.github/workflows/integration-test.yml

name: Docker Integration Test

on:
  workflow_dispatch:

concurrency:
  group: docker-integration-${{ github.ref }}
  cancel-in-progress: true

jobs:
  laravel-to-ai-services:
    runs-on: ubuntu-latest
    timeout-minutes: 90

    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          lfs: true
      - name: Pull and verify Git LFS files
        run: |
          git lfs version
          git lfs pull
          git lfs checkout
          git lfs ls-files

          python - <<'PY'
          from pathlib import Path

          paths = [
              "ai_apps/generation/bundle/models/affinity/config.pkl",
              "ai_apps/generation/bundle/models/affinity/model.pt",
              "ai_apps/generation/bundle/models/generator/egfr_generator.chkpt",
              "ai_apps/generation/bundle/models/generator/reinvent.prior",
          ]

          for p in paths:
              path = Path(p)
              if not path.exists():
                  raise SystemExit(f"Missing required artifact: {p}")

              data = path.read_bytes()[:80]
              size = path.stat().st_size

              print(f"{p}: {size} bytes")

              if data.startswith(b"version https://git-lfs.github.com"):
                  raise SystemExit(f"{p} is still a Git LFS pointer file")
          PY
      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Build and start stack
        run: |
          # Clean up volumes from previous runs
          docker compose down -v 2>/dev/null || true

          docker builder prune -af || true
          docker system df

          COMPOSE_PARALLEL_LIMIT=1 docker compose build
          docker system df

          docker compose up -d --wait


          # Run fresh migrations to ensure clean database state
          docker compose exec -T laravel php artisan migrate:fresh --force

      - name: Seed verified test user
        run: |
          echo "=== Creating verified test user via PHP script ==="
          docker compose exec -T laravel php -r "
          require 'vendor/autoload.php';
          \$app = require_once 'bootstrap/app.php';
          \$kernel = \$app->make(Illuminate\Contracts\Console\Kernel::class);
          \$kernel->bootstrap();

          use App\Models\User;
          use Illuminate\Support\Facades\Hash;

          \$user = User::firstOrCreate(
              ['email' => 'salehyasmeen080@gmail.com'],
              [
                  'name' => 'Test User',
                  'password' => Hash::make('123456789'),
                  'role' => 'normal',
                  'is_verified' => true,
                  'email_verified_at' => now(),
                  'created_at' => now(),
                  'updated_at' => now()
              ]
          );
          echo 'User ID: ' . \$user->id . PHP_EOL;
          echo 'Email: ' . \$user->email . PHP_EOL;
          echo 'Verified: ' . (\$user->is_verified ? 'YES' : 'NO') . PHP_EOL;
          "

      - name: Login and get Bearer token
        run: |
          echo "POST /api/user/login"
          HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST http://localhost:8080/api/user/login \
            -H "Content-Type: application/json" \
            -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
          echo "HTTP Status: $HTTP_CODE"
          cat login.json
          echo ""

          if [ "$HTTP_CODE" != "200" ]; then
            echo "Login failed with HTTP $HTTP_CODE"
            docker compose logs laravel
            exit 1
          fi

          python3 - <<'PY'
          import json, sys
          try:
              data = json.load(open("login.json"))
          except json.JSONDecodeError as e:
              print("Invalid JSON response:", e)
              with open("login.json") as f:
                  print("Raw response:", f.read())
              sys.exit(1)

          if not data.get("success"):
              print("Login failed:", json.dumps(data, indent=2))
              sys.exit(1)

          token = data.get("data", {}).get("token")
          if not token:
              print("No token in response:", json.dumps(data, indent=2))
              sys.exit(1)

          with open("token.txt", "w") as f:
              f.write(token)
          print("Login OK - token saved")
          PY

      - name: Show service status
        if: always()
        run: docker compose ps -a

      - name: Wait for Laravel API
        run: |
          for i in $(seq 1 60); do
            if curl -sf http://localhost:8080/ > /dev/null 2>&1; then
              echo "Laravel is up"
              exit 0
            fi
            echo "Waiting for Laravel ($i/60)..."
            sleep 5
          done
          docker compose logs laravel
          exit 1

