psql demo db build #74
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: 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-latest | |
| container: node:latest | |
| 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: Build mimic-iv concepts | |
| 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: 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 |