Merge pull request #8797 from github/release-prep/2.9.0

Release preparation for version 2.9.0

.bazelrc

@@ -0,0 +1,3 @@
+build --copt="-std=c++17"
+
+try-import %workspace%/local.bazelrc

.bazelversion

@@ -0,0 +1 @@
+5.0.0

.codeqlmanifest.json

@@ -4,14 +4,18 @@
         "*/ql/lib/qlpack.yml",
         "*/ql/test/qlpack.yml",
         "*/ql/examples/qlpack.yml",
-        "*/upgrades/qlpack.yml",
+        "*/ql/consistency-queries/qlpack.yml",
         "cpp/ql/test/query-tests/Security/CWE/CWE-190/semmle/tainted/qlpack.yml",
         "javascript/ql/experimental/adaptivethreatmodeling/lib/qlpack.yml",
+        "javascript/ql/experimental/adaptivethreatmodeling/modelbuilding/qlpack.yml",
         "javascript/ql/experimental/adaptivethreatmodeling/src/qlpack.yml",
+        "csharp/ql/campaigns/Solorigate/lib/qlpack.yml",
+        "csharp/ql/campaigns/Solorigate/src/qlpack.yml",
+        "csharp/ql/campaigns/Solorigate/test/qlpack.yml",
         "misc/legacy-support/*/qlpack.yml",
         "misc/suite-helpers/qlpack.yml",
         "ruby/extractor-pack/codeql-extractor.yml",
-        "ruby/ql/consistency-queries/qlpack.yml"
+        "ql/extractor-pack/codeql-extractor.yml"
     ],
     "versionPolicies": {
       "default": {

.gitattributes

@@ -50,4 +50,15 @@
 *.pdb -text
 
 java/ql/test/stubs/**/*.java linguist-generated=true
-java/ql/test/experimental/stubs/**/*.java linguist-generated=true
+java/ql/test/experimental/stubs/**/*.java linguist-generated=true
+
+# For some languages, upgrade script testing references really old dbscheme
+# files from legacy upgrades that have CRLF line endings. Since upgrade
+# resolution relies on object hashes, we must suppress line ending conversion
+# for those testing dbscheme files.
+*/ql/lib/upgrades/initial/*.dbscheme -text
+
+# Generated test files - these are synced from the standard JavaScript libraries using
+# `javascript/ql/experimental/adaptivethreatmodeling/test/update_endpoint_test_files.py`.
+javascript/ql/experimental/adaptivethreatmodeling/test/endpoint_large_scale/autogenerated/**/*.js linguist-generated=true -merge
+javascript/ql/experimental/adaptivethreatmodeling/test/endpoint_large_scale/autogenerated/**/*.ts linguist-generated=true -merge

.github/actions/fetch-codeql/action.yml

@@ -3,12 +3,22 @@ description: Fetches the latest version of CodeQL
 runs:
   using: composite
   steps:
+    - name: Select platform - Linux
+      if: runner.os == 'Linux'
+      shell: bash
+      run: echo "GA_CODEQL_CLI_PLATFORM=linux64" >> $GITHUB_ENV
+
+    - name: Select platform - MacOS
+      if: runner.os == 'MacOS'
+      shell: bash
+      run: echo "GA_CODEQL_CLI_PLATFORM=osx64" >> $GITHUB_ENV
+
     - name: Fetch CodeQL
       shell: bash
       run: |
         LATEST=$(gh release list --repo https://github.com/github/codeql-cli-binaries | cut -f 1 | grep -v beta | sort --version-sort | tail -1)
-        gh release download --repo https://github.com/github/codeql-cli-binaries --pattern codeql-linux64.zip "$LATEST"
-        unzip -q -d "${RUNNER_TEMP}" codeql-linux64.zip
+        gh release download --repo https://github.com/github/codeql-cli-binaries --pattern codeql-$GA_CODEQL_CLI_PLATFORM.zip "$LATEST"
+        unzip -q -d "${RUNNER_TEMP}" codeql-$GA_CODEQL_CLI_PLATFORM.zip
         echo "${RUNNER_TEMP}/codeql" >> "${GITHUB_PATH}"
       env:
         GITHUB_TOKEN: ${{ github.token }}

.github/labeler.yml

@@ -26,3 +26,6 @@ documentation:
   - "**/*.qhelp"
   - "**/*.md"
   - docs/**/*
+
+"QL-for-QL": 
+  - ql/**/*

.github/workflows/check-change-note.yml

@@ -6,7 +6,11 @@ on:
     paths:
       - "*/ql/src/**/*.ql"
       - "*/ql/src/**/*.qll"
+      - "*/ql/lib/**/*.ql"
+      - "*/ql/lib/**/*.qll"
       - "!**/experimental/**"
+      - "!ql/**"
+      - ".github/workflows/check-change-note.yml"
 
 jobs:
   check-change-note:

.github/workflows/check-qldoc.yml

@@ -0,0 +1,53 @@
+name: "Check QLdoc coverage"
+
+on:
+  pull_request:
+    paths:
+      - "*/ql/lib/**"
+      - .github/workflows/check-qldoc.yml
+    branches:
+      - main
+      - "rc/*"
+
+jobs:
+  qldoc:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Install CodeQL
+        run: |
+          gh extension install github/gh-codeql
+          gh codeql set-channel nightly
+          gh codeql version
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 2
+
+      - name: Check QLdoc coverage
+        shell: bash
+        run: |
+          EXIT_CODE=0
+          changed_lib_packs="$(git diff --name-only --diff-filter=ACMRT HEAD^ HEAD | { grep -o '^[a-z]*/ql/lib' || true; } | sort -u)"
+          for pack_dir in ${changed_lib_packs}; do
+            lang="${pack_dir%/ql/lib}"
+            gh codeql generate library-doc-coverage --output="${RUNNER_TEMP}/${lang}-current.txt" --dir="${pack_dir}"
+          done
+          git checkout HEAD^
+          for pack_dir in ${changed_lib_packs}; do
+            # When we add a new language, pack_dir would not exist in HEAD^.
+            # In this case the right thing to do is to skip the check.
+            [[ ! -d "${pack_dir}" ]] && continue
+            lang="${pack_dir%/ql/lib}"
+            gh codeql generate library-doc-coverage --output="${RUNNER_TEMP}/${lang}-baseline.txt" --dir="${pack_dir}"
+            awk -F, '{gsub(/"/,""); if ($4==0 && $6=="public") print "\""$3"\"" }' "${RUNNER_TEMP}/${lang}-current.txt" | sort -u > "${RUNNER_TEMP}/current-undocumented.txt"
+            awk -F, '{gsub(/"/,""); if ($4==0 && $6=="public") print "\""$3"\"" }' "${RUNNER_TEMP}/${lang}-baseline.txt" | sort -u > "${RUNNER_TEMP}/baseline-undocumented.txt"
+            UNDOCUMENTED="$(grep -f <(comm -13 "${RUNNER_TEMP}/baseline-undocumented.txt" "${RUNNER_TEMP}/current-undocumented.txt") "${RUNNER_TEMP}/${lang}-current.txt" || true)"
+            if [ -n "$UNDOCUMENTED" ]; then
+              echo "$UNDOCUMENTED" | awk -F, '{gsub(/"/,""); print "::warning file='"${pack_dir}"'/"$1",line="$2"::Missing QLdoc for "$5, $3 }'
+              EXIT_CODE=1
+            fi
+          done
+          exit "${EXIT_CODE}"

.github/workflows/codeql-analysis.yml

@@ -27,6 +27,11 @@ jobs:
       pull-requests: read
 
     steps:
+    - name: Setup dotnet
+      uses: actions/setup-dotnet@v1
+      with:
+        dotnet-version: 6.0.101
+
     - name: Checkout repository
       uses: actions/checkout@v2
 
@@ -51,7 +56,7 @@ jobs:
     #    uses a compiled language
 
     - run: |
-       dotnet build csharp
+       dotnet build csharp /p:UseSharedCompilation=false
 
