Ask AI questions to each selected entry in a batch

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

@@ -233,6 +233,7 @@ public enum StandardActions implements Action {
     GROUP_ENTRIES_CLEAR(Localization.lang("Clear group")),
 
     CLEAR_EMBEDDINGS_CACHE(Localization.lang("Clear embeddings cache")),
+    AI_ASK_QUESTIONS(Localization.lang("Ask AI questions...")),
 
     GIT(Localization.lang("Git"), IconTheme.JabRefIcons.GIT_SYNC),
     GIT_PULL(Localization.lang("Pull")),

jabgui/src/main/java/org/jabref/gui/ai/AskQuestionsAction.java

@@ -0,0 +1,238 @@
+package org.jabref.gui.ai;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+import java.util.concurrent.ExecutionException;
+import java.util.regex.Pattern;
+
+import javafx.application.Platform;
+import javafx.collections.ObservableList;
+import javafx.scene.control.ButtonType;
+import javafx.scene.paint.Color;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.gui.util.UiTaskExecutor;
+import org.jabref.logic.FilePreferences;
+import org.jabref.logic.ai.AiService;
+import org.jabref.logic.ai.chatting.ChatModel;
+import org.jabref.logic.ai.chatting.tasks.GenerateRagResponseTask;
+import org.jabref.logic.ai.ingestion.tasks.generateembeddings.GenerateEmbeddingsTaskRequest;
+import org.jabref.logic.ai.preferences.AiPreferences;
+import org.jabref.logic.ai.rag.logic.ResponseEngine;
+import org.jabref.logic.ai.rag.util.ResponseEngineFactory;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.util.BackgroundTask;
+import org.jabref.logic.util.TaskExecutor;
+import org.jabref.model.ai.chatting.ChatMessage;
+import org.jabref.model.ai.identifiers.FullBibEntry;
+import org.jabref.model.ai.pipeline.ResponseEngineKind;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.LinkedFile;
+
+import jfx.incubator.scene.control.richtext.RichTextArea;
+import jfx.incubator.scene.control.richtext.TextPos;
+import jfx.incubator.scene.control.richtext.model.StyleAttributeMap;
+import org.jspecify.annotations.NullMarked;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.jabref.gui.actions.ActionHelper.needsEntriesSelected;
+
+/// Asks a fixed list of questions to each selected entry, one entry after the other, one question after the other.
+/// Questions and answers are appended to the entry's AI chat, so they show up in the entry editor's AI chat tab.
+///
+/// Each question is sent without the previous questions and answers in the context, so the prompt stays small
+/// (system message + retrieved excerpts + question) and works with small models.
+@NullMarked
+public class AskQuestionsAction extends SimpleCommand {
+    private static final Logger LOGGER = LoggerFactory.getLogger(AskQuestionsAction.class);
+    private static final Pattern QUESTION_SEPARATOR = Pattern.compile("(?m)^\\s*---\\s*$");
+    private static final Pattern SEPARATOR_LINE = Pattern.compile("\\s*---\\s*");
+    private static final StyleAttributeMap EVEN_SECTION = StyleAttributeMap.builder().setBackground(Color.TRANSPARENT).build();
+    private static final StyleAttributeMap ODD_SECTION = StyleAttributeMap.builder().setBackground(Color.gray(0.5, 0.15)).build();
+
+    // ponytail: remembered per JabRef run only, add a preference if this survives the experiment
+    private static String lastQuestions = "";
+
+    private final StateManager stateManager;
+    private final DialogService dialogService;
+    private final AiService aiService;
+    private final AiPreferences aiPreferences;
+    private final FilePreferences filePreferences;
+    private final TaskExecutor taskExecutor;
+
+    public AskQuestionsAction(StateManager stateManager,
+                              DialogService dialogService,
+                              AiService aiService,
+                              AiPreferences aiPreferences,
+                              FilePreferences filePreferences,
+                              TaskExecutor taskExecutor) {
+        this.stateManager = stateManager;
+        this.dialogService = dialogService;
+        this.aiService = aiService;
+        this.aiPreferences = aiPreferences;
+        this.filePreferences = filePreferences;
+        this.taskExecutor = taskExecutor;
+        this.executable.bind(needsEntriesSelected(stateManager));
+    }
+
+    @Override
+    public void execute() {
+        Optional<BibDatabaseContext> context = stateManager.getActiveDatabase();
+        if (context.isEmpty() || stateManager.getSelectedEntries().isEmpty()) {
+            return;
+        }
+        if (!aiPreferences.getAiFeaturesEnabled()) {
+            dialogService.notify(Localization.lang("AI features are disabled. Enable them in the preferences."));
+            return;
+        }
+
+        List<BibEntry> entries = new ArrayList<>(stateManager.getSelectedEntries());
+        List<String> questions = askForQuestions();
+        if (questions.isEmpty()) {
+            return;
+        }
+
+        BackgroundTask<Void> task = new BackgroundTask<>() {
+            @Override
+            public Void call() {
+                askAll(this, context.get(), entries, questions);
+                return null;
+            }
+        };
+        task.showToUser(true);
+        task.titleProperty().set(Localization.lang("Asking AI questions"));
+        task.onFailure(ex -> LOGGER.error("Asking AI questions failed", ex));
+        task.executeWith(taskExecutor);
+    }
+
+    private List<String> askForQuestions() {
+        BaseDialog<String> dialog = new BaseDialog<>() {
+        };
+        dialog.setTitle(Localization.lang("Ask AI questions"));
