upgrade to v2 of ecr login action #834
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_RAW_BUCKET: recover-dev-raw-data | ||
DEV_INTERMEDIATE_BUCKET: recover-dev-intermediate-data | ||
DEV_PROCESSED_BUCKET: recover-dev-processed-data | ||
PROD_INPUT_BUCKET: recover-input-data | ||
PROD_RAW_BUCKET: recover-raw-data | ||
PROD_INTERMEDIATE_BUCKET: recover-intermediate-data | ||
INTEGRATION_TEST_NUM_EXPORTS: 28 | ||
ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true | ||
jobs: | ||
pre-commit: | ||
name: Run pre-commit hooks against all files | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v3 | ||
- uses: actions/setup-python@v5 | ||
with: | ||
python-version: ${{ env.PYTHON_VERSION }} | ||
- uses: pre-commit/[email protected] | ||
deploy-snowflake: | ||
name: Deploy Snowflake resources | ||
needs: pre-commit | ||
runs-on: ubuntu-latest | ||
env: | ||
PRIVATE_KEY_PASSPHRASE: ${{ secrets.SNOWFLAKE_PRIVATE_KEY_PASSPHRASE }} | ||
SNOWFLAKE_ENVIRONMENT: ${{ github.ref_name == 'main' && 'staging' || github.ref_name }} | ||
steps: | ||
- uses: actions/checkout@v3 | ||
- name: Configure Snowflake connection | ||
run: | | ||
# Create temporary files for config.toml and our private key | ||
config_file=$(mktemp) | ||
private_key_file=$(mktemp) | ||
# Write to the private key file | ||
echo "${{ secrets.SNOWFLAKE_PRIVATE_KEY }}" > $private_key_file | ||
# Write to config.toml file | ||
echo 'default_connection_name = "recover"' >> $config_file | ||
echo '[connections.recover]' >> $config_file | ||
echo "account = \"${{ vars.SNOWFLAKE_ACCOUNT }}\"" >> $config_file | ||
echo "user = \"${{ vars.SNOWFLAKE_USER }}\"" >> $config_file | ||
echo "role = \"${{ vars.SNOWFLAKE_ROLE }}\"" >> $config_file | ||
echo 'warehouse = "RECOVER_XSMALL"' >> $config_file | ||
echo 'authenticator = "SNOWFLAKE_JWT"' >> $config_file | ||
echo "private_key_path = \"$private_key_file\"" >> $config_file | ||
# Write config.toml path to global environment | ||
echo "SNOWFLAKE_CONFIG_PATH=$config_file" >> $GITHUB_ENV | ||
- name: Configuration file information | ||
run: | | ||
echo "Snowflake configuration is located at $SNOWFLAKE_CONFIG_PATH" | ||
cat $SNOWFLAKE_CONFIG_PATH | ||
- name: Install Snowflake CLI | ||
uses: Snowflake-Labs/[email protected] | ||
with: | ||
default-config-file-path: ${{ env.SNOWFLAKE_CONFIG_PATH }} | ||
- name: Test Snowflake connection | ||
run: | | ||
snow --version | ||
snow connection test | ||
- name: Deploy Snowflake objects | ||
run: | | ||
snow sql \ | ||
-D "git_branch=$GITHUB_REF_NAME" \ | ||
-D "environment=$SNOWFLAKE_ENVIRONMENT" \ | ||
-f snowflake/objects/deploy.sql | ||
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 }} | ||
--shareable-artifacts-bucket ${{ vars.SHAREABLE_ARTIFACTS_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 | ||
pipenv install pytest-datadir | ||
- name: Test scripts with pytest (lambda, etc.) | ||
run: | | ||
pipenv run python -m pytest -v \ | ||
tests/test_s3_event_config_lambda.py \ | ||
tests/test_s3_to_glue_lambda.py \ | ||
tests/test_lambda_dispatch.py \ | ||
tests/test_consume_logs.py \ | ||
tests/test_lambda_raw.py \ | ||
tests/test_lambda_raw_sync.py | ||
- 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@v2 | ||
with: | ||
mask-password: 'false' | ||
- 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['docker_username_' + steps.login-ecr.outputs.registry] }} | ||
Check failure on line 215 in .github/workflows/upload-and-deploy.yaml GitHub Actions / upload-and-deployInvalid workflow file
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||
ecr-password: ${{ steps.login-ecr.outputs['docker_password_' + steps.login-ecr.outputs.registry] }} | ||
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 Glue 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 \ | ||
tests/test_compare_parquet_datasets.py -v" | ||
- name: Run unit tests for JSON to Parquet under AWS Glue 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" | ||
- name: Run unit tests for Great Expectations on Parquet under AWS Glue 4.0 | ||
if: matrix.tag_name == 'aws_glue_4' | ||
run: > | ||
su - glue_user --command "cd $GITHUB_WORKSPACE && | ||
python3 -m pytest tests/test_run_great_expectations_on_parquet.py -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" >> $GITHUB_ENV | ||
- name: "Deploy sceptre stacks to dev" | ||
run: pipenv run sceptre --debug --var "namespace=${{ 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-cleanup: | ||
name: Cleanup non-main branch data before integration tests | ||
runs-on: ubuntu-latest | ||
needs: sceptre-deploy-develop | ||
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: ${{ env.PYTHON_VERSION }} | ||
- name: Set namespace for non-default branch | ||
if: github.ref_name != 'main' | ||
