Address PR review feedback and fix failing integration tests

- Fix databaseLocks memory leak: clean up map entries on release
- Fix bqrs_interpret source-archive: prefer src.zip over src/
- Fix cacheDatabaseAnalyzeResults: use resolved database path
- Fix annotation category search: add COLLATE NOCASE
- Fix resultCount: use ?? 0 instead of ?? null (two locations)
- Fix VS Code tests: wrap mock mutations in try/finally
- Fix codeql_bqrs_info integration tests: files → file in test
  runner, monitoring runner, and test-config.json

Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/52936c89-89e6-4b1d-8c0e-12dcb9ad2388

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

Author: Copilot

client/integration-tests/primitives/tools/codeql_bqrs_info/json_format/test-config.json

@@ -1,7 +1,7 @@
 {
   "toolName": "codeql_bqrs_info",
   "arguments": {
-    "files": ["client/integration-tests/primitives/tools/codeql_bqrs_info/json_format/before/results.bqrs"],
+    "file": "client/integration-tests/primitives/tools/codeql_bqrs_info/json_format/before/results.bqrs",
     "format": "json"
   }
 }

client/src/lib/integration-test-runner.js

@@ -931,7 +931,7 @@ export class IntegrationTestRunner {
       // Use static BQRS file
       const bqrsFile = path.join(staticPath, "src", "ExampleQuery1", "ExampleQuery1.test.bqrs");
       if (fs.existsSync(bqrsFile)) {
-        params.files = [bqrsFile];
+        params.file = bqrsFile;
       } else {
         throw new Error(`Static BQRS file not found: ${bqrsFile}`);
       }

client/src/lib/monitoring-integration-test-runner.js

@@ -361,7 +361,7 @@ export class MonitoringIntegrationTestRunner {
       if (fs.existsSync(beforeDir)) {
         const bqrsFiles = fs.readdirSync(beforeDir).filter((f) => f.endsWith(".bqrs"));
         if (bqrsFiles.length > 0) {
-          params.bqrs = path.join(beforeDir, bqrsFiles[0]);
+          params.file = path.join(beforeDir, bqrsFiles[0]);
         } else {
           throw new Error(`No .bqrs files found in ${beforeDir} for ${toolName}`);
         }

extensions/vscode/test/bridge/environment-builder.test.ts

@@ -281,61 +281,70 @@ describe('EnvironmentBuilder', () => {
   it('should set ENABLE_ANNOTATION_TOOLS=false when setting is disabled', async () => {
     const vscode = await import('vscode');
     const originalGetConfig = vscode.workspace.getConfiguration;
-    vscode.workspace.getConfiguration = () => ({
-      get: (_key: string, defaultVal?: any) => {
-        if (_key === 'enableAnnotationTools') return false;
-        if (_key === 'additionalDatabaseDirs') return [];
-        if (_key === 'additionalQueryRunResultsDirs') return [];
-        if (_key === 'additionalMrvaRunResultsDirs') return [];
-        return defaultVal;
-      },
-      has: () => false,
-      inspect: () => undefined as any,
-      update: () => Promise.resolve(),
-    }) as any;
 
-    builder.invalidate();
-    const env = await builder.build();
-    expect(env.ENABLE_ANNOTATION_TOOLS).toBe('false');
-
-    vscode.workspace.getConfiguration = originalGetConfig;
+    try {
+      vscode.workspace.getConfiguration = () => ({
+        get: (_key: string, defaultVal?: any) => {
+          if (_key === 'enableAnnotationTools') return false;
+          if (_key === 'additionalDatabaseDirs') return [];
+          if (_key === 'additionalQueryRunResultsDirs') return [];
+          if (_key === 'additionalMrvaRunResultsDirs') return [];
+          return defaultVal;
+        },
+        has: () => false,
+        inspect: () => undefined as any,
+        update: () => Promise.resolve(),
+      }) as any;
+
+      builder.invalidate();
+      const env = await builder.build();
+      expect(env.ENABLE_ANNOTATION_TOOLS).toBe('false');
+    } finally {
+      vscode.workspace.getConfiguration = originalGetConfig;
+    }
   });
 
   it('should set MONITORING_STORAGE_LOCATION to scratch dir when annotations enabled with workspace', async () => {
     const vscode = await import('vscode');
     const origFolders = vscode.workspace.workspaceFolders;
-    (vscode.workspace.workspaceFolders as any) = [
-      { uri: { fsPath: '/mock/workspace' }, name: 'ws', index: 0 },
-    ];
 
