Moved Journal Abbreviation from Quality Menu to Cleanup Entries Dialog

CHANGELOG.md

@@ -31,6 +31,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 - Added "$" to the citation key generator preferences default list of characters to remove [#12536](https://github.com/JabRef/jabref/issues/12536)
 - We changed the message displayed in the Integrity Check Progress dialog to "Waiting for the check to finish...". [#12694](https://github.com/JabRef/jabref/issues/12694)
+- We moved journal abbreviation from the Quality menu to the cleanup entries dialog [#11791](https://github.com/JabRef/jabref/issues/11791)
 - We moved the "Generate a new key for imported entries" option from the "Web search" tab to the "Citation key generator" tab in preferences. [#12436](https://github.com/JabRef/jabref/pull/12436)
 - We improved the offline parsing of BibTeX data from PDF-documents. [#12278](https://github.com/JabRef/jabref/issues/12278)
 - The tab bar is now hidden when only one library is open. [#9971](https://github.com/JabRef/jabref/issues/9971)

src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -109,11 +109,6 @@ public enum StandardActions implements Action {
     COPY_LINKED_FILES(Localization.lang("Copy linked files to folder...")),
     COPY_DOI(Localization.lang("Copy DOI")),
     COPY_DOI_URL(Localization.lang("Copy DOI url")),
-    ABBREVIATE(Localization.lang("Abbreviate journal names")),
-    ABBREVIATE_DEFAULT(Localization.lang("default"), Localization.lang("Abbreviate journal names of the selected entries (DEFAULT abbreviation)"), KeyBinding.ABBREVIATE),
-    ABBREVIATE_DOTLESS(Localization.lang("dotless"), Localization.lang("Abbreviate journal names of the selected entries (DOTLESS abbreviation)")),
-    ABBREVIATE_SHORTEST_UNIQUE(Localization.lang("shortest unique"), Localization.lang("Abbreviate journal names of the selected entries (SHORTEST UNIQUE abbreviation)")),
-    UNABBREVIATE(Localization.lang("Unabbreviate journal names"), Localization.lang("Unabbreviate journal names of the selected entries"), KeyBinding.UNABBREVIATE),
 
     MANAGE_CUSTOM_EXPORTS(Localization.lang("Manage custom exports")),
     MANAGE_CUSTOM_IMPORTS(Localization.lang("Manage custom imports")),

src/main/java/org/jabref/gui/cleanup/CleanupAction.java

@@ -20,6 +20,7 @@
 import org.jabref.logic.JabRefException;
 import org.jabref.logic.cleanup.CleanupPreferences;
 import org.jabref.logic.cleanup.CleanupWorker;
+import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.logic.util.BackgroundTask;
@@ -36,6 +37,7 @@ public class CleanupAction extends SimpleCommand {
     private final StateManager stateManager;
     private final TaskExecutor taskExecutor;
     private final UndoManager undoManager;
+    private final JournalAbbreviationRepository abbreviationRepository;
     private final List<JabRefException> failures;
 
     private boolean isCanceled;
@@ -46,13 +48,15 @@ public CleanupAction(Supplier<LibraryTab> tabSupplier,
                          DialogService dialogService,
                          StateManager stateManager,
                          TaskExecutor taskExecutor,
-                         UndoManager undoManager) {
+                         UndoManager undoManager,
+                         JournalAbbreviationRepository abbreviationRepository) {
         this.tabSupplier = tabSupplier;
         this.preferences = preferences;
         this.dialogService = dialogService;
         this.stateManager = stateManager;
         this.taskExecutor = taskExecutor;
         this.undoManager = undoManager;
+        this.abbreviationRepository = abbreviationRepository;
         this.failures = new ArrayList<>();
 
         this.executable.bind(ActionHelper.needsEntriesSelected(stateManager));
@@ -114,7 +118,9 @@ private boolean doCleanup(BibDatabaseContext databaseContext, CleanupPreferences
         CleanupWorker cleaner = new CleanupWorker(
                 databaseContext,
                 preferences.getFilePreferences(),
-                preferences.getTimestampPreferences()
+                preferences.getTimestampPreferences(),
+                preferences.getJournalAbbreviationPreferences().shouldUseFJournalField(),
+                abbreviationRepository
         );
 
