Persist group membership in folder libraries and make pair renames opt-in

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added a library-specific override of the "Auto rename files if entry changes" preference to the library properties. [#769](https://github.com/JabRef/jabref-koppor/pull/769)
 - In directory libraries, a sidecar and its PDF are now renamed together to the configured filename pattern (Preferences > Linked files) whenever the entry is edited — e.g. changing the citation key renames both files. [#741](https://github.com/JabRef/jabref-koppor/pull/741)
 - The groups panel of a directory library now mirrors the folder structure: each subdirectory appears as a group containing the entries whose files live there (updated live as files change). [#740](https://github.com/JabRef/jabref-koppor/pull/740)
 - Directory libraries now save into their sidecar files: edits are written back automatically (debounced until typing pauses; Ctrl+S forces the write and no longer creates a `.bib`), the first edit of a PDF-only entry creates a Markdown sidecar (`X.md` with the Hayagriva data as frontmatter and the comment fields as notes body), renaming a citation key renames the YAML key, and deleting an entry removes it from its file (the file is trashed once empty, the PDF stays). Hand-written content that JabRef does not understand survives rewrites. [#739](https://github.com/JabRef/jabref-koppor/pull/739)

docs/requirements/directory-library.md

@@ -82,11 +82,13 @@ entries or subgroups can be added to them, they cannot be dragged or edited.
 Needs: impl
 
 ## The sidecar and its PDF follow the configured filename pattern
-`req~directory-library.pattern-rename~1`
+`req~directory-library.pattern-rename~2`
 
-When write-back touches a single-entry sidecar, the sidecar and its equally named PDF are
-renamed together to the base name the configured filename pattern (Linked files preferences)
-generates for the entry, keeping the pair in sync. Multi-entry files have no single generating
+When write-back touches a single-entry sidecar and auto-renaming is enabled, the sidecar and
+its equally named PDF are renamed together to the base name the configured filename pattern
+(Linked files preferences) generates for the entry, keeping the pair in sync. Auto-renaming
+follows the global "Auto rename files if entry changes" preference unless the library
+properties override it (General tab; the same override applies to `.bib` libraries). Multi-entry files have no single generating
 entry and keep their name; occupied target names and pattern failures leave the current name
 untouched. Entry file links and the catalog follow the rename; the watcher does not re-import
 the renamed files.

jabgui/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java

@@ -1,5 +1,7 @@
 package org.jabref.gui.collab.metedatachange;
 
+import java.util.Optional;
+
 import javafx.scene.control.Label;
 import javafx.scene.control.ScrollPane;
 import javafx.scene.layout.VBox;
@@ -72,14 +74,23 @@ private ScrollPane createDefaultDiffScrollPane(MetaDataDiff.Difference diff) {
         VBox diffContainer = new VBox(12);
 
         // Show both original and new values
-        diffContainer.getChildren().add(new Label(diff.originalObject().toString()));
-        diffContainer.getChildren().add(new Label(diff.newObject().toString()));
+        diffContainer.getChildren().add(new Label(formatValue(diff, diff.originalObject())));
+        diffContainer.getChildren().add(new Label(formatValue(diff, diff.newObject())));
 
         ScrollPane scrollPane = new ScrollPane(diffContainer);
         scrollPane.setFitToWidth(true);
         return scrollPane;
     }
 
+    private static String formatValue(MetaDataDiff.Difference diff, Object value) {
+        if (diff.differenceType() == MetaDataDiff.DifferenceType.AUTO_RENAME_FILES_ON_CHANGE
+                && value instanceof Optional<?> override) {
+            return override.map(rename -> Boolean.TRUE.equals(rename) ? Localization.lang("Yes") : Localization.lang("No"))
+                           .orElse(Localization.lang("Use global preference"));
+        }
+        return value.toString();
+    }
+
     private String getDifferenceString(MetaDataDiff.DifferenceType changeType) {
         return switch (changeType) {
             case PROTECTED ->
@@ -106,6 +117,8 @@ private String getDifferenceString(MetaDataDiff.DifferenceType changeType) {
                     Localization.lang("Library-specific file directory");
             case CONTENT_SELECTOR ->
                     Localization.lang("Content selectors");
+            case AUTO_RENAME_FILES_ON_CHANGE ->
+                    Localization.lang("Auto rename files if entry changes");
         };
     }
 }

jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java

@@ -2,6 +2,8 @@
 
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.cleanup.RenamePdfCleanup;
+import org.jabref.logic.shared.DatabaseLocation;
+import org.jabref.logic.util.strings.StringUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.event.FieldChangedEvent;
@@ -14,19 +16,27 @@
 public class AutoRenameFileOnEntryChange {
     private static final Logger LOGGER = LoggerFactory.getLogger(AutoRenameFileOnEntryChange.class);
 