-    builder.invalidate();
-    const env = await builder.build();
-    expect(env.MONITORING_STORAGE_LOCATION).toBe('/mock/workspace/.codeql/ql-mcp');
-
-    (vscode.workspace.workspaceFolders as any) = origFolders;
+    try {
+      (vscode.workspace.workspaceFolders as any) = [
+        { uri: { fsPath: '/mock/workspace' }, name: 'ws', index: 0 },
+      ];
+
+      builder.invalidate();
+      const env = await builder.build();
+      expect(env.MONITORING_STORAGE_LOCATION).toBe('/mock/workspace/.codeql/ql-mcp');
+    } finally {
+      (vscode.workspace.workspaceFolders as any) = origFolders;
+    }
   });
 
   it('should allow additionalEnv to override ENABLE_ANNOTATION_TOOLS', async () => {
     const vscode = await import('vscode');
     const originalGetConfig = vscode.workspace.getConfiguration;
-    vscode.workspace.getConfiguration = () => ({
-      get: (_key: string, defaultVal?: any) => {
-        if (_key === 'additionalEnv') return { ENABLE_ANNOTATION_TOOLS: 'false' };
-        if (_key === 'additionalDatabaseDirs') return [];
-        if (_key === 'additionalQueryRunResultsDirs') return [];
-        if (_key === 'additionalMrvaRunResultsDirs') return [];
-        return defaultVal;
-      },
-      has: () => false,
-      inspect: () => undefined as any,
-      update: () => Promise.resolve(),
-    }) as any;
 
-    builder.invalidate();
-    const env = await builder.build();
-    // additionalEnv comes after the default, so it should override
-    expect(env.ENABLE_ANNOTATION_TOOLS).toBe('false');
-
-    vscode.workspace.getConfiguration = originalGetConfig;
+    try {
+      vscode.workspace.getConfiguration = () => ({
+        get: (_key: string, defaultVal?: any) => {
+          if (_key === 'additionalEnv') return { ENABLE_ANNOTATION_TOOLS: 'false' };
+          if (_key === 'additionalDatabaseDirs') return [];
+          if (_key === 'additionalQueryRunResultsDirs') return [];
+          if (_key === 'additionalMrvaRunResultsDirs') return [];
+          return defaultVal;
+        },
+        has: () => false,
+        inspect: () => undefined as any,
+        update: () => Promise.resolve(),
+      }) as any;
+
+      builder.invalidate();
+      const env = await builder.build();
+      // additionalEnv comes after the default, so it should override
+      expect(env.ENABLE_ANNOTATION_TOOLS).toBe('false');
+    } finally {
+      vscode.workspace.getConfiguration = originalGetConfig;
+    }
   });
 });

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

@@ -183584,7 +183584,7 @@ var SqliteStore = class _SqliteStore {
       params.$entity_key_prefix = filter.entityKeyPrefix + "%";
     }
     if (filter?.search) {
-      conditions.push("(id IN (SELECT rowid FROM annotations_fts WHERE annotations_fts MATCH $search) OR category = $search_cat)");
+      conditions.push("(id IN (SELECT rowid FROM annotations_fts WHERE annotations_fts MATCH $search) OR category = $search_cat COLLATE NOCASE)");
       params.$search = filter.search;
       params.$search_cat = filter.search;
     }
@@ -184501,7 +184501,7 @@ Interpreted output saved to: ${outputFilePath}`;
             if (outputFormat.includes("sarif")) {
               try {
                 const sarif = JSON.parse(resultContent);
-                resultCount = sarif?.runs?.[0]?.results?.length ?? null;
+                resultCount = sarif?.runs?.[0]?.results?.length ?? 0;
               } catch {
               }
             }
@@ -184605,7 +184605,7 @@ function cacheDatabaseAnalyzeResults(params, logger2) {
     let resultCount = null;
     try {
       const sarif = JSON.parse(resultContent);
-      resultCount = sarif?.runs?.[0]?.results?.length ?? null;
+      resultCount = sarif?.runs?.[0]?.results?.length ?? 0;
     } catch {
     }
     const cacheKey2 = computeQueryCacheKey({
@@ -187230,15 +187230,20 @@ var databaseLocks = /* @__PURE__ */ new Map();
 function acquireDatabaseLock(dbPath) {
   const key = dbPath;
   const previous = databaseLocks.get(key) ?? Promise.resolve();
-  let release;
+  let resolveGate;
   const gate = new Promise((resolve15) => {
-    release = resolve15;
+    resolveGate = resolve15;
   });
   databaseLocks.set(key, gate);
   return {
     ready: previous.then(() => {
     }),
-    release
+    release: () => {
+      resolveGate();
+      if (databaseLocks.get(key) === gate) {
+        databaseLocks.delete(key);
+      }
+    }
   };
 }
 var defaultCLIResultProcessor = (result, _params) => {
@@ -187483,7 +187488,9 @@ function registerCLITool(server, definition) {
           case "codeql_bqrs_interpret":
             if (options.database) {
               const dbPath = resolveDatabasePath(options.database);
-              options["source-archive"] = join10(dbPath, "src");
+              const srcZipPath = join10(dbPath, "src.zip");
+              const srcDirPath = join10(dbPath, "src");
+              options["source-archive"] = existsSync6(srcZipPath) ? srcZipPath : srcDirPath;
               delete options.database;
             }
             break;
@@ -187621,7 +187628,8 @@ function registerCLITool(server, definition) {
           }
         }
         if (name === "codeql_database_analyze" && result.success && options.output) {
-          cacheDatabaseAnalyzeResults({ ...params, output: options.output, format: options.format }, logger);
+          const resolvedDb = typeof params.database === "string" ? resolveDatabasePath(params.database) : params.database;
+          cacheDatabaseAnalyzeResults({ ...params, database: resolvedDb, output: options.output, format: options.format }, logger);
         }
         const processedResult = resultProcessor(result, params);
         return {