run: echo "NAMESPACE=$GITHUB_REF_NAME" >> $GITHUB_ENV | ||
- name: Clean input data bucket | ||
run: > | ||
pipenv run python src/scripts/manage_artifacts/clean_for_integration_test.py | ||
--bucket $DEV_INPUT_BUCKET | ||
--bucket_prefix "${{ env.NAMESPACE }}/" | ||
- name: Clean raw data bucket | ||
run: > | ||
pipenv run python src/scripts/manage_artifacts/clean_for_integration_test.py | ||
--bucket $DEV_RAW_BUCKET | ||
--bucket_prefix "${{ env.NAMESPACE }}/json/" | ||
- name: Clean intermediate data bucket | ||
run: > | ||
pipenv run python src/scripts/manage_artifacts/clean_for_integration_test.py | ||
--bucket $DEV_INTERMEDIATE_BUCKET | ||
--bucket_prefix "${{ env.NAMESPACE }}/json/" | ||
integration-test-develop: | ||
name: Triggers ETL workflow with S3 test files | ||
runs-on: ubuntu-latest | ||
needs: [sceptre-deploy-develop, integration-test-develop-cleanup] | ||
environment: develop | ||
# These permissions are needed to interact with GitHub's OIDC Token endpoint. | ||
permissions: | ||
id-token: write | ||
contents: read | ||
env: | ||
EXPORT_S3_KEY_PREFIX: pilot-data | ||
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" >> $GITHUB_ENV | ||
- name: Fetch the most recent exports. | ||
id: recent-exports | ||
run: | | ||
# Retrieve the last ~2 weeks of exports from each cohort | ||
# Ignore keys which end with "/" and which match "owner.txt" | ||
echo "KEYS=$( | ||
aws s3api list-objects-v2 \ | ||
--bucket $DEV_INPUT_BUCKET \ | ||
--prefix $EXPORT_S3_KEY_PREFIX \ | ||
--query '((sort_by(Contents[? !ends_with(Key, `/`) && !contains(Key, `owner.txt`)], &LastModified)[::-1])[:${{ env.INTEGRATION_TEST_NUM_EXPORTS }}])[*].Key' | | ||
jq -c | ||
)" >> "$GITHUB_OUTPUT" | ||
- name: Copy most recent exports to this namespace | ||
run: > | ||
echo '${{ 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/${key#"$EXPORT_S3_KEY_PREFIX"/}"; | ||
done | ||
- name: Write most recent exports to S3 cloudformation bucket | ||
run: > | ||
echo '${{ steps.recent-exports.outputs.KEYS }}' | | ||
jq --arg bucket "s3://$DEV_INPUT_BUCKET/" '.[] |= $bucket + .' | | ||
aws s3 cp - "s3://${{ vars.CFN_BUCKET }}/$NAMESPACE/integration_test_exports.json" | ||
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 }} | ||
--shareable-artifacts-bucket ${{ vars.SHAREABLE_ARTIFACTS_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-cleanup: | ||
name: Cleanup main branch staging data before integration tests | ||
runs-on: ubuntu-latest | ||
needs: sceptre-deploy-staging | ||
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: Clean input data bucket | ||
run: > | ||
pipenv run python src/scripts/manage_artifacts/clean_for_integration_test.py | ||
--bucket $PROD_INPUT_BUCKET | ||
--bucket_prefix "staging/" | ||
- name: Clean raw data bucket | ||
run: > | ||
pipenv run python src/scripts/manage_artifacts/clean_for_integration_test.py | ||
--bucket $PROD_RAW_BUCKET | ||
--bucket_prefix "staging/json/" | ||
- name: Clean intermediate data bucket | ||
run: > | ||
pipenv run python src/scripts/manage_artifacts/clean_for_integration_test.py | ||
--bucket $PROD_INTERMEDIATE_BUCKET | ||
--bucket_prefix "staging/json/" | ||
integration-test-staging: | ||
name: Triggers staging workflow with production data | ||
runs-on: ubuntu-latest | ||
needs: [sceptre-deploy-staging, integration-test-staging-cleanup] | ||
environment: prod | ||
# These permissions are needed to interact with GitHub's OIDC Token endpoint. | ||
permissions: | ||
id-token: write | ||
contents: read | ||
env: | ||
EXPORT_S3_KEY_PREFIX: main | ||
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: ${{ env.PYTHON_VERSION }} | ||
- name: Fetch the most recent exports. | ||
id: recent-exports | ||
run: | | ||
# Retrieve the last ~2 weeks of exports from each cohort | ||
# Ignore keys which end with "/" and which match "owner.txt" | ||
echo "KEYS=$( | ||
aws s3api list-objects-v2 \ | ||
--bucket $PROD_INPUT_BUCKET \ | ||
--prefix "$EXPORT_S3_KEY_PREFIX/" \ | ||
--query '((sort_by(Contents[? !ends_with(Key, `/`) && !contains(Key, `owner.txt`)], &LastModified)[::-1])[:${{ env.INTEGRATION_TEST_NUM_EXPORTS }}])[*].Key' | | ||
jq -c | ||
)" >> "$GITHUB_OUTPUT" | ||
- name: Copy most recent exports to this namespace | ||
run: > | ||
echo '${{ steps.recent-exports.outputs.KEYS }}' | jq -r '.[]' | while read -r key; do | ||
aws s3 cp "s3://$PROD_INPUT_BUCKET/$key" "s3://$PROD_INPUT_BUCKET/staging/${key#"$EXPORT_S3_KEY_PREFIX"/}"; | ||
done | ||
- name: Write most recent exports to S3 cloudformation bucket | ||
run: > | ||
echo '${{ steps.recent-exports.outputs.KEYS }}' | | ||
jq --arg bucket "s3://$PROD_INPUT_BUCKET/" '.[] |= $bucket + .' | | ||
aws s3 cp - "s3://${{ vars.CFN_BUCKET }}/staging/integration_test_exports.json" |