Copy linked files on entry transfer

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added the option in Preferences → Linked files → Attached files to adjust the path of attached files and copy them if needed when entries are copied to another library [#12267](https://github.com/JabRef/jabref/issues/12267)
 - We fixed an issue where "Print preview" would throw a `NullPointerException` if no printers were available. [#13708](https://github.com/JabRef/jabref/issues/13708)
 - We added the option to enable the language server in the preferences. [#13697](https://github.com/JabRef/jabref/pull/13697)
 - We introduced an option in Preferences under (under Linked files -> Linked file name conventions) to automatically rename linked files when an entry data changes. [#11316](https://github.com/JabRef/jabref/issues/11316)

docs/requirements/files.md

@@ -0,0 +1,25 @@
+# File Transfer Between Bib Entries
+
+*Note:*  
+"Reachable" here denotes that the linked file can be accessed via a relative path that does **not** climb up the directory structure (i.e., no "`..`" segments beyond the root directory).  
+Additionally, this check respects all configured **directories for files** as defined in JabRef's file linking settings (see [directories for files](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#directories-for-files)).
+
+## File is reachable and should not be copied
+`req~logic.externalfiles.file-transfer.reachable-no-copy~1`
+When a linked file is reachable from the target context, the system must adjust the relative path in the target entry but must not copy the file again.
+
+Needs: impl
+
+## File is not reachable, but the path is the same
+`req~logic.externalfiles.file-transfer.not-reachable-same-path~1`
+When a linked file is not reachable from the target context, and the relative path in both source and target entry is the same, the file must be copied to the target context.
+
+Needs: impl
+
+## File is not reachable, and a different path is used
+`req~logic.externalfiles.file-transfer.not-reachable-different-path~1`
+When a linked file is not reachable from the target context, and the relative path differs between source and target entries, the file must be copied and the directory structure must be created to preserve the relative link.
+
+Needs: impl
+
+<!-- markdownlint-disable-file MD022 -->

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

@@ -7,6 +7,7 @@
 import java.awt.datatransfer.UnsupportedFlavorException;
 import java.io.IOException;
 import java.util.List;
+import java.util.Optional;
 
 import javafx.application.Platform;
 import javafx.scene.control.TextInputControl;
@@ -18,12 +19,14 @@
 import org.jabref.logic.bibtex.BibEntryWriter;
 import org.jabref.logic.bibtex.FieldWriter;
 import org.jabref.logic.preferences.CliPreferences;
+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.entry.BibtexString;
 
 import com.airhacks.afterburner.injection.Injector;
+import org.jspecify.annotations.NonNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -32,8 +35,11 @@ public class ClipBoardManager {
     private static final Logger LOGGER = LoggerFactory.getLogger(ClipBoardManager.class);
 
     private static Clipboard clipboard;
+
     private static java.awt.datatransfer.Clipboard primary;
 
+    private BibDatabaseContext sourceDatabaseContext;
+
     public ClipBoardManager() {
         this(Clipboard.getSystemClipboard(), Toolkit.getDefaultToolkit().getSystemSelection());
     }
@@ -162,6 +168,14 @@ public void setContent(List<BibEntry> entries, BibEntryTypesManager entryTypesMa
         setContent(builder.toString());
     }
 
+    public Optional<BibDatabaseContext> getSourceBibDatabaseContext() {
+      return Optional.ofNullable(sourceDatabaseContext);
+    }
+
+    public void setSourceBibDatabaseContext(@NonNull BibDatabaseContext context) {
+        sourceDatabaseContext = context;
+    }
+
     private String serializeEntries(List<BibEntry> entries, BibEntryTypesManager entryTypesManager) throws IOException {
         CliPreferences preferences = Injector.instantiateModelOrService(CliPreferences.class);
         // BibEntry is not Java serializable. Thus, we need to do the serialization manually

