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 buttons "Add example entry" and "Import existing PDFs" when a library is empty, making it easier for new users to get started. [#12662](https://github.com/JabRef/jabref/issues/12662)
 - In the Open/LibreOffice integration, we added the provision to modify the bibliography title and its format for CSL styles, in the "Select style" dialog. [#12663](https://github.com/JabRef/jabref/issues/12663)
 - We added a new Welcome tab which shows a welcome screen if no database is open. [#12272](https://github.com/JabRef/jabref/issues/12272)

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

@@ -37,6 +37,7 @@
 import org.jabref.logic.util.BuildInfo;
 import org.jabref.logic.util.FallbackExceptionHandler;
 import org.jabref.logic.util.HeadlessExecutorService;
+import org.jabref.logic.util.NotificationService;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.logic.util.WebViewStore;
 import org.jabref.model.entry.BibEntryTypesManager;
@@ -162,6 +163,7 @@ public void initialize() {
 
         JabRefGUI.dialogService = new JabRefDialogService(mainStage);
         Injector.setModelOrService(DialogService.class, dialogService);
+        Injector.setModelOrService(NotificationService.class, dialogService);
 
         JabRefGUI.clipBoardManager = new ClipBoardManager();
         Injector.setModelOrService(ClipBoardManager.class, clipBoardManager);

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

@@ -8,25 +8,33 @@
 <?import javafx.scene.control.TableView?>
 <?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.VBox?>
+<?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="600" 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="150.0" maxWidth="200" text="%Field"/>
+                    <TableColumn fx:id="messageColumn" prefWidth="300" text="%Message"/>
+                    <TableColumn fx:id="fixesColumn" prefWidth="200.0" maxWidth="200" text="%Fix"/>
                 </columns>
                 <columnResizePolicy>
                     <TableView fx:constant="CONSTRAINED_RESIZE_POLICY_FLEX_LAST_COLUMN"/>
                 </columnResizePolicy>
             </TableView>
             <HBox maxHeight="30" spacing="4.0">
-                <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"/>
+                <MenuButton fx:id="keyFilterButton" prefHeight="30.0" maxHeight="30.0" text="%Citation key filter"/>
+                <MenuButton fx:id="fieldFilterButton" prefHeight="30.0" maxHeight="30.0" text="%Field filter"/>
+                <MenuButton fx:id="messageFilterButton" prefHeight="30.0" maxHeight="30.0" text="%Message filter"/>
+            </HBox>
+            <HBox maxHeight="30" spacing="10.0" alignment="CENTER_RIGHT">
+                <HBox spacing="4.0">
+                    <ComboBox fx:id="entryTypeCombo" maxWidth="400"  />
+                    <Button onAction="#fixByType" prefHeight="20.0" text="%Fix by type"/>
+                </HBox>
+                <Button onAction="#fixAll" prefHeight="20.0" text="%Fix all"/>
             </HBox>
         </VBox>
     </content>

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

@@ -1,12 +1,23 @@
 package org.jabref.gui.integrity;
 
+import java.util.Arrays;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.Set;
+import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.function.Function;
 
+import javafx.application.Platform;
 import javafx.beans.property.ReadOnlyStringWrapper;
 import javafx.fxml.FXML;
+import javafx.scene.control.Button;
+import javafx.scene.control.ComboBox;
 import javafx.scene.control.ContextMenu;
+import javafx.scene.control.Label;
 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;
@@ -18,8 +29,10 @@
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.gui.util.ValueTableCellFactory;
 import org.jabref.gui.util.ViewModelTableRowFactory;
+import org.jabref.logic.integrity.IntegrityIssue;
 import org.jabref.logic.integrity.IntegrityMessage;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.util.NotificationService;
 
 import com.airhacks.afterburner.views.ViewLoader;
 import jakarta.inject.Inject;
@@ -31,20 +44,28 @@ 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;
+    @Inject private NotificationService notificationService;
 
     private final List<IntegrityMessage> messages;
     private final LibraryTab libraryTab;
+
     private IntegrityCheckDialogViewModel viewModel;
     private TableFilter<IntegrityMessage> tableFilter;
 
-    public IntegrityCheckDialog(List<IntegrityMessage> messages, LibraryTab libraryTab) {
+    private final double FIX_BUTTON_HEIGHT = 20.0;
+
+    public IntegrityCheckDialog(List<IntegrityMessage> messages,
+                                LibraryTab libraryTab) {
         this.messages = messages;
         this.libraryTab = libraryTab;
+
         this.setTitle(Localization.lang("Check integrity"));
         this.initModality(Modality.NONE);
 
