fix: hydrate worker DB in server mode + fix LadybugDB getAll API mismatch (#398) (#404)

Fix server/bridge mode leaving the web UI with 0 nodes and broken
Query/Processes/embeddings by hydrating the worker-side LadybugDB
and BM25 indexes after loading graph data from the backend.

Also fix LadybugDB QueryResult API mismatch where result.getAll()
does not exist in some @ladybugdb/wasm-core versions — falls back
to getAllObjects() or getAllRows().

gitnexus-web/src/App.tsx

@@ -40,6 +40,7 @@ const AppContent = () => {
     availableRepos,
     setAvailableRepos,
     switchRepo,
+    hydrateWorkerFromServer,
   } = useAppState();
 
   const graphCanvasRef = useRef<GraphCanvasHandle>(null);
@@ -157,21 +158,31 @@ const AppContent = () => {
 
     // Transition directly to exploring view
     setViewMode('exploring');
+    setProgress(null);
 
-    // Initialize agent if LLM is configured
-    if (getActiveProviderConfig()) {
-      initializeAgent(projectName);
-    }
+    // Hydrate the worker-side DB (LadybugDB + BM25) so Query/Processes/embeddings work
+    hydrateWorkerFromServer(result.nodes, result.relationships, result.fileContents).then(() => {
+      // Initialize agent if LLM is configured
+      if (getActiveProviderConfig()) {
+        initializeAgent(projectName);
+      }
 
-    // Auto-start embeddings
-    startEmbeddings().catch((err) => {
-      if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
-        startEmbeddings('wasm').catch(console.warn);
-      } else {
-        console.warn('Embeddings auto-start failed:', err);
+      // Auto-start embeddings (now that LadybugDB is ready)
+      startEmbeddings().catch((err) => {
+        if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
+          startEmbeddings('wasm').catch(console.warn);
+        } else {
+          console.warn('Embeddings auto-start failed:', err);
+        }
+      });
+    }).catch((err) => {
+      console.warn('Worker hydration failed (non-fatal):', err);
+      // Still initialize agent even if hydration fails
+      if (getActiveProviderConfig()) {
+        initializeAgent(projectName);
       }
     });
-  }, [setViewMode, setGraph, setFileContents, setProjectName, initializeAgent, startEmbeddings]);
+  }, [setViewMode, setGraph, setFileContents, setProjectName, setProgress, initializeAgent, startEmbeddings, hydrateWorkerFromServer]);
 
   // Auto-connect when ?server query param is present (bookmarkable shortcut)
   const autoConnectRan = useRef(false);

gitnexus-web/src/core/lbug/lbug-adapter.ts

@@ -190,7 +190,7 @@ export const loadGraphToLbug = async (
     for (const tableName of NODE_TABLES) {
       try {
         const countRes = await conn.query(`MATCH (n:${tableName}) RETURN count(n) AS cnt`);
-        const countRows = await countRes.getAll();
+        const countRows = await (countRes.getAll?.() ?? countRes.getAllObjects?.() ?? countRes.getAllRows?.() ?? []);
         const countRow = countRows[0];
         const count = countRow ? (countRow.cnt ?? countRow[0] ?? 0) : 0;
         totalNodes += Number(count);
@@ -293,8 +293,8 @@ export const executeQuery = async (cypher: string): Promise<any[]> => {
       });
     }
 
-    // Collect all rows
-    const allRows = await result.getAll();
+    // Collect all rows (handle API differences across LadybugDB versions)
+    const allRows = await (result.getAll?.() ?? result.getAllObjects?.() ?? result.getAllRows?.() ?? []);
     const rows: any[] = [];
     for (const row of allRows) {
       // Convert tuple to named object if we have column names and row is array
@@ -331,7 +331,7 @@ export const getLbugStats = async (): Promise<{ nodes: number; edges: number }>
     for (const tableName of NODE_TABLES) {
       try {
         const nodeResult = await conn.query(`MATCH (n:${tableName}) RETURN count(n) AS cnt`);
-        const nodeRows = await nodeResult.getAll();
+        const nodeRows = await (nodeResult.getAll?.() ?? nodeResult.getAllObjects?.() ?? nodeResult.getAllRows?.() ?? []);
         const nodeRow = nodeRows[0];
         totalNodes += Number(nodeRow?.cnt ?? nodeRow?.[0] ?? 0);
       } catch {
@@ -343,7 +343,7 @@ export const getLbugStats = async (): Promise<{ nodes: number; edges: number }>
     let totalEdges = 0;
     try {
       const edgeResult = await conn.query(`MATCH ()-[r:${REL_TABLE_NAME}]->() RETURN count(r) AS cnt`);
-      const edgeRows = await edgeResult.getAll();
+      const edgeRows = await (edgeResult.getAll?.() ?? edgeResult.getAllObjects?.() ?? edgeResult.getAllRows?.() ?? []);
       const edgeRow = edgeRows[0];
       totalEdges = Number(edgeRow?.cnt ?? edgeRow?.[0] ?? 0);
     } catch {
@@ -408,7 +408,7 @@ export const executePrepared = async (
 
