Fix for delete entries should ask user

CHANGELOG.md

@@ -11,6 +11,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added a popup, as well as a preferences setting item, so users can choose whether to delete files linked to selected entries when they delete entries. [#10509](https://github.com/JabRef/jabref/issues/10509)
+
 ### Changed
 
 ### Fixed

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

@@ -8,6 +8,7 @@
 import java.util.Objects;
 import java.util.Optional;
 import java.util.Random;
+import java.util.stream.Collectors;
 
 import javax.swing.undo.UndoManager;
 
@@ -34,7 +35,9 @@
 import org.jabref.gui.collab.DatabaseChangeMonitor;
 import org.jabref.gui.dialogs.AutosaveUiManager;
 import org.jabref.gui.entryeditor.EntryEditor;
+import org.jabref.gui.fieldeditors.LinkedFileViewModel;
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
+import org.jabref.gui.linkedfile.DeleteFileAction;
 import org.jabref.gui.maintable.BibEntryTableViewModel;
 import org.jabref.gui.maintable.MainTable;
 import org.jabref.gui.maintable.MainTableDataModel;
@@ -414,7 +417,7 @@ public void setMode(BasePanelMode mode) {
     }
 
     /**
-     * Removes the selected entries from the database
+     * Removes the selected entries and files linked to selected entries from the database
      *
      * @param cut If false the user will get asked if he really wants to delete the entries, and it will be localized as "deleted". If true the action will be localized as "cut"
      */
@@ -423,7 +426,7 @@ public void delete(boolean cut) {
     }
 
     /**
-     * Removes the selected entries from the database
+     * Removes the selected entries and files linked to selected entries from the database
      *
      * @param cut If false the user will get asked if he really wants to delete the entries, and it will be localized as "deleted". If true the action will be localized as "cut"
      */
@@ -435,8 +438,25 @@ private void delete(boolean cut, List<BibEntry> entries) {
             return;
         }
 
+        // Delete selected entries
         getUndoManager().addEdit(new UndoableRemoveEntries(bibDatabaseContext.getDatabase(), entries, cut));
         bibDatabaseContext.getDatabase().removeEntries(entries);
+
+        if (!cut) {
+            List<LinkedFile> linkedFileList = entries.stream()
+                                                     .flatMap(entry -> entry.getFiles().stream())
+                                                     .distinct()
+                                                     .toList();
+
+            if (!linkedFileList.isEmpty()) {
+                List<LinkedFileViewModel> viewModels = linkedFileList.stream()
+                                                                     .map(linkedFile -> linkedFile.toModel(null, bibDatabaseContext, null, null, preferencesService))
+                                                                     .collect(Collectors.toList());
+
+                new DeleteFileAction(dialogService, preferencesService, bibDatabaseContext, viewModels).execute();
+            }
+        }
+
         ensureNotShowingBottomPanel(entries);
 
         this.changedProperty.setValue(true);
@@ -669,6 +689,14 @@ public BibDatabase getDatabase() {
         return bibDatabaseContext.getDatabase();
     }
 
+    /**
+     * Initializes a pop-up dialog box to confirm whether the user wants to delete the selected entry
+     * Keep track of user preference:
+     * if the user prefers not to ask before deleting, delete the selected entry without displaying the dialog box
+     *
+     * @param numberOfEntries number of entries user is selecting
+     * @return true if user confirm to delete entry
+     */
     private boolean showDeleteConfirmationDialog(int numberOfEntries) {
         if (preferencesService.getWorkspacePreferences().shouldConfirmDelete()) {
             String title = Localization.lang("Delete entry");
@@ -682,7 +710,8 @@ private boolean showDeleteConfirmationDialog(int numberOfEntries) {
                 cancelButton = Localization.lang("Keep entries");
             }
 
-            return dialogService.showConfirmationDialogWithOptOutAndWait(title,
+            return dialogService.showConfirmationDialogWithOptOutAndWait(
+                    title,
                     message,
                     okButton,
                     cancelButton,

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java

@@ -251,8 +251,9 @@ private void setUpKeyBindings() {
             if (keyBinding.isPresent()) {
                 switch (keyBinding.get()) {
                     case DELETE_ENTRY:
-                        new DeleteFileAction(dialogService, preferencesService, databaseContext,
-                                viewModel, listView).execute();
+                        // Delete multiple selected files in currently opened entry
+                        // als
+                        deleteEntry();
                         event.consume();
                         break;
                     default:
@@ -262,6 +263,11 @@ private void setUpKeyBindings() {
         });
     }
 