+    private final BibDatabaseContext bibDatabaseContext;
     private final FilePreferences filePreferences;
     private final RenamePdfCleanup renamePdfCleanup;
 
     public AutoRenameFileOnEntryChange(BibDatabaseContext bibDatabaseContext, FilePreferences filePreferences) {
+        this.bibDatabaseContext = bibDatabaseContext;
         this.filePreferences = filePreferences;
         renamePdfCleanup = new RenamePdfCleanup(false, () -> bibDatabaseContext, filePreferences);
     }
 
+    /// The library properties override the global preference when set (`MetaData#getAutoRenameFilesOnChange`);
+    /// without a filename pattern there is nothing to rename to.
+    public static boolean isEnabled(BibDatabaseContext bibDatabaseContext, FilePreferences filePreferences) {
+        return !StringUtil.isBlank(filePreferences.getFileNamePattern())
+                && bibDatabaseContext.getMetaData().getAutoRenameFilesOnChange().orElseGet(filePreferences::shouldAutoRenameFilesOnChange);
+    }
+
     @Subscribe
     public void listen(FieldChangedEvent event) {
-        if (!filePreferences.shouldAutoRenameFilesOnChange()
-                || filePreferences.getFileNamePattern().isEmpty()
-                || filePreferences.getFileNamePattern() == null) {
+        // A directory library renames its sidecar/PDF pairs in the write-back (see SidecarWriteBack)
+        if (bibDatabaseContext.getLocation() == DatabaseLocation.DIRECTORY || !isEnabled(bibDatabaseContext, filePreferences)) {
             return;
         }
 

jabgui/src/main/java/org/jabref/gui/importer/actions/OpenDirectoryLibraryAction.java

@@ -19,6 +19,7 @@
 import org.jabref.gui.clipboard.ClipBoardManager;
 import org.jabref.gui.desktop.os.NativeDesktop;
 import org.jabref.gui.exporter.SaveDatabaseAction;
+import org.jabref.gui.externalfiles.AutoRenameFileOnEntryChange;
 import org.jabref.gui.git.GitConflictResolverDialog;
 import org.jabref.gui.git.GuiGitConflictResolverStrategy;
 import org.jabref.gui.preferences.GuiPreferences;
@@ -160,8 +161,12 @@ private void showLibraryTab(DirectoryLibraryScanner.ScanResult scanResult, PdfEn
         libraryTab.updateTabTitle(false);
 
         BibDatabaseContext databaseContext = scanResult.databaseContext();
-        Function<BibEntry, Optional<String>> fileNameGenerator = entry -> FileUtil.createFileNameFromPattern(
-                databaseContext.getDatabase(), entry, preferences.getFilePreferences().getFileNamePattern());
+        // Evaluated per write, so a changed preference (global or library) takes effect immediately
+        // [impl->req~directory-library.pattern-rename~2]
+        Function<BibEntry, Optional<String>> fileNameGenerator = entry ->
+                AutoRenameFileOnEntryChange.isEnabled(databaseContext, preferences.getFilePreferences())
+                ? FileUtil.createFileNameFromPattern(databaseContext.getDatabase(), entry, preferences.getFilePreferences().getFileNamePattern())
+                : Optional.empty();
         GuiGitConflictResolverStrategy conflictResolver = new GuiGitConflictResolverStrategy(
                 new GitConflictResolverDialog(dialogService, preferences, stateManager));
         DirectoryLibrarySynchronizer synchronizer = new DirectoryLibrarySynchronizer(

jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesView.java

@@ -2,9 +2,11 @@
 
 import java.nio.charset.Charset;
 import java.nio.file.Path;
+import java.util.Optional;
 import java.util.function.UnaryOperator;
 
