, fileUpdateMonitor, entryTypesManager)),
+
+                new SeparatorMenuItem(),
+
                 factory.createSubMenu(StandardActions.REMOTE_DB,
                         factory.createMenuItem(StandardActions.CONNECT_TO_SHARED_DB, new ConnectToSharedDatabaseCommand(frame, dialogService)),
                         factory.createMenuItem(StandardActions.PULL_CHANGES_FROM_SHARED_DB, new PullChangesFromSharedAction(stateManager))),

jabgui/src/main/java/org/jabref/gui/mergebibfilesintocurrentbib/MergeBibFilesIntoCurrentBibAction.java

@@ -0,0 +1,190 @@
+package org.jabref.gui.mergebibfilesintocurrentbib;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import javax.swing.undo.UndoManager;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.mergeentries.MergeEntriesAction;
+import org.jabref.gui.preferences.GuiPreferences;
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.gui.undo.UndoableInsertEntries;
+import org.jabref.gui.util.DirectoryDialogConfiguration;
+import org.jabref.logic.database.DuplicateCheck;
+import org.jabref.logic.importer.OpenDatabase;
+import org.jabref.logic.importer.ParserResult;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.database.BibDatabaseMode;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.util.FileUpdateMonitor;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.jabref.gui.actions.ActionHelper.needsDatabase;
+
+public class MergeBibFilesIntoCurrentBibAction extends SimpleCommand {
+    private static final Logger LOGGER = LoggerFactory.getLogger(MergeBibFilesIntoCurrentBibAction.class);
+
+    private final DialogService dialogService;
+    private final GuiPreferences preferences;
+    private final StateManager stateManager;
+    private final UndoManager undoManager;
+    private final FileUpdateMonitor fileUpdateMonitor;
+    private final BibEntryTypesManager entryTypesManager;
+
+    private boolean shouldMergeSameKeyEntries;
+    private boolean shouldMergeDuplicateEntries;
+
+    private final List<BibEntry> entriesToMerge = new ArrayList<>();
+    private final List<List<BibEntry>> duplicatePairsToMerge = new ArrayList<>();
+    private final List<List<BibEntry>> sameKeyPairsToMerge = new ArrayList<>();
+
+    public MergeBibFilesIntoCurrentBibAction(DialogService dialogService,
+                                             GuiPreferences preferences,
+                                             StateManager stateManager,
+                                             UndoManager undoManager,
+                                             FileUpdateMonitor fileUpdateMonitor,
+                                             BibEntryTypesManager entryTypesManager) {
+        this.dialogService = dialogService;
+        this.preferences = preferences;
+        this.stateManager = stateManager;
+        this.undoManager = undoManager;
+        this.fileUpdateMonitor = fileUpdateMonitor;
+        this.entryTypesManager = entryTypesManager;
+
+        this.executable.bind(needsDatabase(this.stateManager));
+    }
+
+    @Override
+    public void execute() {
+        Optional<Path> selectedDirectory = getDirectoryToMerge();
+        Optional<BibDatabaseContext> context = stateManager.getActiveDatabase();
+
+        MergeBibFilesIntoCurrentBibPreferences mergeBibFilesIntoCurrentBibPreferences = preferences.getMergeBibFilesIntoCurrentBibPreferences();
+
+        shouldMergeSameKeyEntries = mergeBibFilesIntoCurrentBibPreferences.shouldMergeSameKeyEntries();
+        shouldMergeDuplicateEntries = mergeBibFilesIntoCurrentBibPreferences.shouldMergeDuplicateEntries();
+
+        if (selectedDirectory.isPresent() && context.isPresent()) {
+            mergeBibFilesIntoCurrentBib(selectedDirectory.get(), context.get());
+        }
+    }
+
+    private Optional<Path> getDirectoryToMerge() {
+        DirectoryDialogConfiguration config = new DirectoryDialogConfiguration.Builder()
+                .withInitialDirectory(preferences.getFilePreferences().getWorkingDirectory())
+                .build();
+
+        return dialogService.showDirectorySelectionDialog(config);
+    }
