Only submit most recent ~2 weeks of exports for integration tests #539
Workflow file for this run
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| name: upload-and-deploy | ||
| on: | ||
| push: | ||
| branches: "*" | ||
| tags-ignore: "*" | ||
| env: | ||
| NAMESPACE: main | ||
| PYTHON_VERSION: 3.9 | ||
| DEV_INPUT_BUCKET: recover-dev-input-data | ||
| DEV_PROCESSED_BUCKET: recover-dev-processed-data | ||
| PROD_INPUT_BUCKET: recover-input-data | ||
| 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/action@v3.0.0 | ||
| #upload-files: | ||
| # name: Upload files to S3 bucket in development | ||
| # 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: develop | ||
| # 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: ${{ env.PYTHON_VERSION }} | ||
| # - name: Setup sam | ||
| # uses: aws-actions/setup-sam@v2 | ||
| # - name: Set namespace for non-default branch | ||
| # if: github.ref_name != 'main' | ||
| # run: echo "NAMESPACE=$GITHUB_REF_NAME" >> $GITHUB_ENV | ||
| # - name: Copy files to templates bucket, use dev cloudformation bucket | ||
| # run: > | ||
| # python src/scripts/manage_artifacts/artifacts.py | ||
| # --upload | ||
| # --namespace $NAMESPACE | ||
| # --cfn_bucket ${{ vars.CFN_BUCKET }} | ||
| #nonglue-unit-tests: | ||
| # name: Runs unit tests that are not dependent on aws-glue package resources | ||
| # 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: develop | ||
| # 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: Install additional python dependency | ||
| # run: | | ||
| # pipenv install ecs_logging~=2.0 | ||
| # - name: Test lambda scripts with pytest | ||
| # run: | | ||
| # pipenv run python -m pytest tests/test_s3_event_config_lambda.py -v | ||
| # pipenv run python -m pytest tests/test_s3_to_glue_lambda.py -v | ||
| # - name: Test dev synapse folders for STS access with pytest | ||
| # run: > | ||
| # pipenv run python -m pytest tests/test_setup_external_storage.py | ||
| # --test-bucket $DEV_INPUT_BUCKET | ||
| # --test-synapse-folder-id syn51758510 | ||
| # --namespace $NAMESPACE | ||
| # --test-sts-permission read_only | ||
| # -v | ||
| # pipenv run python -m pytest tests/test_setup_external_storage.py | ||
| # --test-bucket $DEV_PROCESSED_BUCKET | ||
| # --test-synapse-folder-id syn51084525 | ||
| # --namespace $NAMESPACE/parquet | ||
| # --test-sts-permission read_write | ||
| # -v | ||
| #pytest-docker: | ||
| # name: Build and push testing docker images to the pytest ECR repository. | ||
| # needs: pre-commit | ||
| # runs-on: ubuntu-latest | ||
| # # These permissions are needed to interact with GitHub's OIDC Token endpoint. | ||
| # permissions: | ||
| # id-token: write | ||
| # contents: read | ||
| # strategy: | ||
| # matrix: | ||
| # include: | ||
| # - tag_name: aws_glue_3 | ||
| # dockerfile: tests/Dockerfile.aws_glue_3 | ||
| # - tag_name: aws_glue_4 | ||
| # dockerfile: tests/Dockerfile.aws_glue_4 | ||
| # environment: develop | ||
| # steps: | ||
| # - name: Assume AWS role | ||
| # uses: aws-actions/configure-aws-credentials@v2 | ||
| # with: | ||
| # role-to-assume: ${{ vars.AWS_CREDENTIALS_IAM_ROLE }} | ||
| # aws-region: "us-east-1" | ||
| # # unmasking of the AWS account ID allows the acct id to pass through outputs | ||
| # mask-aws-account-id: "no" | ||
| # - name: Login to Amazon ECR | ||
| # id: login-ecr | ||
| # uses: aws-actions/amazon-ecr-login@v1 | ||
| # - name: Get ECR secret names | ||
| # id: ecr | ||
| # run: | | ||
| # usernameKey=docker_username_$(echo ${{ steps.login-ecr.outputs.registry }} | tr '.-' _) | ||