+    private void deleteEntry() {
+        new DeleteFileAction(dialogService, preferencesService, databaseContext,
+                viewModel, listView.getSelectionModel().getSelectedItems()).execute();
+    }
+
     public LinkedFilesEditorViewModel getViewModel() {
         return viewModel;
     }

src/main/java/org/jabref/gui/linkedfile/DeleteFileAction.java

@@ -9,7 +9,6 @@
 import javafx.scene.control.Alert;
 import javafx.scene.control.ButtonBar;
 import javafx.scene.control.ButtonType;
-import javafx.scene.control.ListView;
 
 import org.jabref.gui.DialogService;
 import org.jabref.gui.actions.SimpleCommand;
@@ -31,92 +30,105 @@ public class DeleteFileAction extends SimpleCommand {
     private final PreferencesService preferences;
     private final BibDatabaseContext databaseContext;
     private final LinkedFilesEditorViewModel viewModel;
-    private final ListView<LinkedFileViewModel> listView;
+    private final List<LinkedFileViewModel> linkedFiles;
 
     public DeleteFileAction(DialogService dialogService,
                             PreferencesService preferences,
                             BibDatabaseContext databaseContext,
                             LinkedFilesEditorViewModel viewModel,
-                            ListView<LinkedFileViewModel> listView) {
+                            List<LinkedFileViewModel> linkedFiles) {
         this.dialogService = dialogService;
         this.preferences = preferences;
         this.databaseContext = databaseContext;
         this.viewModel = viewModel;
-        this.listView = listView;
+        this.linkedFiles = List.copyOf(linkedFiles);
+    }
+
+    public DeleteFileAction(DialogService dialogService,
+                            PreferencesService preferences,
+                            BibDatabaseContext databaseContext,
+                            List<LinkedFileViewModel> linkedFiles) {
+        this(dialogService, preferences, databaseContext, null, linkedFiles);
     }
 
     @Override
     public void execute() {
-        List<LinkedFileViewModel> toBeDeleted = List.copyOf(listView.getSelectionModel().getSelectedItems());
-
-        if (toBeDeleted.isEmpty()) {
+        if (linkedFiles.isEmpty()) {
             dialogService.notify(Localization.lang("This operation requires selected linked files."));
             return;
         }
 
+        if (!preferences.getFilePreferences().confirmDeleteLinkedFile()) {
+            deleteFiles(linkedFiles, true);
+            return;
+        }
+
         String dialogTitle;
         String dialogContent;
 
-        if (toBeDeleted.size() != 1) {
-            dialogTitle = Localization.lang("Delete %0 files", toBeDeleted.size());
+        if (linkedFiles.size() != 1) {
+            dialogTitle = Localization.lang("Delete %0 files", linkedFiles.size());
             dialogContent = Localization.lang("Delete %0 files permanently from disk, or just remove the files from the entry? " +
-                    "Pressing Delete will delete the files permanently from disk.", toBeDeleted.size());
+                    "Pressing Delete will delete the files permanently from disk.", linkedFiles.size());
         } else {
-            Optional<Path> file = toBeDeleted.get(0).getFile().findIn(databaseContext, preferences.getFilePreferences());
+            Optional<Path> file = linkedFiles.get(0).getFile().findIn(databaseContext, preferences.getFilePreferences());
 
             if (file.isPresent()) {
                 dialogTitle = Localization.lang("Delete '%0'", file.get().getFileName().toString());
                 dialogContent = Localization.lang("Delete '%0' permanently from disk, or just remove the file from the entry? " +
                         "Pressing Delete will delete the file permanently from disk.", file.get().toString());
             } else {
-                dialogService.notify(Localization.lang("Error accessing file '%0'.", toBeDeleted.get(0).getFile().getLink()));
+                dialogService.notify(Localization.lang("Error accessing file '%0'.", linkedFiles.get(0).getFile().getLink()));
                 return;
             }
         }
 
         ButtonType removeFromEntry = new ButtonType(Localization.lang("Remove from entry"), ButtonBar.ButtonData.YES);
         ButtonType deleteFromEntry = new ButtonType(Localization.lang("Delete from disk"));
+
         Optional<ButtonType> buttonType = dialogService.showCustomButtonDialogAndWait(Alert.AlertType.INFORMATION,
                 dialogTitle, dialogContent, removeFromEntry, deleteFromEntry, ButtonType.CANCEL);
 
         if (buttonType.isPresent()) {
             if (buttonType.get().equals(removeFromEntry)) {
-                deleteFiles(toBeDeleted, false);
+                deleteFiles(linkedFiles, false);
             }
 
             if (buttonType.get().equals(deleteFromEntry)) {
-                deleteFiles(toBeDeleted, true);
+                deleteFiles(linkedFiles, true);
             }
         }
     }
 
