Copy linked files on entry transfer

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

@@ -44,6 +44,7 @@
 import org.jabref.gui.dialogs.AutosaveUiManager;
 import org.jabref.gui.exporter.SaveDatabaseAction;
 import org.jabref.gui.externalfiles.AutoRenameFileOnEntryChange;
+import org.jabref.gui.externalfiles.EntryImportHandlerTracker;
 import org.jabref.gui.externalfiles.ImportHandler;
 import org.jabref.gui.fieldeditors.LinkedFileViewModel;
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
@@ -61,6 +62,7 @@
 import org.jabref.logic.ai.AiService;
 import org.jabref.logic.citationstyle.CitationStyleCache;
 import org.jabref.logic.command.CommandSelectionTab;
+import org.jabref.logic.externalfiles.LinkedFileTransferHelper;
 import org.jabref.logic.importer.FetcherClientException;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.FetcherServerException;
@@ -842,17 +844,48 @@ 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;
         }
+        BibDatabaseContext sourceBibDatabaseContext = clipBoardManager.getSourceBibDatabaseContext().orElse(null);
+        copyEntriesWithFeedback(entriesToAdd, sourceBibDatabaseContext);
+    }
+
+    private void copyEntriesWithFeedback(List<BibEntry> entriesToAdd, BibDatabaseContext sourceBibDatabaseContext) {
+        final List<BibEntry> finalEntriesToAdd = entriesToAdd;
+
+        EntryImportHandlerTracker tracker = new EntryImportHandlerTracker(finalEntriesToAdd.size());
+
+        tracker.setOnFinish(() -> {
+            int importedCount = tracker.getImportedCount();
+            int skippedCount = tracker.getSkippedCount();
+
+            String targetName = bibDatabaseContext.getDatabasePath()
+                .map(path -> path.getFileName().toString())
+                .orElse(Localization.lang("target library"));
+
+            if (importedCount == finalEntriesToAdd.size()) {
+                dialogService.notify(Localization.lang("Pasted %0 entry(s) to %1",
+              String.valueOf(importedCount), targetName));
+            } else if (importedCount == 0) {
+                dialogService.notify(Localization.lang("No entry was pasted to %0", targetName));
+            } else {
+                dialogService.notify(Localization.lang("Pasted %0 entry(s) to %1. %2 were skipped",
+                    String.valueOf(importedCount), targetName, String.valueOf(skippedCount)));
+            }
+            if (sourceBibDatabaseContext != null) {
+                LinkedFileTransferHelper
+                    .adjustLinkedFilesForTarget(sourceBibDatabaseContext,
+                        bibDatabaseContext, preferences.getFilePreferences());
+            }
+        });
 
-        importHandler.importEntriesWithDuplicateCheck(bibDatabaseContext, entriesToAdd);
+        importHandler.importEntriesWithDuplicateCheck(bibDatabaseContext, finalEntriesToAdd, tracker);
     }
 
     private List<BibEntry> handleNonBibTeXStringData(String data) {
@@ -870,8 +903,8 @@ private List<BibEntry> handleNonBibTeXStringData(String data) {
         }
     }
 
-    public void dropEntry(List<BibEntry> entriesToAdd) {
-        importHandler.importEntriesWithDuplicateCheck(bibDatabaseContext, entriesToAdd);
+    public void dropEntry(List<BibEntry> entriesToAdd, BibDatabaseContext sourceBibDatabaseContext) {
+        copyEntriesWithFeedback(entriesToAdd, sourceBibDatabaseContext);
     }
 
     public void cutEntry() {

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

@@ -10,6 +10,8 @@
 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.externalfiles.LinkedFileTransferHelper;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -25,19 +27,22 @@ public class CopyTo extends SimpleCommand {
     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;
@@ -106,6 +111,9 @@ private void copyEntriesWithFeedback(List<BibEntry> entriesToAdd, BibDatabaseCon
         });
 
         importHandler.importEntriesWithDuplicateCheck(targetDatabaseContext, entriesToAdd, tracker);
+        tracker.setOnFinish(() -> LinkedFileTransferHelper
+          .adjustLinkedFilesForTarget(sourceDatabaseContext, targetDatabaseContext, filePreferences)
+        );
     }
 
     public Optional<BibEntry> getCrossRefEntry(BibEntry bibEntryToCheck, BibDatabaseContext sourceDatabaseContext) {