     - name: Perform CodeQL Analysis
       uses: github/codeql-action/analyze@main

.github/workflows/csv-coverage-metrics.yml

@@ -0,0 +1,43 @@
+name: "Publish framework coverage as metrics"
+
+on:
+  schedule:
+    - cron: '5 0 * * *'
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - ".github/workflows/csv-coverage-metrics.yml"
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Setup CodeQL
+        uses: ./.github/actions/fetch-codeql
+      - name: Create empty database
+        run: |
+          DATABASE="${{ runner.temp }}/java-database"
+          PROJECT="${{ runner.temp }}/java-project"
+          mkdir -p "$PROJECT/src/tmp/empty"
+          echo "class Empty {}" >> "$PROJECT/src/tmp/empty/Empty.java"
+          codeql database create "$DATABASE" --language=java --source-root="$PROJECT" --command 'javac src/tmp/empty/Empty.java'
+      - name: Capture coverage information
+        run: |
+          DATABASE="${{ runner.temp }}/java-database"
+          codeql database analyze --format=sarif-latest --output=metrics.sarif -- "$DATABASE" ./java/ql/src/Metrics/Summaries/FrameworkCoverage.ql
+      - uses: actions/upload-artifact@v2
+        with:
+          name: metrics.sarif
+          path: metrics.sarif
+          retention-days: 20
+      - name: Upload SARIF file
+        uses: github/codeql-action/upload-sarif@v1
+        with:
+          sarif_file: metrics.sarif

.github/workflows/js-ml-tests.yml

@@ -0,0 +1,76 @@
+name: JS ML-powered queries tests
+
+on:
+  push:
+    paths:
+      - "javascript/ql/experimental/adaptivethreatmodeling/**"
+      - .github/workflows/js-ml-tests.yml
+    branches:
+      - main
+      - "rc/*"
+  pull_request:
+    paths:
+      - "javascript/ql/experimental/adaptivethreatmodeling/**"
+      - .github/workflows/js-ml-tests.yml
+
+defaults:
+  run:
+    working-directory: javascript/ql/experimental/adaptivethreatmodeling
+
+jobs:
+  qlformat:
+    name: Check QL formatting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: ./.github/actions/fetch-codeql
+
+      - name: Check QL formatting
+        run: |
+          find . "(" -name "*.ql" -or -name "*.qll" ")" -print0 | \
+            xargs -0 codeql query format --check-only
+
+  qlcompile:
+    name: Check QL compilation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: ./.github/actions/fetch-codeql
+
+      - name: Install pack dependencies
+        run: |
+          for pack in modelbuilding src; do
+            codeql pack install --mode verify -- "${pack}"
+          done
+
+      - name: Check QL compilation
+        run: |
+          codeql query compile \
+            --check-only \
+            --ram 5120 \
+            --additional-packs "${{ github.workspace }}" \
+            --threads=0 \
+            -- \
+            lib modelbuilding src
+
+  qltest:
+    name: Run QL tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: ./.github/actions/fetch-codeql
+
+      - name: Install pack dependencies
+        run: codeql pack install -- test
+
+      - name: Run QL tests
+        run: |
+          codeql test run \
+            --threads=0 \
+            --ram 5120 \
+            --additional-packs "${{ github.workspace }}" \
+            -- \
+            test

.github/workflows/mad_modelDiff.yml

@@ -0,0 +1,103 @@
+name: Models as Data - Diff
+
+on:
+  workflow_dispatch:
+    inputs:
+      projects:
+        description: "The projects to generate models for"
+        required: true
+        default: '["netty/netty"]'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "java/ql/src/utils/model-generator/**/*.*"
+      - ".github/workflows/mad_modelDiff.yml"
+
+permissions:
+  contents: read
+
+jobs:
+  model-diff:
+    name: Model Difference
+    runs-on: ubuntu-latest
+    if: github.repository == 'github/codeql'
+    strategy:
+      matrix:
+        slug: ${{fromJson(github.event.inputs.projects || '["apache/commons-codec", "apache/commons-io", "apache/commons-beanutils", "apache/commons-logging", "apache/commons-fileupload", "apache/commons-lang", "apache/commons-validator", "apache/commons-csv", "apache/dubbo"]' )}}
+    steps:
+      - name: Clone github/codeql from PR
+        uses: actions/checkout@v2
+        if: github.event.pull_request
+        with:
+          path: codeql-pr
+      - name: Clone github/codeql from main
+        uses: actions/checkout@v2
+        with:
+          path: codeql-main
+          ref: main
+      - uses: ./codeql-main/.github/actions/fetch-codeql
+      - name: Download database
+        env:
+          SLUG: ${{ matrix.slug }}
+        run: |
+          set -x
+          mkdir lib-dbs
+          SHORTNAME=${SLUG//[^a-zA-Z0-9_]/}
+          projectId=`curl -s https://lgtm.com/api/v1.0/projects/g/${SLUG} | jq .id`
+          curl -L "https://lgtm.com/api/v1.0/snapshots/$projectId/java" -o "$SHORTNAME.zip"
+          unzip -q -d "${SHORTNAME}-db" "${SHORTNAME}.zip"
+          mkdir "lib-dbs/$SHORTNAME/"
+          mv "${SHORTNAME}-db/"$(ls -1 "${SHORTNAME}"-db)/* "lib-dbs/${SHORTNAME}/"
+      - name: Generate Models (PR and main)
+        run: |
+          set -x
+          mkdir tmp-models
+          MODELS=`pwd`/tmp-models
+          DATABASES=`pwd`/lib-dbs
+
+          analyzeDatabaseWithCheckout() {
+            QL_VARIANT=$1
+            DATABASE=$2
+            cd codeql-$QL_VARIANT
+            SHORTNAME=`basename $DATABASE`
+            python java/ql/src/utils/model-generator/GenerateFlowModel.py $DATABASE $MODELS/${SHORTNAME}.qll
+            mv $MODELS/${SHORTNAME}.qll $MODELS/${SHORTNAME}Generated_${QL_VARIANT}.qll
+            cd ..
+          }
+
+          for d in $DATABASES/*/ ; do
+            ls -1 "$d"
+
+            analyzeDatabaseWithCheckout "main" $d
+            if [[ "$GITHUB_EVENT_NAME" == "pull_request" ]]
+            then
+              analyzeDatabaseWithCheckout "pr" $d
+            fi
+          done
+      - name: Install diff2html
+        if: github.event.pull_request
+        run: |
+          npm install -g diff2html-cli
+      - name: Generate Model Diff
+        if: github.event.pull_request
+        run: |
+          set -x
+          MODELS=`pwd`/tmp-models
+          ls -1 tmp-models/
+          for m in $MODELS/*_main.qll ; do
+            t="${m/main/"pr"}"
+            basename=`basename $m`
+            name="diff_${basename/_main.qll/""}"
+            (diff -w -u $m $t | diff2html -i stdin -F $MODELS/$name.html) || true
+          done
+      - uses: actions/upload-artifact@v2
+        with:
+          name: models
+          path: tmp-models/*.qll
+          retention-days: 20
+      - uses: actions/upload-artifact@v2
+        with:
+          name: diffs
+          path: tmp-models/*.html
+          retention-days: 20

.github/workflows/mad_regenerate-models.yml

@@ -0,0 +1,62 @@
+name: Regenerate framework models
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "30 2 * * *"
+  pull_request:
+    branches:
+      - main
+    paths:
+      - ".github/workflows/mad_regenerate-models.yml"
+
+jobs:
+  regenerate-models:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # placeholder required for each axis, excluded below, replaced by the actual combinations (see include)
+        slug: ["placeholder"]
+        ref: ["placeholder"]
+        include:
+          - slug: "apache/commons-io"
+            ref: "8985de8fe74f6622a419b37a6eed0dbc484dc128"
+        exclude:
+          - slug: "placeholder"
+            ref: "placeholder"
+    steps:
+      - name: Clone self (github/codeql)
+        uses: actions/checkout@v2
+      - name: Setup CodeQL binaries
+        uses: ./.github/actions/fetch-codeql
+      - name: Clone repositories
+        uses: actions/checkout@v2
+        with:
+          path: repos/${{ matrix.ref }}
+          ref: ${{ matrix.ref }}
+          repository: ${{ matrix.slug }}
+      - name: Build database
+        env:
+          SLUG: ${{ matrix.slug }}
+          REF: ${{ matrix.ref }}
+        run: |
+          mkdir dbs
+          cd repos/${REF}
+          SHORTNAME=${SLUG//[^a-zA-Z0-9_]/}
+          codeql database create --language=java ../../dbs/${SHORTNAME}
+      - name: Regenerate models in-place
+        env:
+          SLUG: ${{ matrix.slug }}
+        run: |
+          SHORTNAME=${SLUG//[^a-zA-Z0-9_]/}
+          java/ql/src/utils/model-generator/RegenerateModels.py "${SLUG}" dbs/${SHORTNAME}
+      - name: Stage changes
+        run: |
+          find java -name "*.qll" -print0 | xargs -0 git add
+          git status
+          git diff --cached > models.patch
+      - uses: actions/upload-artifact@v2
+        with:
+          name: patch
+          path: models.patch
+          retention-days: 7

