Fix for delete entries should ask user

CHANGELOG.md

@@ -16,6 +16,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a fetcher for [ISIDORE](https://isidore.science/), simply paste in the link into the text field or the last 6 digits in the link that identify that paper. [#10423](https://github.com/JabRef/jabref/issues/10423)
 - When importing entries form the "Citation relations" tab, the field [cites](https://docs.jabref.org/advanced/entryeditor/entrylinks) is now filled according to the relationship between the entries. [#10572](https://github.com/JabRef/jabref/pull/10752)
 - We added a new group icon column to the main table showing the icons of the entry's groups. [#10801](https://github.com/JabRef/jabref/pull/10801)
+- When deleting an entry, the files linked to the entry are now optionally deleted as well. [#10509](https://github.com/JabRef/jabref/issues/10509)
+- We added support to move the file to the system trash (instead of deleting it). [#10591](https://github.com/JabRef/jabref/pull/10591)
 - We added ability to jump to an entry in the command line using `-j CITATIONKEY`. [koppor#540](https://github.com/koppor/jabref/issues/540)
 - We added a new boolean to the style files for Openoffice/Libreoffice integration to switch between ZERO_WIDTH_SPACE (default) and no space. [#10843](https://github.com/JabRef/jabref/pull/10843)
 - When pasting HTML into the abstract or a comment field, the hypertext is automatically converted to Markdown. [#10558](https://github.com/JabRef/jabref/issues/10558)

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;
 
@@ -42,7 +43,9 @@
 import org.jabref.gui.dialogs.AutosaveUiManager;
 import org.jabref.gui.entryeditor.EntryEditor;
 import org.jabref.gui.exporter.SaveDatabaseAction;
+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;
@@ -430,7 +433,7 @@ public SuggestionProviders getSuggestionProviders() {
     }
 
     /**
-     * Removes the selected entries from the database
+     * Removes the selected entries and files linked to selected entries from the database
      *
      * @param mode If DELETE_ENTRY 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"
      */
@@ -439,7 +442,7 @@ public void delete(StandardActions mode) {
     }
 
     /**
-     * Removes the selected entries from the database
+     * Removes the selected entries and files linked to selected entries from the database
      *
      * @param mode If DELETE_ENTRY 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"
      */
@@ -451,16 +454,31 @@ private void delete(StandardActions mode, List<BibEntry> entries) {
             return;
         }
 
+        // Delete selected entries
         getUndoManager().addEdit(new UndoableRemoveEntries(bibDatabaseContext.getDatabase(), entries, mode == StandardActions.CUT));
         bibDatabaseContext.getDatabase().removeEntries(entries);
+
+        if (mode != StandardActions.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.getFilePreferences(), bibDatabaseContext, viewModels).execute();
+            }
+        }
+
         ensureNotShowingBottomPanel(entries);
 
         this.changedProperty.setValue(true);
         switch (mode) {
-            case StandardActions.CUT ->
-                    dialogService.notify(Localization.lang("Cut %0 entry(ies)", entries.size()));
-            case StandardActions.DELETE_ENTRY ->
-                    dialogService.notify(Localization.lang("Deleted %0 entry(ies)", entries.size()));
+            case StandardActions.CUT -> dialogService.notify(Localization.lang("Cut %0 entry(ies)", entries.size()));
+            case StandardActions.DELETE_ENTRY -> dialogService.notify(Localization.lang("Deleted %0 entry(ies)", entries.size()));
         }
 
         // prevent the main table from loosing focus
@@ -678,6 +696,14 @@ 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");
@@ -691,7 +717,8 @@ 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/desktop/JabRefDesktop.java

@@ -1,5 +1,7 @@
 package org.jabref.gui.desktop;
 
+import java.awt.Desktop;
+import java.io.File;
 import java.io.IOException;
 import java.net.URI;
 import java.nio.file.Files;
@@ -52,7 +54,7 @@ private JabRefDesktop() {
 
