nightly_build.yaml

name: Nightly Build

on:
  schedule:
    - cron: "59 23 * * *"
  workflow_dispatch:

permissions: write-all

jobs:
  build-and-publish:
    name: Nightly Report Build
    runs-on: ubuntu-latest
    steps:

      - uses: actions/checkout@v2
        with:
          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token.
          fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository.

      - name: Set up Java
        uses: actions/setup-java@v3
        with:
          java-version: '17'
          distribution: temurin

      - name: Get robot.jar
        run: |
          wget https://github.com/ontodev/robot/releases/download/v1.9.5/robot.jar -O robot/robot.jar
          chmod +x robot/robot.jar

      - name: Set up Python 3.9
        uses: actions/setup-python@v2
        with:
          python-version: 3.9

      - name: Install Project Dependencies
        run: |
          pip install -r requirements.txt

      - name: Templates generation
        run: |
          PYTHONPATH=./src:$PYTHONPATH python src/cl_coverage.py

      - name: Ontology generation
        run: |
          cd robot
          java -jar robot.jar --prefixes template_prefixes.json template --template ../templates/cellxgene_subset.tsv --output ../cellxgene_subset.owl

      - name: Commit files
        run: |
          git config --local user.email "github-actions[bot]@users.noreply.github.com"
          git config --local user.name "github-actions[bot]"
          git commit -a -m "Nightly build"

      - name: Push changes
        uses: ad-m/github-push-action@master
        with:
          branch: ${{ github.head_ref }}