         List<FieldChange> changes = cleaner.cleanup(preset, entry);

src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.fxml

@@ -2,6 +2,7 @@
 
 <?import javafx.geometry.Insets?>
 <?import javafx.scene.control.CheckBox?>
+<?import javafx.scene.control.ComboBox?>
 <?import javafx.scene.control.Label?>
 <?import javafx.scene.control.ToggleGroup?>
 <?import javafx.scene.layout.VBox?>
@@ -44,6 +45,14 @@
          </VBox.margin>
          </VBox>
          <CheckBox fx:id="cleanUpDeletedFiles" text="Remove links to non existent files" />
+      </VBox>
+      <Label text="%Journal-related" />
+      <VBox>
+          <VBox.margin>
+            <Insets left="20.0" />
+          </VBox.margin>
+          <Label text="Choose how to handle journal names:" />
+          <ComboBox fx:id="journalCleanupSelector" />
       </VBox>
             <FieldFormatterCleanupsPanel fx:id="formatterCleanupsPanel" />
  <padding>

src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.java

@@ -8,6 +8,7 @@
 import javafx.collections.FXCollections;
 import javafx.fxml.FXML;
 import javafx.scene.control.CheckBox;
+import javafx.scene.control.ComboBox;
 import javafx.scene.control.Label;
 import javafx.scene.layout.VBox;
 
@@ -22,7 +23,6 @@
 import com.airhacks.afterburner.views.ViewLoader;
 
 public class CleanupPresetPanel extends VBox {
-
     private final BibDatabaseContext databaseContext;
     @FXML private Label cleanupRenamePDFLabel;
     @FXML private CheckBox cleanUpDOI;
@@ -39,6 +39,7 @@ public class CleanupPresetPanel extends VBox {
     @FXML private CheckBox cleanUpBibtex;
     @FXML private CheckBox cleanUpTimestampToCreationDate;
     @FXML private CheckBox cleanUpTimestampToModificationDate;
+    @FXML private ComboBox<String> journalCleanupSelector;
     @FXML private FieldFormatterCleanupsPanel formatterCleanupsPanel;
 
     public CleanupPresetPanel(BibDatabaseContext databaseContext, CleanupPreferences cleanupPreferences, FilePreferences filePreferences) {
@@ -96,6 +97,14 @@ private void init(CleanupPreferences cleanupPreferences, FilePreferences filePre
                         cleanUpTimestampToCreationDate.selectedProperty().setValue(false);
                     }
                 });
+        journalCleanupSelector.setItems(FXCollections.observableArrayList(
+                CleanupPreferences.JOURNAL_CLEANUP_ABBREVIATE_DEFAULT,
+                CleanupPreferences.JOURNAL_CLEANUP_ABBREVIATE_DOTLESS,
+                CleanupPreferences.JOURNAL_CLEANUP_ABBREVIATE_SHORTEST_UNIQUE,
+                CleanupPreferences.JOURNAL_CLEANUP_UNABBREVIATE,
+                CleanupPreferences.JOURNAL_CLEANUP_NO_CHANGES
+        ));
+        journalCleanupSelector.getSelectionModel().select(CleanupPreferences.JOURNAL_CLEANUP_NO_CHANGES);
         updateDisplay(cleanupPreferences);
     }
 
@@ -117,6 +126,8 @@ private void updateDisplay(CleanupPreferences preset) {
         cleanUpTimestampToModificationDate.setSelected(preset.isActive(CleanupPreferences.CleanupStep.CONVERT_TIMESTAMP_TO_MODIFICATIONDATE));
         cleanUpTimestampToModificationDate.setSelected(preset.isActive(CleanupPreferences.CleanupStep.DO_NOT_CONVERT_TIMESTAMP));
         cleanUpISSN.setSelected(preset.isActive(CleanupPreferences.CleanupStep.CLEAN_UP_ISSN));
+        journalCleanupSelector.getSelectionModel().select(preset.getSelectedJournalCleanupOption());
+
         formatterCleanupsPanel.cleanupsDisableProperty().setValue(!preset.getFieldFormatterCleanups().isEnabled());
         formatterCleanupsPanel.cleanupsProperty().setValue(FXCollections.observableArrayList(preset.getFieldFormatterCleanups().getConfiguredActions()));
     }
@@ -167,6 +178,16 @@ public CleanupPreferences getCleanupPreset() {
         if (cleanUpTimestampToModificationDate.isSelected()) {
             activeJobs.add(CleanupPreferences.CleanupStep.CONVERT_TIMESTAMP_TO_MODIFICATIONDATE);
         }
+        String selectedJournalOption = journalCleanupSelector.getSelectionModel().getSelectedItem();
+        if (CleanupPreferences.JOURNAL_CLEANUP_ABBREVIATE_DEFAULT.equals(selectedJournalOption)) {
+            activeJobs.add(CleanupPreferences.CleanupStep.ABBREVIATE_DEFAULT);
+        } else if (CleanupPreferences.JOURNAL_CLEANUP_ABBREVIATE_DOTLESS.equals(selectedJournalOption)) {
+            activeJobs.add(CleanupPreferences.CleanupStep.ABBREVIATE_DOTLESS);
+        } else if (CleanupPreferences.JOURNAL_CLEANUP_ABBREVIATE_SHORTEST_UNIQUE.equals(selectedJournalOption)) {
+            activeJobs.add(CleanupPreferences.CleanupStep.ABBREVIATE_SHORTEST_UNIQUE);
+        } else if (CleanupPreferences.JOURNAL_CLEANUP_UNABBREVIATE.equals(selectedJournalOption)) {
+            activeJobs.add(CleanupPreferences.CleanupStep.UNABBREVIATE);
+        }
 