+
+    public void mergeBibFilesIntoCurrentBib(Path directory, BibDatabaseContext context) {
+        BibDatabase database = context.getDatabase();
+        Optional<Path> databasePath = context.getDatabasePath();
+        DuplicateCheck duplicateCheck = new DuplicateCheck(entryTypesManager);
+
+        entriesToMerge.clear();
+        sameKeyPairsToMerge.clear();
+        duplicatePairsToMerge.clear();
+
+        for (Path path : getAllBibFiles(directory, databasePath.orElseGet(() -> Path.of("")))) {
+            ParserResult result;
+            try {
+                result = OpenDatabase.loadDatabase(path, preferences.getImportFormatPreferences(), fileUpdateMonitor);
+            } catch (IOException e) {
+                LOGGER.error("Could not load file '{}': {}", path, e.getMessage(), e);
+                continue;
+            }
+            for (BibEntry toMergeEntry : result.getDatabase().getEntries()) {
+                processEntry(toMergeEntry, database, duplicateCheck);
+            }
+        }
+
+        database.insertEntries(entriesToMerge);
+        performMerges();
+
+        NamedCompound compound = new NamedCompound(Localization.lang("Merge BibTeX files into current library"));
+        compound.addEdit(new UndoableInsertEntries(database, entriesToMerge));
+        compound.end();
+        undoManager.addEdit(compound);
+    }
+
+    private void processEntry(BibEntry entry, BibDatabase database, DuplicateCheck duplicateCheck) {
+        for (BibEntry existingEntry : database.getEntries()) {
+            if (entry.equals(existingEntry)) {
+                return;
+            } else if (entry.getCitationKey().equals(existingEntry.getCitationKey())) {
+                if (shouldMergeSameKeyEntries) {
+                    sameKeyPairsToMerge.add(List.of(entry, existingEntry));
+                }
+                return;
+            } else if (duplicateCheck.isDuplicate(entry, existingEntry, BibDatabaseMode.BIBTEX)) {
+                if (shouldMergeDuplicateEntries) {
+                    duplicatePairsToMerge.add(List.of(entry, existingEntry));
+                }
+                return;
+            }
+        }
+        entriesToMerge.add(entry);
+    }
+
+    private void performMerges() {
+        for (List<BibEntry> pair : sameKeyPairsToMerge) {
+            mergeEntries(pair);
+        }
+        for (List<BibEntry> pair : duplicatePairsToMerge) {
+            mergeEntries(pair);
+        }
+    }
+
+    private void mergeEntries(List<BibEntry> entries) {
+        stateManager.setSelectedEntries(entries);
+        new MergeEntriesAction(dialogService, stateManager, undoManager, preferences).execute();
+    }
+
+    private List<Path> getAllBibFiles(Path directory, Path databasePath) {
+        if (!isValidPath(directory)) {
+            return List.of();
+        }
+        try (Stream<Path> stream = Files.find(
+                directory,
+                Integer.MAX_VALUE,
+                (path, _) -> path.getFileName().toString().endsWith(".bib") &&
+                        !path.equals(databasePath)
+        )) {
+            return stream.collect(Collectors.toList());
+        } catch (IOException e) {
+            LOGGER.error("Error finding .bib files in '{}': {}", directory.getFileName(), e.getMessage(), e);
+        }
+        return List.of();
+    }
+
+    private boolean isValidPath(Path directory) {
+        if (!Files.exists(directory)) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Chosen folder does not exist:") + " " + directory);
+            return false;
+        }
+        if (!Files.isDirectory(directory)) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Chosen path is not a folder:") + " " + directory);
+            return false;
+        }
+        if (!Files.isReadable(directory)) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Chosen folder is not readable:") + " " + directory);
+            return false;
+        }
+        return true;
+    }
+}

jabgui/src/main/java/org/jabref/gui/mergebibfilesintocurrentbib/MergeBibFilesIntoCurrentBibPreferences.java

