Fix for delete entries should ask user

CHANGELOG.md

@@ -11,6 +11,7 @@ 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)
 - We added a dropdown menu to let users change the reference library during AUX file import. [#10472](https://github.com/JabRef/jabref/issues/10472)
 - We added a button to let users reset the cite command to the default value. [#10569](https://github.com/JabRef/jabref/issues/10569)
 

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

@@ -34,6 +34,7 @@
 import org.jabref.gui.dialogs.AutosaveUiManager;
 import org.jabref.gui.entryeditor.EntryEditor;
 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;
@@ -419,7 +420,7 @@ public JabRefFrame frame() {
     }
 
     /**
-     * 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"
      */
@@ -428,7 +429,7 @@ 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"
      */
@@ -440,8 +441,26 @@ private void delete(boolean cut, List<BibEntry> entries) {
             return;
         }
 
+        // Delete selected entries
         getUndoManager().addEdit(new UndoableRemoveEntries(bibDatabaseContext.getDatabase(), entries, cut));
         bibDatabaseContext.getDatabase().removeEntries(entries);
+
+        // Not delete files when user select cut
+        if (!cut) {
+            // Keep track of linked files from selected entries
+            List<LinkedFile> linkedFileList = new ArrayList<>();
+
+            for (BibEntry entry : entries) {
+                List<LinkedFile> linkedFilesFromEntry = entry.getFiles();
+                linkedFileList.addAll(linkedFilesFromEntry);
+            }
+
+            // Delete files which linked to selected entries when user select deletion
+            if (linkedFileList.size() > 0 && showLinkedFileDeleteConfirmationDialog(linkedFileList)) {
+                new DeleteFileAction(dialogService, preferencesService, bibDatabaseContext, null, null).deleteFileFromDisk(linkedFileList);
+            }
+        }
+
         ensureNotShowingBottomPanel(entries);
 
         this.changedProperty.setValue(true);
@@ -679,6 +698,14 @@ 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");
@@ -692,7 +719,8 @@ private boolean showDeleteConfirmationDialog(int numberOfEntries) {
                 cancelButton = Localization.lang("Keep entries");
             }
 
-            return dialogService.showConfirmationDialogWithOptOutAndWait(title,
+            return dialogService.showConfirmationDialogWithOptOutAndWait(
+                    title,
                     message,
                     okButton,
                     cancelButton,
@@ -703,6 +731,41 @@ private boolean showDeleteConfirmationDialog(int numberOfEntries) {
         }
     }
 
+    /**
+     * Initializes a pop-up dialog box to confirm whether the user wants to delete attached files from selected entry
+     * Keep track of user preference:
+     * if the user prefers always delete attached files, delete the files without displaying the dialog box
+     *
+     * @param linkedFileList A list of LinkedFile to be deleted
+     * @return true if user confirm to delete attached files
+     */
+    private boolean showLinkedFileDeleteConfirmationDialog(List<LinkedFile> linkedFileList) {
+        if (preferencesService.getFilePreferences().alwaysDeleteLinkedFile()) {
+            return true;
+        } else {
+            Optional<Path> file = linkedFileList.get(0).findIn(bibDatabaseContext, preferencesService.getFilePreferences());
+
+            String title = Localization.lang("Delete attached file");
+            String message = Localization.lang("Delete '%0'", file.get().getFileName().toString());
+            String okButton = Localization.lang("Delete attached file");
+            String cancelButton = Localization.lang("Keep attached file");
+            if (linkedFileList.size() > 1) {
+                title = Localization.lang("Delete attached files");
+                message = Localization.lang("Delete %0 attached files", linkedFileList.size());
+                okButton = Localization.lang("Delete attached files");
+                cancelButton = Localization.lang("Keep attached files");
+            }
+
+            return dialogService.showConfirmationDialogWithOptOutAndWait(
+                    title,
+                    message,
+                    okButton,
+                    cancelButton,
+                    Localization.lang("Always delete attached file(s)"),
+                    optOut -> preferencesService.getFilePreferences().setAlwaysDeleteLinkedFile(optOut));
+        }
+    }
+
     /**
      * Depending on whether a preview or an entry editor is showing, save the current divider location in the correct preference setting.
      */

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

@@ -116,7 +116,26 @@ private void deleteFiles(List<LinkedFileViewModel> toBeDeleted, boolean deleteFr
      */
     public void deleteFileFromDisk(LinkedFileViewModel fileViewModel) {
         LinkedFile linkedFile = fileViewModel.getFile();
+        deleteFileHelper(linkedFile);
+    }
+
+    /**
+     * Deletes files from disk without asking the user for confirmation, for a list of files
+     *
+     * @param filesLinkedToEntry A list of LinkedFile to be deleted
+     */
+    public void deleteFileFromDisk(List<LinkedFile> filesLinkedToEntry) {
+        for (LinkedFile linkedFile : filesLinkedToEntry) {
+            deleteFileHelper(linkedFile);
+        }
+    }
 
+    /**
+     * Helper method to delete the specified file from disk
+     *
+     * @param linkedFile The LinkedFile (file which linked to an entry) to be deleted from disk
+     */
+    private void deleteFileHelper(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="%Always delete attached file(s)"/>
+
 </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.alwaysDeleteLinkedFile());
 