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

@@ -104,6 +104,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import static org.jabref.gui.util.CopyUtil.copyEntriesWithFeedback;
+
 /**
  * Represents the ui area where the notifier pane, the library table and the entry editor are shown.
  */
@@ -810,6 +812,7 @@ public void insertEntries(final List<BibEntry> entries) {
     }
 
     public void copyEntry() {
+        clipBoardManager.setSourceBibDatabaseContext(this.getBibDatabaseContext());
         int entriesCopied = doCopyEntry(getSelectedEntries());
         if (entriesCopied >= 0) {
             dialogService.notify(Localization.lang("Copied %0 entry(s)", entriesCopied));
@@ -838,17 +841,27 @@ private int doCopyEntry(List<BibEntry> selectedEntries) {
     }
 
     public void pasteEntry() {
-        List<BibEntry> entriesToAdd;
         String content = ClipBoardManager.getContents();
-        entriesToAdd = importHandler.handleBibTeXData(content);
+        List<BibEntry> entriesToAdd = importHandler.handleBibTeXData(content);
         if (entriesToAdd.isEmpty()) {
             entriesToAdd = handleNonBibTeXStringData(content);
         }
         if (entriesToAdd.isEmpty()) {
             return;
         }
-
-        importHandler.importEntriesWithDuplicateCheck(bibDatabaseContext, entriesToAdd);
+        // Now, the BibEntries to add are known
+        // The definitive insertion needs to happen now.
+        BibDatabaseContext sourceBibDatabaseContext = clipBoardManager.getSourceBibDatabaseContext().orElse(null);
+        copyEntriesWithFeedback(
+            sourceBibDatabaseContext,
+            entriesToAdd,
+            bibDatabaseContext,
+            Localization.lang("Pasted %0 entry(s) to %1"),
+            Localization.lang("Pasted %0 entry(s) to %1. %2 were skipped"),
+            dialogService,
+            preferences.getFilePreferences(),
+            importHandler
+            );
     }
 
     private List<BibEntry> handleNonBibTeXStringData(String data) {
@@ -866,11 +879,21 @@ private List<BibEntry> handleNonBibTeXStringData(String data) {
         }
     }
 
-    public void dropEntry(List<BibEntry> entriesToAdd) {
-        importHandler.importEntriesWithDuplicateCheck(bibDatabaseContext, entriesToAdd);
+    public void dropEntry(BibDatabaseContext sourceBibDatabaseContext, List<BibEntry> entriesToAdd) {
+        copyEntriesWithFeedback(
+            sourceBibDatabaseContext,
+            entriesToAdd,
+            bibDatabaseContext,
+            Localization.lang("Moved %0 entry(s) to %1"),
+            Localization.lang("Moved %0 entry(s) to %1. %2 were skipped"),
+            dialogService,
+            preferences.getFilePreferences(),
+            importHandler
+            );
     }
 
     public void cutEntry() {
+        clipBoardManager.setSourceBibDatabaseContext(this.getBibDatabaseContext());
         int entriesCopied = doCopyEntry(getSelectedEntries());
         int entriesDeleted = doDeleteEntry(StandardActions.CUT, mainTable.getSelectedEntries());
 

jabgui/src/main/java/org/jabref/gui/edit/CopyTo.java

@@ -8,8 +8,8 @@
 import org.jabref.gui.StateManager;
 import org.jabref.gui.actions.ActionHelper;
 import org.jabref.gui.actions.SimpleCommand;
-import org.jabref.gui.externalfiles.EntryImportHandlerTracker;
 import org.jabref.gui.externalfiles.ImportHandler;
+import org.jabref.logic.FilePreferences;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -18,26 +18,31 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import static org.jabref.gui.util.CopyUtil.copyEntriesWithFeedback;
+
 public class CopyTo extends SimpleCommand {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(CopyTo.class);
 
     private final DialogService dialogService;
     private final StateManager stateManager;
     private final CopyToPreferences copyToPreferences;
+    private final FilePreferences filePreferences;
     private final ImportHandler importHandler;
     private final BibDatabaseContext sourceDatabaseContext;
     private final BibDatabaseContext targetDatabaseContext;
 
