Add fix options for integrity issues

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added a feature to fix integrity issues one at a time or similar issues by selecting a type, or to fix all at once. [#11419](https://github.com/JabRef/jabref/issues/11419)
 - We added a new CLI that supports txt, csv, and console-based output for consistency in BibTeX entries. [#11984](https://github.com/JabRef/jabref/issues/11984)
 - We added a new dialog for bibliography consistency check. [#11950](https://github.com/JabRef/jabref/issues/11950)
 - We added a feature for copying entries to libraries, available via the context menu, with an option to include cross-references. [#12374](https://github.com/JabRef/jabref/pull/12374)

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

@@ -250,7 +250,7 @@ private void createMenu() {
         quality.getItems().addAll(
                 factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(frame::getCurrentLibraryTab, dialogService, stateManager, preferences, entryTypesManager, taskExecutor)),
                 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_INTEGRITY, new IntegrityCheckAction(frame::getCurrentLibraryTab, preferences, dialogService, stateManager, (UiTaskExecutor) taskExecutor, preferences, undoManager, 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)),
 

src/main/java/org/jabref/gui/integrity/IntegrityCheckAction.java

@@ -4,6 +4,8 @@
 import java.util.List;
 import java.util.function.Supplier;
 
+import javax.swing.undo.UndoManager;
+
 import javafx.collections.ObservableList;
 import javafx.concurrent.Task;
 
@@ -17,6 +19,7 @@
 import org.jabref.logic.integrity.IntegrityMessage;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 
@@ -29,19 +32,25 @@ public class IntegrityCheckAction extends SimpleCommand {
     private final Supplier<LibraryTab> tabSupplier;
     private final GuiPreferences preferences;
     private final StateManager stateManager;
+    private final CliPreferences cliPreferences;
+    private final UndoManager undoManager;
     private final JournalAbbreviationRepository abbreviationRepository;
 
     public IntegrityCheckAction(Supplier<LibraryTab> tabSupplier,
                                 GuiPreferences preferences,
                                 DialogService dialogService,
                                 StateManager stateManager,
                                 UiTaskExecutor taskExecutor,
+                                CliPreferences cliPreferences,
+                                UndoManager undoManager,
                                 JournalAbbreviationRepository abbreviationRepository) {
         this.tabSupplier = tabSupplier;
         this.stateManager = stateManager;
         this.taskExecutor = taskExecutor;
         this.preferences = preferences;
         this.dialogService = dialogService;
+        this.cliPreferences = cliPreferences;
+        this.undoManager = undoManager;
         this.abbreviationRepository = abbreviationRepository;
         this.executable.bind(needsDatabase(this.stateManager));
     }
@@ -78,7 +87,7 @@ protected List<IntegrityMessage> call() {
             if (messages.isEmpty()) {
                 dialogService.notify(Localization.lang("No problems found."));
             } else {
-                dialogService.showCustomDialogAndWait(new IntegrityCheckDialog(messages, tabSupplier.get()));
+                dialogService.showCustomDialogAndWait(new IntegrityCheckDialog(messages, tabSupplier, dialogService, stateManager, taskExecutor, cliPreferences, undoManager));
             }
         });
         task.setOnFailed(event -> dialogService.showErrorDialogAndWait("Integrity check failed.", task.getException()));

