Merge pull request #1626 from github/henrymercer/diagnostics-ghes

Enable diagnostics functionality on GHES
Pass negative SARIF include diagnostics flag when feature is disabled
2026-10-20 05:15:24 +03:00 · 2023-03-30 10:22:39 +01:00 · 2023-03-29 18:56:19 +01:00 · 2023-03-29 18:45:27 +01:00 · 2023-03-29 13:28:57 +01:00 · 2023-03-29 11:02:16 +02:00
66 changed files with 863 additions and 450 deletions
@@ -40,7 +40,7 @@ runs:
      with:
        output: ${{ runner.temp }}/results
        upload-database: false
-        upload: false
+        upload: never
      env:
        CODEQL_ACTION_TEST_MODE: "true"
    - name: Check SARIF
@@ -52,14 +52,23 @@ jobs:
      id: init
      with:
        languages: javascript
-        queries: security-extended
        tools: ${{ steps.prepare-test.outputs.tools-url }}
-    - name: Manually add a diagnostic
+    - name: Add test diagnostics
      shell: bash
      env:
        CODEQL_PATH: ${{ steps.init.outputs.codeql-path }}
      run: |
-        "$CODEQL_PATH" database add-diagnostic "$RUNNER_TEMP/codeql_databases/javascript" --plaintext-message="Plaintext message" --source-id="lang/diagnostics/example" --source-name="Diagnostic name"
+        for i in {1..2}; do
+          # Use the same location twice to test the workaround for the bug in CodeQL CLI 2.12.5 that
+          # produces an invalid diagnostic with multiple identical location objects.
+          "$CODEQL_PATH" database add-diagnostic \
+            "$RUNNER_TEMP/codeql_databases/javascript" \
+            --file-path /path/to/file \
+            --plaintext-message "Plaintext message $i" \
+            --source-id "lang/diagnostics/example" \
+            --source-name "Diagnostic name" \
+            --ready-for-status-page
+        done
    - uses: ./../action/analyze
      with:
        output: ${{ runner.temp }}/results
@@ -75,22 +84,48 @@ jobs:
      env:
        SARIF_PATH: ${{ runner.temp }}/results/javascript.sarif
      with:
-        script: |-
+        script: |
          const fs = require('fs');

+          function checkStatusPageNotification(n) {
+            const expectedMessage = 'Plaintext message 1\n\nCodeQL also found 1 other diagnostic like this. See the workflow log for details.';
+            if (n.message.text !== expectedMessage) {
+              core.setFailed(`Expected the status page diagnostic to have the message '${expectedMessage}', but found '${n.message.text}'.`);
+            }
+            if (n.locations.length !== 1) {
+              core.setFailed(`Expected the status page diagnostic to have exactly 1 location, but found ${n.locations.length}.`);
+            }
+          }
+
          const sarif = JSON.parse(fs.readFileSync(process.env['SARIF_PATH'], 'utf8'));
          const run = sarif.runs[0];

          const toolExecutionNotifications = run.invocations[0].toolExecutionNotifications;
-          const diagnosticToolExecutionNotification = toolExecutionNotifications.filter(n => n.descriptor.id === 'lang/diagnostics/example' && n.message.text === 'Plaintext message');
-          if (diagnosticToolExecutionNotification.length !== 1) {
-            core.setFailed(`Expected exactly 1 entry for this diagnostic in the 'runs[].invocations[].toolExecutionNotifications[]' SARIF property, found ${diagnosticToolExecutionNotification.length}`);
+          const statusPageNotifications = toolExecutionNotifications.filter(n =>
+            n.descriptor.id === 'lang/diagnostics/example' && n.properties?.visibility?.statusPage
+          );
+          if (statusPageNotifications.length !== 1) {
+            core.setFailed(
+              'Expected exactly one status page reporting descriptor for this diagnostic in the ' +
+                `'runs[].invocations[].toolExecutionNotifications[]' SARIF property, but found ` +
+                `${statusPageNotifications.length}. All notification reporting descriptors: ` + 
+                `${JSON.stringify(toolExecutionNotifications)}.`
+            );
          }
+          checkStatusPageNotification(statusPageNotifications[0]);

          const notifications = run.tool.driver.notifications;
-          const diagnosticNotification = notifications.filter(n => n.id === 'lang/diagnostics/example' && n.name === 'lang/diagnostics/example' && n.fullDescription.text && 'Diagnostic name');
+          const diagnosticNotification = notifications.filter(n =>
+            n.id === 'lang/diagnostics/example' && n.name === 'lang/diagnostics/example' &&
+              n.fullDescription.text === 'Diagnostic name'
+          );
          if (diagnosticNotification.length !== 1) {
-            core.setFailed(`Expected exactly 1 entry for this diagnostic in the 'runs[].tool.driver.notifications[]' SARIF property, found ${diagnosticNotification.length}`);
+            core.setFailed(
+              'Expected exactly one notification for this diagnostic in the ' +
+                `'runs[].tool.driver.notifications[]' SARIF property, but found ` +
+                `${diagnosticNotification.length}. All notifications: ` +
+                `${JSON.stringify(notifications)}.`
+            );
          }

          core.info('Finished diagnostic export test');
@@ -56,7 +56,7 @@ jobs:
      with:
        upload-database: false
        skip-queries: true
-        upload: false
+        upload: never
    - name: Assert database exists
      shell: bash
      run: |
@@ -1,72 +0,0 @@
-# Warning: This file is generated automatically, and should not be modified.
-# Instead, please modify the template in the pr-checks directory and run:
-#     pip install ruamel.yaml && python3 sync.py
-# to regenerate this file.
-
-name: PR Check - Swift analysis using autobuild
-env:
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  GO111MODULE: auto
-  CODEQL_EXTRACTOR_JAVA_AGENT_DISABLE_KOTLIN: 'true'
-on:
-  push:
-    branches:
-    - main
-    - releases/v2
-  pull_request:
-    types:
-    - opened
-    - synchronize
-    - reopened
-    - ready_for_review
-  workflow_dispatch: {}
-jobs:
-  swift-autobuild:
-    strategy:
-      matrix:
-        include:
-        - os: macos-latest
-          version: latest
-        - os: macos-latest
-          version: cached
-        - os: macos-latest
-          version: nightly-latest
-    name: Swift analysis using autobuild
-    timeout-minutes: 45
-    runs-on: ${{ matrix.os }}
-    steps:
-    - name: Check out repository
-      uses: actions/checkout@v3
-    - name: Prepare test
-      id: prepare-test
-      uses: ./.github/prepare-test
-      with:
-        version: ${{ matrix.version }}
-    - uses: ./../action/init
-      id: init
-      with:
-        languages: swift
-        tools: ${{ steps.prepare-test.outputs.tools-url }}
-    - uses: ./../action/.github/setup-swift
-      with:
-        codeql-path: ${{steps.init.outputs.codeql-path}}
-    - name: Check working directory
-      shell: bash
-      run: pwd
-    - uses: ./../action/autobuild
-      timeout-minutes: 10
-    - uses: ./../action/analyze
-      id: analysis
-      with:
-        upload-database: false
-    - name: Check database
-      shell: bash
-      run: |
-        SWIFT_DB="${{ fromJson(steps.analysis.outputs.db-locations).swift }}"
-        if [[ ! -d "$SWIFT_DB" ]]; then
-          echo "Did not create a database for Swift."
-          exit 1
-        fi
-    env:
-      CODEQL_ENABLE_EXPERIMENTAL_FEATURES_SWIFT: 'true' # Remove when Swift is GA.
-      CODEQL_ACTION_TEST_MODE: true
@@ -91,7 +91,7 @@ jobs:
        upload-database: false
        ref: refs/heads/main
        sha: 5e235361806c361d4d3f8859e3c897658025a9a2
-        upload: false
+        upload: never
    - uses: ./../action/upload-sarif
      with:
        ref: refs/heads/main
@@ -103,7 +103,7 @@ jobs:
        checkout_path: x/y/z/some-path/tests/multi-language-repo
        ref: v1.1.0
        sha: 474bbf07f9247ffe1856c6a0f94aeeb10e7afee6
-        upload: false
+        upload: never
        upload-database: false

    - uses: ./../action/upload-sarif
@@ -36,7 +36,7 @@ jobs:
      with:
        output: ${{ runner.temp }}/results
        upload-database: false
-        upload: false
+        upload: never

    - name: Check Sarif
      uses: ./../action/.github/check-sarif
@@ -1,5 +1,19 @@
 # CodeQL Action Changelog

+## [UNRELEASED]
+
+No user facing changes.
+
+## 2.2.9 - 27 Mar 2023
+
+- Customers post-processing the SARIF output of the `analyze` Action before uploading it to Code Scanning will benefit from an improved debugging experience. [#1598](https://github.com/github/codeql-action/pull/1598)
+  - The CodeQL Action will now upload a SARIF file with debugging information to Code Scanning on failed runs for customers using `upload: false`. Previously, this was only available for customers using the default value of the `upload` input.
+  - The `upload` input to the `analyze` Action now accepts the following values:
+    - `always` is the default value, which uploads the SARIF file to Code Scanning for successful and failed runs.
+    - `failure-only` is recommended for customers post-processing the SARIF file before uploading it to Code Scanning. This option uploads debugging information to Code Scanning for failed runs to improve the debugging experience.
+    - `never` avoids uploading the SARIF file to Code Scanning even if the code scanning run fails. This is not recommended for external users since it complicates debugging.
+    - The legacy `true` and `false` options will be interpreted as `always` and `failure-only` respectively.
+
 ## 2.2.8 - 22 Mar 2023

