main-ci.yml

name: main-ci

on:

  pull_request:   # default types: opened, synchronize, reopened
    branches: [main]
    paths:
      - 'modules/**'
      - '.github/workflows/main-ci.yml'
  
  workflow_dispatch:

env:
  SCHEMATIC_VERSION: 24.7.2 # please update .devcontainer as well until this can be set globally somewhere...
  
jobs:
  build:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          ref: ${{ github.event.pull_request.head.ref }}
          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: Get skip flags
        id: check_skip_flags
        run: echo "HEAD_COMMIT_MESSAGE=$(git show -s --format=%s)" >> "$GITHUB_OUTPUT"
      
      - name: Setup custom build tools and make jsonld 
        shell: bash
        run: |
          bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install)
          git clone --depth 1 https://github.com/anngvu/retold.git
          make
  
      - name: Install tools and regenerate registered jsons for Superdataset, PortalDataset, etc
        run: |
          pip install linkml==v1.8.1
          npm install -g json-dereference-cli
          make PortalDataset
          make PortalStudy
          make Superdataset
          make PortalPublication
          make Protocol
      
      # Set up supported python.
      - uses: actions/setup-python@v5
        with:
          python-version: '3.10.12' 
      
      - name: Setup schematic and do another convert pass
        id: schematic-convert
        run: |
          pip install schematicpy==${{ env.SCHEMATIC_VERSION }}
          pip show schematicpy
          schematic schema convert NF.jsonld
    
      - name: Commit files if there are changes
        run: |
          if [[ $(git diff --exit-code) ]]; then 
            echo "Changes in src modules affect final jsonld or json artifacts and will be committed"
            git config --local user.email "nf-osi@sagebionetworks.org"
            git config --local user.name "nf-osi[bot]"
            git add .
            git commit -m "Rebuild NF.jsonld, json"
          else 
            echo "Changes in src modules did not affect final jsonld or json artifacts"
            echo "Note that tests will still be run in the next job"
          fi
    
      - name: Push changes
        uses: ad-m/github-push-action@master
        with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         branch: ${{ github.event.pull_request.head.ref }}
      

  
  # Additionally test PRs
  test:
    name: Test with schematic current version
    needs: [build]
    runs-on: ubuntu-latest
    env:
      SCHEMATIC_SERVICE_ACCT_CREDS: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }}
    permissions:
      pull-requests: write
    if: ${{ !contains(github.event.pull_request.labels.*.name, 'skip tests') }}
    # strategy:
    #  matrix:  
    # cannot actually do parallel/concurrent testing because of API rate limits, 
    # so we currently only test with one schematic version because it takes much too long with sequential

    steps:
      - uses: actions/checkout@v4
        with:
          ref: ${{ github.event.pull_request.head.ref }}
          fetch-depth: 1

      - uses: actions/setup-python@v5
        with:
          python-version: '3.10.12' 
      
      - name: Setup schematic
        id: setup-schematic
        run: |
          pip install schematicpy==${{ env.SCHEMATIC_VERSION }}
          pip show schematicpy

      - name: Test generate
        working-directory: tests/generate
        continue-on-error: true
        run: ./basic_templates.sh

      - name: Test validate
        working-directory: tests/validate
        continue-on-error: true
        run: ./run_config.sh

      - name: Test submit
        working-directory: tests/submit
        continue-on-error: true
        # Only test submit needs SYNAPSE_AUTH_TOKEN
        env:
          SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }}
        # Need to set up csvtool for use in test environment
        run: |
          sudo apt install csvtool
          printf "[authentication]\nSYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN" > .synapseConfig
          ./test_submit.sh
      
      - name: Create test suite report
        working-directory: tests
        continue-on-error: true
        run: docker run -v $(pwd):/tests -e SCHEMATIC=${{ env.SCHEMATIC_VERSION }} rocker/tidyverse R -e "rmarkdown::render('tests/test-suite-report.Rmd')"

      - name: Report on test suite as PR comment
        uses: mshick/add-pr-comment@v2
        with:
          message-id: test-suite-report-${{ env.SCHEMATIC_VERSION }}
          message-path: |
            tests/test-suite-report.md

      - name: Upload test artifacts
        uses:  actions/upload-artifact@v4
        with:
          name: test-logs-${{ env.SCHEMATIC_VERSION }}
          path: tests/**/logs