Extract references from related work section (Part 1)

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added a related work text extractor, which finds and inserts the related work text into bib entries from references in the texts. [#9840](https://github.com/JabRef/jabref/issues/9840)
 - We added a hover button on group rows to quickly add a new group or subgroup. [#12289](https://github.com/JabRef/jabref/issues/12289)
 - We added a shorthand for protecting terms in the fields: user can now select a text and type a opening curling brace to quickly wrap the selection in braces. [#15442](https://github.com/JabRef/jabref/pull/15442)
 - We added fallback search for `[DATE]` patterns in the file finder, so that if an exact date match is not found, progressively less specific dates (year-month, then year) are tried. [#8152](https://github.com/JabRef/jabref/issues/8152)

docs/requirements/dialog-with-text-input.md

@@ -0,0 +1,16 @@
+---
+parent: Requirements
+---
+# Dialog with text input
+
+## Automatic clipboard content detection and focus for text input
+`req~textinput.clipboard.autofocus~1`
+
+When a dialog with text input is opened:
+
+- Text field should be focused.
+- If the clipboard contains contents, it should be in the field and be marked.
+
+Needs: impl
+
+<!-- markdownlint-disable-file MD022 -->

jabgui/src/main/java/org/jabref/gui/actions/ActionHelper.java

@@ -111,6 +111,28 @@ public static BooleanExpression isFilePresentForSelectedEntry(StateManager state
         return BooleanExpression.booleanExpression(fileIsPresent);
     }
 
+    public static BooleanExpression isPdfFilePresentForSelectedEntry(StateManager stateManager, CliPreferences preferences) {
+        ObservableList<BibEntry> selectedEntries = stateManager.getSelectedEntries();
+        Binding<Boolean> pdfFileIsPresent = EasyBind.valueAt(selectedEntries, 0).mapOpt(entry -> {
+            if (stateManager.getActiveDatabase().isEmpty()) {
+                return false;
+            }
+
+            return entry.getFiles().stream()
+                        .filter(linkedFile -> linkedFile.getFileName()
+                                                        .map(Path::of)
+                                                        .map(FileUtil::isPDFFile)
+                                                        .orElse(false))
+                        .anyMatch(linkedFile -> FileUtil.find(
+                                                                stateManager.getActiveDatabase().get(),
+                                                                linkedFile.getLink(),
+                                                                preferences.getFilePreferences())
+                                                        .isPresent());
+        }).orElseOpt(false);
+
+        return BooleanExpression.booleanExpression(pdfFileIsPresent);
+    }
+
     /// Check if at least one of the selected entries has linked files
     /// <br>
     /// Used in {@link org.jabref.gui.maintable.OpenSelectedEntriesFilesAction} when multiple entries selected

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

@@ -43,6 +43,7 @@ public enum StandardActions implements Action {
     OPEN_EXTERNAL_FILE(Localization.lang("Open file"), IconTheme.JabRefIcons.FILE, KeyBinding.OPEN_FILE),
     EXTRACT_FILE_REFERENCES_ONLINE(Localization.lang("Extract references from file (online)"), IconTheme.JabRefIcons.FILE_STAR),
     EXTRACT_FILE_REFERENCES_OFFLINE(Localization.lang("Extract references from file (offline)"), IconTheme.JabRefIcons.FILE_STAR),
+    EXTRACT_RELATED_WORK_COMMENTS(Localization.lang("Extract related work comments"), IconTheme.JabRefIcons.COMMENT),
     OPEN_URL(Localization.lang("Open URL or DOI"), IconTheme.JabRefIcons.WWW, KeyBinding.OPEN_URL_OR_DOI),
     SEARCH(Localization.lang("Search...")),
     SEARCH_GOOGLE_SCHOLAR(Localization.lang("Search Google Scholar")),