@@ -0,0 +1,38 @@
+package org.jabref.gui.mergebibfilesintocurrentbib;
+
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.SimpleBooleanProperty;
+
+public class MergeBibFilesIntoCurrentBibPreferences {
+    private final BooleanProperty shouldMergeSameKeyEntries = new SimpleBooleanProperty();
+    private final BooleanProperty shouldMergeDuplicateEntries = new SimpleBooleanProperty();
+
+    public MergeBibFilesIntoCurrentBibPreferences(boolean shouldMergeSameKeyEntries, boolean shouldMergeDuplicateEntries) {
+        this.shouldMergeSameKeyEntries.set(shouldMergeSameKeyEntries);
+        this.shouldMergeDuplicateEntries.set(shouldMergeDuplicateEntries);
+    }
+
+    public boolean shouldMergeSameKeyEntries() {
+        return this.shouldMergeSameKeyEntries.get();
+    }
+
+    public void setShouldMergeSameKeyEntries(boolean decision) {
+        this.shouldMergeSameKeyEntries.set(decision);
+    }
+
+    public BooleanProperty shouldMergeSameKeyEntriesProperty() {
+        return this.shouldMergeSameKeyEntries;
+    }
+
+    public boolean shouldMergeDuplicateEntries() {
+        return this.shouldMergeDuplicateEntries.get();
+    }
+
+    public void setShouldMergeDuplicateEntries(boolean decision) {
+        this.shouldMergeDuplicateEntries.set(decision);
+    }
+
+    public BooleanProperty shouldMergeDuplicateEntriesProperty() {
+        return this.shouldMergeDuplicateEntries;
+    }
+}

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

@@ -13,6 +13,7 @@
 import org.jabref.gui.maintable.ColumnPreferences;
 import org.jabref.gui.maintable.MainTablePreferences;
 import org.jabref.gui.maintable.NameDisplayPreferences;
+import org.jabref.gui.mergebibfilesintocurrentbib.MergeBibFilesIntoCurrentBibPreferences;
 import org.jabref.gui.mergeentries.MergeDialogPreferences;
 import org.jabref.gui.newentry.NewEntryPreferences;
 import org.jabref.gui.preview.PreviewPreferences;
@@ -58,4 +59,6 @@ public interface GuiPreferences extends CliPreferences {
     KeyBindingRepository getKeyBindingRepository();
 
     NewEntryPreferences getNewEntryPreferences();
+
+    MergeBibFilesIntoCurrentBibPreferences getMergeBibFilesIntoCurrentBibPreferences();
 }

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

@@ -38,6 +38,7 @@
 import org.jabref.gui.maintable.MainTableColumnModel;
 import org.jabref.gui.maintable.MainTablePreferences;
 import org.jabref.gui.maintable.NameDisplayPreferences;
+import org.jabref.gui.mergebibfilesintocurrentbib.MergeBibFilesIntoCurrentBibPreferences;
 import org.jabref.gui.mergeentries.DiffMode;
 import org.jabref.gui.mergeentries.MergeDialogPreferences;
 import org.jabref.gui.newentry.NewEntryDialogTab;
@@ -234,6 +235,11 @@ public class JabRefGuiPreferences extends JabRefCliPreferences implements GuiPre
     private static final String CREATE_ENTRY_INTERPRET_PARSER_NAME = "latestInterpretParserName";
     // endregion
 
