MarkDuplicates flow options now start with FLOW_ #217
Workflow file for this run
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name: Cloud Tests | |
on: | |
push: | |
branches: | |
- 'master' | |
pull_request: | |
workflow_dispatch: | |
env: | |
PICARD_TEST_INPUTS: gs://hellbender/test/resources/ | |
PICARD_TEST_STAGING: gs://hellbender-test-logs/staging/ | |
PICARD_TEST_LOGS: /hellbender-test-logs/build_reports/ | |
PICARD_TEST_PROJECT: broad-dsde-dev | |
jobs: | |
## This workaround is necessary since there is no equivalent to the old TRAVIS_SECURE_ENVIRONMENT variable that indicated | |
## if a run was privileged and had secrets. Since the GCP credentials are necessary for all tests in order to upload their, | |
## results that makes them a reasonable proxy for testing the credentials of this entire execution. https://github.com/actions/runner/issues/520 | |
check-secrets: | |
name: check if the environment has privileges | |
outputs: | |
google-credentials: ${{ steps.google-credentials.outputs.defined }} | |
runs-on: ubuntu-latest | |
steps: | |
- id: google-credentials | |
env: | |
GCP_CREDENTIALS: ${{ secrets.GCP_CREDENTIALS }} | |
if: "${{ env.GCP_CREDENTIALS != '' }}" | |
run: echo defined=true >> $GITHUB_OUTPUT | |
test: | |
runs-on: ubuntu-latest | |
needs: check-secrets | |
strategy: | |
matrix: | |
java: [ 17 ] | |
run_barclay_tests: [true, false] | |
experimental: [ false ] | |
fail-fast: false | |
continue-on-error: ${{ matrix.experimental }} | |
name: Java ${{ matrix.Java }}, Barclay=${{ matrix.run_barclay_tests}} cloud tests | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: 'Set up java ${{ matrix.Java }}' | |
uses: actions/setup-java@v3 | |
with: | |
java-version: ${{ matrix.Java }} | |
distribution: 'temurin' | |
cache: gradle | |
- name: 'Compile with Gradle' | |
run: | | |
./gradlew compileJava | |
./gradlew installDist | |
#Google Cloud stuff | |
- id: 'gcloud-auth' | |
if: needs.check-secrets.outputs.google-credentials == 'true' | |
uses: google-github-actions/auth@v0 | |
with: | |
credentials_json: ${{ secrets.GCP_CREDENTIALS }} | |
project_id: ${{ env.PICARD_TEST_PROJECT }} | |
create_credentials_file: true | |
- name: 'Set up Cloud SDK' | |
if: needs.check-secrets.outputs.google-credentials == 'true' | |
uses: google-github-actions/setup-gcloud@v2 | |
- name: compile test code | |
if: needs.check-secrets.outputs.google-credentials == 'true' | |
run: ./gradlew compileTestJava | |
- name: Run tests | |
if: needs.check-secrets.outputs.google-credentials == 'true' | |
env: | |
TEST_TYPE: cloud | |
run: | | |
if [[ ${{matrix.run_barclay_tests}} == true ]]; then | |
echo "Running tests using the Barclay command line parser." | |
./gradlew barclayTest | |
else | |
echo "Running tests using the legacy Picard command line parser." | |
./gradlew jacocoTestReport | |
fi | |
- name: Upload test results | |
if: always() | |
uses: actions/upload-artifact@v3 | |
with: | |
name: cloud-test-results-${{ matrix.Java }}-barclay-${{ matrix.run_barclay_tests}} | |
path: build/reports/tests |