@@ -76,10 +97,49 @@ private void initialize() {
                 .withOnMouseClickedEvent(this::handleRowClick)
                 .install(messagesTable);
         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);
+                setGraphic(null);
+                button.setOnAction(null);
+
+                if (empty || getTableRow() == null || getTableRow().getItem() == null) {
+                    return;
+                }
+
+                IntegrityMessage rowData = getTableRow().getItem();
+                Optional<IntegrityIssue> issue = IntegrityIssue.fromMessage(rowData);
+
+                if (issue.isEmpty()) {
+                    return;
+                }
+
+                if (issue.get().getFix().isEmpty()) {
+                    setGraphic(new Label(Localization.lang("No fix available")));
+                } else {
+                    configureButton(issue.get().getFix().get(), () -> {
+                        viewModel.fix(issue.get(), rowData);
+                        removeRow(rowData);
+                    });
+                    setGraphic(button);
+                }
+            }
+
+            private void configureButton(String text, Runnable action) {
+                button.setText(text);
+                button.setPrefHeight(FIX_BUTTON_HEIGHT);
+                button.setOnAction(event -> action.run());
+            }
+        });
+
         new ValueTableCellFactory<IntegrityMessage, String>()
                 .withText(Function.identity())
                 .withTooltip(Function.identity())
@@ -91,6 +151,8 @@ private void initialize() {
         addMessageColumnFilter(keyColumn, keyFilterButton);
         addMessageColumnFilter(fieldColumn, fieldFilterButton);
         addMessageColumnFilter(messageColumn, messageFilterButton);
+
+       messagesTable.itemsProperty().bind(viewModel.columnsListProperty());
     }
 
     private void addMessageColumnFilter(TableColumn<IntegrityMessage, String> messageColumn, MenuButton messageFilterButton) {
@@ -121,4 +183,95 @@ public void clearFilters() {
             });
         }
     }
+
+    private void updateEntryTypeCombo() {
+        Set<String> entryTypes = new HashSet<>(viewModel.issueListProperty());
+        Set<String> uniqueTexts = new HashSet<>();
+        entryTypeCombo.getItems().clear();
+
+        Arrays.stream(IntegrityIssue.values())
+              .filter(issue -> issue.getFix().isPresent())
+              .filter(issue -> entryTypes.contains(issue.getText()))
+              .filter(issue -> uniqueTexts.add(issue.getText()))
+              .forEach(issue -> entryTypeCombo.getItems().add(issue.getText()));
+
+        if (entryTypeCombo.getItems().isEmpty()) {
+            entryTypeCombo.getItems().add(Localization.lang("No fix available"));
+        }
+        entryTypeCombo.getSelectionModel().selectFirst();
+    }
+
+    public void fix(IntegrityIssue issue, IntegrityMessage message) {
+        viewModel.fix(issue, message);
+        removeRow(message);
+    }
+
+    public void removeRow(IntegrityMessage message) {
+        Platform.runLater(() ->
+                viewModel.columnsListProperty().getValue().removeIf(column ->
+                        Objects.equals(column.entry().getCitationKey().get(), message.entry().getCitationKey().get()) &&
+                                Objects.equals(column.message(), message.message())
+                )
+        );
+        Platform.runLater(() -> viewModel.issueListProperty().removeIf(issue -> Objects.equals(issue, message.message())));
+        updateEntryTypeCombo();
+    }
+
+    /**
+     * Checks if a given {@link IntegrityMessage} has a fix available.
+     *
+     * @param message the {@link IntegrityMessage} to check
+     * @return {@code true} if a fix is available, {@code false} otherwise
+     */
+    private boolean hasFix(IntegrityMessage message) {
+        return message != null && message.field() != null && IntegrityIssue.fromMessage(message)
+                                                                           .map(issue -> issue.getFix().isPresent())
+                                                                           .orElse(false);
+    }
+
+    /**
+     * Attempts to fix all {@link IntegrityMessage} objects of the selected type.
+     * If fixes are available, they are applied, and the fixed messages are removed.
+     * A notification is shown to indicate success or failure.
+     */
+    @FXML
+    private void fixByType() {
+        AtomicBoolean fixed = new AtomicBoolean(false);
+
+        String selectedType = entryTypeCombo.getSelectionModel().getSelectedItem();
+        Optional<IntegrityIssue> selectedIssue = Arrays.stream(IntegrityIssue.values())
+                                                       .filter(issue -> issue.getText().equals(selectedType))
+                                                       .findFirst();
+
+        selectedIssue.ifPresent(issue -> {
+            messagesTable.getItems().stream()
+                         // Filter messages matching the selected issue type and have a fix
+                         .filter(message -> message.message().equals(issue.getText()) && hasFix(message))
+                         .forEach(message -> {
+                             fix(issue, message);
+                             fixed.set(true);
+                         });
+        });
+
+        updateEntryTypeCombo();
+
+        if (fixed.get()) {
+            notificationService.notify(Localization.lang("Fixed successfully."));
+        } else {
+            notificationService.notify(Localization.lang("No fixes available."));
+        }
+    }
+
+    /**
+     * Attempts to fix all {@link IntegrityMessage} objects that have a fix available.
+     * Messages with applicable fixes are processed, and the corresponding UI elements are updated.
+     */
+    @FXML
+    private void fixAll() {
+        messagesTable.getItems().stream()
+                .filter(this::hasFix)   // Filter all messages that have a fix
+                .forEach(message -> IntegrityIssue.fromMessage(message).ifPresent(issue -> fix(issue, message)));
+
+        updateEntryTypeCombo();
+    }
 }

