Remove grep from cache tools; fix annotation_search API to FTS semantics; always apply SARIF path for SARIF format

Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/219712ee-4c28-4b51-9da5-961020112e6e

Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

Author: Copilot

server/dist/codeql-development-mcp-server.js

@@ -181038,10 +181038,6 @@ var Protocol = class {
     this._progressHandlers.clear();
     this._taskProgressTokens.clear();
     this._pendingDebouncedNotifications.clear();
-    for (const info of this._timeoutInfo.values()) {
-      clearTimeout(info.timeoutId);
-    }
-    this._timeoutInfo.clear();
     for (const controller of this._requestHandlerAbortControllers.values()) {
       controller.abort();
     }
@@ -181172,9 +181168,7 @@ var Protocol = class {
         await capturedTransport?.send(errorResponse);
       }
     }).catch((error2) => this._onerror(new Error(`Failed to send response: ${error2}`))).finally(() => {
-      if (this._requestHandlerAbortControllers.get(request.id) === abortController) {
-        this._requestHandlerAbortControllers.delete(request.id);
-      }
+      this._requestHandlerAbortControllers.delete(request.id);
     });
   }
   _onprogress(notification) {
@@ -183187,9 +183181,6 @@ var McpServer = class {
           annotations = rest.shift();
         }
       } else if (typeof firstArg === "object" && firstArg !== null) {
-        if (Object.values(firstArg).some((v) => typeof v === "object" && v !== null)) {
-          throw new Error(`Tool ${name} expected a Zod schema or ToolAnnotations, but received an unrecognized object`);
-        }
         annotations = rest.shift();
       }
     }
@@ -183308,9 +183299,6 @@ function getZodSchemaObject(schema2) {
   if (isZodRawShapeCompat(schema2)) {
     return objectFromShape(schema2);
   }
-  if (!isZodSchemaInstance(schema2)) {
-    throw new Error("inputSchema must be a Zod schema or raw shape, received an unrecognized object");
-  }
   return schema2;
 }
 function promptArgumentsFromSchema(schema2) {
@@ -185651,7 +185639,7 @@ var SqliteStore = class _SqliteStore {
     return null;
   }
   /**
-   * Retrieve a subset of cached result content via line range, grep, or maxLines.
+   * Retrieve a subset of cached result content via line range or maxLines.
    */
   getCacheContentSubset(cacheKey2, options) {
     const fullContent = this.getCacheContent(cacheKey2);
@@ -185666,10 +185654,6 @@ var SqliteStore = class _SqliteStore {
       const endIdx = Math.min(totalLines, end);
       selectedLines = selectedLines.slice(startIdx, endIdx);
     }
-    if (options.grep) {
-      const term = options.grep.toLowerCase();
-      selectedLines = selectedLines.filter((line) => line.toLowerCase().includes(term));
-    }
     const truncated = selectedLines.length > maxLines;
     if (truncated) {
       selectedLines = selectedLines.slice(0, maxLines);
@@ -195412,16 +195396,16 @@ function registerAnnotationDeleteTool(server) {
 function registerAnnotationSearchTool(server) {
   server.tool(
     "annotation_search",
-    "Substring search across annotation content, metadata, and labels (case-insensitive SQL LIKE matching).",
+    'Full-text search across annotation content, metadata, and labels using SQLite FTS (token-based MATCH; use * suffix for prefix matching, e.g. "vulnerab*").',
     {
-      query: external_exports.string().describe("Search term \u2014 matched as a substring against content, metadata, and label."),
+      search: external_exports.string().describe("Full-text search query matched against annotation content, metadata, and label (SQLite FTS MATCH syntax; use * for prefix matching)."),
       category: external_exports.string().optional().describe("Restrict search to a specific category."),
       limit: external_exports.number().optional().describe("Maximum number of results (default: 50).")
     },
-    async ({ query, category, limit }) => {
+    async ({ search, category, limit }) => {
       const store = sessionDataManager.getStore();
       const results = store.listAnnotations({
-        search: query,
+        search,
         category,
         limit: limit ?? 50
       });
@@ -195637,24 +195621,23 @@ function registerQueryResultsCacheLookupTool(server) {
 function registerQueryResultsCacheRetrieveTool(server) {
   server.tool(
     "query_results_cache_retrieve",
-    "Retrieve cached query results with optional subset selection. Supports line ranges (for graphtext/CSV), SARIF result indices, file filtering, and text search to return only the relevant portion.",
+    "Retrieve cached query results with optional subset selection. Supports line ranges (for graphtext/CSV) and SARIF result indices and file filtering to return only the relevant portion.",
     {
       cacheKey: external_exports.string().describe("The cache key of the result to retrieve."),
-      lineRange: external_exports.tuple([external_exports.number(), external_exports.number()]).optional().describe("Line range [start, end] (1-indexed). For graphtext/CSV output."),
-      resultIndices: external_exports.tuple([external_exports.number(), external_exports.number()]).optional().describe("SARIF result index range [start, end] (0-indexed, inclusive)."),
+      lineRange: external_exports.tuple([external_exports.number(), external_exports.number()]).optional().describe("Line range [start, end] (1-indexed, inclusive). For graphtext/CSV output only."),
+      resultIndices: external_exports.tuple([external_exports.number(), external_exports.number()]).optional().describe("SARIF result index range [start, end] (0-indexed, inclusive). For SARIF output only."),
       fileFilter: external_exports.string().optional().describe("For SARIF: only include results whose file path contains this string."),
-      grep: external_exports.string().optional().describe("Text search filter: only include lines/results containing this term."),
       maxLines: external_exports.number().optional().describe("Maximum number of lines to return for line-based formats (default: 500)."),
       maxResults: external_exports.number().optional().describe("Maximum number of SARIF results to return (default: 100).")
     },
-    async ({ cacheKey: cacheKey2, lineRange, resultIndices, fileFilter, grep, maxLines, maxResults }) => {
+    async ({ cacheKey: cacheKey2, lineRange, resultIndices, fileFilter, maxLines, maxResults }) => {
       const store = sessionDataManager.getStore();
       const meta = store.getCacheEntryMeta(cacheKey2);
       if (!meta) {
         return { content: [{ type: "text", text: `No cached result found for key: ${cacheKey2}` }] };
       }
       const isSarif = meta.outputFormat.includes("sarif");
-      if (isSarif && (resultIndices || fileFilter)) {
+      if (isSarif) {
         const subset2 = store.getCacheSarifSubset(cacheKey2, {
           resultIndices,
           fileFilter,
@@ -195688,7 +195671,6 @@ function registerQueryResultsCacheRetrieveTool(server) {
       }
       const subset = store.getCacheContentSubset(cacheKey2, {
         lineRange,
-        grep,
         maxLines: maxLines ?? 500
       });
       if (!subset) {