     /**
      * Open a http/pdf/ps viewer for the given link string.
-     *
+     * <p>
      * Opening a PDF file at the file field is done at {@link org.jabref.gui.fieldeditors.LinkedFileViewModel#open}
      */
     public static void openExternalViewer(BibDatabaseContext databaseContext,
@@ -239,7 +241,6 @@ public static void openFolderAndSelectFile(Path fileLink,
      * If no command is specified in {@link Globals}, the default system console will be executed.
      *
      * @param file Location the console should be opened at.
-     *
      */
     public static void openConsole(Path file, PreferencesService preferencesService, DialogService dialogService) throws IOException {
         if (file == null) {
@@ -314,4 +315,26 @@ public static void openBrowserShowPopup(String url, DialogService dialogService,
             dialogService.showErrorDialogAndWait(couldNotOpenBrowser, couldNotOpenBrowser + "\n" + openManually + "\n" + copiedToClipboard);
         }
     }
+
+    /**
+     * Moves the given file to the trash.
+     *
+     * @throws UnsupportedOperationException if the current platform does not support the {@link Desktop.Action#MOVE_TO_TRASH} action
+     * @see Desktop#moveToTrash(File)
+     */
+    public static void moveToTrash(Path path) {
+        NATIVE_DESKTOP.moveToTrash(path);
+    }
+
+    public static boolean moveToTrashSupported() {
+        return NATIVE_DESKTOP.moveToTrashSupported();
+    }
+
+    public static Path getApplicationDirectory() {
+        return NATIVE_DESKTOP.getApplicationDirectory();
+    }
+
+    public static Path getFulltextIndexBaseDirectory() {
+        return NATIVE_DESKTOP.getFulltextIndexBaseDirectory();
+    }
 }

src/main/java/org/jabref/gui/desktop/os/NativeDesktop.java

@@ -1,5 +1,6 @@
 package org.jabref.gui.desktop.os;
 
+import java.awt.Desktop;
 import java.io.File;
 import java.io.IOException;
 import java.net.InetAddress;
@@ -8,6 +9,7 @@
 import java.nio.file.Path;
 
 import org.jabref.Launcher;
+import org.jabref.architecture.AllowedToUseAwt;
 import org.jabref.gui.DialogService;
 import org.jabref.logic.util.BuildInfo;
 import org.jabref.logic.util.OS;
@@ -19,15 +21,16 @@
 import org.slf4j.LoggerFactory;
 
 /**
+ * This class is not meant to be used directly. Use {@link org.jabref.gui.desktop.JabRefDesktop} instead.
+ * <p>
  * This class contains bundles OS specific implementations for file directories and file/application open handling methods.
  * In case the default does not work, subclasses provide the correct behavior.
- *
- * <p>
+ * * <p>
  * We cannot use a static logger instance here in this class as the Logger first needs to be configured in the {@link Launcher#addLogToDisk}
  * The configuration of tinylog will become immutable as soon as the first log entry is issued.
  * https://tinylog.org/v2/configuration/
- * </p>
  */
+@AllowedToUseAwt("Because of moveToTrash() is not available elsewhere.")
 public abstract class NativeDesktop {
 
     public abstract void openFile(String filePath, String fileType, FilePreferences filePreferences) throws IOException;
@@ -125,4 +128,18 @@ public String getHostName() {
         }
         return hostName;
     }
+
+    /**
+     * Moves the given file to the trash.
+     *
+     * @throws UnsupportedOperationException if the current platform does not support the {@link Desktop.Action#MOVE_TO_TRASH} action
+     * @see Desktop#moveToTrash(File)
+     */
+    public void moveToTrash(Path path) {
+        Desktop.getDesktop().moveToTrash(path.toFile());
+    }
+
+    public boolean moveToTrashSupported() {
+        return Desktop.getDesktop().isSupported(Desktop.Action.MOVE_TO_TRASH);
+    }
 }

