Add capability to filter queries

This change adds a `query-filters` property to the codeql-config file.

This property is an array of `exclude`/`include` entries for a query
suite. These filters are appended to the generated query suite files
and used to filter queries after they are selected.

A related change is that now, all pack references are run in a single
query suite, which has the query filters appended to them.

lib/analyze.js

@@ -22,7 +22,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.runCleanup = exports.runFinalize = exports.runQueries = exports.CodeQLAnalysisError = void 0;
+exports.validateQueryFilters = exports.runCleanup = exports.runFinalize = exports.createQuerySuiteContents = exports.convertPackToQuerySuiteEntry = exports.runQueries = exports.CodeQLAnalysisError = void 0;
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const toolrunner = __importStar(require("@actions/exec/lib/toolrunner"));
@@ -30,6 +30,7 @@ const del_1 = __importDefault(require("del"));
 const yaml = __importStar(require("js-yaml"));
 const analysisPaths = __importStar(require("./analysis-paths"));
 const codeql_1 = require("./codeql");
+const configUtils = __importStar(require("./config-utils"));
 const count_loc_1 = require("./count-loc");
 const languages_1 = require("./languages");
 const sharedEnv = __importStar(require("./shared-environment"));
@@ -128,6 +129,7 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
     }
     for (const language of config.languages) {
         const queries = config.queries[language];
+        const queryFilters = validateQueryFilters(config.originalUserInput["query-filters"]);
         const packsWithVersion = config.packs[language] || [];
         const hasBuiltinQueries = (queries === null || queries === void 0 ? void 0 : queries.builtin.length) > 0;
         const hasCustomQueries = (queries === null || queries === void 0 ? void 0 : queries.custom.length) > 0;
@@ -150,7 +152,7 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
             const querySuitePaths = [];
             if (queries["builtin"].length > 0) {
                 const startTimeBuiltIn = new Date().getTime();
-                querySuitePaths.push(await runQueryGroup(language, "builtin", createQuerySuiteContents(queries["builtin"]), undefined));
+                querySuitePaths.push(await runQueryGroup(language, "builtin", createQuerySuiteContents(queries["builtin"], queryFilters), undefined));
                 statusReport[`analyze_builtin_queries_${language}_duration_ms`] =
                     new Date().getTime() - startTimeBuiltIn;
             }
@@ -158,12 +160,12 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
             let ranCustom = false;
             for (let i = 0; i < queries["custom"].length; ++i) {
                 if (queries["custom"][i].queries.length > 0) {
-                    querySuitePaths.push(await runQueryGroup(language, `custom-${i}`, createQuerySuiteContents(queries["custom"][i].queries), queries["custom"][i].searchPath));
+                    querySuitePaths.push(await runQueryGroup(language, `custom-${i}`, createQuerySuiteContents(queries["custom"][i].queries, queryFilters), queries["custom"][i].searchPath));
                     ranCustom = true;
                 }
             }
             if (packsWithVersion.length > 0) {
-                querySuitePaths.push(...(await runQueryPacks(language, "packs", packsWithVersion, undefined)));
+                querySuitePaths.push(await runQueryPacks(language, "packs", packsWithVersion, queryFilters));
                 ranCustom = true;
             }
             if (ranCustom) {
@@ -221,23 +223,43 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
         logger.debug(`BQRS results produced for ${language} (queries: ${type})"`);
         return querySuitePath;
     }
-    async function runQueryPacks(language, type, packs, searchPath) {
+    async function runQueryPacks(language, type, packs, queryFilters) {
         const databasePath = util.getCodeQLDatabasePath(config, language);
-        // Run the queries individually instead of all at once to avoid command
-        // line length restrictions, particularly on windows.
         for (const pack of packs) {
             logger.debug(`Running query pack for ${language}-${type}: ${pack}`);
-            const codeql = await (0, codeql_1.getCodeQL)(config.codeQLCmd);
-            await codeql.databaseRunQueries(databasePath, searchPath, pack, memoryFlag, threadsFlag);
-            logger.debug(`BQRS results produced for ${language} (queries: ${type})"`);
         }
-        return packs;
+        // combine the list of packs into a query suite in order to run them all simultaneously.
+        const querySuite = packs
+            .map(convertPackToQuerySuiteEntry)
+            .concat(queryFilters);
+        const querySuitePath = `${databasePath}-queries-${type}.qls`;
+        fs.writeFileSync(querySuitePath, yaml.dump(querySuite));
+        logger.debug(`BQRS results produced for ${language} (queries: ${type})"`);
+        const codeql = await (0, codeql_1.getCodeQL)(config.codeQLCmd);
+        await codeql.databaseRunQueries(databasePath, undefined, querySuitePath, memoryFlag, threadsFlag);
+        return querySuitePath;
     }
 }
 exports.runQueries = runQueries;
-function createQuerySuiteContents(queries) {
-    return queries.map((q) => `- query: ${q}`).join("\n");
+function convertPackToQuerySuiteEntry(packStr) {
+    var _a, _b, _c, _d;
+    const pack = configUtils.parsePacksSpecification(packStr);
+    return {
+        qlpack: !pack.path ? pack.name : undefined,
+        from: pack.path ? pack.name : undefined,
+        version: pack.version,
+        query: ((_a = pack.path) === null || _a === void 0 ? void 0 : _a.endsWith(".ql")) ? pack.path : undefined,
+        queries: !((_b = pack.path) === null || _b === void 0 ? void 0 : _b.endsWith(".ql")) && !((_c = pack.path) === null || _c === void 0 ? void 0 : _c.endsWith(".qls"))
+            ? pack.path
+            : undefined,
+        apply: ((_d = pack.path) === null || _d === void 0 ? void 0 : _d.endsWith(".qls")) ? pack.path : undefined,
+    };
 }
+exports.convertPackToQuerySuiteEntry = convertPackToQuerySuiteEntry;
+function createQuerySuiteContents(queries, queryFilters) {
+    return yaml.dump(queries.map((q) => ({ query: q })).concat(queryFilters));
+}
+exports.createQuerySuiteContents = createQuerySuiteContents;
 async function runFinalize(outputDir, threadsFlag, memoryFlag, config, logger) {
     const codeql = await (0, codeql_1.getCodeQL)(config.codeQLCmd);
     if (await util.codeQlVersionAbove(codeql, codeql_1.CODEQL_VERSION_NEW_TRACING)) {
@@ -298,4 +320,25 @@ function printLinesOfCodeSummary(logger, language, lineCounts) {
         logger.info(`Counted a baseline of ${lineCounts[language]} lines of code for ${language}.`);
     }
 }
+// exported for testing
+function validateQueryFilters(queryFilters) {
+    if (!queryFilters) {
+        return [];
+    }
+    const errors = [];
+    for (const qf of queryFilters) {
+        const keys = Object.keys(qf);
+        if (keys.length !== 1) {
+            errors.push(`Query filter must have exactly one key: ${JSON.stringify(qf)}`);
+        }
+        if (!["exclude", "include"].includes(keys[0])) {
+            errors.push(`Only "include" or "exclude" filters are allowed:\n${JSON.stringify(qf)}`);
+        }
+    }
+    if (errors.length) {
+        throw new Error(`Invalid query filter.\n${errors.join("\n")}`);
+    }
+    return queryFilters;
+}
+exports.validateQueryFilters = validateQueryFilters;
 //# sourceMappingURL=analyze.js.map