server/dist/codeql-development-mcp-server.js.map

@@ -662,13 +662,12 @@ export class SqliteStore {
   }
 
   /**
-   * Retrieve a subset of cached result content via line range, grep, or maxLines.
+   * Retrieve a subset of cached result content via line range or maxLines.
    */
   getCacheContentSubset(
     cacheKey: string,
     options: {
       lineRange?: [number, number];
-      grep?: string;
       maxLines?: number;
     },
   ): { content: string; totalLines: number; returnedLines: number; truncated: boolean } | null {
@@ -687,11 +686,6 @@ export class SqliteStore {
       selectedLines = selectedLines.slice(startIdx, endIdx);
     }
 
-    if (options.grep) {
-      const term = options.grep.toLowerCase();
-      selectedLines = selectedLines.filter(line => line.toLowerCase().includes(term));
-    }
-
     const truncated = selectedLines.length > maxLines;
     if (truncated) {
       selectedLines = selectedLines.slice(0, maxLines);

server/src/lib/sqlite-store.ts

@@ -166,16 +166,16 @@ function registerAnnotationDeleteTool(server: McpServer): void {
 function registerAnnotationSearchTool(server: McpServer): void {
   server.tool(
     'annotation_search',
-    'Substring search across annotation content, metadata, and labels (case-insensitive SQL LIKE matching).',
+    'Full-text search across annotation content, metadata, and labels using SQLite FTS (token-based MATCH; use * suffix for prefix matching, e.g. "vulnerab*").',
     {
-      query: z.string().describe('Search term — matched as a substring against content, metadata, and label.'),
+      search: z.string().describe('Full-text search query matched against annotation content, metadata, and label (SQLite FTS MATCH syntax; use * for prefix matching).'),
       category: z.string().optional().describe('Restrict search to a specific category.'),
       limit: z.number().optional().describe('Maximum number of results (default: 50).'),
     },
-    async ({ query, category, limit }) => {
+    async ({ search, category, limit }) => {
       const store = sessionDataManager.getStore();
       const results = store.listAnnotations({
-        search: query,
+        search,
         category,
         limit: limit ?? 50,
       });