         // Autolink preferences
         switch (autoLinkPreferences.getCitationKeyDependency()) {
@@ -110,6 +112,7 @@ public void storeSettings() {
         }
 
         autoLinkPreferences.setRegularExpression(autolinkRegexKeyProperty.getValue());
+        filePreferences.setAlwaysDeleteLinkedFile(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/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 alwaysDeleteLinkedFile() {
+        return confirmDeleteLinkedFile.get();
+    }
+
+    public BooleanProperty alwaysDeleteLinkedFileProperty() {
+        return confirmDeleteLinkedFile;
+    }
+
+    public void setAlwaysDeleteLinkedFile(boolean confirmLinkedFileDelete) {
+        this.confirmDeleteLinkedFile.set(confirmLinkedFileDelete);
+    }
 }

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

@@ -282,6 +282,7 @@ public class JabRefPreferences implements PreferencesService {
     public static final String DEFAULT_CITATION_KEY_PATTERN = "defaultBibtexKeyPattern";
     public static final String UNWANTED_CITATION_KEY_CHARACTERS = "defaultUnwantedBibtexKeyCharacters";
     public static final String CONFIRM_DELETE = "confirmDelete";
+    public static final String CONFIRM_LINKED_FILE_DELETE = "confirmLinkedFileDelete";
     public static final String WARN_BEFORE_OVERWRITING_KEY = "warnBeforeOverwritingKey";
     public static final String AVOID_OVERWRITING_KEY = "avoidOverwritingKey";
     public static final String AUTOLINK_EXACT_KEY_ONLY = "autolinkExactKeyOnly";
@@ -683,6 +684,7 @@ private JabRefPreferences() {
         defaults.put(AVOID_OVERWRITING_KEY, Boolean.FALSE);
         defaults.put(WARN_BEFORE_OVERWRITING_KEY, Boolean.TRUE);
         defaults.put(CONFIRM_DELETE, Boolean.TRUE);
+        defaults.put(CONFIRM_LINKED_FILE_DELETE, Boolean.FALSE);
         defaults.put(DEFAULT_CITATION_KEY_PATTERN, "[auth][year]");
         defaults.put(UNWANTED_CITATION_KEY_CHARACTERS, "-`ʹ:!;?^+");
         defaults.put(RESOLVE_STRINGS_FOR_FIELDS, "author;booktitle;editor;editora;editorb;editorc;institution;issuetitle;journal;journalsubtitle;journaltitle;mainsubtitle;month;publisher;shortauthor;shorteditor;subtitle;titleaddon");
@@ -2160,7 +2162,8 @@ public FilePreferences getFilePreferences() {
                 ExternalFileTypes.fromString(get(EXTERNAL_FILE_TYPES)),
                 getBoolean(CREATE_BACKUP),
                 // We choose the data directory, because a ".bak" file should survive cache cleanups
-                getPath(BACKUP_DIRECTORY, OS.getNativeDesktop().getBackupDirectory()));
+                getPath(BACKUP_DIRECTORY, OS.getNativeDesktop().getBackupDirectory()),
+                getBoolean(CONFIRM_LINKED_FILE_DELETE));
 
         EasyBind.listen(filePreferences.mainFileDirectoryProperty(), (obs, oldValue, newValue) -> put(MAIN_FILE_DIRECTORY, newValue));
         EasyBind.listen(filePreferences.storeFilesRelativeToBibFileProperty(), (obs, oldValue, newValue) -> putBoolean(STORE_RELATIVE_TO_BIB, newValue));
@@ -2173,6 +2176,7 @@ public FilePreferences getFilePreferences() {
                 put(EXTERNAL_FILE_TYPES, ExternalFileTypes.toStringList(filePreferences.getExternalFileTypes())));
         EasyBind.listen(filePreferences.createBackupProperty(), (obs, oldValue, newValue) -> putBoolean(CREATE_BACKUP, newValue));
         EasyBind.listen(filePreferences.backupDirectoryProperty(), (obs, oldValue, newValue) -> put(BACKUP_DIRECTORY, newValue.toString()));
+        EasyBind.listen(filePreferences.alwaysDeleteLinkedFileProperty(), (obs, oldValue, newValue) -> putBoolean(CONFIRM_LINKED_FILE_DELETE, newValue));
 
         return filePreferences;
     }

src/main/resources/l10n/JabRef_en.properties

@@ -2452,6 +2452,14 @@ Found\ match\ in\ %0=Found match in %0
 On\ page\ %0=On page %0
 Found\ matches\ in\ Annotations\:=Found matches in Annotations:
 
+Attached\ files=Attached files
+Always\ delete\ attached\ file(s)=Always delete attached file(s)
+Delete\ %0\ attached\ files=Delete %0 attached files
+Delete\ attached\ file=Delete attached file
+Delete\ attached\ files=Delete attached files
+Keep\ attached\ file=Keep attached file
+Keep\ attached\ files=Keep attached files
+
 Grobid\ URL=Grobid URL
 Remote\ services=Remote services
 Allow\ sending\ PDF\ files\ and\ raw\ citation\ strings\ to\ a\ JabRef\ online\ service\ (Grobid)\ to\ determine\ Metadata.\ This\ produces\ better\ results.=Allow sending PDF files and raw citation strings to a JabRef online service (Grobid) to determine Metadata. This produces better results.