     /**
      * Deletes the files from the entry and optionally from disk.
      *
-     * @param toBeDeleted the files to be deleted
+     * @param toBeDeleted    the files to be deleted
      * @param deleteFromDisk if true, the files are deleted from disk, otherwise they are only removed from the entry
      */
     private void deleteFiles(List<LinkedFileViewModel> toBeDeleted, boolean deleteFromDisk) {
         for (LinkedFileViewModel fileViewModel : toBeDeleted) {
             if (fileViewModel.getFile().isOnlineLink()) {
-                viewModel.removeFileLink(fileViewModel);
+                if (viewModel != null) {
+                    viewModel.removeFileLink(fileViewModel);
+                }
             } else {
                 if (deleteFromDisk) {
-                    deleteFileFromDisk(fileViewModel);
+                    deleteFileHelper(databaseContext, fileViewModel.getFile());
+                }
+                if (viewModel != null) {
+                    viewModel.getFiles().remove(fileViewModel);
                 }
-                viewModel.getFiles().remove(fileViewModel);
             }
         }
     }
 
     /**
-     * Deletes the file from disk without asking the user for confirmation.
+     * Helper method to delete the specified file from disk
      *
-     * @param fileViewModel the file to be deleted
+     * @param linkedFile The LinkedFile (file which linked to an entry) to be deleted from disk
      */
-    public void deleteFileFromDisk(LinkedFileViewModel fileViewModel) {
-        LinkedFile linkedFile = fileViewModel.getFile();
-
+    private void deleteFileHelper(BibDatabaseContext databaseContext, LinkedFile linkedFile) {
         Optional<Path> file = linkedFile.findIn(databaseContext, preferences.getFilePreferences());
 
         if (file.isEmpty()) {

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

@@ -76,4 +76,8 @@
         <TextField fx:id="fileDirectoryPattern" GridPane.columnIndex="1" GridPane.rowIndex="1"
                    prefWidth="300" minWidth="300" maxWidth="300"/>
     </GridPane>
+
+    <Label styleClass="sectionHeader" text="%Attached files"/>
+    <CheckBox fx:id="confirmLinkedFileDelete" text="%Show confirmation dialog when deleting files"/>
+
 </fx:root>

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

@@ -37,6 +37,7 @@ public class LinkedFilesTab extends AbstractPreferenceTabView<LinkedFilesTabView
 
     @FXML private ComboBox<String> fileNamePattern;
     @FXML private TextField fileDirectoryPattern;
+    @FXML private CheckBox confirmLinkedFileDelete;
 
     private final ControlsFxVisualizer validationVisualizer = new ControlsFxVisualizer();
 
@@ -69,6 +70,7 @@ public void initialize() {
         fileNamePattern.valueProperty().bindBidirectional(viewModel.fileNamePatternProperty());
         fileNamePattern.itemsProperty().bind(viewModel.defaultFileNamePatternsProperty());
         fileDirectoryPattern.textProperty().bindBidirectional(viewModel.fileDirectoryPatternProperty());
+        confirmLinkedFileDelete.selectedProperty().bindBidirectional(viewModel.confirmLinkedFileDeleteProperty());
 
         ActionFactory actionFactory = new ActionFactory(Globals.getKeyPrefs());
         actionFactory.configureIconButton(StandardActions.HELP_REGEX_SEARCH, new HelpAction(HelpFile.REGEX_SEARCH, dialogService, preferencesService.getFilePreferences()), autolinkRegexHelp);

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

@@ -39,6 +39,7 @@ public class LinkedFilesTabViewModel implements PreferenceTabViewModel {
     private final BooleanProperty fulltextIndex = new SimpleBooleanProperty();
     private final StringProperty fileNamePatternProperty = new SimpleStringProperty();
     private final StringProperty fileDirectoryPatternProperty = new SimpleStringProperty();
+    private final BooleanProperty confirmLinkedFileDeleteProperty = new SimpleBooleanProperty();
 
     private final Validator mainFileDirValidator;
 