     public CopyTo(DialogService dialogService,
                   StateManager stateManager,
                   CopyToPreferences copyToPreferences,
+                  FilePreferences filePreferences,
                   ImportHandler importHandler,
                   BibDatabaseContext sourceDatabaseContext,
                   BibDatabaseContext targetDatabaseContext) {
         this.dialogService = dialogService;
         this.stateManager = stateManager;
         this.copyToPreferences = copyToPreferences;
+        this.filePreferences = filePreferences;
         this.importHandler = importHandler;
         this.sourceDatabaseContext = sourceDatabaseContext;
         this.targetDatabaseContext = targetDatabaseContext;
@@ -75,37 +80,29 @@ public void copyEntriesWithCrossRef(List<BibEntry> selectedEntries, BibDatabaseC
                                                             .flatMap(entry -> getCrossRefEntry(entry, sourceDatabaseContext).stream()).toList();
         entriesToAdd.addAll(entriesWithCrossRef);
 
-        copyEntriesWithFeedback(entriesToAdd, targetDatabaseContext,
-                Localization.lang("Copied %0 entry(s) to %1, including cross-references"),
-                Localization.lang("Copied %0 entry(s) to %1. %2 were skipped including cross-references"));
+        copyEntriesWithFeedback(
+            sourceDatabaseContext,
+            entriesToAdd,
+            targetDatabaseContext,
+            Localization.lang("Copied %0 entry(s) to %1, including cross-references"),
+            Localization.lang("Copied %0 entry(s) to %1. %2 were skipped including cross-references"),
+            dialogService,
+            filePreferences,
+            importHandler
+        );
     }
 
     public void copyEntriesWithoutCrossRef(List<BibEntry> selectedEntries, BibDatabaseContext targetDatabaseContext) {
-        copyEntriesWithFeedback(selectedEntries, targetDatabaseContext,
-                Localization.lang("Copied %0 entry(s) to %1 without cross-references"),
-                Localization.lang("Copied %0 entry(s) to %1. %2 were skipped without cross-references"));
-    }
-
-    private void copyEntriesWithFeedback(List<BibEntry> entriesToAdd, BibDatabaseContext targetDatabaseContext, String successMessage, String partialMessage) {
-        EntryImportHandlerTracker tracker = new EntryImportHandlerTracker(entriesToAdd.size());
-        tracker.setOnFinish(() -> {
-            int importedCount = tracker.getImportedCount();
-            int skippedCount = tracker.getSkippedCount();
-
-            String targetName = targetDatabaseContext.getDatabasePath()
-                                                     .map(path -> path.getFileName().toString())
-                                                     .orElse(Localization.lang("target library"));
-
-            if (importedCount == entriesToAdd.size()) {
-                dialogService.notify(Localization.lang(successMessage, String.valueOf(importedCount), targetName));
-            } else if (importedCount == 0) {
-                dialogService.notify(Localization.lang("No entry was copied to %0", targetName));
-            } else {
-                dialogService.notify(Localization.lang(partialMessage, String.valueOf(importedCount), targetName, String.valueOf(skippedCount)));
-            }
-        });
-
-        importHandler.importEntriesWithDuplicateCheck(targetDatabaseContext, entriesToAdd, tracker);
+        copyEntriesWithFeedback(
+            sourceDatabaseContext,
+            selectedEntries,
+            targetDatabaseContext,
+            Localization.lang("Copied %0 entry(s) to %1, without cross-references"),
+            Localization.lang("Copied %0 entry(s) to %1. %2 were skipped without cross-references"),
+            dialogService,
+            filePreferences,
+            importHandler
+        );
     }
 
     public Optional<BibEntry> getCrossRefEntry(BibEntry bibEntryToCheck, BibDatabaseContext sourceDatabaseContext) {

jabgui/src/main/java/org/jabref/gui/edit/EditAction.java

@@ -30,7 +30,8 @@ public class EditAction extends SimpleCommand {
     private final StateManager stateManager;
     private final UndoManager undoManager;
 
