build(deps-dev): bump jinja2 from 3.1.4 to 3.1.5 #699
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: push | |
| jobs: | |
| # first, build the image | |
| build: | |
| name: Build and push image | |
| uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master | |
| secrets: | |
| ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} | |
| ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} | |
| QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} | |
| QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} | |
| # then run the tests | |
| test: | |
| name: Run tests | |
| runs-on: ubuntu-20.04 | |
| needs: build | |
| services: | |
| postgres: | |
| image: postgres:13 | |
| # Provide the password for postgres | |
| env: | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: metadata_db | |
| # 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 | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - name: Installing dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install --yes --no-install-recommends jq postgresql-client python3.9 python3-pip | |
| sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.9 1 | |
| sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.9 1 | |
| - name: Install poetry, python dependencies and tube | |
| run: | | |
| python3.9 -m pip install --upgrade pip poetry requests | |
| python3.9 -m poetry config virtualenvs.create true | |
| python3.9 -m poetry install -vv --no-interaction --with dev | |
| - name: Make dir cor compose-etl | |
| working-directory: .. | |
| run: git clone https://github.com/uc-cdis/compose-etl.git --branch master --single-branch | |
| - name: List all files and current directory | |
| run: | | |
| ls ../.. | |
| ls .. | |
| pwd | |
| - name: Copy configuration files | |
| run: | | |
| cp -f tests/integrated_tests/gen3/tube/etlMapping.yaml ../compose-etl/configs/etlMapping.yaml | |
| cp -f tests/integrated_tests/gen3/tube/user.yaml ../compose-etl/configs/user.yaml | |
| - name: Make XDG_DATA_HOME's tube | |
| run: mkdir -p $XDG_DATA_HOME/gen3/tube | |
| env: | |
| XDG_DATA_HOME: /home/runner/work/tube | |
| - name: Copy file to the XDG_DATA_HOME folder | |
| run: cp tests/integrated_tests/gen3/tube/{creds.json,etlMapping.yaml,user.yaml} $XDG_DATA_HOME/gen3/tube/ | |
| env: | |
| XDG_DATA_HOME: /home/runner/work/tube | |
| - name: Run standalone tests | |
| env: | |
| ES_URL: localhost | |
| POSTGRES_PORT: 5432 | |
| XDG_DATA_HOME: /home/runner/work/tube | |
| # Run the tests that do not require Spark and ElasticSearch | |
| run: python3.9 -m poetry run pytest -v tests/standalone_tests --cov=tube --cov-report term-missing --cov-report xml | |
| - name: Init postgres database | |
| run: psql -d postgresql://postgres:postgres@localhost/metadata_db -f tests/integrated_tests/metadata_db.sql | |
| - name: Create credential file | |
| working-directory: ../compose-etl | |
| run: echo "{\"db_host\":\"host.docker.internal\",\"db_username\":\"postgres\",\"db_password\":\"postgres\",\"db_database\":\"metadata_db\"}" > configs/creds.json | |
| - name: Replace tube branch | |
| working-directory: ../compose-etl | |
| run: | | |
| BRANCH=${{ github.head_ref || github.ref_name }} | |
| BRANCH=$(echo $BRANCH | tr / _) | |
| sed -i "s/tube:master/tube:$BRANCH/g" docker-compose.yml | |
| - name: change max_map_count (needed for running Elasticsearch in container) | |
| working-directory: ../compose-etl | |
| run: sudo sysctl -w vm.max_map_count=262144 | |
| - name: Run spark and ElasticSearch | |
| working-directory: ../compose-etl | |
| run: docker compose up -d spark elasticsearch | |
| - name: Wait for the container to be up and running | |
| run: sleep 60 | |
| - name: Checking logs | |
| working-directory: ../compose-etl | |
| run: docker compose logs | |
| - name: Check all containers | |
| run: docker ps | |
| - name: Check all docker networks | |
| run: docker network ls | |
| - name: Run ETL process | |
| working-directory: ../compose-etl | |
| run: docker compose run tube bash -c "python run_config.py; python run_etl.py" | |
| - name: Run integrated tests | |
| # Run the tests that require Spark and ElasticSearch | |
| env: | |
| ES_URL: localhost | |
| POSTGRES_PORT: 5432 | |
| DICTIONARY_URL: https://s3.amazonaws.com/dictionary-artifacts/ndhdictionary/3.3.8/schema.json | |
| XDG_DATA_HOME: /home/runner/work/tube | |
| ES_INDEX_NAME: etl | |
| # Skip SSL tests marked with `@pytest.mark.ssl` | |
| run: python3.9 -m poetry run pytest -v tests/integrated_tests -m "not ssl" --cov=tube --cov-append --cov-report term-missing --cov-report xml | |
| - name: Run dataframe tests | |
| # Run the tests that require Spark but not ElasticSearch | |
| env: | |
| ES_URL: localhost | |
| POSTGRES_PORT: 5432 | |
| DICTIONARY_URL: https://s3.amazonaws.com/dictionary-artifacts/ibdgc-dictionary/1.6.10/schema.json | |
| XDG_DATA_HOME: /home/runner/work/tube | |
| RUNNING_MODE: Test | |
| HADOOP_VERSION: 3.3.2 | |
| ES_INDEX_NAME: etl | |
| ES_HADOOP_VERSION: 8.3.3 | |
| ES_HADOOP_HOME: /home/runner/work/tube | |
| ES_SPARK_30_2_12: elasticsearch-spark-30_2.12 | |
| ES_SPARK_20_2_11: elasticsearch-spark-20_2.11 | |
| # Skip SSL tests marked with `@pytest.mark.ssl` | |
| run: | | |
| python3.9 -m poetry run pytest -v tests/dataframe_tests -m "schema_ibdgc and not ssl" --cov=tube --cov-append --cov-report term-missing --cov-report xml | |
| python3.9 -m poetry run pytest -v tests/dataframe_tests -m "schema_midrc and not ssl" --cov=tube --cov-append --cov-report term-missing --cov-report xml | |
| python3.9 -m poetry run pytest -v tests/dataframe_tests -m "schema_jcoin and not ssl" --cov=tube --cov-append --cov-report term-missing --cov-report xml | |
| python3.9 -m poetry run pytest -v tests/dataframe_tests -m "schema_parent and not ssl" --cov=tube --cov-append --cov-report term-missing --cov-report xml | |
| # python3.9 -m poetry run pytest -v tests/dataframe_tests -m "not ssl and not schema_ibdgc and not schema_midrc" --cov=tube --cov-append --cov-report term-missing --cov-report xml | |
| - name: Submit coverage report | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_TOKEN }} | |
| run: | | |
| pip install coveralls | |
| coveralls |