 import javafx.application.Platform;
+import javafx.collections.FXCollections;
 import javafx.fxml.FXML;
 import javafx.scene.control.Button;
 import javafx.scene.control.ComboBox;
@@ -37,6 +39,7 @@ public class GeneralPropertiesView extends AbstractPropertiesTabView<GeneralProp
     @FXML private TextField userSpecificFileDirectory;
     @FXML private TextField latexFileDirectory;
     @FXML private TextField keywordSeparator;
+    @FXML private ComboBox<Optional<Boolean>> autoRenameFilesOnChange;
     @FXML private Button libSpecificFileDirSwitchId;
     @FXML private Button userSpecificFileDirSwitchId;
     @FXML private Button laTexSpecificFileDirSwitchId;
@@ -101,6 +104,14 @@ public void initialize() {
                 change -> change.getControlNewText().length() <= 1 ? change : null;
         keywordSeparator.setTextFormatter(new TextFormatter<>(singleCharacterFilter));
 
+        boolean globalAutoRename = preferences.getFilePreferences().shouldAutoRenameFilesOnChange();
+        new ViewModelListCellFactory<Optional<Boolean>>()
+                .withText(choice -> choice.map(GeneralPropertiesView::yesOrNo)
+                                          .orElse(Localization.lang("Use global preference (%0)", yesOrNo(globalAutoRename))))
+                .install(autoRenameFilesOnChange);
+        autoRenameFilesOnChange.setItems(FXCollections.observableArrayList(Optional.empty(), Optional.of(true), Optional.of(false)));
+        autoRenameFilesOnChange.valueProperty().bindBidirectional(viewModel.autoRenameFilesOnChangeProperty());
+
         userSpecificFileDirectoryTooltip.setText(Localization.lang("User-specific file directory: %0", preferences.getFilePreferences().getUserAndHost()));
         userSpecificFileDirectory.setTooltip(userSpecificFileDirectoryTooltip);
 
@@ -179,4 +190,8 @@ void userSpecificFileDirPathSwitch() {
     void laTexSpecificFileDirPathSwitch() {
         viewModel.togglePath(viewModel.laTexFileDirectoryProperty());
     }
+
+    private static String yesOrNo(boolean value) {
+        return value ? Localization.lang("Yes") : Localization.lang("No");
+    }
 }

jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesViewModel.java

@@ -47,6 +47,7 @@ public class GeneralPropertiesViewModel implements PropertiesTabViewModel {
     private final StringProperty userSpecificFileDirectoryProperty = new SimpleStringProperty("");
     private final StringProperty laTexFileDirectoryProperty = new SimpleStringProperty("");
     private final StringProperty keywordSeparatorProperty = new SimpleStringProperty("");
+    private final ObjectProperty<Optional<Boolean>> autoRenameFilesOnChangeProperty = new SimpleObjectProperty<>(Optional.empty());
 
     private final Validator librarySpecificFileDirectoryValidator;
     private final Validator userSpecificFileDirectoryValidator;
@@ -91,6 +92,7 @@ public void setValues(MetaData metaData) {
         userSpecificFileDirectoryProperty.setValue(metaData.getUserFileDirectory(preferences.getFilePreferences().getUserAndHost()).orElse("").trim());
         laTexFileDirectoryProperty.setValue(metaData.getLatexFileDirectory(preferences.getFilePreferences().getUserAndHost()).map(Path::toString).orElse(""));
         keywordSeparatorProperty.setValue(metaData.getKeywordSeparator().map(Object::toString).orElse(""));
+        autoRenameFilesOnChangeProperty.setValue(metaData.getAutoRenameFilesOnChange());
     }
 
     @Override
@@ -120,6 +122,7 @@ public void storeSettings(MetaData metaData) {
         }
 
         storeKeywordSeparator(metaData);
+        autoRenameFilesOnChangeProperty.getValue().ifPresentOrElse(metaData::setAutoRenameFilesOnChange, metaData::clearAutoRenameFilesOnChange);
     }
 
     /// The separator and the group definitions the migration rewrites are both metadata, so the
@@ -225,6 +228,10 @@ public StringProperty keywordSeparatorProperty() {
         return this.keywordSeparatorProperty;
     }
 