+    // region MergeBibFilesPreferences
+    private static final String MERGE_SAME_KEY_ENTRIES = "mergeSameKeyEntries";
+    private static final String MERGE_DUPLICATE_ENTRIES = "mergeDuplicateEntries";
+    // endregion
+
     private static JabRefGuiPreferences singleton;
 
     private EntryEditorPreferences entryEditorPreferences;
@@ -255,6 +261,7 @@ public class JabRefGuiPreferences extends JabRefCliPreferences implements GuiPre
     private KeyBindingRepository keyBindingRepository;
     private CopyToPreferences copyToPreferences;
     private NewEntryPreferences newEntryPreferences;
+    private MergeBibFilesIntoCurrentBibPreferences mergeBibFilesIntoCurrentBibPreferences;
 
     private JabRefGuiPreferences() {
         super();
@@ -431,6 +438,11 @@ private JabRefGuiPreferences() {
         defaults.put(CREATE_ENTRY_ID_FETCHER_NAME, DoiFetcher.NAME);
         defaults.put(CREATE_ENTRY_INTERPRET_PARSER_NAME, PlainCitationParserChoice.RULE_BASED.getLocalizedName());
         // endregion
+
+        // region MergeBibEntriesPreferences
+        defaults.put(MERGE_SAME_KEY_ENTRIES, true);
+        defaults.put(MERGE_DUPLICATE_ENTRIES, true);
+        // endregion
     }
 
     /**
@@ -1300,6 +1312,24 @@ public NewEntryPreferences getNewEntryPreferences() {
         return newEntryPreferences;
     }
 
+    // region MergeBibFilesPreferences
+    @Override
+    public MergeBibFilesIntoCurrentBibPreferences getMergeBibFilesIntoCurrentBibPreferences() {
+        if (mergeBibFilesIntoCurrentBibPreferences != null) {
+            return mergeBibFilesIntoCurrentBibPreferences;
+        }
+        mergeBibFilesIntoCurrentBibPreferences = new MergeBibFilesIntoCurrentBibPreferences(
+                getBoolean(MERGE_SAME_KEY_ENTRIES),
+                getBoolean(MERGE_DUPLICATE_ENTRIES)
+        );
+
+        EasyBind.listen(mergeBibFilesIntoCurrentBibPreferences.shouldMergeSameKeyEntriesProperty(), (_, _, newValue) -> putBoolean(MERGE_SAME_KEY_ENTRIES, newValue));
+        EasyBind.listen(mergeBibFilesIntoCurrentBibPreferences.shouldMergeDuplicateEntriesProperty(), (_, _, newValue) -> putBoolean(MERGE_DUPLICATE_ENTRIES, newValue));
+
+        return mergeBibFilesIntoCurrentBibPreferences;
+    }
+    // endregion
+
     /**
      * In GUI mode, we can lookup the directory better
      */

jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTab.java

@@ -50,6 +50,8 @@ public class GeneralTab extends AbstractPreferenceTabView<GeneralTabViewModel> i
     @FXML private CheckBox shouldAskForIncludingCrossReferences;
     @FXML private CheckBox confirmHideTabBar;
     @FXML private ComboBox<BibDatabaseMode> biblatexMode;
+    @FXML private CheckBox mergeSameKeyEntries;
+    @FXML private CheckBox mergeDuplicateEntries;
     @FXML private CheckBox alwaysReformatBib;
     @FXML private CheckBox autosaveLocalLibraries;
     @FXML private Button autosaveLocalLibrariesHelp;
@@ -130,6 +132,9 @@ public void initialize() {
         biblatexMode.itemsProperty().bind(viewModel.biblatexModeListProperty());
         biblatexMode.valueProperty().bindBidirectional(viewModel.selectedBiblatexModeProperty());
 
+        mergeSameKeyEntries.selectedProperty().bindBidirectional(viewModel.mergeSameKeyEntriesProperty());
+        mergeDuplicateEntries.selectedProperty().bindBidirectional(viewModel.mergeDuplicateEntriesProperty());
+
         alwaysReformatBib.selectedProperty().bindBidirectional(viewModel.alwaysReformatBibProperty());
         autosaveLocalLibraries.selectedProperty().bindBidirectional(viewModel.autosaveLocalLibrariesProperty());
         ActionFactory actionFactory = new ActionFactory();