Fix Kuzu lock: connection cache per dbPath for MCP tools

- graph-store: getCachedOrOpenGraphStore(), invalidateGraphStoreCache()
- MCP tools (context, query, impact, cypher, rename, indexDbGraph) use cache
- indexDbGraph: invalidate before (re)index so write uses fresh connection
- clean_index: invalidate affected paths before cleanIndex()
Avoids 'Could not set lock on file' when tools open same DB repeatedly.

Made-with: Cursor

Author: chouswei

src/graph/graph-store.ts

@@ -1,6 +1,7 @@
 /**
  * GraphStore: open/create Kuzu DB, addDocument, addSymbol, addEdge, getConnection.
  * Phase 2 step 7.
+ * Connection cache: one store per dbPath per process to avoid Kuzu "Could not set lock on file".
  */
 
 import * as kuzu from 'kuzu';
@@ -9,6 +10,8 @@ import { dirname } from 'path';
 import type { NodeLabel, SymbolProps } from '../types.js';
 import { getSchemaDdl, NODE_TABLE } from './schema.js';
 
+const storeCache = new Map<string, GraphStore>();
+
 function escapeCypherString(s: string): string {
   return s.replace(/\\/g, '\\\\').replace(/'/g, "\\'");
 }
@@ -71,3 +74,23 @@ export async function openGraphStore(dbPath: string): Promise<GraphStore> {
     getConnection: () => conn,
   };
 }
+
+/**
+ * Return cached GraphStore for dbPath or open once and cache it.
+ * Use this in MCP tools so repeated/concurrent requests share one connection per DB (avoids Kuzu lock errors).
+ */
+export async function getCachedOrOpenGraphStore(dbPath: string): Promise<GraphStore> {
+  const cached = storeCache.get(dbPath);
+  if (cached) return cached;
+  const store = await openGraphStore(dbPath);
+  storeCache.set(dbPath, store);
+  return store;
+}
+
+/**
+ * Remove cached store for dbPath. Next getCachedOrOpenGraphStore(dbPath) will open a new connection.
+ * Call before re-index or clean so the next access sees the new or removed DB.
+ */
+export function invalidateGraphStoreCache(dbPath: string): void {
+  storeCache.delete(dbPath);
+}

src/index.ts

@@ -6,7 +6,11 @@ export * from './types.js';
 export { findSysmlFiles } from './discovery/find-sysml.js';
 export { applyLoadOrder } from './discovery/load-order.js';
 export { runIndexer } from './indexer/indexer.js';
-export { openGraphStore } from './graph/graph-store.js';
+export {
+  openGraphStore,
+  getCachedOrOpenGraphStore,
+  invalidateGraphStoreCache,
+} from './graph/graph-store.js';
 export { getStorageRoot, setStorageRoot, getDbPathForIndexedPath } from './storage/location.js';
 export { listIndexedPaths } from './storage/list.js';
 export { cleanIndex } from './storage/clean.js';

src/mcp/tools/clean-index.ts

@@ -2,13 +2,22 @@
  * MCP tool: clean_index – remove index for path or all.
  */
 
+import { getDbPathForIndexedPath } from '../../storage/location.js';
+import { listIndexedPaths } from '../../storage/list.js';
 import { cleanIndex } from '../../storage/clean.js';
+import { invalidateGraphStoreCache } from '../../graph/graph-store.js';
 
 export interface CleanIndexArgs {
   path?: string;
 }
 
 export async function handleCleanIndex(args: CleanIndexArgs): Promise<{ ok: boolean; removed?: string[]; error?: string }> {
+  if (args.path !== undefined && args.path !== '') {
+    invalidateGraphStoreCache(getDbPathForIndexedPath(args.path));
+  } else {
+    const paths = await listIndexedPaths();
+    for (const p of paths) invalidateGraphStoreCache(getDbPathForIndexedPath(p));
+  }
   const result = await cleanIndex(args.path);
   if (!result.ok) return { ok: false, error: result.error };
   return { ok: true, removed: result.removed };

src/mcp/tools/context.ts

@@ -5,7 +5,7 @@
 
 import { listIndexedPaths } from '../../storage/list.js';
 import { getDbPathForIndexedPath } from '../../storage/location.js';
-import { openGraphStore } from '../../graph/graph-store.js';
+import { getCachedOrOpenGraphStore } from '../../graph/graph-store.js';
 import { NODE_TABLE } from '../../graph/schema.js';
 import { EDGE_TYPES } from '../../graph/schema.js';
 
