ci.yml

on:
  pull_request:
    branches: [ "master", "main" ]

  push:
    branches: [ "master", "main" ]

jobs:
  check_data_models:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        data_model_file: [
          'PRIMED_phenotype_data_model.json',
          'PRIMED_genotype_data_model.json',
          'PRIMED_GSR_data_model.json'
        ]
    name: Check data model
    steps:

      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: "4.2.3"

      - name: Install dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 1
          packages: github::UW-GAC/AnvilDataModels, any::sessioninfo
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

      - name: Check ${{ matrix.data_model_file }} file
        run: |
          AnvilDataModels::json_to_dm("${{ matrix.data_model_file }}")
        shell: Rscript {0}

  check_test_data:
    runs-on: ubuntu-latest
    name: Check test data
    steps:

      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Checkout primed-file-checks
        uses: actions/checkout@v3
        with:
          repository: UW-GAC/primed-file-checks
          path: primed-file-checks

      # Install Java to this VM. This Java version and distribution is compatible with Cromwell.
      # This is the same step as used by broadinstitute/cromwell/.github/set_up_cromwell_action.
      - name: Setup JDK
        uses: actions/setup-java@v3
        with:
          distribution: temurin
          java-version: 11

      # Get cromwell jar file
      - uses: robinraju/release-downloader@v1.10
        with:
          repository: 'broadinstitute/cromwell'
          tag: '87'
          fileName: 'cromwell-87.jar'

      - name: Validate test data
        run: |
          java -jar cromwell-87.jar run primed-file-checks/validate_phenotype_model.wdl --inputs test_data/wdl_inputs_validate_phenotype_model.json
        shell: bash

      - name: Success!
        run: echo "Success!"