 - Update default CodeQL bundle version to 2.12.5. [#1585](https://github.com/github/codeql-action/pull/1585)
@@ -10,10 +10,14 @@ inputs:
    required: false
    default: "../results"
  upload:
-    description: Upload the SARIF file to Code Scanning
+    description: >-
+      Upload the SARIF file to Code Scanning.
+      Defaults to 'always' which uploads the SARIF file to Code Scanning for successful and failed runs.
+      'failure-only' only uploads debugging information to Code Scanning if the workflow run fails, for users post-processing the SARIF file before uploading it to Code Scanning.
+      'never' avoids uploading the SARIF file to Code Scanning, even if the code scanning run fails. This is not recommended for external users since it complicates debugging.
    required: false
    # If changing this, make sure to update workflow.ts accordingly.
-    default: "true"
+    default: "always"
  cleanup-level:
    description: "Level of cleanup to perform on CodeQL databases at the end of the analyze step. This should either be 'none' to skip cleanup, or be a valid argument for the --mode flag of the CodeQL CLI command 'codeql database cleanup' as documented at https://codeql.github.com/docs/codeql-cli/manual/database-cleanup"
    required: false
@@ -23,7 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
    return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.printDebugLogs = exports.isAnalyzingDefaultBranch = exports.getRelativeScriptPath = exports.isRunningLocalAction = exports.workflowEventName = exports.sendStatusReport = exports.createStatusReportBase = exports.getActionVersion = exports.getActionsStatus = exports.getRef = exports.computeAutomationID = exports.getAutomationID = exports.getAnalysisKey = exports.determineMergeBaseCommitOid = exports.getCommitOid = exports.getTemporaryDirectory = exports.getOptionalInput = exports.getRequiredInput = void 0;
+exports.getUploadValue = exports.printDebugLogs = exports.isAnalyzingDefaultBranch = exports.getRelativeScriptPath = exports.isRunningLocalAction = exports.workflowEventName = exports.sendStatusReport = exports.createStatusReportBase = exports.getActionVersion = exports.getActionsStatus = exports.getRef = exports.computeAutomationID = exports.getAutomationID = exports.getAnalysisKey = exports.determineMergeBaseCommitOid = exports.getCommitOid = exports.getTemporaryDirectory = exports.getOptionalInput = exports.getRequiredInput = void 0;
 const fs = __importStar(require("fs"));
 const os = __importStar(require("os"));
 const path = __importStar(require("path"));
@@ -478,9 +478,14 @@ function getWorkflowEvent() {
 function removeRefsHeadsPrefix(ref) {
    return ref.startsWith("refs/heads/") ? ref.slice("refs/heads/".length) : ref;
 }
-// Is the version of the repository we are currently analyzing from the default branch,
-// or alternatively from another branch or a pull request.
+// Returns whether we are analyzing the default branch for the repository.
+// For cases where the repository information might not be available (e.g.,
+// dynamic workflows), this can be forced by the environment variable
+// CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH.
 async function isAnalyzingDefaultBranch() {
+    if (process.env.CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH === "true") {
+        return true;
+    }
    // Get the current ref and trim and refs/heads/ prefix
    let currentRef = await getRef();
    currentRef = removeRefsHeadsPrefix(currentRef);
@@ -521,4 +526,22 @@ async function printDebugLogs(config) {
    }
 }
 exports.printDebugLogs = printDebugLogs;
+// Parses the `upload` input into an `UploadKind`, converting unspecified and deprecated upload inputs appropriately.
+function getUploadValue(input) {
+    switch (input) {
+        case undefined:
+        case "true":
+        case "always":
+            return "always";
+        case "false":
+        case "failure-only":
+            return "failure-only";
+        case "never":
+            return "never";
+        default:
+            core.warning(`Unrecognized 'upload' input to 'analyze' Action: ${input}. Defaulting to 'always'.`);
+            return "always";
+    }
+}
+exports.getUploadValue = getUploadValue;
 //# sourceMappingURL=actions-util.js.map
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@@ -172,6 +172,9 @@ const util_1 = require("./util");
    t.deepEqual(process.env.CODEQL_ACTION_VERSION, "1.2.3");
 });
 (0, ava_1.default)("isAnalyzingDefaultBranch()", async (t) => {
+    process.env["CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH"] = "true";
+    t.deepEqual(await actionsutil.isAnalyzingDefaultBranch(), true);
+    process.env["CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH"] = "false";
    await (0, util_1.withTmpDir)(async (tmpDir) => {
        (0, testing_utils_1.setupActionsVars)(tmpDir, tmpDir);
        const envFile = path.join(tmpDir, "event.json");
@@ -1 +1 @@
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@@ -155,7 +155,7 @@ async function run() {
        if (hasBadExpectErrorInput()) {
            throw new Error("`expect-error` input parameter is for internal use only. It should only be set by codeql-action or a fork.");
        }
-        await util.enrichEnvironment(await (0, codeql_1.getCodeQL)(config.codeQLCmd));
+        await (0, codeql_1.enrichEnvironment)(await (0, codeql_1.getCodeQL)(config.codeQLCmd));
        const apiDetails = (0, api_client_1.getApiDetails)();
        const outputDir = actionsUtil.getRequiredInput("output");
        const threads = util.getThreadsFlag(actionsUtil.getOptionalInput("threads") || process.env["CODEQL_THREADS"], logger);
@@ -176,7 +176,8 @@ async function run() {
            dbLocations[language] = util.getCodeQLDatabasePath(config, language);
        }
        core.setOutput("db-locations", dbLocations);
-        if (runStats && actionsUtil.getRequiredInput("upload") === "true") {
+        const uploadInput = actionsUtil.getOptionalInput("upload");
+        if (runStats && actionsUtil.getUploadValue(uploadInput) === "always") {
            uploadResult = await upload_lib.uploadFromActions(outputDir, actionsUtil.getRequiredInput("checkout_path"), actionsUtil.getOptionalInput("category"), logger);
            core.setOutput("sarif-id", uploadResult.sarifID);
        }
@@ -1 +1 @@
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@@ -218,7 +218,7 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
    return statusReport;
    async function runInterpretResults(language, queries, sarifFile, enableDebugLogging) {
        const databasePath = util.getCodeQLDatabasePath(config, language);
-        return await codeql.databaseInterpretResults(databasePath, queries, sarifFile, addSnippetsFlag, threadsFlag, enableDebugLogging ? "-vv" : "-v", automationDetailsId, config, features);
+        return await codeql.databaseInterpretResults(databasePath, queries, sarifFile, addSnippetsFlag, threadsFlag, enableDebugLogging ? "-vv" : "-v", automationDetailsId, config, features, logger);
    }
    async function runPrintLinesOfCode(language) {
        const databasePath = util.getCodeQLDatabasePath(config, language);
@@ -1 +1 @@
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truncated
@@ -23,9 +23,10 @@ var __importStar = (this && this.__importStar) || function (mod) {
    return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getExtraOptions = exports.getCodeQLForCmd = exports.getCodeQLForTesting = exports.getCachedCodeQL = exports.setCodeQL = exports.getCodeQL = exports.setupCodeQL = exports.CODEQL_VERSION_INIT_WITH_QLCONFIG = exports.CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE = exports.CODEQL_VERSION_BETTER_RESOLVE_LANGUAGES = exports.CODEQL_VERSION_ML_POWERED_QUERIES_WINDOWS = exports.CODEQL_VERSION_TRACING_GLIBC_2_34 = exports.CODEQL_VERSION_NEW_TRACING = exports.CODEQL_VERSION_GHES_PACK_DOWNLOAD = exports.CommandInvocationError = void 0;
+exports.enrichEnvironment = exports.getExtraOptions = exports.getCodeQLForCmd = exports.getCodeQLForTesting = exports.getCachedCodeQL = exports.setCodeQL = exports.getCodeQL = exports.setupCodeQL = exports.CODEQL_VERSION_INIT_WITH_QLCONFIG = exports.CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE = exports.CODEQL_VERSION_BETTER_RESOLVE_LANGUAGES = exports.CODEQL_VERSION_ML_POWERED_QUERIES_WINDOWS = exports.CODEQL_VERSION_TRACING_GLIBC_2_34 = exports.CODEQL_VERSION_NEW_TRACING = exports.CODEQL_VERSION_GHES_PACK_DOWNLOAD = exports.CommandInvocationError = void 0;
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
+const core = __importStar(require("@actions/core"));
 const toolrunner = __importStar(require("@actions/exec/lib/toolrunner"));
 const yaml = __importStar(require("js-yaml"));
 const actions_util_1 = require("./actions-util");
@@ -34,6 +35,7 @@ const error_matcher_1 = require("./error-matcher");
 const feature_flags_1 = require("./feature-flags");
 const languages_1 = require("./languages");
 const setupCodeql = __importStar(require("./setup-codeql"));
+const shared_environment_1 = require("./shared-environment");
 const toolrunner_error_catcher_1 = require("./toolrunner-error-catcher");
 const trap_caching_1 = require("./trap-caching");
 const util = __importStar(require("./util"));
@@ -505,14 +507,18 @@ async function getCodeQLForCmd(cmd, checkVersion) {
            }
            await (0, toolrunner_error_catcher_1.toolrunnerErrorCatcher)(cmd, codeqlArgs, error_matcher_1.errorMatchers);
        },
-        async databaseInterpretResults(databasePath, querySuitePaths, sarifFile, addSnippetsFlag, threadsFlag, verbosityFlag, automationDetailsId, config, features) {
+        async databaseInterpretResults(databasePath, querySuitePaths, sarifFile, addSnippetsFlag, threadsFlag, verbosityFlag, automationDetailsId, config, features, logger) {
+            const shouldExportDiagnostics = await features.getValue(feature_flags_1.Feature.ExportDiagnosticsEnabled, this);
+            const codeqlOutputFile = shouldExportDiagnostics
+                ? path.join(config.tempDir, "codeql-intermediate-results.sarif")
+                : sarifFile;
            const codeqlArgs = [
                "database",
                "interpret-results",
                threadsFlag,
                "--format=sarif-latest",
                verbosityFlag,
-                `--output=${sarifFile}`,
+                `--output=${codeqlOutputFile}`,
                addSnippetsFlag,
                "--print-diagnostics-summary",
                "--print-metrics-summary",
@@ -528,15 +534,21 @@ async function getCodeQLForCmd(cmd, checkVersion) {
            if (await util.codeQlVersionAbove(this, CODEQL_VERSION_FILE_BASELINE_INFORMATION)) {
                codeqlArgs.push("--sarif-add-baseline-file-info");
            }
-            if (await features.getValue(feature_flags_1.Feature.ExportDiagnosticsEnabled, this)) {
+            if (shouldExportDiagnostics) {
                codeqlArgs.push("--sarif-include-diagnostics");
            }
+            else if (await util.codeQlVersionAbove(this, "2.12.4")) {
+                codeqlArgs.push("--no-sarif-include-diagnostics");
+            }
            codeqlArgs.push(databasePath);
            if (querySuitePaths) {
                codeqlArgs.push(...querySuitePaths);
            }
            // capture stdout, which contains analysis summaries
            const returnState = await (0, toolrunner_error_catcher_1.toolrunnerErrorCatcher)(cmd, codeqlArgs, error_matcher_1.errorMatchers);
+            if (shouldExportDiagnostics) {
+                util.fixInvalidNotificationsInFile(codeqlOutputFile, sarifFile, logger);
+            }
            return returnState.stdout;
        },
        async databasePrintBaseline(databasePath) {
@@ -613,14 +625,15 @@ async function getCodeQLForCmd(cmd, checkVersion) {
            ];
            await new toolrunner.ToolRunner(cmd, args).exec();
        },
-        async databaseExportDiagnostics(databasePath, sarifFile, automationDetailsId) {
+        async databaseExportDiagnostics(databasePath, sarifFile, automationDetailsId, tempDir, logger) {
+            const intermediateSarifFile = path.join(tempDir, "codeql-intermediate-results.sarif");
            const args = [
                "database",
                "export-diagnostics",
                `${databasePath}`,
                "--db-cluster",
                "--format=sarif-latest",
-                `--output=${sarifFile}`,
+                `--output=${intermediateSarifFile}`,
                "--sarif-include-diagnostics",
                "-vvv",
                ...getExtraOptionsFromEnv(["diagnostics", "export"]),
@@ -629,6 +642,8 @@ async function getCodeQLForCmd(cmd, checkVersion) {
                args.push("--sarif-category", automationDetailsId);
            }
            await new toolrunner.ToolRunner(cmd, args).exec();
+            // Fix invalid notifications in the SARIF file output by CodeQL.
+            util.fixInvalidNotificationsInFile(intermediateSarifFile, sarifFile, logger);
        },
        async diagnosticsExport(sarifFile, automationDetailsId, config, features) {
            const args = [
@@ -829,4 +844,19 @@ async function getCodeScanningConfigExportArguments(config, codeql, features) {
    }
    return [];
 }
+/**
+ * Enrich the environment variables with further flags that we cannot
+ * know the value of until we know what version of CodeQL we're running.
+ */
+async function enrichEnvironment(codeql) {
+    if (await util.codeQlVersionAbove(codeql, exports.CODEQL_VERSION_NEW_TRACING)) {
+        core.exportVariable(shared_environment_1.EnvVar.FEATURE_MULTI_LANGUAGE, "false");
+        core.exportVariable(shared_environment_1.EnvVar.FEATURE_SANDWICH, "false");
+    }
+    else {
+        core.exportVariable(shared_environment_1.EnvVar.FEATURE_MULTI_LANGUAGE, "true");
+        core.exportVariable(shared_environment_1.EnvVar.FEATURE_SANDWICH, "true");
+    }
+}
+exports.enrichEnvironment = enrichEnvironment;
 //# sourceMappingURL=codeql.js.map
@@ -1 +1 @@
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truncated
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truncated
@@ -424,7 +424,7 @@ for (const isBundleVersionInUrl of [true, false]) {
    sinon.stub(codeqlObject, "getVersion").resolves("2.7.0");
    // safeWhich throws because of the test CodeQL object.
    sinon.stub(safeWhich, "safeWhich").resolves("");
-    await codeqlObject.databaseInterpretResults("", [], "", "", "", "-v", "", stubConfig, (0, testing_utils_1.createFeatures)([]));
+    await codeqlObject.databaseInterpretResults("", [], "", "", "", "-v", "", stubConfig, (0, testing_utils_1.createFeatures)([]), (0, logging_1.getRunnerLogger)(true));
    t.false(runnerConstructorStub.firstCall.args[1].includes("--sarif-add-query-help"), "--sarif-add-query-help should be absent, but it is present");
 });
 (0, ava_1.default)("databaseInterpretResults() sets --sarif-add-query-help for 2.7.1", async (t) => {
@@ -433,7 +433,7 @@ for (const isBundleVersionInUrl of [true, false]) {
    sinon.stub(codeqlObject, "getVersion").resolves("2.7.1");
    // safeWhich throws because of the test CodeQL object.
    sinon.stub(safeWhich, "safeWhich").resolves("");
-    await codeqlObject.databaseInterpretResults("", [], "", "", "", "-v", "", stubConfig, (0, testing_utils_1.createFeatures)([]));
+    await codeqlObject.databaseInterpretResults("", [], "", "", "", "-v", "", stubConfig, (0, testing_utils_1.createFeatures)([]), (0, logging_1.getRunnerLogger)(true));
    t.true(runnerConstructorStub.firstCall.args[1].includes("--sarif-add-query-help"), "--sarif-add-query-help should be present, but it is absent");
 });
 (0, ava_1.default)("databaseInitCluster() without injected codescanning config", async (t) => {
@@ -733,7 +733,7 @@ const injectedConfigMacro = ava_1.default.macro({
    sinon.stub(codeqlObject, "getVersion").resolves("2.11.3");
    // safeWhich throws because of the test CodeQL object.
    sinon.stub(safeWhich, "safeWhich").resolves("");
-    await codeqlObject.databaseInterpretResults("", [], "", "", "", "-v", "", stubConfig, (0, testing_utils_1.createFeatures)([]));
+    await codeqlObject.databaseInterpretResults("", [], "", "", "", "-v", "", stubConfig, (0, testing_utils_1.createFeatures)([]), (0, logging_1.getRunnerLogger)(true));
    t.true(runnerConstructorStub.firstCall.args[1].includes("--sarif-add-baseline-file-info"), "--sarif-add-baseline-file-info should be present, but it is absent");
 });
 (0, ava_1.default)("databaseInterpretResults() does not set --sarif-add-baseline-file-info for 2.11.2", async (t) => {
@@ -742,7 +742,7 @@ const injectedConfigMacro = ava_1.default.macro({
    sinon.stub(codeqlObject, "getVersion").resolves("2.11.2");
    // safeWhich throws because of the test CodeQL object.
    sinon.stub(safeWhich, "safeWhich").resolves("");
-    await codeqlObject.databaseInterpretResults("", [], "", "", "", "-v", "", stubConfig, (0, testing_utils_1.createFeatures)([]));
+    await codeqlObject.databaseInterpretResults("", [], "", "", "", "-v", "", stubConfig, (0, testing_utils_1.createFeatures)([]), (0, logging_1.getRunnerLogger)(true));
