Auto-sync: 201d269f287526269b8ffded5f450ff36b46c740

.editorconfig

@@ -0,0 +1,18 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+indent_size = 4
+indent_style = space
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.md]
+trim_trailing_whitespace = false
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[compose.yaml]
+indent_size = 4

.env.docker

@@ -0,0 +1,36 @@
+APP_NAME=AILIXIR
+APP_ENV=production
+APP_KEY=base64:CHANGEME_GENERATE_ON_FIRST_BOOT=
+APP_DEBUG=false
+APP_URL=http://localhost:8080
+
+LOG_CHANNEL=stderr
+LOG_LEVEL=info
+
+DB_CONNECTION=sqlite
+DB_DATABASE=/var/www/html/database/ailixir.sqlite
+
+SESSION_DRIVER=database
+SESSION_LIFETIME=120
+
+CACHE_STORE=database
+QUEUE_CONNECTION=database
+
+# AI microservices (Docker internal DNS)
+GENERATION_SERVICE_URL=http://generation:8000
+CHEMICAL_AI_URL=http://chemical-rag:5000
+ADMET_AI_URL=http://admet:8000
+AI_ADMET_SERVICE_URL=http://admet:8000
+DRUG_REPURPOSING_URL=http://drug-repurposing:8000
+AI_SERVICE_URL=http://drug-repurposing:8000
+
+AI_INTEGRATION_ROUTES_ENABLED=true
+
+MAIL_MAILER=smtp
+MAIL_HOST=smtp.gmail.com
+MAIL_PORT=587
+MAIL_USERNAME=yasmeensaleh747@gmail.com
+MAIL_PASSWORD="fghu ijct vhfu xnud"
+MAIL_ENCRYPTION=tls
+MAIL_FROM_ADDRESS=yasmeensaleh747@gmail.com
+MAIL_FROM_NAME="AILIXIR"

.env.example

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+# AILIXIR API Test Configuration
+# Copy this to .env and fill in your values
+
+# API URLs
+BASE_URL=https://america-hyperlipemic-grazyna.ngrok-free.dev/api
+AUTH_BASE_URL=https://america-hyperlipemic-grazyna.ngrok-free.dev/api
+
+# Test User Credentials
+TEST_EMAIL=your_email@example.com
+TEST_PASSWORD=your_password
+TEST_NAME=Your Name
+
+# Database (SQLite)
+DB_CONNECTION=sqlite
+DB_DATABASE=database/ailixir.sqlite
+MD_SIMULATION_URL=http://localhost:5005

.env.hf

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+# AILIXIR Hugging Face Spaces Environment
+# Copy the relevant values to HF Space secrets/settings
+
+APP_NAME=AILIXIR
+APP_ENV=production
+APP_DEBUG=false
+APP_URL=https://Ailixir-AI-Team-ailixir-api.hf.space
+
+LOG_CHANNEL=stderr
+LOG_LEVEL=info
+
+DB_CONNECTION=sqlite
+DB_DATABASE=/var/www/html/database/ailixir.sqlite
+
+SESSION_DRIVER=database
+SESSION_LIFETIME=120
+CACHE_STORE=database
+QUEUE_CONNECTION=database
+
+# AI Microservice URLs (HF Spaces)
+GENERATION_SERVICE_URL=https://shdwRow-ailixir-generation.hf.space
+CHEMICAL_AI_URL=https://RottenShadow-ailixir-chemical-rag.hf.space
+ADMET_AI_URL=https://shdwRow-ailixir-admet.hf.space
+AI_ADMET_SERVICE_URL=https://shdwRow-ailixir-admet.hf.space
+DRUG_REPURPOSING_URL=https://RottenShadow-ailixir-drug-repurposing.hf.space
+AI_SERVICE_URL=https://RottenShadow-ailixir-drug-repurposing.hf.space
+
+AI_INTEGRATION_ROUTES_ENABLED=true
+MAIL_MAILER=log
+
+CLOUDINARY_URL=cloudinary://dummy_key:dummy_secret@dummy_cloud
+CLOUDINARY_CLOUD_NAME=dummy_cloud
+CLOUDINARY_API_KEY=dummy_key
+CLOUDINARY_API_SECRET=dummy_secret
+
+# Hugging Face Spaces mode (triggers supervisord)
+RUN_MODE=hf

.gitattributes

@@ -1,35 +1,11 @@
-*.7z filter=lfs diff=lfs merge=lfs -text
-*.arrow filter=lfs diff=lfs merge=lfs -text
-*.bin filter=lfs diff=lfs merge=lfs -text
-*.bz2 filter=lfs diff=lfs merge=lfs -text
-*.ckpt filter=lfs diff=lfs merge=lfs -text
-*.ftz filter=lfs diff=lfs merge=lfs -text
-*.gz filter=lfs diff=lfs merge=lfs -text
-*.h5 filter=lfs diff=lfs merge=lfs -text
-*.joblib filter=lfs diff=lfs merge=lfs -text
-*.lfs.* filter=lfs diff=lfs merge=lfs -text
-*.mlmodel filter=lfs diff=lfs merge=lfs -text
-*.model filter=lfs diff=lfs merge=lfs -text
-*.msgpack filter=lfs diff=lfs merge=lfs -text
-*.npy filter=lfs diff=lfs merge=lfs -text
-*.npz filter=lfs diff=lfs merge=lfs -text
-*.onnx filter=lfs diff=lfs merge=lfs -text
-*.ot filter=lfs diff=lfs merge=lfs -text
-*.parquet filter=lfs diff=lfs merge=lfs -text
-*.pb filter=lfs diff=lfs merge=lfs -text
-*.pickle filter=lfs diff=lfs merge=lfs -text
-*.pkl filter=lfs diff=lfs merge=lfs -text
-*.pt filter=lfs diff=lfs merge=lfs -text
-*.pth filter=lfs diff=lfs merge=lfs -text
-*.rar filter=lfs diff=lfs merge=lfs -text
-*.safetensors filter=lfs diff=lfs merge=lfs -text
-saved_model/**/* filter=lfs diff=lfs merge=lfs -text
-*.tar.* filter=lfs diff=lfs merge=lfs -text
-*.tar filter=lfs diff=lfs merge=lfs -text
-*.tflite filter=lfs diff=lfs merge=lfs -text
-*.tgz filter=lfs diff=lfs merge=lfs -text
-*.wasm filter=lfs diff=lfs merge=lfs -text
-*.xz filter=lfs diff=lfs merge=lfs -text
-*.zip filter=lfs diff=lfs merge=lfs -text
-*.zst filter=lfs diff=lfs merge=lfs -text
-*tfevents* filter=lfs diff=lfs merge=lfs -text
+* text=auto eol=lf
+
+*.blade.php diff=html
+*.css diff=css
+*.html diff=html
+*.md diff=markdown
+*.php diff=php
+
+/.github export-ignore
+CHANGELOG.md export-ignore
+.styleci.yml export-ignore

.github/workflows/api-tests-hf.yml

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+name: AILIXIR API Tests (HF Spaces)
+
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 6 * * *"
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install test dependencies
+        run: pip install -r requirements.txt
+
+      - name: Wake up HF Space
+        run: |
+          echo "Waiting for ailixir-api HF Space to be ready..."
+          for i in $(seq 1 60); do
+            if curl -sf https://Ailixir-AI-Team-ailixir-api.hf.space/ > /dev/null 2>&1; then
+              echo "ailixir-api is up"
+              sleep 5
+              exit 0
+            fi
+            echo "Attempt $i/60: not ready yet..."
+            sleep 5
+          done
+          echo "ailixir-api failed to become healthy in time"
+          exit 1
+
+      - name: Run API tests
+        env:
+          BASE_URL: https://Ailixir-AI-Team-ailixir-api.hf.space/api
+          TEST_EMAIL: test@example.com
+          TEST_PASSWORD: password123
+          TEST_NAME: testuser
+        run: |
+          python -m pytest tests/ -v --tb=short --junitxml=junit.xml || true
+
+      - name: Upload test results
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: test-results-hf
+          path: junit.xml
+
+      - name: Test Summary
+        uses: test-summary/action@v2
+        with:
+          paths: junit.xml
+        if: always()

.github/workflows/api-tests.yml

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+name: AILIXIR API Tests (Docker)
+
+on:
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        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: Create .env file for Docker
+        run: |
+          cp docker/laravel.env .env
+
+      - name: Start Docker containers
+        run: |
+          docker compose up -d --build
+
+      - name: Wait for services to be healthy
+        run: |
+          echo "Waiting for Laravel API to be ready..."
+          for i in {1..60}; do
+            if docker exec ailixir-laravel curl -f http://127.0.0.1:8000 > /dev/null 2>&1; then
+              echo "Laravel API is ready"
+              break
+            fi
+            echo "Attempt $i/60: Laravel API not ready yet..."
+            sleep 3
+          done
+
+          echo "Waiting for ADMET service to be healthy..."
+          for i in {1..120}; do
+            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
+              break
+            fi
+            echo "Attempt $i/120: ADMET service not ready yet..."
+            sleep 5
+          done
+
+          echo "All services are up and running!"
+          docker compose ps
+
+      - name: Run database migrations
+        run: |
+          docker exec ailixir-laravel php artisan migrate --force
+
+      - name: Run API tests
+        env:
+          BASE_URL: http://localhost:8080/api
+          TEST_EMAIL: test@example.com
+          TEST_PASSWORD: password123
+          TEST_NAME: testuser
+        run: |
+          docker exec ailixir-laravel \
+            python -m pytest tests/ -v --tb=short --junitxml=junit.xml || true
+
+      - name: Copy test results from container
+        if: always()
+        run: |
+          docker cp ailixir-laravel:/var/www/html/junit.xml ./junit.xml || true
+
+      - name: Upload test results
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: test-results
+          path: junit.xml
+
+      - name: Test Summary
+        uses: test-summary/action@v2
+        with:
+          paths: "junit.xml"
+        if: always()
+
+      - name: Collect Docker logs
+        if: failure()
+        run: |
+          mkdir -p logs
+          docker compose logs laravel > logs/laravel.log
+          docker compose logs admet > logs/admet.log
+          docker compose logs drug-repurposing > logs/drug-repurposing.log
+          docker compose logs chemical-rag > logs/chemical-rag.log
+
+      - name: Upload Docker logs
+        uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: docker-logs
+          path: logs/
+
+      - name: Cleanup Docker containers
+        if: always()
+        run: |
+          docker compose down -v

.github/workflows/e2e-md-test.yml

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+name: MD Simulation E2E Test
+
+on:
+  push:
+    branches: [main, develop, MD-integration]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 6 * * *"
+  workflow_dispatch:
+
+concurrency:
+  group: e2e-md-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  e2e-md-simulation:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build Laravel image
+        run: docker build -t ailixir-laravel .
+
+      - name: Build MD simulation image
+        run: docker build -t md-simulation ai_apps/Protein-Ligand-MD-Simulation/
+
+      - name: Create Docker network
+        run: docker network create ailixir-md
+
+      - name: Start Redis
+        run: |
+          docker run -d --name md-redis \
+            --network ailixir-md \
+            --network-alias md-redis \
+            redis:7-alpine
+
+      - name: Start MD Simulation API
+        run: |
+          docker run -d --name md-api \
+            --network ailixir-md \
+            -p 5005:5005 \
+            -e REDIS_HOST=md-redis \
+            -e REDIS_PORT=6379 \
+            -e USE_REDIS=true \
+            -e OPENMM_PLATFORM=CPU \
+            -e FLASK_HOST=0.0.0.0 \
+            -e FLASK_PORT=5005 \
+            -e MD_DATA_DIR=/app/data \
+            -e LOG_LEVEL=INFO \
+            md-simulation
+
+      - name: Start Laravel API
+        run: |
+          docker run -d --name ailixir-laravel \
+            --network ailixir-md \
+            -p 8000:8000 \
+            --env-file docker/laravel.env \
+            -e MD_SIMULATION_URL=http://md-api:5005 \
+            -e QUEUE_CONNECTION=sync \
+            -e APP_KEY=base64:l+P8vPcH6w+2qV6vYC3h8K9xN0mR4sT5uW6xY7zA8bB= \
+            ailixir-laravel
+
+      - name: Wait for Laravel API to be ready
+        run: |
+          echo "Waiting for Laravel API to be ready..."
+          for i in $(seq 1 30); do
+            if curl -sf http://localhost:8000/ > /dev/null 2>&1; then
+              echo "Laravel API is ready"
+              exit 0
+            fi
+            echo "Waiting for Laravel ($i/30)..."
+            sleep 2
+          done
+          docker logs ailixir-laravel
+          exit 1
+
+      - name: Wait for MD Simulation API to be healthy
+        run: |
+          echo "Waiting for MD Simulation API to be healthy..."
+          for i in $(seq 1 60); do
+            if curl -sf http://localhost:5005/health > /dev/null 2>&1; then
+              echo "MD Simulation API is healthy"
+              exit 0
+            fi
+            echo "Waiting for MD API ($i/60)..."
+            sleep 5
+          done
+          docker logs md-api
+          exit 1
+
+      - name: Run MD Simulation E2E tests
+        run: |
+          docker exec \
+            -e MD_E2E_BASE_URL=http://localhost:8000/api \
+            ailixir-laravel \
+            ./vendor/bin/pest --filter=MdSimulationE2ETest --log-junit=/var/www/html/junit.xml
+
+      - name: Copy test results from container
+        if: always()
+        run: |
+          docker cp ailixir-laravel:/var/www/html/junit.xml ./junit.xml || true
+
+      - name: Upload test results
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: e2e-md-test-results
+          path: junit.xml
+
+      - name: Test Summary
+        uses: test-summary/action@v2
+        if: always()
+        with:
+          paths: junit.xml
+
+      - name: Dump logs on failure
+        if: failure()
+        run: |
+          echo "=== Laravel logs ==="
+          docker logs ailixir-laravel || true
+          echo "=== MD API logs ==="
+          docker logs md-api || true
+          echo "=== Redis logs ==="
+          docker logs md-redis || true
+
+      - name: Cleanup
+        if: always()
+        run: |
+          docker rm -f ailixir-laravel md-api md-redis 2>/dev/null || true
+          docker network rm ailixir-md 2>/dev/null || true

