python-apollo.yml

name: Python-Apollo

on:
  push:
    branches: [develop, apollo_g7]
  pull_request:
    branches: [develop]

jobs:
  test-python-apollo:
    name: test-python-apollo
    runs-on: ubuntu-latest

    steps:
      - name: Checkout Apollo
        uses: actions/checkout@v4

      - name: Set up JDK 17
        uses: actions/setup-java@v4
        with:
          distribution: temurin
          java-version: 17

      - name: Setup Gradle
        uses: gradle/actions/setup-gradle@v4

      - name: Build Apollo
        run: ./gradlew classes

      - name: Start Apollo
        run: |
          ./gradlew bootRun > apollo.log 2>&1 &

          # Wait for health endpoint
          for i in $(seq 1 300); do
            response=$(curl -s 'http://localhost:8080/apollo/health/index' 2>/dev/null || true)
            if echo "$response" | grep -q '"status":"ready"'; then
              echo "Apollo is ready (${i}s)"
              break
            fi
            if [ $i -eq 300 ]; then
              echo "FAIL: Apollo not ready after 300 seconds"
              cat apollo.log
              exit 1
            fi
            sleep 1
          done

      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.12'

      - name: Checkout python-apollo
        uses: actions/checkout@v4
        with:
          repository: galaxy-genome-annotation/python-apollo
          path: python-apollo
          ref: master

      - name: Install python-apollo
        run: |
          cd python-apollo
          pip install 'biopython<1.86' apollo pytest

      - name: Bootstrap test data
        run: |
          cd python-apollo
          export ARROW_GLOBAL_CONFIG_PATH=$(pwd)/test-data/local-apollo2-arrow.yml
          ./bootstrap_apollo.sh --nodocker

      - name: Diagnose test failures
        run: |
          cd python-apollo
          export ARROW_GLOBAL_CONFIG_PATH=$(pwd)/test-data/local-apollo2-arrow.yml
          python3 -c "
          import traceback, json, sys
          try:
              from apollo import ApolloInstance
              wa = ApolloInstance('http://localhost:8080/apollo', 'admin@local.host', 'password')

              print('=== Organisms ===')
              orgs = wa.organisms.get_organisms()
              for o in orgs:
                  print(f\"  {o.get('commonName')}: sequences={o.get('sequences')}\")

              print()
              print('=== Test load_gff3 ===')
              feature_data = wa.annotations.load_gff3('test_organism', 'test-data/mrna-top.gff')
              print(f'load_gff3 returned: {feature_data}')

              print()
              print('=== Remote API test ===')
              import tempfile, tarfile, glob, os
              with tempfile.NamedTemporaryFile(suffix='.tar.gz', delete=False) as archive:
                  archive_path = archive.name
                  with tarfile.open(archive_path, mode='w:gz') as tar:
                      base = 'test-data/dataset_1_files/data/'
                      for root, dirs, files in os.walk(base):
                          for f in files:
                              full = os.path.join(root, f)
                              arcname = os.path.relpath(full, base)
                              tar.add(full, arcname=arcname)
                  with tarfile.open(archive_path, mode='r:gz') as tar:
                      print(f'  Archive has {len(tar.getmembers())} entries')
                      for m in tar.getmembers()[:5]:
                          print(f'    {m.name}')
                  with open(archive_path, 'rb') as f:
                      result = wa.remote.add_organism('diag_remote_org', f)
                      print(f'  add_organism result: {json.dumps(result, indent=2, default=str)[:500]}')
                  os.unlink(archive_path)

          except Exception as e:
              print(f'DIAGNOSTIC FAILED: {type(e).__name__}: {e}')
              traceback.print_exc()
          " 2>&1 || true

          echo ""
          echo "=== Apollo ERROR/WARN log lines ==="
          grep -E 'ERROR|WARN' ../apollo.log | tail -200 || true

      - name: Run tests
        run: |
          cd python-apollo
          export ARROW_GLOBAL_CONFIG_PATH=$(pwd)/test-data/local-apollo2-arrow.yml
          python -m pytest -v

      - name: Print Apollo log on failure
        if: failure()
        run: |
          echo "=== Delete-related log lines ==="
          grep -iE 'deleteOrganism|features to delete|Deleted.*features|problem removing|not authorized to delete' apollo.log | tail -50 || true
          echo ""
          echo "=== Last 500 lines of Apollo log ==="
          tail -500 apollo.log