@@ -80,6 +81,7 @@ public void setValues() {
         fulltextIndex.setValue(filePreferences.shouldFulltextIndexLinkedFiles());
         fileNamePatternProperty.setValue(filePreferences.getFileNamePattern());
         fileDirectoryPatternProperty.setValue(filePreferences.getFileDirectoryPattern());
+        confirmLinkedFileDeleteProperty.setValue(filePreferences.confirmDeleteLinkedFile());
 
         // Autolink preferences
         switch (autoLinkPreferences.getCitationKeyDependency()) {
@@ -110,6 +112,7 @@ public void storeSettings() {
         }
 
         autoLinkPreferences.setRegularExpression(autolinkRegexKeyProperty.getValue());
+        filePreferences.confirmDeleteLinkedFile(confirmLinkedFileDeleteProperty.getValue());
     }
 
     ValidationStatus mainFileDirValidationStatus() {
@@ -178,5 +181,9 @@ public StringProperty fileDirectoryPatternProperty() {
     public BooleanProperty useMainFileDirectoryProperty() {
         return useMainFileDirectoryProperty;
     }
+
+    public BooleanProperty confirmLinkedFileDeleteProperty() {
+        return this.confirmLinkedFileDeleteProperty;
+    }
 }
 

src/main/java/org/jabref/model/entry/LinkedFile.java

@@ -18,9 +18,13 @@
 import javafx.beans.property.StringProperty;
 
 import org.jabref.architecture.AllowedToUseLogic;
+import org.jabref.gui.DialogService;
+import org.jabref.gui.fieldeditors.LinkedFileViewModel;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.preferences.FilePreferences;
+import org.jabref.preferences.PreferencesService;
 
 /**
  * Represents the link to an external file (e.g. associated PDF file).
@@ -199,4 +203,18 @@ public Optional<Path> findIn(List<Path> directories) {
             return Optional.empty();
         }
     }
+
+    public LinkedFileViewModel toModel(BibEntry entry,
+                                       BibDatabaseContext databaseContext,
+                                       TaskExecutor taskExecutor,
+                                       DialogService dialogService,
+                                       PreferencesService preferencesService) {
+        return new LinkedFileViewModel(
+                this,
+                entry,
+                databaseContext,
+                taskExecutor,
+                dialogService,
+                preferencesService);
+    }
 }

src/main/java/org/jabref/preferences/FilePreferences.java

@@ -36,6 +36,7 @@ public class FilePreferences {
     private final ObservableSet<ExternalFileType> externalFileTypes = FXCollections.observableSet(new TreeSet<>(Comparator.comparing(ExternalFileType::getName)));
     private final BooleanProperty createBackup = new SimpleBooleanProperty();
     private final ObjectProperty<Path> backupDirectory = new SimpleObjectProperty<>();
+    private final BooleanProperty confirmDeleteLinkedFile;
 
     public FilePreferences(String userAndHost,
                            String mainFileDirectory,
@@ -47,7 +48,8 @@ public FilePreferences(String userAndHost,
                            Path workingDirectory,
                            Set<ExternalFileType> externalFileTypes,
                            boolean createBackup,
-                           Path backupDirectory) {
+                           Path backupDirectory,
+                           boolean confirmDeleteLinkedFile) {
         this.userAndHost.setValue(userAndHost);
         this.mainFileDirectory.setValue(mainFileDirectory);
         this.storeFilesRelativeToBibFile.setValue(storeFilesRelativeToBibFile);
@@ -59,6 +61,7 @@ public FilePreferences(String userAndHost,
         this.externalFileTypes.addAll(externalFileTypes);
         this.createBackup.setValue(createBackup);
         this.backupDirectory.setValue(backupDirectory);
+        this.confirmDeleteLinkedFile = new SimpleBooleanProperty(confirmDeleteLinkedFile);
     }
 
     public String getUserAndHost() {
@@ -180,4 +183,16 @@ public void setBackupDirectory(Path backupPath) {
     public Path getBackupDirectory() {
         return this.backupDirectory.getValue();
     }
+
+    public boolean confirmDeleteLinkedFile() {
+        return confirmDeleteLinkedFile.get();
+    }
+
+    public BooleanProperty confirmDeleteLinkedFileProperty() {
+        return confirmDeleteLinkedFile;
+    }
+
+    public void confirmDeleteLinkedFile(boolean confirmLinkedFileDelete) {
+        this.confirmDeleteLinkedFile.set(confirmLinkedFileDelete);
+    }
 }