.github/workflows/post-pr-comment.yml

@@ -1,12 +1,17 @@
-name: Post pull-request comment
+# This workflow is the second part of the process described in
+# .github/workflows/qhelp-pr-preview.yml
+# See that file for more info.
+
+name: Post PR comment
 on:
   workflow_run:
-    workflows: ["Query help preview"]
+    workflows: [Render QHelp changes]
     types:
       - completed
 
 permissions:
   pull-requests: write
+  actions: read
 
 jobs:
   post_comment:
@@ -17,15 +22,53 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ github.token }}
           WORKFLOW_RUN_ID: ${{ github.event.workflow_run.id }}
-      - run: |
-          PR="$(grep -o '^[0-9]\+$' pr.txt)"
+
+      - name: Check that PR SHA matches workflow SHA
+        run: |
+          PR="$(grep -o '^[0-9]\+$' pr_number.txt)"
           PR_HEAD_SHA="$(gh api "/repos/${GITHUB_REPOSITORY}/pulls/${PR}" --jq .head.sha)"
           # Check that the pull-request head SHA matches the head SHA of the workflow run
           if [ "${WORKFLOW_RUN_HEAD_SHA}" != "${PR_HEAD_SHA}" ]; then
             echo "PR head SHA ${PR_HEAD_SHA} does not match workflow_run event SHA ${WORKFLOW_RUN_HEAD_SHA}. Stopping." 1>&2
             exit 1
           fi
-          gh pr comment "${PR}" --repo "${GITHUB_REPOSITORY}" -F comment.txt
         env:
           GITHUB_TOKEN: ${{ github.token }}
           WORKFLOW_RUN_HEAD_SHA: ${{ github.event.workflow_run.head_commit.id }}
+
+      - name: Create or update comment
+        run: |
+          COMMENT_PREFIX="QHelp previews"
+          COMMENT_AUTHOR="github-actions[bot]"
+          PR_NUMBER="$(grep -o '^[0-9]\+$' pr_number.txt)"
+
+          # If there is no existing comment, comment_id.txt will contain just a
+          # newline (due to jq & gh behaviour). This will cause grep to fail, so
+          # we catch that.
+          RAW_COMMENT_ID=$(grep -o '^[0-9]\+$' comment_id.txt || true)
+
+          if [ $RAW_COMMENT_ID ]
+          then
+            # Fetch existing comment, and validate:
+            # - comment belongs to the PR with number $PR_NUMBER
+            # - comment starts with the expected prefix ("QHelp previews")
+            # - comment author is github-actions[bot]
+            FILTER='select(.issue_url | endswith($repo+"/issues/"+$pr))
+                  | select(.body | startswith($prefix))
+                  | select(.user.login == $author)
+                  | .id'
+            COMMENT_ID=$(gh api "repos/${GITHUB_REPOSITORY}/issues/comments/${RAW_COMMENT_ID}" | jq --arg repo "${GITHUB_REPOSITORY}" --arg pr "${PR_NUMBER}" --arg prefix "${COMMENT_PREFIX}" --arg author "${COMMENT_AUTHOR}" "${FILTER}")
+            if [ $COMMENT_ID ]
+            then
+              # Update existing comment
+              jq --rawfile body comment_body.txt '{"body":$body}' -n | gh api "repos/${GITHUB_REPOSITORY}/issues/comments/${COMMENT_ID}" -X PATCH --input -
+            else
+              echo "Comment ${RAW_COMMENT_ID} did not pass validations: not editing." >&2
+              exit 1
+            fi
+          else
+            # Create new comment
+            jq --rawfile body comment_body.txt '{"body":$body}' -n | gh api "repos/${GITHUB_REPOSITORY}/issues/${PR_NUMBER}/comments" -X POST --input -
+          fi
+        env:
+          GITHUB_TOKEN: ${{ github.token }}

.github/workflows/qhelp-pr-preview.yml

@@ -1,7 +1,25 @@
-name: Query help preview
+# This workflow checks for any changes in .qhelp files in pull requests.
+# For any changed files, it renders them to markdown in a file called `comment_body.txt`.
+# It then checks if there's an existing comment on the pull request generated by
+# this workflow, and writes the comment ID to `comment_id.txt`.
+# It also writes the PR number to `pr_number.txt`.
+# These three files are uploaded as an artifact.
+
+# When this workflow completes, the workflow "Post PR comment" runs.
+# It downloads the artifact and adds a comment to the PR with the rendered
+# QHelp.
+
+# The task is split like this because creating PR comments requires extra
+# permissions that we don't want to expose to PRs from external forks.
+
+# For more info see:
+# https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#workflow_run
+# https://docs.github.com/en/actions/security-guides/automatic-token-authentication#permissions-for-the-github_token
+name: Render QHelp changes
 
 permissions:
   contents: read
+  pull-requests: read
 
 on:
   pull_request:
@@ -15,12 +33,16 @@ jobs:
   qhelp:
     runs-on: ubuntu-latest
     steps:
-      - run: echo "${{  github.event.number }}" > pr.txt
+      - run: echo "${PR_NUMBER}" > pr_number.txt
+        env:
+          PR_NUMBER: ${{ github.event.number }}
       - uses: actions/upload-artifact@v2
         with:
           name: comment
-          path: pr.txt
+          path: pr_number.txt
+          if-no-files-found: error
           retention-days: 1
+
       - uses: actions/checkout@v2
         with:
           fetch-depth: 2
@@ -36,7 +58,7 @@ jobs:
       - name: QHelp preview
         run: |
           EXIT_CODE=0
-          echo "QHelp previews:" > comment.txt
+          echo "QHelp previews:" > comment_body.txt
           while read -r -d $'\0' path; do
             if [ ! -f "${path}" ]; then
                exit 1
@@ -52,12 +74,29 @@ jobs:
                echo '```'
             fi
             echo "</details>"
-          done < "${RUNNER_TEMP}/paths.txt" >> comment.txt
+          done < "${RUNNER_TEMP}/paths.txt" >> comment_body.txt
           exit "${EXIT_CODE}"
 
       - if: always()
         uses: actions/upload-artifact@v2
         with:
           name: comment
-          path: comment.txt
+          path: comment_body.txt
+          if-no-files-found: error
+          retention-days: 1
+
+      - name: Save ID of existing QHelp comment (if it exists)
+        run: |
+          # Find the latest comment starting with "QHelp previews"
+          COMMENT_PREFIX="QHelp previews"
+          gh api "repos/${GITHUB_REPOSITORY}/issues/${PR_NUMBER}/comments" --paginate | jq --arg prefix "${COMMENT_PREFIX}" '[.[] | select(.body|startswith($prefix)) | .id] | max' > comment_id.txt
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+          PR_NUMBER: ${{ github.event.number }}
+
+      - uses: actions/upload-artifact@v2
+        with:
+          name: comment
+          path: comment_id.txt
+          if-no-files-found: error
           retention-days: 1

