mimic-code/.github/workflows/docker-build.yml at main · MIT-LCP/mimic-code · GitHub

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# Build and run the containerized MIMIC-IV builds against the demo dataset.
name: docker build

on:
  pull_request:
    paths:
      - 'mimic-iv/buildmimic/postgres/**'
      - 'mimic-iv/buildmimic/duckdb/**'
      - 'mimic-iv/buildmimic/download_data.sh'
      - '.github/workflows/docker-build.yml'
  push:
    branches:
      - main
    paths:
      - 'mimic-iv/buildmimic/postgres/**'
      - 'mimic-iv/buildmimic/duckdb/**'
      - '.github/workflows/docker-build.yml'

# Cancel superseded runs when a PR is pushed again.
concurrency:
  group: docker-build-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

permissions:
  contents: read

jobs:
  build:
    runs-on: ubuntu-latest

    defaults:
      run:
        # Name bash explicitly to get `-eo pipefail`.
        shell: bash

    env:
      DUCKDB_DOCKER: mimic-iv/buildmimic/duckdb/docker
      POSTGRES_DOCKER: mimic-iv/buildmimic/postgres/docker
      MIMIC_DATA_DIR: ${{ github.workspace }}
      MIMIC_OUTPUT_DIR: ${{ github.workspace }}/duckdb-out

    steps:
      - uses: actions/checkout@v7
      - uses: ./.github/actions/download-demo
      - uses: ./.github/actions/setup-duckdb

      - name: Build both images
        run: |
          docker compose -f "$DUCKDB_DOCKER/docker-compose.yml" build
          docker compose -f "$POSTGRES_DOCKER/docker-compose.yml" build

      # --exit-code-from implies --abort-on-container-exit and returns the build
      # job's own status, so a failed build fails the step.
      - name: Build MIMIC-IV in DuckDB
        run: |
          mkdir -p "$MIMIC_OUTPUT_DIR"
          docker compose -f "$DUCKDB_DOCKER/docker-compose.yml" \
            up --exit-code-from mimic-build | tee duckdb.log
          if grep -F -q "FAILED" duckdb.log; then
            echo "::error::DuckDB container row-count validation failed:"
            grep -F "FAILED" duckdb.log
            exit 1
          fi

      - name: Read the built database with the runner's own duckdb
        run: |
          rows=$(duckdb "$MIMIC_OUTPUT_DIR/mimic4.db" -noheader -list \
            -c "SELECT count(*) FROM mimiciv_derived.sepsis3")
          echo "mimiciv_derived.sepsis3: ${rows} rows"
          if [ -z "${rows}" ] || [ "${rows}" -eq 0 ]; then
            echo "::error::The concepts are missing from the container-built database."
            exit 1
          fi

      - name: Build MIMIC-IV in PostgreSQL
        run: |
          docker compose -f "$POSTGRES_DOCKER/docker-compose.yml" \
            up --exit-code-from mimic-build | tee psql.log
          if grep -F -q "FAILED" psql.log; then
            echo "::error::PostgreSQL container row-count validation failed:"
            grep -F "FAILED" psql.log
            exit 1
          fi

      - name: Tear down
        if: always()
        run: |
          docker compose -f "$DUCKDB_DOCKER/docker-compose.yml" down -v || true
          docker compose -f "$POSTGRES_DOCKER/docker-compose.yml" down -v || true