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

@@ -7,6 +7,7 @@
 import javafx.scene.control.TextInputControl;
 import javafx.scene.web.WebView;
 
+import org.jabref.gui.ClipBoardManager;
 import org.jabref.gui.LibraryTab;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.actions.ActionHelper;
@@ -29,12 +30,15 @@ public class EditAction extends SimpleCommand {
     private final StandardActions action;
     private final StateManager stateManager;
     private final UndoManager undoManager;
+    private final ClipBoardManager clipBoardManager;
 
-    public EditAction(StandardActions action, Supplier<LibraryTab> tabSupplier, StateManager stateManager, UndoManager undoManager) {
+    public EditAction(StandardActions action, Supplier<LibraryTab> tabSupplier, StateManager stateManager,
+                      UndoManager undoManager, ClipBoardManager clipBoardManager) {
         this.action = action;
         this.tabSupplier = tabSupplier;
         this.stateManager = stateManager;
         this.undoManager = undoManager;
+        this.clipBoardManager = clipBoardManager;
 
         if (action == StandardActions.PASTE) {
             this.executable.bind(ActionHelper.needsDatabase(stateManager));
@@ -77,8 +81,14 @@ public void execute() {
                 // Not sure what is selected -> copy/paste/cut selected entries except for Preview and CodeArea
 
                 switch (action) {
-                    case COPY -> tabSupplier.get().copyEntry();
-                    case CUT -> tabSupplier.get().cutEntry();
+                    case COPY -> {
+                        clipBoardManager.setSourceBibDatabaseContext(tabSupplier.get().getBibDatabaseContext());
+                        tabSupplier.get().copyEntry();
+                    }
+                    case CUT -> {
+                        clipBoardManager.setSourceBibDatabaseContext(tabSupplier.get().getBibDatabaseContext());
+                        tabSupplier.get().cutEntry();
+                    }
                     case PASTE -> tabSupplier.get().pasteEntry();
                     case DELETE_ENTRY -> tabSupplier.get().deleteEntry();
                     case UNDO -> {

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

@@ -251,7 +251,7 @@ public void importEntryWithDuplicateCheck(BibDatabaseContext bibDatabaseContext,
     }
 
     private void importEntryWithDuplicateCheck(BibDatabaseContext bibDatabaseContext, BibEntry entry, DuplicateResolverDialog.DuplicateResolverResult decision, EntryImportHandlerTracker tracker) {
-        BibEntry entryToInsert = cleanUpEntry(bibDatabaseContext, entry);
+        BibEntry entryToInsert = new BibEntry(cleanUpEntry(bibDatabaseContext, entry));
 
         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(entryCopies, sourceBibDatabaseContext);
             } 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(groupTreeNodeToCopy.getEntriesInGroup(allEntries), stateManager.getActiveDatabase().get());
         // List of all children of groupTreeNodeToCopy
         List<GroupTreeNode> children = groupTreeNodeToCopy.getChildren();
 

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

@@ -206,10 +206,10 @@ private void createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.CUT, new EditAction(StandardActions.CUT, frame::getCurrentLibraryTab, stateManager, undoManager)),
-                factory.createMenuItem(StandardActions.COPY, new EditAction(StandardActions.COPY, frame::getCurrentLibraryTab, stateManager, undoManager)),
+                factory.createMenuItem(StandardActions.CUT, new EditAction(StandardActions.CUT, frame::getCurrentLibraryTab, stateManager, undoManager, clipBoardManager)),
+                factory.createMenuItem(StandardActions.COPY, new EditAction(StandardActions.COPY, frame::getCurrentLibraryTab, stateManager, undoManager, clipBoardManager)),
                 RightClickMenu.createCopySubMenu(factory, dialogService, stateManager, preferences, clipBoardManager, abbreviationRepository, taskExecutor),
-                factory.createMenuItem(StandardActions.PASTE, new EditAction(StandardActions.PASTE, frame::getCurrentLibraryTab, stateManager, undoManager)),
+                factory.createMenuItem(StandardActions.PASTE, new EditAction(StandardActions.PASTE, frame::getCurrentLibraryTab, stateManager, undoManager, clipBoardManager)),
 
