Upgrade JSON to Parquet large job worker type (#109) #21
Workflow file for this run
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| name: upload-and-deploy-to-prod-main | |
| on: | |
| push: | |
| tags: | |
| - "v[0-9]+.[0-9]+.[0-9]+" | |
| env: | |
| NAMESPACE: main | |
| PYTHON_VERSION: 3.9 | |
| jobs: | |
| pre-commit: | |
| name: Run pre-commit hooks against all files | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| - uses: pre-commit/[email protected] | |
| upload-files: | |
| name: Upload files to S3 bucket in prod/main | |
| runs-on: ubuntu-latest | |
| needs: pre-commit | |
| # These permissions are needed to interact with GitHub's OIDC Token endpoint. | |
| permissions: | |
| id-token: write | |
| contents: read | |
| environment: prod | |
| steps: | |
| - name: Setup code, pipenv, aws | |
| uses: Sage-Bionetworks/action-pipenv-aws-setup@v3 | |
| with: | |
| role_to_assume: ${{ vars.AWS_CREDENTIALS_IAM_ROLE }} | |
| role_session_name: GitHubActions-${{ github.repository_owner }}-${{ github.event.repository.name }}-${{ github.run_id }} | |
| python_version: ${{ env.PYTHON_VERSION }} | |
| - name: Copy files to templates bucket | |
| run: python src/scripts/manage_artifacts/artifacts.py --upload --namespace $NAMESPACE --cfn_bucket ${{ vars.CFN_BUCKET }} | |
| sceptre-deploy-main: | |
| name: Deploys to prod/main using sceptre | |
| runs-on: ubuntu-latest | |
| needs: [pre-commit, upload-files] | |
| environment: prod | |
| # These permissions are needed to interact with GitHub's OIDC Token endpoint. | |
| permissions: | |
| id-token: write | |
| contents: read | |
| steps: | |
| - name: Setup code, pipenv, aws | |
| uses: Sage-Bionetworks/action-pipenv-aws-setup@v3 | |
| with: | |
| role_to_assume: ${{ vars.AWS_CREDENTIALS_IAM_ROLE }} | |
| role_session_name: GitHubActions-${{ github.repository_owner }}-${{ github.event.repository.name }}-${{ github.run_id }} | |
| python_version: ${{ env.PYTHON_VERSION }} | |
| - name: Create directory for remote sceptre templates | |
| run: mkdir -p templates/remote/ | |
| - name: Deploy sceptre stacks to prod/main | |
| run: pipenv run sceptre --var "namespace=${{ env.NAMESPACE }}" launch prod --yes | |
| - name: Delete preexisting S3 event notification for this namespace | |
| uses: gagoar/invoke-aws-lambda@v3 | |
| with: | |
| AWS_ACCESS_KEY_ID: ${{ env.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ env.AWS_SECRET_ACCESS_KEY }} | |
| AWS_SESSION_TOKEN: ${{ env.AWS_SESSION_TOKEN }} | |
| REGION: ${{ env.AWS_REGION }} | |
| FunctionName: ${{ env.NAMESPACE }}-S3EventConfig | |
| Payload: '{"RequestType": "Delete"}' | |
| LogType: Tail | |
| - name: Create S3 event notification for this namespace | |
| uses: gagoar/invoke-aws-lambda@v3 | |
| with: | |
| AWS_ACCESS_KEY_ID: ${{ env.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ env.AWS_SECRET_ACCESS_KEY }} | |
| AWS_SESSION_TOKEN: ${{ env.AWS_SESSION_TOKEN }} | |
| REGION: ${{ env.AWS_REGION }} | |
| FunctionName: ${{ env.NAMESPACE }}-S3EventConfig | |
| Payload: '{"RequestType": "Create"}' | |
| LogType: Tail | |
| sts-access-test: | |
| name: Runs STS access tests on prod synapse folders | |
| runs-on: ubuntu-latest | |
| needs: sceptre-deploy-main | |
| environment: prod | |
| # These permissions are needed to interact with GitHub's OIDC Token endpoint. | |
| permissions: | |
| id-token: write | |
| contents: read | |
| steps: | |
| - name: Setup code, pipenv, aws | |
| uses: Sage-Bionetworks/action-pipenv-aws-setup@v3 | |
| with: | |
| role_to_assume: ${{ vars.AWS_CREDENTIALS_IAM_ROLE }} | |
| role_session_name: ${{ github.event.repository.name }}-${{ github.run_id }}-nonglue-unit-tests | |
| python_version: ${{ env.PYTHON_VERSION }} | |
| - name: Test prod synapse folders for STS access with pytest | |
| run: > | |
| pipenv run python -m pytest tests/test_setup_external_storage.py | |
| --test-bucket recover-input-data | |
| --test-synapse-folder-id syn51714264 | |
| --namespace $NAMESPACE | |
| --test-sts-permission read_only | |
| -v | |
| pipenv run python -m pytest tests/test_setup_external_storage.py | |
| --test-bucket recover-processed-data | |
| --test-synapse-folder-id syn51406699 | |
| --namespace $NAMESPACE/parquet | |
| --test-sts-permission read_write | |
| -v |