ci(pr-check): add tsv output verification #27
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| name: PR checks on algorithm submission | |
| on: | |
| pull_request: | |
| paths: | |
| - 'algorithms/*.yaml' | |
| - '.github/workflows/1-pr-check.yml' | |
| push: | |
| paths: | |
| - 'algorithms/*.yaml' | |
| - '.github/workflows/1-pr-check.yml' | |
| jobs: | |
| check_yaml: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/${{ github.repository }}-algo-checks:main | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.github_token }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: find algorithm files | |
| run: | | |
| { | |
| echo 'FILELIST<<EOF' | |
| find ./algorithms -name '*.yaml' -print | |
| echo EOF | |
| } >> "$GITHUB_ENV" | |
| - name: Convert and validate using jsonschema | |
| run: | | |
| for algo in ${FILELIST}; do | |
| yq -o json $algo > algo.json \ | |
| && jsonschema-cli -i algo.json "config/schema.json" | |
| done | |
| rm algo.json | |
| check_image: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: find algorithm files | |
| run: | | |
| { | |
| echo 'FILELIST<<EOF' | |
| find ./algorithms -name '*.yaml' -print | |
| echo EOF | |
| } >> "$GITHUB_ENV" | |
| - name: Pull image | |
| run: | | |
| for algo in ${FILELIST}; do | |
| IMAGE=$(grep '^image: ' $algo | sed 's/^image: \+//' | tr -d \'\") | |
| if ! docker pull $IMAGE ; then | |
| echo "Cannot pull image: $IMAGE" | |
| exit 1 | |
| fi | |
| done | |
| - name: Check output | |
| run: | | |
| HEADER_REGEX='onset duration eventType confidence channels dateTime recordingDuration' | |
| for algo in ${FILELIST}; do | |
| IMAGE=$(grep '^image: ' $algo | sed 's/^image: \+//' | tr -d \'\") | |
| OUT=$(tr -cd '[:alnum:]' < <(echo $IMAGE) ) | |
| echo "running: $IMAGE" | |
| docker run -v ./tests/data:/data -v /tmp:/output -e INPUT=unipolar.edf -e OUTPUT="${OUT}.tsv" $IMAGE | |
| if ! [[ $(head -n1 "/tmp/${OUT}.tsv") =~ "$HEADER_REGEX" ]]; then | |
| echo "Output does not have the expected header" | |
| exit 1 | |
| fi | |
| done | |