-    public EditAction(StandardActions action, Supplier<LibraryTab> tabSupplier, StateManager stateManager, UndoManager undoManager) {
+    public EditAction(StandardActions action, Supplier<LibraryTab> tabSupplier, StateManager stateManager,
+                      UndoManager undoManager) {
         this.action = action;
         this.tabSupplier = tabSupplier;
         this.stateManager = stateManager;

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

@@ -250,8 +250,20 @@ public void importEntryWithDuplicateCheck(BibDatabaseContext bibDatabaseContext,
         importEntryWithDuplicateCheck(bibDatabaseContext, entry, BREAK, new EntryImportHandlerTracker());
     }
 
+    /**
+     * Imports an entry into the database with duplicate checking and handling.
+     * Creates a copy of the entry for processing - the original entry parameter is not modified.
+     * The copied entry may be modified during cleanup and duplicate handling.
+     *
+     * @param bibDatabaseContext the database context to import into
+     * @param entry the entry to import (original will not be modified)
+     * @param decision the duplicate resolution strategy to apply
+     * @param tracker tracks the import status of the entry
+     */
     private void importEntryWithDuplicateCheck(BibDatabaseContext bibDatabaseContext, BibEntry entry, DuplicateResolverDialog.DuplicateResolverResult decision, EntryImportHandlerTracker tracker) {
-        BibEntry entryToInsert = cleanUpEntry(bibDatabaseContext, entry);
+        // The original entry should not be modified
+        BibEntry entryCopy = new BibEntry(entry);
+        BibEntry entryToInsert = cleanUpEntry(bibDatabaseContext, entryCopy);
 
         BackgroundTask.wrap(() -> findDuplicate(bibDatabaseContext, entryToInsert))
                       .onFailure(e -> {

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

@@ -21,6 +21,7 @@
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.io.FileUtil;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.groups.GroupTreeNode;
 
@@ -106,7 +107,8 @@ private void onTabDragDropped(Node destinationTabNode, DragEvent tabDragEvent, T
             if (hasEntries(dragboard)) {
                 List<BibEntry> entryCopies = stateManager.getLocalDragboard().getBibEntries().stream()
                                                          .map(BibEntry::new).toList();
-                destinationLibraryTab.dropEntry(entryCopies);
+                BibDatabaseContext sourceBibDatabaseContext = stateManager.getActiveDatabase().orElse(null);
+                destinationLibraryTab.dropEntry(sourceBibDatabaseContext, entryCopies);
             } else if (hasGroups(dragboard)) {
                 dropGroups(dragboard, destinationLibraryTab);
             }
@@ -213,7 +215,7 @@ private void copyGroupTreeNode(LibraryTab destinationLibraryTab, GroupTreeNode p
         // add groupTreeNodeToCopy to the parent-- in the first run that will the source/main GroupTreeNode
         GroupTreeNode copiedNode = parent.addSubgroup(groupTreeNodeToCopy.copyNode().getGroup());
         // add all entries of a groupTreeNode to the new library.
-        destinationLibraryTab.dropEntry(groupTreeNodeToCopy.getEntriesInGroup(allEntries));
+        destinationLibraryTab.dropEntry(stateManager.getActiveDatabase().get(), groupTreeNodeToCopy.getEntriesInGroup(allEntries));
         // List of all children of groupTreeNodeToCopy
         List<GroupTreeNode> children = groupTreeNodeToCopy.getChildren();
 

jabgui/src/main/java/org/jabref/gui/maintable/RightClickMenu.java

@@ -152,7 +152,7 @@ private static Menu createCopyToMenu(ActionFactory factory,
                     factory.createCustomMenuItem(
                             StandardActions.COPY_TO,
                             new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(),
-                                    importHandler, sourceDatabaseContext, targetDatabaseContext),
+                                    preferences.getFilePreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext),
                             targetDatabaseName
                     )
             );

jabgui/src/main/java/org/jabref/gui/preferences/linkedfiles/LinkedFilesTab.java

@@ -42,6 +42,7 @@ public class LinkedFilesTab extends AbstractPreferenceTabView<LinkedFilesTabView
     @FXML private TextField fileDirectoryPattern;
     @FXML private CheckBox confirmLinkedFileDelete;
     @FXML private CheckBox moveToTrash;
+    @FXML private CheckBox adjustOrCopyLinkedFilesOnTransfer;
 
     private final ControlsFxVisualizer validationVisualizer = new ControlsFxVisualizer();
 