      - name: Wait for ADMET Service to be Healthy
        run: |
          echo "Waiting for ADMET service to be healthy..."
          for i in $(seq 1 120); do
            if curl -sf http://localhost:8002/health > /dev/null 2>&1; then
              echo "ADMET service is healthy and responding on port 8002"
              echo "Waiting additional 10 seconds for service to fully initialize..."
              sleep 10
              exit 0
            fi
            if docker exec ailixir-admet python -c "import urllib.request; urllib.request.urlopen('http://localhost:8000/health')" > /dev/null 2>&1; then
              echo "ADMET service is healthy internally inside container"
              echo "Waiting additional 10 seconds for service to fully initialize..."
              sleep 10
              exit 0
            fi
            echo "Attempt $i/120: ADMET service not ready yet..."
            sleep 5
          done
          echo "ADMET service failed to become healthy in time"
          docker compose logs admet
          exit 1

      - name: Test aggregated AI health via Laravel
        run: |
          TOKEN=$(cat token.txt)
          echo "GET /api/ai-services/health"
          curl -sf http://localhost:8080/api/ai-services/health \
            -H "Authorization: Bearer $TOKEN" | tee health.json
          python3 - <<'PY'
          import json, sys
          data = json.load(open("health.json"))
          if not data.get("success"):
              print("AI services health check failed:", json.dumps(data, indent=2))
              sys.exit(1)
          print("All AI services healthy via Laravel")
          PY

      - name: Test ADMET prediction via
        run: |
          TOKEN=$(cat token.txt)
          echo "POST /api/admet/predict"
          HTTP_CODE=$(curl -s -o admet.json -w "%{http_code}" -X POST http://localhost:8080/api/admet/predict \
            -H "Authorization: Bearer $TOKEN" \
            -H "Content-Type: application/json" \
            -d '{"smiles": "c1ccccc1, CCO, CCC"}')
          
          echo "HTTP Status: $HTTP_CODE"
          cat admet.json
          echo ""
          
          if [ "$HTTP_CODE" != "200" ]; then
            echo "ADMET prediction request failed with HTTP $HTTP_CODE"
            docker compose logs laravel
            exit 1
          fi

          python3 - <<'PY'
          import json, sys
          try:
              data = json.load(open("admet.json"))
          except json.JSONDecodeError as e:
              print("Invalid JSON response:", e)
              with open("admet.json") as f:
                  print("Raw response:", f.read())
              sys.exit(1)
          
          if not data.get("success"):
              print("ADMET prediction test failed:", json.dumps(data, indent=2))
              sys.exit(1)

          results = data.get("data", {}).get("results", [])
          if len(results) < 3:
              print(f"Expected at least 3 results, got {len(results)}")
              sys.exit(1)

          print(f"ADMET prediction OK - {len(results)} compounds processed")
          PY

      - name: Test Chemical RAG proxy via Laravel
        run: |
          TOKEN=$(cat token.txt)
          echo "POST /api/ai-services/test/chemical-search"
          HTTP_CODE=$(curl -s -o chemical.json -w "%{http_code}" -X POST http://localhost:8080/api/ai-services/test/chemical-search \
            -H "Authorization: Bearer $TOKEN" \
            -H "Content-Type: application/json" \
            -d '{"query": "malaria drug"}')
          echo "HTTP Status: $HTTP_CODE"
          cat chemical.json
          echo ""
          python3 - <<'PY'
          import json, sys
          data = json.load(open("chemical.json"))
          if not data.get("success"):
              print("Chemical RAG proxy test failed:", json.dumps(data, indent=2))
              sys.exit(1)
          print("Chemical RAG proxy OK")
          PY

      - name: Test Drug Repurposing proxy via Laravel
        run: |
          TOKEN=$(cat token.txt)
          echo "GET /api/ai-services/test/drug-repurposing"
          HTTP_CODE=$(curl -s -o drug.json -w "%{http_code}" http://localhost:8080/api/ai-services/test/drug-repurposing \
            -H "Authorization: Bearer $TOKEN")
          echo "HTTP Status: $HTTP_CODE"
          cat drug.json
          echo ""
          python3 - <<'PY'
          import json, sys
          data = json.load(open("drug.json"))
          if not data.get("success"):
              print("Drug Repurposing proxy test failed:", json.dumps(data, indent=2))
              sys.exit(1)
          print("Drug Repurposing proxy OK")
          PY