.github/workflows/ql-for-ql-build.yml

@@ -0,0 +1,203 @@
+name: Run QL for QL
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  queries:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Find codeql
+        id: find-codeql
+        uses: github/codeql-action/init@aa93aea877e5fb8841bcb1193f672abf6e9f2980
+        with:
+          languages: javascript # does not matter
+          tools: latest
+      - name: Get CodeQL version
+        id: get-codeql-version
+        run: |
+          echo "::set-output name=version::$("${CODEQL}" --version | head -n 1 | rev | cut -d " " -f 1 | rev)"
+        shell: bash
+        env:
+          CODEQL: ${{ steps.find-codeql.outputs.codeql-path }}
+      - name: Cache queries
+        id: cache-queries
+        uses: actions/cache@v2
+        with:
+          path: ${{ runner.temp }}/query-pack.zip
+          key: queries-${{ hashFiles('ql/**/*.ql*') }}-${{ hashFiles('ql/**/qlpack.yml') }}-${{ hashFiles('ql/ql/src/ql.dbscheme*') }}-${{ steps.get-codeql-version.outputs.version }}
+      - name: Build query pack
+        if: steps.cache-queries.outputs.cache-hit != 'true'
+        run: |
+          cd ql/ql/src
+          "${CODEQL}" pack create
+          cd .codeql/pack/codeql/ql/0.0.0
+          zip "${PACKZIP}" -r .
+        env:
+          CODEQL: ${{ steps.find-codeql.outputs.codeql-path }}
+          PACKZIP: ${{ runner.temp }}/query-pack.zip
+      - name: Upload query pack
+        uses: actions/upload-artifact@v2
+        with:
+          name: query-pack-zip
+          path: ${{ runner.temp }}/query-pack.zip
+
+  extractors:
+    strategy:
+      fail-fast: false
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Cache entire extractor
+        id: cache-extractor
+        uses: actions/cache@v2
+        with:
+          path: |
+            ql/target/release/ql-autobuilder
+            ql/target/release/ql-autobuilder.exe
+            ql/target/release/ql-extractor
+            ql/target/release/ql-extractor.exe
+          key: ${{ runner.os }}-extractor-${{ hashFiles('ql/**/Cargo.lock') }}-${{ hashFiles('ql/**/*.rs') }}
+      - name: Cache cargo
+        if: steps.cache-extractor.outputs.cache-hit != 'true'
+        uses: actions/cache@v2
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            ql/target
+          key: ${{ runner.os }}-rust-cargo-${{ hashFiles('ql/**/Cargo.lock') }}
+      - name: Check formatting
+        if: steps.cache-extractor.outputs.cache-hit != 'true'
+        run: cd ql; cargo fmt --all -- --check
+      - name: Build
+        if: steps.cache-extractor.outputs.cache-hit != 'true'
+        run: cd ql; cargo build --verbose
+      - name: Run tests
+        if: steps.cache-extractor.outputs.cache-hit != 'true'
+        run: cd ql; cargo test --verbose
+      - name: Release build
+        if: steps.cache-extractor.outputs.cache-hit != 'true'
+        run: cd ql; cargo build --release
+      - name: Generate dbscheme
+        if: steps.cache-extractor.outputs.cache-hit != 'true'
+        run: ql/target/release/ql-generator --dbscheme ql/ql/src/ql.dbscheme --library ql/ql/src/codeql_ql/ast/internal/TreeSitter.qll
+      - uses: actions/upload-artifact@v2
+        with:
+          name: extractor-ubuntu-latest
+          path: |
+            ql/target/release/ql-autobuilder
+            ql/target/release/ql-autobuilder.exe
+            ql/target/release/ql-extractor
+            ql/target/release/ql-extractor.exe
+          retention-days: 1
+  package:
+    runs-on: ubuntu-latest
+
+    needs:
+      - extractors
+      - queries
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/download-artifact@v2
+        with:
+          name: query-pack-zip
+          path: query-pack-zip
+      - uses: actions/download-artifact@v2
+        with:
+          name: extractor-ubuntu-latest
+          path: linux64
+      - run: |
+          unzip query-pack-zip/*.zip -d pack
+          cp -r ql/codeql-extractor.yml ql/tools ql/ql/src/ql.dbscheme.stats pack/
+          mkdir -p pack/tools/linux64
+          if [[ -f linux64/ql-autobuilder ]]; then
+            cp linux64/ql-autobuilder pack/tools/linux64/autobuilder
+            chmod +x pack/tools/linux64/autobuilder
+          fi
+          if [[ -f linux64/ql-extractor ]]; then
+            cp linux64/ql-extractor pack/tools/linux64/extractor
+            chmod +x pack/tools/linux64/extractor
+          fi
+          cd pack
+          zip -rq ../codeql-ql.zip .
+      - uses: actions/upload-artifact@v2
+        with:
+          name: codeql-ql-pack
+          path: codeql-ql.zip
+          retention-days: 1
+  analyze:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        folder: [cpp, csharp, java, javascript, python, ql, ruby]
+
+    needs:
+      - package
+
+    steps:
+      - name: Download pack
+        uses: actions/download-artifact@v2
+        with:
+          name: codeql-ql-pack
+          path: ${{ runner.temp }}/codeql-ql-pack-artifact
+
+      - name: Prepare pack
+        run: |
+          unzip "${PACK_ARTIFACT}/*.zip" -d "${PACK}"
+        env:
+          PACK_ARTIFACT: ${{ runner.temp }}/codeql-ql-pack-artifact
+          PACK: ${{ runner.temp }}/pack
+      - name: Hack codeql-action options
+        run: |
+          JSON=$(jq -nc --arg pack "${PACK}" '.database."run-queries"=["--search-path", $pack] | .resolve.queries=["--search-path", $pack] | .resolve.extractor=["--search-path", $pack] | .database.init=["--search-path", $pack]')
+          echo "CODEQL_ACTION_EXTRA_OPTIONS=${JSON}" >> ${GITHUB_ENV}
+        env:
+          PACK: ${{ runner.temp }}/pack
+
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Create CodeQL config file
+        run: |
+          echo "paths:" > ${CONF}
+          echo "  - ${FOLDER}" >> ${CONF}
+          echo "paths-ignore:" >> ${CONF}
+          echo "  - ql/ql/test" >> ${CONF} 
+          echo "disable-default-queries: true" >> ${CONF}
+          echo "packs:" >> ${CONF}
+          echo "  - codeql/ql" >> ${CONF}
+          echo "Config file: "
+          cat ${CONF}
+        env: 
+          CONF: ./ql-for-ql-config.yml
+          FOLDER: ${{ matrix.folder }}
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@aa93aea877e5fb8841bcb1193f672abf6e9f2980
+        with:
+          languages: ql
+          db-location: ${{ runner.temp }}/db
+          config-file: ./ql-for-ql-config.yml
+          tools: latest
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@aa93aea877e5fb8841bcb1193f672abf6e9f2980
+        with: 
+          category: "ql-for-ql-${{ matrix.folder }}"
+      - name: Copy sarif file to CWD
+        run: cp ../results/ql.sarif ./${{ matrix.folder }}.sarif
+      - name: Sarif as artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ matrix.folder }}.sarif
+          path: ${{ matrix.folder }}.sarif
+

.github/workflows/ql-for-ql-dataset_measure.yml

@@ -0,0 +1,84 @@
+name: Collect database stats for QL for QL
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - ql/ql/src/ql.dbscheme
+  pull_request:
+    branches: [main]
+    paths:
+      - ql/ql/src/ql.dbscheme
+  workflow_dispatch:
+
+jobs:
+  measure:
+    env:
+      CODEQL_THREADS: 4 # TODO: remove this once it's set by the CLI
+    strategy:
+      matrix:
+        repo:
+          - github/codeql
+          - github/codeql-go
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Find codeql
+        id: find-codeql
+        uses: github/codeql-action/init@aa93aea877e5fb8841bcb1193f672abf6e9f2980
+        with:
+          languages: javascript # does not matter
+      - uses: actions/cache@v2
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            ql/target
+          key: ${{ runner.os }}-qltest-cargo-${{ hashFiles('ql/**/Cargo.lock') }}
+      - name: Build Extractor
+        run: cd ql; env "PATH=$PATH:`dirname ${CODEQL}`" ./create-extractor-pack.sh
+        env:
+          CODEQL: ${{ steps.find-codeql.outputs.codeql-path }}
+      - name: Checkout ${{ matrix.repo }}
+        uses: actions/checkout@v2
+        with:
+          repository: ${{ matrix.repo }}
+          path: ${{ github.workspace }}/repo
+      - name: Create database
+        run: |
+          "${CODEQL}" database create \
+            --search-path "ql/extractor-pack" \
+            --threads 4 \
+            --language ql --source-root "${{ github.workspace }}/repo" \
+            "${{ runner.temp }}/database"
+        env:
+          CODEQL: ${{ steps.find-codeql.outputs.codeql-path }}
+      - name: Measure database
+        run: |
+          mkdir -p "stats/${{ matrix.repo }}"
+          "${CODEQL}" dataset measure --threads 4 --output "stats/${{ matrix.repo }}/stats.xml" "${{ runner.temp }}/database/db-ql"
+        env:
+          CODEQL: ${{ steps.find-codeql.outputs.codeql-path }}
+      - uses: actions/upload-artifact@v2
+        with:
+          name: measurements
+          path: stats
+          retention-days: 1
+
+  merge:
+    runs-on: ubuntu-latest
+    needs: measure
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/download-artifact@v2
+        with:
+          name: measurements
+          path: stats
+      - run: |
+          python -m pip install --user lxml
+          find stats -name 'stats.xml' -print0 | sort -z | xargs -0 python ql/scripts/merge_stats.py --output ql/ql/src/ql.dbscheme.stats --normalise ql_tokeninfo
+      - uses: actions/upload-artifact@v2
+        with:
+          name: ql.dbscheme.stats
+          path: ql/ql/src/ql.dbscheme.stats