lib/analyze.test.js

@@ -210,4 +210,136 @@ const util = __importStar(require("./util"));
         }
     }
 });
+(0, ava_1.default)("validateQueryFilters", (t) => {
+    t.notThrows(() => (0, analyze_1.validateQueryFilters)([]));
+    t.notThrows(() => (0, analyze_1.validateQueryFilters)(undefined));
+    t.notThrows(() => {
+        return (0, analyze_1.validateQueryFilters)([
+            {
+                exclude: {
+                    "problem.severity": "recommendation",
+                },
+            },
+            {
+                exclude: {
+                    "tags contain": ["foo", "bar"],
+                },
+            },
+            {
+                include: {
+                    "problem.severity": "something-to-think-about",
+                },
+            },
+            {
+                include: {
+                    "tags contain": ["baz", "bop"],
+                },
+            },
+        ]);
+    });
+    t.throws(() => {
+        return (0, analyze_1.validateQueryFilters)([
+            {
+                exclude: {
+                    "tags contain": ["foo", "bar"],
+                },
+                include: {
+                    "tags contain": ["baz", "bop"],
+                },
+            },
+        ]);
+    }, { message: /Query filter must have exactly one key/ });
+    t.throws(() => {
+        return (0, analyze_1.validateQueryFilters)([{ xxx: "foo" }]);
+    }, { message: /Only "include" or "exclude" filters are allowed/ });
+});
+const convertPackToQuerySuiteEntryMacro = ava_1.default.macro({
+    exec: (t, packSpec, suiteEntry) => t.deepEqual((0, analyze_1.convertPackToQuerySuiteEntry)(packSpec), suiteEntry),
+    title: (_providedTitle, packSpec) => `Query Suite Entry: ${packSpec}`,
+});
+(0, ava_1.default)(convertPackToQuerySuiteEntryMacro, "a/b", {
+    qlpack: "a/b",
+    from: undefined,
+    version: undefined,
+    query: undefined,
+    queries: undefined,
+    apply: undefined,
+});
+(0, ava_1.default)(convertPackToQuerySuiteEntryMacro, "a/b@~1.2.3", {
+    qlpack: "a/b",
+    from: undefined,
+    version: "~1.2.3",
+    query: undefined,
+    queries: undefined,
+    apply: undefined,
+});
+(0, ava_1.default)(convertPackToQuerySuiteEntryMacro, "a/b:my/path", {
+    qlpack: undefined,
+    from: "a/b",
+    version: undefined,
+    query: undefined,
+    queries: "my/path",
+    apply: undefined,
+});
+(0, ava_1.default)(convertPackToQuerySuiteEntryMacro, "a/b@~1.2.3:my/path", {
+    qlpack: undefined,
+    from: "a/b",
+    version: "~1.2.3",
+    query: undefined,
+    queries: "my/path",
+    apply: undefined,
+});
+(0, ava_1.default)(convertPackToQuerySuiteEntryMacro, "a/b:my/path/query.ql", {
+    qlpack: undefined,
+    from: "a/b",
+    version: undefined,
+    query: "my/path/query.ql",
+    queries: undefined,
+    apply: undefined,
+});
+(0, ava_1.default)(convertPackToQuerySuiteEntryMacro, "a/b@~1.2.3:my/path/query.ql", {
+    qlpack: undefined,
+    from: "a/b",
+    version: "~1.2.3",
+    query: "my/path/query.ql",
+    queries: undefined,
+    apply: undefined,
+});
+(0, ava_1.default)(convertPackToQuerySuiteEntryMacro, "a/b:my/path/suite.qls", {
+    qlpack: undefined,
+    from: "a/b",
+    version: undefined,
+    query: undefined,
+    queries: undefined,
+    apply: "my/path/suite.qls",
+});
+(0, ava_1.default)(convertPackToQuerySuiteEntryMacro, "a/b@~1.2.3:my/path/suite.qls", {
+    qlpack: undefined,
+    from: "a/b",
+    version: "~1.2.3",
+    query: undefined,
+    queries: undefined,
+    apply: "my/path/suite.qls",
+});
+(0, ava_1.default)("convertPackToQuerySuiteEntry Failure", (t) => {
+    t.throws(() => (0, analyze_1.convertPackToQuerySuiteEntry)("this-is-not-a-pack"));
+});
+(0, ava_1.default)("createQuerySuiteContents", (t) => {
+    const yamlResult = (0, analyze_1.createQuerySuiteContents)(["query1.ql", "query2.ql"], [
+        {
+            exclude: { "problem.severity": "recommendation" },
+        },
+        {
+            include: { "problem.severity": "recommendation" },
+        },
+    ]);
+    const expected = `- query: query1.ql
+- query: query2.ql
+- exclude:
+    problem.severity: recommendation
+- include:
+    problem.severity: recommendation
+`;
+    t.deepEqual(yamlResult, expected);
+});
 //# sourceMappingURL=analyze.test.js.map