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

@@ -67,6 +67,7 @@
 import org.jabref.gui.preview.PreviewControls;
 import org.jabref.gui.pseudonymize.PseudonymizeAction;
 import org.jabref.gui.push.GuiPushToApplicationCommand;
+import org.jabref.gui.relatedwork.RelatedWorkAction;
 import org.jabref.gui.search.RebuildFulltextSearchIndexAction;
 import org.jabref.gui.shared.ConnectToSharedDatabaseCommand;
 import org.jabref.gui.shared.PullChangesFromSharedAction;
@@ -326,6 +327,7 @@ private void createMenu() {
                 factory.createMenuItem(StandardActions.NEW_SUB_LIBRARY_FROM_AUX, new NewSubLibraryAction(frame, stateManager, dialogService)),
                 factory.createMenuItem(StandardActions.NEW_LIBRARY_FROM_PDF_ONLINE, new NewLibraryFromPdfActionOnline(frame, stateManager, dialogService, preferences, taskExecutor)),
                 factory.createMenuItem(StandardActions.NEW_LIBRARY_FROM_PDF_OFFLINE, new NewLibraryFromPdfActionOffline(frame, stateManager, dialogService, preferences, taskExecutor)),
+                factory.createMenuItem(StandardActions.EXTRACT_RELATED_WORK_COMMENTS, new RelatedWorkAction(dialogService, stateManager, preferences)),
                 factory.createMenuItem(StandardActions.PSEUDONYMIZE_LIBRARY, new PseudonymizeAction(stateManager, dialogService, preferences)),
 
                 new SeparatorMenuItem(),

jabgui/src/main/java/org/jabref/gui/maintable/RightClickMenu.java

@@ -30,6 +30,7 @@
 import org.jabref.gui.preferences.GuiPreferences;
 import org.jabref.gui.preview.CopyCitationAction;
 import org.jabref.gui.preview.PreviewPreferences;
+import org.jabref.gui.relatedwork.RelatedWorkAction;
 import org.jabref.gui.specialfields.SpecialFieldMenuItemFactory;
 import org.jabref.logic.citationstyle.CitationStyleOutputFormat;
 import org.jabref.logic.importer.WebFetchers;
@@ -94,6 +95,7 @@ public static ContextMenu create(LibraryTab libraryTab,
                 factory.createMenuItem(StandardActions.OPEN_EXTERNAL_FILE, new OpenSelectedEntriesFilesAction(dialogService, stateManager, preferences, taskExecutor)),
                 extractFileReferencesOnline,
                 extractFileReferencesOffline,
+                factory.createMenuItem(StandardActions.EXTRACT_RELATED_WORK_COMMENTS, new RelatedWorkAction(dialogService, stateManager, preferences)),
 
                 factory.createMenuItem(StandardActions.OPEN_URL, new OpenUrlAction(dialogService, stateManager, preferences)),
 

jabgui/src/main/java/org/jabref/gui/newentry/NewEntryView.java

@@ -370,6 +370,7 @@ private void initializeLookupIdentifier() {
     }
 
     private void initializeInterpretCitations() {
+        // [impl->req~textinput.clipboard.autofocus~1]
         interpretText.textProperty().bindBidirectional(viewModel.interpretTextProperty());
         final String clipboardText = ClipBoardManager.getContents().trim();
         if (!StringUtil.isBlank(clipboardText)) {
@@ -443,6 +444,7 @@ private void switchInterpretCitations() {
         currentApproach = NewEntryDialogTab.INTERPRET_CITATIONS;
         newEntryPreferences.setLatestApproach(NewEntryDialogTab.INTERPRET_CITATIONS);
 
+        // [impl->req~textinput.clipboard.autofocus~1]
         if (interpretText != null) {
             Platform.runLater(() -> interpretText.requestFocus());
         }

jabgui/src/main/java/org/jabref/gui/relatedwork/RelatedWorkAction.java

@@ -0,0 +1,69 @@
+package org.jabref.gui.relatedwork;
+
+import java.nio.file.Path;
+import java.util.Optional;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.ActionHelper;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.preferences.CliPreferences;
+import org.jabref.logic.util.io.FileUtil;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.LinkedFile;
+
+public class RelatedWorkAction extends SimpleCommand {
+
+    private final DialogService dialogService;
+    private final StateManager stateManager;
+
+    public RelatedWorkAction(DialogService dialogService, StateManager stateManager, CliPreferences preferences) {
+        this.dialogService = dialogService;
+        this.stateManager = stateManager;
+        executable.bind(ActionHelper.needsDatabase(stateManager)
+                                    .and(ActionHelper.needsEntriesSelected(1, stateManager))
+                                    .and(ActionHelper.isPdfFilePresentForSelectedEntry(stateManager, preferences)));
+    }
+
+    @Override
+    public void execute() {
+        BibDatabaseContext databaseContext = stateManager.getActiveDatabase().orElseThrow();
+        BibEntry sourceEntry = stateManager.getSelectedEntries().getFirst();
+        Optional<LinkedFile> linkedPDFFile = sourceEntry.getFiles().stream()
+                                                        .filter(this::isPDFLinkedFile)
+                                                        .findFirst();
+
+        if (linkedPDFFile.isEmpty()) {
+            dialogService.showWarningDialogAndWait(
+                    Localization.lang("No PDF files available"),
+                    Localization.lang("Please attach PDF files")
+            );
+            return;
+        }
+
+        Optional<String> citationKey = sourceEntry.getCitationKey();
+        if (citationKey.isEmpty()) {
+            dialogService.showWarningDialogAndWait(
+                    Localization.lang("Insert related work text"),
+                    Localization.lang("Selected entry does not have an associated citation key.")
+            );
+            return;
+        }
+
+        dialogService.showCustomDialogAndWait(new RelatedWorkDialogView(
+                databaseContext,
+                sourceEntry,
+                linkedPDFFile.get(),
+                citationKey.get()
+        ));
+    }
+
+    private boolean isPDFLinkedFile(LinkedFile linkedFile) {
+        return linkedFile.getFileName()
+                         .map(Path::of)
+                         .map(FileUtil::isPDFFile)
+                         .orElse(false);
+    }
+}