      - name: Dump logs on failure
        if: failure()
        run: |
          docker compose logs --no-color

      - name: Tear down
        if: always()
        run: docker compose down -v

  drug-repurposing-integration-test:
    runs-on: ubuntu-latest
    timeout-minutes: 45

    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          lfs: true
      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Build and start stack
       
        run: |
          docker compose down -v 2>/dev/null || true
          docker builder prune -af || true
          docker system df

          COMPOSE_PARALLEL_LIMIT=1 docker compose build
          docker system df

          docker compose up -d --wait

      - name: Verify drug-repurposing reachable from Laravel container
        run: |
          echo "=== Laravel → drug-repurposing DNS ==="
          docker compose exec -T laravel getent hosts drug-repurposing

          echo "=== Health check from Laravel container ==="
          docker compose exec -T laravel curl -sf http://drug-repurposing:8000/health | tee /tmp/drug-repurposing-health.json
          python3 - <<'PY'
          import json, sys
          data = json.load(open("/tmp/drug-repurposing-health.json"))
          if data.get("status") != "healthy":
              print("Expected healthy status:", data)
              sys.exit(1)
          print("drug-repurposing reachable from Laravel:", data.get("service"))
          PY

          echo "=== DRUG_REPURPOSING_URL in Laravel env ==="
          docker compose exec -T laravel php -r 'echo "DRUG_REPURPOSING_URL=" . getenv("DRUG_REPURPOSING_URL") . PHP_EOL;'

      - name: Run drug repurposing integration tests
        run: |
          # Match phpunit.xml: sync queue + sqlite so jobs run inside the test process
          docker compose exec -T \
            -e QUEUE_CONNECTION=sync \
            laravel php artisan test --filter=DrugRepurposingIntegrationTest
            

      - name: Dump logs on failure
        if: failure()
        run: |
          docker compose logs --no-color laravel drug-repurposing queue

      - name: Tear down
        if: always()
        run: docker compose down -v

  docking-integration-test:
    runs-on: ubuntu-latest
    timeout-minutes: 45

    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          lfs: true
      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Build and start stack
        run: |
          docker compose down -v 2>/dev/null || true
          docker compose build --build-arg COMPOSER_DEV="" laravel
          docker compose up -d laravel

      - name: Verify RDKit, Vina, and Open Babel in container
        run: |
          echo "Verifying python3 import rdkit"
          docker compose exec -T laravel python3 -c "import rdkit; print(rdkit.__version__)"
          echo "Verifying vina --help"
          docker compose exec -T laravel vina --help
          echo "Verifying obabel -V"
          docker compose exec -T laravel obabel -V

      - name: Run Laravel Feature Tests
        run: |
          docker compose exec -T laravel php artisan test --filter=DockingSubmitTest

      - name: Tear down
        if: always()
        run: docker compose down -v

  rag-integration-test:
    runs-on: ubuntu-latest
    timeout-minutes: 90

    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          lfs: true
      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Build and start stack
        run: |
          docker compose down -v 2>/dev/null || true
          docker builder prune -af || true
          docker system df

          COMPOSE_PARALLEL_LIMIT=1 docker compose build
          docker system df

          docker compose up -d --wait

          # Run fresh migrations to ensure clean database state
          docker compose exec -T laravel php artisan migrate:fresh --force

      - name: Seed verified test user
        run: |
          echo "=== Creating verified test user via PHP script ==="
          docker compose exec -T laravel php -r "
          require 'vendor/autoload.php';
          \$app = require_once 'bootstrap/app.php';
          \$kernel = \$app->make(Illuminate\Contracts\Console\Kernel::class);
          \$kernel->bootstrap();

          use App\Models\User;
          use Illuminate\Support\Facades\Hash;

          \$user = User::firstOrCreate(
              ['email' => 'salehyasmeen080@gmail.com'],
              [
                  'name' => 'Test User',
                  'password' => Hash::make('123456789'),
                  'role' => 'normal',
                  'is_verified' => true,
                  'email_verified_at' => now(),
                  'created_at' => now(),
                  'updated_at' => now()
              ]
          );
          echo 'User ID: ' . \$user->id . PHP_EOL;
          echo 'Email: ' . \$user->email . PHP_EOL;
          echo 'Verified: ' . (\$user->is_verified ? 'YES' : 'NO') . PHP_EOL;
          "