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

@@ -19,9 +19,6 @@
 import javafx.beans.property.SimpleDoubleProperty;
 import javafx.beans.property.StringProperty;
 import javafx.scene.Node;
-import javafx.scene.control.Alert.AlertType;
-import javafx.scene.control.ButtonBar.ButtonData;
-import javafx.scene.control.ButtonType;
 
 import org.jabref.gui.AbstractViewModel;
 import org.jabref.gui.DialogService;
@@ -30,6 +27,7 @@
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.icon.JabRefIcon;
+import org.jabref.gui.linkedfile.DeleteFileAction;
 import org.jabref.gui.linkedfile.DownloadLinkedFileAction;
 import org.jabref.gui.linkedfile.LinkedFileEditDialogView;
 import org.jabref.gui.mergeentries.MultiMergeEntriesView;
@@ -86,7 +84,6 @@ public LinkedFileViewModel(LinkedFile linkedFile,
                                TaskExecutor taskExecutor,
                                DialogService dialogService,
                                PreferencesService preferencesService) {
-
         this.linkedFile = linkedFile;
         this.preferencesService = preferencesService;
         this.linkedFileHandler = new LinkedFileHandler(linkedFile, entry, databaseContext, preferencesService.getFilePreferences());
@@ -365,42 +362,16 @@ public void moveToDefaultDirectoryAndRename() {
     }
 
     /**
-     * Asks the user for confirmation that he really wants to the delete the file from disk (or just remove the link).
+     * Asks the user for confirmation that he really wants to the delete the file from disk (or just remove the link)
+     * and then proceeds accordingly.
      *
-     * @return true if the linked file should be removed afterwards from the entry (i.e because it was deleted
-     * successfully, does not exist in the first place or the user choose to remove it)
+     * @return true if the linked file has been removed afterward from the entry (i.e., because it was deleted
+     * successfully, does not exist in the first place, or the user choose to remove it)
      */
     public boolean delete() {
-        Optional<Path> file = linkedFile.findIn(databaseContext, preferencesService.getFilePreferences());
-
-        if (file.isEmpty()) {
-            LOGGER.warn("Could not find file {}", linkedFile.getLink());
-            return true;
-        }
-
-        ButtonType removeFromEntry = new ButtonType(Localization.lang("Remove from entry"), ButtonData.YES);
-        ButtonType deleteFromEntry = new ButtonType(Localization.lang("Delete from disk"));
-        Optional<ButtonType> buttonType = dialogService.showCustomButtonDialogAndWait(AlertType.INFORMATION,
-                Localization.lang("Delete '%0'", file.get().getFileName().toString()),
-                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()),
-                removeFromEntry, deleteFromEntry, ButtonType.CANCEL);
-
-        if (buttonType.isPresent()) {
-            if (buttonType.get().equals(removeFromEntry)) {
-                return true;
-            }
-
-            if (buttonType.get().equals(deleteFromEntry)) {
-                try {
-                    Files.delete(file.get());
-                    return true;
-                } catch (IOException ex) {
-                    dialogService.showErrorDialogAndWait(Localization.lang("Cannot delete file"), Localization.lang("File permission error"));
-                    LOGGER.warn("File permission error while deleting: {}", linkedFile, ex);
-                }
-            }
-        }
-        return false;
+        DeleteFileAction deleteFileAction = new DeleteFileAction(dialogService, preferencesService.getFilePreferences(), databaseContext, null, List.of(this));
+        deleteFileAction.execute();
+        return deleteFileAction.isSuccess();
     }
 
     public void edit() {

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

@@ -254,8 +254,7 @@ private void setUpKeyBindings() {
             if (keyBinding.isPresent()) {
                 switch (keyBinding.get()) {
                     case DELETE_ENTRY:
-                        new DeleteFileAction(dialogService, preferencesService, databaseContext,
-                                viewModel, listView).execute();
+                        deleteAttachedFilesWithConfirmation();
                         event.consume();
                         break;
                     default:
@@ -265,6 +264,11 @@ private void setUpKeyBindings() {
         });
     }
 
+    private void deleteAttachedFilesWithConfirmation() {
+        new DeleteFileAction(dialogService, preferencesService.getFilePreferences(), databaseContext,
+                viewModel, listView.getSelectionModel().getSelectedItems()).execute();
+    }
+
     public LinkedFilesEditorViewModel getViewModel() {
         return viewModel;
     }