    t.false(runnerConstructorStub.firstCall.args[1].includes("--sarif-add-baseline-file-info"), "--sarif-add-baseline-file-info must be absent, but it is present");
 });
 function stubToolRunnerConstructor() {
@@ -1 +1 @@
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Line truncated
+{"version":3,"file":"codeql.test.js","sourceRoot":"","sources":["../src/codeql.test.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uCAAyB;AACzB,gDAAwB;AAExB,yEAA2D;AAC3D,+DAAiD;AACjD,kEAAoD;AACpD,8CAA6C;AAC7C,8CAAsB;AACtB,8CAAgC;AAChC,gDAAwB;AACxB,6CAA+B;AAE/B,4DAA8C;AAC9C,kDAAoC;AAEpC,iDAAmC;AAEnC,0DAA4C;AAC5C,mDAIyB;AACzB,iCAAqC;AACrC,2CAAuC;AACvC,uCAA4C;AAC5C,mDAA+E;AAC/E,6CAA+B;AAC/B,iCAA+C;AAE/C,IAAA,0BAAU,EAAC,aAAI,CAAC,CAAC;AAEjB,MAAM,gBAAgB,GAAG;IACvB,IAAI,EAAE,OAAO;IACb,GAAG,EAAE,oBAAoB;IACzB,MAAM,EAAE,wBAAwB;CACjC,CAAC;AAEF,MAAM,oBAAoB,GAAG;IAC3B,IAAI,EAAE,OAAO;IACb,GAAG,EAAE,sCAAsC;IAC3C,MAAM,EAAE,6CAA6C;CACtD,CAAC;AAEF,MAAM,0BAA0B,GAA6B;IAC3D,UAAU,EAAE,OAAO;IACnB,OAAO,EAAE,IAAI,CAAC,aAAa,CAAC,MAAM;CACnC,CAAC;AAEF,IAAI,UAAkB,CAAC;AAEvB,aAAI,CAAC,UAAU,CAAC,GAAG,EAAE;IACnB,IAAA,4BAAqB,EAAC,OAAO,CAAC,CAAC;IAE/B,UAAU,GAAG;QACX,SAAS,EAAE,CAAC,oBAAQ,CAAC,GAAG,CAAC;QACzB,OAAO,EAAE,EAAE;QACX,WAAW,EAAE,EAAE;QACf,KAAK,EAAE,EAAE;QACT,iBAAiB,EAAE,EAAE;QACrB,OAAO,EAAE,EAAE;QACX,SAAS,EAAE,EAAE;QACb,aAAa,EAAE;YACb,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,MAAM;SACV;QACvB,UAAU,EAAE,EAAE;QACd,KAAK,EAAE,EAAE;QACT,SAAS,EAAE,KAAK;QAChB,iBAAiB,EAAE,IAAI,CAAC,2BAA2B;QACnD,iBAAiB,EAAE,IAAI,CAAC,2BAA2B;QACnD,sBAAsB,EAAE;YACtB,iBAAiB,EAAE,KAAK;YACxB,kBAAkB,EAAE,KAAK;YACzB,oBAAoB,EAAE,KAAK;SAC5B;QACD,UAAU,EAAE,EAAE;QACd,qBAAqB,EAAE,CAAC;KACzB,CAAC;AACJ,CAAC,CAAC,CAAC;AAEH;;;;;GAKG;AACH,SAAS,eAAe,CAAC,EACvB,UAAU,GAAG,gBAAgB,EAC7B,QAAQ,EACR,IAAI,GAAG,sBAAsB,EAC7B,gBAAgB,GAAG,IAAI,EACvB,OAAO,GAOR;IACC,MAAM,QAAQ,GACZ,OAAO,CAAC,QAAQ,KAAK,OAAO;QAC1B,CAAC,CAAC,OAAO;QACT,CAAC,CAAC,OAAO,CAAC,QAAQ,KAAK,OAAO;YAC9B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,OAAO,CAAC;IAEd,MAAM,OAAO,GAAG,UAAU,EAAE,GAAG,IAAI,qBAAqB,CAAC;IACzD,MAAM,WAAW,GAAG,UAAU;QAC5B,CAAC,CAAC,IAAI,IAAI,sBAAsB,OAAO,iBACnC,gBAAgB,CAAC,CAAC,CAAC,IAAI,QAAQ,EAAE,CAAC,CAAC,CAAC,EACtC,SAAS;QACX,CAAC,CAAC,aAAa,OAAO,uBAAuB,CAAC;IAEhD,IAAA,cAAI,EAAC,OAAO,CAAC;SACV,GAAG,CAAC,WAAW,CAAC;SAChB,aAAa,CACZ,GAAG,EACH,cAAI,CAAC,IAAI,CACP,SAAS,EACT,iCAAiC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,SAAS,CACpE,CACF,CAAC;IAEJ,OAAO,GAAG,OAAO,GAAG,WAAW,EAAE,CAAC;AACpC,CAAC;AAED,KAAK,UAAU,oBAAoB,CAAC,EAClC,UAAU,GAAG,gBAAgB,EAC7B,UAAU,EACV,QAAQ,EACR,OAAO,EACP,MAAM,GAOP;IACC,MAAM,GAAG,GAAG,eAAe,CAAC,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAC,CAAC;IAC/D,MAAM,MAAM,CAAC,WAAW,CACtB,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,EAC1C,UAAU,EACV,MAAM,EACN,IAAI,CAAC,aAAa,CAAC,IAAI,EACvB,UAAU,KAAK,SAAS;QACtB,CAAC,CAAC,EAAE,UAAU,EAAE,OAAO,EAAE,OAAO,EAAE,IAAI,CAAC,aAAa,CAAC,IAAI,EAAE;QAC3D,CAAC,CAAC,0BAA0B,EAC9B,IAAA,yBAAe,EAAC,IAAI,CAAC,EACrB,KAAK,CACN,CAAC;AACJ,CAAC;AAED,SAAS,cAAc,CAAC,EACtB,UAAU,GAAG,gBAAgB,EAC7B,UAAU,EACV,OAAO,GAKR;IACC,OAAO,IAAA,cAAI,EAAC,UAAU,CAAC,MAAO,CAAC;SAC5B,GAAG,CAAC,6CAA6C,OAAO,EAAE,CAAC;SAC3D,KAAK,CAAC,GAAG,EAAE;QACV,MAAM,EAAE,UAAU,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;YAChC,IAAI;SACL,CAAC,CAAC;QACH,QAAQ,EAAE,OAAO;KAClB,CAAC,CAAC;AACP,CAAC;AAED,SAAS,cAAc,CAAC,UAA4B;IAClD,6FAA6F;IAC7F,oFAAoF;IACpF,gFAAgF;IAChF,kDAAkD;IAClD,KAAK;SACF,IAAI,CAAC,WAAW,EAAE,kBAAkB,CAAC;SACrC,QAAQ,CAAC,OAAO,CAAC;SACjB,OAAO,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC;IAC5B,MAAM,oBAAoB,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,EAAE,qBAAqB,CAAC,CAAC;IACrE,oBAAoB,CAAC,QAAQ,CAAC,mBAAmB,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;IAC3E,oBAAoB;SACjB,QAAQ,CAAC,gBAAgB,CAAC;SAC1B,OAAO,CAAC,UAAU,CAAC,MAAM,IAAI,EAAE,CAAC,CAAC;AACtC,CAAC;AAED,IAAA,aAAI,EAAC,gFAAgF,EAAE,KAAK,EAAE,CAAC,EAAE,EAAE;IACjG,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QACrC,IAAA,gCAAgB,EAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QAEjC,MAAM,QAAQ,GAAG,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC;QAE1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;YAE5B,MAAM,GAAG,GAAG,eAAe,CAAC;gBAC1B,OAAO,EAAE,iBAAiB,OAAO,EAAE;gBACnC,QAAQ,EAAE,KAAK;aAChB,CAAC,CAAC;YACH,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,WAAW,CACrC,GAAG,EACH,gBAAgB,EAChB,MAAM,EACN,IAAI,CAAC,aAAa,CAAC,MAAM,EACzB,0BAA0B,EAC1B,IAAA,yBAAe,EAAC,IAAI,CAAC,EACrB,KAAK,CACN,CAAC;YAEF,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,EAAE,SAAS,OAAO,EAAE,CAAC,CAAC,CAAC;YACvD,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC,YAAY,EAAE,SAAS,OAAO,EAAE,CAAC,CAAC;YAC9C,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC,WAAW,EAAE,kBAAW,CAAC,QAAQ,CAAC,CAAC;YAC/C,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,uBAAuB,CAAC,CAAC,CAAC;SAC5D;QAED,CAAC,CAAC,EAAE,CAAC,SAAS,CAAC,eAAe,CAAC,QAAQ,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC;IACtD,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC;AAEH,IAAA,aAAI,EAAC,gFAAgF,EAAE,KAAK,EAAE,CAAC,EAAE,EAAE;IACjG,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QACrC,IAAA,gCAAgB,EAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QAEjC,MAAM,oBAAoB,CAAC;YACzB,OAAO,EAAE,wBAAwB;YACjC,QAAQ,EAAE,IAAI;YACd,MAAM;SACP,CAAC,CAAC;QAEH,MAAM,GAAG,GAAG,eAAe,CAAC;YAC1B,OAAO,EAAE,wBAAwB;SAClC,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,WAAW,CACrC,GAAG,EACH,gBAAgB,EAChB,MAAM,EACN,IAAI,CAAC,aAAa,CAAC,MAAM,EACzB,0BAA0B,EAC1B,IAAA,yBAAe,EAAC,IAAI,CAAC,EACrB,KAAK,CACN,CAAC;QACF,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,EAAE,gBAAgB,CAAC,CAAC,CAAC;QACrLine truncated
@@ -55,12 +55,12 @@ exports.featureConfig = {
    [Feature.ExportCodeScanningConfigEnabled]: {
        envVar: "CODEQL_ACTION_EXPORT_CODE_SCANNING_CONFIG",
        minimumVersion: "2.12.3",
-        defaultValue: false,
+        defaultValue: true,
    },
    [Feature.ExportDiagnosticsEnabled]: {
        envVar: "CODEQL_ACTION_EXPORT_DIAGNOSTICS",
        minimumVersion: "2.12.4",
-        defaultValue: false,
+        defaultValue: true,
    },
    [Feature.MlPoweredQueriesEnabled]: {
        envVar: "CODEQL_ML_POWERED_QUERIES",
@@ -70,7 +70,7 @@ exports.featureConfig = {
    [Feature.UploadFailedSarifEnabled]: {
        envVar: "CODEQL_ACTION_UPLOAD_FAILED_SARIF",
        minimumVersion: "2.11.3",
-        defaultValue: false,
+        defaultValue: true,
    },
 };
 exports.FEATURE_FLAGS_FILE_NAME = "cached-feature-flags.json";
@@ -1 +1 @@
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@@ -54,7 +54,8 @@ async function maybeUploadFailedSarif(config, repositoryNwo, features, logger) {
    const workflow = await (0, workflow_1.getWorkflow)();
    const jobName = (0, util_1.getRequiredEnvParam)("GITHUB_JOB");
    const matrix = (0, util_1.parseMatrixInput)(actionsUtil.getRequiredInput("matrix"));
-    if ((0, workflow_1.getUploadInputOrThrow)(workflow, jobName, matrix) !== "true" ||
+    const shouldUpload = (0, workflow_1.getUploadInputOrThrow)(workflow, jobName, matrix);
+    if (!["always", "failure-only"].includes(actionsUtil.getUploadValue(shouldUpload)) ||
        (0, util_1.isInTestMode)()) {
        return { upload_failed_run_skipped_because: "SARIF upload is disabled" };
    }
@@ -69,7 +70,7 @@ async function maybeUploadFailedSarif(config, repositoryNwo, features, logger) {
    }
    else {
        // We call 'database export-diagnostics' to find any per-database diagnostics.
-        await codeql.databaseExportDiagnostics(databasePath, sarifFile, category);
+        await codeql.databaseExportDiagnostics(databasePath, sarifFile, category, config.tempDir, logger);
    }
    core.info(`Uploading failed SARIF file ${sarifFile}`);
    const uploadResult = await uploadLib.uploadFromActions(sarifFile, checkoutPath, category, logger);
@@ -1 +1 @@
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@@ -159,33 +159,64 @@ const workflow = __importStar(require("./workflow"));
        exportDiagnosticsEnabled: true,
    });
 });
-(0, ava_1.default)("doesn't upload failed SARIF for workflow with upload: false", async (t) => {
-    const actionsWorkflow = createTestWorkflow([
-        {
-            name: "Checkout repository",
-            uses: "actions/checkout@v3",
-        },
-        {
-            name: "Initialize CodeQL",
-            uses: "github/codeql-action/init@v2",
-            with: {
-                languages: "javascript",
+const UPLOAD_INPUT_TEST_CASES = [
+    {
+        uploadInput: "true",
+        shouldUpload: true,
+    },
+    {
+        uploadInput: "false",
+        shouldUpload: true,
+    },
+    {
+        uploadInput: "always",
+        shouldUpload: true,
+    },
+    {
+        uploadInput: "failure-only",
+        shouldUpload: true,
+    },
+    {
+        uploadInput: "never",
+        shouldUpload: false,
+    },
+    {
+        uploadInput: "unrecognized-value",
+        shouldUpload: true,
+    },
+];
+for (const { uploadInput, shouldUpload } of UPLOAD_INPUT_TEST_CASES) {
+    (0, ava_1.default)(`does ${shouldUpload ? "" : "not "}upload failed SARIF run for workflow with upload: ${uploadInput}`, async (t) => {
+        const actionsWorkflow = createTestWorkflow([
+            {
+                name: "Checkout repository",
+                uses: "actions/checkout@v3",
            },
-        },
-        {
-            name: "Perform CodeQL Analysis",
-            uses: "github/codeql-action/analyze@v2",
-            with: {
-                category: "my-category",
-                upload: false,
+            {
+                name: "Initialize CodeQL",
+                uses: "github/codeql-action/init@v2",
+                with: {
+                    languages: "javascript",
+                },
            },
-        },
-    ]);
-    const result = await testFailedSarifUpload(t, actionsWorkflow, {
-        expectUpload: false,
+            {
+                name: "Perform CodeQL Analysis",
+                uses: "github/codeql-action/analyze@v2",
+                with: {
+                    category: "my-category",
+                    upload: uploadInput,
+                },
+            },
+        ]);
+        const result = await testFailedSarifUpload(t, actionsWorkflow, {
+            category: "my-category",
+            expectUpload: shouldUpload,
+        });
+        if (!shouldUpload) {
+            t.is(result.upload_failed_run_skipped_because, "SARIF upload is disabled");
+        }
    });
-    t.is(result.upload_failed_run_skipped_because, "SARIF upload is disabled");
-});
+}
 (0, ava_1.default)("uploading failed SARIF run succeeds when workflow uses an input with a matrix var", async (t) => {
    const actionsWorkflow = createTestWorkflow([
        {
@@ -273,7 +304,7 @@ function createTestWorkflow(steps) {
        },
    };
 }
-async function testFailedSarifUpload(t, actionsWorkflow, { category, databaseExists = true, exportDiagnosticsEnabled = false, expectUpload = true, matrix = {}, } = {}) {
+async function testFailedSarifUpload(t, actionsWorkflow, { category, databaseExists = true, expectUpload = true, exportDiagnosticsEnabled = false, matrix = {}, } = {}) {
    const config = {
        codeQLCmd: "codeql",
        debugMode: true,
@@ -312,10 +343,8 @@ async function testFailedSarifUpload(t, actionsWorkflow, { category, databaseExi
            raw_upload_size_bytes: 20,
            zipped_upload_size_bytes: 10,
        });
-    }
-    if (expectUpload) {
        if (databaseExists && exportDiagnosticsEnabled) {
-            t.true(databaseExportDiagnosticsStub.calledOnceWith(config.dbLocation, sinon.match.string, category), `Actual args were: ${databaseExportDiagnosticsStub.args}`);
+            t.true(databaseExportDiagnosticsStub.calledOnceWith(config.dbLocation, sinon.match.string, category, sinon.match.any, sinon.match.any), `Actual args were: ${databaseExportDiagnosticsStub.args}`);
        }
        else {
            t.true(diagnosticsExportStub.calledOnceWith(sinon.match.string, category, config, sinon.match.any), `Actual args were: ${diagnosticsExportStub.args}`);
@@ -1 +1 @@
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@@ -129,7 +129,7 @@ async function run() {
        toolsDownloadDurationMs = initCodeQLResult.toolsDownloadDurationMs;
        toolsVersion = initCodeQLResult.toolsVersion;
        toolsSource = initCodeQLResult.toolsSource;
-        await (0, util_1.enrichEnvironment)(codeql);
+        await (0, codeql_1.enrichEnvironment)(codeql);
        config = await (0, init_1.initConfig)((0, actions_util_1.getOptionalInput)("languages"), (0, actions_util_1.getOptionalInput)("queries"), (0, actions_util_1.getOptionalInput)("packs"), registriesInput, (0, actions_util_1.getOptionalInput)("config-file"), (0, actions_util_1.getOptionalInput)("db-location"), getTrapCachingEnabled(), 
        // Debug mode is enabled if:
        // - The `init` Action is passed `debug: true`.
@@ -1 +1 @@
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@@ -1,6 +1,38 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ODASA_TRACER_CONFIGURATION = exports.CODEQL_WORKFLOW_STARTED_AT = exports.CODEQL_ACTION_TEST_MODE = exports.CODEQL_ACTION_TESTING_ENVIRONMENT = exports.CODEQL_ACTION_ANALYZE_DID_COMPLETE_SUCCESSFULLY = exports.CODEQL_ACTION_DID_AUTOBUILD_GOLANG = void 0;
+exports.ODASA_TRACER_CONFIGURATION = exports.CODEQL_WORKFLOW_STARTED_AT = exports.CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX = exports.CODEQL_ACTION_TEST_MODE = exports.CODEQL_ACTION_TESTING_ENVIRONMENT = exports.CODEQL_ACTION_ANALYZE_DID_COMPLETE_SUCCESSFULLY = exports.CODEQL_ACTION_DID_AUTOBUILD_GOLANG = exports.EnvVar = void 0;
+/**
+ * Environment variables to be set by codeql-action and used by the
+ * CLI.
+ */
+var EnvVar;
+(function (EnvVar) {
+    /**
+     * Semver of the codeql-action as specified in package.json.
+     */
+    EnvVar["VERSION"] = "CODEQL_ACTION_VERSION";
+    /**
+     * If set to a truthy value, then the codeql-action might combine SARIF
+     * output from several `interpret-results` runs for the same Language.
+     */
+    EnvVar["FEATURE_SARIF_COMBINE"] = "CODEQL_ACTION_FEATURE_SARIF_COMBINE";
+    /**
+     * If set to the "true" string, then the codeql-action will upload SARIF,
+     * not the cli.
+     */
+    EnvVar["FEATURE_WILL_UPLOAD"] = "CODEQL_ACTION_FEATURE_WILL_UPLOAD";
+    /**
+     * If set to the "true" string, then the codeql-action is using its
+     * own deprecated and non-standard way of scanning for multiple
+     * languages.
+     */
+    EnvVar["FEATURE_MULTI_LANGUAGE"] = "CODEQL_ACTION_FEATURE_MULTI_LANGUAGE";
+    /**
+     * If set to the "true" string, then the codeql-action is using its
+     * own sandwiched workflow mechanism
+     */
+    EnvVar["FEATURE_SANDWICH"] = "CODEQL_ACTION_FEATURE_SANDWICH";
+})(EnvVar = exports.EnvVar || (exports.EnvVar = {}));
 /**
 * Environment variable that is set to true when the CodeQL Action has invoked
 * the Go autobuilder.
@@ -14,6 +46,11 @@ exports.CODEQL_ACTION_ANALYZE_DID_COMPLETE_SUCCESSFULLY = "CODEQL_ACTION_ANALYZE
 exports.CODEQL_ACTION_TESTING_ENVIRONMENT = "CODEQL_ACTION_TESTING_ENVIRONMENT";
 /** Used to disable uploading SARIF results or status reports to the GitHub API */
 exports.CODEQL_ACTION_TEST_MODE = "CODEQL_ACTION_TEST_MODE";
+/**
+ * Used to disable the SARIF post-processing in the Action that removes duplicate locations from
+ * notifications in the `run[].invocations[].toolExecutionNotifications` SARIF property.
+ */
+exports.CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX = "CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX";
 /**
 * The time at which the first action (normally init) started executing.
 * If a workflow invokes a different action without first invoking the init
@@ -1 +1 @@
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@@ -38,7 +38,7 @@ const actionsUtil = __importStar(require("./actions-util"));
 const api = __importStar(require("./api-client"));
 const fingerprints = __importStar(require("./fingerprints"));
 const repository_1 = require("./repository");
-const sharedEnv = __importStar(require("./shared-environment"));
+const shared_environment_1 = require("./shared-environment");
 const util = __importStar(require("./util"));
 const workflow = __importStar(require("./workflow"));
 // Takes a list of paths to sarif files and combines them together,
@@ -206,7 +206,7 @@ function buildPayload(commitOid, ref, analysisKey, analysisName, zippedSarif, wo
        workflow_run_id: workflowRunID,
        checkout_uri: checkoutURI,
        environment,
-        started_at: process.env[sharedEnv.CODEQL_WORKFLOW_STARTED_AT],
+        started_at: process.env[shared_environment_1.CODEQL_WORKFLOW_STARTED_AT],
        tool_names: toolNames,
        base_ref: undefined,
        base_sha: undefined,
@@ -1 +1 @@