.github/workflows/integration-test-hf.yml

@@ -0,0 +1,492 @@
+name: HF Spaces Integration Test
+
+on:
+  push:
+    branches: [main, develop, "feature/**"]
+  pull_request:
+    branches: [main, develop]
+  workflow_dispatch:
+
+concurrency:
+  group: hf-integration-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  core-ai-proxy:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Warm up ailixir-api Space
+        run: |
+          echo "Waiting for ailixir-api HF Space..."
+          for i in $(seq 1 60); do
+            if curl -sf https://Ailixir-AI-Team-ailixir-api.hf.space/ > /dev/null 2>&1; then
+              echo "ailixir-api is up"
+              sleep 5
+              exit 0
+            fi
+            echo "Attempt $i/60..."
+            sleep 5
+          done
+          exit 1
+
+      - name: Warm up ailixir-drug-repurposing Space
+        run: |
+          echo "Waiting for ailixir-drug-repurposing HF Space..."
+          for i in $(seq 1 60); do
+            if curl -sf https://RottenShadow-ailixir-drug-repurposing.hf.space/health > /dev/null 2>&1; then
+              echo "ailixir-drug-repurposing is up"
+              sleep 3
+              exit 0
+            fi
+            echo "Attempt $i/60..."
+            sleep 5
+          done
+          exit 1
+
+      - name: Warm up ailixir-admet Space
+        run: |
+          echo "Waiting for ailixir-admet HF Space..."
+          for i in $(seq 1 60); do
+            if curl -sf https://shdwRow-ailixir-admet.hf.space/health > /dev/null 2>&1; then
+              echo "ailixir-admet is up"
+              sleep 3
+              exit 0
+            fi
+            echo "Attempt $i/60..."
+            sleep 5
+          done
+          exit 1
+
+      - name: Warm up ailixir-chemical-rag Space
+        run: |
+          echo "Waiting for ailixir-chemical-rag HF Space..."
+          for i in $(seq 1 60); do
+            if curl -sf https://RottenShadow-ailixir-chemical-rag.hf.space/health > /dev/null 2>&1; then
+              echo "ailixir-chemical-rag is up"
+              sleep 3
+              exit 0
+            fi
+            echo "Attempt $i/60..."
+            sleep 5
+          done
+          exit 1
+
+      - name: Login and get Bearer token
+        run: |
+          echo "POST /api/user/login"
+          HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/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 $HTTP_CODE"
+            exit 1
+          fi
+
+          python3 - <<'PY'
+          import json, sys
+          try:
+              data = json.load(open("login.json"))
+          except json.JSONDecodeError as e:
+              print("Invalid JSON response:", e)
+              with open("login.json") as f:
+                  print("Raw response:", f.read())
+              sys.exit(1)
+
+          if not data.get("success"):
+              print("Login failed:", json.dumps(data, indent=2))
+              sys.exit(1)
+
+          token = data.get("data", {}).get("token")
+          if not token:
+              print("No token in response:", json.dumps(data, indent=2))
+              sys.exit(1)
+
+          with open("token.txt", "w") as f:
+              f.write(token)
+          print("Login OK - token saved")
+          PY
+
+      - name: Test aggregated AI health via Laravel
+        run: |
+          TOKEN=$(cat token.txt)
+          echo "GET /api/ai-services/health"
+          HTTP_CODE=$(curl -s -o health.json -w "%{http_code}" https://Ailixir-AI-Team-ailixir-api.hf.space/api/ai-services/health \
+            -H "Authorization: Bearer $TOKEN")
+          echo "HTTP Status: $HTTP_CODE"
+          cat health.json
+          echo ""
+          python3 - <<'PY'
+          import json, sys
+          data = json.load(open("health.json"))
+          if not data.get("success"):
+              print("AI services health check failed:", json.dumps(data, indent=2))
+              sys.exit(1)
+          print("All AI services healthy via Laravel proxy")
+          PY
+
+      - name: Test ADMET prediction via Laravel proxy
+        run: |
+          TOKEN=$(cat token.txt)
+          echo "POST /api/admet/predict"
+          HTTP_CODE=$(curl -s -o admet.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/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 failed with HTTP $HTTP_CODE"
+            exit 1
+          fi
+
+          python3 - <<'PY'
+          import json, sys
+          try:
+              data = json.load(open("admet.json"))
+          except json.JSONDecodeError as e:
+              print("Invalid JSON response:", e)
+              with open("admet.json") as f:
+                  print("Raw response:", f.read())
+              sys.exit(1)
+
+          if not data.get("success"):
+              print("ADMET prediction test failed:", json.dumps(data, indent=2))
+              sys.exit(1)
+
+          results = data.get("data", {}).get("results", [])
+          if len(results) < 3:
+              print(f"Expected at least 3 results, got {len(results)}")
+              sys.exit(1)
+
+          print(f"ADMET prediction OK - {len(results)} compounds processed")
+          PY
+
+      - name: Test Chemical RAG proxy via Laravel
+        run: |
+          TOKEN=$(cat token.txt)
+          echo "POST /api/ai-services/test/chemical-search"
+          HTTP_CODE=$(curl -s -o chemical.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/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}" https://Ailixir-AI-Team-ailixir-api.hf.space/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
+
+  chemical-search:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Warm up ailixir-api Space
+        run: |
+          for i in $(seq 1 60); do
+            if curl -sf https://Ailixir-AI-Team-ailixir-api.hf.space/ > /dev/null 2>&1; then
+              echo "ailixir-api is up"
+              sleep 5
+              exit 0
+            fi
+            echo "Waiting ($i/60)..."
+            sleep 5
+          done
+          exit 1
+
+      - name: Login and get Bearer token
+        run: |
+          HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
+            -H "Content-Type: application/json" \
+            -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
+          if [ "$HTTP_CODE" != "200" ]; then exit 1; fi
+          python3 - <<'PY'
+          import json
+          with open('login.json') as f: data = json.load(f)
+          token = data.get('data', {}).get('token')
+          if not token: exit(1)
+          with open('token.txt','w') as f: f.write(token)
+          print('Login OK')
+          PY
+
+      - name: Test retrieval-only chemical search
+        run: |
+          TOKEN=$(cat token.txt)
+          echo "POST /api/chemical-search (retrieval-only)"
+          HTTP_CODE=$(curl -s -o search.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/chemical-search \
+            -H "Authorization: Bearer $TOKEN" \
+            -H "Content-Type: application/json" \
+            -d '{"smiles":"CC(=O)O"}')
+          echo "HTTP Status: $HTTP_CODE"
+          cat search.json
+          echo ""
+          python3 - <<'PY'
+          import json, sys
+          data = json.load(open("search.json"))
+          if not data.get("success"):
+              print("Chemical search (retrieval-only) failed:", json.dumps(data, indent=2))
+              sys.exit(1)
+          if not isinstance(data.get("compounds"), list):
+              print("Missing 'compounds' array in response")
+              sys.exit(1)
+          if data.get("metadata", {}).get("source") != "retrieval":
+              print("Expected source='retrieval', got:", data.get("metadata", {}).get("source"))
+              sys.exit(1)
+          print("Chemical search (retrieval-only) OK - found", len(data["compounds"]), "compounds")
+          PY
+
+      - name: Test full RAG chemical search
+        run: |
+          TOKEN=$(cat token.txt)
+          echo "POST /api/chemical-search/full-rag"
+          HTTP_CODE=$(curl -s -o rag.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/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 rag.json
+          echo ""
+          python3 - <<'PY'
+          import json, sys
+          data = json.load(open("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)
+          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
+
+  drug-repurposing-integration:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Warm up ailixir-api Space
+        run: |
+          for i in $(seq 1 60); do
+            if curl -sf https://Ailixir-AI-Team-ailixir-api.hf.space/ > /dev/null 2>&1; then
+              echo "ailixir-api is up"
+              sleep 5
+              exit 0
+            fi
+            echo "Waiting ($i/60)..."
+            sleep 5
+          done
+          exit 1
+
+      - name: Login and get Bearer token
+        run: |
+          HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
+            -H "Content-Type: application/json" \
+            -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
+          if [ "$HTTP_CODE" != "200" ]; then exit 1; fi
+          python3 - <<'PY'
+          import json
+          with open('login.json') as f: data = json.load(f)
+          token = data.get('data', {}).get('token')
+          if not token: exit(1)
+          with open('token.txt','w') as f: f.write(token)
+          print('Login OK')
+          PY
+
+      - name: Test unauthenticated DR request is rejected
+        run: |
+          echo "POST /api/drug-repurposing/targets (no auth)"
+          HTTP_CODE=$(curl -s -o dr_unauth.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/drug-repurposing/targets \
+            -H "Content-Type: application/json" \
+            -d '{"disease_name":"Type 2 Diabetes"}')
+          if [ "$HTTP_CODE" != "401" ]; then
+            echo "Expected 401, got $HTTP_CODE"
+            exit 1
+          fi
+          python3 - <<'PY'
+          import json
+          with open('dr_unauth.json') as f: data = json.load(f)
+          assert not data.get('success', True), 'Expected success=false'
+          print('Unauthenticated DR request correctly rejected')
+          PY
+
+      - name: Test DR target lookup requires disease_name
+        run: |
+          TOKEN=$(cat token.txt)
+          echo "POST /api/drug-repurposing/targets (missing disease_name)"
+          HTTP_CODE=$(curl -s -o dr_validation.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/drug-repurposing/targets \
+            -H "Authorization: Bearer $TOKEN" \
+            -H "Content-Type: application/json" \
+            -d '{"top_n": 2}')
+          if [ "$HTTP_CODE" != "422" ]; then
+            echo "Expected 422, got $HTTP_CODE"
+            exit 1
+          fi
+          echo "Missing disease_name correctly rejected"
+
+      - name: Test DR target lookup via Laravel proxy
+        run: |
+          TOKEN=$(cat token.txt)
+          echo "POST /api/drug-repurposing/targets"
+          HTTP_CODE=$(curl -s -o dr_targets.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/drug-repurposing/targets \
+            -H "Authorization: Bearer $TOKEN" \
+            -H "Content-Type: application/json" \
+            -d '{"disease_name":"Type 2 Diabetes","top_n":2}')
+          echo "HTTP Status: $HTTP_CODE"
+          cat dr_targets.json
+          echo ""
+
+          if [ "$HTTP_CODE" != "200" ]; then
+            echo "DR target lookup failed with HTTP $HTTP_CODE"
+            exit 1
+          fi
+
+          python3 - <<'PY'
+          import json, sys
+          data = json.load(open("dr_targets.json"))
+          if not data.get("success"):
+              print("DR target lookup failed:", json.dumps(data, indent=2))
+              sys.exit(1)
+          job_id = data.get("data", {}).get("job_id")
+          status = data.get("data", {}).get("status")
+          print(f"DR target lookup OK - job_id={job_id}, status={status}")
+
+          # Poll for completion
+          import time, urllib.request
+          base = "https://Ailixir-AI-Team-ailixir-api.hf.space/api/drug-repurposing/targets"
+          with open("token.txt") as f: token = f.read().strip()
+          for i in range(30):
+              req = urllib.request.Request(f"{base}/{job_id}")
+              req.add_header("Authorization", f"Bearer {token}")
+              resp = urllib.request.urlopen(req)
+              status_data = json.loads(resp.read())
+              s = status_data.get("data", {}).get("status")
+              if s == "completed":
+                  output = status_data.get("data", {}).get("output", {})
+                  assert len(output.get("targets", [])) > 0, "No targets found"
+                  print(f"DR targets completed - {len(output['targets'])} targets found")
+                  sys.exit(0)
+              elif s == "failed":
+                  print("DR target lookup failed:", json.dumps(status_data, indent=2))
+                  sys.exit(1)
+              print(f"  Polling... attempt {i+1}/30, status={s}")
+              time.sleep(5)
+          print("DR target lookup did not complete in time")
+          sys.exit(1)
+          PY
+
+  docking-integration:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Warm up ailixir-api Space
+        run: |
+          for i in $(seq 1 60); do
+            if curl -sf https://Ailixir-AI-Team-ailixir-api.hf.space/ > /dev/null 2>&1; then
+              echo "ailixir-api is up"
+              sleep 5
+              exit 0
+            fi
+            echo "Waiting ($i/60)..."
+            sleep 5
+          done
+          exit 1
+
+      - name: Login and get Bearer token
+        run: |
+          HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
+            -H "Content-Type: application/json" \
+            -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
+          if [ "$HTTP_CODE" != "200" ]; then exit 1; fi
+          python3 - <<'PY'
+          import json
+          with open('login.json') as f: data = json.load(f)
+          token = data.get('data', {}).get('token')
+          if not token: exit(1)
+          with open('token.txt','w') as f: f.write(token)
+          print('Login OK')
+          PY
+
+      - name: Test docking submit
+        run: |
+          TOKEN=$(cat token.txt)
+          echo "POST /api/docking/submit"
+          HTTP_CODE=$(curl -s -o docking.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/docking/submit \
+            -H "Authorization: Bearer $TOKEN" \
+            -F "protein_name=EGFR" \
+            -F "protein_file=@tests/Fixtures/docking/egfr_clean.pdbqt" \
+            -F "ligand_name=Erlotinib" \
+            -F "ligand_file=@tests/Fixtures/docking/ligand.pdbqt" \
+            -F "center_x=10.0" \
+            -F "center_y=15.0" \
+            -F "center_z=20.0" \
+            -F "box_size_x=25.0" \
+            -F "box_size_y=25.0" \
+            -F "box_size_z=25.0" \
+            -F "exhaustiveness=8")
+          echo "HTTP Status: $HTTP_CODE"
+          cat docking.json
+          echo ""
+
+          if [ "$HTTP_CODE" != "200" ]; then
+            echo "Docking submit failed with HTTP $HTTP_CODE"
+            exit 1
+          fi
+
+          python3 - <<'PY'
+          import json, sys
+          data = json.load(open("docking.json"))
+          if not data.get("success"):
+              print("Docking submit failed:", json.dumps(data, indent=2))
+              sys.exit(1)
+          print("Docking submit OK - job created")
+          PY

.github/workflows/integration-test.yml

@@ -0,0 +1,553 @@
+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

.github/workflows/keep-hf-alive.yml

@@ -0,0 +1,21 @@
+name: Keep HF Alive
+
+on:
+  schedule:
+    - cron: "0 */24 * * *"
+  workflow_dispatch:
+
+jobs:
+  keep_hf_alive_job:
+    name: keep hf alive job
+    runs-on: ubuntu-latest
+    steps:
+      - name: Hit main API health endpoint
+        run: |
+          curl -s -o /dev/null -w "%{http_code}" \
+            "https://Ailixir-AI-Team-ailixir-api.hf.space/api/ai-services/health"
+
+      - name: Hit generation health endpoint
+        run: |
+          curl -s -o /dev/null -w "%{http_code}" \
+            "https://shdwrow-ailixir-generation.hf.space/health"

.github/workflows/md-simulation-health.yml

@@ -0,0 +1,117 @@
+name: MD Simulation Health Check
+
+on:
+  push:
+    branches: [MD-integration]
+  workflow_dispatch:
+
+concurrency:
+  group: md-simulation-health-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  md-simulation-health-check:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build Laravel image
+        run: docker build -t ailixir-laravel .
+
+      - name: Build MD simulation image
+        run: docker build -t md-simulation ai_apps/Protein-Ligand-MD-Simulation/
+
+      - name: Create Docker network
+        run: docker network create ailixir-md
+
+      - name: Start Laravel API
+        run: |
+          docker run -d --name ailixir-laravel \
+            --network ailixir-md \
+            -p 8000:8000 \
+            --env-file docker/laravel.env \
+            -e MD_SIMULATION_URL=http://md-api:5005 \
+            ailixir-laravel
+
+      - name: Start Redis
+        run: |
+          docker run -d --name md-redis \
+            --network ailixir-md \
+            --network-alias md-redis \
+            redis:7-alpine
+
+      - name: Start MD Simulation API
+        run: |
+          docker run -d --name md-api \
+            --network ailixir-md \
+            -p 5005:5005 \
+            -e REDIS_HOST=md-redis \
+            -e REDIS_PORT=6379 \
+            -e USE_REDIS=true \
+            -e OPENMM_PLATFORM=CPU \
+            -e FLASK_HOST=0.0.0.0 \
+            -e FLASK_PORT=5005 \
+            -e MD_DATA_DIR=/app/data \
+            -e LOG_LEVEL=INFO \
+            md-simulation
+
+      - name: Wait for Laravel API to be ready
+        run: |
+          echo "Waiting for Laravel API to be ready..."
+          for i in $(seq 1 30); do
+            if curl -sf http://localhost:8000/ > /dev/null 2>&1; then
+              echo "Laravel API is ready"
+              exit 0
+            fi
+            echo "Waiting for Laravel ($i/30)..."
+            sleep 2
+          done
+          docker logs ailixir-laravel
+          exit 1
+
+      - name: Wait for MD Simulation API to be healthy
+        run: |
+          echo "Waiting for MD Simulation API to be healthy..."
+          for i in $(seq 1 60); do
+            if curl -sf http://localhost:5005/health > /dev/null 2>&1; then
+              echo "MD Simulation API is healthy"
+              exit 0
+            fi
+            echo "Waiting for MD API ($i/60)..."
+            sleep 5
+          done
+          docker logs md-api
+          exit 1
+
+      - name: Test MD simulation health via Laravel proxy
+        run: |
+          echo "GET /api/md-simulation/health via Laravel proxy"
+          RESPONSE=$(curl -sf http://localhost:8000/api/md-simulation/health)
+          echo "$RESPONSE"
+          STATUS=$(echo "$RESPONSE" | python3 -c "import json,sys; print(json.load(sys.stdin).get('status'))")
+          if [ "$STATUS" != "ok" ]; then
+            echo "Expected status 'ok', got '$STATUS'"
+            exit 1
+          fi
+          echo "MD Simulation service is healthy via Laravel proxy!"
+
+      - name: Dump logs on failure
+        if: failure()
+        run: |
+          docker logs ailixir-laravel || true
+          docker logs md-api || true
+          docker logs md-redis || true
+
+      - name: Cleanup
+        if: always()
+        run: |
+          docker rm -f ailixir-laravel md-api md-redis 2>/dev/null || true
+          docker network rm ailixir-md 2>/dev/null || true

.github/workflows/push-models-to-hf.yml

@@ -0,0 +1,31 @@
+name: Push Models to HF Generation Space
+
+on:
+  workflow_dispatch:
+
+jobs:
+  push-models:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Upload models to HF dataset
+        run: |
+          pip install huggingface_hub
+          python -c "
+          from huggingface_hub import HfApi
+          api = HfApi()
+          api.upload_folder(
+              repo_id='shdwRow/ailixir-generation-models',
+              folder_path='ai_apps/generation/bundle/models',
+              repo_type='dataset',
+              token='${{ secrets.HF_TOKEN_SHDWROW }}'
+          )
+          print('Models uploaded successfully')
+          "
+
+      - name: Rebuild HF Space with latest models
+        run: |
+          curl -X POST \
+            "https://huggingface.co/api/spaces/shdwRow/ailixir-generation/restart" \
+            -H "Authorization: Bearer ${{ secrets.HF_TOKEN_SHDWROW }}"

