integration-tests.yml

name: Integration Tests

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  workflow_dispatch:
  schedule:
    # Run integration tests nightly at 3 AM UTC to catch integration issues early
    - cron: "0 3 * * *"

env:
  REGISTRY: ghcr.io
  IMAGE_PREFIX: ghcr.io/${{ github.repository_owner }}/nexuslims-test

jobs:
  integration-test:
    name: Integration Tests (Python ${{ matrix.python-version }})
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.11", "3.12"]

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

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Log in to Container Registry
        uses: docker/login-action@v3
        with:
          registry: ${{ env.REGISTRY }}
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}

      - name: Pull pre-built test images
        run: |
          docker pull ${{ env.IMAGE_PREFIX }}-nemo:latest || echo "NEMO image not found, will build locally"
          docker pull ${{ env.IMAGE_PREFIX }}-cdcs:latest || echo "CDCS image not found, will build locally"

      - name: Tag images for local use
        continue-on-error: true
        run: |
          docker tag ${{ env.IMAGE_PREFIX }}-nemo:latest nexuslims-test-nemo:latest 2>/dev/null || true
          docker tag ${{ env.IMAGE_PREFIX }}-cdcs:latest nexuslims-test-cdcs:latest 2>/dev/null || true

      - name: Start Docker services
        working-directory: tests/integration/docker
        run: |
          # Try to use pre-built images first, fall back to building if needed
          if docker image inspect nexuslims-test-nemo:latest >/dev/null 2>&1 && \
             docker image inspect nexuslims-test-cdcs:latest >/dev/null 2>&1; then
            echo "Using pre-built images from registry"
            docker compose -f docker-compose.ci.yml up -d
          else
            echo "Building images locally (pre-built images not available)"
            docker compose up -d
          fi

      - name: Wait for services to be healthy
        run: |
          echo "Waiting for NEMO to be ready..."
          timeout 180 bash -c 'until curl -f http://localhost:8000/ > /dev/null 2>&1; do echo -n "."; sleep 3; done'
          echo "✓ NEMO is ready"

          echo "Waiting for CDCS to be ready..."
          timeout 240 bash -c 'until curl -f http://localhost:8080/ > /dev/null 2>&1; do echo -n "."; sleep 5; done'
          echo "✓ CDCS is ready"

          echo "Waiting for MailPit to be ready..."
          timeout 60 bash -c 'until curl -f http://localhost:8025/ > /dev/null 2>&1; do echo -n "."; sleep 2; done'
          echo "✓ MailPit is ready"

      - name: Show Docker service status
        if: always()
        working-directory: tests/integration/docker
        run: docker compose ps

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y findutils

      - name: Set up uv
        uses: astral-sh/setup-uv@v4
        with:
          enable-cache: true

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install dependencies
        run: uv sync

      - name: Create test environment for module imports
        run: |
          # Create test directories
          mkdir -p /tmp/nexuslims-test-instrument-data
          mkdir -p /tmp/nexuslims-test-data

          # Create empty database file (Settings validates it exists)
          touch /tmp/nexuslims-test-data/nexuslims_test.db

          # Create .env file with minimal config for import-time validation
          cat > .env << 'EOF'
          # CI Integration Test Environment
          # These values allow NexusLIMS modules to be imported during test collection
          # The actual test fixtures will override these with monkeypatch

          # Test data paths
          NX_INSTRUMENT_DATA_PATH=/tmp/nexuslims-test-instrument-data
          NX_DATA_PATH=/tmp/nexuslims-test-data
          NX_DB_PATH=/tmp/nexuslims-test-data/nexuslims_test.db

          # CDCS configuration (will be overridden by fixtures)
          NX_CDCS_URL=http://localhost:8080
          NX_CDCS_USER=admin
          NX_CDCS_PASS=admin
          EOF

      - name: Run unit tests
        run: |
          uv run pytest tests/ \
            --ignore=tests/integration \
            -v \
            --mpl \
            --mpl-baseline-path=tests/unit/files/figs \
            --cov=nexusLIMS \
            --cov-report term-missing \
            --tb=short \
            --maxfail=5

      - name: Run integration tests
        run: |
          uv run pytest tests/integration/ \
            -v \
            -m integration \
            --cov=nexusLIMS \
            --cov-append \
            --cov-report html:tests/coverage-combined \
            --cov-report term-missing \
            --cov-report=xml:coverage-combined.xml \
            --tb=short \
            --maxfail=5
        env:
          # Integration test environment variables
          PYTEST_TIMEOUT: 600

      - name: Upload combined test coverage
        uses: actions/upload-artifact@v4
        with:
          name: coverage-combined-${{ matrix.python-version }}
          path: |
            .coverage
            coverage-combined.xml
          include-hidden-files: true

      - name: Upload HTML coverage report
        if: matrix.python-version == '3.11'
        uses: actions/upload-artifact@v4
        with:
          name: coverage-combined-html
          path: tests/coverage-combined

      - name: Show Docker logs on failure
        if: failure()
        working-directory: tests/integration/docker
        run: |
          echo "=== NEMO Logs ==="
          docker compose logs nemo | tail -100
          echo ""
          echo "=== CDCS Logs ==="
          docker compose logs cdcs | tail -100
          echo ""
          echo "=== MongoDB Logs ==="
          docker compose logs cdcs-mongo | tail -50
          echo ""
          echo "=== PostgreSQL Logs ==="
          docker compose logs cdcs-postgres | tail -50

      - name: Cleanup Docker services
        if: always()
        working-directory: tests/integration/docker
        run: |
          docker compose down -v --remove-orphans || true

  upload-coverage:
    name: Upload Combined Coverage to Codecov
    needs: integration-test
    runs-on: ubuntu-latest
    if: always()

    steps:
      - uses: actions/checkout@v4

      - name: Download all coverage artifacts
        uses: actions/download-artifact@v4
        with:
          pattern: coverage-combined-*
          path: coverage-reports

      - name: Upload combined coverage to Codecov
        uses: codecov/codecov-action@v5
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: ./coverage-reports/**/*.xml
          flags: combined
          fail_ci_if_error: false