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@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseMatrixInput = exports.isHostedRunner = exports.checkForTimeout = exports.withTimeout = exports.tryGetFolderBytes = exports.listFolder = exports.doesDirectoryExist = exports.logCodeScanningConfigInCli = exports.useCodeScanningConfigInCli = exports.isInTestMode = exports.getMlPoweredJsQueriesStatus = exports.getMlPoweredJsQueriesPack = exports.ML_POWERED_JS_QUERIES_PACK_NAME = exports.supportExpectDiscardedCache = exports.isGoodVersion = exports.delay = exports.bundleDb = exports.codeQlVersionAbove = exports.getCachedCodeQlVersion = exports.cacheCodeQlVersion = exports.isHTTPError = exports.UserError = exports.HTTPError = exports.getRequiredEnvParam = exports.enrichEnvironment = exports.initializeEnvironment = exports.EnvVar = exports.assertNever = exports.apiVersionInRange = exports.DisallowedAPIVersionReason = exports.checkGitHubVersionInRange = exports.getGitHubVersion = exports.GitHubVariant = exports.parseGitHubUrl = exports.getCodeQLDatabasePath = exports.getThreadsFlag = exports.getThreadsFlagValue = exports.getAddSnippetsFlag = exports.getMemoryFlag = exports.getMemoryFlagValue = exports.withTmpDir = exports.getToolNames = exports.getExtraOptionsEnvParam = exports.DEFAULT_DEBUG_DATABASE_NAME = exports.DEFAULT_DEBUG_ARTIFACT_NAME = exports.GITHUB_DOTCOM_URL = void 0;
+exports.fixInvalidNotificationsInFile = exports.fixInvalidNotifications = exports.parseMatrixInput = exports.isHostedRunner = exports.checkForTimeout = exports.withTimeout = exports.tryGetFolderBytes = exports.listFolder = exports.doesDirectoryExist = exports.logCodeScanningConfigInCli = exports.useCodeScanningConfigInCli = exports.isInTestMode = exports.getMlPoweredJsQueriesStatus = exports.getMlPoweredJsQueriesPack = exports.ML_POWERED_JS_QUERIES_PACK_NAME = exports.supportExpectDiscardedCache = exports.isGoodVersion = exports.delay = exports.bundleDb = exports.codeQlVersionAbove = exports.getCachedCodeQlVersion = exports.cacheCodeQlVersion = exports.isHTTPError = exports.UserError = exports.HTTPError = exports.getRequiredEnvParam = exports.initializeEnvironment = exports.assertNever = exports.apiVersionInRange = exports.DisallowedAPIVersionReason = exports.checkGitHubVersionInRange = exports.getGitHubVersion = exports.GitHubVariant = exports.parseGitHubUrl = exports.getCodeQLDatabasePath = exports.getThreadsFlag = exports.getThreadsFlagValue = exports.getAddSnippetsFlag = exports.getMemoryFlag = exports.getMemoryFlagValue = exports.withTmpDir = exports.getToolNames = exports.getExtraOptionsEnvParam = exports.DEFAULT_DEBUG_DATABASE_NAME = exports.DEFAULT_DEBUG_ARTIFACT_NAME = exports.GITHUB_DOTCOM_URL = void 0;
 const fs = __importStar(require("fs"));
 const os = __importStar(require("os"));
 const path = __importStar(require("path"));
@@ -37,7 +37,6 @@ const get_folder_size_1 = __importDefault(require("get-folder-size"));
 const semver = __importStar(require("semver"));
 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");
 const feature_flags_1 = require("./feature-flags");
 const shared_environment_1 = require("./shared-environment");
@@ -333,63 +332,16 @@ function assertNever(value) {
    throw new ExhaustivityCheckingError(value);
 }
 exports.assertNever = assertNever;
-/**
- * Environment variables to be set by codeql-action and used by the
- * CLI.
- */
-var EnvVar;
-(function (EnvVar) {
-    /**
-     * Semver of the codeql-action as specified in package.json.
-     */
-    EnvVar["VERSION"] = "CODEQL_ACTION_VERSION";
-    /**
-     * If set to a truthy value, then the codeql-action might combine SARIF
-     * output from several `interpret-results` runs for the same Language.
-     */
-    EnvVar["FEATURE_SARIF_COMBINE"] = "CODEQL_ACTION_FEATURE_SARIF_COMBINE";
-    /**
-     * If set to the "true" string, then the codeql-action will upload SARIF,
-     * not the cli.
-     */
-    EnvVar["FEATURE_WILL_UPLOAD"] = "CODEQL_ACTION_FEATURE_WILL_UPLOAD";
-    /**
-     * If set to the "true" string, then the codeql-action is using its
-     * own deprecated and non-standard way of scanning for multiple
-     * languages.
-     */
-    EnvVar["FEATURE_MULTI_LANGUAGE"] = "CODEQL_ACTION_FEATURE_MULTI_LANGUAGE";
-    /**
-     * If set to the "true" string, then the codeql-action is using its
-     * own sandwiched workflow mechanism
-     */
-    EnvVar["FEATURE_SANDWICH"] = "CODEQL_ACTION_FEATURE_SANDWICH";
-})(EnvVar = exports.EnvVar || (exports.EnvVar = {}));
 /**
 * Set some initial environment variables that we can set even without
 * knowing what version of CodeQL we're running.
 */
 function initializeEnvironment(version) {
-    core.exportVariable(EnvVar.VERSION, version);
-    core.exportVariable(EnvVar.FEATURE_SARIF_COMBINE, "true");
-    core.exportVariable(EnvVar.FEATURE_WILL_UPLOAD, "true");
+    core.exportVariable(shared_environment_1.EnvVar.VERSION, version);
+    core.exportVariable(shared_environment_1.EnvVar.FEATURE_SARIF_COMBINE, "true");
+    core.exportVariable(shared_environment_1.EnvVar.FEATURE_WILL_UPLOAD, "true");
 }
 exports.initializeEnvironment = initializeEnvironment;
-/**
- * Enrich the environment variables with further flags that we cannot
- * know the value of until we know what version of CodeQL we're running.
- */
-async function enrichEnvironment(codeql) {
-    if (await codeQlVersionAbove(codeql, codeql_1.CODEQL_VERSION_NEW_TRACING)) {
-        core.exportVariable(EnvVar.FEATURE_MULTI_LANGUAGE, "false");
-        core.exportVariable(EnvVar.FEATURE_SANDWICH, "false");
-    }
-    else {
-        core.exportVariable(EnvVar.FEATURE_MULTI_LANGUAGE, "true");
-        core.exportVariable(EnvVar.FEATURE_SANDWICH, "true");
-    }
-}
-exports.enrichEnvironment = enrichEnvironment;
 /**
 * Get an environment parameter, but throw an error if it is not set.
 */
@@ -707,4 +659,73 @@ function parseMatrixInput(matrixInput) {
    return JSON.parse(matrixInput);
 }
 exports.parseMatrixInput = parseMatrixInput;
+function removeDuplicateLocations(locations) {
+    const newJsonLocations = new Set();
+    return locations.filter((location) => {
+        const jsonLocation = JSON.stringify(location);
+        if (!newJsonLocations.has(jsonLocation)) {
+            newJsonLocations.add(jsonLocation);
+            return true;
+        }
+        return false;
+    });
+}
+function fixInvalidNotifications(sarif, logger) {
+    if (process.env[shared_environment_1.CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX] === "true") {
+        logger.info("SARIF notification object duplicate location fix disabled by the " +
+            `${shared_environment_1.CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX} environment variable.`);
+        return sarif;
+    }
+    if (!Array.isArray(sarif.runs)) {
+        return sarif;
+    }
+    // Ensure that the array of locations for each SARIF notification contains unique locations.
+    // This is a workaround for a bug in the CodeQL CLI that causes duplicate locations to be
+    // emitted in some cases.
+    let numDuplicateLocationsRemoved = 0;
+    const newSarif = {
+        ...sarif,
+        runs: sarif.runs.map((run) => {
+            if (run.tool?.driver?.name !== "CodeQL" ||
+                !Array.isArray(run.invocations)) {
+                return run;
+            }
+            return {
+                ...run,
+                invocations: run.invocations.map((invocation) => {
+                    if (!Array.isArray(invocation.toolExecutionNotifications)) {
+                        return invocation;
+                    }
+                    return {
+                        ...invocation,
+                        toolExecutionNotifications: invocation.toolExecutionNotifications.map((notification) => {
+                            if (!Array.isArray(notification.locations)) {
+                                return notification;
+                            }
+                            const newLocations = removeDuplicateLocations(notification.locations);
+                            numDuplicateLocationsRemoved +=
+                                notification.locations.length - newLocations.length;
+                            return {
+                                ...notification,
+                                locations: newLocations,
+                            };
+                        }),
+                    };
+                }),
+            };
+        }),
+    };
+    if (numDuplicateLocationsRemoved > 0) {
+        logger.info(`Removed ${numDuplicateLocationsRemoved} duplicate locations from SARIF notification ` +
+            "objects.");
+    }
+    return newSarif;
+}
+exports.fixInvalidNotifications = fixInvalidNotifications;
+function fixInvalidNotificationsInFile(inputPath, outputPath, logger) {
+    let sarif = JSON.parse(fs.readFileSync(inputPath, "utf8"));
+    sarif = fixInvalidNotifications(sarif, logger);
+    fs.writeFileSync(outputPath, JSON.stringify(sarif));
+}
+exports.fixInvalidNotificationsInFile = fixInvalidNotificationsInFile;
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Line truncated
@@ -330,4 +330,49 @@ const shortTime = 10;
    t.deepEqual(shortTaskTimedOut, false);
    t.deepEqual(result, 99);
 });
+function createMockSarifWithNotification(locations) {
+    return {
+        runs: [
+            {
+                tool: {
+                    driver: {
+                        name: "CodeQL",
+                    },
+                },
+                invocations: [
+                    {
+                        toolExecutionNotifications: [
+                            {
+                                locations,
+                            },
+                        ],
+                    },
+                ],
+            },
+        ],
+    };
+}
+const stubLocation = {
+    physicalLocation: {
+        artifactLocation: {
+            uri: "file1",
+        },
+    },
+};
+(0, ava_1.default)("fixInvalidNotifications leaves notifications with unique locations alone", (t) => {
+    const messages = [];
+    const result = util.fixInvalidNotifications(createMockSarifWithNotification([stubLocation]), (0, testing_utils_1.getRecordingLogger)(messages));
+    t.deepEqual(result, createMockSarifWithNotification([stubLocation]));
+    t.is(messages.length, 0);
+});
+(0, ava_1.default)("fixInvalidNotifications removes duplicate locations", (t) => {
+    const messages = [];
+    const result = util.fixInvalidNotifications(createMockSarifWithNotification([stubLocation, stubLocation]), (0, testing_utils_1.getRecordingLogger)(messages));
+    t.deepEqual(result, createMockSarifWithNotification([stubLocation]));
+    t.is(messages.length, 1);
+    t.deepEqual(messages[0], {
+        type: "info",
+        message: "Removed 1 duplicate locations from SARIF notification objects.",
+    });
+});
 //# sourceMappingURL=util.test.js.map
@@ -1 +1 @@
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@@ -84,8 +84,6 @@ function toCodedErrors(errors) {
 exports.WorkflowErrors = toCodedErrors({
    MismatchedBranches: `Please make sure that every branch in on.pull_request is also in on.push so that Code Scanning can compare pull requests against the state of the base branch.`,
    MissingPushHook: `Please specify an on.push hook so that Code Scanning can compare pull requests against the state of the base branch.`,
-    PathsSpecified: `Using on.push.paths can prevent Code Scanning annotating new alerts in your pull requests.`,
-    PathsIgnoreSpecified: `Using on.push.paths-ignore can prevent Code Scanning annotating new alerts in your pull requests.`,
    CheckoutWrongHead: `git checkout HEAD^2 is no longer necessary. Please remove this step as Code Scanning recommends analyzing the merge commit for best results.`,
 });
 function getWorkflowErrors(doc) {
@@ -130,19 +128,6 @@ function getWorkflowErrors(doc) {
        if (!hasPush && hasPullRequest) {
            missingPush = true;
        }
-        if (hasPush && hasPullRequest) {
-            const paths = doc.on.push?.paths;
-            // if you specify paths or paths-ignore you can end up with commits that have no baseline
-            // if they didn't change any files
-            // currently we cannot go back through the history and find the most recent baseline
-            if (Array.isArray(paths) && paths.length > 0) {
-                errors.push(exports.WorkflowErrors.PathsSpecified);
-            }
-            const pathsIgnore = doc.on.push?.["paths-ignore"];
-            if (Array.isArray(pathsIgnore) && pathsIgnore.length > 0) {
-                errors.push(exports.WorkflowErrors.PathsIgnoreSpecified);
-            }
-        }
        // if doc.on.pull_request is null that means 'all branches'
        // if doc.on.pull_request is undefined that means 'off'
        // we only want to check for mismatched branches if pull_request is on.
@@ -339,12 +324,11 @@ exports.getCategoryInputOrThrow = getCategoryInputOrThrow;
 *
 * Typically you'll want to wrap this function in a try/catch block and handle the error.
 *
- * @returns the upload input
+ * @returns the user input to upload, or undefined if input was unspecified
 * @throws an error if the upload input could not be determined
 */
 function getUploadInputOrThrow(workflow, jobName, matrixVars) {
-    return (getInputOrThrow(workflow, jobName, getAnalyzeActionName(), "upload", matrixVars) || "true" // if unspecified, upload defaults to true
-    );
+    return getInputOrThrow(workflow, jobName, getAnalyzeActionName(), "upload", matrixVars);
 }
 exports.getUploadInputOrThrow = getUploadInputOrThrow;
 /**
@@ -1 +1 @@
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Line truncated
@@ -58,15 +58,6 @@ function errorCodes(actual, expected) {
    });
    t.deepEqual(...errorCodes(errors, []));
 });
-(0, ava_1.default)("getWorkflowErrors() when on.push should not have a path", (t) => {
-    const errors = (0, workflow_1.getWorkflowErrors)({
-        on: {
-            push: { branches: ["main"], paths: ["test/*"] },
-            pull_request: { branches: ["main"] },
-        },
-    });
-    t.deepEqual(...errorCodes(errors, [workflow_1.WorkflowErrors.PathsSpecified]));
-});
 (0, ava_1.default)("getWorkflowErrors() when on.push is a correct object", (t) => {
    const errors = (0, workflow_1.getWorkflowErrors)({
        on: { push: { branches: ["main"] }, pull_request: { branches: ["main"] } },
@@ -227,7 +218,7 @@ function errorCodes(actual, expected) {
 (0, ava_1.default)("formatWorkflowErrors() when there are multiple errors", (t) => {
    const message = (0, workflow_1.formatWorkflowErrors)([
        workflow_1.WorkflowErrors.CheckoutWrongHead,
-        workflow_1.WorkflowErrors.PathsSpecified,
+        workflow_1.WorkflowErrors.MismatchedBranches,
    ]);
    t.true(message.startsWith("2 issues were detected with this workflow:"));
 });
@@ -238,9 +229,9 @@ function errorCodes(actual, expected) {
 (0, ava_1.default)("formatWorkflowCause()", (t) => {
    const message = (0, workflow_1.formatWorkflowCause)([
        workflow_1.WorkflowErrors.CheckoutWrongHead,
-        workflow_1.WorkflowErrors.PathsSpecified,
+        workflow_1.WorkflowErrors.MismatchedBranches,
    ]);
-    t.deepEqual(message, "CheckoutWrongHead,PathsSpecified");
+    t.deepEqual(message, "CheckoutWrongHead,MismatchedBranches");
    t.deepEqual((0, workflow_1.formatWorkflowCause)([]), undefined);
 });
 (0, ava_1.default)("patternIsSuperset()", (t) => {
@@ -1 +1 @@
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Line truncated
@@ -1,6 +1,6 @@
 {
  "name": "codeql",
-  "version": "2.2.8",
+  "version": "2.2.10",
  "lockfileVersion": 3,
  "requires": true,
  "packages": {
@@ -1,12 +1,12 @@
 {
  "name": "codeql",
-  "version": "2.2.8",
+  "version": "2.2.10",
  "lockfileVersion": 3,
  "requires": true,
  "packages": {
    "": {
      "name": "codeql",
-      "version": "2.2.8",
+      "version": "2.2.10",
      "license": "MIT",
      "dependencies": {
        "@actions/artifact": "^1.1.0",
@@ -1,6 +1,6 @@
 {
  "name": "codeql",
-  "version": "2.2.8",
+  "version": "2.2.10",
  "private": true,
  "description": "CodeQL action",
  "scripts": {
@@ -1,5 +1,5 @@
 name: "Diagnostic export"
-description: "Tests that a manually added diagnostic is exported to SARIF."
+description: "Tests that manually added diagnostics are correctly exported to SARIF."
 versions: ["latest", "nightly-latest"]
 env:
  CODEQL_ACTION_EXPORT_DIAGNOSTICS: true
@@ -8,14 +8,23 @@ steps:
    id: init
    with:
      languages: javascript
-      queries: security-extended
      tools: ${{ steps.prepare-test.outputs.tools-url }}
-  - name: Manually add a diagnostic
+  - name: Add test diagnostics
    shell: bash
    env:
      CODEQL_PATH: ${{ steps.init.outputs.codeql-path }}
    run: |
-      "$CODEQL_PATH" database add-diagnostic "$RUNNER_TEMP/codeql_databases/javascript" --plaintext-message="Plaintext message" --source-id="lang/diagnostics/example" --source-name="Diagnostic name"
+      for i in {1..2}; do
+        # Use the same location twice to test the workaround for the bug in CodeQL CLI 2.12.5 that
+        # produces an invalid diagnostic with multiple identical location objects.
+        "$CODEQL_PATH" database add-diagnostic \
+          "$RUNNER_TEMP/codeql_databases/javascript" \
+          --file-path /path/to/file \
+          --plaintext-message "Plaintext message $i" \
+          --source-id "lang/diagnostics/example" \
+          --source-name "Diagnostic name" \
+          --ready-for-status-page
+      done
  - uses: ./../action/analyze
    with:
      output: "${{ runner.temp }}/results"
@@ -34,19 +43,45 @@ steps:
      script: |
        const fs = require('fs');