     const result = await conn.execute(stmt, params);
 
-    const rows = await result.getAll();
+    const rows = await (result.getAll?.() ?? result.getAllObjects?.() ?? result.getAllRows?.() ?? []);
 
     await stmt.close();
     return rows;
@@ -472,7 +472,7 @@ export const testArrayParams = async (): Promise<{ success: boolean; error?: str
     for (const tableName of NODE_TABLES) {
       try {
         const nodeResult = await conn.query(`MATCH (n:${tableName}) RETURN n.id AS id LIMIT 1`);
-        const nodeRows = await nodeResult.getAll();
+        const nodeRows = await (nodeResult.getAll?.() ?? nodeResult.getAllObjects?.() ?? nodeResult.getAllRows?.() ?? []);
         const nodeRow = nodeRows[0];
         if (nodeRow) {
           testNodeId = nodeRow.id ?? nodeRow[0];
@@ -509,7 +509,7 @@ export const testArrayParams = async (): Promise<{ success: boolean; error?: str
     const verifyResult = await conn.query(
       `MATCH (e:${EMBEDDING_TABLE_NAME} {nodeId: '${testNodeId}'}) RETURN e.embedding AS emb`
     );
-    const verifyRows = await verifyResult.getAll();
+    const verifyRows = await (verifyResult.getAll?.() ?? verifyResult.getAllObjects?.() ?? verifyResult.getAllRows?.() ?? []);
     const verifyRow = verifyRows[0];
     const storedEmb = verifyRow?.emb ?? verifyRow?.[0];
 

gitnexus-web/src/hooks/useAppState.tsx

@@ -125,6 +125,7 @@ interface AppState {
   runPipelineFromFiles: (files: FileEntry[], onProgress: (p: PipelineProgress) => void, clusteringConfig?: ProviderConfig) => Promise<PipelineResult>;
   runQuery: (cypher: string) => Promise<any[]>;
   isDatabaseReady: () => Promise<boolean>;
+  hydrateWorkerFromServer: (nodes: any[], relationships: any[], fileContents: Record<string, string>) => Promise<void>;
 
   // Embedding state
   embeddingStatus: EmbeddingStatus;
@@ -482,6 +483,16 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     }
   }, []);
 
+  const hydrateWorkerFromServer = useCallback(async (
+    nodes: any[],
+    relationships: any[],
+    fileContents: Record<string, string>
+  ): Promise<void> => {
+    const api = apiRef.current;
+    if (!api) throw new Error('Worker not initialized');
+    await api.hydrateFromServerData(nodes, relationships, fileContents);
+  }, []);
+
   // Embedding methods
   const startEmbeddings = useCallback(async (forceDevice?: 'webgpu' | 'wasm'): Promise<void> => {
     const api = apiRef.current;
@@ -1018,15 +1029,23 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
       setFileContents(fileMap);
 
       setViewMode('exploring');
+      setProgress(null);
 
-      if (getActiveProviderConfig()) initializeAgent(pName);
+      // Hydrate the worker-side DB (LadybugDB + BM25) so Query/Processes/embeddings work
+      hydrateWorkerFromServer(result.nodes, result.relationships, result.fileContents).then(() => {
+        if (getActiveProviderConfig()) initializeAgent(pName);
 