lib/config-utils.js

@@ -19,7 +19,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getConfig = exports.getPathToParsedConfigFile = exports.initConfig = exports.parsePacks = exports.validatePacksSpecification = exports.parsePacksFromConfig = exports.getDefaultConfig = exports.getUnknownLanguagesError = exports.getNoLanguagesError = exports.getConfigFileDirectoryGivenMessage = exports.getConfigFileFormatInvalidMessage = exports.getConfigFileRepoFormatInvalidMessage = exports.getConfigFileDoesNotExistErrorMessage = exports.getConfigFileOutsideWorkspaceErrorMessage = exports.getLocalPathDoesNotExist = exports.getLocalPathOutsideOfRepository = exports.getPacksStrInvalid = exports.getPacksInvalid = exports.getPacksInvalidSplit = exports.getPacksRequireLanguage = exports.getPathsInvalid = exports.getPathsIgnoreInvalid = exports.getQueryUsesInvalid = exports.getQueriesInvalid = exports.getDisableDefaultQueriesInvalid = exports.getNameInvalid = exports.validateAndSanitisePath = void 0;
+exports.getConfig = exports.getPathToParsedConfigFile = exports.initConfig = exports.parsePacks = exports.validatePackSpecification = exports.prettyPrintPack = exports.parsePacksSpecification = exports.parsePacksFromConfig = exports.getDefaultConfig = exports.getUnknownLanguagesError = exports.getNoLanguagesError = exports.getConfigFileDirectoryGivenMessage = exports.getConfigFileFormatInvalidMessage = exports.getConfigFileRepoFormatInvalidMessage = exports.getConfigFileDoesNotExistErrorMessage = exports.getConfigFileOutsideWorkspaceErrorMessage = exports.getLocalPathDoesNotExist = exports.getLocalPathOutsideOfRepository = exports.getPacksStrInvalid = exports.getPacksInvalid = exports.getPacksInvalidSplit = exports.getPacksRequireLanguage = exports.getPathsInvalid = exports.getPathsIgnoreInvalid = exports.getQueryUsesInvalid = exports.getQueriesInvalid = exports.getDisableDefaultQueriesInvalid = exports.getNameInvalid = exports.validateAndSanitisePath = void 0;
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const yaml = __importStar(require("js-yaml"));
@@ -150,9 +150,7 @@ async function addBuiltinSuiteQueries(languages, codeQL, resultMap, packs, suite
     return injectedMlQueries;
 }
 function isMlPoweredJsQueriesPack(pack) {
-    return (pack === util_1.ML_POWERED_JS_QUERIES_PACK_NAME ||
-        pack.startsWith(`${util_1.ML_POWERED_JS_QUERIES_PACK_NAME}@`) ||
-        pack.startsWith(`${util_1.ML_POWERED_JS_QUERIES_PACK_NAME}:`));
+    return parsePacksSpecification(pack).name === util_1.ML_POWERED_JS_QUERIES_PACK_NAME;
 }
 /**
  * Retrieve the set of queries at localQueryPath and add them to resultMap.
@@ -638,10 +636,7 @@ function parsePacksFromConfig(packsByLanguage, languages, configFile) {
         if (!languages.includes(lang)) {
             throw new Error(getPacksRequireLanguage(lang, configFile));
         }
-        packs[lang] = [];
-        for (const packStr of packsArr) {
-            packs[lang].push(validatePacksSpecification(packStr, configFile));
-        }
+        packs[lang] = packsArr.map((packStr) => validatePackSpecification(packStr, configFile));
     }
     return packs;
 }
@@ -665,7 +660,7 @@ function parsePacksFromInput(packsInput, languages) {
     }
     return {
         [languages[0]]: packsInput.split(",").reduce((packs, pack) => {
-            packs.push(validatePacksSpecification(pack, ""));
+            packs.push(validatePackSpecification(pack));
             return packs;
         }, []),
     };
@@ -688,7 +683,7 @@ function parsePacksFromInput(packsInput, languages) {
  * @param packStr the package specification to verify.
  * @param configFile Config file to use for error reporting
  */
-function validatePacksSpecification(packStr, configFile) {
+function parsePacksSpecification(packStr, configFile) {
     if (typeof packStr !== "string") {
         throw new Error(getPacksStrInvalid(packStr, configFile));
     }
@@ -730,9 +725,21 @@ function validatePacksSpecification(packStr, configFile) {
         // 0 length path
         throw new Error(getPacksStrInvalid(packStr, configFile));
     }
-    return (packName + (version ? `@${version}` : "") + (packPath ? `:${packPath}` : ""));
+    return {
+        name: packName,
+        version,
+        path: packPath,
+    };
 }
-exports.validatePacksSpecification = validatePacksSpecification;
+exports.parsePacksSpecification = parsePacksSpecification;
+function prettyPrintPack(pack) {
+    return `${pack.name}${pack.version ? `@${pack.version}` : ""}${pack.path ? `:${pack.path}` : ""}`;
+}
+exports.prettyPrintPack = prettyPrintPack;
+function validatePackSpecification(pack, configFile) {
+    return prettyPrintPack(parsePacksSpecification(pack, configFile));
+}
+exports.validatePackSpecification = validatePackSpecification;
 // exported for testing
 function parsePacks(rawPacksFromConfig, rawPacksInput, languages, configFile) {
     const packsFromInput = parsePacksFromInput(rawPacksInput, languages);