+        function checkStatusPageNotification(n) {
+          const expectedMessage = 'Plaintext message 1\n\nCodeQL also found 1 other diagnostic like this. See the workflow log for details.';
+          if (n.message.text !== expectedMessage) {
+            core.setFailed(`Expected the status page diagnostic to have the message '${expectedMessage}', but found '${n.message.text}'.`);
+          }
+          if (n.locations.length !== 1) {
+            core.setFailed(`Expected the status page diagnostic to have exactly 1 location, but found ${n.locations.length}.`);
+          }
+        }
+
        const sarif = JSON.parse(fs.readFileSync(process.env['SARIF_PATH'], 'utf8'));
        const run = sarif.runs[0];

        const toolExecutionNotifications = run.invocations[0].toolExecutionNotifications;
-        const diagnosticToolExecutionNotification = toolExecutionNotifications.filter(n => n.descriptor.id === 'lang/diagnostics/example' && n.message.text === 'Plaintext message');
-        if (diagnosticToolExecutionNotification.length !== 1) {
-          core.setFailed(`Expected exactly 1 entry for this diagnostic in the 'runs[].invocations[].toolExecutionNotifications[]' SARIF property, found ${diagnosticToolExecutionNotification.length}`);
+        const statusPageNotifications = toolExecutionNotifications.filter(n =>
+          n.descriptor.id === 'lang/diagnostics/example' && n.properties?.visibility?.statusPage
+        );
+        if (statusPageNotifications.length !== 1) {
+          core.setFailed(
+            'Expected exactly one status page reporting descriptor for this diagnostic in the ' +
+              `'runs[].invocations[].toolExecutionNotifications[]' SARIF property, but found ` +
+              `${statusPageNotifications.length}. All notification reporting descriptors: ` + 
+              `${JSON.stringify(toolExecutionNotifications)}.`
+          );
        }
+        checkStatusPageNotification(statusPageNotifications[0]);