.github/workflows/sync-hf-all.yml

@@ -0,0 +1,232 @@
+name: Sync to Hugging Face Spaces
+
+# Automatically syncs code from GitHub main branch to all 5 Hugging Face Spaces.
+# Each job syncs a different subset of the repo to a specific HF Space.
+#
+# Two HF accounts are used:
+#   - RottenShadow: ailixir-drug-repurposing, ailixir-chemical-rag
+#   - shdwRow (secondary): ailixir-admet, ailixir-generation
+#   - Ailixir-AI-Team: ailixir-api
+#
+# Required GitHub secrets:
+#   HF_TOKEN            — HF access token for RottenShadow account (read+write permissions)
+#   HF_TOKEN_AILIXIR    — HF access token for Ailixir-AI-Team account (read+write permissions)
+#   HF_TOKEN_SHDWROW    — HF access token for shdwRow account (read+write permissions)
+#   GOOGLE_CLIENT_ID    — Google OAuth client ID
+#   GOOGLE_CLIENT_SECRET — Google OAuth client secret
+
+on:
+  push:
+    branches: [main, feature/hugging-face-deploy]
+  workflow_dispatch:
+
+jobs:
+  # ── Backend API (Laravel) ──────────────────────────────────────
+  # Syncs the full repo minus AI app directories to Ailixir-AI-Team/ailixir-api.
+  # The live SQLite database (database/ailixir.sqlite) is preserved across syncs:
+  #   - Excluded from rsync so it's never overwritten
+  #   - Restored from HEAD via git checkout so live data isn't committed
+  backend:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Sync ailixir-api
+        env:
+          HF_TOKEN_AILIXIR: ${{ secrets.HF_TOKEN_AILIXIR }}
+        run: |
+          SPACE="Ailixir-AI-Team/ailixir-api"
+          REPO_URL="https://Ailixir-AI-Team:${HF_TOKEN_AILIXIR}@huggingface.co/spaces/${SPACE}"
+          git clone --depth 1 "$REPO_URL" /tmp/hf-space
+          cd /tmp/hf-space
+          # Sync files (new, modified, deleted) but preserve the live database
+          rsync -av --delete --exclude=ai_apps --exclude=.git --exclude=.env --exclude=.dockerignore --exclude=public/imgs --exclude=storage --exclude=Diagrams --exclude=database/ailixir.sqlite "$GITHUB_WORKSPACE/" .
+          cp "$GITHUB_WORKSPACE/README_HF.md" README.md 2>/dev/null || true
+          # Write .env with all required environment variables for HF Spaces
+          printf '%s\n' \
+            'RUN_MODE=hf' \
+            'APP_KEY=base64:T/MgQZht16genNJN3aZ5flCuvfe7Zfs4yFhuAFO2itU=' \
+            'AI_INTEGRATION_ROUTES_ENABLED=true' \
+            'APP_URL=https://Ailixir-AI-Team-ailixir-api.hf.space' \
+            'APP_DEBUG=true' \
+            'ADMET_AI_URL=https://shdwRow-ailixir-admet.hf.space' \
+            'CHEMICAL_AI_URL=https://RottenShadow-ailixir-chemical-rag.hf.space' \
+            'DRUG_REPURPOSING_URL=https://RottenShadow-ailixir-drug-repurposing.hf.space' \
+            'GENERATION_SERVICE_URL=https://shdwRow-ailixir-generation.hf.space' \
+            'GOOGLE_CLIENT_ID=${{ secrets.GOOGLE_CLIENT_ID }}' \
+            'GOOGLE_CLIENT_SECRET=${{ secrets.GOOGLE_CLIENT_SECRET }}' \
+            'GOOGLE_REDIRECT_URI=https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/auth/google' \
+            'CLOUDINARY_CLOUD_NAME=dummy_cloud' \
+            'CLOUDINARY_API_KEY=dummy_key' \
+            'CLOUDINARY_API_SECRET=dummy_secret' \
+            'QUEUE_CONNECTION=sync' \
+            > .env
+          git config user.name "AILIXIR Bot"
+          git config user.email "bot@ailixir.app"
+          # Prevent the live database from being tracked/committed
+          git checkout HEAD -- database/ailixir.sqlite 2>/dev/null || true
+          git add -A
+          if git diff --cached --quiet; then echo "  No changes"; else git commit -m "Auto-sync: $GITHUB_SHA"; git push; fi
+
+  # ── Drug Repurposing (FastAPI) ─────────────────────────────────
+  # Syncs ai_apps/Drug Reporposing/ to RottenShadow/ailixir-drug-repurposing.
+  # Renames Dockerfile.hf → Dockerfile if present.
+  # Can run in mock mode for testing (set USE_MOCK_MODEL=true in HF secrets).
+  drug-repurposing:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Sync ailixir-drug-repurposing
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: |
+          SPACE="RottenShadow/ailixir-drug-repurposing"
+          REPO_URL="https://RottenShadow:${HF_TOKEN}@huggingface.co/spaces/${SPACE}"
+          git clone --depth 1 "$REPO_URL" /tmp/hf-space
+          cd /tmp/hf-space
+          rsync -av --delete --exclude=.git --exclude=__pycache__ --exclude='*.pyc' --exclude=digrams --exclude=docs --exclude=docker "$GITHUB_WORKSPACE/ai_apps/Drug Reporposing/" .
+          cp "$GITHUB_WORKSPACE/ai_apps/Drug Reporposing/README_HF.md" README.md 2>/dev/null || true
+          if [ -f Dockerfile.hf ]; then mv Dockerfile.hf Dockerfile; fi
+          git config user.name "AILIXIR Bot"
+          git config user.email "bot@ailixir.app"
+          git add -A
+          if git diff --cached --quiet; then echo "  No changes"; else git commit -m "Auto-sync: $GITHUB_SHA"; git push; fi
+
+  # ── ADMET Prediction (FastAPI + PyTorch) ───────────────────────
+  # Syncs ai_apps/ADMIT/admet_inference/ to shdwRow/ailixir-admet.
+  # Uses HF Xet for binary .ckpt model files.
+  # Requires HF_TOKEN_SHDWROW secret (shdwRow account).
+  admet:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Install git-xet for binary file support
+        run: |
+          curl --proto '=https' --tlsv1.2 -sSf https://raw.githubusercontent.com/huggingface/xet-core/refs/heads/main/git_xet/install.sh | sh
+          git xet install
+      - name: Sync ailixir-admet
+        env:
+          HF_TOKEN_SHDWROW: ${{ secrets.HF_TOKEN_SHDWROW }}
+        run: |
+          SPACE="shdwRow/ailixir-admet"
+          REPO_URL="https://shdwRow:${HF_TOKEN_SHDWROW}@huggingface.co/spaces/${SPACE}"
+          git clone --depth 1 "$REPO_URL" /tmp/hf-space
+          cd /tmp/hf-space
+          rsync -av --delete --exclude=.git --exclude=datasets.rar "$GITHUB_WORKSPACE/ai_apps/ADMIT/admet_inference/" .
+          cp README_HF.md README.md 2>/dev/null || true
+          git config user.name "AILIXIR Bot"
+          git config user.email "bot@ailixir.app"
+          git config lfs.allowincompletepush true
+          git lfs install
+          git lfs track '*.ckpt'
+          git add -A
+          if git diff --cached --quiet; then echo "  No changes"; else git commit -m "Auto-sync: $GITHUB_SHA"; git push; fi
+
+  # ── Chemical RAG (FastAPI + ChromaDB) ─────────────────────────
+  # Syncs ai_apps/chemical-rag-system/chemical-rag-system/ to RottenShadow/ailixir-chemical-rag.
+  chemical-rag:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Sync ailixir-chemical-rag
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: |
+          SPACE="RottenShadow/ailixir-chemical-rag"
+          REPO_URL="https://RottenShadow:${HF_TOKEN}@huggingface.co/spaces/${SPACE}"
+          git clone --depth 1 "$REPO_URL" /tmp/hf-space
+          cd /tmp/hf-space
+          rsync -av --delete --exclude=.git --exclude=digrams "$GITHUB_WORKSPACE/ai_apps/chemical-rag-system/chemical-rag-system/" .
+          cp README_HF.md README.md 2>/dev/null || true
+          git config user.name "AILIXIR Bot"
+          git config user.email "bot@ailixir.app"
+          git add -A
+          if git diff --cached --quiet; then echo "  No changes"; else git commit -m "Auto-sync: $GITHUB_SHA"; git push; fi
+
+  # ── Molecular Generation (FastAPI + REINVENT4) ────────────────
+  # Syncs ai_apps/generation/ to shdwRow/ailixir-generation.
+  # Renames Dockerfile.hf → Dockerfile (or Dockerfile.api → Dockerfile as fallback).
+  # Uses HF Xet for binary .ckpt, .pt, .pkl model files.
+  # Requires HF_TOKEN_SHDWROW secret (shdwRow account).
+  generation:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Install git-xet for binary file support
+        run: |
+          curl --proto '=https' --tlsv1.2 -sSf https://raw.githubusercontent.com/huggingface/xet-core/refs/heads/main/git_xet/install.sh | sh
+          git xet install
+      - name: Sync ailixir-generation
+        env:
+          HF_TOKEN_SHDWROW: ${{ secrets.HF_TOKEN_SHDWROW }}
+        run: |
+          SPACE="shdwRow/ailixir-generation"
+          REPO_URL="https://shdwRow:${HF_TOKEN_SHDWROW}@huggingface.co/spaces/${SPACE}"
+          git clone --depth 1 "$REPO_URL" /tmp/hf-space
+          cd /tmp/hf-space
+          rsync -av --delete --exclude=.git --exclude=bundle/models "$GITHUB_WORKSPACE/ai_apps/generation/" .
+          cp "$GITHUB_WORKSPACE/ai_apps/generation/README_HF.md" README.md 2>/dev/null || true
+          if [ -f Dockerfile.hf ]; then mv Dockerfile.hf Dockerfile; elif [ -f Dockerfile.api ]; then mv Dockerfile.api Dockerfile; fi
+          git config user.name "AILIXIR Bot"
+          git config user.email "bot@ailixir.app"
+          git add -A
+          if git diff --cached --quiet; then echo "  No changes"; else git commit -m "Auto-sync: $GITHUB_SHA"; git push; fi
+
+  chat-bot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install Hugging Face CLI
+        run: pip install -U "huggingface_hub[cli]"
+
+      - name: Add Gemini key to Hugging Face Space secrets
+        env:
+          HF_TOKEN_SHDWROW: ${{ secrets.HF_TOKEN_SHDWROW }}
+          GEMINI_API_KEY: ${{ secrets.GEMINI_API_KEY }}
+        run: |
+          hf spaces secrets add shdwRow/ailixir-chat-bot \
+            -s GEMINI_API_KEY="$GEMINI_API_KEY" \
+            --token "$HF_TOKEN_SHDWROW"
+
+      - name: Sync ailixir-chat-bot
+        env:
+          HF_TOKEN_SHDWROW: ${{ secrets.HF_TOKEN_SHDWROW }}
+        run: |
+          SPACE="shdwRow/ailixir-chat-bot"
+          REPO_URL="https://shdwRow:${HF_TOKEN_SHDWROW}@huggingface.co/spaces/${SPACE}"
+
+          git clone --depth 1 "$REPO_URL" /tmp/hf-chat-bot
+          cd /tmp/hf-chat-bot
+
+          rsync -av --delete \
+            --exclude=.git \
+            --exclude=.env \
+            --exclude=__pycache__ \
+            --exclude='*.pyc' \
+            --exclude='*.db' \
+            --exclude='*.db-shm' \
+            --exclude='*.db-wal' \
+            "$GITHUB_WORKSPACE/ai_apps/chem_agent_api/" .
+
+          git config user.name "AILIXIR Bot"
+          git config user.email "bot@ailixir.app"
+
+          git add -A
+          if git diff --cached --quiet; then
+            echo "No changes"
+          else
+            git commit -m "Auto-sync chat bot: $GITHUB_SHA"
+            git push
+          fi

.gitignore

@@ -0,0 +1,37 @@
+*.log
+.DS_Store
+.env
+.env.backup
+.env.production
+.phpactor.json
+.phpunit.result.cache
+/.fleet
+/.idea
+/.nova
+/.phpunit.cache
+/.vscode
+/.zed
+/auth.json
+/node_modules
+/public/build
+/public/hot
+/public/storage
+/storage/*.key
+/storage/pail
+/vendor
+Homestead.json
+Homestead.yaml
+Thumbs.db
+.env
+__pycache__/
+*.pyc
+*.sqlite
+*.sqlite-wal
+*.sqlite-shm
+
+ai_apps/chem_agent_api/.env
+ai_apps/chem_agent_api/_pycache_/
+ai_apps/chem_agent_api/pycache/
+ai_apps/chem_agent_api/*.db
+ai_apps/chem_agent_api/*.db-shm
+ai_apps/chem_agent_api/*.db-wal

.scribe/.filehashes

@@ -0,0 +1,4 @@
+# GENERATED. YOU SHOULDN'T MODIFY OR DELETE THIS FILE.
+# Scribe uses this file to know when you change something manually in your docs.
+.scribe/intro.md=ac7eb5bb370d74c7b07631610e041687
+.scribe/auth.md=9bee2b1ef8a238b2e58613fa636d5f39

.scribe/auth.md

@@ -0,0 +1,3 @@
+# Authenticating requests
+
+This API is not authenticated.

.scribe/endpoints.cache/00.yaml

@@ -0,0 +1,1503 @@
+## Autogenerated by Scribe. DO NOT MODIFY.
+
+name: Endpoints
+description: ''
+endpoints:
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/awards
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/awards could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/awards/{id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      id:
+        custom: []
+        name: id
+        description: 'The ID of the award.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/awards\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/awards/{id}/scientists'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      id:
+        custom: []
+        name: id
+        description: 'The ID of the award.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/awards\/consequatur\/scientists could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/scientists
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/scientists could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/scientists/{id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      id:
+        custom: []
+        name: id
+        description: 'The ID of the scientist.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/scientists\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/scientists/{id}/awards'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      id:
+        custom: []
+        name: id
+        description: 'The ID of the scientist.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/scientists\/consequatur\/awards could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/register
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: '---------------- Auth ----------------'
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      name:
+        custom: []
+        name: name
+        description: 'Must not be greater than 255 characters.'
+        required: true
+        example: vmqeopfuudtdsufvyvddq
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address.'
+        required: true
+        example: kunde.eloisa@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      password:
+        custom: []
+        name: password
+        description: 'Must be at least 6 characters.'
+        required: true
+        example: '4[*UyPJ"}6'
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      name: vmqeopfuudtdsufvyvddq
+      email: kunde.eloisa@example.com
+      password: '4[*UyPJ"}6'
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/login
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      password:
+        custom: []
+        name: password
+        description: ''
+        required: true
+        example: 'O[2UZ5ij-e/dl4m{o,'
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+      password: 'O[2UZ5ij-e/dl4m{o,'
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/verify-email
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: '---------------- Email Verification ----------------'
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      otp:
+        custom: []
+        name: otp
+        description: 'Must be 6 digits.'
+        required: true
+        example: '810798'
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+      otp: '810798'
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/resend-otp
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/forgot-password
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: '---------------- Password Reset ----------------'
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/reset-password
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      otp:
+        custom: []
+        name: otp
+        description: 'Must be 6 digits.'
+        required: true
+        example: '810798'
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      password:
+        custom: []
+        name: password
+        description: 'Must be at least 6 characters.'
+        required: true
+        example: '[2UZ5ij-e/dl4'
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+      otp: '810798'
+      password: '[2UZ5ij-e/dl4'
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/resend-reset-password-otp
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/auth/google
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: '---------------- Google OAuth ----------------'
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      access_token:
+        custom: []
+        name: access_token
+        description: ''
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      access_token: consequatur
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/user/profile
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: '---------------- Profile ----------------'
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/user\/profile could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/logout
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/news
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/news could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/news/refresh
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/news\/refresh could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/news/clear
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/news\/clear could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/news/categories
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/news\/categories could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: 'api/news/{articleId}/share'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      articleId:
+        custom: []
+        name: articleId
+        description: ''
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      articleId: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: 'api/news/{articleId}/save'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      articleId:
+        custom: []
+        name: articleId
+        description: ''
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      articleId: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/news/saved
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/news\/saved could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - DELETE
+    uri: 'api/news/saved/{savedArticleId}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      savedArticleId:
+        custom: []
+        name: savedArticleId
+        description: ''
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      savedArticleId: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/ai/run
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      num_smiles:
+        custom: []
+        name: num_smiles
+        description: ''
+        required: true
+        example: 17
+        type: integer
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      top_k:
+        custom: []
+        name: top_k
+        description: ''
+        required: true
+        example: 17
+        type: integer
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      Docking:
+        custom: []
+        name: Docking
+        description: ''
+        required: true
+        example: 11613.31890586
+        type: number
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      DeepPurpose_Affinity:
+        custom: []
+        name: DeepPurpose_Affinity
+        description: ''
+        required: true
+        example: 11613.31890586
+        type: number
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      SA:
+        custom: []
+        name: SA
+        description: ''
+        required: true
+        example: 11613.31890586
+        type: number
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      TPSA:
+        custom: []
+        name: TPSA
+        description: ''
+        required: true
+        example: 11613.31890586
+        type: number
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      MW:
+        custom: []
+        name: MW
+        description: ''
+        required: true
+        example: 11613.31890586
+        type: number
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      num_smiles: 17
+      top_k: 17
+      Docking: 11613.31890586
+      DeepPurpose_Affinity: 11613.31890586
+      SA: 11613.31890586
+      TPSA: 11613.31890586
+      MW: 11613.31890586
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/ai/status/{job_job_id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      job_job_id:
+        custom: []
+        name: job_job_id
+        description: 'The ID of the job job.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      job_job_id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/ai\/status\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/ai/preview/{job_job_id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      job_job_id:
+        custom: []
+        name: job_job_id
+        description: 'The ID of the job job.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      job_job_id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/ai\/preview\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/ai/download/top/{job_job_id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      job_job_id:
+        custom: []
+        name: job_job_id
+        description: 'The ID of the job job.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      job_job_id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/ai\/download\/top\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/ai/download/full/{job_job_id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      job_job_id:
+        custom: []
+        name: job_job_id
+        description: 'The ID of the job job.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      job_job_id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/ai\/download\/full\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/ai/history
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/ai\/history could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/upload-file
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null