lib/config-utils.test.js

@@ -828,6 +828,46 @@ const invalidPackNameMacro = ava_1.default.macro({
 (0, ava_1.default)(invalidPackNameMacro, "c/d@../a");
 (0, ava_1.default)(invalidPackNameMacro, "c/d@b/../a");
 (0, ava_1.default)(invalidPackNameMacro, "c/d:z@1");
+/**
+ * Test macro for pretty printing pack specs
+ */
+const packSpecPrettyPrintingMacro = ava_1.default.macro({
+    exec: (t, packStr, packObj) => {
+        const parsed = configUtils.parsePacksSpecification(packStr);
+        t.deepEqual(parsed, packObj, "parsed pack spec is correct");
+        const stringified = configUtils.prettyPrintPack(packObj);
+        t.deepEqual(stringified, packStr.trim(), "pretty-printed pack spec is correct");
+        t.deepEqual(configUtils.validatePackSpecification(packStr), packStr.trim(), "pack spec is valid");
+    },
+    title: (_providedTitle, packStr, 
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    _packObj) => `Prettyprint pack spec: '${packStr}'`,
+});
+(0, ava_1.default)(packSpecPrettyPrintingMacro, "a/b", {
+    name: "a/b",
+    version: undefined,
+    path: undefined,
+});
+(0, ava_1.default)(packSpecPrettyPrintingMacro, "a/b@~1.2.3", {
+    name: "a/b",
+    version: "~1.2.3",
+    path: undefined,
+});
+(0, ava_1.default)(packSpecPrettyPrintingMacro, "a/b@~1.2.3:abc/def", {
+    name: "a/b",
+    version: "~1.2.3",
+    path: "abc/def",
+});
+(0, ava_1.default)(packSpecPrettyPrintingMacro, "a/b:abc/def", {
+    name: "a/b",
+    version: undefined,
+    path: "abc/def",
+});
+(0, ava_1.default)(packSpecPrettyPrintingMacro, "    a/b:abc/def    ", {
+    name: "a/b",
+    version: undefined,
+    path: "abc/def",
+});
 /**
  * Test macro for testing the packs block and the packs input
  */

lib/util.js

@@ -33,6 +33,7 @@ const api = __importStar(require("./api-client"));
 const api_client_1 = require("./api-client");
 const apiCompatibility = __importStar(require("./api-compatibility.json"));
 const codeql_1 = require("./codeql");
+const config_utils_1 = require("./config-utils");
 /**
  * Specifies bundle versions that are known to be broken
  * and will not be used if found in the toolcache.
@@ -552,10 +553,13 @@ exports.ML_POWERED_JS_QUERIES_PACK_NAME = "codeql/javascript-experimental-atm-qu
  * queries beta.
  */
 async function getMlPoweredJsQueriesPack(codeQL) {
-    if (await codeQlVersionAbove(codeQL, "2.8.4")) {
-        return `${exports.ML_POWERED_JS_QUERIES_PACK_NAME}@~0.2.0`;
-    }
-    return `${exports.ML_POWERED_JS_QUERIES_PACK_NAME}@~0.1.0`;
+    const version = (await codeQlVersionAbove(codeQL, "2.8.4"))
+        ? "~0.2.0"
+        : "~0.1.0";
+    return (0, config_utils_1.prettyPrintPack)({
+        name: exports.ML_POWERED_JS_QUERIES_PACK_NAME,
+        version,
+    });
 }
 exports.getMlPoweredJsQueriesPack = getMlPoweredJsQueriesPack;
 /**
@@ -581,9 +585,8 @@ exports.getMlPoweredJsQueriesPack = getMlPoweredJsQueriesPack;
  */
 function getMlPoweredJsQueriesStatus(config) {
     const mlPoweredJsQueryPacks = (config.packs.javascript || [])
-        .map((pack) => pack.split("@"))
-        .filter((packNameVersion) => packNameVersion[0] === "codeql/javascript-experimental-atm-queries" &&
-        packNameVersion.length <= 2);
+        .map((p) => (0, config_utils_1.parsePacksSpecification)(p))
+        .filter((pack) => pack.name === "codeql/javascript-experimental-atm-queries" && !pack.path);
     switch (mlPoweredJsQueryPacks.length) {
         case 1:
             // We should always specify an explicit version string in `getMlPoweredJsQueriesPack`,
@@ -591,7 +594,7 @@ function getMlPoweredJsQueriesStatus(config) {
             // with each version of the CodeQL Action. Therefore in practice we should only hit the
             // `latest` case here when customers have explicitly added the ML-powered query pack to their
             // CodeQL config.
-            return mlPoweredJsQueryPacks[0][1] || "latest";
+            return mlPoweredJsQueryPacks[0].version || "latest";
         case 0:
             return "false";
         default:

lib/util.test.js

@@ -209,13 +209,13 @@ const ML_POWERED_JS_STATUS_TESTS = [
     // If no packs are loaded, status is false.
     [[], "false"],
     // If another pack is loaded but not the ML-powered query pack, status is false.
-    [["someOtherPack"], "false"],
+    [["some-other/pack"], "false"],
     // If the ML-powered query pack is loaded with a specific version, status is that version.
     [[`${util.ML_POWERED_JS_QUERIES_PACK_NAME}@~0.1.0`], "~0.1.0"],
     // If the ML-powered query pack is loaded with a specific version and another pack is loaded, the
     // status is the version of the ML-powered query pack.
     [
-        ["someOtherPack", `${util.ML_POWERED_JS_QUERIES_PACK_NAME}@~0.1.0`],
+        ["some-other/pack", `${util.ML_POWERED_JS_QUERIES_PACK_NAME}@~0.1.0`],
         "~0.1.0",
     ],
     // If the ML-powered query pack is loaded without a version, the status is "latest".
@@ -230,7 +230,7 @@ const ML_POWERED_JS_STATUS_TESTS = [
     ],
     // If the ML-powered query pack is loaded with no specific version, and another pack is loaded,
     // the status is "latest".
-    [["someOtherPack", util.ML_POWERED_JS_QUERIES_PACK_NAME], "latest"],
+    [["some-other/pack", util.ML_POWERED_JS_QUERIES_PACK_NAME], "latest"],
 ];
 for (const [packs, expectedStatus] of ML_POWERED_JS_STATUS_TESTS) {
     const packDescriptions = `[${packs

src/analyze.test.ts

@@ -1,11 +1,16 @@
 import * as fs from "fs";
 import * as path from "path";
 
-import test from "ava";
+import test, { ExecutionContext } from "ava";
 import * as yaml from "js-yaml";
 import * as sinon from "sinon";
 
-import { runQueries } from "./analyze";
+import {
+  convertPackToQuerySuiteEntry,
+  createQuerySuiteContents,
+  runQueries,
+  validateQueryFilters,
+} from "./analyze";
 import { setCodeQL } from "./codeql";
 import { Config } from "./config-utils";
 import * as count from "./count-loc";
@@ -249,3 +254,161 @@ test("status report fields and search path setting", async (t) => {
     }
   }
 });
+
+test("validateQueryFilters", (t) => {
+  t.notThrows(() => validateQueryFilters([]));
+  t.notThrows(() => validateQueryFilters(undefined));
+  t.notThrows(() => {
+    return validateQueryFilters([
+      {
+        exclude: {
+          "problem.severity": "recommendation",
+        },
+      },
+      {
+        exclude: {
+          "tags contain": ["foo", "bar"],
+        },
+      },
+      {
+        include: {
+          "problem.severity": "something-to-think-about",
+        },
+      },
+      {
+        include: {
+          "tags contain": ["baz", "bop"],
+        },
+      },
+    ]);
+  });
+
+  t.throws(
+    () => {
+      return validateQueryFilters([
+        {
+          exclude: {
+            "tags contain": ["foo", "bar"],
+          },
+          include: {
+            "tags contain": ["baz", "bop"],
+          },
+        },
+      ]);
+    },
+    { message: /Query filter must have exactly one key/ }
+  );
+
+  t.throws(
+    () => {
+      return validateQueryFilters([{ xxx: "foo" } as any]);
+    },
+    { message: /Only "include" or "exclude" filters are allowed/ }
+  );
+});
+
+const convertPackToQuerySuiteEntryMacro = test.macro({
+  exec: (t: ExecutionContext<unknown>, packSpec: string, suiteEntry: any) =>
+    t.deepEqual(convertPackToQuerySuiteEntry(packSpec), suiteEntry),
+
+  title: (_providedTitle, packSpec: string) => `Query Suite Entry: ${packSpec}`,
+});
+
+test(convertPackToQuerySuiteEntryMacro, "a/b", {
+  qlpack: "a/b",
+  from: undefined,
+  version: undefined,
+  query: undefined,
+  queries: undefined,
+  apply: undefined,
+});
+
+test(convertPackToQuerySuiteEntryMacro, "a/b@~1.2.3", {
+  qlpack: "a/b",
+  from: undefined,
+  version: "~1.2.3",
+  query: undefined,
+  queries: undefined,
+  apply: undefined,
+});
+
+test(convertPackToQuerySuiteEntryMacro, "a/b:my/path", {
+  qlpack: undefined,
+  from: "a/b",
+  version: undefined,
+  query: undefined,
+  queries: "my/path",
+  apply: undefined,
+});
+
+test(convertPackToQuerySuiteEntryMacro, "a/b@~1.2.3:my/path", {
+  qlpack: undefined,
+  from: "a/b",
+  version: "~1.2.3",
+  query: undefined,
+  queries: "my/path",
+  apply: undefined,
+});
+
+test(convertPackToQuerySuiteEntryMacro, "a/b:my/path/query.ql", {
+  qlpack: undefined,
+  from: "a/b",
+  version: undefined,
+  query: "my/path/query.ql",
+  queries: undefined,
+  apply: undefined,
+});
+
+test(convertPackToQuerySuiteEntryMacro, "a/b@~1.2.3:my/path/query.ql", {
+  qlpack: undefined,
+  from: "a/b",
+  version: "~1.2.3",
+  query: "my/path/query.ql",
+  queries: undefined,
+  apply: undefined,
+});
+
+test(convertPackToQuerySuiteEntryMacro, "a/b:my/path/suite.qls", {
+  qlpack: undefined,
+  from: "a/b",
+  version: undefined,
+  query: undefined,
+  queries: undefined,
+  apply: "my/path/suite.qls",
+});
+
+test(convertPackToQuerySuiteEntryMacro, "a/b@~1.2.3:my/path/suite.qls", {
+  qlpack: undefined,
+  from: "a/b",
+  version: "~1.2.3",
+  query: undefined,
+  queries: undefined,
+  apply: "my/path/suite.qls",
+});
+
+test("convertPackToQuerySuiteEntry Failure", (t) => {
+  t.throws(() => convertPackToQuerySuiteEntry("this-is-not-a-pack"));
+});
+
+test("createQuerySuiteContents", (t) => {
+  const yamlResult = createQuerySuiteContents(
+    ["query1.ql", "query2.ql"],
+    [
+      {
+        exclude: { "problem.severity": "recommendation" },
+      },
+      {
+        include: { "problem.severity": "recommendation" },
+      },
+    ]
+  );
+  const expected = `- query: query1.ql
+- query: query2.ql
+- exclude:
+    problem.severity: recommendation
+- include:
+    problem.severity: recommendation
+`;
+
+  t.deepEqual(yamlResult, expected);
+});