.github/workflows/ql-for-ql-tests.yml

@@ -0,0 +1,52 @@
+name: Run QL for QL Tests
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - "ql/**"
+  pull_request:
+    branches: [main]
+    paths:
+      - "ql/**"
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  qltest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Find codeql
+        id: find-codeql
+        uses: github/codeql-action/init@aa93aea877e5fb8841bcb1193f672abf6e9f2980
+        with:
+          languages: javascript # does not matter
+      - uses: actions/cache@v2
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            ql/target
+          key: ${{ runner.os }}-qltest-cargo-${{ hashFiles('ql/**/Cargo.lock') }}
+      - name: Build extractor
+        run: |
+          cd ql;
+          codeqlpath=$(dirname ${{ steps.find-codeql.outputs.codeql-path }});
+          env "PATH=$PATH:$codeqlpath" ./create-extractor-pack.sh
+      - name: Run QL tests
+        run: |
+          "${CODEQL}" test run --check-databases --check-unused-labels --check-repeated-labels --check-redefined-labels --check-use-before-definition --search-path "${{ github.workspace }}/ql/extractor-pack" --consistency-queries ql/ql/consistency-queries ql/ql/test
+        env:
+          CODEQL: ${{ steps.find-codeql.outputs.codeql-path }}
+      - name: Check QL formatting
+        run: |
+          find ql/ql "(" -name "*.ql" -or -name "*.qll" ")" -print0 | xargs -0 "${CODEQL}" query format --check-only
+        env:
+          CODEQL: ${{ steps.find-codeql.outputs.codeql-path }}
+      - name: Check QL compilation
+        run: |
+          "${CODEQL}" query compile --check-only --threads=4 --warnings=error --search-path "${{ github.workspace }}/ql/extractor-pack" "ql/ql/src" "ql/ql/examples"
+        env:
+          CODEQL: ${{ steps.find-codeql.outputs.codeql-path }}

.github/workflows/ruby-build.yml

@@ -50,7 +50,7 @@ jobs:
             ~/.cargo/registry
             ~/.cargo/git
             ruby/target
-          key: ${{ runner.os }}-rust-cargo-${{ hashFiles('**/Cargo.lock') }}
+          key: ${{ runner.os }}-ruby-rust-cargo-${{ hashFiles('ruby/rust-toolchain.toml', 'ruby/**/Cargo.lock') }}
       - name: Check formatting
         run: cargo fmt --all -- --check
       - name: Build

.github/workflows/ruby-qltest.yml

@@ -24,27 +24,54 @@ defaults:
     working-directory: ruby
 
 jobs:
-  qltest:
+  qlformat:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - uses: ./.github/actions/fetch-codeql
-      - uses: ./ruby/actions/create-extractor-pack
-      - name: Run QL tests
-        run: |
-          codeql test run --search-path "${{ github.workspace }}/ruby/extractor-pack" --check-databases --check-unused-labels --check-repeated-labels --check-redefined-labels --check-use-before-definition --consistency-queries ql/consistency-queries ql/test
-        env:
-          GITHUB_TOKEN: ${{ github.token }}
       - name: Check QL formatting
         run: find ql "(" -name "*.ql" -or -name "*.qll" ")" -print0 | xargs -0 codeql query format --check-only
+  qlcompile:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: ./.github/actions/fetch-codeql
       - name: Check QL compilation
         run: |
-          codeql query compile --check-only --threads=4 --warnings=error "ql/src" "ql/examples"
+          codeql query compile --check-only --threads=0 --ram 5000 --warnings=error "ql/src" "ql/examples"
         env:
           GITHUB_TOKEN: ${{ github.token }}
+  qlupgrade:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: ./.github/actions/fetch-codeql
       - name: Check DB upgrade scripts
         run: |
           echo >empty.trap
           codeql dataset import -S ql/lib/upgrades/initial/ruby.dbscheme testdb empty.trap
           codeql dataset upgrade testdb --additional-packs ql/lib
           diff -q testdb/ruby.dbscheme ql/lib/ruby.dbscheme
+      - name: Check DB downgrade scripts
+        run: |
+          echo >empty.trap
+          rm -rf testdb; codeql dataset import -S ql/lib/ruby.dbscheme testdb empty.trap
+          codeql resolve upgrades --format=lines --allow-downgrades --additional-packs downgrades \
+           --dbscheme=ql/lib/ruby.dbscheme --target-dbscheme=downgrades/initial/ruby.dbscheme |
+           xargs codeql execute upgrades testdb
+          diff -q testdb/ruby.dbscheme downgrades/initial/ruby.dbscheme
+  qltest:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        slice: ["1/2", "2/2"]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: ./.github/actions/fetch-codeql
+      - uses: ./ruby/actions/create-extractor-pack
+      - name: Run QL tests
+        run: |
+          codeql test run --threads=0 --ram 5000 --slice ${{ matrix.slice }} --search-path "${{ github.workspace }}/ruby/extractor-pack" --check-databases --check-unused-labels --check-repeated-labels --check-redefined-labels --check-use-before-definition --consistency-queries ql/consistency-queries ql/test
+        env:
+          GITHUB_TOKEN: ${{ github.token }}

.github/workflows/swift-qltest.yml

@@ -0,0 +1,51 @@
+name: "Swift: Run QL Tests"
+
+on:
+  pull_request:
+    paths:
+      - "swift/**"
+      - .github/workflows/swift-qltest.yml
+    branches:
+      - main
+defaults:
+  run:
+    working-directory: swift
+
+jobs:
+  qlformat:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: ./.github/actions/fetch-codeql
+      - name: Check QL formatting
+        run: find ql "(" -name "*.ql" -or -name "*.qll" ")" -print0 | xargs -0 codeql query format --check-only
+  qltest:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os : [ubuntu-20.04, macos-latest]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: ./.github/actions/fetch-codeql
+      - name: Install bazelisk - Linux
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y wget
+          wget https://github.com/bazelbuild/bazelisk/releases/download/v1.11.0/bazelisk-linux-amd64
+          mv bazelisk-linux-amd64 /usr/local/bin/bazel
+          chmod +x /usr/local/bin/bazel
+      - name: Install bazelisk - macOS
+        if: runner.os == 'MacOS'
+        run: |
+          brew install bazelisk
+      - name: Build Swift extractor
+        run: |
+          bazel run //swift:create-extractor-pack
+      - name: Run QL tests
+        run: |
+          codeql test run --threads=0 --ram 5000 --search-path "${{ github.workspace }}/swift/extractor-pack" --check-databases --check-unused-labels --check-repeated-labels --check-redefined-labels --check-use-before-definition ql/test
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+

.github/workflows/validate-change-notes.yml

@@ -0,0 +1,29 @@
+name: Validate change notes
+
+on:
+  push:
+    paths:
+      - "*/ql/*/change-notes/**/*"
+      - ".github/workflows/validate-change-notes.yml"
+    branches:
+      - main
+      - "rc/*"
+  pull_request:
+    paths:
+      - "*/ql/*/change-notes/**/*"
+      - ".github/workflows/validate-change-notes.yml"
+
+jobs:
+  check-change-note:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Setup CodeQL
+        uses: ./.github/actions/fetch-codeql
+
+      - name: Fail if there are any errors with existing change notes
+
+        run: |
+          codeql pack release --groups cpp,csharp,java,javascript,python,ruby,-examples,-test,-experimental

.gitignore

@@ -17,7 +17,7 @@
 # Byte-compiled python files
 *.pyc
 
-# python virtual environment folder 
+# python virtual environment folder
 .venv/
 
 # It's useful (though not required) to be able to unpack codeql in the ql checkout itself
@@ -29,4 +29,10 @@ csharp/extractor/Semmle.Extraction.CSharp.Driver/Properties/launchSettings.json
 .codeql
 
 # Compiled class file
-*.class
+*.class
+
+# links created by bazel
+/bazel-*
+
+# CLion project files
+/.clwb

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+exclude: /test/.*$(?<!\.ql)(?<!\.qll)(?<!\.qlref)
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+
+-   repo: local
+    hooks:
+    -   id: codeql-format
+        name: Fix QL file formatting
+        files: \.qll?$
+        language: system
+        entry: codeql query format --in-place
+
+    -   id: sync-files
+        name: Fix files required to be identical
+        language: system
+        entry: python3 config/sync-files.py --latest
+        pass_filenames: false
+
+    -   id: qhelp
+        name: Check query help generation
+        files: \.qhelp$
+        language: system
+        entry: python3 misc/scripts/check-qhelp.py

CODEOWNERS

@@ -5,13 +5,8 @@
 /python/ @github/codeql-python
 /ruby/ @github/codeql-ruby
 
-# Make @xcorail (GitHub Security Lab) a code owner for experimental queries so he gets pinged when we promote a query out of experimental
-/cpp/**/experimental/**/* @github/codeql-c-analysis @xcorail
-/csharp/**/experimental/**/* @github/codeql-csharp @xcorail
-/java/**/experimental/**/* @github/codeql-java @xcorail
-/javascript/**/experimental/**/* @github/codeql-javascript @xcorail
-/python/**/experimental/**/* @github/codeql-python @xcorail
-/ruby/**/experimental/**/* @github/codeql-ruby @xcorail
+# ML-powered queries
+/javascript/ql/experimental/adaptivethreatmodeling/ @github/codeql-ml-powered-queries-reviewers
 
 # Notify members of codeql-go about PRs to the shared data-flow library files
 /java/ql/src/semmle/code/java/dataflow/internal/DataFlowImpl.qll @github/codeql-java @github/codeql-go
@@ -25,3 +20,14 @@
 /docs/codeql-for-visual-studio-code/ @github/codeql-vscode-reviewers
 /docs/ql-language-reference/ @github/codeql-frontend-reviewers
 /docs/query-*-style-guide.md @github/codeql-analysis-reviewers
+
+# QL for QL reviewers
+/ql/ @github/codeql-ql-for-ql-reviewers
+
+# Bazel
+**/*.bazel @github/codeql-ci-reviewers
+**/*.bzl @github/codeql-ci-reviewers
+
+# Documentation etc
+/*.md @github/code-scanning-product
+/LICENSE @github/code-scanning-product

CONTRIBUTING.md

@@ -4,6 +4,9 @@ We welcome contributions to our CodeQL libraries and queries. Got an idea for a
 
 There is lots of useful documentation to help you write queries, ranging from information about query file structure to tutorials for specific target languages. For more information on the documentation available, see [CodeQL queries](https://help.semmle.com/QL/learn-ql/writing-queries/writing-queries.html) on [help.semmle.com](https://help.semmle.com).
 
