Add support for loading .blg warnings in Integrity Check Dialog

CHANGELOG.md

@@ -27,6 +27,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a feature for enabling drag-and-drop of files into groups  [#12540](https://github.com/JabRef/jabref/issues/12540)
 - We added support for reordering keywords via drag and drop, automatic alphabetical ordering, and improved pasting and editing functionalities in the keyword editor. [#10984](https://github.com/JabRef/jabref/issues/10984)
 - We added a new functionality where author names having multiple spaces in-between will be considered as separate user block as it does for " and ". [#12701](https://github.com/JabRef/jabref/issues/12701)
+- We added support for loading and displaying BibTeX .blg warnings in the Check integrity dialog, with custom path selection and metadata persistence. [#11998](https://github.com/JabRef/jabref/issues/11998)
 - We added an option to choose whether to open the file explorer in the files directory or in the last opened directory when attaching files. [#12554](https://github.com/JabRef/jabref/issues/12554)
 - We enhanced support for parsing XMP metadata from PDF files. [#12829](https://github.com/JabRef/jabref/issues/12829)
 - We added a "Preview" header in the JStyles tab in the "Select style" dialog, to make it consistent with the CSL styles tab. [#12838](https://github.com/JabRef/jabref/pull/12838)

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

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.control.TextField?>
+<?import javafx.scene.layout.HBox?>
+
+<HBox xmlns="http://javafx.com/javafx"
+      xmlns:fx="http://javafx.com/fxml"
+      spacing="10"
+      alignment="CENTER_LEFT"
+      fx:controller="org.jabref.gui.integrity.BibLogSettingsPane"
+      fx:id="bibLogSettingsPane">
+    <Label text="BibTeX log (.blg) file:"/>
+    <TextField fx:id="pathField" prefWidth="300"/>
+    <Button onAction="#onBrowse" text="Browse..."/>
+    <Button onAction="#onReset" text="Reset"/>
+</HBox>

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

@@ -0,0 +1,88 @@
+package org.jabref.gui.integrity;
+
+import java.nio.file.Path;
+
+import javafx.collections.ObservableList;
+import javafx.fxml.FXML;
+import javafx.scene.control.TextField;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.util.FileDialogConfiguration;
+import org.jabref.logic.JabRefException;
+import org.jabref.logic.integrity.IntegrityMessage;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.util.StandardFileType;
+import org.jabref.model.database.BibDatabaseContext;
+
+import jakarta.inject.Inject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Controller for the .blg file settings panel.
+ *
+ * Binds the path text field to the ViewModel,
+ * and handles browse/reset button actions.
+ */
+public class BibLogSettingsPane {
+    private static final Logger LOGGER = LoggerFactory.getLogger(BibLogSettingsPane.class);
+    @FXML
+    private TextField pathField;
+    private BibLogSettingsViewModel viewModel;
+    @Inject private DialogService dialogService;
+    private Runnable onBlgPathChanged;
+
+    public void initializeViewModel(BibDatabaseContext context, Runnable onBlgPathChanged) throws JabRefException {
+        this.onBlgPathChanged = onBlgPathChanged;
+        this.viewModel = new BibLogSettingsViewModel(context.getMetaData(), context.getDatabasePath());
+        pathField.textProperty().bindBidirectional(viewModel.pathProperty());
+        viewModel.getBlgWarnings(context);
+    }
+
+    public ObservableList<IntegrityMessage> getBlgWarnings() {
+        return viewModel.getBlgWarningsObservable();
+    }
+
+    public void refreshWarnings(BibDatabaseContext context) throws JabRefException {
+        viewModel.getBlgWarnings(context);
+    }
+
+    @FXML
+    private void onBrowse() {
+        FileDialogConfiguration fileDialogConfiguration = createBlgFileDialogConfig();
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(path -> {
+            viewModel.setBlgFilePath(path);
+            notifyPathChanged();
+        });
+    }
+
+    @FXML
+    private void onReset() {
+        viewModel.resetBlgFilePath();
+        notifyPathChanged();
+    }
+
+    private void notifyPathChanged() {
+        if (onBlgPathChanged != null) {
+            onBlgPathChanged.run();
+        }
+    }
+
+    public BibLogSettingsViewModel getViewModel() {
+        return viewModel;
+    }
+
+    private FileDialogConfiguration createBlgFileDialogConfig() {
+        Path initialDir = viewModel.getInitialDirectory();
+        FileDialogConfiguration config = new FileDialogConfiguration.Builder()
+                .addExtensionFilter(Localization.lang("BibTeX log files"), StandardFileType.BLG)
+                .withDefaultExtension(Localization.lang("BibTeX log files"), StandardFileType.BLG)
+                .withInitialDirectory(viewModel.getInitialDirectory())
+                .build();
+        return config;
+    }
+
+    public boolean wasBlgFileManuallySelected() {
+        return viewModel.wasBlgFileManuallySelected();
+    }
+}

