Fix bugs

src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -46,6 +46,7 @@
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.TaskExecutor;
+import org.jabref.logic.ai.AiService;
 import org.jabref.logic.bibtex.TypedBibEntry;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.EntryBasedFetcher;
@@ -88,6 +89,9 @@ public class EntryEditor extends BorderPane {
     private final ExternalFilesEntryLinker fileLinker;
     private final DirectoryMonitorManager directoryMonitorManager;
 
+    // TODO: Move this out.
+    private final AiService aiService;
+
     private Subscription typeSubscription;
 
     /*
@@ -132,6 +136,8 @@ public EntryEditor(LibraryTab libraryTab) {
                   .root(this)
                   .load();
 
+        this.aiService = new AiService(preferencesService.getAiPreferences());
+
         this.entryEditorPreferences = preferencesService.getEntryEditorPreferences();
         this.fileLinker = new ExternalFilesEntryLinker(preferencesService.getFilePreferences(), databaseContext, dialogService);
 
@@ -315,7 +321,7 @@ private List<EntryEditorTab> createTabs() {
         entryEditorTabs.add(sourceTab);
         entryEditorTabs.add(new LatexCitationsTab(databaseContext, preferencesService, dialogService, directoryMonitorManager));
         entryEditorTabs.add(new FulltextSearchResultsTab(stateManager, preferencesService, dialogService, taskExecutor));
-        entryEditorTabs.add(new AiChatTab(preferencesService, databaseContext, taskExecutor));
+        entryEditorTabs.add(new AiChatTab(preferencesService, aiService, databaseContext, taskExecutor));
 
         return entryEditorTabs;
     }

src/main/java/org/jabref/gui/entryeditor/aichattab/AiChatTab.java

@@ -57,9 +57,6 @@ public class AiChatTab extends EntryEditorTab {
 
     private BibEntry currentBibEntry = null;
 
-    // TODO: Proper embeddings.
-    private EmbeddingStore<TextSegment> embeddingStore = null;
-
     public AiChatTab(PreferencesService preferencesService, AiService aiService,
                      BibDatabaseContext bibDatabaseContext, TaskExecutor taskExecutor) {
         this.filePreferences = preferencesService.getFilePreferences();
@@ -117,12 +114,12 @@ private void bindToCorrectEntry(BibEntry entry) {
     }
 
     private void createAiChat() {
-        aiChat = new AiChat(aiService, MetadataFilterBuilder.metadataKey("linkedFile").isIn(currentBibEntry.getFiles()));
+        aiChat = new AiChat(aiService, MetadataFilterBuilder.metadataKey("linkedFile").isIn(currentBibEntry.getFiles().stream().map(LinkedFile::getLink).toList()));
         aiChat.setSystemMessage(QA_SYSTEM_MESSAGE);
     }
 
     private void ingestFiles(BibEntry entry) {
-        AiIngestor aiIngestor = new AiIngestor(embeddingStore, aiService.getEmbeddingModel());
+        AiIngestor aiIngestor = new AiIngestor(aiService.getEmbeddingStore(), aiService.getEmbeddingModel());
         entry.getFiles().forEach(file -> {
             aiIngestor.ingestLinkedFile(file, bibDatabaseContext, filePreferences);
         });

src/main/java/org/jabref/gui/importer/actions/LoadChatHistoryAction.java

@@ -17,6 +17,7 @@
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
 
+import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -41,7 +42,10 @@ private void readAiChatsFile(BibDatabase bibDatabase, Path databasePath) {
         File chatFile = chatPath.toFile();
         try {
             InputStream inputStream = new FileInputStream(chatFile);
+
             ObjectMapper objectMapper = new ObjectMapper();
+            // Jackson JSON adds an unknown field "typeLabel".
+            objectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
             AiChatsFile aiChatFile = objectMapper.readValue(inputStream, AiChatsFile.class);
             loadAiChatHistory(bibDatabase, aiChatFile);
         } catch (FileNotFoundException e) {

src/main/java/org/jabref/logic/ai/AiIngestor.java

@@ -53,7 +53,7 @@ public AiIngestor(EmbeddingStore<TextSegment> embeddingStore, EmbeddingModel emb
     public void ingestLinkedFile(LinkedFile linkedFile, BibDatabaseContext bibDatabaseContext, FilePreferences filePreferences) {
         Optional<Path> path = linkedFile.findIn(bibDatabaseContext, filePreferences);
         if (path.isPresent()) {
-            ingestFile(path.get(), new Metadata().add("linkedFile", linkedFile));
+            ingestFile(path.get(), new Metadata().add("linkedFile", linkedFile.getLink()));
         } else {
             LOGGER.error("Could not find path for a linked file: " + linkedFile.getLink());
         }

src/main/java/org/jabref/logic/ai/AiService.java

@@ -32,6 +32,10 @@ public class AiService {
     private final EventBus eventBus = new EventBus();
 
     public AiService(AiPreferences aiPreferences) {
+        if (aiPreferences.getEnableChatWithFiles() && !aiPreferences.getOpenAiToken().isEmpty()) {
+            setOpenAiToken(aiPreferences.getOpenAiToken());
+        }
+
         EasyBind.listen(aiPreferences.enableChatWithFilesProperty(), (property, oldValue, newValue) -> {
             if (newValue) {
                 if (!aiPreferences.getOpenAiToken().isEmpty()) {