Add search for citations in LaTeX files (back-end and GUI)

CHANGELOG.md

@@ -69,6 +69,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We moved the dropdown menu for selecting the push-application from the toolbar into the external application preferences. [#674](https://github.com/JabRef/jabref/issues/674)
 - We removed the alphabetical ordering of the custom tabs and updated the error message when trying to create a general field with a name containing an illegal character. [#5019](https://github.com/JabRef/jabref/issues/5019)
 - We added a context menu to the bib(la)tex-source-editor to copy'n'paste. [#5007](https://github.com/JabRef/jabref/pull/5007)
+- We added a bibliographic references search, for finding references in several LaTeX files. This tool scans directories and shows which entries are used, how many times and where.
 
 
 ### Fixed

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

@@ -101,6 +101,7 @@
 import org.jabref.gui.search.GlobalSearchBar;
 import org.jabref.gui.shared.ConnectToSharedDatabaseCommand;
 import org.jabref.gui.specialfields.SpecialFieldMenuItemFactory;
+import org.jabref.gui.texparser.ParseTexAction;
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.DefaultTaskExecutor;
@@ -768,6 +769,7 @@ private MenuBar createMenu() {
         pushToApplicationsManager.setMenuItem(pushToApplicationMenuItem);
 
         tools.getItems().addAll(
+                factory.createMenuItem(StandardActions.PARSE_TEX, new ParseTexAction(stateManager)),
                 factory.createMenuItem(StandardActions.NEW_SUB_LIBRARY_FROM_AUX, new NewSubLibraryAction(this, stateManager)),
                 factory.createMenuItem(StandardActions.FIND_UNLINKED_FILES, new FindUnlinkedFilesAction(this, stateManager)),
                 factory.createMenuItem(StandardActions.WRITE_XMP, new OldDatabaseCommandWrapper(Actions.WRITE_XMP, this, stateManager)),

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

@@ -85,6 +85,7 @@ public enum StandardActions implements Action {
     TOOGLE_OO(Localization.lang("OpenOffice/LibreOffice"), IconTheme.JabRefIcons.FILE_OPENOFFICE, KeyBinding.OPEN_OPEN_OFFICE_LIBRE_OFFICE_CONNECTION),
     TOGGLE_WEB_SEARCH(Localization.lang("Web search"), Localization.lang("Toggle web search interface"), IconTheme.JabRefIcons.WWW, KeyBinding.WEB_SEARCH),
 
+    PARSE_TEX(Localization.lang("LaTeX references search"), IconTheme.JabRefIcons.APPLICATION_TEXSTUDIO),
     NEW_SUB_LIBRARY_FROM_AUX(Localization.lang("New sublibrary based on AUX file") + "...", Localization.lang("New BibTeX sublibrary") + Localization.lang("This feature generates a new library based on which entries are needed in an existing LaTeX document."), IconTheme.JabRefIcons.NEW),
     WRITE_XMP(Localization.lang("Write XMP-metadata to PDFs"), Localization.lang("Will write XMP-metadata to the PDFs linked from selected entries."), KeyBinding.WRITE_XMP),
     OPEN_FOLDER(Localization.lang("Open folder"), Localization.lang("Open folder"), KeyBinding.OPEN_FOLDER),

src/main/java/org/jabref/gui/texparser/FileNodeViewModel.java

@@ -0,0 +1,58 @@
+package org.jabref.gui.texparser;
+
+import java.nio.file.Path;
+import java.util.StringJoiner;
+
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+
+import org.jabref.logic.l10n.Localization;
+
+class FileNodeViewModel {
+
+    private final Path path;
+    private final ObservableList<FileNodeViewModel> children;
+    private int fileCount;
+
+    public FileNodeViewModel(Path path) {
+        this.path = path;
+        this.fileCount = 0;
+        this.children = FXCollections.observableArrayList();
+    }
+
+    public Path getPath() {
+        return path;
+    }
+
+    public int getFileCount() {
+        return fileCount;
+    }
+
+    public void setFileCount(int fileCount) {
+        this.fileCount = fileCount;
+    }
+
+    public ObservableList<FileNodeViewModel> getChildren() {
+        return children;
+    }
+
+    /**
+     * Return a string for displaying a node name (and its number of children if it is a directory).
+     */
+    public String getDisplayText() {
+        if (path.toFile().isDirectory()) {
+            return String.format("%s (%s %s)", path.getFileName(), fileCount,
+                    fileCount == 1 ? Localization.lang("file") : Localization.lang("files"));
+        }
+        return path.getFileName().toString();
+    }
+
+    @Override
+    public String toString() {
+        return new StringJoiner(", ", FileNodeViewModel.class.getSimpleName() + "[", "]")
+                .add("path=" + path)
+                .add("fileCount=" + fileCount)
+                .add("children=" + children)
+                .toString();
+    }
+}

src/main/java/org/jabref/gui/texparser/ParseTexAction.java

@@ -0,0 +1,25 @@
+package org.jabref.gui.texparser;
+
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.model.database.BibDatabaseContext;
+
+import static org.jabref.gui.actions.ActionHelper.needsDatabase;
+
+public class ParseTexAction extends SimpleCommand {
+
+    private final StateManager stateManager;
+
+    public ParseTexAction(StateManager stateManager) {
+        this.stateManager = stateManager;
+        this.executable.bind(needsDatabase(stateManager));
+    }
+
+    @Override
+    public void execute() {
+        BibDatabaseContext database = stateManager.getActiveDatabase().orElseThrow(NullPointerException::new);
+        ParseTexDialogView dialog = new ParseTexDialogView(database);
+
+        dialog.showAndWait();
+    }
+}

src/main/java/org/jabref/gui/texparser/ParseTexDialog.fxml

@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.ButtonType?>
+<?import javafx.scene.control.DialogPane?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.control.ProgressIndicator?>
+<?import javafx.scene.control.TextField?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
+<?import org.controlsfx.control.CheckTreeView?>
+
+<DialogPane xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1"
+            fx:controller="org.jabref.gui.texparser.ParseTexDialogView"
+            prefWidth="500.0" prefHeight="650.0">
+    <content>
+        <VBox spacing="10.0">
+            <VBox spacing="5.0">
+                <Label text="%LaTeX files directory:"/>
+                <HBox spacing="10.0">
+                    <TextField fx:id="texDirectoryField" HBox.hgrow="ALWAYS"/>
+                    <Button fx:id="browseButton" onAction="#browseButtonClicked" text="%Browse"/>
+                    <Button fx:id="searchButton" defaultButton="true" onAction="#searchButtonClicked" text="%Search"/>
+                </HBox>
+            </VBox>
+            <VBox spacing="5.0">
+                <Label text="%LaTeX files found:"/>
+                <CheckTreeView fx:id="fileTreeView" prefHeight="500.0" VBox.vgrow="ALWAYS"/>
+            </VBox>
+            <VBox spacing="5.0">
+                <HBox spacing="10.0">
+                    <Button fx:id="selectAllButton" text="%Select all" styleClass="text-button" onAction="#selectAll"/>
+                    <Button fx:id="unselectAllButton" text="%Unselect all" styleClass="text-button"
+                            onAction="#unselectAll"/>
+                </HBox>
+            </VBox>
+            <ProgressIndicator fx:id="progressIndicator" prefHeight="200.0"/>
+        </VBox>
+    </content>
+    <ButtonType fx:constant="CLOSE"/>
+    <ButtonType fx:id="parseButtonType" text="%Parse"/>
+</DialogPane>

src/main/java/org/jabref/gui/texparser/ParseTexDialogView.java

@@ -0,0 +1,113 @@
+package org.jabref.gui.texparser;
+
+import javax.inject.Inject;
+
+import javafx.beans.binding.Bindings;
+import javafx.fxml.FXML;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.CheckBoxTreeItem;
+import javafx.scene.control.ProgressIndicator;
+import javafx.scene.control.SelectionMode;
+import javafx.scene.control.TextField;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.ControlHelper;
+import org.jabref.gui.util.IconValidationDecorator;
+import org.jabref.gui.util.RecursiveTreeItem;
+import org.jabref.gui.util.TaskExecutor;
+import org.jabref.gui.util.ViewModelTreeCellFactory;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.preferences.PreferencesService;
+
+import com.airhacks.afterburner.views.ViewLoader;
+import de.saxsys.mvvmfx.utils.validation.visualization.ControlsFxVisualizer;
+import org.controlsfx.control.CheckTreeView;
+import org.fxmisc.easybind.EasyBind;
+
+public class ParseTexDialogView extends BaseDialog<Void> {
+
+    private final BibDatabaseContext databaseContext;
+    private final ControlsFxVisualizer validationVisualizer;
+    @FXML private TextField texDirectoryField;
+    @FXML private Button browseButton;
+    @FXML private Button searchButton;
+    @FXML private ProgressIndicator progressIndicator;
+    @FXML private CheckTreeView<FileNodeViewModel> fileTreeView;
+    @FXML private Button selectAllButton;
+    @FXML private Button unselectAllButton;
+    @FXML private ButtonType parseButtonType;
+    @Inject private DialogService dialogService;
+    @Inject private TaskExecutor taskExecutor;
+    @Inject private PreferencesService preferencesService;
+    private ParseTexDialogViewModel viewModel;
+
+    public ParseTexDialogView(BibDatabaseContext databaseContext) {
+        this.databaseContext = databaseContext;
+        this.validationVisualizer = new ControlsFxVisualizer();
+
+        this.setTitle(Localization.lang("LaTeX references search"));
+
+        ViewLoader.view(this)
+                  .load()
+                  .setAsDialogPane(this);
+
+        ControlHelper.setAction(parseButtonType, getDialogPane(), event -> viewModel.parseButtonClicked());
+        Button parseButton = (Button) getDialogPane().lookupButton(parseButtonType);
+        parseButton.disableProperty().bind(viewModel.noFilesFoundProperty().or(
+                Bindings.isEmpty(viewModel.getCheckedFileList())));
+    }
+
+    @FXML
+    private void initialize() {
+        viewModel = new ParseTexDialogViewModel(databaseContext, dialogService, taskExecutor, preferencesService);
+
+        fileTreeView.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
+        fileTreeView.showRootProperty().bindBidirectional(viewModel.successfulSearchProperty());
+        fileTreeView.rootProperty().bind(EasyBind.map(viewModel.rootProperty(), fileNode ->
+                new RecursiveTreeItem<>(fileNode, FileNodeViewModel::getChildren)));
+
+        EasyBind.subscribe(fileTreeView.rootProperty(), root -> {
+            ((CheckBoxTreeItem<FileNodeViewModel>) root).setSelected(true);
+            root.setExpanded(true);
+            EasyBind.listBind(viewModel.getCheckedFileList(), fileTreeView.getCheckModel().getCheckedItems());
+        });
+
+        new ViewModelTreeCellFactory<FileNodeViewModel>()
+                .withText(FileNodeViewModel::getDisplayText)
+                .install(fileTreeView);
+
+        texDirectoryField.textProperty().bindBidirectional(viewModel.texDirectoryProperty());
+        validationVisualizer.setDecoration(new IconValidationDecorator());
+        validationVisualizer.initVisualization(viewModel.texDirectoryValidation(), texDirectoryField);
+
+        browseButton.disableProperty().bindBidirectional(viewModel.searchInProgressProperty());
+        searchButton.disableProperty().bind(viewModel.texDirectoryValidation().validProperty().not());
+        selectAllButton.disableProperty().bindBidirectional(viewModel.noFilesFoundProperty());
+        unselectAllButton.disableProperty().bindBidirectional(viewModel.noFilesFoundProperty());
+
+        progressIndicator.visibleProperty().bindBidirectional(viewModel.searchInProgressProperty());
+    }
+
+    @FXML
+    private void browseButtonClicked() {
+        viewModel.browseButtonClicked();
+    }
+
+    @FXML
+    private void searchButtonClicked() {
+        viewModel.searchButtonClicked();
+    }
+
+    @FXML
+    private void selectAll() {
+        fileTreeView.getCheckModel().checkAll();
+    }
+
+    @FXML
+    private void unselectAll() {
+        fileTreeView.getCheckModel().clearChecks();
+    }
+}