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

@@ -32,15 +32,20 @@ function acquireDatabaseLock(dbPath: string): { ready: Promise<void>; release: (
   const key = dbPath;
   const previous = databaseLocks.get(key) ?? Promise.resolve();
 
-  let release!: () => void;
+  let resolveGate!: () => void;
   const gate = new Promise<void>(resolve => {
-    release = resolve;
+    resolveGate = resolve;
   });
   databaseLocks.set(key, gate);
 
   return {
     ready: previous.then(() => {}),
-    release,
+    release: () => {
+      resolveGate();
+      if (databaseLocks.get(key) === gate) {
+        databaseLocks.delete(key);
+      }
+    },
   };
 }
 
@@ -382,7 +387,9 @@ export function registerCLITool(server: McpServer, definition: CLIToolDefinition
             // Map 'database' to '--source-archive' for codeql bqrs interpret
             if (options.database) {
               const dbPath = resolveDatabasePath(options.database as string);
-              options['source-archive'] = join(dbPath, 'src');
+              const srcZipPath = join(dbPath, 'src.zip');
+              const srcDirPath = join(dbPath, 'src');
+              options['source-archive'] = existsSync(srcZipPath) ? srcZipPath : srcDirPath;
               delete options.database;
             }
             break;
@@ -607,7 +614,10 @@ export function registerCLITool(server: McpServer, definition: CLIToolDefinition
 
         // Post-execution: cache database_analyze results in query results cache
         if (name === 'codeql_database_analyze' && result.success && options.output) {
-          cacheDatabaseAnalyzeResults({ ...params, output: options.output, format: options.format }, logger);
+          const resolvedDb = typeof params.database === 'string'
+            ? resolveDatabasePath(params.database)
+            : params.database;
+          cacheDatabaseAnalyzeResults({ ...params, database: resolvedDb, output: options.output, format: options.format }, logger);
         }
 
         // Process the result

server/src/lib/cli-tool-registry.ts

@@ -238,7 +238,7 @@ export async function processQueryRunResults(
             if (outputFormat.includes('sarif')) {
               try {
                 const sarif = JSON.parse(resultContent);
-                resultCount = (sarif?.runs?.[0]?.results as unknown[] | undefined)?.length ?? null;
+                resultCount = (sarif?.runs?.[0]?.results as unknown[] | undefined)?.length ?? 0;
               } catch { /* non-SARIF content — leave count null */ }
             }
 
@@ -358,7 +358,7 @@ export function cacheDatabaseAnalyzeResults(
     let resultCount: number | null = null;
     try {
       const sarif = JSON.parse(resultContent);
-      resultCount = (sarif?.runs?.[0]?.results as unknown[] | undefined)?.length ?? null;
+      resultCount = (sarif?.runs?.[0]?.results as unknown[] | undefined)?.length ?? 0;
     } catch { /* non-SARIF content */ }
 
     const cacheKey = computeQueryCacheKey({

server/src/lib/result-processor.ts

@@ -459,7 +459,7 @@ export class SqliteStore {
       // across content, label, and metadata fields. Also match the category
       // column directly (not in FTS) so searches like "performance" find
       // annotations whose category is "performance".
-      conditions.push('(id IN (SELECT rowid FROM annotations_fts WHERE annotations_fts MATCH $search) OR category = $search_cat)');
+      conditions.push('(id IN (SELECT rowid FROM annotations_fts WHERE annotations_fts MATCH $search) OR category = $search_cat COLLATE NOCASE)');
       params.$search = filter.search;
       params.$search_cat = filter.search;
     }