src/main/java/org/jabref/gui/integrity/IntegrityCheckDialog.fxml

@@ -8,15 +8,18 @@
 <?import javafx.scene.control.TableView?>
 <?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.VBox?>
+<?import javafx.scene.layout.Region?>
+<?import javafx.scene.control.ComboBox?>
 <DialogPane xmlns:fx="http://javafx.com/fxml/1" prefHeight="600.0" prefWidth="700.0"
             xmlns="http://javafx.com/javafx/8.0.121" fx:controller="org.jabref.gui.integrity.IntegrityCheckDialog">
     <content>
-        <VBox spacing="4.0">
-            <TableView fx:id="messagesTable" prefHeight="550" prefWidth="700.0" VBox.vgrow="ALWAYS" HBox.hgrow="ALWAYS">
+        <VBox spacing="10.0">
+            <TableView fx:id="messagesTable" prefHeight="550" prefWidth="750.0" VBox.vgrow="ALWAYS" HBox.hgrow="ALWAYS">
                 <columns>
                     <TableColumn fx:id="keyColumn" prefWidth="150.0" maxWidth="200"  text="%Citation key"/>
-                    <TableColumn fx:id="fieldColumn" prefWidth="110.0" maxWidth="200" text="%Field"/>
-                    <TableColumn fx:id="messageColumn" prefWidth="400" text="%Message"/>
+                    <TableColumn fx:id="fieldColumn" prefWidth="100.0" maxWidth="200" text="%Field"/>
+                    <TableColumn fx:id="messageColumn" prefWidth="300" text="%Message"/>
+                    <TableColumn fx:id="fixesColumn" prefWidth="200.0" maxWidth="200" text="%Fixes"/>
                 </columns>
                 <columnResizePolicy>
                     <TableView fx:constant="CONSTRAINED_RESIZE_POLICY_FLEX_LAST_COLUMN"/>
@@ -26,7 +29,12 @@
                 <MenuButton fx:id="keyFilterButton" prefHeight="30.0" maxHeight="30.0" text="%Citation key filters"/>
                 <MenuButton fx:id="fieldFilterButton" prefHeight="30.0" maxHeight="30.0" text="%Field filters"/>
                 <MenuButton fx:id="messageFilterButton" prefHeight="30.0" maxHeight="30.0" text="%Message filters"/>
-                <Button onAction="#clearFilters" text="%Clear filters"/>
+            </HBox>
+            <HBox maxHeight="30" spacing="4.0" alignment="CENTER">
+                <Button prefHeight="20.0" text="%Fix all"/>
+                <Region HBox.hgrow="ALWAYS" />
+                <ComboBox fx:id="entryTypeCombo" maxWidth="400"  />
+                <Button onAction="#fixByType" alignment="CENTER_RIGHT" prefHeight="20.0" text="%Fix by type"/>
             </HBox>
         </VBox>
     </content>

src/main/java/org/jabref/gui/integrity/IntegrityCheckDialog.java

@@ -1,24 +1,40 @@
 package org.jabref.gui.integrity;
 
+import java.util.Arrays;
 import java.util.List;
+import java.util.Optional;
+import java.util.Set;
 import java.util.function.Function;
+import java.util.function.Supplier;
+
+import javax.swing.undo.UndoManager;
 
 import javafx.beans.property.ReadOnlyStringWrapper;
+import javafx.collections.FXCollections;
 import javafx.collections.ListChangeListener;
+import javafx.collections.ObservableList;
 import javafx.fxml.FXML;
+import javafx.scene.control.Button;
+import javafx.scene.control.ComboBox;
 import javafx.scene.control.ContextMenu;
 import javafx.scene.control.MenuButton;
+import javafx.scene.control.TableCell;
 import javafx.scene.control.TableColumn;
 import javafx.scene.control.TableView;
 import javafx.scene.input.MouseButton;
 import javafx.stage.Modality;
 
+import org.jabref.gui.DialogService;
 import org.jabref.gui.LibraryTab;
+import org.jabref.gui.StateManager;
 import org.jabref.gui.theme.ThemeManager;
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.gui.util.ValueTableCellFactory;
 import org.jabref.logic.integrity.IntegrityMessage;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.preferences.CliPreferences;
+import org.jabref.logic.util.TaskExecutor;
+import org.jabref.model.entry.field.Field;
 
 import com.airhacks.afterburner.views.ViewLoader;
 import jakarta.inject.Inject;
@@ -30,20 +46,40 @@ public class IntegrityCheckDialog extends BaseDialog<Void> {
     @FXML private TableColumn<IntegrityMessage, String> keyColumn;
     @FXML private TableColumn<IntegrityMessage, String> fieldColumn;
     @FXML private TableColumn<IntegrityMessage, String> messageColumn;
+    @FXML private TableColumn<IntegrityMessage, String> fixesColumn;
     @FXML private MenuButton keyFilterButton;
     @FXML private MenuButton fieldFilterButton;
     @FXML private MenuButton messageFilterButton;
+    @FXML private ComboBox<String> entryTypeCombo;
 
     @Inject private ThemeManager themeManager;
 
     private final List<IntegrityMessage> messages;
-    private final LibraryTab libraryTab;
+    private final Supplier<LibraryTab> tabSupplier;
+    private final DialogService dialogService;
+    private final StateManager stateManager;
+    private final TaskExecutor taskExecutor;
+    private final CliPreferences preferences;
+    private final UndoManager undoManager;
+
     private IntegrityCheckDialogViewModel viewModel;
     private TableFilter<IntegrityMessage> tableFilter;
 
-    public IntegrityCheckDialog(List<IntegrityMessage> messages, LibraryTab libraryTab) {
+    public IntegrityCheckDialog(List<IntegrityMessage> messages,
+                                Supplier<LibraryTab> tabSupplier,
+                                DialogService dialogService,
+                                StateManager stateManager,
+                                TaskExecutor taskExecutor,
+                                CliPreferences preferences,
+                                UndoManager undoManager) {
         this.messages = messages;
-        this.libraryTab = libraryTab;
+        this.tabSupplier = tabSupplier;
+        this.dialogService = dialogService;
+        this.stateManager = stateManager;
+        this.taskExecutor = taskExecutor;
+        this.preferences = preferences;
+        this.undoManager = undoManager;
+
         this.setTitle(Localization.lang("Check integrity"));
         this.initModality(Modality.NONE);
 
