GUI for consistency check

CHANGELOG.md

@@ -11,6 +11,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added a GUI for bibliography consistency check. [#11950](https://github.com/JabRef/jabref/pull/12433)
+
 ### Changed
 
 - We improved the offline parsing of BibTeX data from PDF-documents. [#12278](https://github.com/JabRef/jabref/issues/12278)

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

@@ -141,6 +141,7 @@ public enum StandardActions implements Action {
     MERGE_ENTRIES(Localization.lang("Merge entries"), IconTheme.JabRefIcons.MERGE_ENTRIES, KeyBinding.MERGE_ENTRIES),
     RESOLVE_DUPLICATE_KEYS(Localization.lang("Resolve duplicate citation keys"), Localization.lang("Find and remove duplicate citation keys"), KeyBinding.RESOLVE_DUPLICATE_CITATION_KEYS),
     CHECK_INTEGRITY(Localization.lang("Check integrity"), KeyBinding.CHECK_INTEGRITY),
+    CHECK_CONSISTENCY(Localization.lang("Check consistency"), KeyBinding.CHECK_CONSISTENCY),
     FIND_UNLINKED_FILES(Localization.lang("Search for unlinked local files"), IconTheme.JabRefIcons.SEARCH, KeyBinding.FIND_UNLINKED_FILES),
     AUTO_LINK_FILES(Localization.lang("Automatically set file links"), IconTheme.JabRefIcons.AUTO_FILE_LINK, KeyBinding.AUTOMATICALLY_LINK_FILES),
     LOOKUP_DOC_IDENTIFIER(Localization.lang("Search document identifier online")),

src/main/java/org/jabref/gui/consistency/ConsistencyCheckAction.java

@@ -0,0 +1,35 @@
+package org.jabref.gui.consistency;
+
+import java.util.List;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.preferences.GuiPreferences;
+import org.jabref.logic.quality.consistency.BibliographyConsistencyCheck;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+
+public class ConsistencyCheckAction extends SimpleCommand {
+
+    private final DialogService dialogService;
+    private final StateManager stateManager;
+    private final GuiPreferences preferences;
+
+    public ConsistencyCheckAction(DialogService dialogService, StateManager stateManager, GuiPreferences preferences) {
+        this.dialogService = dialogService;
+        this.stateManager = stateManager;
+        this.preferences = preferences;
+    }
+
+    @Override
+    public void execute() {
+        BibDatabaseContext databaseContext = stateManager.getActiveDatabase().orElseThrow(() -> new NullPointerException("Database null"));
+        List<BibEntry> entries = databaseContext.getDatabase().getEntries();
+
+        BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
+        BibliographyConsistencyCheck.Result result = consistencyCheck.check(entries);
+
+        dialogService.showCustomDialogAndWait(new ConsistencyCheckDialog(result, dialogService, preferences));
+    }
+}

src/main/java/org/jabref/gui/consistency/ConsistencyCheckDialog.fxml

@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.ButtonType?>
+<?import javafx.scene.control.ComboBox?>
+<?import javafx.scene.control.DialogPane?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.control.TableView?>
+<?import javafx.scene.control.Tooltip?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
+<DialogPane xmlns:fx="http://javafx.com/fxml/1" prefHeight="600.0" prefWidth="1200.0"
+            xmlns="http://javafx.com/javafx/8.0.121" fx:controller="org.jabref.gui.consistency.ConsistencyCheckDialog">
+    <content>
+        <VBox spacing="10.0">
+            <TableView fx:id="tableView" prefHeight="550" prefWidth="1200.0" VBox.vgrow="ALWAYS" HBox.hgrow="ALWAYS">
+                <columns>
+                </columns>
+                <columnResizePolicy>
+                    <TableView fx:constant="CONSTRAINED_RESIZE_POLICY_FLEX_LAST_COLUMN"/>
+                </columnResizePolicy>
+            </TableView>
+            <HBox spacing="4.0" alignment="CENTER">
+                <Label text="%Entry type"/>
+                <ComboBox fx:id="entryTypeCombo" maxWidth="Infinity" HBox.hgrow="ALWAYS" />
+                <Button onAction="#selectEntry" text="%Select">
+                    <tooltip>
+                        <Tooltip text="%Shows results for the selected entry type."/>
+                    </tooltip>
+                </Button>
+            </HBox>
+            <HBox spacing="4.0">
+                <Button onAction="#exportAsCsv" text="%Export as csv file" />
+                <Button onAction="#exportAsTxt" text="%Export as txt file" alignment="CENTER_LEFT" />
+            </HBox>
+        </VBox>
+    </content>
+    <ButtonType fx:constant="CLOSE"/>
+</DialogPane>