src/analyze.ts

@@ -152,7 +152,7 @@ function dbIsFinalized(
   try {
     const dbInfo = yaml.load(
       fs.readFileSync(path.resolve(dbPath, "codeql-database.yml"), "utf8")
-    );
+    ) as { inProgress?: boolean };
     return !("inProgress" in dbInfo);
   } catch (e) {
     logger.warning(
@@ -224,6 +224,9 @@ export async function runQueries(
 
   for (const language of config.languages) {
     const queries = config.queries[language];
+    const queryFilters = validateQueryFilters(
+      config.originalUserInput["query-filters"]
+    );
     const packsWithVersion = config.packs[language] || [];
 
     const hasBuiltinQueries = queries?.builtin.length > 0;
@@ -261,7 +264,7 @@ export async function runQueries(
           await runQueryGroup(
             language,
             "builtin",
-            createQuerySuiteContents(queries["builtin"]),
+            createQuerySuiteContents(queries["builtin"], queryFilters),
             undefined
           )
         );
@@ -276,7 +279,10 @@ export async function runQueries(
             await runQueryGroup(
               language,
               `custom-${i}`,
-              createQuerySuiteContents(queries["custom"][i].queries),
+              createQuerySuiteContents(
+                queries["custom"][i].queries,
+                queryFilters
+              ),
               queries["custom"][i].searchPath
             )
           );
@@ -285,12 +291,7 @@ export async function runQueries(
       }
       if (packsWithVersion.length > 0) {
         querySuitePaths.push(
-          ...(await runQueryPacks(
-            language,
-            "packs",
-            packsWithVersion,
-            undefined
-          ))
+          await runQueryPacks(language, "packs", packsWithVersion, queryFilters)
         );
         ranCustom = true;
       }
@@ -392,32 +393,59 @@ export async function runQueries(
     language: Language,
     type: string,
     packs: string[],
-    searchPath: string | undefined
-  ): Promise<string[]> {
+    queryFilters: configUtils.QueryFilter[]
+  ): Promise<string> {
     const databasePath = util.getCodeQLDatabasePath(config, language);
-    // Run the queries individually instead of all at once to avoid command
-    // line length restrictions, particularly on windows.
 
     for (const pack of packs) {
       logger.debug(`Running query pack for ${language}-${type}: ${pack}`);
-
-      const codeql = await getCodeQL(config.codeQLCmd);
-      await codeql.databaseRunQueries(
-        databasePath,
-        searchPath,
-        pack,
-        memoryFlag,
-        threadsFlag
-      );
-
-      logger.debug(`BQRS results produced for ${language} (queries: ${type})"`);
     }
-    return packs;
+
+    // combine the list of packs into a query suite in order to run them all simultaneously.
+    const querySuite = packs
+      .map(convertPackToQuerySuiteEntry)
+      .concat(queryFilters as any[]);
+
+    const querySuitePath = `${databasePath}-queries-${type}.qls`;
+    fs.writeFileSync(querySuitePath, yaml.dump(querySuite));
+
+    logger.debug(`BQRS results produced for ${language} (queries: ${type})"`);
+
+    const codeql = await getCodeQL(config.codeQLCmd);
+    await codeql.databaseRunQueries(
+      databasePath,
+      undefined,
+      querySuitePath,
+      memoryFlag,
+      threadsFlag
+    );
+
+    return querySuitePath;
   }
 }
 
-function createQuerySuiteContents(queries: string[]) {
-  return queries.map((q: string) => `- query: ${q}`).join("\n");
+export function convertPackToQuerySuiteEntry(packStr: string) {
+  const pack = configUtils.parsePacksSpecification(packStr);
+  return {
+    qlpack: !pack.path ? pack.name : undefined,
+    from: pack.path ? pack.name : undefined,
+    version: pack.version,
+    query: pack.path?.endsWith(".ql") ? pack.path : undefined,
+    queries:
+      !pack.path?.endsWith(".ql") && !pack.path?.endsWith(".qls")
+        ? pack.path
+        : undefined,
+    apply: pack.path?.endsWith(".qls") ? pack.path : undefined,
+  };
+}
+
+export function createQuerySuiteContents(
+  queries: string[],
+  queryFilters: configUtils.QueryFilter[]
+) {
+  return yaml.dump(
+    queries.map((q: string) => ({ query: q })).concat(queryFilters as any)
+  );
 }
 
