WM-2560: Update GDCWholeGenomeSomaticSingleSample to 1.3.1 #2773
Workflow file for this run
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| # This workflow triggers tests on PRs | |
| name: Tests on Pull Requests | |
| on: | |
| pull_request: | |
| paths: | |
| - api/** | |
| - database/** | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| services: | |
| postgres: | |
| image: postgres:11 | |
| # Provide the password for postgres | |
| env: | |
| POSTGRES_PASSWORD: postgres | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| # Maps tcp port 5432 on service container to the host | |
| - 5432:5432 | |
| env: | |
| MODULES: api functions/aou functions/sg | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Setup Java | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: '11' | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@e73bf2b6435244b2c9c5c226ae5022d91d0ce702 | |
| with: | |
| cli: '1.10.1.739' | |
| - name: Setup Python3 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.8' # Version range or exact version of a Python version to use, using SemVer's version range syntax | |
| # Get secret from vault | |
| - name: Authenticate to GCloud | |
| id: gcloud | |
| env: | |
| ROLE_ID: ${{ secrets.ROLE_ID }} | |
| SECRET_ID: ${{ secrets.SECRET_ID }} | |
| VAULT_ADDR: ${{ secrets.VAULT_ADDR }} | |
| run: | | |
| # get vault token using role-id and secret-id | |
| VAULT_TOKEN=$(curl \ | |
| --request POST \ | |
| --data "{\"role_id\":\"${ROLE_ID}\",\"secret_id\":\"${SECRET_ID}\"}" \ | |
| ${VAULT_ADDR}/v1/auth/approle/login | jq -r .auth.client_token) | |
| if [ -z "${VAULT_TOKEN}" ] ; then | |
| echo "Vault authentication failed!" | |
| exit 1 | |
| fi | |
| echo ::add-mask::${VAULT_TOKEN} | |
| echo "VAULT_TOKEN=${VAULT_TOKEN}" >> $GITHUB_ENV | |
| echo ${VAULT_TOKEN} > ~/.vault-token | |
| # use vault token to read secret - service account json | |
| curl --silent -H "X-Vault-Token: ${VAULT_TOKEN}" -X GET \ | |
| ${VAULT_ADDR}/v1/secret/dsde/gotc/dev/wfl/wfl-non-prod-service-account.json \ | |
| | jq .data > sa.json | |
| if [ ! -s sa.json ] ; then | |
| echo "Retrieval of Gcloud SA credentials failed" | |
| exit 1 | |
| fi | |
| # auth as service account | |
| gcloud auth activate-service-account --key-file=sa.json | |
| if [ $? -ne 0 ] ; then | |
| echo "Gcloud auth failed!" | |
| exit 1 | |
| fi | |
| # get bearer token and set it to a specific env var that | |
| # subsequent steps expect. bearer token good for 1 hour | |
| GOOGLE_OAUTH_ACCESS_TOKEN=$(gcloud auth print-access-token) | |
| if [ -z "${GOOGLE_OAUTH_ACCESS_TOKEN}" ] ; then | |
| echo "Generating Gcloud access token failed" | |
| exit 1 | |
| fi | |
| echo ::add-mask::${GOOGLE_OAUTH_ACCESS_TOKEN} | |
| echo "GOOGLE_OAUTH_ACCESS_TOKEN=${GOOGLE_OAUTH_ACCESS_TOKEN}" >> $GITHUB_ENV | |
| echo "GOOGLE_APPLICATION_CREDENTIALS=$(find `pwd` -maxdepth 1 -name sa.json)" >> $GITHUB_ENV | |
| - name: Fetch Dependency Cache | |
| uses: actions/cache@v2 | |
| with: | |
| key: ${{ runner.os }}-depedency-cache | |
| path: ~/.m2 | |
| - name: Pre-Build | |
| run: make ${MODULES} TARGET=prebuild | |
| - name: Lint | |
| run: make ${MODULES} TARGET=lint | |
| - name: Build | |
| run: make ${MODULES} TARGET=build | |
| - name: Unit Test | |
| run: make ${MODULES} TARGET=unit | |
| - name: Integration Test | |
| env: | |
| WFL_POSTGRES_USERNAME: postgres | |
| WFL_POSTGRES_PASSWORD: postgres | |
| # | |
| # Assign env variables from Atlantis-managed GitHub Secrets: | |
| # https://github.com/broadinstitute/terraform-ap-deployments/blob/master/github/tfvars/broadinstitute-wfl.tfvars | |
| # | |
| WFL_SLACK_TOKEN: ${{ secrets.WFL_SLACK_TOKEN }} | |
| run: make ${MODULES} TARGET=integration |