src/main/java/org/jabref/gui/consistency/ConsistencyCheckDialog.java

@@ -0,0 +1,81 @@
+package org.jabref.gui.consistency;
+
+import java.util.Collection;
+
+import javafx.fxml.FXML;
+import javafx.scene.control.ComboBox;
+import javafx.scene.control.TableColumn;
+import javafx.scene.control.TableView;
+import javafx.scene.control.cell.PropertyValueFactory;
+import javafx.stage.Modality;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.preferences.GuiPreferences;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.quality.consistency.BibliographyConsistencyCheck;
+import org.jabref.logic.quality.consistency.ConsistencyMessage;
+import org.jabref.model.entry.field.Field;
+
+import com.airhacks.afterburner.views.ViewLoader;
+
+public class ConsistencyCheckDialog extends BaseDialog<Void> {
+
+    @FXML private TableView<ConsistencyMessage> tableView;
+    @FXML private ComboBox<String> entryTypeCombo;
+
+    private final BibliographyConsistencyCheck.Result result;
+    private final DialogService dialogService;
+    private final GuiPreferences preferences;
+    private String selectedEntry;
+
+    private ConsistencyCheckDialogViewModel viewModel;
+
+    public ConsistencyCheckDialog(BibliographyConsistencyCheck.Result result, DialogService dialogService, GuiPreferences preferences) {
+        this.result = result;
+        this.dialogService = dialogService;
+        this.preferences = preferences;
+
+        this.setTitle(Localization.lang("Check consistency"));
+        this.initModality(Modality.NONE);
+
+        ViewLoader.view(this)
+                  .load()
+                  .setAsDialogPane(this);
+    }
+
+    public ConsistencyCheckDialogViewModel getViewModel() {
+        return viewModel;
+    }
+
+    @FXML
+    public void initialize() {
+        viewModel = new ConsistencyCheckDialogViewModel(result, dialogService, preferences);
+
+        result.entryTypeToResultMap().forEach((entrySet, entryTypeResult) -> {
+            entryTypeCombo.getItems().add(entrySet.toString());
+
+            Collection<Field> fields = entryTypeResult.fields();
+            for (Field field: fields) {
+                TableColumn<ConsistencyMessage, String> tableColumn = new TableColumn<>(field.toString());
+                tableColumn.setCellValueFactory(new PropertyValueFactory<>(field.toString()));
+                tableView.getColumns().add(tableColumn);
+            }
+        });
+
+        entryTypeCombo.getSelectionModel().select(entryTypeCombo.getItems().getFirst());
+    }
+
+    public void selectEntry() {
+        selectedEntry = entryTypeCombo.getSelectionModel().getSelectedItem();
+    }
+
+    public void exportAsCsv() {
+        viewModel.startExportAsCsv();
+    }
+
+    public void exportAsTxt() {
+        viewModel.startExportAsTxt();
+    }
+}
+

src/main/java/org/jabref/gui/consistency/ConsistencyCheckDialogViewModel.java

@@ -0,0 +1,66 @@
+package org.jabref.gui.consistency;
+
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.Writer;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Optional;
+
+import org.jabref.gui.AbstractViewModel;
+import org.jabref.gui.DialogService;
+import org.jabref.gui.preferences.GuiPreferences;
+import org.jabref.gui.util.FileDialogConfiguration;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.quality.consistency.BibliographyConsistencyCheck;
+import org.jabref.logic.quality.consistency.BibliographyConsistencyCheckResultCsvWriter;
+import org.jabref.logic.quality.consistency.BibliographyConsistencyCheckResultTxtWriter;
+import org.jabref.logic.util.StandardFileType;
+
+public class ConsistencyCheckDialogViewModel extends AbstractViewModel {
+    private final DialogService dialogService;
+    private final GuiPreferences preferences;
+    private final BibliographyConsistencyCheck.Result result;
+
+    public ConsistencyCheckDialogViewModel(BibliographyConsistencyCheck.Result result, DialogService dialogService, GuiPreferences preferences) {
+        this.result = result;
+        this.dialogService = dialogService;
+        this.preferences = preferences;
+    }
+
+    public void startExportAsTxt() {
+        FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
+                .withInitialDirectory(preferences.getFilePreferences().getWorkingDirectory())
+                .addExtensionFilter(StandardFileType.TXT)
+                .withDefaultExtension(StandardFileType.TXT)
+                .build();
+        Optional<Path> exportPath = dialogService.showFileSaveDialog(fileDialogConfiguration);
+
+        if (exportPath.isEmpty()) {
+            return;
+        }
+
+        try (Writer writer = new OutputStreamWriter(Files.newOutputStream(exportPath.get()))) {
+            BibliographyConsistencyCheckResultTxtWriter bibliographyConsistencyCheckResultTxtWriter = new BibliographyConsistencyCheckResultTxtWriter(result, writer);
+            bibliographyConsistencyCheckResultTxtWriter.writeFindings();
+        } catch (IOException e) {
+            dialogService.notify(Localization.lang("Failed to export file!"));
+        }
+    }
+
+    public void startExportAsCsv() {
+        FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
+                .withInitialDirectory(preferences.getFilePreferences().getWorkingDirectory())
+                .addExtensionFilter(StandardFileType.TXT)
+                .withDefaultExtension(StandardFileType.TXT)
+                .build();
+        Optional<Path> exportPath = dialogService.showFileSaveDialog(fileDialogConfiguration);
+
+        try (Writer writer = new OutputStreamWriter(Files.newOutputStream(exportPath.get()))) {
+            BibliographyConsistencyCheckResultCsvWriter bibliographyConsistencyCheckResultTxtWriter = new BibliographyConsistencyCheckResultCsvWriter(result, writer);
+            bibliographyConsistencyCheckResultTxtWriter.writeFindings();
+        } catch (IOException e) {
+            dialogService.notify(Localization.lang("Failed to export file!"));
+        }
+    }
+}