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

@@ -1,22 +1,47 @@
 package org.jabref.gui.integrity;
 
 import java.util.List;
+import java.util.stream.Collectors;
 
+import javafx.beans.property.ListProperty;
+import javafx.beans.property.SimpleListProperty;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 
 import org.jabref.gui.AbstractViewModel;
+import org.jabref.logic.integrity.IntegrityIssue;
 import org.jabref.logic.integrity.IntegrityMessage;
 
 public class IntegrityCheckDialogViewModel extends AbstractViewModel {
 
+    private final ListProperty<IntegrityMessage> columnsListProperty;
+    private final ObservableList<String> issuesListProperty;
     private final ObservableList<IntegrityMessage> messages;
 
     public IntegrityCheckDialogViewModel(List<IntegrityMessage> messages) {
         this.messages = FXCollections.observableArrayList(messages);
+
+        List<String> issuesList = messages.stream()
+                                          .map(IntegrityMessage::message)
+                                          .collect(Collectors.toList());
+        this.issuesListProperty = FXCollections.observableArrayList(issuesList);
+
+        this.columnsListProperty = new SimpleListProperty<>(FXCollections.observableArrayList(messages));
+    }
+
+    public ObservableList<String> issueListProperty() {
+        return issuesListProperty;
+    }
+
+    public ListProperty<IntegrityMessage> columnsListProperty() {
+        return this.columnsListProperty;
     }
 
     public ObservableList<IntegrityMessage> getMessages() {
         return messages;
     }
+
+    public void fix(IntegrityIssue issue, IntegrityMessage message) {
+        // fixes
+    }
 }

src/main/java/org/jabref/logic/integrity/ASCIICharacterChecker.java

@@ -4,7 +4,6 @@
 import java.util.List;
 import java.util.Map;
 
-import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.Field;
 
@@ -21,7 +20,7 @@ public List<IntegrityMessage> check(BibEntry entry) {
         for (Map.Entry<Field, String> field : entry.getFieldMap().entrySet()) {
             boolean asciiOnly = CharMatcher.ascii().matchesAllOf(field.getValue());
             if (!asciiOnly) {
-                results.add(new IntegrityMessage(Localization.lang("Non-ASCII encoded character found"), entry,
+                results.add(new IntegrityMessage(IntegrityIssue.NON_ASCII_ENCODED_CHARACTER_FOUND.getText(), entry,
                         field.getKey()));
             }
         }

src/main/java/org/jabref/logic/integrity/AbbreviationChecker.java

@@ -6,7 +6,6 @@
 import java.util.Set;
 
 import org.jabref.logic.journals.JournalAbbreviationRepository;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.FieldFactory;
@@ -26,7 +25,7 @@ public List<IntegrityMessage> check(BibEntry entry) {
         for (Field field : fields) {
             Optional<String> value = entry.getFieldLatexFree(field);
             value.filter(abbreviationRepository::isAbbreviatedName)
-                 .ifPresent(val -> messages.add(new IntegrityMessage(Localization.lang("abbreviation detected"), entry, field)));
+                 .ifPresent(val -> messages.add(new IntegrityMessage(IntegrityIssue.ABBREVIATION_DETECTED.getText(), entry, field)));
         }
         return messages;
     }

src/main/java/org/jabref/logic/integrity/BibStringChecker.java

@@ -7,7 +7,6 @@
 import java.util.regex.Pattern;
 
 import org.jabref.logic.bibtex.FieldWriter;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.FieldFactory;
@@ -35,7 +34,7 @@ public List<IntegrityMessage> check(BibEntry entry) {
                 }
                 if ((hashCount & 1) == 1) { // Check if odd
                     // # is FieldWriter.BIBTEX_STRING_START_END_SYMBOL
-                    results.add(new IntegrityMessage(Localization.lang("odd number of unescaped '#'"), entry,
+                    results.add(new IntegrityMessage(IntegrityIssue.ODD_NUMBER_OF_UNESCAPED.getText(), entry,
                             field.getKey()));
                 }
             }