@@ -19,7 +19,7 @@ export async function handleContext(args: ContextArgs): Promise<{ ok: boolean; n
     return { ok: false, error: 'No indexed paths; run indexDbGraph first' };
   }
   const dbPath = getDbPathForIndexedPath(paths[0]);
-  const store = await openGraphStore(dbPath);
+  const store = await getCachedOrOpenGraphStore(dbPath);
   const conn = store.getConnection();
   const name = (args.name || '').trim().replace(/\\/g, '\\\\').replace(/'/g, "\\'");
   if (!name) {

src/mcp/tools/cypher.ts

@@ -5,7 +5,7 @@
 
 import { listIndexedPaths } from '../../storage/list.js';
 import { getDbPathForIndexedPath } from '../../storage/location.js';
-import { openGraphStore } from '../../graph/graph-store.js';
+import { getCachedOrOpenGraphStore } from '../../graph/graph-store.js';
 
 export interface CypherArgs {
   query: string;
@@ -17,7 +17,7 @@ export async function handleCypher(args: CypherArgs): Promise<{ ok: boolean; row
     return { ok: false, error: 'No indexed paths; run indexDbGraph first' };
   }
   const dbPath = getDbPathForIndexedPath(paths[0]);
-  const store = await openGraphStore(dbPath);
+  const store = await getCachedOrOpenGraphStore(dbPath);
   const conn = store.getConnection();
   try {
     const result = await conn.query(args.query.trim());

src/mcp/tools/impact.ts

@@ -5,7 +5,7 @@
 
 import { listIndexedPaths } from '../../storage/list.js';
 import { getDbPathForIndexedPath } from '../../storage/location.js';
-import { openGraphStore } from '../../graph/graph-store.js';
+import { getCachedOrOpenGraphStore } from '../../graph/graph-store.js';
 import { NODE_TABLE } from '../../graph/schema.js';
 import { EDGE_TYPES } from '../../graph/schema.js';
 
@@ -20,7 +20,7 @@ export async function handleImpact(args: ImpactArgs): Promise<{ ok: boolean; nod
     return { ok: false, error: 'No indexed paths; run indexDbGraph first' };
   }
   const dbPath = getDbPathForIndexedPath(paths[0]);
-  const store = await openGraphStore(dbPath);
+  const store = await getCachedOrOpenGraphStore(dbPath);
   const conn = store.getConnection();
   const target = (args.target || '').trim().replace(/\\/g, '\\\\').replace(/'/g, "\\'");
   if (!target) {

src/mcp/tools/index-db-graph.ts

@@ -4,7 +4,7 @@
 
 import { getDbPathForIndexedPath } from '../../storage/location.js';
 import { addToRegistry } from '../../storage/registry.js';
-import { openGraphStore } from '../../graph/graph-store.js';
+import { getCachedOrOpenGraphStore, invalidateGraphStoreCache } from '../../graph/graph-store.js';
 import { runIndexer } from '../../indexer/indexer.js';
 
 export interface IndexDbGraphArgs {
@@ -19,7 +19,8 @@ export async function handleIndexDbGraph(args: IndexDbGraphArgs): Promise<{ ok:
   }
   for (const p of paths) {
     const dbPath = getDbPathForIndexedPath(p);
-    const store = await openGraphStore(dbPath);
+    invalidateGraphStoreCache(dbPath);
+    const store = await getCachedOrOpenGraphStore(dbPath);
     const result = await runIndexer(store, { roots: [p] });
     if (!result.ok) return { ok: false, error: result.error };
     await addToRegistry(p);

src/mcp/tools/query.ts

@@ -5,7 +5,7 @@
 
 import { listIndexedPaths } from '../../storage/list.js';
 import { getDbPathForIndexedPath } from '../../storage/location.js';
-import { openGraphStore } from '../../graph/graph-store.js';
+import { getCachedOrOpenGraphStore } from '../../graph/graph-store.js';
 import { NODE_TABLE } from '../../graph/schema.js';
 
 export interface QueryArgs {
@@ -19,7 +19,7 @@ export async function handleQuery(args: QueryArgs): Promise<{ ok: boolean; nodes
     return { ok: false, error: 'No indexed paths; run indexDbGraph first' };
   }
   const dbPath = getDbPathForIndexedPath(paths[0]);
-  const store = await openGraphStore(dbPath);
+  const store = await getCachedOrOpenGraphStore(dbPath);
   const conn = store.getConnection();
   const q = (args.query || '').trim().toLowerCase();
   if (!q) {

src/mcp/tools/rename.ts

@@ -5,7 +5,7 @@
 
 import { listIndexedPaths } from '../../storage/list.js';
 import { getDbPathForIndexedPath } from '../../storage/location.js';
-import { openGraphStore } from '../../graph/graph-store.js';
+import { getCachedOrOpenGraphStore } from '../../graph/graph-store.js';
 import { NODE_TABLE } from '../../graph/schema.js';
 
 export interface RenameArgs {
@@ -20,7 +20,7 @@ export async function handleRename(args: RenameArgs): Promise<{ ok: boolean; pre
     return { ok: false, error: 'No indexed paths; run indexDbGraph first' };
   }
   const dbPath = getDbPathForIndexedPath(paths[0]);
-  const store = await openGraphStore(dbPath);
+  const store = await getCachedOrOpenGraphStore(dbPath);
   const conn = store.getConnection();
   const symbol = (args.symbol || '').trim().replace(/\\/g, '\\\\').replace(/'/g, "\\'");
   const newName = (args.newName ?? '').trim();