| # echo "username-key=$usernameKey" >> $GITHUB_OUTPUT | ||
| # passwordKey=docker_password_$(echo ${{ steps.login-ecr.outputs.registry }} | tr '.-' _) | ||
| # echo "password-key=$passwordKey" >> $GITHUB_OUTPUT | ||
| # - uses: actions/checkout@v3 | ||
| # - name: Set up Docker Buildx | ||
| # uses: docker/setup-buildx-action@v2 | ||
| # - name: Build and push to ECR | ||
| # id: docker-build-push | ||
| # uses: docker/build-push-action@v4 | ||
| # with: | ||
| # push: true | ||
| # tags: ${{ steps.login-ecr.outputs.registry }}/pytest:${{ github.ref_name }}_${{ matrix.tag_name }} | ||
| # file: ${{ matrix.dockerfile }} | ||
| # cache-from: type=local,src=/tmp/.buildx-cache | ||
| # cache-to: type=local,dest=/tmp/.buildx-cache | ||
| # outputs: | ||
| # ecr-registry: ${{ steps.login-ecr.outputs.registry }} | ||
| # ecr-username: ${{ steps.login-ecr.outputs[steps.ecr.outputs.username-key] }} | ||
| # ecr-password: ${{ steps.login-ecr.outputs[steps.ecr.outputs.password-key] }} | ||
| #glue-unit-tests: | ||
| # name: Run Pytest unit tests for AWS glue | ||
| # needs: pytest-docker | ||
| # environment: develop | ||
| # runs-on: ubuntu-latest | ||
| # # These permissions are needed to interact with GitHub's OIDC Token endpoint. | ||
| # permissions: | ||
| # id-token: write | ||
| # contents: read | ||
| # strategy: | ||
| # matrix: | ||
| # tag_name: | ||
| # ["aws_glue_3", "aws_glue_4"] | ||
| # container: | ||
| # image: ${{ needs.pytest-docker.outputs.ecr-registry }}/pytest:${{ github.ref_name }}_${{ matrix.tag_name }} | ||
| # credentials: | ||
| # username: ${{ needs.pytest-docker.outputs.ecr-username }} | ||
| # password: ${{ needs.pytest-docker.outputs.ecr-password }} | ||
| # env: | ||
| # DISABLE_SSL: true | ||
| # options: "--user root" | ||
| # steps: | ||
| # - name: Assume AWS role | ||
| # uses: aws-actions/configure-aws-credentials@v2 | ||
| # with: | ||
| # role-to-assume: ${{ vars.AWS_CREDENTIALS_IAM_ROLE }} | ||
| # aws-region: "us-east-1" | ||
| # - uses: actions/checkout@v3 | ||
| # - run: chown -R glue_user $GITHUB_WORKSPACE | ||
| # - run: su - glue_user --command "aws configure set aws_access_key_id $AWS_ACCESS_KEY_ID" | ||
| # - run: su - glue_user --command "aws configure set aws_secret_access_key $AWS_SECRET_ACCESS_KEY" | ||
| # - run: su - glue_user --command "aws configure set aws_session_token $AWS_SESSION_TOKEN" | ||
| # - run: su - glue_user --command "aws configure set region $AWS_REGION" | ||
| # - name: Set namespace for non-default branch or for tag | ||
| # if: github.ref_name != 'main' | ||
| # run: echo "NAMESPACE=$GITHUB_REF_NAME" >> $GITHUB_ENV | ||
| # - name: Run Pytest unit tests under AWS 3.0 | ||
| # if: matrix.tag_name == 'aws_glue_3' | ||
| # run: | | ||
| # su - glue_user --command "cd $GITHUB_WORKSPACE && python3 -m pytest tests/test_s3_to_json.py -v" | ||
| # su - glue_user --command "cd $GITHUB_WORKSPACE && python3 -m pytest tests/test_compare_parquet_datasets.py -v" | ||
| # - name: Run Pytest unit tests under AWS 4.0 | ||
| # if: matrix.tag_name == 'aws_glue_4' | ||
| # run: > | ||
| # su - glue_user --command "cd $GITHUB_WORKSPACE && | ||
| # python3 -m pytest tests/test_json_to_parquet.py --namespace $NAMESPACE -v" | ||
| #sceptre-deploy-develop: | ||
| # name: Deploys branch using sceptre | ||
| # runs-on: ubuntu-latest | ||
| # needs: [upload-files, nonglue-unit-tests, glue-unit-tests] | ||
| # environment: develop | ||
| # # 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: ${{ env.PYTHON_VERSION }} | ||
