Fix/copy linked files on entry transfer

docs/requirements/filed.md

@@ -0,0 +1,21 @@
+# File Transfer Between Bib Entries
+
+## 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;
@@ -19,6 +20,7 @@
 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;
@@ -35,6 +37,8 @@ public class ClipBoardManager {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(ClipBoardManager.class);
 
+    private BibDatabaseContext sourceDatabaseContext;
+
     private static Clipboard clipboard;
     private static java.awt.datatransfer.Clipboard primary;
 
@@ -117,6 +121,10 @@ public static String getContentsPrimary() {
         return getContents();
     }
 
+    public Optional<BibDatabaseContext> getSourceBibDatabaseContext() {
+      return Optional.ofNullable(sourceDatabaseContext);
+    }
+
     /**
      * Puts content onto the system clipboard.
      *
@@ -166,6 +174,12 @@ public void setContent(List<BibEntry> entries, BibEntryTypesManager entryTypesMa
         setContent(builder.toString());
     }
 
+    public void setSourceBibDatabaseContext(BibDatabaseContext context) {
+      if (context != null) {
+        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

@@ -43,6 +43,7 @@
 import org.jabref.gui.collab.DatabaseChangeMonitor;
 import org.jabref.gui.dialogs.AutosaveUiManager;
 import org.jabref.gui.exporter.SaveDatabaseAction;
+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;
@@ -60,6 +61,7 @@
 import org.jabref.gui.util.UiTaskExecutor;
 import org.jabref.logic.ai.AiService;
 import org.jabref.logic.citationstyle.CitationStyleCache;
+import org.jabref.logic.externalfiles.LinkedFileTransferHelper;
 import org.jabref.logic.importer.FetcherClientException;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.FetcherServerException;
@@ -816,21 +818,53 @@ private int doCopyEntry(List<BibEntry> selectedEntries) {
         }
     }
 
-    public void pasteEntry() {
-        List<BibEntry> entriesToAdd;
-        String content = ClipBoardManager.getContents();
-        entriesToAdd = importHandler.handleBibTeXData(content);
-        if (entriesToAdd.isEmpty()) {
-            entriesToAdd = handleNonBibTeXStringData(content);
-        }
-        if (entriesToAdd.isEmpty()) {
-            return;
-        }
+  public void pasteEntry() {
+    String content = ClipBoardManager.getContents();
+    List<BibEntry> entriesToAdd = importHandler.handleBibTeXData(content);
+    if (entriesToAdd.isEmpty()) {
+      entriesToAdd = handleNonBibTeXStringData(content);
+    }
+    if (entriesToAdd.isEmpty()) {
+      return;
+    }
+    copyEntriesWithFeedback(entriesToAdd);
+  }
 
-        importHandler.importEntriesWithDuplicateCheck(bibDatabaseContext, entriesToAdd);
+  private void copyEntriesWithFeedback(List<BibEntry> entriesToAdd) {
+    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)));
+      }
+    });
+
+    importHandler.importEntriesWithDuplicateCheck(bibDatabaseContext, finalEntriesToAdd, tracker);
+
+    if (clipBoardManager.getSourceBibDatabaseContext().isPresent()) {
+      tracker.setOnFinish(() -> LinkedFileTransferHelper
+        .adjustLinkedFilesForTarget(clipBoardManager.getSourceBibDatabaseContext().get(),
+          bibDatabaseContext, preferences.getFilePreferences()));
     }
+  }
+
 
-    private List<BibEntry> handleNonBibTeXStringData(String data) {
+  private List<BibEntry> handleNonBibTeXStringData(String data) {
         try {
             return this.importHandler.handleStringData(data);
         } catch (FetcherException exception) {

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/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 = (BibEntry) cleanUpEntry(bibDatabaseContext, entry).clone();
 
         BackgroundTask.wrap(() -> findDuplicate(bibDatabaseContext, entryToInsert))
                       .onFailure(e -> {

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

@@ -73,7 +73,7 @@ public static ContextMenu create(BibEntryTableViewModel entry,
 
         contextMenu.getItems().addAll(
                 factory.createMenuItem(StandardActions.COPY, new EditAction(StandardActions.COPY, () -> libraryTab, stateManager, undoManager)),
-                createCopySubMenu(factory, dialogService, stateManager, preferences, clipBoardManager, abbreviationRepository, taskExecutor),
+                createCopySubMenu(factory, dialogService, stateManager, preferences, libraryTab, clipBoardManager, abbreviationRepository, taskExecutor),
                 createCopyToMenu(factory, dialogService, stateManager, preferences, libraryTab, importHandler),
                 factory.createMenuItem(StandardActions.PASTE, new EditAction(StandardActions.PASTE, () -> libraryTab, stateManager, undoManager)),
                 factory.createMenuItem(StandardActions.CUT, new EditAction(StandardActions.CUT, () -> libraryTab, stateManager, undoManager)),
@@ -157,7 +157,8 @@ private static Menu createCopyToMenu(ActionFactory factory,
                 copyToMenu.getItems().addAll(
                         factory.createCustomMenuItem(
                                 StandardActions.COPY_TO,
-                                new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(), importHandler, sourceDatabaseContext, bibDatabaseContext),
+                                new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(),
+                                  preferences.getFilePreferences(), importHandler, sourceDatabaseContext, bibDatabaseContext),
                                 destinationDatabaseName
                         )
                 );
@@ -171,11 +172,14 @@ private static Menu createCopySubMenu(ActionFactory factory,
                                           DialogService dialogService,
                                           StateManager stateManager,
                                           GuiPreferences preferences,
+                                          LibraryTab libraryTab,
                                           ClipBoardManager clipBoardManager,
                                           JournalAbbreviationRepository abbreviationRepository,
                                           TaskExecutor taskExecutor) {
         Menu copySpecialMenu = factory.createMenu(StandardActions.COPY_MORE);
 