      - name: Login and get Bearer token
        run: |
          echo "POST /api/user/login"
          HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST http://localhost:8080/api/user/login \
            -H "Content-Type: application/json" \
            -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
          echo "HTTP Status: $HTTP_CODE"
          cat login.json
          echo ""

          if [ "$HTTP_CODE" != "200" ]; then
            echo "Login failed with HTTP $HTTP_CODE"
            docker compose logs laravel
            exit 1
          fi

          python3 - <<'PY'
          import json, sys
          try:
              data = json.load(open("login.json"))
          except json.JSONDecodeError as e:
              print("Invalid JSON response:", e)
              with open("login.json") as f:
                  print("Raw response:", f.read())
              sys.exit(1)

          if not data.get("success"):
              print("Login failed:", json.dumps(data, indent=2))
              sys.exit(1)

          token = data.get("data", {}).get("token")
          if not token:
              print("No token in response:", json.dumps(data, indent=2))
              sys.exit(1)

          with open("token.txt", "w") as f:
              f.write(token)
          print("Login OK - token saved")
          PY

      - name: Show service status
        if: always()
        run: docker compose ps -a

      - name: Wait for Laravel API
        run: |
          for i in $(seq 1 60); do
            if curl -sf http://localhost:8080/ > /dev/null 2>&1; then
              echo "Laravel is up"
              exit 0
            fi
            echo "Waiting for Laravel ($i/60)..."
            sleep 5
          done
          docker compose logs laravel
          exit 1

      - name: Test retrieval-only chemical search
        run: |
          TOKEN=$(cat token.txt)
          echo "POST /api/chemical-search (retrieval-only)"
          HTTP_CODE=$(curl -s -o chemical_search.json -w "%{http_code}" -X POST http://localhost:8080/api/chemical-search \
            -H "Authorization: Bearer $TOKEN" \
            -H "Content-Type: application/json" \
            -d '{"smiles":"CC(=O)O"}')
          echo "HTTP Status: $HTTP_CODE"
          cat chemical_search.json
          echo ""
          python3 - <<'PY'
          import json, sys
          data = json.load(open("chemical_search.json"))
          if not data.get("success"):
              print("Chemical search (retrieval-only) failed:", json.dumps(data, indent=2))
              sys.exit(1)
          if not isinstance(data.get("compounds"), list):
              print("Missing 'compounds' array in response")
              sys.exit(1)
          if data.get("metadata", {}).get("source") != "retrieval":
              print("Expected source='retrieval', got:", data.get("metadata", {}).get("source"))
              sys.exit(1)
          print("Chemical search (retrieval-only) OK - found", len(data["compounds"]), "compounds")
          PY

      - name: Test full RAG chemical search
        run: |
          TOKEN=$(cat token.txt)
          echo "POST /api/chemical-search/full-rag"
          HTTP_CODE=$(curl -s -o chemical_rag.json -w "%{http_code}" -X POST http://localhost:8080/api/chemical-search/full-rag \
            -H "Authorization: Bearer $TOKEN" \
            -H "Content-Type: application/json" \
            -d '{"smiles":"CC(=O)O"}')
          echo "HTTP Status: $HTTP_CODE"
          cat chemical_rag.json
          echo ""
          python3 - <<'PY'
          import json, sys
          data = json.load(open("chemical_rag.json"))
          if not data.get("success"):
              print("Chemical search (full RAG) failed:", json.dumps(data, indent=2))
              sys.exit(1)
          if not isinstance(data.get("compounds"), list):
              print("Missing 'compounds' array in response")
              sys.exit(1)
          if data.get("metadata", {}).get("source") != "full_rag":
              print("Expected source='full_rag', got:", data.get("metadata", {}).get("source"))
              sys.exit(1)
          # Verify explanations exist for full RAG
          for compound in data["compounds"]:
              if not compound.get("explanation"):
                  print("Missing explanation for compound:", compound.get("name"))
                  sys.exit(1)
          print("Chemical search (full RAG) OK - found", len(data["compounds"]), "compounds with explanations")
          PY

      - name: Dump logs on failure
        if: failure()
        run: |
          docker compose logs --no-color

      - name: Tear down
        if: always()
        run: docker compose down -v