+    public ObjectProperty<Optional<Boolean>> autoRenameFilesOnChangeProperty() {
+        return this.autoRenameFilesOnChangeProperty;
+    }
+
     private Path getBrowseDirectory(String configuredDir) {
         Optional<Path> libPath = this.databaseContext.getDatabasePath();
         Path workingDir = preferences.getFilePreferences().getWorkingDirectory();

jabgui/src/main/resources/org/jabref/gui/libraryproperties/general/GeneralProperties.fxml

@@ -135,6 +135,10 @@
                GridPane.columnIndex="0" GridPane.rowIndex="7"/>
         <TextField fx:id="keywordSeparator" prefWidth="50.0" maxWidth="50.0"
                    GridPane.columnIndex="1" GridPane.rowIndex="7"/>
+        <Label text="%Auto rename files if entry changes"
+               GridPane.columnIndex="0" GridPane.rowIndex="8"/>
+        <ComboBox fx:id="autoRenameFilesOnChange" prefWidth="150.0"
+                  GridPane.columnIndex="1" GridPane.hgrow="ALWAYS" GridPane.rowIndex="8"/>
 
     </GridPane>
 </fx:root>

jabgui/src/test/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChangeTest.java

@@ -34,6 +34,7 @@
 
 class AutoRenameFileOnEntryChangeTest {
     private FilePreferences filePreferences;
+    private BibDatabaseContext bibDatabaseContext;
     private BibEntry entry;
     private Path tempDir;
 
@@ -42,7 +43,7 @@ void setUp(@TempDir Path tempDir) {
         this.tempDir = tempDir;
         MetaData metaData = new MetaData();
         metaData.setLibrarySpecificFileDirectory(tempDir.toString());
-        BibDatabaseContext bibDatabaseContext = new BibDatabaseContext(new BibDatabase(), metaData);
+        bibDatabaseContext = new BibDatabaseContext(new BibDatabase(), metaData);
         GlobalCitationKeyPatterns keyPattern = GlobalCitationKeyPatterns.fromPattern("[auth][year]");
         GuiPreferences guiPreferences = mock(GuiPreferences.class);
         filePreferences = mock(FilePreferences.class);
@@ -110,6 +111,45 @@ void noFileRenameOnEmptyFilePattern() throws IOException {
         assertFileExists(tempDir.resolve("oldKey2081.pdf"));
     }
 
+    @Test
+    void libraryOverrideEnablesRenameDespiteDisabledGlobalPreference() throws IOException {
+        Files.createFile(tempDir.resolve("oldKey2081.pdf"));
+        entry.setFiles(List.of(new LinkedFile("", "oldKey2081.pdf", "PDF")));
+        when(filePreferences.shouldAutoRenameFilesOnChange()).thenReturn(false);
+        bibDatabaseContext.getMetaData().setAutoRenameFilesOnChange(true);
+
+        entry.setField(StandardField.AUTHOR, "newKey");
+
+        assertEquals("newKey2081.pdf", entry.getFiles().getFirst().getLink());
+        assertFileExists(tempDir.resolve("newKey2081.pdf"));
+    }
+
+    @Test
+    void libraryOverrideDisablesRenameDespiteEnabledGlobalPreference() throws IOException {
+        Files.createFile(tempDir.resolve("oldKey2081.pdf"));
+        entry.setFiles(List.of(new LinkedFile("", "oldKey2081.pdf", "PDF")));
+        when(filePreferences.shouldAutoRenameFilesOnChange()).thenReturn(true);
+        bibDatabaseContext.getMetaData().setAutoRenameFilesOnChange(false);
+
+        entry.setField(StandardField.AUTHOR, "newKey");
+
+        assertEquals("oldKey2081.pdf", entry.getFiles().getFirst().getLink());
+        assertFileExists(tempDir.resolve("oldKey2081.pdf"));
+    }
+
+    @Test
+    void directoryLibrariesLeaveRenamesToTheSidecarWriteBack() throws IOException {
+        Files.createFile(tempDir.resolve("oldKey2081.pdf"));
+        entry.setFiles(List.of(new LinkedFile("", "oldKey2081.pdf", "PDF")));
+        when(filePreferences.shouldAutoRenameFilesOnChange()).thenReturn(true);
+        bibDatabaseContext.convertToDirectoryLibrary(tempDir);
+
+        entry.setField(StandardField.AUTHOR, "newKey");
+
+        assertEquals("oldKey2081.pdf", entry.getFiles().getFirst().getLink());
+        assertFileExists(tempDir.resolve("oldKey2081.pdf"));
+    }
+
     @Test
     void singleFileRenameOnEntryChange() throws IOException {
         Files.createFile(tempDir.resolve("oldKey2081.pdf"));