 export async function runFinalize(
@@ -505,3 +533,33 @@ function printLinesOfCodeSummary(
     );
   }
 }
+
+// exported for testing
+export function validateQueryFilters(queryFilters?: configUtils.QueryFilter[]) {
+  if (!queryFilters) {
+    return [];
+  }
+
+  const errors: string[] = [];
+  for (const qf of queryFilters) {
+    const keys = Object.keys(qf);
+    if (keys.length !== 1) {
+      errors.push(
+        `Query filter must have exactly one key: ${JSON.stringify(qf)}`
+      );
+    }
+    if (!["exclude", "include"].includes(keys[0])) {
+      errors.push(
+        `Only "include" or "exclude" filters are allowed:\n${JSON.stringify(
+          qf
+        )}`
+      );
+    }
+  }
+
+  if (errors.length) {
+    throw new Error(`Invalid query filter.\n${errors.join("\n")}`);
+  }
+
+  return queryFilters;
+}

src/config-utils.test.ts

@@ -1572,6 +1572,60 @@ test(invalidPackNameMacro, "c/d@../a");
 test(invalidPackNameMacro, "c/d@b/../a");
 test(invalidPackNameMacro, "c/d:z@1");
 
+/**
+ * Test macro for pretty printing pack specs
+ */
+const packSpecPrettyPrintingMacro = test.macro({
+  exec: (t: ExecutionContext, packStr: string, packObj: configUtils.Pack) => {
+    const parsed = configUtils.parsePacksSpecification(packStr);
+    t.deepEqual(parsed, packObj, "parsed pack spec is correct");
+    const stringified = configUtils.prettyPrintPack(packObj);
+    t.deepEqual(
+      stringified,
+      packStr.trim(),
+      "pretty-printed pack spec is correct"
+    );
+
+    t.deepEqual(
+      configUtils.validatePackSpecification(packStr),
+      packStr.trim(),
+      "pack spec is valid"
+    );
+  },
+  title: (
+    _providedTitle: string | undefined,
+    packStr: string,
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    _packObj: configUtils.Pack
+  ) => `Prettyprint pack spec: '${packStr}'`,
+});
+
+test(packSpecPrettyPrintingMacro, "a/b", {
+  name: "a/b",
+  version: undefined,
+  path: undefined,
+});
+test(packSpecPrettyPrintingMacro, "a/b@~1.2.3", {
+  name: "a/b",
+  version: "~1.2.3",
+  path: undefined,
+});
+test(packSpecPrettyPrintingMacro, "a/b@~1.2.3:abc/def", {
+  name: "a/b",
+  version: "~1.2.3",
+  path: "abc/def",
+});
+test(packSpecPrettyPrintingMacro, "a/b:abc/def", {
+  name: "a/b",
+  version: undefined,
+  path: "abc/def",
+});
+test(packSpecPrettyPrintingMacro, "    a/b:abc/def    ", {
+  name: "a/b",
+  version: undefined,
+  path: "abc/def",
+});
+
 /**
  * Test macro for testing the packs block and the packs input
  */

src/config-utils.ts

@@ -49,6 +49,20 @@ export interface UserConfig {
   // language. If this is a single language analysis, then no split by
   // language is necessary.
   packs?: Record<string, string[]> | string[];
+
+  // Set of query filters to include and exclude extra queries based on
+  // codeql query suite `include` and `exclude` properties
+  "query-filters"?: QueryFilter[];
+}
+
+export type QueryFilter = ExcludeQueryFilter | IncludeQueryFilter;
+
+interface ExcludeQueryFilter {
+  exclude: Record<string, string[] | string>;
+}
+
+interface IncludeQueryFilter {
+  include: Record<string, string[] | string>;
 }
 
 /**
@@ -157,6 +171,12 @@ export interface Config {
 
 export type Packs = Partial<Record<Language, string[]>>;
 
+export interface Pack {
+  name: string;
+  version?: string;
+  path?: string;
+}
+
 /**
  * A list of queries from https://github.com/github/codeql that
  * we don't want to run. Disabling them here is a quicker alternative to
@@ -319,11 +339,7 @@ async function addBuiltinSuiteQueries(
 }
 
 function isMlPoweredJsQueriesPack(pack: string) {
-  return (
-    pack === ML_POWERED_JS_QUERIES_PACK_NAME ||
-    pack.startsWith(`${ML_POWERED_JS_QUERIES_PACK_NAME}@`) ||
-    pack.startsWith(`${ML_POWERED_JS_QUERIES_PACK_NAME}:`)
-  );
+  return parsePacksSpecification(pack).name === ML_POWERED_JS_QUERIES_PACK_NAME;
 }
 
 /**
@@ -1170,10 +1186,10 @@ export function parsePacksFromConfig(
     if (!languages.includes(lang as Language)) {
       throw new Error(getPacksRequireLanguage(lang, configFile));
     }
-    packs[lang] = [];
-    for (const packStr of packsArr) {
-      packs[lang].push(validatePacksSpecification(packStr, configFile));
-    }
+
+    packs[lang] = packsArr.map((packStr) =>
+      validatePackSpecification(packStr, configFile)
+    );
   }
   return packs;
 }
@@ -1206,7 +1222,7 @@ function parsePacksFromInput(
 
   return {
     [languages[0]]: packsInput.split(",").reduce((packs, pack) => {
-      packs.push(validatePacksSpecification(pack, ""));
+      packs.push(validatePackSpecification(pack));
       return packs;
     }, [] as string[]),
   };
@@ -1230,10 +1246,10 @@ function parsePacksFromInput(
  * @param packStr the package specification to verify.
  * @param configFile Config file to use for error reporting
  */
-export function validatePacksSpecification(
+export function parsePacksSpecification(
   packStr: string,
   configFile?: string
-): string {
+): Pack {
   if (typeof packStr !== "string") {
     throw new Error(getPacksStrInvalid(packStr, configFile));
   }
@@ -1286,9 +1302,21 @@ export function validatePacksSpecification(
     throw new Error(getPacksStrInvalid(packStr, configFile));
   }
 