         activeJobs.add(CleanupPreferences.CleanupStep.FIX_FILE_LINKS);
 

src/main/java/org/jabref/gui/cleanup/CleanupSingleAction.java

@@ -16,6 +16,7 @@
 import org.jabref.logic.JabRefException;
 import org.jabref.logic.cleanup.CleanupPreferences;
 import org.jabref.logic.cleanup.CleanupWorker;
+import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.model.FieldChange;
@@ -29,16 +30,18 @@ public class CleanupSingleAction extends SimpleCommand {
     private final StateManager stateManager;
     private final BibEntry entry;
     private final UndoManager undoManager;
+    private final JournalAbbreviationRepository abbreviationRepository;
 
     private boolean isCanceled;
     private int modifiedEntriesCount;
 
-    public CleanupSingleAction(BibEntry entry, CliPreferences preferences, DialogService dialogService, StateManager stateManager, UndoManager undoManager) {
+    public CleanupSingleAction(BibEntry entry, CliPreferences preferences, DialogService dialogService, StateManager stateManager, UndoManager undoManager, JournalAbbreviationRepository abbreviationRepository) {
         this.entry = entry;
         this.preferences = preferences;
         this.dialogService = dialogService;
         this.stateManager = stateManager;
         this.undoManager = undoManager;
+        this.abbreviationRepository = abbreviationRepository;
 
         this.executable.bind(ActionHelper.needsEntriesSelected(stateManager));
     }
@@ -84,7 +87,9 @@ private void doCleanup(BibDatabaseContext databaseContext, CleanupPreferences pr
         CleanupWorker cleaner = new CleanupWorker(
                 databaseContext,
                 preferences.getFilePreferences(),
-                preferences.getTimestampPreferences()
+                preferences.getTimestampPreferences(),
+                preferences.getJournalAbbreviationPreferences().shouldUseFJournalField(),
+                abbreviationRepository
         );
 
         List<FieldChange> changes = cleaner.cleanup(preset, entry);

src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -268,7 +268,7 @@ void generateCiteKeyButton() {
 
     @FXML
     void generateCleanupButton() {
-        CleanupSingleAction action = new CleanupSingleAction(getCurrentlyEditedEntry(), preferences, dialogService, stateManager, undoManager);
+        CleanupSingleAction action = new CleanupSingleAction(getCurrentlyEditedEntry(), preferences, dialogService, stateManager, undoManager, journalAbbreviationRepository);
         action.execute();
     }
 

src/main/java/org/jabref/gui/frame/JabRefFrame.java

@@ -207,7 +207,8 @@ private void initLayout() {
                 taskExecutor,
                 entryTypesManager,
                 clipBoardManager,
-                undoManager);
+                undoManager,
+                Injector.instantiateModelOrService(JournalAbbreviationRepository.class));
 