jablib/src/main/java/org/jabref/logic/bibtex/comparator/MetaDataDiff.java

@@ -16,6 +16,7 @@
 
 public class MetaDataDiff {
     public enum DifferenceType {
+        AUTO_RENAME_FILES_ON_CHANGE,
         CONTENT_SELECTOR,
         DEFAULT_KEY_PATTERN,
         ENCODING,
@@ -112,6 +113,7 @@ public List<Difference> getDifferences(GlobalCitationKeyPatterns globalCitationK
         addToListIfDiff(changes, DifferenceType.MODE, originalMetaData.getMode(), newMetaData.getMode());
         addToListIfDiff(changes, DifferenceType.LIBRARY_SPECIFIC_FILE_DIRECTORY, originalMetaData.getLibrarySpecificFileDirectory(), newMetaData.getLibrarySpecificFileDirectory());
         addToListIfDiff(changes, DifferenceType.CONTENT_SELECTOR, originalMetaData.getContentSelectors(), newMetaData.getContentSelectors());
+        addToListIfDiff(changes, DifferenceType.AUTO_RENAME_FILES_ON_CHANGE, originalMetaData.getAutoRenameFilesOnChange(), newMetaData.getAutoRenameFilesOnChange());
         return changes;
     }
 

jablib/src/main/java/org/jabref/logic/directorylibrary/BibMirror.java

@@ -20,6 +20,7 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.groups.DirectoryStructureGroup;
 import org.jabref.model.groups.GroupTreeNode;
+import org.jabref.model.metadata.MetaData;
 
 import org.jspecify.annotations.NullMarked;
 import org.slf4j.Logger;
@@ -120,9 +121,12 @@ void doInitialize() {
                 writeScheduler.accept(mirror);
                 return;
             }
-            // The mirror's metadata is the only place user-defined groups of a directory
-            // library survive a restart — the sidecars carry entries, not library metadata
-            readBibContext(mirror).ifPresent(this::adoptUserGroups);
+            // The mirror's metadata is the only place library settings and user-defined groups of
+            // a directory library survive a restart — the sidecars carry entries, not library metadata
+            readBibContext(mirror).ifPresent(remote -> {
+                adoptLibrarySettings(remote);
+                adoptUserGroups(remote);
+            });
             try {
                 if (Files.exists(baseFile(root)) && Files.mismatch(mirror, baseFile(root)) == -1L) {
                     return;
@@ -180,6 +184,22 @@ private void merge(BibDatabaseContext remote) {
         markDirty();
     }
 
+    /// Restores the library properties that the sidecars do not carry. The keyword separator
+    /// comes first: explicit group memberships in the sidecars are separated by it.
+    private void adoptLibrarySettings(BibDatabaseContext remote) {
+        MetaData remoteMetaData = remote.getMetaData();
+        Optional<Character> keywordSeparator = remoteMetaData.getKeywordSeparator();
+        Optional<Boolean> autoRename = remoteMetaData.getAutoRenameFilesOnChange();
+        if (keywordSeparator.isEmpty() && autoRename.isEmpty()) {
+            return;
+        }
+        modelUpdateMarshaller.accept(() -> {
+            MetaData metaData = databaseContext.getMetaData();
+            keywordSeparator.ifPresent(metaData::setKeywordSeparator);
+            autoRename.ifPresent(metaData::setAutoRenameFilesOnChange);
+        });
+    }
+
     /// Restores user-defined groups from the mirror's metadata into the freshly scanned
     /// context (whose tree only holds the automatic directory-structure group). The
     /// serialized directory-structure group itself is skipped — the scanner installs it with

jablib/src/main/java/org/jabref/logic/directorylibrary/SidecarWriteBack.java

@@ -43,7 +43,7 @@
 /// The debounce, retry, and reporting of pending writes live in [PendingWrites]; this class
 /// only knows how to write one file. Callers hold the synchronizer's monitor.
 // [impl->req~directory-library.write-back~2]
-// [impl->req~directory-library.pattern-rename~1]
+// [impl->req~directory-library.pattern-rename~2]
 @NullMarked
 class SidecarWriteBack {