server/src/tools/annotation-tools.ts

@@ -80,27 +80,27 @@ function registerQueryResultsCacheLookupTool(server: McpServer): void {
 function registerQueryResultsCacheRetrieveTool(server: McpServer): void {
   server.tool(
     'query_results_cache_retrieve',
-    'Retrieve cached query results with optional subset selection. Supports line ranges (for graphtext/CSV), SARIF result indices, file filtering, and text search to return only the relevant portion.',
+    'Retrieve cached query results with optional subset selection. Supports line ranges (for graphtext/CSV) and SARIF result indices and file filtering to return only the relevant portion.',
     {
       cacheKey: z.string().describe('The cache key of the result to retrieve.'),
-      lineRange: z.tuple([z.number(), z.number()]).optional().describe('Line range [start, end] (1-indexed). For graphtext/CSV output.'),
-      resultIndices: z.tuple([z.number(), z.number()]).optional().describe('SARIF result index range [start, end] (0-indexed, inclusive).'),
+      lineRange: z.tuple([z.number(), z.number()]).optional().describe('Line range [start, end] (1-indexed, inclusive). For graphtext/CSV output only.'),
+      resultIndices: z.tuple([z.number(), z.number()]).optional().describe('SARIF result index range [start, end] (0-indexed, inclusive). For SARIF output only.'),
       fileFilter: z.string().optional().describe('For SARIF: only include results whose file path contains this string.'),
-      grep: z.string().optional().describe('Text search filter: only include lines/results containing this term.'),
       maxLines: z.number().optional().describe('Maximum number of lines to return for line-based formats (default: 500).'),
       maxResults: z.number().optional().describe('Maximum number of SARIF results to return (default: 100).'),
     },
-    async ({ cacheKey, lineRange, resultIndices, fileFilter, grep, maxLines, maxResults }) => {
+    async ({ cacheKey, lineRange, resultIndices, fileFilter, maxLines, maxResults }) => {
       const store = sessionDataManager.getStore();
       const meta = store.getCacheEntryMeta(cacheKey);
 
       if (!meta) {
         return { content: [{ type: 'text' as const, text: `No cached result found for key: ${cacheKey}` }] };
       }
 
-      // For SARIF format with SARIF-specific filters, use SARIF subset retrieval
+      // SARIF format: always use the SARIF-aware subset retrieval so that
+      // maxResults is applied and result-level filters (indices, file path) work correctly.
       const isSarif = meta.outputFormat.includes('sarif');
-      if (isSarif && (resultIndices || fileFilter)) {
+      if (isSarif) {
         const subset = store.getCacheSarifSubset(cacheKey, {
           resultIndices,
           fileFilter,
@@ -134,10 +134,9 @@ function registerQueryResultsCacheRetrieveTool(server: McpServer): void {
         };
       }
 
-      // Line-based subset for graphtext, CSV, or any text format
+      // Line-based subset for graphtext, CSV, or any other text format.
       const subset = store.getCacheContentSubset(cacheKey, {
         lineRange,
-        grep,
         maxLines: maxLines ?? 500,
       });
       if (!subset) {

server/src/tools/cache-tools.ts

@@ -291,9 +291,9 @@ describe('SqliteStore', () => {
       expect(subset!.totalLines).toBe(6); // 5 lines + trailing newline
     });
 
-    it('should retrieve subset by grep', () => {
+    it('should retrieve subset by maxLines without lineRange', () => {
       store.putCacheEntry({
-        cacheKey: 'grep',
+        cacheKey: 'nolimit',
         queryName: 'PrintAST',
         queryPath: '/p.ql',
         databasePath: '/db',
@@ -303,11 +303,11 @@ describe('SqliteStore', () => {
         resultContent: 'Function foo\n  Param x\nFunction bar\n  Param y\n',
       });
 
-      const subset = store.getCacheContentSubset('grep', { grep: 'Function' });
+      const subset = store.getCacheContentSubset('nolimit', { maxLines: 2 });
       expect(subset).not.toBeNull();
       expect(subset!.returnedLines).toBe(2);
-      expect(subset!.content).toContain('Function foo');
-      expect(subset!.content).toContain('Function bar');
+      expect(subset!.truncated).toBe(true);
+      expect(subset!.content).toBe('Function foo\n  Param x');
     });
 
     it('should enforce maxLines cap', () => {