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

@@ -17,6 +17,7 @@
 import org.jabref.gui.auximport.NewSubLibraryAction;
 import org.jabref.gui.citationkeypattern.GenerateCitationKeyAction;
 import org.jabref.gui.cleanup.CleanupAction;
+import org.jabref.gui.consistency.ConsistencyCheckAction;
 import org.jabref.gui.copyfiles.CopyFilesAction;
 import org.jabref.gui.documentviewer.ShowDocumentViewerAction;
 import org.jabref.gui.duplicationFinder.DuplicateSearch;
@@ -245,6 +246,7 @@ private void createMenu() {
                 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_CONSISTENCY, new ConsistencyCheckAction(dialogService, stateManager, preferences)),
                 factory.createMenuItem(StandardActions.CLEANUP_ENTRIES, new CleanupAction(frame::getCurrentLibraryTab, preferences, dialogService, stateManager, taskExecutor, undoManager)),
 
                 new SeparatorMenuItem(),

src/main/java/org/jabref/gui/keyboard/KeyBinding.java

@@ -30,6 +30,7 @@ public enum KeyBinding {
     ACCEPT("Accept", Localization.lang("Accept"), "ctrl+ENTER", KeyBindingCategory.EDIT),
     AUTOMATICALLY_LINK_FILES("Automatically link files", Localization.lang("Automatically set file links"), "F7", KeyBindingCategory.QUALITY),
     CHECK_INTEGRITY("Check integrity", Localization.lang("Check integrity"), "ctrl+F8", KeyBindingCategory.QUALITY),
+    CHECK_CONSISTENCY("Check consistency", Localization.lang("Check consistency"), "ctrl+F9", KeyBindingCategory.QUALITY),
     CLEANUP("Cleanup", Localization.lang("Cleanup entries"), "alt+F8", KeyBindingCategory.QUALITY),
     CLOSE_DATABASE("Close library", Localization.lang("Close library"), "ctrl+W", KeyBindingCategory.FILE),
     CLOSE("Close dialog", Localization.lang("Close dialog"), "Esc", KeyBindingCategory.VIEW),

src/main/java/org/jabref/logic/quality/consistency/ConsistencyMessage.java

@@ -0,0 +1,6 @@
+package org.jabref.logic.quality.consistency;
+
+public class ConsistencyMessage {
+
+    public ConsistencyMessage() { }
+}

src/main/resources/l10n/JabRef_en.properties

@@ -1023,6 +1023,14 @@ Line\ %0\:\ Found\ corrupted\ citation\ key\ %1\ (comma\ missing).=Line %0: Foun
 Check\ integrity=Check integrity
 Checking\ integrity...=Checking integrity...
 
+Check\ consistency=Check consistency
+Select=Select
+Entry\ type=Entry type
+Export\ as\ csv\ file =Export as csv file
+Export\ as\ txt\ file =Export as txt file
+Shows\ results\ for\ the\ selected\ entry\ type.=Show results for the selected entry type.
+Failed\ to\ export\ file!=Failed to export file!
+
 Field\ Presence\ Consistency\ Check\ Result=Field Presence Consistency Check Result
 required\ field\ is\ present=required field is present
 optional\ field\ is\ present=optional field is present