@@ -57,7 +93,7 @@ public IntegrityCheckDialog(List<IntegrityMessage> messages, LibraryTab libraryT
     private void onSelectionChanged(ListChangeListener.Change<? extends IntegrityMessage> change) {
         if (change.next()) {
             change.getAddedSubList().stream().findFirst().ifPresent(message ->
-                    libraryTab.editEntryAndFocusField(message.entry(), message.field()));
+                    tabSupplier.get().editEntryAndFocusField(message.entry(), message.field()));
         }
     }
 
@@ -67,14 +103,49 @@ public IntegrityCheckDialogViewModel getViewModel() {
 
     @FXML
     private void initialize() {
-        viewModel = new IntegrityCheckDialogViewModel(messages);
+        viewModel = new IntegrityCheckDialogViewModel(messages, tabSupplier, dialogService, stateManager, taskExecutor, preferences, undoManager);
 
         messagesTable.getSelectionModel().getSelectedItems().addListener(this::onSelectionChanged);
         messagesTable.setItems(viewModel.getMessages());
+        updateEntryTypeCombo();
         keyColumn.setCellValueFactory(row -> new ReadOnlyStringWrapper(row.getValue().entry().getCitationKey().orElse("")));
         fieldColumn.setCellValueFactory(row -> new ReadOnlyStringWrapper(row.getValue().field().getDisplayName()));
         messageColumn.setCellValueFactory(row -> new ReadOnlyStringWrapper(row.getValue().message()));
 
+        fixesColumn.setCellFactory(row -> new TableCell<>() {
+            private final Button button = new Button();
+
+            @Override
+            protected void updateItem(String item, boolean empty) {
+                super.updateItem(item, empty);
+                if (empty || getTableRow() == null || getTableRow().getItem() == null) {
+                    setGraphic(null);
+                    return;
+                }
+                IntegrityMessage rowData = getTableRow().getItem();
+                configureAction(rowData);
+            }
+
+            private void configureAction(IntegrityMessage message) {
+                Optional<IntegrityIssue> issue = IntegrityIssue.fromField(message.field());
+                if (issue.isPresent() && issue.get().getFix() != null) {
+                    configureButton(issue.get().getFix(), () -> {
+                        viewModel.fix(issue.get(), message);
+                        removeRowFromTable(message);
+                    });
+                    setGraphic(button);
+                    return;
+                }
+                setGraphic(null);
+            }
+
+            private void configureButton(String text, Runnable action) {
+                button.setText(text);
+                button.setPrefHeight(20.0);
+                button.setOnAction(event -> action.run());
+            }
+        });
+
         new ValueTableCellFactory<IntegrityMessage, String>()
                 .withText(Function.identity())
                 .withTooltip(Function.identity())
@@ -116,4 +187,41 @@ public void clearFilters() {
             });
         }
     }
+
+    private void removeRowFromTable(IntegrityMessage message) {
+        ObservableList<IntegrityMessage> mutableMessages = FXCollections.observableArrayList(messagesTable.getItems());
+        mutableMessages.remove(message);
+        messagesTable.setItems(mutableMessages);
+    }
+
+    private void updateEntryTypeCombo() {
+        Set<Field> entryTypes = viewModel.getEntryTypes();
+        entryTypeCombo.getItems().clear();
+
+        Arrays.stream(IntegrityIssue.values())
+              .filter(issue -> entryTypes.contains(issue.getField()))
+              .forEach(issue -> entryTypeCombo.getItems().add(issue.getText()));
+
+        if (!entryTypeCombo.getItems().isEmpty()) {
+            entryTypeCombo.getSelectionModel().selectFirst();
+        }
+    }
+
+    @FXML
+    private void fixByType() {
+        String selectedType = entryTypeCombo.getSelectionModel().getSelectedItem();
+        Optional<IntegrityIssue> selectedIssue = Arrays.stream(IntegrityIssue.values())
+                                                       .filter(issue -> issue.getText().equals(selectedType))
+                                                       .findFirst();
+        if (selectedIssue.isPresent()) {
+            for (IntegrityMessage message : messages) {
+                if (message.field().equals(selectedIssue.get().getField())) {
+                    viewModel.fix(selectedIssue.get(), message);
+                    removeRowFromTable(message);
+                    viewModel.removeFromEntryTypes(message.field().getDisplayName());
+                }
+            }
+        }
+        updateEntryTypeCombo();
+    }
 }