                 new SeparatorMenuItem(),
 
@@ -248,7 +248,7 @@ private void createMenu() {
                 factory.createMenuItem(StandardActions.ADD_ENTRY, new NewEntryAction(false, frame::getCurrentLibraryTab, dialogService, preferences, stateManager)),
                 factory.createMenuItem(StandardActions.ADD_ENTRY_IDENTIFIER, new NewEntryAction(NewEntryDialogTab.ENTER_IDENTIFIER, frame::getCurrentLibraryTab, dialogService, preferences, stateManager)),
                 factory.createMenuItem(StandardActions.ADD_ENTRY_PLAINTEXT, new NewEntryAction(NewEntryDialogTab.INTERPRET_CITATIONS, frame::getCurrentLibraryTab, dialogService, preferences, stateManager)),
-                factory.createMenuItem(StandardActions.DELETE_ENTRY, new EditAction(StandardActions.DELETE_ENTRY, frame::getCurrentLibraryTab, stateManager, undoManager)),
+                factory.createMenuItem(StandardActions.DELETE_ENTRY, new EditAction(StandardActions.DELETE_ENTRY, frame::getCurrentLibraryTab, stateManager, undoManager, clipBoardManager)),
 
                 new SeparatorMenuItem(),
 

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

@@ -117,16 +117,16 @@ private void createToolBar() {
                 new HBox(
                         factory.createIconButton(StandardActions.ADD_ENTRY_IMMEDIATE, new NewEntryAction(true, frame::getCurrentLibraryTab, dialogService, preferences, stateManager)),
                         factory.createIconButton(StandardActions.ADD_ENTRY, new NewEntryAction(false, frame::getCurrentLibraryTab, dialogService, preferences, stateManager)),
-                        factory.createIconButton(StandardActions.DELETE_ENTRY, new EditAction(StandardActions.DELETE_ENTRY, frame::getCurrentLibraryTab, stateManager, undoManager))),
+                        factory.createIconButton(StandardActions.DELETE_ENTRY, new EditAction(StandardActions.DELETE_ENTRY, frame::getCurrentLibraryTab, stateManager, undoManager, clipBoardManager))),
 
                 new Separator(Orientation.VERTICAL),
 
                 new HBox(
                         factory.createIconButton(StandardActions.UNDO, new UndoAction(frame::getCurrentLibraryTab, undoManager, dialogService, stateManager)),
                         factory.createIconButton(StandardActions.REDO, new RedoAction(frame::getCurrentLibraryTab, undoManager, dialogService, stateManager)),
-                        factory.createIconButton(StandardActions.CUT, new EditAction(StandardActions.CUT, frame::getCurrentLibraryTab, stateManager, undoManager)),
-                        factory.createIconButton(StandardActions.COPY, new EditAction(StandardActions.COPY, frame::getCurrentLibraryTab, stateManager, undoManager)),
-                        factory.createIconButton(StandardActions.PASTE, new EditAction(StandardActions.PASTE, frame::getCurrentLibraryTab, stateManager, undoManager))),
+                        factory.createIconButton(StandardActions.CUT, new EditAction(StandardActions.CUT, frame::getCurrentLibraryTab, stateManager, undoManager, clipBoardManager)),
+                        factory.createIconButton(StandardActions.COPY, new EditAction(StandardActions.COPY, frame::getCurrentLibraryTab, stateManager, undoManager, clipBoardManager)),
+                        factory.createIconButton(StandardActions.PASTE, new EditAction(StandardActions.PASTE, frame::getCurrentLibraryTab, stateManager, undoManager, clipBoardManager))),
 
                 new Separator(Orientation.VERTICAL),