+        dialog.setHeaderText(Localization.lang("Each question is asked to every selected entry. Separate questions with a line containing only ---"));
+        RichTextArea textArea = new RichTextArea();
+        textArea.setWrapText(true);
+        textArea.setPrefSize(600, 300);
+        textArea.appendText(lastQuestions);
+        textArea.getModel().addListener(change -> {
+            if (change.isEdit()) {
+                // Restyling inside the change callback would modify the model while it is being edited
+                Platform.runLater(() -> colorSections(textArea));
+            }
+        });
+        colorSections(textArea);
+        dialog.getDialogPane().setContent(textArea);
+        dialog.getDialogPane().getButtonTypes().addAll(ButtonType.OK, ButtonType.CANCEL);
+        dialog.setResultConverter(button -> button == ButtonType.OK ? plainText(textArea) : null);
+
+        Optional<String> text = dialogService.showCustomDialogAndWait(dialog);
+        if (text.isEmpty()) {
+            return List.of();
+        }
+        lastQuestions = text.get();
+        return QUESTION_SEPARATOR.splitAsStream(text.get())
+                                 .map(String::strip)
+                                 .filter(question -> !question.isEmpty())
+                                 .toList();
+    }
+
+    /// Alternates the paragraph background per `---` section, like the rows of the main table.
+    private static void colorSections(RichTextArea textArea) {
+        boolean odd = false;
+        for (int i = 0; i < textArea.getParagraphCount(); i++) {
+            if (SEPARATOR_LINE.matcher(textArea.getModel().getPlainText(i)).matches()) {
+                odd = !odd;
+            }
+            textArea.applyStyle(TextPos.ofLeading(i, 0), textArea.getParagraphEnd(i), odd ? ODD_SECTION : EVEN_SECTION);
+        }
+    }
+
+    private static String plainText(RichTextArea textArea) {
+        StringBuilder text = new StringBuilder();
+        for (int i = 0; i < textArea.getParagraphCount(); i++) {
+            text.append(textArea.getModel().getPlainText(i)).append('\n');
+        }
+        return text.toString();
+    }
+
+    private void askAll(BackgroundTask<Void> task, BibDatabaseContext context, List<BibEntry> entries, List<String> questions) {
+        ChatModel chatModel = aiService.getCurrentChatModel();
+        ResponseEngine responseEngine = ResponseEngineFactory.create(
+                aiPreferences,
+                filePreferences,
+                aiService.getCurrentEmbeddingModel(),
+                aiService.getEmbeddingsStore());
+
+        int total = entries.size() * questions.size();
+        int done = 0;
+        task.updateProgress(done, total);
+
+        for (BibEntry entry : entries) {
+            if (task.isCancelled()) {
+                return;
+            }
+            String entryName = entry.getCitationKey().orElse(entry.getId());
+            FullBibEntry fullEntry = new FullBibEntry(context, entry);
+            ObservableList<ChatMessage> chatHistory = aiService.getChatHistoryCache().getForEntry(context, entry);
+
+            if (responseEngine.getKind() == ResponseEngineKind.EMBEDDINGS_SEARCH) {
+                task.updateMessage(Localization.lang("Generating embeddings for %0", entryName));
+                ingestFiles(context, entry);
+            }
+
+            for (String question : questions) {
+                if (task.isCancelled()) {
+                    return;
+                }
+                task.updateMessage(entryName + ": " + question);
+
+                ChatMessage userMessage = ChatMessage.userMessage(question);
+                ChatMessage answer;
+                try {
+                    answer = new GenerateRagResponseTask(
+                            chatModel,
+                            responseEngine,
+                            List.of(userMessage),
+                            List.of(fullEntry),
+                            aiPreferences.getChattingSystemMessageTemplate(),
+                            aiPreferences.getChattingUserMessageTemplate()
+                    ).call();
+                } catch (Exception e) {
+                    LOGGER.warn("Question '{}' failed for entry {}", question, entryName, e);
+                    answer = ChatMessage.errorMessage(e);
+                }
+                ChatMessage finalAnswer = answer;
+                UiTaskExecutor.runInJavaFXThread(() -> chatHistory.addAll(userMessage, finalAnswer));
+
+                task.updateProgress(++done, total);
+            }
+        }
+    }
+
+    private void ingestFiles(BibDatabaseContext context, BibEntry entry) {
+        for (LinkedFile linkedFile : entry.getFiles()) {
+            try {
+                aiService.getIngestionTaskAggregator().startWithFuture(new GenerateEmbeddingsTaskRequest(
+                        filePreferences,
+                        aiService.getIngestedDocumentsRepository(),
+                        aiService.getEmbeddingsStore(),
+                        aiService.getCurrentEmbeddingModel(),
+                        aiService.getCurrentDocumentSplitter(),
+                        context,
+                        linkedFile
+                ), false).getKey().get();
+            } catch (InterruptedException _) {
+                Thread.currentThread().interrupt();
+                return;
+            } catch (ExecutionException e) {
+                LOGGER.warn("Embedding generation failed for {}", linkedFile.getLink(), e);
+            }
+        }
+    }
+}

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

@@ -11,6 +11,7 @@
 import org.jabref.gui.actions.ActionFactory;
 import org.jabref.gui.actions.ActionHelper;
 import org.jabref.gui.actions.StandardActions;
+import org.jabref.gui.ai.AskQuestionsAction;
 import org.jabref.gui.clipboard.ClipBoardManager;
 import org.jabref.gui.edit.CopyMoreAction;
 import org.jabref.gui.edit.CopyTo;
@@ -32,6 +33,7 @@
 import org.jabref.gui.relatedwork.RelatedWorkAction;
 import org.jabref.gui.specialfields.SpecialFieldMenuItemFactory;
 import org.jabref.gui.util.UiTaskExecutor;
+import org.jabref.logic.ai.AiService;
 import org.jabref.logic.citationstyle.CitationStyleOutputFormat;
 import org.jabref.logic.importer.fetcher.CrossRef;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
@@ -44,6 +46,7 @@
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.entry.field.SpecialField;
 
+import com.airhacks.afterburner.injection.Injector;
 import com.tobiasdiez.easybind.EasyBind;
 
 public class RightClickMenu {
@@ -92,6 +95,7 @@ public static ContextMenu create(LibraryTab libraryTab,
                 extractFileReferencesOnline,
                 extractFileReferencesOffline,
                 factory.createMenuItem(StandardActions.EXTRACT_RELATED_WORK_COMMENTS, new RelatedWorkAction(dialogService, stateManager, preferences)),
+                factory.createMenuItem(StandardActions.AI_ASK_QUESTIONS, new AskQuestionsAction(stateManager, dialogService, Injector.instantiateModelOrService(AiService.class), preferences.getAiPreferences(), preferences.getFilePreferences(), taskExecutor)),
 
                 factory.createMenuItem(StandardActions.OPEN_URL, new OpenUrlAction(dialogService, stateManager, preferences)),
 

jablib/src/main/resources/l10n/JabRef_en.properties

@@ -3723,3 +3723,8 @@ Move\ group=Move group
 Sort\ subgroups=Sort subgroups
 Change\ string\ constants=Change string constants
 Founded\ by\ Morten\ O.\ Alver\ and\ Nizar\ Batada.=Founded by Morten O. Alver and Nizar Batada.
+Ask\ AI\ questions...=Ask AI questions...
+Ask\ AI\ questions=Ask AI questions
+Asking\ AI\ questions=Asking AI questions
+Each\ question\ is\ asked\ to\ every\ selected\ entry.\ Separate\ questions\ with\ a\ line\ containing\ only\ ---=Each question is asked to every selected entry. Separate questions with a line containing only ---
+AI\ features\ are\ disabled.\ Enable\ them\ in\ the\ preferences.=AI features are disabled. Enable them in the preferences.