+        clipBoardManager.setSourceBibDatabaseContext(libraryTab.getBibDatabaseContext());
+
         copySpecialMenu.getItems().addAll(
                 factory.createMenuItem(StandardActions.COPY_TITLE, new CopyMoreAction(StandardActions.COPY_TITLE, dialogService, stateManager, clipBoardManager, preferences, abbreviationRepository)),
                 factory.createMenuItem(StandardActions.COPY_KEY, new CopyMoreAction(StandardActions.COPY_KEY, dialogService, stateManager, clipBoardManager, preferences, abbreviationRepository)),

jabgui/src/test/java/org/jabref/gui/edit/CopyToTest.java

@@ -84,7 +84,7 @@ void executeCopyEntriesWithoutCrossRef() {
         selectedEntries.add(entry);
         when(stateManager.getSelectedEntries()).thenReturn((ObservableList<BibEntry>) selectedEntries);
 
-        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(),
+        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(), preferences.getFilePreferences(),
                 importHandler, sourceDatabaseContext, targetDatabaseContext);
 
         ArgumentCaptor<EntryImportHandlerTracker> trackerCaptor = ArgumentCaptor.forClass(EntryImportHandlerTracker.class);
@@ -98,7 +98,8 @@ void executeCopyEntriesWithCrossRef() {
         selectedEntries.add(entryWithCrossRef);
         when(stateManager.getSelectedEntries()).thenReturn((ObservableList<BibEntry>) selectedEntries);
 
-        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext);
+        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(),
+          preferences.getFilePreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext);
 
         ArgumentCaptor<EntryImportHandlerTracker> trackerCaptor = ArgumentCaptor.forClass(EntryImportHandlerTracker.class);
         copyTo.copyEntriesWithCrossRef(selectedEntries, targetDatabaseContext);
@@ -111,7 +112,8 @@ void executeCopyEntriesWithCrossRef() {
 
     @Test
     void executeGetCrossRefEntry() {
-        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext);
+        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(),
+          preferences.getFilePreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext);
 
         BibEntry result = copyTo.getCrossRefEntry(entryWithCrossRef, sourceDatabaseContext).orElse(null);
 
@@ -125,7 +127,8 @@ void executeExecuteWithoutCrossRef() {
         when(stateManager.getSelectedEntries()).thenReturn((ObservableList<BibEntry>) selectedEntries);
         when(preferences.getCopyToPreferences().getShouldAskForIncludingCrossReferences()).thenReturn(false);
 
-        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext);
+        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(),
+          preferences.getFilePreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext);
 
         ArgumentCaptor<EntryImportHandlerTracker> trackerCaptor = ArgumentCaptor.forClass(EntryImportHandlerTracker.class);
         copyTo.execute();
@@ -140,7 +143,8 @@ void executeExecuteWithCrossRefAndUserIncludes() {
         when(preferences.getCopyToPreferences().getShouldAskForIncludingCrossReferences()).thenReturn(true);
         when(dialogService.showConfirmationDialogWithOptOutAndWait(anyString(), anyString(), anyString(), anyString(), anyString(), any())).thenReturn(true);
 
-        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext);
+        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(),
+          preferences.getFilePreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext);
 
         ArgumentCaptor<EntryImportHandlerTracker> trackerCaptor = ArgumentCaptor.forClass(EntryImportHandlerTracker.class);
         copyTo.execute();
@@ -158,7 +162,8 @@ void executeWithCrossRefAndUserExcludes() {
         when(preferences.getCopyToPreferences().getShouldAskForIncludingCrossReferences()).thenReturn(true);
         when(dialogService.showConfirmationDialogWithOptOutAndWait(anyString(), anyString(), anyString(), anyString(), anyString(), any())).thenReturn(false);
 
-        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext);
+        copyTo = new CopyTo(dialogService, stateManager, preferences.getCopyToPreferences(),
+          preferences.getFilePreferences(), importHandler, sourceDatabaseContext, targetDatabaseContext);
 
         ArgumentCaptor<EntryImportHandlerTracker> trackerCaptor = ArgumentCaptor.forClass(EntryImportHandlerTracker.class);
         copyTo.execute();

jablib/src/main/java/module-info.java

@@ -107,17 +107,14 @@
     exports org.jabref.logic.pseudonymization;
     exports org.jabref.logic.citation.repository;
 
-    requires java.base;
-
-    requires javafx.base;
+  requires javafx.base;
     requires javafx.graphics; // because of javafx.scene.paint.Color
     requires afterburner.fx;
     requires com.tobiasdiez.easybind;
 
     // for java.awt.geom.Rectangle2D required by org.jabref.logic.pdf.TextExtractor
-    requires java.desktop;
 
-    // SQL
+  // SQL
     requires java.sql;
     requires java.sql.rowset;
 
@@ -249,6 +246,6 @@
     requires mslinks;
     requires org.antlr.antlr4.runtime;
     requires org.libreoffice.uno;
-    requires org.jetbrains.annotations;
-    // endregion
+  requires org.jetbrains.annotations;
+  // endregion
 }