@@ -81,6 +82,7 @@ public void initialize() {
         confirmLinkedFileDelete.selectedProperty().bindBidirectional(viewModel.confirmLinkedFileDeleteProperty());
         openFileExplorerInFilesDirectory.selectedProperty().bindBidirectional(viewModel.openFileExplorerInFilesDirectoryProperty());
         openFileExplorerInLastDirectory.selectedProperty().bindBidirectional(viewModel.openFileExplorerInLastDirectoryProperty());
+        adjustOrCopyLinkedFilesOnTransfer.selectedProperty().bindBidirectional(viewModel.adjustOrCopyLinkedFilesOnTransferProperty());
 
         ActionFactory actionFactory = new ActionFactory();
         actionFactory.configureIconButton(StandardActions.HELP_REGEX_SEARCH, new HelpAction(HelpFile.REGEX_SEARCH, dialogService, preferences.getExternalApplicationsPreferences()), autolinkRegexHelp);

jabgui/src/main/java/org/jabref/gui/preferences/linkedfiles/LinkedFilesTabViewModel.java

@@ -42,6 +42,7 @@ public class LinkedFilesTabViewModel implements PreferenceTabViewModel {
     private final StringProperty fileDirectoryPatternProperty = new SimpleStringProperty();
     private final BooleanProperty confirmLinkedFileDeleteProperty = new SimpleBooleanProperty();
     private final BooleanProperty moveToTrashProperty = new SimpleBooleanProperty();
+    private final BooleanProperty adjustOrCopyLinkedFilesOnTransferProperty = new SimpleBooleanProperty();
     private final BooleanProperty openFileExplorerInFilesDirectory = new SimpleBooleanProperty();
     private final BooleanProperty openFileExplorerInLastDirectory = new SimpleBooleanProperty();
 
@@ -90,6 +91,7 @@ public void setValues() {
         moveToTrashProperty.setValue(filePreferences.moveToTrash());
         openFileExplorerInFilesDirectory.setValue(filePreferences.shouldOpenFileExplorerInFileDirectory());
         openFileExplorerInLastDirectory.setValue(filePreferences.shouldOpenFileExplorerInLastUsedDirectory());
+        adjustOrCopyLinkedFilesOnTransferProperty.setValue(filePreferences.shouldAdjustOrCopyLinkedFilesOnTransfer());
 
         // Autolink preferences
         switch (autoLinkPreferences.getCitationKeyDependency()) {
@@ -125,6 +127,7 @@ public void storeSettings() {
         autoLinkPreferences.setRegularExpression(autolinkRegexKeyProperty.getValue());
         filePreferences.confirmDeleteLinkedFile(confirmLinkedFileDeleteProperty.getValue());
         filePreferences.moveToTrash(moveToTrashProperty.getValue());
+        filePreferences.setAdjustOrCopyLinkedFilesOnTransfer(adjustOrCopyLinkedFilesOnTransferProperty.getValue());
     }
 
     ValidationStatus mainFileDirValidationStatus() {
@@ -206,6 +209,10 @@ public BooleanProperty moveToTrashProperty() {
         return this.moveToTrashProperty;
     }
 
+    public BooleanProperty adjustOrCopyLinkedFilesOnTransferProperty() {
+        return adjustOrCopyLinkedFilesOnTransferProperty;
+    }
+
     public BooleanProperty openFileExplorerInFilesDirectoryProperty() {
         return openFileExplorerInFilesDirectory;
     }