| # - name: Create directory for remote sceptre templates | ||
| # run: mkdir -p templates/remote/ | ||
| # - name: Set namespace for non-default branch | ||
| # if: github.ref_name != 'main' | ||
| # run: echo "NAMESPACE=$GITHUB_REF_NAME" >> $GITHUB_ENV | ||
| # - name: "Deploy sceptre stacks to dev" | ||
| # run: pipenv run sceptre --var "namespace=${{ env.NAMESPACE }}" launch develop --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 | ||
| integration-test-develop: | ||
| name: Triggers ETL workflow with S3 test files | ||
| runs-on: ubuntu-latest | ||
| needs: sceptre-deploy-develop | ||
|
Check failure on line 262 in .github/workflows/upload-and-deploy.yaml
|
||
| environment: develop | ||
| # 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: ${{ vars.AWS_CREDENTIALS_IAM_ROLE }} | ||
| role_session_name: integration-test-${{ github.run_id }} | ||
| python_version: ${{ env.PYTHON_VERSION }} | ||
| - name: Set namespace for non-default branch or for tag | ||
| if: github.ref_name != 'main' | ||
| run: echo "NAMESPACE=$GITHUB_REF_NAME" >> $GITHUB_ENV | ||
| - name: Fetch the most recent exports. | ||
| id: recent-exports | ||
| run: | | ||
| # Retrieve the last ~2 weeks of exports from each cohort | ||
| # Ignore files which end with "/" | ||
| echo "KEYS=$( | ||
| aws s3api list-objects-v2 \ | ||
| --bucket $DEV_INPUT_BUCKET \ | ||
| --prefix 'pilot-data/' \ | ||
| --query '((sort_by(Contents[? !ends_with(Key, `/`) && !contains(Key, `owner.txt`))], &LastModified)[::-1])[:28])[*].Key' | ||
| )" >> "$GITHUB_OUTPUT" | ||
| - name: Copies over test files from ingestion bucket | ||
| run: > | ||
| echo ${{ steps.recent-exports.outputs.KEYS }} | jq -r '.[]' | while read -r key; do | ||
| aws s3 cp "s3://$DEV_INPUT_BUCKET/$key" "s3://$DEV_INPUT_BUCKET/$NAMESPACE/$key" | ||
| done | ||
| sceptre-deploy-staging: | ||
| name: Deploys to staging of prod using sceptre | ||
| runs-on: ubuntu-latest | ||
| needs: integration-test-develop | ||
| if: github.ref_name == '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: ${{ vars.AWS_CREDENTIALS_IAM_ROLE }} | ||
| role_session_name: GitHubActions-${{ 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 staging | ||
| --cfn_bucket ${{ vars.CFN_BUCKET }} | ||
| - name: Create directory for remote sceptre templates | ||
| run: mkdir -p templates/remote/ | ||
| - name: Deploy sceptre stacks to staging on prod | ||
| run: pipenv run sceptre --var "namespace=staging" launch prod --yes | ||
| integration-test-staging: | ||
| name: Triggers staging workflow with production data | ||
| runs-on: ubuntu-latest | ||
| needs: sceptre-deploy-staging | ||
| 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: ${{ vars.AWS_CREDENTIALS_IAM_ROLE }} | ||
| role_session_name: integration-test-${{ github.run_id }} | ||
| python_version: ${{ env.PYTHON_VERSION }} | ||
| - name: generate test events | ||
| run: > | ||
| pipenv run python src/lambda_function/s3_to_glue/events/generate_test_event.py | ||
| --input-bucket $PROD_INPUT_BUCKET | ||
| --input-key-prefix $NAMESPACE | ||
| --output-directory ./src/lambda_function/s3_to_glue/events/ | ||
| - name: Setup sam | ||
| uses: aws-actions/setup-sam@v2 | ||
| - name: sam build lambda | ||
| run: > | ||
| sam build | ||
| -t src/lambda_function/s3_to_glue/template.yaml | ||
| - name: Invoke Lambda | ||
| run: | | ||
| cd src/lambda_function/s3_to_glue/ | ||
| sam local invoke -e events/records.json --parameter-overrides "S3ToJsonWorkflowName=staging-S3ToJsonWorkflow" | ||
