test.yml

name: Test

concurrency:
  group: ci-${{ github.head_ref }}
  cancel-in-progress: true

on:
  pull_request:
    types: [opened, reopened, synchronize, ready_for_review]
    paths:
      - *.sh
      - *.sql
      - Dockerfile

jobs:
  lint:
    runs-on: ubuntu-latest
    steps:
    - name: Checkout
      uses: actions/checkout@v2
    - name: Build container
      run: |
        docker build -t chado .

    - name: Test Running Container
      run: |
        container_id=$(docker run -it -e INSTALL_YEAST_DATA=1 -d --name chado chado)

        while true; do
          date

          # Check that it's ready to run
          start_count=$(docker logs $container_id | grep 'database system is ready to accept connections' | wc -l)
          if (( start_count > 1 )); then
            break
          fi

          # If it's not output some logs
          docker logs $container_id | tail

          # And wait a bit
          sleep 5
        done

        # Check that yeast is, in fact loaded.
        docker exec $container_id psql -U postgres -c "select * from organism where common_name = 'yeast' " | grep '1 row'

        # Dump something useful
        docker exec $container_id psql -U postgres -c "select type_id, count(*) from feature group by type_id ;"

        docker kill $container_id
        docker rm -f $container_id

        # Done!
        exit 0