-  return (
-    packName + (version ? `@${version}` : "") + (packPath ? `:${packPath}` : "")
-  );
+  return {
+    name: packName,
+    version,
+    path: packPath,
+  };
+}
+
+export function prettyPrintPack(pack: Pack) {
+  return `${pack.name}${pack.version ? `@${pack.version}` : ""}${
+    pack.path ? `:${pack.path}` : ""
+  }`;
+}
+
+export function validatePackSpecification(pack: string, configFile?: string) {
+  return prettyPrintPack(parsePacksSpecification(pack, configFile));
 }
 
 // exported for testing
@@ -1448,7 +1476,7 @@ function getLocalConfig(configFile: string, workspacePath: string): UserConfig {
     throw new Error(getConfigFileDoesNotExistErrorMessage(configFile));
   }
 
-  return yaml.load(fs.readFileSync(configFile, "utf8"));
+  return yaml.load(fs.readFileSync(configFile, "utf8")) as UserConfig;
 }
 
 async function getRemoteConfig(
@@ -1483,7 +1511,9 @@ async function getRemoteConfig(
     throw new Error(getConfigFileFormatInvalidMessage(configFile));
   }
 
-  return yaml.load(Buffer.from(fileContents, "base64").toString("binary"));
+  return yaml.load(
+    Buffer.from(fileContents, "base64").toString("binary")
+  ) as UserConfig;
 }
 
 /**

src/util.test.ts

@@ -298,13 +298,13 @@ const ML_POWERED_JS_STATUS_TESTS: Array<[string[], string]> = [
   // If no packs are loaded, status is false.
   [[], "false"],
   // If another pack is loaded but not the ML-powered query pack, status is false.
-  [["someOtherPack"], "false"],
+  [["some-other/pack"], "false"],
   // If the ML-powered query pack is loaded with a specific version, status is that version.
   [[`${util.ML_POWERED_JS_QUERIES_PACK_NAME}@~0.1.0`], "~0.1.0"],
   // If the ML-powered query pack is loaded with a specific version and another pack is loaded, the
   // status is the version of the ML-powered query pack.
   [
-    ["someOtherPack", `${util.ML_POWERED_JS_QUERIES_PACK_NAME}@~0.1.0`],
+    ["some-other/pack", `${util.ML_POWERED_JS_QUERIES_PACK_NAME}@~0.1.0`],
     "~0.1.0",
   ],
   // If the ML-powered query pack is loaded without a version, the status is "latest".
@@ -319,7 +319,7 @@ const ML_POWERED_JS_STATUS_TESTS: Array<[string[], string]> = [
   ],
   // If the ML-powered query pack is loaded with no specific version, and another pack is loaded,
   // the status is "latest".
-  [["someOtherPack", util.ML_POWERED_JS_QUERIES_PACK_NAME], "latest"],
+  [["some-other/pack", util.ML_POWERED_JS_QUERIES_PACK_NAME], "latest"],
 ];
 
 for (const [packs, expectedStatus] of ML_POWERED_JS_STATUS_TESTS) {

src/util.ts

@@ -11,7 +11,11 @@ import * as api from "./api-client";
 import { getApiClient, GitHubApiDetails } from "./api-client";
 import * as apiCompatibility from "./api-compatibility.json";
 import { CodeQL, CODEQL_VERSION_NEW_TRACING } from "./codeql";
-import { Config } from "./config-utils";
+import {
+  Config,
+  parsePacksSpecification,
+  prettyPrintPack,
+} from "./config-utils";
 import { Language } from "./languages";
 import { Logger } from "./logging";
 
@@ -664,10 +668,13 @@ export const ML_POWERED_JS_QUERIES_PACK_NAME =
 export async function getMlPoweredJsQueriesPack(
   codeQL: CodeQL
 ): Promise<string> {
-  if (await codeQlVersionAbove(codeQL, "2.8.4")) {
-    return `${ML_POWERED_JS_QUERIES_PACK_NAME}@~0.2.0`;
-  }
-  return `${ML_POWERED_JS_QUERIES_PACK_NAME}@~0.1.0`;
+  const version = (await codeQlVersionAbove(codeQL, "2.8.4"))
+    ? "~0.2.0"
+    : "~0.1.0";
+  return prettyPrintPack({
+    name: ML_POWERED_JS_QUERIES_PACK_NAME,
+    version,
+  });
 }
 
 /**
@@ -693,11 +700,10 @@ export async function getMlPoweredJsQueriesPack(
  */
 export function getMlPoweredJsQueriesStatus(config: Config): string {
   const mlPoweredJsQueryPacks = (config.packs.javascript || [])
-    .map((pack) => pack.split("@"))
+    .map((p) => parsePacksSpecification(p))
     .filter(
-      (packNameVersion) =>
-        packNameVersion[0] === "codeql/javascript-experimental-atm-queries" &&
-        packNameVersion.length <= 2
+      (pack) =>
+        pack.name === "codeql/javascript-experimental-atm-queries" && !pack.path
     );
   switch (mlPoweredJsQueryPacks.length) {
     case 1:
@@ -706,7 +712,7 @@ export function getMlPoweredJsQueriesStatus(config: Config): string {
       // with each version of the CodeQL Action. Therefore in practice we should only hit the
       // `latest` case here when customers have explicitly added the ML-powered query pack to their
       // CodeQL config.
-      return mlPoweredJsQueryPacks[0][1] || "latest";
+      return mlPoweredJsQueryPacks[0].version || "latest";
     case 0:
       return "false";
     default: