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", "3.13", "3.14"]

    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: Determine image tag
        id: image-tag
        run: |
          # Match the tag generation from build-test-images.yml
          # For branches: use branch name
          # For PRs: use pr-<number>
          # For other: use sha
          if [[ "${{ github.ref }}" == refs/heads/* ]]; then
            TAG="${{ github.ref_name }}"
          elif [[ "${{ github.event_name }}" == "pull_request" ]]; then
            TAG="pr-${{ github.event.pull_request.number }}"
          else
            TAG="sha-${{ github.sha }}"
          fi
          # Replace / with - for valid Docker tags
          TAG="${TAG//\//-}"
          echo "tag=${TAG}" >> $GITHUB_OUTPUT
          echo "Using image tag: ${TAG}"

      - name: Pull pre-built test images
        continue-on-error: true
        run: |
          docker pull ${{ env.IMAGE_PREFIX }}-nemo:${{ steps.image-tag.outputs.tag }} || echo "Tagged NEMO image not found"
          docker pull ${{ env.IMAGE_PREFIX }}-cdcs:${{ steps.image-tag.outputs.tag }} || echo "Tagged CDCS image not found"
          docker pull ${{ env.IMAGE_PREFIX }}-elabftw:${{ steps.image-tag.outputs.tag }} || echo "Tagged eLabFTW image not found"

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

      - name: Start Docker services
        working-directory: tests/integration/docker
        env:
          REGISTRY: ${{ env.REGISTRY }}
          IMAGE_OWNER: ${{ github.repository_owner }}
          IMAGE_TAG: ${{ steps.image-tag.outputs.tag }}
        run: |
          # Try to use pre-built images with the PR/branch tag from build-test-images.yml
          if docker image inspect nexuslims-test-nemo:latest >/dev/null 2>&1 && \
             docker image inspect nexuslims-test-cdcs:latest >/dev/null 2>&1 && \
             docker image inspect nexuslims-test-elabftw:latest >/dev/null 2>&1; then
            echo "Using pre-built images from registry (tag: ${{ steps.image-tag.outputs.tag }})"
            docker compose -f docker-compose.ci.yml up -d
          else
            echo "Pre-built images not available - building locally"
            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:48000/ > /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:48080/ > /dev/null 2>&1; do echo -n "."; sleep 5; done'
          echo "✓ CDCS is ready"

          echo "Waiting for eLabFTW to be ready..."
          timeout 240 bash -c 'until curl -fk https://localhost:48148/login.php > /dev/null 2>&1; do echo -n "."; sleep 5; done'
          echo "✓ eLabFTW is ready"

          echo "Waiting for MailPit to be ready..."
          timeout 60 bash -c 'until curl -f http://localhost:48025/ > /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: Run all tests (unit + integration)
        run: |
          uv run pytest tests/ \
            -v \
            --override-ini=addopts= \
            --mpl \
            --mpl-baseline-path=tests/unit/files/figs \
            --cov=nexusLIMS \
            --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: Collect Docker container logs
        if: always()
        working-directory: tests/integration/docker
        run: |
          mkdir -p ../../docker-logs

          # Debug: Show what containers exist
          echo "=== Running Containers ==="
          docker ps -a --filter "name=nexuslims-test" || true
          echo ""

          # Determine which compose file was used and collect logs
          if docker image inspect nexuslims-test-nemo:latest >/dev/null 2>&1 && \
             docker image inspect nexuslims-test-cdcs:latest >/dev/null 2>&1 && \
             docker image inspect nexuslims-test-elabftw:latest >/dev/null 2>&1; then
            COMPOSE_FILE="docker-compose.ci.yml"
          else
            COMPOSE_FILE="docker-compose.yml"
          fi

          echo "Collecting logs from compose stack (using $COMPOSE_FILE)..."

          # Collect full compose logs (try both approaches)
          docker compose -f "$COMPOSE_FILE" logs --no-color > ../../docker-logs/docker-compose.log 2>&1 || true

          # Also try collecting by container name directly as fallback
          for container in nexuslims-test-nemo nexuslims-test-cdcs nexuslims-test-cdcs-mongo nexuslims-test-cdcs-postgres nexuslims-test-cdcs-redis nexuslims-test-elabftw nexuslims-test-elabftw-mysql nexuslims-test-mailpit nexuslims-test-caddy-proxy; do
            docker logs "$container" > "../../docker-logs/${container##*-}.log" 2>&1 || true
          done

          # Display summary to action logs
          echo "=== Docker Logs Summary ==="
          du -sh ../../docker-logs/* 2>/dev/null || echo "No logs collected"
          echo ""
          echo "=== Log Files Created ==="
          ls -lh ../../docker-logs/ 2>/dev/null || echo "No log directory"

      - name: Display Docker logs on failure
        if: failure()
        run: |
          echo "=== Docker Compose Full Log ==="
          cat docker-logs/docker-compose.log 2>/dev/null || echo "No compose log available"
          echo ""
          echo "=== NEMO Log ==="
          cat docker-logs/nemo.log 2>/dev/null || echo "No NEMO log available"
          echo ""
          echo "=== CDCS Log ==="
          cat docker-logs/cdcs.log 2>/dev/null || echo "No CDCS log available"
          echo ""
          echo "=== MongoDB Log ==="
          cat docker-logs/mongo.log 2>/dev/null || echo "No MongoDB log available"
          echo ""
          echo "=== PostgreSQL Log ==="
          cat docker-logs/postgres.log 2>/dev/null || echo "No PostgreSQL log available"
          echo ""
          echo "=== Redis Log ==="
          cat docker-logs/redis.log 2>/dev/null || echo "No Redis log available"
          echo ""
          echo "=== eLabFTW Log ==="
          cat docker-logs/elabftw.log 2>/dev/null || echo "No eLabFTW log available"
          echo ""
          echo "=== eLabFTW MySQL Log ==="
          cat docker-logs/mysql.log 2>/dev/null || echo "No eLabFTW MySQL log available"
          echo ""
          echo "=== Mailpit Log ==="
          cat docker-logs/mailpit.log 2>/dev/null || echo "No Mailpit log available"
          echo ""
          echo "=== Caddy Proxy Log ==="
          cat docker-logs/proxy.log 2>/dev/null || echo "No Caddy Proxy log available"

      - name: Upload Docker logs artifact
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: docker-logs-${{ matrix.python-version }}
          path: tests/docker-logs/
          if-no-files-found: ignore

      - 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