+## Change notes
+
+Any nontrivial user-visible change to a query pack or library pack should have a change note. For details on how to add a change note for your change, see [this guide](docs/change-notes.md).
 
 ## Submitting a new experimental query
 
@@ -33,13 +36,17 @@ If you have an idea for a query that you would like to share with other CodeQL u
 
     For details, see the [guide on query metadata](docs/query-metadata-style-guide.md).
 
-    Make sure the `select` statement is compatible with the query `@kind`. See [About CodeQL queries](https://help.semmle.com/QL/learn-ql/writing-queries/introduction-to-queries.html#select-clause) on help.semmle.com.
+    Make sure the `select` statement is compatible with the query `@kind`. See [About CodeQL queries](https://codeql.github.com/docs/writing-codeql-queries/about-codeql-queries/#select-clause) on codeql.github.com.
 
 3. **Formatting**
 
     - The queries and libraries must be autoformatted, for example using the "Format Document" command in [CodeQL for Visual Studio Code](https://help.semmle.com/codeql/codeql-for-vscode/procedures/about-codeql-for-vscode.html).
 
-    If you prefer, you can use this [pre-commit hook](misc/scripts/pre-commit) that automatically checks whether your files are correctly formatted. See the [pre-commit hook installation guide](docs/pre-commit-hook-setup.md) for instructions on how to install the hook.
+    If you prefer, you can either:
+    1. install the [pre-commit framework](https://pre-commit.com/) and install the configured hooks on this repo via `pre-commit install`, or
+    2. use this [pre-commit hook](misc/scripts/pre-commit) that automatically checks whether your files are correctly formatted.
+
+    See the [pre-commit hook installation guide](docs/pre-commit-hook-setup.md) for instructions on the two approaches.
 
 4. **Compilation**
 
@@ -60,6 +67,10 @@ After the experimental query is merged, we welcome pull requests to improve it.
 
 ## Using your personal data
 
-If you contribute to this project, we will record your name and email address (as provided by you with your contributions) as part of the code repositories, which are public. We might also use this information to contact you in relation to your contributions, as well as in the normal course of software development. We also store records of CLA agreements signed in the past, but no longer require contributors to sign a CLA. Under GDPR legislation, we do this on the basis of our legitimate interest in creating the CodeQL product. 
+If you contribute to this project, we will record your name and email address (as provided by you with your contributions) as part of the code repositories, which are public. We might also use this information to contact you in relation to your contributions, as well as in the normal course of software development. We also store records of CLA agreements signed in the past, but no longer require contributors to sign a CLA. Under GDPR legislation, we do this on the basis of our legitimate interest in creating the CodeQL product.
 
 Please do get in touch (privacy@github.com) if you have any questions about this or our data protection policies.
+
+## Bazel
+Please notice that any bazel targets and definitions in this repository are currently experimental
+and for internal use only.

README.md

@@ -1,11 +1,11 @@
 # CodeQL
 
-This open source repository contains the standard CodeQL libraries and queries that power [LGTM](https://lgtm.com) and the other CodeQL products that [GitHub](https://github.com) makes available to its customers worldwide. For the queries, libraries, and extractor that power Go analysis, visit the [CodeQL for Go repository](https://github.com/github/codeql-go).
+This open source repository contains the standard CodeQL libraries and queries that power [GitHub Advanced Security](https://github.com/features/security/code) and the other application security products that [GitHub](https://github.com/features/security/) makes available to its customers worldwide. For the queries, libraries, and extractor that power Go analysis, visit the [CodeQL for Go repository](https://github.com/github/codeql-go).
 
 ## How do I learn CodeQL and run queries?
 
 There is [extensive documentation](https://codeql.github.com/docs/) on getting started with writing CodeQL.
-You can use the [interactive query console](https://lgtm.com/help/lgtm/using-query-console) on LGTM.com or the [CodeQL for Visual Studio Code](https://codeql.github.com/docs/codeql-for-visual-studio-code/) extension to try out your queries on any open source project that's currently being analyzed.
+You can use the [CodeQL for Visual Studio Code](https://codeql.github.com/docs/codeql-for-visual-studio-code/) extension or the [interactive query console](https://lgtm.com/help/lgtm/using-query-console) on LGTM.com (Semmle Legacy product) to try out your queries on any open source project that's currently being analyzed.
 
 ## Contributing
 
@@ -15,6 +15,8 @@ We welcome contributions to our standard library and standard checks. Do you hav
 
 The code in this repository is licensed under the [MIT License](LICENSE) by [GitHub](https://github.com).
 
+The CodeQL CLI (including the CodeQL engine) is hosted in a [different repository](https://github.com/github/codeql-cli-binaries) and is [licensed separately](https://github.com/github/codeql-cli-binaries/blob/main/LICENSE.md). If you'd like to use the CodeQL CLI to analyze closed-source code, you will need a separate commercial license; please [contact us](https://github.com/enterprise/contact) for further help.
+
 ## Visual Studio Code integration
 
 If you use Visual Studio Code to work in this repository, there are a few integration features to make development easier.

WORKSPACE.bazel

@@ -0,0 +1,12 @@
+# Please notice that any bazel targets and definitions in this repository are currently experimental
+# and for internal use only.
+
+workspace(name = "codeql")
+
+load("//misc/bazel:workspace.bzl", "codeql_workspace")
+
+codeql_workspace()
+
+load("//misc/bazel:workspace_deps.bzl", "codeql_workspace_deps")
+
+codeql_workspace_deps()

config/blame-deprecations.mjs

@@ -0,0 +1,58 @@
+import fs from "fs";
+import path from "path";
+import cp from "child_process";
+function* walk(dir) {
+  for (const file of fs.readdirSync(dir)) {
+    const filePath = path.join(dir, file);
+    if (fs.statSync(filePath).isDirectory()) {
+      yield* walk(filePath);
+    } else {
+      yield filePath;
+    }
+  }
+}
+
+function* deprecatedFiles(dir) {
+  for (const file of walk(dir)) {
+    if (file.endsWith(".ql") || file.endsWith(".qll")) {
+      const contents = fs.readFileSync(file, "utf8");
+      if (/\sdeprecated\s/.test(contents)) {
+        yield file;
+      }
+    }
+  }
+}
+
+const blameRegExp =
+  /^(\^?\w+)\s.+\s+(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2} (?:\+|-)\d{4})\s+(\d+)\).*$/;
+
+function* deprecationMessages(dir) {
+  for (const file of deprecatedFiles(dir)) {
+    const blame = cp.execFileSync("git", ["blame", "--", file]);
+    const lines = blame.toString().split("\n");
+    for (let i = 0; i < lines.length; i++) {
+      const line = lines[i];
+      if (line.includes(" deprecated ")) {
+        try {
+          const [_, sha, time, lineNumber] = line.match(blameRegExp);
+          const date = new Date(time);
+          // check if it's within the last 14 months (a year, plus 2 months for safety, in case a PR was delayed)
+          if (date.getTime() >= Date.now() - 14 * 31 * 24 * 60 * 60 * 1000) {
+            continue;
+          }
+          const message = `${file}:${lineNumber} was last updated on ${date.getFullYear()}-${date.getMonth()}-${date.getDate()}`;
+          yield [message, date];
+        } catch (e) {
+          console.log(e);
+          console.log("----");
+          console.log(line);
+          console.log("----");
+          process.exit(0);
+        }
+      }
+    }
+  }
+}
+[...deprecationMessages(".")]
+  .sort((a, b) => a[1].getTime() - b[1].getTime())
+  .forEach((msg) => console.log(msg[0]));

