IT-8483 Remove codeql.yml workflows from affected repos #409
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| name: WDL Integration Tests v2 | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - develop | |
| pull_request: | |
| branches: | |
| - main | |
| - develop | |
| types: | |
| - opened | |
| - synchronize | |
| - ready_for_review | |
| - labeled | |
| workflow_dispatch: | |
| permissions: | |
| contents: read | |
| actions: write | |
| packages: read | |
| jobs: | |
| test: | |
| name: WDL Integration Tests (Staging) v2 | |
| if: contains(github.event.pull_request.labels.*.name, 'integration2') | |
| runs-on: ubuntu-24.04 | |
| env: | |
| PROJECT: dxCompiler_playground | |
| steps: | |
| - name: Git checkout | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| # performance optimizations https://abbbi.github.io/actions/ | |
| - uses: abbbi/github-actions-tune@81fb919e588c20b7ab52b2cac097d2efd765c714 # v1 | |
| - name: Install java | |
| uses: actions/setup-java@d202f5dbf7256730fb690ec59f6381650114feb2 # v1.4.3 | |
| with: | |
| java-version: 11 | |
| - name: Install SBT | |
| run: | | |
| sudo apt-get update | |
| echo "deb https://repo.scala-sbt.org/scalasbt/debian all main" | sudo tee /etc/apt/sources.list.d/sbt.list | |
| curl -sL "https://keyserver.ubuntu.com/pks/lookup?op=get&search=0x99E82A75642AC823" | sudo apt-key add | |
| sudo apt-get update | |
| sudo apt-get install -y sbt | |
| - name: Install Poetry | |
| uses: snok/install-poetry@76e04a911780d5b312d89783f7b1cd627778900a # v1.4.1 | |
| with: | |
| version: 1.4.2 | |
| virtualenvs-create: true | |
| - name: Install dxpy and other dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y apt-transport-https wget git openssh-server tree python3 python3-pip python3-venv | |
| cwltool=`jq -r '.execDepends.cwl[0].name' scripts/bundled_dependencies.json` | |
| pip3 install --upgrade pip setuptools==76.0.0 | |
| pip3 install termcolor dxpy==0.393.0 $cwltool pyOpenSSL==25.0.0 | |
| # install dxda | |
| dxda_version=`jq -r '.dxda' scripts/bundled_dependencies.json` | |
| sudo wget -O/usr/local/bin/dx-download-agent https://github.com/dnanexus/dxda/releases/download/${dxda_version}/dx-download-agent-linux | |
| sudo chmod +x /usr/local/bin/dx-download-agent | |
| - name: Install dxcint | |
| run: | | |
| cd dxcint | |
| poetry install | |
| cd .. | |
| - name: Set-up | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| ROBOT_TOKEN: ${{ secrets.DX_STAGING_ROBOT_TOKEN }} | |
| TEST_ROBOT_TOKEN: ${{ secrets.DX_STAGING_TEST_ROBOT_TOKEN }} | |
| run: | | |
| export PATH="$PATH:$HOME/.local/bin" | |
| # Set up DNAnexus staging environment | |
| dx login --noprojects --staging --token $ROBOT_TOKEN | |
| dx select $PROJECT | |
| cd ${GITHUB_WORKSPACE} | |
| - name: Run medium integration test suite with dxcint | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| ROBOT_TOKEN: ${{ secrets.DX_STAGING_ROBOT_TOKEN }} | |
| run: | | |
| cd dxcint | |
| poetry run dxcint integration -t 'M' ../ --clean | |
| - name: Run multi-user tests | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| ROBOT_TOKEN: ${{ secrets.DX_STAGING_ROBOT_TOKEN }} | |
| TEST_ROBOT_TOKEN: ${{ secrets.DX_STAGING_TEST_ROBOT_TOKEN }} | |
| run: | | |
| FOLDER=/builds/test_gha_dxcompiler_$(date +%s)_$RANDOM | |
| dx mkdir -p $FOLDER | |
| python3 scripts/run_multiuser_tests.py --folder $FOLDER --project $PROJECT \ | |
| --alice-token $ROBOT_TOKEN \ | |
| --bob-token $TEST_ROBOT_TOKEN | |