psql demo db build #77
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| name: psql demo db build | |
| on: | |
| pull_request_review: | |
| types: [submitted] | |
| jobs: | |
| mimic-iv-psql: | |
| # only run if PR is approved | |
| if: github.event.review.state == 'approved' | |
| runs-on: ubuntu-20.04 | |
| container: python:3.10 | |
| services: | |
| # Label used to access the service container | |
| postgres: | |
| # Docker Hub image | |
| image: 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 | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - name: Download demo data | |
| uses: ./.github/actions/download-demo | |
| - name: Install postgresql-client | |
| run: | | |
| apt-get update | |
| apt-get install --yes --no-install-recommends postgresql-client | |
| - name: Load icu/hosp data into PostgreSQL | |
| run: | | |
| echo "Loading data into psql." | |
| psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/create.sql | |
| psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/load_gz.sql | |
| echo "Validating build." | |
| psql -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/validate_demo.sql > results | |
| # if we find "FAILED", then we did not pass the build | |
| if grep -F -q "FAILED" results; then | |
| echo "Failed the following row counts:" | |
| head -n 1 results | |
| grep "FAILED" results | |
| exit 1 | |
| else | |
| echo "Built and loaded demo data successfully." | |
| cat results | |
| fi | |
| env: | |
| POSTGRES_HOST: postgres | |
| PGPASSWORD: postgres | |
| BUILDCODE_PATH: mimic-iv/buildmimic/postgres | |
| - name: mimic-iv/concepts psql build | |
| run: | | |
| psql -h $POSTGRES_HOST -U postgres -f postgres-functions.sql | |
| psql -h $POSTGRES_HOST -U postgres -f postgres-make-concepts.sql | |
| working-directory: ./mimic-iv/concepts_postgres | |
| env: | |
| POSTGRES_HOST: postgres | |
| PGPASSWORD: postgres | |
| - name: mimic_utils - convert mimic-iv concepts to PostgreSQL and rebuild | |
| run: | | |
| pip install . | |
| mimic_utils convert_folder mimic-iv/concepts mimic-iv/concepts_postgres --source_dialect bigquery --destination_dialect postgres | |
| psql -h $POSTGRES_HOST -U postgres -f mimic-iv/concepts_postgres/postgres-make-concepts.sql | |
| working-directory: ./ | |
| env: | |
| POSTGRES_HOST: postgres | |
| PGPASSWORD: postgres | |
| - name: Load ed data into PostgreSQL | |
| run: | | |
| echo "Loading data into psql." | |
| psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/create.sql | |
| psql -q -h $POSTGRES_HOST -U postgres -v mimic_data_dir=ed/ -f ${BUILDCODE_PATH}/load_gz.sql | |
| echo "Validating build." | |
| psql -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/validate_demo.sql > results | |
| # if we find "FAILED", then we did not pass the build | |
| if grep -F -q "FAILED" results; then | |
| echo "Failed the following row counts:" | |
| head -n 1 results | |
| grep "FAILED" results | |
| exit 1 | |
| else | |
| echo "Built and loaded demo data successfully." | |
| cat results | |
| fi | |
| env: | |
| # The hostname used to communicate with the PostgreSQL service container | |
| POSTGRES_HOST: postgres | |
| PGPASSWORD: postgres | |
| # The default PostgreSQL port | |
| POSTGRES_PORT: 5432 | |
| BUILDCODE_PATH: mimic-iv-ed/buildmimic/postgres |