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Add support for loading .blg warnings in Integrity Check Dialog (#12866)
* Add .blg warning support in IntegrityCheckDialog with Browse/Reset and path resolution * Apply review suggestions * Apply changes based on review feedback * add missing localization key for BibTeX log files * apply OpenRewrite suggestions * Fix preferences and Reset logic for .blg file settings * Apply review suggestions * Apply review suggestions * Fix failing unit tests * Apply review suggestions * Apply review suggestions and improve separation of concerns for blg warning panel * Fix localization key + apply bot suggestions * Apply bot suggestions on fast-fail, fix Rewrite and test failures * Remove star imports * Remove unnecessary @nonnull annotations and fix misleading UI warning logic * Apply review suggestions: simplify test and update Javadoc * Revert unintended submodule change to csl-styles
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‎CHANGELOG.md

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@@ -27,6 +27,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
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- We added a feature for enabling drag-and-drop of files into groups [#12540](https://github.com/JabRef/jabref/issues/12540)
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- 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)
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- 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)
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- 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)
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- 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)
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- We enhanced support for parsing XMP metadata from PDF files. [#12829](https://github.com/JabRef/jabref/issues/12829)
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- 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

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

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

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

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

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

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

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result.addAll(check.checkEntry(entry));
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updateProgress(i, entries.size());
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}
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return result;
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}
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};
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if (messages.isEmpty()) {
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dialogService.notify(Localization.lang("No problems found."));
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} else {
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dialogService.showCustomDialogAndWait(new IntegrityCheckDialog(messages, tabSupplier.get()));
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dialogService.showCustomDialogAndWait(new IntegrityCheckDialog(messages, tabSupplier.get(), dialogService));
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}
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});
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task.setOnFailed(event -> dialogService.showErrorDialogAndWait("Integrity check failed.", task.getException()));

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

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<?import javafx.scene.control.Button?>
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<?import javafx.scene.control.ButtonType?>
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<?import javafx.scene.control.DialogPane?>
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<?import javafx.scene.control.Label?>
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<?import javafx.scene.control.MenuButton?>
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<?import javafx.scene.control.TableColumn?>
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<?import javafx.scene.control.TableView?>
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<?import javafx.scene.control.TextField?>
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<?import javafx.scene.layout.HBox?>
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<?import javafx.scene.layout.VBox?>
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<DialogPane xmlns:fx="http://javafx.com/fxml/1" prefHeight="600.0" prefWidth="700.0"
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xmlns="http://javafx.com/javafx/8.0.121" fx:controller="org.jabref.gui.integrity.IntegrityCheckDialog">
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<content>
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<VBox spacing="4.0">
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<VBox fx:id="dialogVBox" spacing="4.0">
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<TableView fx:id="messagesTable" prefHeight="550" prefWidth="700.0" VBox.vgrow="ALWAYS" HBox.hgrow="ALWAYS">
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<columns>
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<TableColumn fx:id="keyColumn" prefWidth="150.0" maxWidth="200" text="%Citation key"/>

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