config/identical-files.json

@@ -7,6 +7,7 @@
     "java/ql/lib/semmle/code/java/dataflow/internal/DataFlowImpl5.qll",
     "java/ql/lib/semmle/code/java/dataflow/internal/DataFlowImpl6.qll",
     "java/ql/lib/semmle/code/java/dataflow/internal/DataFlowImplForSerializability.qll",
+    "java/ql/lib/semmle/code/java/dataflow/internal/DataFlowImplForOnActivityResult.qll",
     "cpp/ql/lib/semmle/code/cpp/dataflow/internal/DataFlowImpl.qll",
     "cpp/ql/lib/semmle/code/cpp/dataflow/internal/DataFlowImpl2.qll",
     "cpp/ql/lib/semmle/code/cpp/dataflow/internal/DataFlowImpl3.qll",
@@ -26,7 +27,8 @@
     "python/ql/lib/semmle/python/dataflow/new/internal/DataFlowImpl3.qll",
     "python/ql/lib/semmle/python/dataflow/new/internal/DataFlowImpl4.qll",
     "ruby/ql/lib/codeql/ruby/dataflow/internal/DataFlowImpl.qll",
-    "ruby/ql/lib/codeql/ruby/dataflow/internal/DataFlowImpl2.qll"
+    "ruby/ql/lib/codeql/ruby/dataflow/internal/DataFlowImpl2.qll",
+    "ruby/ql/lib/codeql/ruby/dataflow/internal/DataFlowImplForLibraries.qll"
   ],
   "DataFlow Java/C++/C#/Python Common": [
     "java/ql/lib/semmle/code/java/dataflow/internal/DataFlowImplCommon.qll",
@@ -53,7 +55,8 @@
     "python/ql/lib/semmle/python/dataflow/new/internal/tainttracking2/TaintTrackingImpl.qll",
     "python/ql/lib/semmle/python/dataflow/new/internal/tainttracking3/TaintTrackingImpl.qll",
     "python/ql/lib/semmle/python/dataflow/new/internal/tainttracking4/TaintTrackingImpl.qll",
-    "ruby/ql/lib/codeql/ruby/dataflow/internal/tainttracking1/TaintTrackingImpl.qll"
+    "ruby/ql/lib/codeql/ruby/dataflow/internal/tainttracking1/TaintTrackingImpl.qll",
+    "ruby/ql/lib/codeql/ruby/dataflow/internal/tainttrackingforlibraries/TaintTrackingImpl.qll"
   ],
   "DataFlow Java/C++/C#/Python Consistency checks": [
     "java/ql/lib/semmle/code/java/dataflow/internal/DataFlowImplConsistency.qll",
@@ -72,6 +75,10 @@
     "java/ql/lib/semmle/code/java/dataflow/internal/rangeanalysis/SsaReadPositionCommon.qll",
     "csharp/ql/lib/semmle/code/csharp/dataflow/internal/rangeanalysis/SsaReadPositionCommon.qll"
   ],
+  "Model as Data Generation Java/C# - CaptureModels": [
+    "java/ql/src/utils/model-generator/internal/CaptureModels.qll",
+    "csharp/ql/src/utils/model-generator/internal/CaptureModels.qll"
+  ],
   "Sign Java/C#": [
     "java/ql/lib/semmle/code/java/dataflow/internal/rangeanalysis/Sign.qll",
     "csharp/ql/lib/semmle/code/csharp/dataflow/internal/rangeanalysis/Sign.qll"
@@ -376,7 +383,8 @@
     "csharp/ql/test/TestUtilities/InlineExpectationsTest.qll",
     "java/ql/test/TestUtilities/InlineExpectationsTest.qll",
     "python/ql/test/TestUtilities/InlineExpectationsTest.qll",
-    "ruby/ql/test/TestUtilities/InlineExpectationsTest.qll"
+    "ruby/ql/test/TestUtilities/InlineExpectationsTest.qll",
+    "ql/ql/test/TestUtilities/InlineExpectationsTest.qll"
   ],
   "C++ ExternalAPIs": [
     "cpp/ql/src/Security/CWE/CWE-020/ExternalAPIs.qll",
@@ -425,7 +433,6 @@
     "python/ql/src/Lexical/CommentedOutCodeMetricOverview.inc.qhelp"
   ],
   "FLinesOfDuplicatedCodeCommon.inc.qhelp": [
-    "cpp/ql/src/Metrics/Files/FLinesOfDuplicatedCodeCommon.inc.qhelp",
     "java/ql/src/Metrics/Files/FLinesOfDuplicatedCodeCommon.inc.qhelp",
     "javascript/ql/src/Metrics/FLinesOfDuplicatedCodeCommon.inc.qhelp",
     "python/ql/src/Metrics/FLinesOfDuplicatedCodeCommon.inc.qhelp"
@@ -452,24 +459,32 @@
     "ruby/ql/lib/codeql/ruby/dataflow/internal/SsaImplCommon.qll",
     "cpp/ql/lib/semmle/code/cpp/ir/dataflow/internal/SsaImplCommon.qll"
   ],
-  "CryptoAlgorithms Python/JS": [
+  "CryptoAlgorithms Python/JS/Ruby": [
     "javascript/ql/lib/semmle/javascript/security/CryptoAlgorithms.qll",
-    "python/ql/lib/semmle/python/concepts/CryptoAlgorithms.qll"
+    "python/ql/lib/semmle/python/concepts/CryptoAlgorithms.qll",
+    "ruby/ql/lib/codeql/ruby/security/CryptoAlgorithms.qll"
+  ],
+  "CryptoAlgorithmNames Python/JS/Ruby": [
+    "javascript/ql/lib/semmle/javascript/security/internal/CryptoAlgorithmNames.qll",
+    "python/ql/lib/semmle/python/concepts/internal/CryptoAlgorithmNames.qll",
+    "ruby/ql/lib/codeql/ruby/security/internal/CryptoAlgorithmNames.qll"
   ],
   "SensitiveDataHeuristics Python/JS": [
     "javascript/ql/lib/semmle/javascript/security/internal/SensitiveDataHeuristics.qll",
-    "python/ql/lib/semmle/python/security/internal/SensitiveDataHeuristics.qll"
+    "python/ql/lib/semmle/python/security/internal/SensitiveDataHeuristics.qll",
+    "ruby/ql/lib/codeql/ruby/security/internal/SensitiveDataHeuristics.qll"
   ],
   "ReDoS Util Python/JS/Ruby": [
     "javascript/ql/lib/semmle/javascript/security/performance/ReDoSUtil.qll",
     "python/ql/lib/semmle/python/security/performance/ReDoSUtil.qll",
     "ruby/ql/lib/codeql/ruby/security/performance/ReDoSUtil.qll"
   ],
-  "ReDoS Exponential Python/JS": [
+  "ReDoS Exponential Python/JS/Ruby": [
     "javascript/ql/lib/semmle/javascript/security/performance/ExponentialBackTracking.qll",
-    "python/ql/lib/semmle/python/security/performance/ExponentialBackTracking.qll"
+    "python/ql/lib/semmle/python/security/performance/ExponentialBackTracking.qll",
+    "ruby/ql/lib/codeql/ruby/security/performance/ExponentialBackTracking.qll"
   ],
-  "ReDoS Polynomial Python/JS": [
+  "ReDoS Polynomial Python/JS/Ruby": [
     "javascript/ql/lib/semmle/javascript/security/performance/SuperlinearBackTracking.qll",
     "python/ql/lib/semmle/python/security/performance/SuperlinearBackTracking.qll",
     "ruby/ql/lib/codeql/ruby/security/performance/SuperlinearBackTracking.qll"
@@ -494,5 +509,45 @@
     "javascript/ql/lib/tutorial.qll",
     "python/ql/lib/tutorial.qll",
     "ruby/ql/lib/tutorial.qll"
+  ],
+  "AccessPathSyntax": [
+    "csharp/ql/lib/semmle/code/csharp/dataflow/internal/AccessPathSyntax.qll",
+    "java/ql/lib/semmle/code/java/dataflow/internal/AccessPathSyntax.qll",
+    "javascript/ql/lib/semmle/javascript/frameworks/data/internal/AccessPathSyntax.qll",
+    "ruby/ql/lib/codeql/ruby/dataflow/internal/AccessPathSyntax.qll"
+  ],
+  "IncompleteUrlSubstringSanitization": [
+    "javascript/ql/src/Security/CWE-020/IncompleteUrlSubstringSanitization.qll",
+    "ruby/ql/src/queries/security/cwe-020/IncompleteUrlSubstringSanitization.qll"
+  ],
+  "Concepts Python/Ruby/JS": [
+    "python/ql/lib/semmle/python/internal/ConceptsShared.qll",
+    "ruby/ql/lib/codeql/ruby/internal/ConceptsShared.qll",
+    "javascript/ql/lib/semmle/javascript/internal/ConceptsShared.qll"
+  ],
+  "Hostname Regexp queries": [
+    "javascript/ql/src/Security/CWE-020/HostnameRegexpShared.qll",
+    "python/ql/src/Security/CWE-020/HostnameRegexpShared.qll",
+    "ruby/ql/src/queries/security/cwe-020/HostnameRegexpShared.qll"
+  ],
+  "ApiGraphModels": [
+    "javascript/ql/lib/semmle/javascript/frameworks/data/internal/ApiGraphModels.qll",
+    "ruby/ql/lib/codeql/ruby/frameworks/data/internal/ApiGraphModels.qll"
+  ],
+  "TaintedFormatStringQuery Ruby/JS": [
+    "javascript/ql/lib/semmle/javascript/security/dataflow/TaintedFormatStringQuery.qll",
+    "ruby/ql/lib/codeql/ruby/security/TaintedFormatStringQuery.qll"
+  ],
+  "TaintedFormatStringCustomizations Ruby/JS": [
+    "javascript/ql/lib/semmle/javascript/security/dataflow/TaintedFormatStringCustomizations.qll",
+    "ruby/ql/lib/codeql/ruby/security/TaintedFormatStringCustomizations.qll"
+  ],
+  "HttpToFileAccessQuery JS/Ruby": [
+    "javascript/ql/lib/semmle/javascript/security/dataflow/HttpToFileAccessQuery.qll",
+    "ruby/ql/lib/codeql/ruby/security/HttpToFileAccessQuery.qll"
+  ],
+  "HttpToFileAccessCustomizations JS/Ruby": [
+    "javascript/ql/lib/semmle/javascript/security/dataflow/HttpToFileAccessCustomizations.qll",
+    "ruby/ql/lib/codeql/ruby/security/HttpToFileAccessCustomizations.qll"
   ]
-}
+}