-      startEmbeddings().catch((err) => {
-        if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
-          startEmbeddings('wasm').catch(console.warn);
-        } else {
-          console.warn('Embeddings auto-start failed:', err);
-        }
+        startEmbeddings().catch((err) => {
+          if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
+            startEmbeddings('wasm').catch(console.warn);
+          } else {
+            console.warn('Embeddings auto-start failed:', err);
+          }
+        });
+      }).catch((err) => {
+        console.warn('Worker hydration failed (non-fatal):', err);
+        // Still initialize agent even if hydration fails
+        if (getActiveProviderConfig()) initializeAgent(pName);
       });
     } catch (err) {
       console.error('Repo switch failed:', err);
@@ -1037,7 +1056,7 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
       });
       setTimeout(() => { setViewMode('exploring'); setProgress(null); }, 3000);
     }
-  }, [serverBaseUrl, setProgress, setViewMode, setProjectName, setGraph, setFileContents, initializeAgent, startEmbeddings, setHighlightedNodeIds, clearAIToolHighlights, clearBlastRadius, setSelectedNode, setQueryResult, setCodeReferences, setCodePanelOpen, setCodeReferenceFocus]);
+  }, [serverBaseUrl, setProgress, setViewMode, setProjectName, setGraph, setFileContents, initializeAgent, startEmbeddings, hydrateWorkerFromServer, setHighlightedNodeIds, clearAIToolHighlights, clearBlastRadius, setSelectedNode, setQueryResult, setCodeReferences, setCodePanelOpen, setCodeReferenceFocus]);
 
   const removeCodeReference = useCallback((id: string) => {
     setCodeReferences(prev => {
@@ -1142,6 +1161,7 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     runPipelineFromFiles,
     runQuery,
     isDatabaseReady,
+    hydrateWorkerFromServer,
     // Embedding state and methods
     embeddingStatus,
     embeddingProgress,

gitnexus-web/src/workers/ingestion.worker.ts

@@ -1,5 +1,7 @@
 import * as Comlink from 'comlink';
 import { runIngestionPipeline, runPipelineFromFiles } from '../core/ingestion/pipeline';
+import { createKnowledgeGraph } from '../core/graph/graph';
+import type { GraphNode, GraphRelationship } from '../core/graph/types';
 import { PipelineProgress, SerializablePipelineResult, serializePipelineResult } from '../types/pipeline';
 import { FileEntry } from '../services/zip';
 import {
@@ -207,6 +209,50 @@ const workerApi = {
     return serializePipelineResult(result);
   },
 
+  /**
+   * Hydrate the worker-side database and indexes from server-loaded data.
+   * This is the missing step when using server/bridge mode — the main thread
+   * builds the React graph, but the worker's LadybugDB + BM25 stay empty.
+   */
+  async hydrateFromServerData(
+    nodes: GraphNode[],
+    relationships: GraphRelationship[],
+    fileContents: Record<string, string>
+  ): Promise<void> {
+    // 1. Build a KnowledgeGraph the same way the pipeline does
+    const graph = createKnowledgeGraph();
+    for (const node of nodes) graph.addNode(node);
+    for (const rel of relationships) graph.addRelationship(rel);
+
+    // 2. Store file contents for grep/read tools
+    storedFileContents = new Map(Object.entries(fileContents));
+
+    // 3. Build BM25 keyword index
+    const bm25DocCount = buildBM25Index(storedFileContents);
+    if (import.meta.env.DEV) {
+      console.log(`🔍 BM25 index built (server mode): ${bm25DocCount} documents`);
+    }
+
+    // 4. Set currentGraphResult so the agent context builder works
+    currentGraphResult = { graph, fileContents: storedFileContents };
+
+    // 5. Load graph into LadybugDB for Cypher queries (optional — gracefully degrades)
+    try {
+      const lbug = await getLbugAdapter();
+      await lbug.loadGraphToLbug(graph, storedFileContents);
+
+      if (import.meta.env.DEV) {
+        const stats = await lbug.getLbugStats();
+        console.log('✅ LadybugDB hydrated (server mode):', stats);
+      }
+    } catch (err) {
+      // LadybugDB is optional — silently continue without it
+      if (import.meta.env.DEV) {
+        console.warn('⚠️ LadybugDB hydration failed (non-fatal):', err);
+      }
+    }
+  },
+
   /**
    * Execute a Cypher query against the LadybugDB database
    * @param cypher - The Cypher query string