.scribe/endpoints/00.yaml

@@ -0,0 +1,1501 @@
+name: Endpoints
+description: ''
+endpoints:
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/awards
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/awards could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/awards/{id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      id:
+        custom: []
+        name: id
+        description: 'The ID of the award.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/awards\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/awards/{id}/scientists'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      id:
+        custom: []
+        name: id
+        description: 'The ID of the award.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/awards\/consequatur\/scientists could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/scientists
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/scientists could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/scientists/{id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      id:
+        custom: []
+        name: id
+        description: 'The ID of the scientist.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/scientists\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/scientists/{id}/awards'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      id:
+        custom: []
+        name: id
+        description: 'The ID of the scientist.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/scientists\/consequatur\/awards could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/register
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: '---------------- Auth ----------------'
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      name:
+        custom: []
+        name: name
+        description: 'Must not be greater than 255 characters.'
+        required: true
+        example: vmqeopfuudtdsufvyvddq
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address.'
+        required: true
+        example: kunde.eloisa@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      password:
+        custom: []
+        name: password
+        description: 'Must be at least 6 characters.'
+        required: true
+        example: '4[*UyPJ"}6'
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      name: vmqeopfuudtdsufvyvddq
+      email: kunde.eloisa@example.com
+      password: '4[*UyPJ"}6'
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/login
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      password:
+        custom: []
+        name: password
+        description: ''
+        required: true
+        example: 'O[2UZ5ij-e/dl4m{o,'
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+      password: 'O[2UZ5ij-e/dl4m{o,'
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/verify-email
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: '---------------- Email Verification ----------------'
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      otp:
+        custom: []
+        name: otp
+        description: 'Must be 6 digits.'
+        required: true
+        example: '810798'
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+      otp: '810798'
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/resend-otp
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/forgot-password
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: '---------------- Password Reset ----------------'
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/reset-password
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      otp:
+        custom: []
+        name: otp
+        description: 'Must be 6 digits.'
+        required: true
+        example: '810798'
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      password:
+        custom: []
+        name: password
+        description: 'Must be at least 6 characters.'
+        required: true
+        example: '[2UZ5ij-e/dl4'
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+      otp: '810798'
+      password: '[2UZ5ij-e/dl4'
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/resend-reset-password-otp
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      email:
+        custom: []
+        name: email
+        description: 'Must be a valid email address. The <code>email</code> of an existing record in the users table.'
+        required: true
+        example: qkunze@example.com
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      email: qkunze@example.com
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/auth/google
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: '---------------- Google OAuth ----------------'
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      access_token:
+        custom: []
+        name: access_token
+        description: ''
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      access_token: consequatur
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/user/profile
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: '---------------- Profile ----------------'
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/user\/profile could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/user/logout
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/news
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/news could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/news/refresh
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/news\/refresh could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/news/clear
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/news\/clear could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/news/categories
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/news\/categories could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: 'api/news/{articleId}/share'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      articleId:
+        custom: []
+        name: articleId
+        description: ''
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      articleId: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: 'api/news/{articleId}/save'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      articleId:
+        custom: []
+        name: articleId
+        description: ''
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      articleId: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/news/saved
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/news\/saved could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - DELETE
+    uri: 'api/news/saved/{savedArticleId}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      savedArticleId:
+        custom: []
+        name: savedArticleId
+        description: ''
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      savedArticleId: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/ai/run
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters:
+      num_smiles:
+        custom: []
+        name: num_smiles
+        description: ''
+        required: true
+        example: 17
+        type: integer
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      top_k:
+        custom: []
+        name: top_k
+        description: ''
+        required: true
+        example: 17
+        type: integer
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      Docking:
+        custom: []
+        name: Docking
+        description: ''
+        required: true
+        example: 11613.31890586
+        type: number
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      DeepPurpose_Affinity:
+        custom: []
+        name: DeepPurpose_Affinity
+        description: ''
+        required: true
+        example: 11613.31890586
+        type: number
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      SA:
+        custom: []
+        name: SA
+        description: ''
+        required: true
+        example: 11613.31890586
+        type: number
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      TPSA:
+        custom: []
+        name: TPSA
+        description: ''
+        required: true
+        example: 11613.31890586
+        type: number
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+      MW:
+        custom: []
+        name: MW
+        description: ''
+        required: true
+        example: 11613.31890586
+        type: number
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanBodyParameters:
+      num_smiles: 17
+      top_k: 17
+      Docking: 11613.31890586
+      DeepPurpose_Affinity: 11613.31890586
+      SA: 11613.31890586
+      TPSA: 11613.31890586
+      MW: 11613.31890586
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/ai/status/{job_job_id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      job_job_id:
+        custom: []
+        name: job_job_id
+        description: 'The ID of the job job.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      job_job_id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/ai\/status\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/ai/preview/{job_job_id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      job_job_id:
+        custom: []
+        name: job_job_id
+        description: 'The ID of the job job.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      job_job_id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/ai\/preview\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/ai/download/top/{job_job_id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      job_job_id:
+        custom: []
+        name: job_job_id
+        description: 'The ID of the job job.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      job_job_id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/ai\/download\/top\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: 'api/ai/download/full/{job_job_id}'
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters:
+      job_job_id:
+        custom: []
+        name: job_job_id
+        description: 'The ID of the job job.'
+        required: true
+        example: consequatur
+        type: string
+        enumValues: []
+        exampleWasSpecified: false
+        nullable: false
+        deprecated: false
+    cleanUrlParameters:
+      job_job_id: consequatur
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/ai\/download\/full\/consequatur could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - GET
+    uri: api/ai/history
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses:
+      -
+        custom: []
+        status: 404
+        content: '{"success":false,"message":"The route api\/ai\/history could not be found."}'
+        headers:
+          cache-control: 'no-cache, private'
+          content-type: application/json
+          access-control-allow-origin: '*'
+        description: null
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null
+  -
+    custom: []
+    httpMethods:
+      - POST
+    uri: api/upload-file
+    metadata:
+      custom: []
+      groupName: Endpoints
+      groupDescription: ''
+      subgroup: ''
+      subgroupDescription: ''
+      title: ''
+      description: ''
+      authenticated: false
+      deprecated: false
+    headers:
+      Content-Type: application/json
+      Accept: application/json
+    urlParameters: []
+    cleanUrlParameters: []
+    queryParameters: []
+    cleanQueryParameters: []
+    bodyParameters: []
+    cleanBodyParameters: []
+    fileParameters: []
+    responses: []
+    responseFields: []
+    auth: []
+    controller: null
+    method: null
+    route: null

.scribe/endpoints/custom.0.yaml

@@ -0,0 +1,53 @@
+# To include an endpoint that isn't a part of your Laravel app (or belongs to a vendor package),
+# you can define it in a custom.*.yaml file, like this one.
+# Each custom file should contain an array of endpoints. Here's an example:
+# See https://scribe.knuckles.wtf/laravel/documenting/custom-endpoints#extra-sorting-groups-in-custom-endpoint-files for more options
+
+#- httpMethods:
+#    - POST
+#  uri: api/doSomething/{param}
+#  metadata:
+#    groupName: The group the endpoint belongs to. Can be a new group or an existing group.
+#    groupDescription: A description for the group. You don't need to set this for every endpoint; once is enough.
+#    subgroup: You can add a subgroup, too.
+#    title: Do something
+#    description: 'This endpoint allows you to do something.'
+#    authenticated: false
+#  headers:
+#    Content-Type: application/json
+#    Accept: application/json
+#  urlParameters:
+#    param:
+#      name: param
+#      description: A URL param for no reason.
+#      required: true
+#      example: 2
+#      type: integer
+#  queryParameters:
+#    speed:
+#      name: speed
+#      description: How fast the thing should be done. Can be `slow` or `fast`.
+#      required: false
+#      example: fast
+#      type: string
+#  bodyParameters:
+#    something:
+#      name: something
+#      description: The things we should do.
+#      required: true
+#      example:
+#        - string 1
+#        - string 2
+#      type: 'string[]'
+#  responses:
+#    - status: 200
+#      description: 'When the thing was done smoothly.'
+#      content: # Your response content can be an object, an array, a string or empty.
+#         {
+#           "hey": "ho ho ho"
+#         }
+#  responseFields:
+#    hey:
+#      name: hey
+#      description: Who knows?
+#      type: string # This is optional

.scribe/intro.md

@@ -0,0 +1,13 @@
+# Introduction
+
+
+
+<aside>
+    <strong>Base URL</strong>: <code>https://america-hyperlipemic-grazyna.ngrok-free.dev/</code>
+</aside>
+
+    This documentation aims to provide all the information you need to work with our API.
+
+    <aside>As you scroll, you'll see code examples for working with the API in different programming languages in the dark area to the right (or as part of the content on mobile).
+    You can switch the language used with the tabs at the top right (or from the nav menu at the top left on mobile).</aside>
+

ARCHITECTURE.md

@@ -0,0 +1,224 @@
+# AILIXIR Architecture & Component Documentation
+
+Last updated: 2026-05-29
+
+This document provides detailed diagrams and per-component explanations for the AILIXIR BackEnd. It is intended for developers and SREs onboarding onto the project and for inclusion in production runbooks.
+
+Contents
+--------
+- System-level architecture (diagram + explanation)
+- Data flow and request lifecycle
+- Per-service component diagrams and responsibilities
+  - Laravel (orchestration)
+  - ADMET inference (FastAPI)
+  - Drug Repurposing (FastAPI)
+  - Chemical RAG (FAISS + RAG)
+- Environment variables & configuration locations
+- Deployment notes and scaling considerations
+- Troubleshooting checkpoints
+
+System-level architecture (Mermaid)
+----------------------------------
+
+```mermaid
+flowchart LR
+  subgraph CLIENTS [Clients]
+    A[Web UI / Frontend]
+    B[External Integrations / APIs]
+  end
+
+  subgraph DOCKER_NET [Docker network: ailixir]
+    direction TB
+    LAR(Laravel API)
+    Q(Queue Worker)
+    MYSQL[(MariaDB)]
+    ADMET(ADMET Inference)
+    DRUG(Drug Repurposing)
+    CRAG(Chemical RAG)
+  end
+
+  A -->|HTTP| LAR
+  B -->|HTTP| LAR
+  LAR -->|DB| MYSQL
+  LAR -->|enqueue| Q
+  LAR -->|AI calls| ADMET
+  LAR -->|AI calls| DRUG
+  LAR -->|AI calls| CRAG
+  ADMET -->|models stored on disk| ADMET
+  CRAG -->|FAISS index on volume| CRAG
+  DRUG -->|model artifacts| DRUG
+```
+
+Explanation
+-----------
+
+- Clients (web, CLI, external services) interact with the `laravel` orchestration API. The Laravel layer handles authentication, request validation, and orchestration of multi-step workflows.
+- Long-running tasks are delegated to the `queue` worker via Laravel's queue system. The queue worker communicates with the same Laravel codebase and uses the internal database for job bookkeeping.
+- AI microservices are independent FastAPI services: `admet`, `drug-repurposing`, and `chemical-rag`. Laravel calls these services over the internal Docker network by service name.
+- Persistent storage: `mysql` holds application state, users, and job metadata; AI services use container volumes for model artifacts and FAISS indexes.
+
+Request lifecycle — typical screening flow
+---------------------------------------
+
+1. Client POSTs request to Laravel endpoint (e.g., run screening).
+2. Laravel validates and creates a job record in MySQL and either performs synchronous work or enqueues a background job.
+3. Background job triggers calls to AI services in parallel or sequence depending on pipeline stage:
+   - `drug-repurposing` to run virtual screening
+   - `admet` to score ADMET properties
+   - `chemical-rag` to fetch similar compounds or augment results
+4. AI services return raw predictions to Laravel which aggregates results, persists summary, and notifies the client.
+
+Per-service diagrams & responsibilities
+--------------------------------------
+
+1) Laravel (orchestration)
+
+```mermaid
+flowchart TD
+  In[HTTP Request]
+  Auth[Auth Layer]
+  Validate[Validation]
+  Controller[Controller]
+  DB[(MySQL)]
+  Queue[Queue Worker]
+  AIcalls[AI Service Calls]
+  Response[Response to Client]
+
+  In --> Auth --> Validate --> Controller --> DB
+  Controller -->|enqueue| Queue
+  Controller -->|direct call| AIcalls
+  AIcalls --> Response
+```
+
+Responsibilities:
+
+- Authentication and authorization (API tokens, OAuth, or guards configured in `config/auth.php`).
+- Centralized error handling and logging.
+- Exposes REST endpoints used by UI and third-party clients; routes live under `routes/`.
+- Job dispatching and scheduling; queue worker executes heavy pipelines.
+
+Where to look in repository:
+
+- `app/Http/Controllers/` — controllers and endpoints
+- `routes/api.php` — API routes and versioning
+- `jobs/` and `app/Jobs` — background job implementations
+- `docker/laravel.env` — example env values
+
+2) ADMET inference (FastAPI)
+
+```mermaid
+flowchart TD
+  Req[POST /predict]
+  Validate[SMILES Validation (RDKit)]
+  Feat[Featurization / Graph builder]
+  Models[MPNN Models (5 tasks)]
+  Aggregate[Aggregate predictions]
+  Return[JSON response]
+
+  Req --> Validate --> Feat --> Models --> Aggregate --> Return
+```
+
+Responsibilities:
+
+- Load pre-trained MPNN models on startup (check `models/` inside service).
+- Validate SMILES strings with RDKit and sanitize input.
+- Support single and batch prediction endpoints; expose `/health` and `/docs`.
+- CPU-optimized inference (no GPU assumed by default) and async handling via Uvicorn.
+
+Where to look:
+
+- `ai_apps/ADMIT/admet_inference/` — service code, `README.md`, `Dockerfile`, `requirements.txt`.
+- Health and docs endpoints available at `http://<host>:<port>/health` and `/docs`.
+
+3) Drug Repurposing (FastAPI)
+
+```mermaid
+flowchart TD
+  Req[POST /api/v1/screen]
+  Targets[OpenTargets integration]
+  Sequences[UniProt fetch]
+  Drugs[Drug library (TDC / fallback)]
+  Model[DeepPurpose MPNN-CNN]
+  Results[Rank & postprocess]
+  Return[JSON summary]
+
+  Req --> Targets --> Sequences --> Drugs --> Model --> Results --> Return
+```
+
+Responsibilities:
+
+- Full screening pipeline: disease→targets→proteins→screening→results.
+- Integrates external APIs (OpenTargets, UniProt) and TDC for drug libraries.
+- Provides mock modes for offline testing (use env `USE_MOCK_MODEL` and `USE_MOCK_DRUGS`).
+
+Where to look:
+
+- `ai_apps/Drug Reporposing/` — service implementation, `docker/` folder, `requirements.txt`, `README.md` and helper scripts (`start.sh`, `start.bat`).
+
+4) Chemical RAG (FAISS + LLM)
+
+```mermaid
+flowchart TD
+  Req[/search/full-rag]
+  Validate[SMILES validation]
+  FP[Morgan fingerprint / embedding]
+  FAISS[FAISS-IVF index lookup]
+  LLM[LLM explanation (optional)]
+  Format[Result formatting]
+  Return[JSON results]
+
+  Req --> Validate --> FP --> FAISS --> LLM --> Format --> Return
+```
+
+Responsibilities:
+
+- High-performance similarity search for large compound libraries (1M+).
+- Persistent FAISS index stored on volume (`chemical-rag-data`).
+- Two endpoints: retrieval-only and full RAG (with LLM explanations); auto-detects and ingests compounds on first run.
+
+Where to look:
+
+- `ai_apps/chemical-rag-system/chemical-rag-system/` — engine, ingestion scripts, FAISS index code, `run_server.py`, and `README.md`.
+
+Environment variables & configuration locations
+---------------------------------------------
+
+- Root compose: `docker-compose.yml` — service names, build contexts, ports, and env files.
+- Laravel env template: `docker/laravel.env` — application and DB defaults.
+- Each AI service: check `ai_apps/<service>/` for `requirements.txt`, `Dockerfile`, and service-specific config (e.g., `app/config.py`).
+
+Production deployment notes
+-------------------------
+
+- Resource limits: `docker-compose.yml` contains `deploy.resources.limits` for AI services; tune these for production (memory, CPU).
+- Secrets: move sensitive env values into secret managers (Kubernetes Secrets, Vault) in production.
+- HTTPS: terminate TLS at a reverse proxy in front of `laravel` (Nginx/Load Balancer) and restrict internal-only exposure for AI services.
+
+Scaling considerations
+---------------------
+
+- Horizontal scaling of AI services: deploy multiple replicas behind a load balancer. Ensure models are loaded on container start and center model size is within available RAM.
+- FAISS index: store on a shared volume or use a dedicated retrieval service with replicated indices.
+- Database: use managed RDS/MariaDB clusters or replicas for HA.
+
+Troubleshooting checkpoints
+--------------------------
+
+- Service not healthy: `docker compose logs -f <service>` and `docker compose ps` to check ports and status.
+- Model load errors: inspect service logs, confirm model files under `models/` or configured model path.
+- FAISS ingestion slow: watch `chemical-rag` logs on first-run ingestion; ensure sufficient CPU and disk I/O.
+
+Appendix — quick visual references
+---------------------------------
+
+- Root system diagram: see top of this file (Mermaid block).
+- Per-service diagrams: each service section above contains its own Mermaid block.
+
+Next steps I can implement for you
+----------------------------------
+
+1. Generate PNG/SVG exports of these Mermaid diagrams and add them to the repo docs folder.
+2. Standardize and replace `ai_apps/*/README.md` with a consistent template including: purpose, architecture diagram, setup (Docker + local), env vars, run commands, API endpoints, troubleshooting.
+3. Create `docs/` folder and add `QUICK_START.md`, per-service `.env.example`, and the generated diagrams.
+
+Tell me which of the next steps you'd like me to do now (1, 2, 3), or if you want all of them performed.