         MainMenu mainMenu = new MainMenu(
                 this,

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

@@ -48,7 +48,6 @@
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.gui.importer.fetcher.LookupIdentifierAction;
 import org.jabref.gui.integrity.IntegrityCheckAction;
-import org.jabref.gui.journals.AbbreviateAction;
 import org.jabref.gui.libraryproperties.LibraryPropertiesAction;
 import org.jabref.gui.linkedfile.RedownloadMissingFilesAction;
 import org.jabref.gui.maintable.NewLibraryFromPdfActionOffline;
@@ -254,20 +253,11 @@ private void createMenu() {
                 factory.createMenuItem(StandardActions.MERGE_ENTRIES, new MergeEntriesAction(dialogService, stateManager, undoManager, preferences)),
                 factory.createMenuItem(StandardActions.CHECK_INTEGRITY, new IntegrityCheckAction(frame::getCurrentLibraryTab, preferences, dialogService, stateManager, (UiTaskExecutor) taskExecutor, abbreviationRepository)),
                 factory.createMenuItem(StandardActions.CHECK_CONSISTENCY, new ConsistencyCheckAction(frame::getCurrentLibraryTab, dialogService, stateManager, preferences, entryTypesManager, (UiTaskExecutor) taskExecutor)),
-                factory.createMenuItem(StandardActions.CLEANUP_ENTRIES, new CleanupAction(frame::getCurrentLibraryTab, preferences, dialogService, stateManager, taskExecutor, undoManager)),
+                factory.createMenuItem(StandardActions.CLEANUP_ENTRIES, new CleanupAction(frame::getCurrentLibraryTab, preferences, dialogService, stateManager, taskExecutor, undoManager, abbreviationRepository)),
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(dialogService, preferences, stateManager, undoManager, (UiTaskExecutor) taskExecutor)),
-
-                new SeparatorMenuItem(),
-
-                factory.createSubMenu(StandardActions.ABBREVIATE,
-                        factory.createMenuItem(StandardActions.ABBREVIATE_DEFAULT, new AbbreviateAction(StandardActions.ABBREVIATE_DEFAULT, frame::getCurrentLibraryTab, dialogService, stateManager, preferences.getJournalAbbreviationPreferences(), abbreviationRepository, taskExecutor, undoManager)),
-                        factory.createMenuItem(StandardActions.ABBREVIATE_DOTLESS, new AbbreviateAction(StandardActions.ABBREVIATE_DOTLESS, frame::getCurrentLibraryTab, dialogService, stateManager, preferences.getJournalAbbreviationPreferences(), abbreviationRepository, taskExecutor, undoManager)),
-                        factory.createMenuItem(StandardActions.ABBREVIATE_SHORTEST_UNIQUE, new AbbreviateAction(StandardActions.ABBREVIATE_SHORTEST_UNIQUE, frame::getCurrentLibraryTab, dialogService, stateManager, preferences.getJournalAbbreviationPreferences(), abbreviationRepository, taskExecutor, undoManager))),
-
-                factory.createMenuItem(StandardActions.UNABBREVIATE, new AbbreviateAction(StandardActions.UNABBREVIATE, frame::getCurrentLibraryTab, dialogService, stateManager, preferences.getJournalAbbreviationPreferences(), abbreviationRepository, taskExecutor, undoManager))
+                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(dialogService, preferences, stateManager, undoManager, (UiTaskExecutor) taskExecutor))
         );
 
         Menu lookupIdentifiers = factory.createSubMenu(StandardActions.LOOKUP_DOC_IDENTIFIER);

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

@@ -39,6 +39,7 @@
 import org.jabref.gui.undo.RedoAction;
 import org.jabref.gui.undo.UndoAction;
 import org.jabref.logic.ai.AiService;
+import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.entry.BibEntryTypesManager;
@@ -63,6 +64,7 @@ public class MainToolBar extends ToolBar {
     private final BibEntryTypesManager entryTypesManager;
     private final ClipBoardManager clipBoardManager;
     private final CountingUndoManager undoManager;
+    private final JournalAbbreviationRepository abbreviationRepository;
 
     private PopOver entryFromIdPopOver;
     private PopOver progressViewPopOver;
@@ -79,7 +81,8 @@ public MainToolBar(LibraryTabContainer tabContainer,
                        TaskExecutor taskExecutor,
                        BibEntryTypesManager entryTypesManager,
                        ClipBoardManager clipBoardManager,
-                       CountingUndoManager undoManager) {
+                       CountingUndoManager undoManager,
+                       JournalAbbreviationRepository abbreviationRepository) {
         this.frame = tabContainer;
         this.pushToApplicationCommand = pushToApplicationCommand;
         this.globalSearchBar = globalSearchBar;
@@ -92,6 +95,7 @@ public MainToolBar(LibraryTabContainer tabContainer,
         this.entryTypesManager = entryTypesManager;
         this.clipBoardManager = clipBoardManager;
         this.undoManager = undoManager;
+        this.abbreviationRepository = abbreviationRepository;
 
         createToolBar();
     }
@@ -140,7 +144,7 @@ private void createToolBar() {
                 new HBox(
                         pushToApplicationButton,
                         factory.createIconButton(StandardActions.GENERATE_CITE_KEYS, new GenerateCitationKeyAction(frame::getCurrentLibraryTab, dialogService, stateManager, taskExecutor, preferences, undoManager)),
-                        factory.createIconButton(StandardActions.CLEANUP_ENTRIES, new CleanupAction(frame::getCurrentLibraryTab, preferences, dialogService, stateManager, taskExecutor, undoManager))),
+                        factory.createIconButton(StandardActions.CLEANUP_ENTRIES, new CleanupAction(frame::getCurrentLibraryTab, preferences, dialogService, stateManager, taskExecutor, undoManager, abbreviationRepository))),
 
                 new Separator(Orientation.VERTICAL),