        const notifications = run.tool.driver.notifications;
-        const diagnosticNotification = notifications.filter(n => n.id === 'lang/diagnostics/example' && n.name === 'lang/diagnostics/example' && n.fullDescription.text && 'Diagnostic name');
+        const diagnosticNotification = notifications.filter(n =>
+          n.id === 'lang/diagnostics/example' && n.name === 'lang/diagnostics/example' &&
+            n.fullDescription.text === 'Diagnostic name'
+        );
        if (diagnosticNotification.length !== 1) {
-          core.setFailed(`Expected exactly 1 entry for this diagnostic in the 'runs[].tool.driver.notifications[]' SARIF property, found ${diagnosticNotification.length}`);
+          core.setFailed(
+            'Expected exactly one notification for this diagnostic in the ' +
+              `'runs[].tool.driver.notifications[]' SARIF property, but found ` +
+              `${diagnosticNotification.length}. All notifications: ` +
+              `${JSON.stringify(notifications)}.`
+          );
        }

-        core.info('Finished diagnostic export test');
+        core.info('Finished diagnostic export test');
@@ -17,7 +17,7 @@ steps:
    with:
      upload-database: false
      skip-queries: true
-      upload: false
+      upload: never
  - name: Assert database exists
    shell: bash
    run: |
@@ -1,33 +0,0 @@
-name: "Swift analysis using autobuild"
-description: "Tests creation of a Swift database using autobuild"
-versions: ["latest", "cached", "nightly-latest"]
-# Swift autobuilder is only supported on MacOS for private beta
-operatingSystems: ["macos"]
-env:
-  CODEQL_ENABLE_EXPERIMENTAL_FEATURES_SWIFT: "true" # Remove when Swift is GA.
-steps:
-  - uses: ./../action/init
-    id: init
-    with:
-      languages: swift
-      tools: ${{ steps.prepare-test.outputs.tools-url }}
-  - uses: ./../action/.github/setup-swift
-    with:
-      codeql-path: ${{steps.init.outputs.codeql-path}}
-  - name: Check working directory
-    shell: bash
-    run: pwd
-  - uses: ./../action/autobuild
-    timeout-minutes: 10
-  - uses: ./../action/analyze
-    id: analysis
-    with:
-      upload-database: false
-  - name: Check database
-    shell: bash
-    run: |
-      SWIFT_DB="${{ fromJson(steps.analysis.outputs.db-locations).swift }}"
-      if [[ ! -d "$SWIFT_DB" ]]; then
-        echo "Did not create a database for Swift."
-        exit 1
-      fi
@@ -14,7 +14,7 @@ steps:
      upload-database: false
      ref: 'refs/heads/main'
      sha: '5e235361806c361d4d3f8859e3c897658025a9a2'
-      upload: false
+      upload: never
  - uses: ./../action/upload-sarif
    with:
      ref: 'refs/heads/main'
@@ -29,7 +29,7 @@ steps:
      checkout_path: x/y/z/some-path/tests/multi-language-repo
      ref: v1.1.0
      sha: 474bbf07f9247ffe1856c6a0f94aeeb10e7afee6
-      upload: false
+      upload: never
      upload-database: false

  - uses: ./../action/upload-sarif
@@ -214,6 +214,10 @@ test("initializeEnvironment", (t) => {
 });

 test("isAnalyzingDefaultBranch()", async (t) => {
+  process.env["CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH"] = "true";
+  t.deepEqual(await actionsutil.isAnalyzingDefaultBranch(), true);
+  process.env["CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH"] = "false";
+
  await withTmpDir(async (tmpDir) => {
    setupActionsVars(tmpDir, tmpDir);
    const envFile = path.join(tmpDir, "event.json");
@@ -627,9 +627,15 @@ function removeRefsHeadsPrefix(ref: string): string {
  return ref.startsWith("refs/heads/") ? ref.slice("refs/heads/".length) : ref;
 }

-// Is the version of the repository we are currently analyzing from the default branch,
-// or alternatively from another branch or a pull request.
+// Returns whether we are analyzing the default branch for the repository.
+// For cases where the repository information might not be available (e.g.,
+// dynamic workflows), this can be forced by the environment variable
+// CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH.
 export async function isAnalyzingDefaultBranch(): Promise<boolean> {
+  if (process.env.CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH === "true") {
+    return true;
+  }
+
  // Get the current ref and trim and refs/heads/ prefix
  let currentRef = await getRef();
  currentRef = removeRefsHeadsPrefix(currentRef);
@@ -674,3 +680,25 @@ export async function printDebugLogs(config: Config) {
    walkLogFiles(logsDirectory);
  }
 }
+
+export type UploadKind = "always" | "failure-only" | "never";
+
+// Parses the `upload` input into an `UploadKind`, converting unspecified and deprecated upload inputs appropriately.
+export function getUploadValue(input: string | undefined): UploadKind {
+  switch (input) {
+    case undefined:
+    case "true":
+    case "always":
+      return "always";
+    case "false":
+    case "failure-only":
+      return "failure-only";
+    case "never":
+      return "never";
+    default:
+      core.warning(
+        `Unrecognized 'upload' input to 'analyze' Action: ${input}. Defaulting to 'always'.`
+      );
+      return "always";
+  }
+}
@@ -16,7 +16,7 @@ import {
 } from "./analyze";
 import { getApiDetails, getGitHubVersion } from "./api-client";
 import { runAutobuild } from "./autobuild";
-import { getCodeQL } from "./codeql";
+import { enrichEnvironment, getCodeQL } from "./codeql";
 import { Config, getConfig } from "./config-utils";
 import { uploadDatabases } from "./database-upload";
 import { Features } from "./feature-flags";
@@ -207,7 +207,7 @@ async function run() {
      );
    }

-    await util.enrichEnvironment(await getCodeQL(config.codeQLCmd));
+    await enrichEnvironment(await getCodeQL(config.codeQLCmd));

    const apiDetails = getApiDetails();
    const outputDir = actionsUtil.getRequiredInput("output");
@@ -268,8 +268,8 @@ async function run() {
      dbLocations[language] = util.getCodeQLDatabasePath(config, language);
    }
    core.setOutput("db-locations", dbLocations);
-
-    if (runStats && actionsUtil.getRequiredInput("upload") === "true") {
+    const uploadInput = actionsUtil.getOptionalInput("upload");
+    if (runStats && actionsUtil.getUploadValue(uploadInput) === "always") {
      uploadResult = await upload_lib.uploadFromActions(
        outputDir,
        actionsUtil.getRequiredInput("checkout_path"),
@@ -369,7 +369,8 @@ export async function runQueries(
      enableDebugLogging ? "-vv" : "-v",
      automationDetailsId,
      config,
-      features
+      features,
+      logger
    );
  }

@@ -637,7 +637,8 @@ test("databaseInterpretResults() does not set --sarif-add-query-help for 2.7.0",
    "-v",
    "",
    stubConfig,
-    createFeatures([])
+    createFeatures([]),
+    getRunnerLogger(true)
  );
  t.false(
    runnerConstructorStub.firstCall.args[1].includes("--sarif-add-query-help"),
@@ -660,7 +661,8 @@ test("databaseInterpretResults() sets --sarif-add-query-help for 2.7.1", async (
    "-v",
    "",
    stubConfig,
-    createFeatures([])
+    createFeatures([]),
+    getRunnerLogger(true)
  );
  t.true(
    runnerConstructorStub.firstCall.args[1].includes("--sarif-add-query-help"),
@@ -1158,7 +1160,8 @@ test("databaseInterpretResults() sets --sarif-add-baseline-file-info for 2.11.3"
    "-v",
    "",
    stubConfig,
-    createFeatures([])
+    createFeatures([]),
+    getRunnerLogger(true)
  );
  t.true(
    runnerConstructorStub.firstCall.args[1].includes(
@@ -1183,7 +1186,8 @@ test("databaseInterpretResults() does not set --sarif-add-baseline-file-info for
    "-v",
    "",
    stubConfig,
-    createFeatures([])
+    createFeatures([]),
+    getRunnerLogger(true)
  );
  t.false(
    runnerConstructorStub.firstCall.args[1].includes(
@@ -1,6 +1,7 @@
 import * as fs from "fs";
 import * as path from "path";

+import * as core from "@actions/core";
 import * as toolrunner from "@actions/exec/lib/toolrunner";
 import * as yaml from "js-yaml";

@@ -17,6 +18,7 @@ import { ToolsSource } from "./init";
 import { isTracedLanguage, Language } from "./languages";
 import { Logger } from "./logging";
 import * as setupCodeql from "./setup-codeql";
+import { EnvVar } from "./shared-environment";
 import { toolrunnerErrorCatcher } from "./toolrunner-error-catcher";
 import {
  getTrapCachingExtractorConfigArgs,
@@ -179,7 +181,8 @@ export interface CodeQL {
    verbosityFlag: string | undefined,
    automationDetailsId: string | undefined,
    config: Config,
-    features: FeatureEnablement
+    features: FeatureEnablement,
+    logger: Logger
  ): Promise<string>;
  /**
   * Run 'codeql database print-baseline'.
@@ -194,7 +197,9 @@ export interface CodeQL {
  databaseExportDiagnostics(
    databasePath: string,
    sarifFile: string,
-    automationDetailsId: string | undefined
+    automationDetailsId: string | undefined,
+    tempDir: string,
+    logger: Logger
  ): Promise<void>;
  /**
   * Run 'codeql diagnostics export'.
@@ -866,15 +871,23 @@ export async function getCodeQLForCmd(
      verbosityFlag: string,
      automationDetailsId: string | undefined,
      config: Config,
-      features: FeatureEnablement
+      features: FeatureEnablement,
+      logger: Logger
    ): Promise<string> {
+      const shouldExportDiagnostics = await features.getValue(
+        Feature.ExportDiagnosticsEnabled,
+        this
+      );
+      const codeqlOutputFile = shouldExportDiagnostics
+        ? path.join(config.tempDir, "codeql-intermediate-results.sarif")
+        : sarifFile;
      const codeqlArgs = [
        "database",
        "interpret-results",
        threadsFlag,
        "--format=sarif-latest",
        verbosityFlag,
-        `--output=${sarifFile}`,
+        `--output=${codeqlOutputFile}`,
        addSnippetsFlag,
        "--print-diagnostics-summary",
        "--print-metrics-summary",
@@ -895,8 +908,10 @@ export async function getCodeQLForCmd(
      ) {
        codeqlArgs.push("--sarif-add-baseline-file-info");
      }
-      if (await features.getValue(Feature.ExportDiagnosticsEnabled, this)) {
+      if (shouldExportDiagnostics) {
        codeqlArgs.push("--sarif-include-diagnostics");
+      } else if (await util.codeQlVersionAbove(this, "2.12.4")) {
+        codeqlArgs.push("--no-sarif-include-diagnostics");
      }
      codeqlArgs.push(databasePath);
      if (querySuitePaths) {
@@ -908,6 +923,11 @@ export async function getCodeQLForCmd(
        codeqlArgs,
        errorMatchers
      );
+
+      if (shouldExportDiagnostics) {
+        util.fixInvalidNotificationsInFile(codeqlOutputFile, sarifFile, logger);
+      }
+
      return returnState.stdout;
    },
    async databasePrintBaseline(databasePath: string): Promise<string> {
@@ -1003,15 +1023,21 @@ export async function getCodeQLForCmd(
    async databaseExportDiagnostics(
      databasePath: string,
      sarifFile: string,
-      automationDetailsId: string | undefined
+      automationDetailsId: string | undefined,
+      tempDir: string,
+      logger: Logger
    ): Promise<void> {
+      const intermediateSarifFile = path.join(
+        tempDir,
+        "codeql-intermediate-results.sarif"
+      );
      const args = [
        "database",
        "export-diagnostics",
        `${databasePath}`,
        "--db-cluster", // Database is always a cluster for CodeQL versions that support diagnostics.
        "--format=sarif-latest",
-        `--output=${sarifFile}`,
+        `--output=${intermediateSarifFile}`,
        "--sarif-include-diagnostics", // ExportDiagnosticsEnabled is always true if this command is run.
        "-vvv",
        ...getExtraOptionsFromEnv(["diagnostics", "export"]),
@@ -1020,6 +1046,13 @@ export async function getCodeQLForCmd(
        args.push("--sarif-category", automationDetailsId);
      }
      await new toolrunner.ToolRunner(cmd, args).exec();
+
+      // Fix invalid notifications in the SARIF file output by CodeQL.
+      util.fixInvalidNotificationsInFile(
+        intermediateSarifFile,
+        sarifFile,
+        logger
+      );
    },
    async diagnosticsExport(
      sarifFile: string,
@@ -1270,3 +1303,17 @@ async function getCodeScanningConfigExportArguments(
  }
  return [];
 }
+
+/**
+ * Enrich the environment variables with further flags that we cannot
+ * know the value of until we know what version of CodeQL we're running.
+ */
+export async function enrichEnvironment(codeql: CodeQL) {
+  if (await util.codeQlVersionAbove(codeql, CODEQL_VERSION_NEW_TRACING)) {
+    core.exportVariable(EnvVar.FEATURE_MULTI_LANGUAGE, "false");
+    core.exportVariable(EnvVar.FEATURE_SANDWICH, "false");
+  } else {
+    core.exportVariable(EnvVar.FEATURE_MULTI_LANGUAGE, "true");
+    core.exportVariable(EnvVar.FEATURE_SANDWICH, "true");
+  }
+}
@@ -62,12 +62,12 @@ export const featureConfig: Record<
  [Feature.ExportCodeScanningConfigEnabled]: {
    envVar: "CODEQL_ACTION_EXPORT_CODE_SCANNING_CONFIG",
    minimumVersion: "2.12.3",
-    defaultValue: false,
+    defaultValue: true,
  },
  [Feature.ExportDiagnosticsEnabled]: {
    envVar: "CODEQL_ACTION_EXPORT_DIAGNOSTICS",
    minimumVersion: "2.12.4",
-    defaultValue: false,
+    defaultValue: true,
  },

  [Feature.MlPoweredQueriesEnabled]: {
@@ -78,7 +78,7 @@ export const featureConfig: Record<
  [Feature.UploadFailedSarifEnabled]: {
    envVar: "CODEQL_ACTION_UPLOAD_FAILED_SARIF",
    minimumVersion: "2.11.3",
-    defaultValue: false,
+    defaultValue: true,
  },
 };

@@ -161,33 +161,70 @@ test("uploads failed SARIF run with database export-diagnostics if the database
  });
 });