jabgui/src/main/java/org/jabref/gui/relatedwork/RelatedWorkDialogView.java

@@ -0,0 +1,96 @@
+package org.jabref.gui.relatedwork;
+
+import java.util.List;
+
+import javafx.application.Platform;
+import javafx.fxml.FXML;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.TextArea;
+import javafx.scene.control.TextField;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.clipboard.ClipBoardManager;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.ControlHelper;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.preferences.CliPreferences;
+import org.jabref.logic.relatedwork.RelatedWorkMatchResult;
+import org.jabref.logic.util.strings.StringUtil;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.LinkedFile;
+
+import com.airhacks.afterburner.views.ViewLoader;
+import jakarta.inject.Inject;
+
+public class RelatedWorkDialogView extends BaseDialog<Void> {
+
+    private final BibDatabaseContext databaseContext;
+    private final BibEntry sourceEntry;
+    private final LinkedFile linkedFile;
+    private final String sourceEntryCitationKey;
+
+    @FXML private TextField entryField;
+    @FXML private TextField linkedFileField;
+    @FXML private TextField userNameField;
+    @FXML private TextArea relatedWorkTextArea;
+    @FXML private ButtonType parseButtonType;
+
+    @Inject private DialogService dialogService;
+    @Inject private CliPreferences preferences;
+    @Inject private BibEntryTypesManager entryTypesManager;
+
+    private RelatedWorkDialogViewModel viewModel;
+
+    public RelatedWorkDialogView(BibDatabaseContext databaseContext,
+                                 BibEntry sourceEntry,
+                                 LinkedFile linkedPdfFile,
+                                 String sourceEntryCitationKey) {
+        this.databaseContext = databaseContext;
+        this.sourceEntry = sourceEntry;
+        this.linkedFile = linkedPdfFile;
+        this.sourceEntryCitationKey = sourceEntryCitationKey;
+
+        setTitle(Localization.lang("Insert related work text"));
+
+        ViewLoader.view(this).load().setAsDialogPane(this);
+
+        ControlHelper.setAction(parseButtonType, getDialogPane(), event -> viewModel.matchRelatedWork().ifPresent(this::openResultDialog));
+
+        Button parseButton = (Button) getDialogPane().lookupButton(parseButtonType);
+        parseButton.disableProperty().bind(viewModel.parseDisabledProperty());
+    }
+
+    @FXML
+    private void initialize() {
+        this.viewModel = new RelatedWorkDialogViewModel(
+                databaseContext,
+                sourceEntry,
+                linkedFile,
+                sourceEntryCitationKey,
+                dialogService,
+                preferences,
+                entryTypesManager
+        );
+
+        this.entryField.textProperty().bind(viewModel.sourceEntryCitationKeyProperty());
+        this.linkedFileField.textProperty().bind(viewModel.linkedPDFFileProperty());
+        this.userNameField.textProperty().bind(viewModel.userNameProperty());
+        this.relatedWorkTextArea.textProperty().bindBidirectional(viewModel.relatedWorkTextProperty());
+
+        // [impl->req~textinput.clipboard.autofocus~1]
+        String clipboardText = ClipBoardManager.getContents().trim();
+        if (!StringUtil.isBlank(clipboardText)) {
+            relatedWorkTextArea.setText(clipboardText);
+            relatedWorkTextArea.selectAll();
+        }
+
+        Platform.runLater(relatedWorkTextArea::requestFocus);
+    }
+
+    private void openResultDialog(List<RelatedWorkMatchResult> matchedResults) {
+        dialogService.showCustomDialogAndWait(new RelatedWorkResultDialogView(sourceEntry, matchedResults, viewModel.userNameProperty().get()));
+    }
+}