cpp/BUILD.bazel

@@ -0,0 +1,17 @@
+package(default_visibility = ["//visibility:public"])
+
+load("@rules_pkg//:mappings.bzl", "pkg_filegroup")
+
+alias(
+    name = "dbscheme",
+    actual = "//cpp/ql/lib:dbscheme",
+)
+
+pkg_filegroup(
+    name = "db-files",
+    srcs = [
+        ":dbscheme",
+        "//cpp/downgrades",
+        "//cpp/ql/lib:dbscheme-stats",
+    ],
+)

cpp/autobuilder/Semmle.Autobuild.Cpp.Tests/Semmle.Autobuild.Cpp.Tests.csproj

@@ -2,7 +2,7 @@
 
   <PropertyGroup>
     <OutputType>Exe</OutputType>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <GenerateAssemblyInfo>false</GenerateAssemblyInfo>
     <RuntimeIdentifiers>win-x64;linux-x64;osx-x64</RuntimeIdentifiers>
     <Nullable>enable</Nullable>

cpp/autobuilder/Semmle.Autobuild.Cpp/Semmle.Autobuild.Cpp.csproj

@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <AssemblyName>Semmle.Autobuild.Cpp</AssemblyName>
     <RootNamespace>Semmle.Autobuild.Cpp</RootNamespace>
     <ApplicationIcon />

cpp/change-notes/2021-11-01-isFromSystemMacroDefinition.md

@@ -1,4 +0,0 @@
-lgtm,codescanning
-* The QL library `semmle.code.cpp.commons.Exclusions` now contains a predicate
-  `isFromSystemMacroDefinition` for identifying code that originates from a
-  macro outside the project being analyzed.

cpp/change-notes/2021-11-09-use-of-http.md

@@ -1,2 +0,0 @@
-lgtm,codescanning
-* A new query `cpp/non-https-url` has been added for C/C++. The query flags uses of `http` URLs that might be better replaced with `https`.

cpp/change-notes/2021-11-25-certificate-not-checked.md

@@ -1,2 +0,0 @@
-lgtm,codescanning
-* A new query `cpp/certificate-not-checked` has been added for C/C++. The query flags unsafe use of OpenSSL and similar libraries.

cpp/change-notes/2021-11-25-certificate-result-conflation.md

@@ -1,2 +0,0 @@
-lgtm,codescanning
-* A new query `cpp/certificate-result-conflation` has been added for C/C++. The query flags unsafe use of OpenSSL and similar libraries.

cpp/config/suites/c/correctness

@@ -31,6 +31,7 @@
 + semmlecode-cpp-queries/Critical/NewArrayDeleteMismatch.ql: /Correctness/Common Errors
 + semmlecode-cpp-queries/Critical/NewDeleteArrayMismatch.ql: /Correctness/Common Errors
 + semmlecode-cpp-queries/Critical/NewFreeMismatch.ql: /Correctness/Common Errors
++ semmlecode-cpp-queries/Likely Bugs/Memory Management/UsingExpiredStackAddress.ql: /Correctness/Common Errors
   # Use of Libraries
 + semmlecode-cpp-queries/Likely Bugs/Memory Management/SuspiciousCallToMemset.ql: /Correctness/Use of Libraries
 + semmlecode-cpp-queries/Likely Bugs/Memory Management/SuspiciousSizeof.ql: /Correctness/Use of Libraries

cpp/config/suites/cpp/correctness

@@ -34,6 +34,7 @@
 + semmlecode-cpp-queries/Critical/NewArrayDeleteMismatch.ql: /Correctness/Common Errors
 + semmlecode-cpp-queries/Critical/NewDeleteArrayMismatch.ql: /Correctness/Common Errors
 + semmlecode-cpp-queries/Critical/NewFreeMismatch.ql: /Correctness/Common Errors
++ semmlecode-cpp-queries/Likely Bugs/Memory Management/UsingExpiredStackAddress.ql: /Correctness/Common Errors
   # Exceptions
 + semmlecode-cpp-queries/Best Practices/Exceptions/AccidentalRethrow.ql: /Correctness/Exceptions
 + semmlecode-cpp-queries/Best Practices/Exceptions/CatchingByValue.ql: /Correctness/Exceptions

cpp/config/suites/security/cwe-120

@@ -5,9 +5,11 @@
   @name Badly bounded write (CWE-120)
 + semmlecode-cpp-queries/Security/CWE/CWE-120/OverrunWrite.ql: /CWE/CWE-120
   @name Potentially overrunning write (CWE-120)
++ semmlecode-cpp-queries/Security/CWE/CWE-120/VeryLikelyOverrunWrite.ql: /CWE/CWE-120
+  @name Likely overrunning write
 + semmlecode-cpp-queries/Security/CWE/CWE-120/OverrunWriteFloat.ql: /CWE/CWE-120
   @name Potentially overrunning write with float to string conversion (CWE-120)
 + semmlecode-cpp-queries/Best Practices/Likely Errors/OffsetUseBeforeRangeCheck.ql: /CWE/CWE-120
   @name Array offset used before range check (CWE-120)
 + semmlecode-cpp-queries/Likely Bugs/Memory Management/UnsafeUseOfStrcat.ql: /CWE/CWE-120
-    @name Potentially unsafe use of strcat (CWE-120)
+  @name Potentially unsafe use of strcat (CWE-120)

cpp/downgrades/2cd420191e5f782589b4e4efb70127de265390dd/upgrade.properties

@@ -0,0 +1,2 @@
+description: Remove unused legacy relations
+compatibility: backwards

cpp/downgrades/BUILD.bazel

@@ -0,0 +1,12 @@
+load("@rules_pkg//:mappings.bzl", "pkg_files", "strip_prefix")
+
+pkg_files(
+    name = "downgrades",
+    srcs = glob(
+        ["**"],
+        exclude = ["BUILD.bazel"],
+    ),
+    prefix = "cpp/downgrades",
+    strip_prefix = strip_prefix.from_pkg(),
+    visibility = ["//cpp:__pkg__"],
+)

cpp/downgrades/bb0f279f2acd793105a347d589b5afc8715d94c4/upgrade.properties

@@ -0,0 +1,3 @@
+description: Add relation for tracking variables from structured binding declarations
+compatibility: full
+is_structured_binding.rel: delete

cpp/downgrades/e9a518baf14f4322ac243578a8e1391386ff030f/upgrade.properties

@@ -0,0 +1,2 @@
+description: Remove uniqueness constraint from the uuid property
+compatibility: full

cpp/downgrades/qlpack.yml

@@ -0,0 +1,4 @@
+name: codeql/cpp-downgrades
+groups: cpp
+downgrades: .
+library: true