-test("doesn't upload failed SARIF for workflow with upload: false", async (t) => {
-  const actionsWorkflow = createTestWorkflow([
-    {
-      name: "Checkout repository",
-      uses: "actions/checkout@v3",
-    },
-    {
-      name: "Initialize CodeQL",
-      uses: "github/codeql-action/init@v2",
-      with: {
-        languages: "javascript",
+const UPLOAD_INPUT_TEST_CASES = [
+  {
+    uploadInput: "true",
+    shouldUpload: true,
+  },
+  {
+    uploadInput: "false",
+    shouldUpload: true,
+  },
+  {
+    uploadInput: "always",
+    shouldUpload: true,
+  },
+  {
+    uploadInput: "failure-only",
+    shouldUpload: true,
+  },
+  {
+    uploadInput: "never",
+    shouldUpload: false,
+  },
+  {
+    uploadInput: "unrecognized-value",
+    shouldUpload: true,
+  },
+];
+
+for (const { uploadInput, shouldUpload } of UPLOAD_INPUT_TEST_CASES) {
+  test(`does ${
+    shouldUpload ? "" : "not "
+  }upload failed SARIF run for workflow with upload: ${uploadInput}`, async (t) => {
+    const actionsWorkflow = createTestWorkflow([
+      {
+        name: "Checkout repository",
+        uses: "actions/checkout@v3",
      },
-    },
-    {
-      name: "Perform CodeQL Analysis",
-      uses: "github/codeql-action/analyze@v2",
-      with: {
-        category: "my-category",
-        upload: false,
+      {
+        name: "Initialize CodeQL",
+        uses: "github/codeql-action/init@v2",
+        with: {
+          languages: "javascript",
+        },
      },
-    },
-  ]);
-  const result = await testFailedSarifUpload(t, actionsWorkflow, {
-    expectUpload: false,
+      {
+        name: "Perform CodeQL Analysis",
+        uses: "github/codeql-action/analyze@v2",
+        with: {
+          category: "my-category",
+          upload: uploadInput,
+        },
+      },
+    ]);
+    const result = await testFailedSarifUpload(t, actionsWorkflow, {
+      category: "my-category",
+      expectUpload: shouldUpload,
+    });
+    if (!shouldUpload) {
+      t.is(
+        result.upload_failed_run_skipped_because,
+        "SARIF upload is disabled"
+      );
+    }
  });
-  t.is(result.upload_failed_run_skipped_because, "SARIF upload is disabled");
-});
+}

 test("uploading failed SARIF run succeeds when workflow uses an input with a matrix var", async (t) => {
  const actionsWorkflow = createTestWorkflow([
@@ -294,14 +331,14 @@ async function testFailedSarifUpload(
  {
    category,
    databaseExists = true,
-    exportDiagnosticsEnabled = false,
    expectUpload = true,
+    exportDiagnosticsEnabled = false,
    matrix = {},
  }: {
    category?: string;
    databaseExists?: boolean;
-    exportDiagnosticsEnabled?: boolean;
    expectUpload?: boolean;
+    exportDiagnosticsEnabled?: boolean;
    matrix?: { [key: string]: string };
  } = {}
 ): Promise<initActionPostHelper.UploadFailedSarifResult> {
@@ -356,14 +393,14 @@ async function testFailedSarifUpload(
      raw_upload_size_bytes: 20,
      zipped_upload_size_bytes: 10,
    });
-  }
-  if (expectUpload) {
    if (databaseExists && exportDiagnosticsEnabled) {
      t.true(
        databaseExportDiagnosticsStub.calledOnceWith(
          config.dbLocation,
          sinon.match.string,
-          category
+          category,
+          sinon.match.any,
+          sinon.match.any
        ),
        `Actual args were: ${databaseExportDiagnosticsStub.args}`
      );
@@ -56,8 +56,11 @@ async function maybeUploadFailedSarif(
  const workflow = await getWorkflow();
  const jobName = getRequiredEnvParam("GITHUB_JOB");
  const matrix = parseMatrixInput(actionsUtil.getRequiredInput("matrix"));
+  const shouldUpload = getUploadInputOrThrow(workflow, jobName, matrix);
  if (
-    getUploadInputOrThrow(workflow, jobName, matrix) !== "true" ||
+    !["always", "failure-only"].includes(
+      actionsUtil.getUploadValue(shouldUpload)
+    ) ||
    isInTestMode()
  ) {
    return { upload_failed_run_skipped_because: "SARIF upload is disabled" };
@@ -76,7 +79,13 @@ async function maybeUploadFailedSarif(
    await codeql.diagnosticsExport(sarifFile, category, config, features);
  } else {
    // We call 'database export-diagnostics' to find any per-database diagnostics.
-    await codeql.databaseExportDiagnostics(databasePath, sarifFile, category);
+    await codeql.databaseExportDiagnostics(
+      databasePath,
+      sarifFile,
+      category,
+      config.tempDir,
+      logger
+    );
  }

  core.info(`Uploading failed SARIF file ${sarifFile}`);
@@ -14,7 +14,11 @@ import {
  StatusReportBase,
 } from "./actions-util";
 import { getGitHubVersion } from "./api-client";
-import { CodeQL, CODEQL_VERSION_NEW_TRACING } from "./codeql";
+import {
+  CodeQL,
+  CODEQL_VERSION_NEW_TRACING,
+  enrichEnvironment,
+} from "./codeql";
 import * as configUtils from "./config-utils";
 import { Feature, Features } from "./feature-flags";
 import {
@@ -35,7 +39,6 @@ import {
  codeQlVersionAbove,
  DEFAULT_DEBUG_ARTIFACT_NAME,
  DEFAULT_DEBUG_DATABASE_NAME,
-  enrichEnvironment,
  getMemoryFlagValue,
  getMlPoweredJsQueriesStatus,
  getRequiredEnvParam,
@@ -1,3 +1,39 @@
+/**
+ * Environment variables to be set by codeql-action and used by the
+ * CLI.
+ */
+export enum EnvVar {
+  /**
+   * Semver of the codeql-action as specified in package.json.
+   */
+  VERSION = "CODEQL_ACTION_VERSION",
+
+  /**
+   * If set to a truthy value, then the codeql-action might combine SARIF
+   * output from several `interpret-results` runs for the same Language.
+   */
+  FEATURE_SARIF_COMBINE = "CODEQL_ACTION_FEATURE_SARIF_COMBINE",
+
+  /**
+   * If set to the "true" string, then the codeql-action will upload SARIF,
+   * not the cli.
+   */
+  FEATURE_WILL_UPLOAD = "CODEQL_ACTION_FEATURE_WILL_UPLOAD",
+
+  /**
+   * If set to the "true" string, then the codeql-action is using its
+   * own deprecated and non-standard way of scanning for multiple
+   * languages.
+   */
+  FEATURE_MULTI_LANGUAGE = "CODEQL_ACTION_FEATURE_MULTI_LANGUAGE",
+
+  /**
+   * If set to the "true" string, then the codeql-action is using its
+   * own sandwiched workflow mechanism
+   */
+  FEATURE_SANDWICH = "CODEQL_ACTION_FEATURE_SANDWICH",
+}
+
 /**
 * Environment variable that is set to true when the CodeQL Action has invoked
 * the Go autobuilder.
@@ -18,6 +54,13 @@ export const CODEQL_ACTION_TESTING_ENVIRONMENT =
 /** Used to disable uploading SARIF results or status reports to the GitHub API */
 export const CODEQL_ACTION_TEST_MODE = "CODEQL_ACTION_TEST_MODE";

+/**
+ * Used to disable the SARIF post-processing in the Action that removes duplicate locations from
+ * notifications in the `run[].invocations[].toolExecutionNotifications` SARIF property.
+ */
+export const CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX =
+  "CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX";
+
 /**
 * The time at which the first action (normally init) started executing.
 * If a workflow invokes a different action without first invoking the init
@@ -13,7 +13,7 @@ import * as api from "./api-client";
 import * as fingerprints from "./fingerprints";
 import { Logger } from "./logging";
 import { parseRepositoryNwo, RepositoryNwo } from "./repository";
-import * as sharedEnv from "./shared-environment";
+import { CODEQL_WORKFLOW_STARTED_AT } from "./shared-environment";
 import * as util from "./util";
 import { SarifFile, SarifResult, SarifRun } from "./util";
 import * as workflow from "./workflow";
@@ -272,7 +272,7 @@ export function buildPayload(
    workflow_run_id: workflowRunID,
    checkout_uri: checkoutURI,
    environment,
-    started_at: process.env[sharedEnv.CODEQL_WORKFLOW_STARTED_AT],
+    started_at: process.env[CODEQL_WORKFLOW_STARTED_AT],
    tool_names: toolNames,
    base_ref: undefined as undefined | string,
    base_sha: undefined as undefined | string,
@@ -9,7 +9,7 @@ import * as sinon from "sinon";
 import * as api from "./api-client";
 import { Config } from "./config-utils";
 import { getRunnerLogger } from "./logging";
-import { setupTests } from "./testing-utils";
+import { getRecordingLogger, LoggedMessage, setupTests } from "./testing-utils";
 import * as util from "./util";

 setupTests(test);
@@ -400,3 +400,60 @@ test("withTimeout doesn't call callback if promise resolves", async (t) => {
  t.deepEqual(shortTaskTimedOut, false);
  t.deepEqual(result, 99);
 });
+
+function createMockSarifWithNotification(
+  locations: util.SarifLocation[]
+): util.SarifFile {
+  return {
+    runs: [
+      {
+        tool: {
+          driver: {
+            name: "CodeQL",
+          },
+        },
+        invocations: [
+          {
+            toolExecutionNotifications: [
+              {
+                locations,
+              },
+            ],
+          },
+        ],
+      },
+    ],
+  };
+}
+
+const stubLocation: util.SarifLocation = {
+  physicalLocation: {
+    artifactLocation: {
+      uri: "file1",
+    },
+  },
+};
+
+test("fixInvalidNotifications leaves notifications with unique locations alone", (t) => {
+  const messages: LoggedMessage[] = [];
+  const result = util.fixInvalidNotifications(
+    createMockSarifWithNotification([stubLocation]),
+    getRecordingLogger(messages)
+  );
+  t.deepEqual(result, createMockSarifWithNotification([stubLocation]));
+  t.is(messages.length, 0);
+});
+
+test("fixInvalidNotifications removes duplicate locations", (t) => {
+  const messages: LoggedMessage[] = [];
+  const result = util.fixInvalidNotifications(
+    createMockSarifWithNotification([stubLocation, stubLocation]),
+    getRecordingLogger(messages)
+  );
+  t.deepEqual(result, createMockSarifWithNotification([stubLocation]));
+  t.is(messages.length, 1);
+  t.deepEqual(messages[0], {
+    type: "info",
+    message: "Removed 1 duplicate locations from SARIF notification objects.",
+  });
+});
@@ -10,7 +10,7 @@ import * as semver from "semver";

 import { getApiClient, GitHubApiDetails } from "./api-client";
 import * as apiCompatibility from "./api-compatibility.json";
-import { CodeQL, CODEQL_VERSION_NEW_TRACING } from "./codeql";
+import { CodeQL } from "./codeql";
 import {
  Config,
  parsePacksSpecification,
@@ -19,7 +19,11 @@ import {
 import { Feature, FeatureEnablement } from "./feature-flags";
 import { Language } from "./languages";
 import { Logger } from "./logging";
-import { CODEQL_ACTION_TEST_MODE } from "./shared-environment";
+import {
+  CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX,
+  CODEQL_ACTION_TEST_MODE,
+  EnvVar,
+} from "./shared-environment";

 /**
 * Specifies bundle versions that are known to be broken
@@ -58,9 +62,14 @@ export interface SarifRun {
    id?: string;
  };
  artifacts?: string[];
+  invocations?: SarifInvocation[];
  results?: SarifResult[];
 }

+export interface SarifInvocation {
+  toolExecutionNotifications?: SarifNotification[];
+}
+
 export interface SarifResult {
  ruleId?: string;
  message?: {
@@ -81,6 +90,18 @@ export interface SarifResult {
  };
 }

+export interface SarifNotification {
+  locations?: SarifLocation[];
+}
+
+export interface SarifLocation {
+  physicalLocation?: {
+    artifactLocation?: {
+      uri?: string;
+    };
+  };
+}
+
 /**
 * Get the extra options for the codeql commands.
 */
@@ -412,42 +433,6 @@ export function assertNever(value: never): never {
  throw new ExhaustivityCheckingError(value);
 }

-/**
- * Environment variables to be set by codeql-action and used by the
- * CLI.
- */
-export enum EnvVar {
-  /**
-   * Semver of the codeql-action as specified in package.json.
-   */
-  VERSION = "CODEQL_ACTION_VERSION",
-
-  /**
-   * If set to a truthy value, then the codeql-action might combine SARIF
-   * output from several `interpret-results` runs for the same Language.
-   */
-  FEATURE_SARIF_COMBINE = "CODEQL_ACTION_FEATURE_SARIF_COMBINE",
-
-  /**
-   * If set to the "true" string, then the codeql-action will upload SARIF,
-   * not the cli.
-   */
-  FEATURE_WILL_UPLOAD = "CODEQL_ACTION_FEATURE_WILL_UPLOAD",
-
-  /**
-   * If set to the "true" string, then the codeql-action is using its
-   * own deprecated and non-standard way of scanning for multiple
-   * languages.
-   */
-  FEATURE_MULTI_LANGUAGE = "CODEQL_ACTION_FEATURE_MULTI_LANGUAGE",
-
-  /**
-   * If set to the "true" string, then the codeql-action is using its
-   * own sandwiched workflow mechanism
-   */
-  FEATURE_SANDWICH = "CODEQL_ACTION_FEATURE_SANDWICH",
-}
-
 /**
 * Set some initial environment variables that we can set even without
 * knowing what version of CodeQL we're running.
@@ -458,20 +443,6 @@ export function initializeEnvironment(version: string) {
  core.exportVariable(EnvVar.FEATURE_WILL_UPLOAD, "true");
 }

-/**
- * Enrich the environment variables with further flags that we cannot
- * know the value of until we know what version of CodeQL we're running.
- */
-export async function enrichEnvironment(codeql: CodeQL) {
-  if (await codeQlVersionAbove(codeql, CODEQL_VERSION_NEW_TRACING)) {
-    core.exportVariable(EnvVar.FEATURE_MULTI_LANGUAGE, "false");
-    core.exportVariable(EnvVar.FEATURE_SANDWICH, "false");
-  } else {
-    core.exportVariable(EnvVar.FEATURE_MULTI_LANGUAGE, "true");
-    core.exportVariable(EnvVar.FEATURE_SANDWICH, "true");
-  }
-}
-
 /**
 * Get an environment parameter, but throw an error if it is not set.
 */
@@ -828,3 +799,92 @@ export function parseMatrixInput(
  }
  return JSON.parse(matrixInput);
 }
+
+function removeDuplicateLocations(locations: SarifLocation[]): SarifLocation[] {
+  const newJsonLocations = new Set<string>();
+  return locations.filter((location) => {
+    const jsonLocation = JSON.stringify(location);
+    if (!newJsonLocations.has(jsonLocation)) {
+      newJsonLocations.add(jsonLocation);
+      return true;
+    }
+    return false;
+  });
+}
+
+export function fixInvalidNotifications(
+  sarif: SarifFile,
+  logger: Logger
+): SarifFile {
+  if (process.env[CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX] === "true") {
+    logger.info(
+      "SARIF notification object duplicate location fix disabled by the " +
+        `${CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX} environment variable.`
+    );
+    return sarif;
+  }
+  if (!Array.isArray(sarif.runs)) {
+    return sarif;
+  }
+
+  // Ensure that the array of locations for each SARIF notification contains unique locations.
+  // This is a workaround for a bug in the CodeQL CLI that causes duplicate locations to be
+  // emitted in some cases.
+  let numDuplicateLocationsRemoved = 0;
+
+  const newSarif = {
+    ...sarif,
+    runs: sarif.runs.map((run) => {
+      if (
+        run.tool?.driver?.name !== "CodeQL" ||
+        !Array.isArray(run.invocations)
+      ) {
+        return run;
+      }
+      return {
+        ...run,
+        invocations: run.invocations.map((invocation) => {
+          if (!Array.isArray(invocation.toolExecutionNotifications)) {
+            return invocation;
+          }
+          return {
+            ...invocation,
+            toolExecutionNotifications:
+              invocation.toolExecutionNotifications.map((notification) => {
+                if (!Array.isArray(notification.locations)) {
+                  return notification;
+                }
+                const newLocations = removeDuplicateLocations(
+                  notification.locations
+                );
+                numDuplicateLocationsRemoved +=
+                  notification.locations.length - newLocations.length;
+                return {
+                  ...notification,
+                  locations: newLocations,
+                };
+              }),
+          };
+        }),
+      };
+    }),
+  };
+
+  if (numDuplicateLocationsRemoved > 0) {
+    logger.info(
+      `Removed ${numDuplicateLocationsRemoved} duplicate locations from SARIF notification ` +
+        "objects."
+    );
+  }
+  return newSarif;
+}
+
+export function fixInvalidNotificationsInFile(
+  inputPath: string,
+  outputPath: string,
+  logger: Logger
+): void {
+  let sarif = JSON.parse(fs.readFileSync(inputPath, "utf8")) as SarifFile;
+  sarif = fixInvalidNotifications(sarif, logger);
+  fs.writeFileSync(outputPath, JSON.stringify(sarif));
+}
@@ -56,17 +56,6 @@ test("getWorkflowErrors() when on.push is a valid superset", (t) => {
  t.deepEqual(...errorCodes(errors, []));
 });

-test("getWorkflowErrors() when on.push should not have a path", (t) => {
-  const errors = getWorkflowErrors({
-    on: {
-      push: { branches: ["main"], paths: ["test/*"] },
-      pull_request: { branches: ["main"] },
-    },
-  });
-
-  t.deepEqual(...errorCodes(errors, [WorkflowErrors.PathsSpecified]));
-});
-
 test("getWorkflowErrors() when on.push is a correct object", (t) => {
  const errors = getWorkflowErrors({
    on: { push: { branches: ["main"] }, pull_request: { branches: ["main"] } },
@@ -317,7 +306,7 @@ test("formatWorkflowErrors() when there is one error", (t) => {
 test("formatWorkflowErrors() when there are multiple errors", (t) => {
  const message = formatWorkflowErrors([
    WorkflowErrors.CheckoutWrongHead,
-    WorkflowErrors.PathsSpecified,
+    WorkflowErrors.MismatchedBranches,
  ]);
  t.true(message.startsWith("2 issues were detected with this workflow:"));
 });
@@ -331,10 +320,10 @@ test("formatWorkflowCause() with no errors", (t) => {
 test("formatWorkflowCause()", (t) => {
  const message = formatWorkflowCause([
    WorkflowErrors.CheckoutWrongHead,
-    WorkflowErrors.PathsSpecified,
+    WorkflowErrors.MismatchedBranches,
  ]);

-  t.deepEqual(message, "CheckoutWrongHead,PathsSpecified");
+  t.deepEqual(message, "CheckoutWrongHead,MismatchedBranches");
  t.deepEqual(formatWorkflowCause([]), undefined);
 });

@@ -108,8 +108,6 @@ function toCodedErrors(errors: {
 export const WorkflowErrors = toCodedErrors({
  MismatchedBranches: `Please make sure that every branch in on.pull_request is also in on.push so that Code Scanning can compare pull requests against the state of the base branch.`,
  MissingPushHook: `Please specify an on.push hook so that Code Scanning can compare pull requests against the state of the base branch.`,
-  PathsSpecified: `Using on.push.paths can prevent Code Scanning annotating new alerts in your pull requests.`,
-  PathsIgnoreSpecified: `Using on.push.paths-ignore can prevent Code Scanning annotating new alerts in your pull requests.`,
  CheckoutWrongHead: `git checkout HEAD^2 is no longer necessary. Please remove this step as Code Scanning recommends analyzing the merge commit for best results.`,
 });

@@ -162,19 +160,6 @@ export function getWorkflowErrors(doc: Workflow): CodedError[] {
    if (!hasPush && hasPullRequest) {
      missingPush = true;
    }
-    if (hasPush && hasPullRequest) {
-      const paths = doc.on.push?.paths;
-      // if you specify paths or paths-ignore you can end up with commits that have no baseline
-      // if they didn't change any files
-      // currently we cannot go back through the history and find the most recent baseline
-      if (Array.isArray(paths) && paths.length > 0) {
-        errors.push(WorkflowErrors.PathsSpecified);
-      }
-      const pathsIgnore = doc.on.push?.["paths-ignore"];
-      if (Array.isArray(pathsIgnore) && pathsIgnore.length > 0) {
-        errors.push(WorkflowErrors.PathsIgnoreSpecified);
-      }
-    }

    // if doc.on.pull_request is null that means 'all branches'
    // if doc.on.pull_request is undefined that means 'off'
@@ -426,22 +411,20 @@ export function getCategoryInputOrThrow(
 *
 * Typically you'll want to wrap this function in a try/catch block and handle the error.
 *
- * @returns the upload input
+ * @returns the user input to upload, or undefined if input was unspecified
 * @throws an error if the upload input could not be determined
 */
 export function getUploadInputOrThrow(
  workflow: Workflow,
  jobName: string,
  matrixVars: { [key: string]: string } | undefined
-): string {
-  return (
-    getInputOrThrow(
-      workflow,
-      jobName,
-      getAnalyzeActionName(),
-      "upload",
-      matrixVars
-    ) || "true" // if unspecified, upload defaults to true
+): string | undefined {
+  return getInputOrThrow(
+    workflow,
+    jobName,
+    getAnalyzeActionName(),
+    "upload",
+    matrixVars
  );
 }

@@ -2,28 +2,28 @@ name: Use custom queries

 disable-default-queries: true

-queries: 
+queries:
 # Query suites
-  - name: Select a query suite 
+  - name: Select a query suite
    uses: ./codeql-qlpacks/complex-python-qlpack/rootAndBar.qls
 # QL pack subset
-  - name: Select a ql file 
+  - name: Select a ql file
    uses: ./codeql-qlpacks/complex-javascript-qlpack/show_ifs.ql
  - name: Select a subfolder
    uses: ./codeql-qlpacks/complex-javascript-qlpack/foo
-  - name: Select a folder with two subfolders 
+  - name: Select a folder with two subfolders
    uses: ./codeql-qlpacks/complex-javascript-qlpack/foo2
 # Inrepo QL pack
  - name: Select an inrepo ql pack
    uses: ./codeql-qlpacks/csharp-qlpack
-  - name: Java queries 
+  - name: Java queries
    uses: ./codeql-qlpacks/java-qlpack
 # External QL packs
-  - name: Go queries 
-    uses: Anthophila/go-querypack@master
-  - name: Cpp queries 
-    uses: Anthophila/cpp-querypack@second-branch
-  - name: JavaScript queries 
-    uses: Anthophila/javascript-querypack/show_ifs2.ql@master
-  - name: Python queries 
-    uses: Anthophila/python-querypack/show_ifs2.ql@second-branch 
+  - name: Go queries
+    uses: codeql-testing/go-querypack@master
+  - name: Cpp queries
+    uses: codeql-testing/cpp-querypack@second-branch
+  - name: JavaScript queries
+    uses: codeql-testing/javascript-querypack/show_ifs2.ql@master
+  - name: Python queries
+    uses: codeql-testing/python-querypack/show_ifs2.ql@second-branch
Author	SHA1	Message	Date
Henry Mercer	bb28e7e59e	Merge pull request #1626 from github/henrymercer/diagnostics-ghes Enable diagnostics functionality on GHES	2023-03-30 10:22:39 +01:00
Henry Mercer	69aec345f1	Pass negative SARIF include diagnostics flag when feature is disabled In preparation for enabling this flag by default in the CLI	2023-03-29 18:56:19 +01:00
Henry Mercer	29a4713933	Enable diagnostics functionality on GHES	2023-03-29 18:45:27 +01:00
Robin Neatherway	dc81ae3368	Merge pull request #1625 from github/rneatherway/rm-old-checks Remove checks for triggering on specific paths	2023-03-29 13:28:57 +01:00
Robin Neatherway	f6e4cff38a	Remove checks for triggering on specific paths These are no longer necessary with the new approach to selecting alerts to show on pull requests.	2023-03-29 11:02:16 +02:00
Henry Mercer	fff3a80b5b	Merge pull request #1620 from github/henrymercer/disable-flaky-check Disable flaky Swift autobuild checks	2023-03-28 21:01:11 +01:00
Henry Mercer	ff39eb8d6a	Disable flaky Swift autobuild checks	2023-03-28 20:40:23 +01:00
Andrew Eisenberg	f9c159f4fd	Merge pull request #1613 from github/aeisenberg/codeql-testing Use new location for external queries	2023-03-27 17:35:01 -07:00
Andrew Eisenberg	0af0653ef4	Use new location for external queries They have moved from `dsp-testing` to `codeql-testing`.	2023-03-27 16:11:45 -07:00
Henry Mercer	bc0ed6a6c3	Merge pull request #1610 from github/henrymercer/diagnostics-workaround-improvements Follow-up improvements to the diagnostics workaround	2023-03-27 17:12:07 +01:00
Henry Mercer	b0e191ecbc	Merge pull request #1609 from github/mergeback/v2.2.9-to-main-04df1262 Mergeback v2.2.9 refs/heads/releases/v2 into main	2023-03-27 16:42:07 +01:00
Henry Mercer	57eca7cbb2	Use `Array.isArray`	2023-03-27 15:59:29 +01:00
Henry Mercer	1e7a38893c	Wrap reading and writing SARIF files	2023-03-27 15:44:47 +01:00
github-actions[bot]	2deae45400	Update checked-in dependencies	2023-03-27 14:03:17 +00:00
github-actions[bot]	32daed70e7	Update changelog and version after v2.2.9	2023-03-27 13:41:15 +00:00
Henry Mercer	04df1262e6	Merge pull request #1608 from github/update-v2.2.9-fb32c3fef Merge main into releases/v2	2023-03-27 14:36:30 +01:00
Henry Mercer	f0988cbd79	Move changelog note to correct section	2023-03-27 11:57:26 +01:00
github-actions[bot]	fef20d6c35	Update changelog for v2.2.9	2023-03-27 10:53:14 +00:00
Henry Mercer	fb32c3fefd	Merge pull request #1605 from github/henrymercer/diagnostics-grouping-workaround Work around duplicate locations bug in diagnostics export	2023-03-27 11:43:33 +01:00
Henry Mercer	329c022f48	Just check the number of locations Only tests the property we are looking for and avoids problems with different cross-platform behavior.	2023-03-24 21:50:26 +00:00
Henry Mercer	c8935d5a9d	Remove duplicate locations from failed run SARIF	2023-03-24 20:30:57 +00:00
Henry Mercer	ade432fd68	Remove duplicate locations from output of `database interpret-results`	2023-03-24 20:30:57 +00:00
Henry Mercer	6f852eeb38	Implement removing duplicate locations from a SARIF file	2023-03-24 20:30:57 +00:00
Henry Mercer	097ab4665f	Speed up checks a bit by just running the standard suite	2023-03-24 20:30:57 +00:00
Henry Mercer	befd804b8b	Extend diagnostics export integration test to capture location bug	2023-03-24 19:48:36 +00:00
Angela P WenandHenry Mercer	a21bb7f968	Update `upload` input values and logic (#1598 ) - The `upload` input to the `analyze` Action now accepts the following values: - `always` is the default value, which uploads the SARIF file to Code Scanning for successful and failed runs. - `failure-only` is recommended for customers post-processing the SARIF file before uploading it to Code Scanning. This option uploads debugging information to Code Scanning for failed runs to improve the debugging experience. - `never` avoids uploading the SARIF file to Code Scanning even if the code scanning run fails. This is not recommended for external users since it complicates debugging. - The legacy `true` and `false` options will be interpreted as `always` and `failure-only` respectively. --------- Co-authored-by: Henry Mercer <henry.mercer@me.com>	2023-03-23 17:23:25 +00:00
Charis Kyriakou	0214d1d378	Merge pull request #1603 from github/charisk/default-branch-analayzing-override Add override for code scanning analysis of default branch	2023-03-23 14:21:05 +00:00
Charis Kyriakou	94cc1dea00	Add override for code scanning analysis of default branch	2023-03-23 13:31:00 +00:00
Henry Mercer	04f256d7e2	Merge pull request #1602 from github/mergeback/v2.2.8-to-main-67a35a08 Mergeback v2.2.8 refs/heads/releases/v2 into main	2023-03-22 19:48:28 +00:00
github-actions[bot]	0b08c9f2ff	Update checked-in dependencies	2023-03-22 19:14:19 +00:00
github-actions[bot]	1196b1ac0c	Update changelog and version after v2.2.8	2023-03-22 19:04:40 +00:00