From b4a9c944f6361508ea59a4744acb9d7ff5a16444 Mon Sep 17 00:00:00 2001
From: InAnYan <ruslanpopov1512@gmail.com>
Date: Thu, 26 Sep 2024 00:35:28 +0300
Subject: [PATCH 1/3] Add options to auto generate embeddings and summaries.
 Unfortunately, they don't work...

---
 src/main/java/org/jabref/gui/JabRefGUI.java   |  2 ++
 .../chathistory/ChatHistoryService.java       | 22 +++++-------
 .../org/jabref/gui/preferences/ai/AiTab.fxml  | 15 ++++++++
 .../org/jabref/gui/preferences/ai/AiTab.java  |  6 ++++
 .../gui/preferences/ai/AiTabViewModel.java    | 24 +++++++++++++
 .../jabref/logic/ai/AiDefaultPreferences.java |  2 ++
 .../org/jabref/logic/ai/AiPreferences.java    | 30 ++++++++++++++++
 .../java/org/jabref/logic/ai/AiService.java   | 18 ++++++++--
 .../logic/ai/ingestion/IngestionService.java  | 34 ++++++++++++++++++-
 .../ai/summarization/SummariesService.java    | 31 ++++++++++++++++-
 .../preferences/JabRefCliPreferences.java     |  8 +++++
 11 files changed, 174 insertions(+), 18 deletions(-)

diff --git a/src/main/java/org/jabref/gui/JabRefGUI.java b/src/main/java/org/jabref/gui/JabRefGUI.java
index d6a80bf3947..d17c06bd035 100644
--- a/src/main/java/org/jabref/gui/JabRefGUI.java
+++ b/src/main/java/org/jabref/gui/JabRefGUI.java
@@ -166,6 +166,7 @@ public void initialize() {
         Injector.setModelOrService(ClipBoardManager.class, clipBoardManager);
 
         JabRefGUI.aiService = new AiService(
+                stateManager,
                 preferences.getAiPreferences(),
                 preferences.getFilePreferences(),
                 dialogService,
@@ -173,6 +174,7 @@ public void initialize() {
         Injector.setModelOrService(AiService.class, aiService);
 
         JabRefGUI.chatHistoryService = new ChatHistoryService(
+                stateManager,
                 preferences.getCitationKeyPatternPreferences(),
                 dialogService);
         Injector.setModelOrService(ChatHistoryService.class, chatHistoryService);
diff --git a/src/main/java/org/jabref/gui/ai/chatting/chathistory/ChatHistoryService.java b/src/main/java/org/jabref/gui/ai/chatting/chathistory/ChatHistoryService.java
index 872a263c7a1..7ae8b69bc2c 100644
--- a/src/main/java/org/jabref/gui/ai/chatting/chathistory/ChatHistoryService.java
+++ b/src/main/java/org/jabref/gui/ai/chatting/chathistory/ChatHistoryService.java
@@ -25,7 +25,6 @@
 import org.jabref.model.groups.AbstractGroup;
 import org.jabref.model.groups.GroupTreeNode;
 
-import com.airhacks.afterburner.injection.Injector;
 import com.google.common.eventbus.Subscribe;
 import dev.langchain4j.data.message.ChatMessage;
 import org.slf4j.Logger;
@@ -58,7 +57,7 @@ public class ChatHistoryService implements AutoCloseable {
 
     private static final String CHAT_HISTORY_FILE_NAME = "chat-histories.mv";
 
-    private final StateManager stateManager = Injector.instantiateModelOrService(StateManager.class);
+    private final StateManager stateManager;
 
     private final CitationKeyPatternPreferences citationKeyPatternPreferences;
 
@@ -79,31 +78,25 @@ private record ChatHistoryManagementRecord(Optional<BibDatabaseContext> bibDatab
         return o1 == o2 ? 0 : o1.getGroup().getName().compareTo(o2.getGroup().getName());
     });
 
-    public ChatHistoryService(CitationKeyPatternPreferences citationKeyPatternPreferences, NotificationService notificationService) {
+    public ChatHistoryService(StateManager stateManager, CitationKeyPatternPreferences citationKeyPatternPreferences, NotificationService notificationService) {
+        this.stateManager = stateManager;
         this.citationKeyPatternPreferences = citationKeyPatternPreferences;
         this.implementation = new MVStoreChatHistoryStorage(Directories.getAiFilesDirectory().resolve(CHAT_HISTORY_FILE_NAME), notificationService);
-        configureHistoryTransfer();
-    }
-
-    public ChatHistoryService(CitationKeyPatternPreferences citationKeyPatternPreferences,
-                              ChatHistoryStorage implementation) {
-        this.citationKeyPatternPreferences = citationKeyPatternPreferences;
-        this.implementation = implementation;
 
-        configureHistoryTransfer();
+        configureDatabaseListeners();
     }
 
-    private void configureHistoryTransfer() {
+    private void configureDatabaseListeners() {
         stateManager.getOpenDatabases().addListener((ListChangeListener<BibDatabaseContext>) change -> {
             while (change.next()) {
                 if (change.wasAdded()) {
-                    change.getAddedSubList().forEach(this::configureHistoryTransfer);
+                    change.getAddedSubList().forEach(this::configureDatabaseListeners);
                 }
             }
         });
     }
 
-    private void configureHistoryTransfer(BibDatabaseContext bibDatabaseContext) {
+    private void configureDatabaseListeners(BibDatabaseContext bibDatabaseContext) {
         bibDatabaseContext.getMetaData().getGroups().ifPresent(rootGroupTreeNode -> {
             rootGroupTreeNode.iterateOverTree().forEach(groupNode -> {
                 groupNode.getGroup().nameProperty().addListener((observable, oldValue, newValue) -> {
@@ -264,6 +257,7 @@ public void close() {
         new HashSet<>(groupsChatHistory.keySet()).forEach(this::closeChatHistoryForGroup);
 
         implementation.commit();
+        implementation.close();
     }
 
     private void transferGroupHistory(BibDatabaseContext bibDatabaseContext, GroupTreeNode groupTreeNode, String oldName, String newName) {
diff --git a/src/main/java/org/jabref/gui/preferences/ai/AiTab.fxml b/src/main/java/org/jabref/gui/preferences/ai/AiTab.fxml
index 820cb029eec..b2b3a408a14 100644
--- a/src/main/java/org/jabref/gui/preferences/ai/AiTab.fxml
+++ b/src/main/java/org/jabref/gui/preferences/ai/AiTab.fxml
@@ -43,6 +43,21 @@
             </children>
         </HBox>
 
+        <CheckBox fx:id="autoGenerateEmbeddings"
+                  mnemonicParsing="false"
+                  text="%Automatically generate embeddings for new entries"
+                  HBox.hgrow="ALWAYS"
+                  maxWidth="Infinity"/>
+
+        <CheckBox fx:id="autoGenerateSummaries"
+                  mnemonicParsing="false"
+                  text="%Automatically generate summaries for new entries"
+                  HBox.hgrow="ALWAYS"
+                  maxWidth="Infinity"/>
+
+        <Label styleClass="sectionHeader"
+               text="%Connection"/>
+
         <HBox alignment="CENTER_LEFT"
               layoutX="10.0"
               layoutY="306.0"
diff --git a/src/main/java/org/jabref/gui/preferences/ai/AiTab.java b/src/main/java/org/jabref/gui/preferences/ai/AiTab.java
index b9f21355b5d..5bad5b2f2f9 100644
--- a/src/main/java/org/jabref/gui/preferences/ai/AiTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ai/AiTab.java
@@ -29,6 +29,8 @@ public class AiTab extends AbstractPreferenceTabView<AiTabViewModel> implements
     private static final String HUGGING_FACE_CHAT_MODEL_PROMPT = "TinyLlama/TinyLlama_v1.1 (or any other model name)";
 
     @FXML private CheckBox enableAi;
+    @FXML private CheckBox autoGenerateEmbeddings;
+    @FXML private CheckBox autoGenerateSummaries;
 
     @FXML private ComboBox<AiProvider> aiProviderComboBox;
     @FXML private ComboBox<String> chatModelComboBox;
@@ -72,6 +74,10 @@ public void initialize() {
         this.viewModel = new AiTabViewModel(preferences);
 
         enableAi.selectedProperty().bindBidirectional(viewModel.enableAi());
+        autoGenerateSummaries.selectedProperty().bindBidirectional(viewModel.autoGenerateSummaries());
+        autoGenerateSummaries.disableProperty().bind(viewModel.disableAutoGenerateSummaries());
+        autoGenerateEmbeddings.selectedProperty().bindBidirectional(viewModel.autoGenerateEmbeddings());
+        autoGenerateEmbeddings.disableProperty().bind(viewModel.disableAutoGenerateEmbeddings());
 
         new ViewModelListCellFactory<AiProvider>()
                 .withText(AiProvider::toString)
diff --git a/src/main/java/org/jabref/gui/preferences/ai/AiTabViewModel.java b/src/main/java/org/jabref/gui/preferences/ai/AiTabViewModel.java
index 8ba7c3a66c0..877bf17b499 100644
--- a/src/main/java/org/jabref/gui/preferences/ai/AiTabViewModel.java
+++ b/src/main/java/org/jabref/gui/preferences/ai/AiTabViewModel.java
@@ -37,6 +37,10 @@ public class AiTabViewModel implements PreferenceTabViewModel {
     private final Locale oldLocale;
 
     private final BooleanProperty enableAi = new SimpleBooleanProperty();
+    private final BooleanProperty autoGenerateEmbeddings = new SimpleBooleanProperty();
+    private final BooleanProperty disableAutoGenerateEmbeddings = new SimpleBooleanProperty();
+    private final BooleanProperty autoGenerateSummaries = new SimpleBooleanProperty();
+    private final BooleanProperty disableAutoGenerateSummaries = new SimpleBooleanProperty();
 
     private final ListProperty<AiProvider> aiProvidersList =
             new SimpleListProperty<>(FXCollections.observableArrayList(AiProvider.values()));
@@ -295,6 +299,8 @@ public void setValues() {
         huggingFaceChatModel.setValue(aiPreferences.getHuggingFaceChatModel());
 
         enableAi.setValue(aiPreferences.getEnableAi());
+        autoGenerateSummaries.setValue(aiPreferences.getAutoGenerateSummaries());
+        autoGenerateEmbeddings.setValue(aiPreferences.getAutoGenerateEmbeddings());
 
         selectedAiProvider.setValue(aiPreferences.getAiProvider());
 
@@ -313,6 +319,8 @@ public void setValues() {
     @Override
     public void storeSettings() {
         aiPreferences.setEnableAi(enableAi.get());
+        aiPreferences.setAutoGenerateEmbeddings(autoGenerateEmbeddings.get());
+        aiPreferences.setAutoGenerateSummaries(autoGenerateSummaries.get());
 
         aiPreferences.setAiProvider(selectedAiProvider.get());
 
@@ -407,6 +415,22 @@ public BooleanProperty enableAi() {
         return enableAi;
     }
 
+    public BooleanProperty autoGenerateEmbeddings() {
+        return autoGenerateEmbeddings;
+    }
+
+    public BooleanProperty disableAutoGenerateEmbeddings() {
+        return disableAutoGenerateEmbeddings;
+    }
+
+    public BooleanProperty autoGenerateSummaries() {
+        return autoGenerateSummaries;
+    }
+
+    public BooleanProperty disableAutoGenerateSummaries() {
+        return disableAutoGenerateSummaries;
+    }
+
     public ReadOnlyListProperty<AiProvider> aiProvidersProperty() {
         return aiProvidersList;
     }
diff --git a/src/main/java/org/jabref/logic/ai/AiDefaultPreferences.java b/src/main/java/org/jabref/logic/ai/AiDefaultPreferences.java
index b17fa670867..2228de6eb84 100644
--- a/src/main/java/org/jabref/logic/ai/AiDefaultPreferences.java
+++ b/src/main/java/org/jabref/logic/ai/AiDefaultPreferences.java
@@ -52,6 +52,8 @@ public class AiDefaultPreferences {
     );
 
     public static final boolean ENABLE_CHAT = false;
+    public static final boolean AUTO_GENERATE_EMBEDDINGS = false;
+    public static final boolean AUTO_GENERATE_SUMMARIES = false;
 
     public static final AiProvider PROVIDER = AiProvider.OPEN_AI;
 
diff --git a/src/main/java/org/jabref/logic/ai/AiPreferences.java b/src/main/java/org/jabref/logic/ai/AiPreferences.java
index d3c8bb345ae..f675ab37a35 100644
--- a/src/main/java/org/jabref/logic/ai/AiPreferences.java
+++ b/src/main/java/org/jabref/logic/ai/AiPreferences.java
@@ -31,6 +31,8 @@ public class AiPreferences {
     private static final String KEYRING_AI_SERVICE_ACCOUNT = "apiKey";
 
     private final BooleanProperty enableAi;
+    private final BooleanProperty autoGenerateEmbeddings;
+    private final BooleanProperty autoGenerateSummaries;
 
     private final ObjectProperty<AiProvider> aiProvider;
 
@@ -58,6 +60,8 @@ public class AiPreferences {
     private Runnable apiKeyChangeListener;
 
     public AiPreferences(boolean enableAi,
+                         boolean autoGenerateEmbeddings,
+                         boolean autoGenerateSummaries,
                          AiProvider aiProvider,
                          String openAiChatModel,
                          String mistralAiChatModel,
@@ -78,6 +82,8 @@ public AiPreferences(boolean enableAi,
                          double ragMinScore
     ) {
         this.enableAi = new SimpleBooleanProperty(enableAi);
+        this.autoGenerateEmbeddings = new SimpleBooleanProperty(autoGenerateEmbeddings);
+        this.autoGenerateSummaries = new SimpleBooleanProperty(autoGenerateSummaries);
 
         this.aiProvider = new SimpleObjectProperty<>(aiProvider);
 
@@ -143,6 +149,30 @@ public void setEnableAi(boolean enableAi) {
         this.enableAi.set(enableAi);
     }
 
+    public BooleanProperty autoGenerateEmbeddingsProperty() {
+        return autoGenerateEmbeddings;
+    }
+
+    public boolean getAutoGenerateEmbeddings() {
+        return autoGenerateEmbeddings.get();
+    }
+
+    public void setAutoGenerateEmbeddings(boolean autoGenerateEmbeddings) {
+        this.autoGenerateEmbeddings.set(autoGenerateEmbeddings);
+    }
+
+    public BooleanProperty autoGenerateSummariesProperty() {
+        return autoGenerateSummaries;
+    }
+
+    public boolean getAutoGenerateSummaries() {
+        return autoGenerateSummaries.get();
+    }
+
+    public void setAutoGenerateSummaries(boolean autoGenerateSummaries) {
+        this.autoGenerateSummaries.set(autoGenerateSummaries);
+    }
+
     public ObjectProperty<AiProvider> aiProviderProperty() {
         return aiProvider;
     }
diff --git a/src/main/java/org/jabref/logic/ai/AiService.java b/src/main/java/org/jabref/logic/ai/AiService.java
index 30655f1721c..a3d332bb567 100644
--- a/src/main/java/org/jabref/logic/ai/AiService.java
+++ b/src/main/java/org/jabref/logic/ai/AiService.java
@@ -6,6 +6,7 @@
 import javafx.beans.property.BooleanProperty;
 import javafx.beans.property.SimpleBooleanProperty;
 
+import org.jabref.gui.StateManager;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.ai.chatting.AiChatService;
 import org.jabref.logic.ai.chatting.model.JabRefChatLanguageModel;
@@ -52,7 +53,8 @@ public class AiService implements AutoCloseable {
     private final IngestionService ingestionService;
     private final SummariesService summariesService;
 
-    public AiService(AiPreferences aiPreferences,
+    public AiService(StateManager stateManager,
+                     AiPreferences aiPreferences,
                      FilePreferences filePreferences,
                      NotificationService notificationService,
                      TaskExecutor taskExecutor
@@ -64,8 +66,11 @@ public AiService(AiPreferences aiPreferences,
         this.mvStoreSummariesStorage = new MVStoreSummariesStorage(Directories.getAiFilesDirectory().resolve(SUMMARIES_FILE_NAME), notificationService);
 
         this.jabRefEmbeddingModel = new JabRefEmbeddingModel(aiPreferences, notificationService, taskExecutor);
+
         this.aiChatService = new AiChatService(aiPreferences, jabRefChatLanguageModel, jabRefEmbeddingModel, mvStoreEmbeddingStore, cachedThreadPool);
+
         this.ingestionService = new IngestionService(
+                stateManager,
                 aiPreferences,
                 shutdownSignal,
                 jabRefEmbeddingModel,
@@ -74,7 +79,16 @@ public AiService(AiPreferences aiPreferences,
                 filePreferences,
                 taskExecutor
         );
-        this.summariesService = new SummariesService(aiPreferences, mvStoreSummariesStorage, jabRefChatLanguageModel, shutdownSignal, filePreferences, taskExecutor);
+
+        this.summariesService = new SummariesService(
+                stateManager,
+                aiPreferences,
+                mvStoreSummariesStorage,
+                jabRefChatLanguageModel,
+                shutdownSignal,
+                filePreferences,
+                taskExecutor
+        );
     }
 
     public JabRefChatLanguageModel getChatLanguageModel() {
diff --git a/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java b/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java
index 6d113891a36..27ca3c976fe 100644
--- a/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java
+++ b/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java
@@ -7,13 +7,16 @@
 
 import javafx.beans.property.ReadOnlyBooleanProperty;
 import javafx.beans.property.StringProperty;
+import javafx.collections.ListChangeListener;
 
+import org.jabref.gui.StateManager;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.ai.AiPreferences;
 import org.jabref.logic.ai.processingstatus.ProcessingInfo;
 import org.jabref.logic.ai.processingstatus.ProcessingState;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
 
 import dev.langchain4j.data.segment.TextSegment;
@@ -29,6 +32,7 @@ public class IngestionService {
 
     private final List<List<LinkedFile>> listsUnderIngestion = new ArrayList<>();
 
+    private final AiPreferences aiPreferences;
     private final FilePreferences filePreferences;
     private final TaskExecutor taskExecutor;
 
@@ -36,7 +40,8 @@ public class IngestionService {
 
     private final ReadOnlyBooleanProperty shutdownSignal;
 
-    public IngestionService(AiPreferences aiPreferences,
+    public IngestionService(StateManager stateManager,
+                            AiPreferences aiPreferences,
                             ReadOnlyBooleanProperty shutdownSignal,
                             EmbeddingModel embeddingModel,
                             EmbeddingStore<TextSegment> embeddingStore,
@@ -44,6 +49,7 @@ public IngestionService(AiPreferences aiPreferences,
                             FilePreferences filePreferences,
                             TaskExecutor taskExecutor
     ) {
+        this.aiPreferences = aiPreferences;
         this.filePreferences = filePreferences;
         this.taskExecutor = taskExecutor;
 
@@ -56,6 +62,32 @@ public IngestionService(AiPreferences aiPreferences,
         );
 
         this.shutdownSignal = shutdownSignal;
+
+        configureDatabaseListeners(stateManager);
+    }
+
+    private void configureDatabaseListeners(StateManager stateManager) {
+        stateManager.getOpenDatabases().addListener((ListChangeListener<BibDatabaseContext>) change -> {
+            while (change.next()) {
+                if (change.wasAdded()) {
+                    change.getAddedSubList().forEach(this::configureDatabaseListeners);
+                }
+            }
+        });
+    }
+
+    private void configureDatabaseListeners(BibDatabaseContext bibDatabaseContext) {
+        bibDatabaseContext.getDatabase().getEntries().addListener((ListChangeListener<BibEntry>) change -> {
+            while (change.next()) {
+                if (change.wasAdded()) {
+                    change.getAddedSubList().forEach(entry -> {
+                        if (aiPreferences.getAutoGenerateEmbeddings()) {
+                            entry.getFiles().forEach(linkedFile -> ingest(linkedFile, bibDatabaseContext));
+                        }
+                    });
+                }
+            }
+        });
     }
 
     /**
diff --git a/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java b/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java
index c71db69cdf8..b63aecdb751 100644
--- a/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java
+++ b/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java
@@ -6,7 +6,9 @@
 import java.util.Optional;
 
 import javafx.beans.property.BooleanProperty;
+import javafx.collections.ListChangeListener;
 
+import org.jabref.gui.StateManager;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.ai.AiPreferences;
 import org.jabref.logic.ai.processingstatus.ProcessingInfo;
@@ -34,6 +36,7 @@ public class SummariesService {
 
     private final Map<BibEntry, ProcessingInfo<BibEntry, Summary>> summariesStatusMap = new HashMap<>();
 
+    private final StateManager stateManager;
     private final AiPreferences aiPreferences;
     private final SummariesStorage summariesStorage;
     private final ChatLanguageModel chatLanguageModel;
@@ -41,13 +44,15 @@ public class SummariesService {
     private final FilePreferences filePreferences;
     private final TaskExecutor taskExecutor;
 
-    public SummariesService(AiPreferences aiPreferences,
+    public SummariesService(StateManager stateManager,
+                            AiPreferences aiPreferences,
                             SummariesStorage summariesStorage,
                             ChatLanguageModel chatLanguageModel,
                             BooleanProperty shutdownSignal,
                             FilePreferences filePreferences,
                             TaskExecutor taskExecutor
     ) {
+        this.stateManager = stateManager;
         this.aiPreferences = aiPreferences;
         this.summariesStorage = summariesStorage;
         this.chatLanguageModel = chatLanguageModel;
@@ -56,6 +61,30 @@ public SummariesService(AiPreferences aiPreferences,
         this.taskExecutor = taskExecutor;
     }
 
+    private void configureDatabaseListeners(StateManager stateManager) {
+        stateManager.getOpenDatabases().addListener((ListChangeListener<BibDatabaseContext>) change -> {
+            while (change.next()) {
+                if (change.wasAdded()) {
+                    change.getAddedSubList().forEach(this::configureDatabaseListeners);
+                }
+            }
+        });
+    }
+
+    private void configureDatabaseListeners(BibDatabaseContext bibDatabaseContext) {
+        bibDatabaseContext.getDatabase().getEntries().addListener((ListChangeListener<BibEntry>) change -> {
+            while (change.next()) {
+                if (change.wasAdded()) {
+                    change.getAddedSubList().forEach(entry -> {
+                        if (aiPreferences.getAutoGenerateEmbeddings()) {
+                            summarize(entry, bibDatabaseContext);
+                        }
+                    });
+                }
+            }
+        });
+    }
+
     /**
      * Start generating summary of a {@link BibEntry}, if it was already generated.
      * This method returns a {@link ProcessingInfo} that can be used for tracking state of the summarization.
diff --git a/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java b/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java
index 3423df38a8d..336c6b7f749 100644
--- a/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java
+++ b/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java
@@ -340,6 +340,8 @@ public class JabRefCliPreferences implements CliPreferences {
     private static final String REMOTE_SERVER_PORT = "remoteServerPort";
 
     private static final String AI_ENABLED = "aiEnabled";
+    private static final String AI_AUTO_GENERATE_EMBEDDINGS = "aiAutoGenerateEmbeddings";
+    private static final String AI_AUTO_GENERATE_SUMMARIES = "aiAutoGenerateSummaries";
     private static final String AI_PROVIDER = "aiProvider";
     private static final String AI_OPEN_AI_CHAT_MODEL = "aiOpenAiChatModel";
     private static final String AI_MISTRAL_AI_CHAT_MODEL = "aiMistralAiChatModel";
@@ -620,6 +622,8 @@ protected JabRefCliPreferences() {
 
         // region:AI
         defaults.put(AI_ENABLED, AiDefaultPreferences.ENABLE_CHAT);
+        defaults.put(AI_AUTO_GENERATE_EMBEDDINGS, AiDefaultPreferences.AUTO_GENERATE_EMBEDDINGS);
+        defaults.put(AI_AUTO_GENERATE_SUMMARIES, AiDefaultPreferences.AUTO_GENERATE_SUMMARIES);
         defaults.put(AI_PROVIDER, AiDefaultPreferences.PROVIDER.name());
         defaults.put(AI_OPEN_AI_CHAT_MODEL, AiDefaultPreferences.CHAT_MODELS.get(AiProvider.OPEN_AI));
         defaults.put(AI_MISTRAL_AI_CHAT_MODEL, AiDefaultPreferences.CHAT_MODELS.get(AiProvider.MISTRAL_AI));
@@ -1811,6 +1815,8 @@ public AiPreferences getAiPreferences() {
 
         aiPreferences = new AiPreferences(
                 aiEnabled,
+                getBoolean(AI_AUTO_GENERATE_EMBEDDINGS),
+                getBoolean(AI_AUTO_GENERATE_SUMMARIES),
                 AiProvider.valueOf(get(AI_PROVIDER)),
                 get(AI_OPEN_AI_CHAT_MODEL),
                 get(AI_MISTRAL_AI_CHAT_MODEL),
@@ -1831,6 +1837,8 @@ public AiPreferences getAiPreferences() {
                 getDouble(AI_RAG_MIN_SCORE));
 
         EasyBind.listen(aiPreferences.enableAiProperty(), (obs, oldValue, newValue) -> putBoolean(AI_ENABLED, newValue));
+        EasyBind.listen(aiPreferences.autoGenerateEmbeddingsProperty(), (obs, oldValue, newValue) -> putBoolean(AI_AUTO_GENERATE_EMBEDDINGS, newValue));
+        EasyBind.listen(aiPreferences.autoGenerateSummariesProperty(), (obs, oldValue, newValue) -> putBoolean(AI_AUTO_GENERATE_SUMMARIES, newValue));
 
         EasyBind.listen(aiPreferences.aiProviderProperty(), (obs, oldValue, newValue) -> put(AI_PROVIDER, newValue.name()));
 

From 57717fa8c875a58b0c7e80310e1305cc68242a97 Mon Sep 17 00:00:00 2001
From: InAnYan <ruslanpopov1512@gmail.com>
Date: Thu, 26 Sep 2024 09:14:36 +0300
Subject: [PATCH 2/3] GC ate my listeners

---
 .../logic/ai/ingestion/IngestionService.java  | 45 ++++++++++++++----
 .../ai/summarization/SummariesService.java    | 46 ++++++++++++++-----
 2 files changed, 69 insertions(+), 22 deletions(-)

diff --git a/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java b/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java
index 27ca3c976fe..39f506fc3ca 100644
--- a/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java
+++ b/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java
@@ -4,6 +4,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.TreeMap;
 
 import javafx.beans.property.ReadOnlyBooleanProperty;
 import javafx.beans.property.StringProperty;
@@ -16,9 +17,15 @@
 import org.jabref.logic.ai.processingstatus.ProcessingState;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.database.event.EntriesAddedEvent;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
+import org.jabref.model.entry.event.FieldAddedOrRemovedEvent;
+import org.jabref.model.entry.event.FieldChangedEvent;
+import org.jabref.model.entry.field.SpecialField;
+import org.jabref.model.entry.field.StandardField;
 
+import com.google.common.eventbus.Subscribe;
 import dev.langchain4j.data.segment.TextSegment;
 import dev.langchain4j.model.embedding.EmbeddingModel;
 import dev.langchain4j.store.embedding.EmbeddingStore;
@@ -28,7 +35,8 @@
  * Use this class in the logic and UI.
  */
 public class IngestionService {
-    private final Map<LinkedFile, ProcessingInfo<LinkedFile, Void>> ingestionStatusMap = new HashMap<>();
+    // We use a {@link TreeMap} here for the same reasons we use it in {@link ChatHistoryService}.
+    private final TreeMap<LinkedFile, ProcessingInfo<LinkedFile, Void>> ingestionStatusMap = new TreeMap<>((o1, o2) -> o1 == o2 ? 0 : o1.getLink().compareTo(o2.getLink()));
 
     private final List<List<LinkedFile>> listsUnderIngestion = new ArrayList<>();
 
@@ -77,17 +85,34 @@ private void configureDatabaseListeners(StateManager stateManager) {
     }
 
     private void configureDatabaseListeners(BibDatabaseContext bibDatabaseContext) {
-        bibDatabaseContext.getDatabase().getEntries().addListener((ListChangeListener<BibEntry>) change -> {
-            while (change.next()) {
-                if (change.wasAdded()) {
-                    change.getAddedSubList().forEach(entry -> {
-                        if (aiPreferences.getAutoGenerateEmbeddings()) {
-                            entry.getFiles().forEach(linkedFile -> ingest(linkedFile, bibDatabaseContext));
-                        }
-                    });
+        // GC was eating the listeners, so we have to fall back to the event bus.
+        bibDatabaseContext.getDatabase().registerListener(new EntriesChangedListener(bibDatabaseContext));
+    }
+
+    private class EntriesChangedListener {
+        private final BibDatabaseContext bibDatabaseContext;
+
+        public EntriesChangedListener(BibDatabaseContext bibDatabaseContext) {
+            this.bibDatabaseContext = bibDatabaseContext;
+        }
+
+        @Subscribe
+        public void listen(EntriesAddedEvent e) {
+            e.getBibEntries().forEach(entry -> {
+                if (aiPreferences.getAutoGenerateEmbeddings()) {
+                    entry.getFiles().forEach(linkedFile -> ingest(linkedFile, bibDatabaseContext));
                 }
+
+                entry.registerListener(this);
+            });
+        }
+
+        @Subscribe
+        public void listen(FieldChangedEvent e) {
+            if (e.getField() == StandardField.FILE && aiPreferences.getAutoGenerateEmbeddings()) {
+                e.getBibEntry().getFiles().forEach(linkedFile -> ingest(linkedFile, bibDatabaseContext));
             }
-        });
+        }
     }
 
     /**
diff --git a/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java b/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java
index b63aecdb751..59056148a2e 100644
--- a/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java
+++ b/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java
@@ -1,9 +1,11 @@
 package org.jabref.logic.ai.summarization;
 
 import java.time.LocalDateTime;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Optional;
+import java.util.TreeMap;
 
 import javafx.beans.property.BooleanProperty;
 import javafx.collections.ListChangeListener;
@@ -11,13 +13,18 @@
 import org.jabref.gui.StateManager;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.ai.AiPreferences;
+import org.jabref.logic.ai.ingestion.IngestionService;
 import org.jabref.logic.ai.processingstatus.ProcessingInfo;
 import org.jabref.logic.ai.processingstatus.ProcessingState;
 import org.jabref.logic.ai.util.CitationKeyCheck;
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.database.event.EntriesAddedEvent;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.event.FieldChangedEvent;
+import org.jabref.model.entry.field.StandardField;
 
+import com.google.common.eventbus.Subscribe;
 import dev.langchain4j.model.chat.ChatLanguageModel;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -34,9 +41,8 @@
 public class SummariesService {
     private static final Logger LOGGER = LoggerFactory.getLogger(SummariesService.class);
 
-    private final Map<BibEntry, ProcessingInfo<BibEntry, Summary>> summariesStatusMap = new HashMap<>();
+    private final TreeMap<BibEntry, ProcessingInfo<BibEntry, Summary>> summariesStatusMap = new TreeMap<>(Comparator.comparing(BibEntry::getId));
 
-    private final StateManager stateManager;
     private final AiPreferences aiPreferences;
     private final SummariesStorage summariesStorage;
     private final ChatLanguageModel chatLanguageModel;
@@ -52,13 +58,14 @@ public SummariesService(StateManager stateManager,
                             FilePreferences filePreferences,
                             TaskExecutor taskExecutor
     ) {
-        this.stateManager = stateManager;
         this.aiPreferences = aiPreferences;
         this.summariesStorage = summariesStorage;
         this.chatLanguageModel = chatLanguageModel;
         this.shutdownSignal = shutdownSignal;
         this.filePreferences = filePreferences;
         this.taskExecutor = taskExecutor;
+
+        configureDatabaseListeners(stateManager);
     }
 
     private void configureDatabaseListeners(StateManager stateManager) {
@@ -72,17 +79,32 @@ private void configureDatabaseListeners(StateManager stateManager) {
     }
 
     private void configureDatabaseListeners(BibDatabaseContext bibDatabaseContext) {
-        bibDatabaseContext.getDatabase().getEntries().addListener((ListChangeListener<BibEntry>) change -> {
-            while (change.next()) {
-                if (change.wasAdded()) {
-                    change.getAddedSubList().forEach(entry -> {
-                        if (aiPreferences.getAutoGenerateEmbeddings()) {
-                            summarize(entry, bibDatabaseContext);
-                        }
-                    });
+        // GC was eating the listeners, so we have to fall back to the event bus.
+        bibDatabaseContext.getDatabase().registerListener(new EntriesChangedListener(bibDatabaseContext));
+    }
+
+    private class EntriesChangedListener {
+        private final BibDatabaseContext bibDatabaseContext;
+
+        public EntriesChangedListener(BibDatabaseContext bibDatabaseContext) {
+            this.bibDatabaseContext = bibDatabaseContext;
+        }
+
+        @Subscribe
+        public void listen(EntriesAddedEvent e) {
+            e.getBibEntries().forEach(entry -> {
+                if (aiPreferences.getAutoGenerateSummaries()) {
+                    summarize(entry, bibDatabaseContext);
                 }
+            });
+        }
+
+        @Subscribe
+        public void listen(FieldChangedEvent e) {
+            if (e.getField() == StandardField.FILE && aiPreferences.getAutoGenerateSummaries()) {
+                summarize(e.getBibEntry(), bibDatabaseContext);
             }
-        });
+        }
     }
 
     /**

From 2f1990e70a1e5b5bf8d532e5a77ba6aa5b57c90a Mon Sep 17 00:00:00 2001
From: InAnYan <ruslanpopov1512@gmail.com>
Date: Thu, 26 Sep 2024 09:28:46 +0300
Subject: [PATCH 3/3] Fix checkers

---
 .../java/org/jabref/logic/ai/ingestion/IngestionService.java | 5 -----
 .../org/jabref/logic/ai/summarization/SummariesService.java  | 3 ---
 src/main/resources/l10n/JabRef_en.properties                 | 3 +++
 3 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java b/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java
index 39f506fc3ca..a5779b92cbb 100644
--- a/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java
+++ b/src/main/java/org/jabref/logic/ai/ingestion/IngestionService.java
@@ -1,9 +1,7 @@
 package org.jabref.logic.ai.ingestion;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 import java.util.TreeMap;
 
 import javafx.beans.property.ReadOnlyBooleanProperty;
@@ -18,11 +16,8 @@
 import org.jabref.logic.util.TaskExecutor;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.event.EntriesAddedEvent;
-import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
-import org.jabref.model.entry.event.FieldAddedOrRemovedEvent;
 import org.jabref.model.entry.event.FieldChangedEvent;
-import org.jabref.model.entry.field.SpecialField;
 import org.jabref.model.entry.field.StandardField;
 
 import com.google.common.eventbus.Subscribe;
diff --git a/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java b/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java
index 59056148a2e..0942ffec8a9 100644
--- a/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java
+++ b/src/main/java/org/jabref/logic/ai/summarization/SummariesService.java
@@ -2,8 +2,6 @@
 
 import java.time.LocalDateTime;
 import java.util.Comparator;
-import java.util.HashMap;
-import java.util.Map;
 import java.util.Optional;
 import java.util.TreeMap;
 
@@ -13,7 +11,6 @@
 import org.jabref.gui.StateManager;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.ai.AiPreferences;
-import org.jabref.logic.ai.ingestion.IngestionService;
 import org.jabref.logic.ai.processingstatus.ProcessingInfo;
 import org.jabref.logic.ai.processingstatus.ProcessingState;
 import org.jabref.logic.ai.util.CitationKeyCheck;
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 2ec8827add2..3817d94749a 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2633,6 +2633,9 @@ RAG\ minimum\ score\ must\ be\ a\ number=RAG minimum score must be a number
 RAG\ minimum\ score\ must\ be\ greater\ than\ 0\ and\ less\ than\ 1=RAG minimum score must be greater than 0 and less than 1
 Temperature\ must\ be\ a\ number=Temperature must be a number
 If\ you\ have\ chosen\ %0\ as\ an\ AI\ provider,\ the\ privacy\ policy\ of\ %0\ applies.\ You\ find\ it\ at\ %1.=If you have chosen %0 as an AI provider, the privacy policy of %0 applies. You find it at %1.
+Automatically\ generate\ embeddings\ for\ new\ entries=Automatically generate embeddings for new entries
+Automatically\ generate\ summaries\ for\ new\ entries=Automatically generate summaries for new entries
+Connection=Connection
 
 Link=Link
 Source\ URL=Source URL