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

@@ -0,0 +1,129 @@
+package org.jabref.gui.integrity;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.Optional;
+
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+
+import org.jabref.gui.AbstractViewModel;
+import org.jabref.logic.JabRefException;
+import org.jabref.logic.biblog.BibLogPathResolver;
+import org.jabref.logic.biblog.BibWarningToIntegrityMessageConverter;
+import org.jabref.logic.biblog.BibtexLogParser;
+import org.jabref.logic.integrity.IntegrityMessage;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.biblog.BibWarning;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.metadata.MetaData;
+
+/// 1. Connects MetaData with the view.
+/// 2. Wraps .blg warnings as IntegrityMessages.
+/// 3. Supports file browsing and reset actions.
+public class BibLogSettingsViewModel extends AbstractViewModel {
+    private final ObservableList<IntegrityMessage> blgWarnings = FXCollections.observableArrayList();
+    private final StringProperty path = new SimpleStringProperty("");
+    private final MetaData metaData;
+    private final Optional<Path> bibPath;
+    private final String user;
+    private Optional<Path> lastResolvedBlgPath = Optional.empty();
+    private boolean userManuallySelectedBlgFile = false;
+
+    public BibLogSettingsViewModel(MetaData metaData, Optional<Path> bibPath) {
+        this.metaData = metaData;
+        this.bibPath = bibPath;
+        this.user = System.getProperty("user.name");
+
+        BibLogPathResolver.resolve(metaData, bibPath, user)
+                          .ifPresent(resolvedPath -> {
+                              this.path.set(resolvedPath.toString());
+                              if (metaData.getBlgFilePath(user).isEmpty()) {
+                                  metaData.setBlgFilePath(user, resolvedPath);
+                                  this.lastResolvedBlgPath = Optional.of(resolvedPath);
+                              }
+                          });
+    }
+
+    /**
+     * Parses the .blg file (if it exists) into the observable list.
+     *
+     * @param databaseContext the current database context used to resolve citation keys in warnings.
+     * @return An Optional containing the list of integrity messages if the file exists and can be parsed,
+     *         or an empty Optional if the file does not exist.
+     * @throws JabRefException if the .blg file cannot be parsed or read
+     */
+    public Optional<List<IntegrityMessage>> getBlgWarnings(BibDatabaseContext databaseContext) throws JabRefException {
+        Optional<Path> resolved = getResolvedBlgPath();
+        if (resolved.isEmpty()) {
+            blgWarnings.clear();
+            return Optional.empty();
+        }
+
+        Path path = resolved.get();
+
+        this.lastResolvedBlgPath = Optional.of(path);
+        try {
+            BibtexLogParser parser = new BibtexLogParser();
+            List<BibWarning> warnings = parser.parseBiblog(path);
+            List<IntegrityMessage> newWarnings = BibWarningToIntegrityMessageConverter.convert(warnings, databaseContext);
+            blgWarnings.setAll(newWarnings);
+            return Optional.of(newWarnings);
+        } catch (IOException e) {
+            blgWarnings.clear();
+            throw new JabRefException(
+                    "Failed to parse .blg file",
+                    Localization.lang("Could not read BibTeX log file. Please check the file path and try again."),
+                    e
+            );
+        }
+    }
+
+    public ObservableList<IntegrityMessage> getBlgWarningsObservable() {
+        return blgWarnings;
+    }
+
+    public StringProperty pathProperty() {
+        return path;
+    }
+
+    public void setBlgFilePath(Path path) {
+        metaData.setBlgFilePath(user, path);
+        this.path.set(path.toString());
+        this.lastResolvedBlgPath = Optional.of(path);
+        this.userManuallySelectedBlgFile = true;
+    }
+
+    public void resetBlgFilePath() {
+        metaData.clearBlgFilePath(user);
+        userManuallySelectedBlgFile = false;
+        Optional<Path> resolved = BibLogPathResolver.resolve(metaData, bibPath, user);
+        if (resolved.isEmpty()) {
+            path.set("");
+            lastResolvedBlgPath = Optional.empty();
+            return;
+        }
+
+        Path resolvedPath = resolved.get();
+        path.set(resolvedPath.toString());
+        lastResolvedBlgPath = Optional.of(resolvedPath);
+    }
+
+    public Optional<Path> getResolvedBlgPath() {
+        return BibLogPathResolver.resolve(metaData, bibPath, user)
+                                 .filter(Files::exists);
+    }
+
+    public Path getInitialDirectory() {
+        return bibPath.flatMap(path -> Optional.ofNullable(path.getParent()))
+                      .orElse(Path.of(System.getProperty("user.home")));
+    }
+
+    public boolean wasBlgFileManuallySelected() {
+        return userManuallySelectedBlgFile;
+    }
+}

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

@@ -69,7 +69,6 @@ protected List<IntegrityMessage> call() {
                     result.addAll(check.checkEntry(entry));
                     updateProgress(i, entries.size());
                 }
-
                 return result;
             }
         };
@@ -78,7 +77,7 @@ 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.get(), dialogService));
             }
         });
         task.setOnFailed(event -> dialogService.showErrorDialogAndWait("Integrity check failed.", task.getException()));

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

@@ -3,15 +3,17 @@
 <?import javafx.scene.control.Button?>
 <?import javafx.scene.control.ButtonType?>
 <?import javafx.scene.control.DialogPane?>
+<?import javafx.scene.control.Label?>
 <?import javafx.scene.control.MenuButton?>
 <?import javafx.scene.control.TableColumn?>
 <?import javafx.scene.control.TableView?>
+<?import javafx.scene.control.TextField?>
 <?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.VBox?>
 <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">
+        <VBox fx:id="dialogVBox" spacing="4.0">
             <TableView fx:id="messagesTable" prefHeight="550" prefWidth="700.0" VBox.vgrow="ALWAYS" HBox.hgrow="ALWAYS">
                 <columns>
                     <TableColumn fx:id="keyColumn" prefWidth="150.0" maxWidth="200"  text="%Citation key"/>