CHANGELOG_SQLITE_HF.md

@@ -0,0 +1,214 @@
+# Changelog: SQLite Migration & Hugging Face Spaces Deployment
+
+> **Date:** 2026-06-09  
+> **Branch:** `feature/hugging-face-deploy`  
+> **Commits:** `fd94aa0..1cbbcaa` (3 commits)
+
+---
+
+## Overview
+
+Migrated AILIXIR from **MySQL/MariaDB** to **SQLite** and deployed the entire platform to **5 Hugging Face Spaces** with GitHub-to-HF auto-sync.
+
+---
+
+## Part 1: SQLite Database Migration
+
+### Migration Fixes
+
+**4 migration files were modified** to remove MySQL-specific syntax:
+
+| File | Problem | Fix |
+|------|---------|-----|
+| `database/migrations/2026_04_20_135553_create_admets_table.php` | `useCurrentOnUpdate()` — MySQL-only | Replaced manual timestamps with `$table->timestamps()` |
+| `database/migrations/2026_04_20_044726_create_screening_results_table.php` | `output` column not nullable, causing `->change()` failure | Changed `json('output')` to `json('output')->nullable()` |
+| `database/migrations/2026_04_20_055149_create_target_lookups_table.php` | Same as above | Same fix |
+| `database/migrations/2026_04_21_155344_add_status_to_screening_tables.php` | Used `->change()` which requires MySQL-like `ALTER TABLE MODIFY` | Rewritten to only add `status` column, removed all `->change()` calls |
+
+### Configuration Changes
+
+- **`config/database.php`** — SQLite connection configured with:
+  - `journal_mode` = `wal` (Write-Ahead Logging for concurrent reads)
+  - `busy_timeout` = `5000` (5 second wait on locked DB)
+  - `transaction_mode` = `IMMEDIATE` (prevents "database is locked" errors)
+
+### Environment Files Updated
+
+| File | Before | After |
+|------|--------|-------|
+| `.env.example` | `DB_CONNECTION=mysql` + host/port/user/pass | `DB_CONNECTION=sqlite`, `DB_DATABASE=database/ailixir.sqlite` |
+| `.env.docker` | Same MySQL config | Same SQLite config |
+| `docker/laravel.env` | Same MySQL config | Same SQLite config |
+
+### `.gitignore`
+Added `*.sqlite`, `*.sqlite-wal`, `*.sqlite-shm` to prevent accidental commits of database files.
+
+---
+
+## Part 2: Docker Infrastructure Changes
+
+### `Dockerfile`
+- **PHP extension**: `pdo_mysql` → `pdo_sqlite`
+- **System packages**: Added `libsqlite3-dev`, `supervisor`
+- **Ports**: Added `EXPOSE 7860` for Hugging Face Spaces
+- **Database directory**: Creates `database/` directory during build
+- Removed `COPY docker/laravel.env .env` (env vars now come from HF Space secrets)
+
+### `docker/supervisord.conf` (new)
+Runs two processes in a single container for HF Spaces:
+- `[program:laravel]` — `php artisan serve --host=0.0.0.0 --port=7860`
+- `[program:queue]` — `php artisan queue:work --sleep=3 --tries=3 --timeout=300`
+
+### `docker/entrypoint.sh`
+- Creates SQLite database file at runtime if it doesn't exist
+- Checks `RUN_MODE=hf` environment variable — if set, starts supervisord instead of the default CMD
+- Still supports Docker Compose mode (runs migrations, then exec's the passed CMD)
+
+### `docker-compose.yml`
+- **Removed** the entire `mysql:` service (was MariaDB 11.4)
+- **Removed** `mysql-data` volume
+- **Removed** `depends_on: mysql` from `laravel` and `queue` services
+- **Removed** `DB_HOST: mysql` environment overrides
+- AI microservice configs remain unchanged
+
+### `.env.hf` (new)
+Template file with all HF Space URLs pre-configured for the AI microservice URLs.
+
+---
+
+## Part 3: Hugging Face Spaces Deployment
+
+### Spaces Created (5)
+
+| Space | Type | Content |
+|-------|------|---------|
+| `ailixir-api` | Docker (Laravel) | Root repo (excludes `ai_apps/`, `Diagrams/`) |
+| `ailixir-admet` | Docker (FastAPI) | `ai_apps/ADMIT/admet_inference/` |
+| `ailixir-drug-repurposing` | Docker (FastAPI) | `ai_apps/Drug Reporposing/` |
+| `ailixir-chemical-rag` | Docker (FastAPI) | `ai_apps/chemical-rag-system/chemical-rag-system/` |
+| `ailixir-generation` | Docker (FastAPI) | `ai_apps/generation/` (CPU-only Dockerfile) |
+
+### Space Configuration
+- All spaces use `cpu-basic` hardware (free tier)
+- Port configured to **7860** in each Dockerfile
+- `README.md` with proper YAML frontmatter added to each space
+- 15-minute sleep timeout for free tier cost savings
+
+### Generation Service Adaptation
+The generation service originally required NVIDIA CUDA + GPU. For HF Spaces (CPU-only), a **lightweight Dockerfile** was created that:
+- Uses `python:3.10-slim` base (instead of `nvidia/cuda`)
+- Installs only `fastapi`, `uvicorn`, `pydantic`, `requests`, `rdkit`
+- Disables AutoDock-GPU and DeepPurpose (CPU-only)
+- Provides basic molecule generation and docking scoring
+
+---
+
+## Part 4: GitHub-to-HF Auto-Sync
+
+### 5 GitHub Actions Workflows
+
+| File | Triggers | Syncs |
+|------|----------|-------|
+| `.github/workflows/sync-hf-backend.yml` | Push to `main`/`develop` (excl. `ai_apps/`) | Whole repo → `ailixir-api` |
+| `.github/workflows/sync-hf-admet.yml` | Push to `ai_apps/ADMIT/admet_inference/` | Subdir → `ailixir-admet` |
+| `.github/workflows/sync-hf-drug-repurposing.yml` | Push to `ai_apps/Drug Reporposing/` | Subdir → `ailixir-drug-repurposing` |
+| `.github/workflows/sync-hf-chemical-rag.yml` | Push to `ai_apps/chemical-rag-system/` | Subdir → `ailixir-chemical-rag` |
+| `.github/workflows/sync-hf-generation.yml` | Push to `ai_apps/generation/` | Subdir → `ailixir-generation` |
+
+Each workflow:
+1. Clones the target HF Space repo
+2. Rsyncs the relevant files (excluding `.git`, `__pycache__`, etc.)
+3. Commits with the GitHub commit SHA
+4. Pushes to HF Space
+
+### GitHub Actions Workflow Updates
+- **`api-tests.yml`** — Removed MySQL wait loop and health check; removed MySQL log collection
+- **`integration-test.yml`** — Same changes across all 4 job definitions
+
+---
+
+## Part 5: Files Modified/Created Summary
+
+### Modified (15 files)
+```
+.config/database.php
+.env.docker
+.env.example
+.gitignore
+Dockerfile
+docker-compose.yml
+docker/entrypoint.sh
+docker/laravel.env
+.github/workflows/api-tests.yml
+.github/workflows/integration-test.yml
+database/migrations/2026_04_20_044726_create_screening_results_table.php
+database/migrations/2026_04_20_055149_create_target_lookups_table.php
+database/migrations/2026_04_20_135553_create_admets_table.php
+database/migrations/2026_04_21_155344_add_status_to_screening_tables.php
+database/ailixir.sqlite (new, empty)
+```
+
+### Created (9 files)
+```
+.env.hf
+docker/supervisord.conf
+.github/workflows/sync-hf-backend.yml
+.github/workflows/sync-hf-admet.yml
+.github/workflows/sync-hf-drug-repurposing.yml
+.github/workflows/sync-hf-chemical-rag.yml
+.github/workflows/sync-hf-generation.yml
+HF_SPACES_GUIDE.md (this file)
+CHANGELOG_SQLITE_HF.md (this file)
+```
+
+---
+
+## Architecture Diagram
+
+```
+┌─────────────────────────────────────────────────────────┐
+│                    GitHub Repository                      │
+│                     RottenShadow/                         │
+│                   AILIXIR_BackEnd                         │
+└────────────────────┬────────────────────────────────────┘
+                     │ Push triggers
+                     ▼
+       ┌─────────────────────────────┐
+       │   GitHub Actions (5 WFs)    │
+       │   Auto-sync to HF Spaces    │
+       └─────────────┬───────────────┘
+                     │
+     ┌───────────────┼───────────────────────┐
+     │               │                       │
+     ▼               ▼                       ▼
+┌──────────┐  ┌──────────┐  ┌──────────┐  ┌──────────┐  ┌──────────┐
+│ailixir-  │  │ailixir-  │  │ailixir-  │  │ailixir-  │  │ailixir-  │
+│api       │  │admet     │  │drug-     │  │chemical- │  │generation│
+│(Laravel) │  │(ADMET)   │  │repurpos. │  │rag       │  │(Molec.   │
+│SQLite    │  │          │  │          │  │          │  │Gen.)     │
+└────┬─────┘  └──────────┘  └──────────┘  └──────────┘  └──────────┘
+     │
+     │  HTTP proxying to AI microservices
+      ├──→ https://shdwRow-ailixir-admet.hf.space
+     ├──→ https://RottenShadow-ailixir-drug-repurposing.hf.space
+     ├──→ https://RottenShadow-ailixir-chemical-rag.hf.space
+      └──→ https://shdwRow-ailixir-generation.hf.space
+```
+
+---
+
+## Remaining Steps (Manual)
+
+1. **Set HF tokens as GitHub secrets** — Required for auto-sync workflows
+   - Go to: https://github.com/RottenShadow/AILIXIR_BackEnd/settings/secrets/actions
+   - Add secret: `HF_TOKEN` = `YOUR_ROTTENSHADOW_TOKEN`
+   - Add secret: `HF_TOKEN_AILIXIR` = `YOUR_AILIXIR_AI_TEAM_TOKEN`
+
+2. **Set backend Space secrets** — Required for `ailixir-api` to function
+   - Go to: https://huggingface.co/spaces/Ailixir-AI-Team/ailixir-api/settings
+   - Add all secrets listed in `HF_SPACES_GUIDE.md` section 3.1
+   - **Minimum:** `APP_KEY`, `RUN_MODE=hf`, and all AI service URLs
+
+3. **Wait for builds to complete** — Backend Docker image is large (~5GB) and takes 15–45 minutes to build on HF free tier
+
+4. **Verify connectivity** — Test the health endpoints and ensure the backend can reach all AI services

DOCKER.md

@@ -0,0 +1,63 @@
+# AILIXIR Docker Stack
+
+Monorepo stack: **Laravel API** + **ADMET** + **Drug Repurposing** + **Chemical RAG**.
+
+## Requirements
+
+- Docker 24+ with Compose v2
+- ~16 GB RAM recommended (PyTorch + ADMET models)
+- Model artifacts present locally:
+  - `ai_apps/ADMIT/admet_inference/models/*/best_model.ckpt`
+  - `ai_apps/Drug Reporposing/save_folder/pretrained_models/...`
+
+## Quick start
+
+```bash
+# From repository root
+docker compose build
+docker compose up -d
+```
+
+| Service | Host URL |
+|---------|----------|
+| Laravel API | http://localhost:8080 |
+| ADMET | http://localhost:8002 |
+| Drug Repurposing | http://localhost:8001 |
+| Chemical RAG | http://localhost:5000 |
+
+## Laravel → AI integration endpoints
+
+Enabled when `AI_INTEGRATION_ROUTES_ENABLED=true` (set in `docker/laravel.env`).
+
+| Method | Endpoint | Description |
+|--------|----------|-------------|
+| GET | `/api/ai-services/health` | Ping all AI `/health` endpoints |
+| POST | `/api/ai-services/test/admet` | Proxy ADMET `/predict` |
+| POST | `/api/ai-services/test/chemical-search` | Proxy Chemical RAG retrieval |
+| GET | `/api/ai-services/test/drug-repurposing` | Health + model status |
+
+Example:
+
+```bash
+curl http://localhost:8080/api/ai-services/health
+curl -X POST http://localhost:8080/api/ai-services/test/admet \
+  -H "Content-Type: application/json" \
+  -d '{"smiles":"c1ccccc1"}'
+```
+
+## Images
+
+- **Laravel**: multi-stage (`composer` + `node` + `php:8.3-cli-alpine`), runs as `www-data`
+- **ADMET / Drug Repurposing**: existing multi-stage Python slim images, non-root UID 1000
+- **Chemical RAG**: multi-stage `python:3.11-slim`, non-root `raguser`
+- **MySQL**: `mariadb:11.4`
+
+## CI
+
+GitHub Actions workflow: `.github/workflows/integration-test.yml`
+
+Builds the full stack and tests Laravel proxy endpoints against all AI services.
+
+## Environment
+
+Copy and adjust `docker/laravel.env` for container-specific values. For local (non-Docker) development, set URLs in `.env` using `.env.example` as reference.

DOCKER_FIXES.md

@@ -0,0 +1,231 @@
+# 🔧 Docker Build Fixes - AILIXIR v2.0
+
+**Last Updated**: 2026 | **Status**: ✅ All Issues Resolved
+
+This document outlines the Docker build failures discovered in CI/CD and the solutions applied.
+
+---
+
+## 🚨 Issues Resolved
+
+### Issue #1: PyTorch Version Incompatibility (CRITICAL)
+
+#### Problem
+```
+ERROR: Could not find a version that satisfies the requirement 
+       torchaudio==0.15.2
+```
+
+#### Root Cause
+- **File**: `ai_apps/Drug Reporposing/requirements.txt`
+- **Line**: 24 (originally specified `torchaudio==0.15.2`)
+- **Issue**: `torchaudio==0.15.2` does not exist on PyPI
+- **Version Gap**: PyPI contains versions 0.11.0 through 2.11.0, but the 0.15.x and 1.x ranges were never released
+- **Incompatibility**: The version was inconsistent with torch==2.0.1 and torchvision==0.15.2
+
+#### Solution
+Updated to compatible PyTorch audio library version:
+
+**Before:**
+```txt
+torch==2.0.1
+torchvision==0.15.2
+torchaudio==0.15.2  # ❌ Does not exist
+```
+
+**After:**
+```txt
+torch==2.0.1
+torchvision==0.15.2
+torchaudio==2.0.1   # ✅ Compatible with torch 2.0.1
+```
+
+#### Files Changed
+- `ai_apps/Drug Reporposing/requirements.txt` (line 24)
+
+#### Verification
+```bash
+# These versions are now available and compatible
+pip install torch==2.0.1 torchvision==0.15.2 torchaudio==2.0.1
+```
+
+---
+
+### Issue #2: Dockerfile Casing Warnings (STYLE)
+
+#### Problem
+```
+FromAsCasing: 'as' and 'FROM' keywords' casing do not match
+```
+
+#### Root Cause
+- Docker Dockerfile linter enforces consistent keyword casing
+- Multi-stage build syntax uses `FROM ... as builder` (mixed case)
+- Should be `FROM ... AS builder` (uppercase AS)
+- **Affected Files**: 2 of 4 Dockerfiles had this warning
+
+#### Solution
+Updated all multi-stage Dockerfile build syntax to use uppercase `AS`:
+
+**Before:**
+```dockerfile
+FROM python:3.10-slim as builder  # ❌ Mixed case
+```
+
+**After:**
+```dockerfile
+FROM python:3.10-slim AS builder  # ✅ Proper casing
+```
+
+#### Files Changed
+1. `ai_apps/ADMIT/admet_inference/Dockerfile` (line 4)
+   - Changed: `FROM python:3.11-slim as builder` → `FROM python:3.11-slim AS builder`
+
+2. `ai_apps/Drug Reporposing/docker/Dockerfile` (line 1)
+   - Changed: `FROM python:3.10-slim as builder` → `FROM python:3.10-slim AS builder`
+
+#### Status Note
+- `ai_apps/chemical-rag-system/chemical-rag-system/Dockerfile` already had correct casing (`AS builder`)
+- No changes were needed for this file
+
+---
+
+## 📊 Fix Summary
+
+| Issue | File(s) | Change | Status |
+|-------|---------|--------|--------|
+| PyTorch incompatibility | Drug Reporposing/requirements.txt | torchaudio 0.15.2 → 2.0.1 | ✅ Fixed |
+| Dockerfile casing | ADMET/Dockerfile | `as` → `AS` | ✅ Fixed |
+| Dockerfile casing | Drug Repurposing/Dockerfile | `as` → `AS` | ✅ Fixed |
+| Dockerfile casing | Chemical-RAG/Dockerfile | Already correct | ✅ OK |
+
+---
+
+## ✅ Verification Steps
+
+After fixes, verify the Docker build succeeds:
+
+```bash
+# Clear Docker cache (optional)
+docker compose down
+docker system prune -a
+
+# Build all services with fixes applied
+cd AILIXIR_BackEnd
+docker compose build --parallel
+
+# Expected output:
+# [+] Building 5/5
+#  - Image ailixir-admet          Built
+#  - Image ailixir-drug-repurposing Built
+#  - Image ailixir-chemical-rag    Built
+#  - Image ailixir-laravel         Built
+#  - Image ailixir-queue           Built
+```
+
+### Verify Individual Services
+```bash
+# Check each image built successfully
+docker images | grep ailixir
+
+# Test container startup
+docker compose up -d
+docker compose ps
+# All services should show "Up" status ✅
+```
+
+---
+
+## 🔍 Technical Details
+
+### PyTorch Version Compatibility Matrix
+
+For Python 3.10 with CUDA-free (CPU) installation:
+
+| torch | torchvision | torchaudio | Status |
+|-------|-------------|-----------|--------|
+| 2.0.1 | 0.15.2 | 0.15.2 | ❌ torchaudio doesn't exist |
+| 2.0.1 | 0.15.2 | 2.0.1 | ✅ Valid (current) |
+| 2.0.1 | 0.15.2 | 2.0.2 | ✅ Valid alternative |
+| 1.13.1 | 0.14.1 | 0.13.1 | ✅ Legacy option |
+
+**Selected**: torch 2.0.1 + torchaudio 2.0.1 (latest stable, best compatibility)
+
+### Dockerfile Multi-Stage Build Syntax
+
+The styleguide requires proper case:
+
+```dockerfile
+# Correct syntax
+FROM <image> AS <name>
+COPY --from=<name> /path /path
+
+# Example (Drug Repurposing)
+FROM python:3.10-slim AS builder
+RUN apt-get update && pip install -r requirements.txt
+FROM python:3.10-slim
+COPY --from=builder /opt/venv /opt/venv
+```
+
+---
+
+## 📋 Checklist for Future Updates
+
+When updating dependencies or Dockerfiles:
+
+- [ ] Verify PyPI has the exact version (search on pypi.org)
+- [ ] Check PyTorch compatibility: https://pytorch.org/get-started/locally/
+- [ ] Test locally: `docker compose build --parallel`
+- [ ] Check for Dockerfile linter warnings: `docker build --check`
+- [ ] Run services: `docker compose up -d`
+- [ ] Verify API endpoints respond: `curl http://localhost:8000`
+
+---
+
+## 🆘 Troubleshooting
+
+### If Docker Build Still Fails
+
+1. **Clear Docker cache**:
+   ```bash
+   docker compose down
+   docker system prune -a -f
+   docker compose build --no-cache --parallel
+   ```
+
+2. **Check individual service logs**:
+   ```bash
+   docker compose build admet 2>&1 | tail -50
+   docker compose build drug-repurposing 2>&1 | tail -50
+   ```
+
+3. **Verify file changes**:
+   ```bash
+   # Check torchaudio version
+   grep -n "torchaudio" ai_apps/Drug\ Reporposing/requirements.txt
+   
+   # Check Dockerfile casing
+   grep "FROM.*as\|FROM.*AS" ai_apps/*/*/Dockerfile ai_apps/*/*/Dockerfile
+   ```
+
+4. **Network/Registry Issues**:
+   - Ensure internet connectivity for PyPI, Docker Hub
+   - Try building at different time (registry mirrors may have delays)
+
+---
+
+## 📚 References
+
+- PyPI Package Index: https://pypi.org/
+- PyTorch Installation: https://pytorch.org/get-started/locally/
+- Docker Best Practices: https://docs.docker.com/develop/dev-best-practices/
+- Dockerfile Reference: https://docs.docker.com/engine/reference/builder/
+
+---
+
+## 🎯 Next Steps
+
+- Monitor CI/CD pipeline for successful builds: `docker compose build --parallel`
+- Add pre-commit hooks to validate Dockerfile syntax
+- Document dependency update procedures
+- Set up automated version compatibility checks

DOCUMENTATION_STRUCTURE.md

@@ -0,0 +1,449 @@
+# AILIXIR Documentation Structure (Recommended)
+
+**Status:** Documentation refactoring complete | **Last Updated:** May 2026
+
+---
+
+## 📋 Overview
+
+The AILIXIR project has been refactored to follow modern open-source documentation standards:
+
+- **Concise main README** (~800 lines, down from 2500+) focused on high-level overview
+- **Dedicated documentation files** for specific topics
+- **Service-specific READMEs** in each microservice directory
+- **Clear navigation** with links between related documents
+
+---
+
+## 📁 Recommended Documentation File Structure
+
+### Root Documentation Files
+
+```
+ailixir-backend/
+├── README.md                    ✅ REFACTORED (concise, high-level)
+├── QUICK_START.md              📝 REFERENCED (needs creation/verification)
+├── ARCHITECTURE.md             ✅ EXISTS (link from README)
+├── DOCKER.md                   ✅ EXISTS (link from README)
+├── PRODUCTION_GUIDE.md         📝 REFERENCED (needs creation/verification)
+├── TROUBLESHOOTING.md          📝 REFERENCED (needs creation)
+├── API_REFERENCE.md            📝 REFERENCED (needs creation)
+├── CONTRIBUTING.md             ✅ REFERENCED (guidelines included in README)
+├── DOCKER_FIXES.md             ✅ EXISTS (known issues)
+└── LICENSE                     ✅ EXISTS
+```
+
+### Service Documentation Files
+
+```
+ai_apps/
+├── ADMIT/
+│   ├── README.md               ✅ UPDATED (training + inference)
+│   └── train_ADMET_model.ipynb ✅ EXISTS
+│
+├── Drug Reporposing/
+│   ├── README.md               ✅ GOOD (keep as-is)
+│   ├── QUICK_START.md          ✅ EXISTS
+│   ├── PRODUCTION_GUIDE.md     ✅ EXISTS
+│   └── IMPLEMENTATION_SUMMARY.md ✅ EXISTS
+│
+└── chemical-rag-system/
+    └── README.md               ✅ UPDATED (v2.1)
+```
+
+---
+
+## 📄 Documentation Files Detail
+
+### 1. **README.md** ✅ (Completed)
+
+**Purpose:** Landing page, high-level overview
+
+**Current Status:** ✅ Refactored and polished
+
+**Length:** ~800 lines (reduced from 2500+)
+
+**Content:**
+- System overview and positioning
+- Feature table
+- Architecture diagram (ASCII, fixed alignment)
+- Quick start (minimal, links to detailed guides)
+- Services overview table
+- API summary with examples
+- Environment variables reference
+- Project structure tree
+- Links to all detailed documentation
+
+**Strengths:**
+- Professional and concise
+- Clear navigation to other docs
+- Suitable for GitHub landing page
+- Impresses recruiters and contributors
+
+---
+
+### 2. **QUICK_START.md** 📝 (Reference, needs verification)
+
+**Purpose:** 5-minute setup for developers
+
+**Recommended Content:**
+- System requirements (minimal)
+- Docker setup (3 commands)
+- Local setup (per service, brief)
+- Health check verification
+- "Next Steps" links to detailed docs
+
+**File Structure:**
+```markdown
+# Quick Start
+
+## Prerequisites
+- Docker & Docker Compose v2+
+- OR: PHP 8.2+, Python 3.10+, MariaDB
+
+## Docker (5 minutes)
+# 3-4 commands
+
+## Local Development
+# Brief per-service setup
+
+## Verify Installation
+# Health checks
+
+## Next Steps
+# Links to detailed guides
+```
+
+**Cross-references:** README.md → QUICK_START.md → DOCKER.md
+
+---
+
+### 3. **ARCHITECTURE.md** ✅ (Exists, referenced)
+
+**Purpose:** System design, diagrams, component details
+
+**Current Status:** ✅ Already comprehensive (use as-is)
+
+**Content:**
+- System-level architecture diagram (Mermaid)
+- Component responsibilities table
+- Data flow explanation
+- Request lifecycle walkthrough
+- Per-service component details
+- Environment variables location guide
+- Deployment notes and scaling
+
+**Cross-references:** README.md ← ARCHITECTURE.md
+
+---
+
+### 4. **DOCKER.md** ✅ (Exists, referenced)
+
+**Purpose:** Docker-specific setup and configuration
+
+**Current Status:** ✅ Comprehensive (use as-is)
+
+**Content:**
+- Docker requirements
+- Quick start with docker-compose
+- Service URLs and ports table
+- Laravel AI integration endpoints
+- Docker image details
+- CI/CD workflow
+- Environment configuration
+
+**Cross-references:** README.md → DOCKER.md
+
+---
+
+### 5. **PRODUCTION_GUIDE.md** 📝 (Reference, needs verification)
+
+**Purpose:** Deployment architecture, scaling, monitoring, security
+
+**Recommended Content:**
+```markdown
+# Production Guide
+
+## Pre-Deployment Checklist
+- Configuration review
+- Security setup
+- Backup strategy
+- Monitoring setup
+
+## Deployment Architecture
+- Architecture diagram (Kubernetes vs Docker Swarm)
+- Service replication strategies
+- Load balancing setup
+- Database replication
+
+## Scaling Strategies
+- Horizontal scaling for stateless services
+- Database scaling and replication
+- Queue worker scaling
+- Memory and resource limits
+
+## Monitoring & Observability
+- Health check endpoints
+- Log aggregation setup
+- Metrics collection (Prometheus)
+- Alert configuration
+
+## Security Hardening
+- Environment variable management
+- HTTPS/TLS setup
+- API authentication
+- Database security
+
+## Performance Tuning
+- Connection pooling
+- Cache configuration
+- Query optimization
+- Rate limiting
+```
+
+**Cross-references:** README.md → PRODUCTION_GUIDE.md
+
+---
+
+### 6. **TROUBLESHOOTING.md** 📝 (Reference, needs creation)
+
+**Purpose:** Common issues and solutions
+
+**Recommended Content:**
+```markdown
+# Troubleshooting
+
+## Quick Reference Table
+| Problem | Cause | Solution |
+| ... |
+
+## Container Issues
+- Service won't start
+- Port already in use
+- Out of memory
+
+## Database Issues
+- Connection failures
+- Migration errors
+- Data persistence
+
+## AI Service Issues
+- Model loading errors
+- GPU out of memory
+- Timeout issues
+- FAISS index slow
+
+## Development Issues
+- Python environment setup
+- Dependency conflicts
+- CUDA not found
+- Permission errors
+
+## Debugging
+- How to check logs
+- Health check procedures
+- Debug mode configuration
+
+## FAQ
+- Common questions
+- Best practices
+- Performance optimization
+```
+
+**Cross-references:** README.md → TROUBLESHOOTING.md
+
+---
+
+### 7. **API_REFERENCE.md** 📝 (Reference, needs creation)
+
+**Purpose:** Complete API endpoint documentation
+
+**Recommended Content:**
+```markdown
+# API Reference
+
+## Overview
+- Base URLs
+- Authentication
+- Error handling
+- Rate limiting
+
+## Laravel Orchestration API
+- Health endpoints
+- AI service proxy endpoints
+- Job management endpoints
+- Result retrieval endpoints
+
+## ADMET Service API
+- Health endpoint
+- Info endpoint
+- Predict endpoints (single & batch)
+- Model status endpoint
+
+## Drug Repurposing Service API
+- Disease targets endpoint
+- Drug library endpoint
+- Screening endpoint
+- Model status endpoint
+
+## Chemical RAG Service API
+- Retrieval-only endpoint
+- Full RAG endpoint
+- Health endpoint
+- Stats endpoint
+
+## Response Formats
+- Success responses
+- Error responses
+- Status codes
+
+## Examples
+- Real curl requests for each endpoint
+- Request/response pairs
+- Error scenarios
+```
+
+**Cross-references:** README.md → API_REFERENCE.md, Service READMEs
+
+---
+
+### 8. **CONTRIBUTING.md** ✅ (Referenced in README)
+
+**Purpose:** Development guidelines
+
+**Current Status:** ✅ Guidelines included in README.md
+
+**Recommended Dedicated File:**
+```markdown
+# Contributing
+
+## Getting Started
+- Fork and clone
+- Setup development environment
+- Create feature branch
+
+## Code Style
+- PHP: PSR-12
+- Python: PEP 8
+- Commits: Conventional format
+
+## Development Workflow
+- Local development
+- Testing requirements
+- Documentation updates
+- Pull request process
+
+## Testing
+- Unit tests
+- Integration tests
+- Running test suites
+
+## Commit Messages
+- Format guidelines
+- Examples
+
+## Pull Request Process
+- Description template
+- Code review expectations
+- Merge requirements
+```
+
+---
+
+## 🎯 Implementation Checklist
+
+### Completed ✅
+- [x] README.md refactored (concise, professional, links to docs)
+- [x] ARCHITECTURE.md (exists, comprehensive)
+- [x] DOCKER.md (exists, comprehensive)
+- [x] ADMET/README.md (updated with full training + inference)
+- [x] Chemical-RAG/README.md (updated with v2.1 focus)
+- [x] Drug Reporposing/README.md (already excellent, kept as-is)
+
+### Recommended Verification/Creation 📝
+- [ ] QUICK_START.md - Verify or create based on template
+- [ ] PRODUCTION_GUIDE.md - Create based on template
+- [ ] TROUBLESHOOTING.md - Create based on template
+- [ ] API_REFERENCE.md - Create based on template
+- [ ] CONTRIBUTING.md - Extract to standalone file (optional)
+
+---
+
+## 📊 Documentation Standards Applied
+
+### Format & Structure
+✅ Consistent markdown formatting across all files
+✅ Clear section hierarchy (H1-H4)
+✅ Emoji headers for visual organization
+✅ Markdown best practices (lists, tables, code blocks)
+
+### Navigation
+✅ Table of contents in root README
+✅ Cross-references between related docs
+✅ Clear "Next Steps" links at end of each section
+✅ Service-specific READMEs with complete info
+
+### Content Quality
+✅ Professional tone (enterprise-grade)
+✅ Concise main README with detailed docs
+✅ Real examples (ports, commands, endpoints)
+✅ Troubleshooting guides with solutions
+
+### GitHub Readability
+✅ Clean whitespace between sections
+✅ Compact tables
+✅ Reduced code block sizes
+✅ Links instead of repetition
+
+---
+
+## 🎓 Best Practices References
+
+This documentation structure follows conventions from:
+- **Apache Software Foundation** - Modular documentation
+- **Kubernetes** - Clear architecture docs with links
+- **Popular open-source projects** - Concise main README with satellite docs
+- **Enterprise software standards** - Professional, scalable approach
+
+---
+
+## 📋 File Status Summary
+
+| File | Status | Purpose |
+|------|--------|---------|
+| README.md | ✅ Complete | High-level overview + navigation |
+| ARCHITECTURE.md | ✅ Exists | System design details |
+| DOCKER.md | ✅ Exists | Container setup |
+| PRODUCTION_GUIDE.md | 📝 Recommended | Deployment & scaling |
+| TROUBLESHOOTING.md | 📝 Recommended | Problem solving |
+| API_REFERENCE.md | 📝 Recommended | Endpoint documentation |
+| CONTRIBUTING.md | ✅ Included in README | Contributing guidelines |
+| Service READMEs | ✅ All updated | Component-specific docs |
+
+---
+
+## 🚀 Next Steps
+
+1. **Verify** QUICK_START.md exists and is up-to-date
+2. **Create or verify** PRODUCTION_GUIDE.md using template
+3. **Create** TROUBLESHOOTING.md from existing content
+4. **Create** API_REFERENCE.md for clarity
+5. **(Optional) Extract** CONTRIBUTING.md as standalone file
+6. **Update** navigation links once all files are created
+7. **Test** all links render correctly on GitHub
+
+---
+
+## 📞 Questions?
+
+Reference this document when:
+- Creating new documentation files
+- Updating existing docs
+- Organizing repository documentation
+- Onboarding new contributors
+
+**Maintain consistency:** Keep all docs at the same quality level and style for professional appearance.
+
+---
+
+**Last Updated:** May 2026 | **Status:** Documentation structure defined ✅

Dockerfile

@@ -0,0 +1,115 @@
+# syntax=docker/dockerfile:1
+
+# ============================================================
+# Stage 1: Composer dependencies
+# ============================================================
+FROM composer:2.8 AS vendor
+
+WORKDIR /app
+
+RUN apk add --no-cache icu-dev libzip-dev oniguruma-dev \
+    && docker-php-ext-install intl zip mbstring bcmath pcntl
+
+# Add build argument for composer dev dependencies
+
+COPY composer.json composer.lock ./
+RUN composer install \
+    --no-interaction \
+    --no-scripts \
+    --prefer-dist \
+    --optimize-autoloader
+
+COPY . .
+RUN composer dump-autoload --optimize --classmap-authoritative
+
+# ============================================================
+# Stage 2: Frontend assets (Vite)
+# ============================================================
+FROM node:22-alpine AS assets
+
+WORKDIR /app
+
+COPY package.json package-lock.json ./
+RUN npm ci
+
+COPY vite.config.js ./
+COPY resources ./resources
+COPY public ./public
+
+RUN npm run build
+
+# ============================================================
+# Stage 3: Runtime (PHP CLI on Debian — artisan serve)
+# ============================================================
+FROM php:8.3-cli AS runtime
+
+RUN apt-get update && apt-get install -y \
+    libicu-dev \
+    libzip-dev \
+    libonig-dev \
+    libsqlite3-dev \
+    wget \
+    bzip2 \
+    ca-certificates \
+    openbabel \
+    supervisor \
+    && docker-php-ext-install \
+    pdo_sqlite \
+    zip \
+    intl \
+    mbstring \
+    bcmath \
+    opcache \
+    pcntl \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY docker/php/opcache.ini /usr/local/etc/php/conf.d/opcache.ini
+
+# Install Miniconda
+ENV CONDA_DIR=/opt/conda
+
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh && \
+    /bin/bash /tmp/miniconda.sh -b -p $CONDA_DIR && \
+    rm /tmp/miniconda.sh
+
+ENV PATH=$CONDA_DIR/bin:$PATH
+
+# Accept Anaconda ToS (required in CI/Docker)
+RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main && \
+    conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r
+
+# Create environment
+RUN conda create -y -p /var/www/html/vina_env -c conda-forge \
+    vina=1.2.5 \
+    python=3.10 \
+    pip
+
+# Install RDKit via pip to bypass Boost C++ solver compatibility conflicts
+RUN /var/www/html/vina_env/bin/pip install rdkit==2025.09.5
+
+# Install testing and service dependencies from requirements.txt
+COPY requirements.txt /tmp/requirements.txt
+RUN /var/www/html/vina_env/bin/pip install -r /tmp/requirements.txt
+
+ENV PATH=/var/www/html/vina_env/bin:$PATH
+
+WORKDIR /var/www/html
+
+COPY --from=vendor --chown=www-data:www-data /app /var/www/html
+COPY --from=assets --chown=www-data:www-data /app/public/build /var/www/html/public/build
+
+COPY docker/entrypoint.sh /usr/local/bin/entrypoint.sh
+COPY docker/supervisord.conf /etc/supervisor/conf.d/supervisord.conf
+RUN chmod +x /usr/local/bin/entrypoint.sh \
+    && mkdir -p storage/framework/{cache,sessions,views} storage/logs bootstrap/cache database \
+    && chown -R www-data:www-data storage bootstrap/cache database /var/www/html/vina_env
+
+USER www-data
+
+EXPOSE 8000 7860
+
+HEALTHCHECK --interval=15s --timeout=5s --start-period=40s --retries=5 \
+    CMD php -r "exit((int)(@file_get_contents('http://127.0.0.1:7860') === false));"
+
+ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
+CMD ["php", "artisan", "serve", "--host=0.0.0.0", "--port=8000"]

HF_SPACES_GUIDE.md

@@ -0,0 +1,277 @@
+# AILIXIR Hugging Face Spaces Deployment Guide
+
+## Overview
+
+The AILIXIR platform is deployed across **5 Hugging Face Spaces**:
+
+| Space | Purpose | URL |
+|-------|---------|-----|
+| `ailixir-api` | Backend API (Laravel + SQLite) | https://huggingface.co/spaces/Ailixir-AI-Team/ailixir-api |
+| `ailixir-admet` | ADMET Prediction Service | https://huggingface.co/spaces/shdwRow/ailixir-admet |
+| `ailixir-drug-repurposing` | Drug Repurposing Service | https://huggingface.co/spaces/RottenShadow/ailixir-drug-repurposing |
+| `ailixir-chemical-rag` | Chemical RAG Service | https://huggingface.co/spaces/RottenShadow/ailixir-chemical-rag |
+| `ailixir-generation` | Molecular Generation Service | https://huggingface.co/spaces/shdwRow/ailixir-generation |
+
+---
+
+## 1. Accessing the Spaces
+
+Each Space builds a Docker container from its respective `Dockerfile`. Once built and running, the services are accessible at:
+
+```
+https://RottenShadow-{space-name}.hf.space
+```
+
+For example:
+- **Backend API:** `https://Ailixir-AI-Team-ailixir-api.hf.space`
+- **ADMET:** `https://shdwRow-ailixir-admet.hf.space`
+- **Drug Repurposing:** `https://RottenShadow-ailixir-drug-repurposing.hf.space`
+- **Chemical RAG:** `https://RottenShadow-ailixir-chemical-rag.hf.space`
+- **Generation:** `https://shdwRow-ailixir-generation.hf.space`
+
+---
+
+## 2. Space Lifecycle
+
+### Wake-up / Sleep
+Spaces on the **free tier** (CPU Basic) go to sleep after **15 minutes of inactivity**. When you access a sleeping Space's URL, it will take **30–120 seconds** to wake up.
+
+To keep a Space awake, you can:
+- Use a **cron job** to ping the health endpoint every 10 minutes
+- Upgrade to a **paid hardware tier** (CPU Upgrade or GPU)
+- Set a **longer sleep timeout** in the Space settings
+
+### Health Check
+Each Space exposes a `/health` endpoint. You can check if a service is running:
+
+  ```bash
+  curl https://shdwRow-ailixir-admet.hf.space/health
+  ```
+
+Expected response: `{"status": "healthy", ...}`
+
+---
+
+## 3. Environment Variables (Secrets)
+
+Each Space requires certain environment variables. These are set as **Space Secrets** in the Hugging Face Space settings.
+
+### 3.1 Backend Space: `ailixir-api`
+
+These are **required** secrets — set them in:  
+https://huggingface.co/spaces/Ailixir-AI-Team/ailixir-api/settings
+
+| Secret | Value | Description |
+|--------|-------|-------------|
+| `APP_KEY` | *(generate one)* | Laravel app key. Run: `php artisan key:generate --show` |
+| `APP_ENV` | `production` | Application environment |
+| `APP_DEBUG` | `false` | Debug mode (keep false in production) |
+| `DB_CONNECTION` | `sqlite` | Database engine |
+| `SESSION_DRIVER` | `database` | Session storage |
+| `CACHE_STORE` | `database` | Cache storage |
+| `QUEUE_CONNECTION` | `database` | Queue driver |
+| `RUN_MODE` | `hf` | **Must be set to `hf`** to enable supervisor mode |
+| `AI_INTEGRATION_ROUTES_ENABLED` | `true` | Enable AI proxy routes |
+| `CHEMICAL_AI_URL` | `https://RottenShadow-ailixir-chemical-rag.hf.space` | Chemical RAG service URL |
+| `ADMET_AI_URL` | `https://shdwRow-ailixir-admet.hf.space` | ADMET service URL |
+| `AI_ADMET_SERVICE_URL` | `https://shdwRow-ailixir-admet.hf.space` | ADMET service URL (alias) |
+| `DRUG_REPURPOSING_URL` | `https://RottenShadow-ailixir-drug-repurposing.hf.space` | Drug repurposing service URL |
+| `AI_SERVICE_URL` | `https://RottenShadow-ailixir-drug-repurposing.hf.space` | Drug repurposing URL (alias) |
+| `GENERATION_SERVICE_URL` | `https://shdwRow-ailixir-generation.hf.space` | Generation service URL |
+| `MAIL_MAILER` | `log` | Mail driver (log to console) |
+| `CLOUDINARY_URL` | `cloudinary://dummy_key:dummy_secret@dummy_cloud` | Cloudinary (can be dummy) |
+| `CLOUDINARY_CLOUD_NAME` | `dummy_cloud` | Cloudinary cloud name |
+| `CLOUDINARY_API_KEY` | `dummy_key` | Cloudinary API key |
+| `CLOUDINARY_API_SECRET` | `dummy_secret` | Cloudinary API secret |
+| `LOG_CHANNEL` | `stderr` | Log output channel |
+| `LOG_LEVEL` | `info` | Log level |
+
+**How to generate APP_KEY:**
+```bash
+# If you have PHP locally:
+php artisan key:generate --show
+
+# If not, use any online base64 generator to create a random 32-byte base64 string
+# Format: base64:XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
+```
+
+### 3.2 ADMET Space: `ailixir-admet` (owner: shdwRow)
+
+**Space settings:** https://huggingface.co/spaces/shdwRow/ailixir-admet/settings
+
+| Secret | Value | Description |
+|--------|-------|-------------|
+| `PYTHONUNBUFFERED` | `1` | Python unbuffered output |
+| `LOG_LEVEL` | `INFO` | Logging level |
+
+### 3.3 Drug Repurposing Space: `ailixir-drug-repurposing`
+
+| Secret | Value | Description |
+|--------|-------|-------------|
+| `HOST` | `0.0.0.0` | Bind address |
+| `PORT` | `7860` | Port (must match Dockerfile) |
+| `DEBUG` | `False` | Debug mode |
+| `LOG_LEVEL` | `INFO` | Log level |
+| `USE_MOCK_MODEL` | `False` | Use mock model (for testing) |
+| `USE_MOCK_DRUGS` | `False` | Use mock drug list (for testing) |
+
+### 3.4 Chemical RAG Space: `ailixir-chemical-rag`
+
+| Secret | Value | Description |
+|--------|-------|-------------|
+| `PYTHONUNBUFFERED` | `1` | Python unbuffered output |
+| `API_PORT` | `7860` | API port |
+| `API_HOST` | `0.0.0.0` | Bind address |
+
+### 3.5 Generation Space: `ailixir-generation` (owner: shdwRow)
+
+**Space settings:** https://huggingface.co/spaces/shdwRow/ailixir-generation/settings
+
+| Secret | Value | Description |
+|--------|-------|-------------|
+| `PUBLIC_BASE_URL` | `https://shdwRow-ailixir-generation.hf.space` | Public URL of the service |
+| `REINVENT_DEVICE` | `cpu` | Device for REINVENT (CPU-only on HF free tier) |
+| `DEEPPURPOSE_URL` | *(leave empty)* | DeepPurpose service URL (CPU-only version) |
+| `ADGPU_BIN` | *(leave empty)* | AutoDock-GPU binary (not available on CPU) |
+
+---
+
+## 4. Setting Secrets in HF Spaces
+
+1. Go to the Space's settings page:  
+   `https://huggingface.co/spaces/RottenShadow/{space-name}/settings`
+
+2. Scroll down to **"Repository Secrets"** section
+
+3. Click **"New secret"**
+
+4. Enter the key-value pair and click **"Add"**
+
+5. The Space will automatically **rebuild** with the new secrets
+
+---
+
+## 5. API Endpoints
+
+Once all spaces are running, the backend API is available at:
+
+```
+https://Ailixir-AI-Team-ailixir-api.hf.space/api
+```
+
+### Authentication
+```bash
+# Register
+curl -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/register \
+  -H "Content-Type: application/json" \
+  -d '{"name":"User","email":"user@example.com","password":"password123"}'
+
+# Login
+curl -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
+  -H "Content-Type: application/json" \
+  -d '{"email":"user@example.com","password":"password123"}'
+
+# Response includes Bearer token
+```
+
+### AI Service Proxies (via Backend)
+All AI endpoints are proxied through the backend:
+
+```bash
+# ADMET prediction
+curl -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/admet/predict \
+  -H "Authorization: Bearer YOUR_TOKEN" \
+  -H "Content-Type: application/json" \
+  -d '{"smiles": "c1ccccc1"}'
+
+# Chemical search
+curl -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/chemical-search \
+  -H "Authorization: Bearer YOUR_TOKEN" \
+  -H "Content-Type: application/json" \
+  -d '{"smiles": "CC(=O)O"}'
+
+# Health check (no auth needed)
+curl https://Ailixir-AI-Team-ailixir-api.hf.space/api/ai-services/health
+```
+
+---
+
+## 6. Auto-Sync from GitHub
+
+The repository has **5 GitHub Actions workflows** that automatically sync code pushes to HF Spaces:
+
+| Workflow | Triggers On | Syncs To |
+|----------|-------------|----------|
+| `sync-hf-all.yml` | Push to `main` | All 5 spaces (matrix job) |
+
+### ❗ PREREQUISITE: Set `HF_TOKEN` as a GitHub Secret
+
+For the auto-sync to work, you **must** add both HF tokens as GitHub Actions secrets:
+
+1. Go to: https://github.com/RottenShadow/AILIXIR_BackEnd/settings/secrets/actions
+2. Click **"New repository secret"**
+3. **Name:** `HF_TOKEN` — **Value:** RottenShadow account token (for `RottenShadow` spaces)
+4. **Name:** `HF_TOKEN_SHDWROW` — **Value:** shdwRow account token (for `shdwRow` spaces)
+5. **Name:** `HF_TOKEN_AILIXIR` — **Value:** Ailixir-AI-Team account token (for `ailixir-api`)
+
+Without these, the auto-sync workflows will fail with an authentication error.
+
+---
+
+## 7. Troubleshooting
+
+### Space stuck at `BUILDING`
+- Large Docker images can take **15–45 minutes** to build on HF free tier
+- Check the build logs: Space page → **"Factory"** or **"Builder"** tab
+- Common issues: missing files, Dockerfile errors, out of memory
+
+### Space shows `NO_APP_FILE`
+- The Dockerfile is missing from the root of the Space repo
+- Ensure `Dockerfile` exists at the root (not in a subdirectory)
+
+### Space shows `CONFIG_ERROR`
+- Missing or invalid `README.md` YAML frontmatter
+- Ensure the `README.md` has the correct format:
+  ```yaml
+  ---
+  title: Space Name
+  emoji: 🧬
+  colorFrom: blue
+  colorTo: green
+  sdk: docker
+  app_port: 7860
+  ---
+  ```
+
+### API returns 500 errors
+- Check the Space logs: Space page → **"Factory"** tab
+- Verify all required environment secrets are set
+- For the backend, ensure `APP_KEY` is a valid Laravel key
+
+### Service not reachable from backend
+- Verify the AI service URL in the backend's secrets is correct
+- The URLs should use the format: `https://RottenShadow-{name}.hf.space` (or `https://shdwRow-{name}.hf.space` for ADMET/Generation)
+- Test the AI service directly first:
+  ```bash
+curl https://shdwRow-ailixir-admet.hf.space/health
+  ```
+
+### Space keeps going to sleep
+- Free tier spaces sleep after 15 minutes of inactivity
+- Use a cron job (e.g., GitHub Actions scheduled workflow) to ping every 10 minutes
+- Or upgrade to a paid hardware tier (starting at $5/month)
+
+---
+
+## 8. Upgrading Hardware
+
+To upgrade a Space from CPU Basic to a paid tier:
+
+1. Go to the Space settings
+2. Under **"Hardware"**, select a tier:
+   - `cpu-upgrade` — 4 vCPU, 16GB RAM ($5/month)
+   - `cpu-basic` — 2 vCPU, 16GB RAM (free)
+   - `t4-small` — NVIDIA T4 GPU ($20/month, for generation service)
+3. Save — the Space will rebuild
+
+**Note:** The generation service (`ailixir-generation`) can benefit from a GPU upgrade for AutoDock-GPU docking.

HUGGINGFACE_FLOW.md

@@ -0,0 +1,186 @@
+# AILIXIR Hugging Face Spaces — Migration Flow
+
+> **Base commit:** `fd94aa0` — pre-HF, Docker Compose with MySQL+Redis
+
+---
+
+## 1. Why Hugging Face Spaces?
+
+| Need | Solution |
+|------|----------|
+| Free hosting for 5 microservices | 5 HF Spaces (2 accounts to keep more awake) |
+| No MySQL/Redis infrastructure | SQLite for storage, `database` queue driver |
+| Simple CI/CD | GitHub Actions auto-syncs code to each HF Space |
+| Binary model files | Git LFS + Xet storage on HF |
+
+---
+
+## 2. Architecture Decisions
+
+### SQLite over MySQL
+- **Why:** HF Spaces provide ephemeral storage; SQLite has zero dependencies
+- **Trade-off:** No concurrent write scaling; fine for single-user/small-team usage
+- **DB Location:** `database/ailixir.sqlite` (mounted in the container)
+- **Migrations:** Run automatically via `entrypoint.sh` on startup
+
+### Two HF Accounts
+- **`Ailixir-AI-Team`**: Backend API
+- **`RottenShadow`**: Chemical RAG, Drug Repurposing
+- **`shdwRow`** (secondary): ADMET, Generation
+- **Why:** HF Spaces free tier puts unused spaces to sleep; spreading across 2 accounts keeps more services warm
+
+### Queue: `sync` driver
+- **Why:** No need for Redis/DB-backed queue worker; jobs run inline
+- **Note:** For production scale, switch back to `database` and run a queue worker
+
+### Binary Model Files: Git LFS + Xet
+- **Why:** HF rejects large files in raw Git; Xet provides efficient binary storage
+- **Tracked:** `*.ckpt`, `*.pt`, `*.pkl`
+
+---
+
+## 3. Per-Service Details
+
+### Backend API (`Ailixir-AI-Team/ailixir-api`)
+- **Tech:** Laravel 12 + PHP 8.3 CLI
+- **Port:** 7860 (HF default)
+- **Dockerfile:** Multi-stage (composer → vite → runtime)
+- **Entrypoint:** Sources `RUN_MODE=hf` → starts supervisord (laravel serve + queue worker)
+- **Fixes applied:**
+  - `config/view.php` — explicit compiled path (fixes 500 on `/`)
+  - `bootstrap/app.php` — `trustProxies(at: '*')` (fixes mixed-content CSS)
+  - `config/scribe.php` — `docs_url` moved to `/scribe-docs`
+  - `/docs` route — serves rendered `API.md` (curl examples, responses, grouped)
+  - `QUEUE_CONNECTION=sync` — no worker needed
+
+### ADMET Prediction (`shdwRow/ailixir-admet`)
+- **Tech:** FastAPI + PyTorch
+- **Port:** 7860
+- **Model:** `best_model.ckpt` (LFS-tracked)
+- **Sync:** Xet-enabled checkout in workflow
+
+### Chemical RAG (`RottenShadow/ailixir-chemical-rag`)
+- **Tech:** FastAPI + ChromaDB
+- **Port:** 7860
+
+### Drug Repurposing (`RottenShadow/ailixir-drug-repurposing`)
+- **Tech:** FastAPI + DeepPurpose
+- **Port:** 7860
+- **Special:** `Dockerfile.hf` with mock-mode fallback
+
+### Generation (`shdwRow/ailixir-generation`)
+- **Tech:** FastAPI + REINVENT4 + RDKit + DeepPurpose (optional)
+- **Port:** 7860
+- **Fixes applied:**
+  - **REINVENT4** — git cloned and `install.py cpu` in `Dockerfile.hf`
+  - **libXrender** — `libxrender1 libxext6` added (RDKit image rendering)
+  - **DeepPurpose** — optional install; integrated `/reinvent_predict` route on same port 7860
+  - **Graceful fallback** — if DeepPurpose unavailable, enrichment returns null affinity values
+  - **Enrichment** — catches connection errors, sets `pred_pAff_mean` to `None`
+
+---
+
+## 4. Sync Workflow
+
+**File:** `.github/workflows/sync-hf-all.yml`
+
+### Trigger
+- Push to `main` branch
+- Manual dispatch via GitHub UI
+
+### Jobs (5 total)
+
+| Job | HF Space | Account | Token | Notes |
+|-----|----------|---------|-------|-------|
+| `backend` | `ailixir-api` | Ailixir-AI-Team | `HF_TOKEN_AILIXIR` | Excludes `ai_apps/`, `database/ailixir.sqlite`, `storage/` |
+| `drug-repurposing` | `ailixir-drug-repurposing` | RottenShadow | `HF_TOKEN` | Renames `Dockerfile.hf` → `Dockerfile` |
+| `admet` | `ailixir-admet` | shdwRow | `HF_TOKEN_SHDWROW` | LFS + Xet for `.ckpt` |
+| `chemical-rag` | `ailixir-chemical-rag` | RottenShadow | `HF_TOKEN` | |
+| `generation` | `ailixir-generation` | shdwRow | `HF_TOKEN_SHDWROW` | LFS + Xet for `.ckpt`, `.pt`, `.pkl` |
+
+### How each job works
+1. Clone the HF Space repo (shallow, depth 1)
+2. `rsync -av --delete` — sync files from main repo, delete files removed in source
+3. Write `.env` with all required vars
+4. Rename `Dockerfile.hf` → `Dockerfile` if present
+5. Setup LFS/Xet for model files (ADMET, Generation)
+6. Commit and push to HF Space
+
+### Key exclusions (backend job)
+```
+--exclude=ai_apps
+--exclude=.git
+--exclude=.env
+--exclude=.dockerignore
+--exclude=public/imgs
+--exclude=storage
+--exclude=Diagrams
+--exclude=database/ailixir.sqlite
+```
+
+### Required GitHub Secrets
+| Secret | Used by |
+|--------|---------|
+| `HF_TOKEN` | drug-repurposing, chemical-rag |
+| `HF_TOKEN_AILIXIR` | backend |
+| `HF_TOKEN_SHDWROW` | admet, generation |
+| `GOOGLE_CLIENT_ID` | backend .env |
+| `GOOGLE_CLIENT_SECRET` | backend .env |
+
+---
+
+## 5. Environment Variables (`.env` written by sync)
+
+```
+RUN_MODE=hf
+APP_KEY=base64:...
+AI_INTEGRATION_ROUTES_ENABLED=true
+APP_URL=https://Ailixir-AI-Team-ailixir-api.hf.space
+APP_DEBUG=true
+QUEUE_CONNECTION=sync
+ADMET_AI_URL=https://shdwRow-ailixir-admet.hf.space
+CHEMICAL_AI_URL=https://RottenShadow-ailixir-chemical-rag.hf.space
+DRUG_REPURPOSING_URL=https://RottenShadow-ailixir-drug-repurposing.hf.space
+GENERATION_SERVICE_URL=https://shdwRow-ailixir-generation.hf.space
+GOOGLE_CLIENT_ID=...
+GOOGLE_CLIENT_SECRET=...
+GOOGLE_REDIRECT_URI=https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/auth/google
+CLOUDINARY_CLOUD_NAME=dummy_cloud
+CLOUDINARY_API_KEY=dummy_key
+CLOUDINARY_API_SECRET=dummy_secret
+```
+
+---
+
+## 6. Database Protection
+
+The sync workflow **excludes** `database/ailixir.sqlite` from rsync and runs `git checkout HEAD -- database/ailixir.sqlite` before commit to prevent the live database from being pushed to git.
+
+On HF Spaces, the database file persists across restarts (HF Spaces keep filesystem between restarts) but is **reset** when the Space rebuilds (code push).
+
+---
+
+## 7. Known Issues & Future Work
+
+| Issue | Status | Resolution |
+|-------|--------|------------|
+| DeepPurpose on Python 3.10 | Unstable | Falls back to null affinity predictions; could switch to conda base image |
+| Google OAuth secrets | Not set | Needs `GOOGLE_CLIENT_ID` / `GOOGLE_CLIENT_SECRET` added to GitHub secrets |
+| Space sleep on free tier | Ongoing | Two-account setup mitigates; upgrade to HF Pro for always-on |
+| Cloudinary credentials | Dummy values | Set real Cloudinary keys for image upload features |
+| ADMET model files in Xet | Working | Large `.ckpt` files stored via HF Xet |
+| Docs route `/docs` | Working | Serves rendered `API.md` with all examples and grouping |
+
+---
+
+## 8. Commit History (cleaned)
+
+```
+c49c94f Add HF Spaces sync workflow with two-account setup, DB protection
+30f0a11 Generation HF: REINVENT4, DeepPurpose, libXrender, graceful fallback
+a342297 AI microservices HF: ports 8000→7860, Dockerfiles, README_HF
+af62962 Backend HF fixes: trustProxies, view cache path, docs route with API.md
+fd80b74 Add HF Spaces environment config, deployment guide, and changelog
+b4a5d77 Foundation: migrate MySQL→SQLite, add supervisor, port 7860, APP_KEY auto-gen
+fd94aa0 Limit Docker Compose build parallelism in CI (original base)
+```

README.md

@@ -1,44 +1,24 @@
 ---
-title: EGFR AI Demo
-emoji: 🧪
+title: AILIXIR - Backend API
+emoji: 🧠
 colorFrom: blue
-colorTo: green
-sdk: gradio
-sdk_version: 6.13.0
-python_version: "3.10"
-app_file: app.py
-pinned: false
-license: other
+colorTo: indigo
+sdk: docker
+app_port: 7860
 ---
 
-# EGFR AI Demo
+# AILIXIR Backend API
 
-Private Gradio demo for the EGFR AI backend workflow.
+Laravel backend with SQLite database for the AILIXIR drug discovery platform.
 
-This Space is a CPU demo version.
+- **Port:** 7860
+- **SDK:** Docker
+- **Database:** SQLite
 
-It demonstrates:
+## Endpoints
 
-- SMILES property calculation
-- response schema for generated molecules
-- `pred_pAff_mean` field placeholder / integration point
-- docking columns and backend contract
-- example response from the private artifact bundle
-
-## Docking note
-
-Real AutoDock-GPU docking is not enabled in this CPU Space.
-
-The backend schema already supports:
-
-- `docking_score`
-- `docking_status`
-- `docking_pose_file`
-
-Supported docking modes in the full backend:
-
-- `off`
-- `top_k`
-- `all`
-
-In this CPU demo Space, docking status is returned as `not_run`.
+- `GET /api/ai-services/health` — Health check
+- `POST /api/admet/predict` — ADMET prediction
+- `POST /api/chemical-search` — Chemical search
+- `POST /api/user/register` — User registration
+- `POST /api/user/login` — User login

README_HF.md

@@ -0,0 +1,24 @@
+---
+title: AILIXIR - Backend API
+emoji: 🧠
+colorFrom: blue
+colorTo: indigo
+sdk: docker
+app_port: 7860
+---
+
+# AILIXIR Backend API
+
+Laravel backend with SQLite database for the AILIXIR drug discovery platform.
+
+- **Port:** 7860
+- **SDK:** Docker
+- **Database:** SQLite
+
+## Endpoints
+
+- `GET /api/ai-services/health` — Health check
+- `POST /api/admet/predict` — ADMET prediction
+- `POST /api/chemical-search` — Chemical search
+- `POST /api/user/register` — User registration
+- `POST /api/user/login` — User login

_ide_helper_models.php

@@ -0,0 +1,774 @@
+<?php
+
+// @formatter:off
+// phpcs:ignoreFile
+/**
+ * A helper file for your Eloquent Models
+ * Copy the phpDocs from this file to the correct Model,
+ * And remove them from this file, to prevent double declarations.
+ *
+ * @author Barry vd. Heuvel <barryvdh@gmail.com>
+ */
+
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property string $smiles
+ * @property float|null $absorption
+ * @property float|null $distribution
+ * @property float|null $metabolism
+ * @property float|null $excretion
+ * @property float|null $toxicity
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet whereAbsorption($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet whereDistribution($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet whereExcretion($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet whereMetabolism($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet whereSmiles($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet whereToxicity($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Admet whereUpdatedAt($value)
+ */
+	class Admet extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+ * @property string $job_id
+ * @property string $status
+ * @property string $preset
+ * @property int $num_molecules
+ * @property int $return_top_k
+ * @property string $docking_mode
+ * @property int $dock_top_k
+ * @property array<array-key, mixed>|null $summary
+ * @property array<array-key, mixed>|null $files
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property array<array-key, mixed>|null $ligands
+ * @property string|null $stage
+ * @property-read \App\Models\User $user
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob completed()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob failed()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob running()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereDockTopK($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereDockingMode($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereFiles($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereJobId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereLigands($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereNumMolecules($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob wherePreset($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereReturnTopK($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereStage($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereStatus($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereSummary($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|AiJob whereUserId($value)
+ */
+	class AiJob extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property string $name
+ * @property string|null $category
+ * @property array<array-key, mixed>|null $images
+ * @property string|null $description
+ * @property string|null $notable_winners
+ * @property string|null $country
+ * @property int|null $year_started
+ * @property string|null $website
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \App\Models\Scientist> $scientists
+ * @property-read int|null $scientists_count
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereCategory($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereCountry($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereDescription($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereImages($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereName($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereNotableWinners($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereWebsite($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Award whereYearStarted($value)
+ */
+	class Award extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $job_id
+ * @property int $rank
+ * @property string $smiles
+ * @property string|null $name
+ * @property string|null $cid
+ * @property float|null $similarity
+ * @property string|null $explanation
+ * @property string|null $image_url
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \App\Models\ChemicalSearchJob $job
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereCid($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereExplanation($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereImageUrl($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereJobId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereName($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereRank($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereSimilarity($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereSmiles($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalCompound whereUpdatedAt($value)
+ */
+	class ChemicalCompound extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+ * @property string $query_smiles
+ * @property int $top_k
+ * @property string $status
+ * @property array<array-key, mixed>|null $results
+ * @property array<array-key, mixed>|null $reason
+ * @property array<array-key, mixed>|null $image_urls
+ * @property array<array-key, mixed>|null $metadata
+ * @property string|null $error_message
+ * @property \Illuminate\Support\Carbon|null $started_at
+ * @property \Illuminate\Support\Carbon|null $completed_at
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \App\Models\ChemicalCompound> $compounds
+ * @property-read int|null $compounds_count
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereCompletedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereErrorMessage($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereImageUrls($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereMetadata($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereQuerySmiles($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereReason($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereResults($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereStartedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereStatus($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereTopK($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemicalSearchJob whereUserId($value)
+ */
+	class ChemicalSearchJob extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+ * @property int|null $chemistry_thread_id
+ * @property string $type
+ * @property string $input_data
+ * @property string|null $response
+ * @property array<array-key, mixed>|null $properties
+ * @property array<array-key, mixed>|null $drug_likeness
+ * @property array<array-key, mixed>|null $admet
+ * @property int|null $processing_time_ms
+ * @property string $status
+ * @property string|null $error_message
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \App\Models\ChemistryThread|null $thread
+ * @property-read \App\Models\User $user
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereAdmet($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereChemistryThreadId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereDrugLikeness($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereErrorMessage($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereInputData($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereProcessingTimeMs($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereProperties($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereResponse($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereStatus($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereType($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryAnalysis whereUserId($value)
+ */
+	class ChemistryAnalysis extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+ * @property string $job_id
+ * @property string $filename
+ * @property string $analysis_type
+ * @property int $total_rows
+ * @property int $completed_rows
+ * @property int $failed_rows
+ * @property int $progress_percent
+ * @property string $status
+ * @property string|null $result_file_path
+ * @property string|null $error_message
+ * @property \Illuminate\Support\Carbon|null $started_at
+ * @property \Illuminate\Support\Carbon|null $completed_at
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \App\Models\User $user
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereAnalysisType($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereCompletedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereCompletedRows($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereErrorMessage($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereFailedRows($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereFilename($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereJobId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereProgressPercent($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereResultFilePath($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereStartedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereStatus($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereTotalRows($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryCsvJob whereUserId($value)
+ */
+	class ChemistryCsvJob extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+ * @property string $thread_id
+ * @property string|null $title
+ * @property string $status
+ * @property \Illuminate\Support\Carbon|null $last_used_at
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \App\Models\ChemistryAnalysis> $analyses
+ * @property-read int|null $analyses_count
+ * @property-read \App\Models\User $user
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread whereLastUsedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread whereStatus($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread whereThreadId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread whereTitle($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ChemistryThread whereUserId($value)
+ */
+	class ChemistryThread extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+ * @property string $input_type
+ * @property string|null $smiles
+ * @property string|null $protein_name
+ * @property string|null $ligand_name
+ * @property string $protein_path
+ * @property string $ligand_path
+ * @property string $status
+ * @property array<array-key, mixed>|null $result_data
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \App\Models\User $user
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereInputType($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereLigandName($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereLigandPath($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereProteinName($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereProteinPath($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereResultData($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereSmiles($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereStatus($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|DockingJob whereUserId($value)
+ */
+	class DockingJob extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property string $job_id
+ * @property string $status
+ * @property string $file_format
+ * @property string $smiles
+ * @property string|null $filename
+ * @property string|null $download_url
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport whereDownloadUrl($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport whereFileFormat($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport whereFilename($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport whereJobId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport whereSmiles($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport whereStatus($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|LigandExport whereUpdatedAt($value)
+ */
+	class LigandExport extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property string $experiment_name
+ * @property string|null $description
+ * @property string|null $SYS_pdb
+ * @property string|null $SYS_nw_pdb
+ * @property string|null $ligand_H_pdb
+ * @property string|null $ligand_gaff_pdb
+ * @property string|null $ligand_h_1_pdb
+ * @property string|null $ligand_h_nonprot_pdb
+ * @property string|null $protein_ligand_pdb
+ * @property string|null $prot_lig_equil_pdb
+ * @property string|null $starting_end_pdb
+ * @property string|null $prot_lig_equil_dcd
+ * @property string|null $prot_lig_prod1_1_nw_dcd
+ * @property string|null $SYS_gaff2_crd
+ * @property string|null $SYS_nw_crd
+ * @property string|null $SYS_gaff2_prmtop
+ * @property string|null $SYS_nw_prmtop
+ * @property string|null $prot_lig_equil_rst
+ * @property string|null $prepareforleap_in
+ * @property string|null $tleap_in
+ * @property string|null $lig_lib
+ * @property string|null $ligand_frcmod
+ * @property string|null $ligand_mol2
+ * @property string|null $ligand_h_renum_txt
+ * @property string|null $ligand_h_sslink
+ * @property string|null $prot_lig_equil_log
+ * @property string|null $_2D_rmsd_csv
+ * @property string|null $Interaction_energy_eelec_csv
+ * @property string|null $Interaction_energy_evdw_csv
+ * @property string|null $PC1_csv
+ * @property string|null $PC2_csv
+ * @property string|null $cross_correlation_csv
+ * @property string|null $distance_csv
+ * @property string|null $distance_select_csv
+ * @property string|null $radius_gyration_csv
+ * @property string|null $rmsd_ca_csv
+ * @property string|null $rmsf_ca_csv
+ * @property string|null $_2D_rmsd_png
+ * @property string|null $Interaction_energy_png
+ * @property string|null $PCA_png
+ * @property string|null $PCA_dist_png
+ * @property string|null $cross_correlation_png
+ * @property string|null $distance_png
+ * @property string|null $distance_select_png
+ * @property string|null $radius_gyration_png
+ * @property string|null $radius_gyration_dist_png
+ * @property string|null $rmsd_ca_png
+ * @property string|null $rmsd_dist_png
+ * @property string|null $rmsf_ca_png
+ * @property string|null $Interaction_html
+ * @property string|null $initial_html
+ * @property string|null $FINAL_RESULTS_MMPBSA_dat
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile where2DRmsdCsv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile where2DRmsdPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereCrossCorrelationCsv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereCrossCorrelationPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereDescription($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereDistanceCsv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereDistancePng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereDistanceSelectCsv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereDistanceSelectPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereExperimentName($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereFINALRESULTSMMPBSADat($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereInitialHtml($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereInteractionEnergyEelecCsv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereInteractionEnergyEvdwCsv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereInteractionEnergyPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereInteractionHtml($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereLigLib($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereLigandFrcmod($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereLigandGaffPdb($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereLigandH1Pdb($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereLigandHNonprotPdb($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereLigandHPdb($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereLigandHRenumTxt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereLigandHSslink($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereLigandMol2($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile wherePC1Csv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile wherePC2Csv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile wherePCADistPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile wherePCAPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile wherePrepareforleapIn($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereProtLigEquilDcd($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereProtLigEquilLog($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereProtLigEquilPdb($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereProtLigEquilRst($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereProtLigProd11NwDcd($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereProteinLigandPdb($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereRadiusGyrationCsv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereRadiusGyrationDistPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereRadiusGyrationPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereRmsdCaCsv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereRmsdCaPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereRmsdDistPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereRmsfCaCsv($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereRmsfCaPng($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereSYSGaff2Crd($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereSYSGaff2Prmtop($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereSYSNwCrd($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereSYSNwPdb($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereSYSNwPrmtop($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereSYSPdb($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereStartingEndPdb($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereTleapIn($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|MdFile whereUpdatedAt($value)
+ */
+	class MdFile extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property string $title
+ * @property string|null $summary
+ * @property string $source
+ * @property string $url
+ * @property \Illuminate\Support\Carbon|null $published_at
+ * @property string|null $category
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News whereCategory($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News wherePublishedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News whereSource($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News whereSummary($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News whereTitle($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|News whereUrl($value)
+ */
+	class News extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property string $name
+ * @property string $type
+ * @property string|null $billing_period
+ * @property numeric $price
+ * @property string $currency
+ * @property string|null $stripe_product_id
+ * @property string|null $stripe_price_id
+ * @property bool $is_active
+ * @property string|null $description
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereBillingPeriod($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereCurrency($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereDescription($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereIsActive($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereName($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan wherePrice($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereStripePriceId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereStripeProductId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereType($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Plan whereUpdatedAt($value)
+ */
+	class Plan extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+ * @property string|null $specialization
+ * @property string|null $university
+ * @property int|null $years_of_experience
+ * @property string|null $bio
+ * @property string|null $photo
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \App\Models\User $user
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher whereBio($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher wherePhoto($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher whereSpecialization($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher whereUniversity($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher whereUserId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Researcher whereYearsOfExperience($value)
+ */
+	class Researcher extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+ * @property int $news_id
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \App\Models\News $news
+ * @property-read \App\Models\User $user
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|SavedArticle newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|SavedArticle newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|SavedArticle query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|SavedArticle whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|SavedArticle whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|SavedArticle whereNewsId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|SavedArticle whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|SavedArticle whereUserId($value)
+ */
+	class SavedArticle extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property string $name
+ * @property string|null $nationality
+ * @property int|null $birth_year
+ * @property int|null $death_year
+ * @property array<array-key, mixed>|null $images
+ * @property string $bio
+ * @property string|null $impact
+ * @property string|null $field
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \App\Models\Award> $awards
+ * @property-read int|null $awards_count
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereBio($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereBirthYear($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereDeathYear($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereField($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereImages($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereImpact($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereName($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereNationality($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Scientist whereUpdatedAt($value)
+ */
+	class Scientist extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+ * @property array<array-key, mixed> $input
+ * @property array<array-key, mixed>|null $output
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property string $status
+ * @property-read \App\Models\User $user
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ScreeningResult newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ScreeningResult newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ScreeningResult query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ScreeningResult whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ScreeningResult whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ScreeningResult whereInput($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ScreeningResult whereOutput($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ScreeningResult whereStatus($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ScreeningResult whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|ScreeningResult whereUserId($value)
+ */
+	class ScreeningResult extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+ * @property string $protein
+ * @property string|null $ligand
+ * @property string $status
+ * @property int $progress
+ * @property string|null $error_message
+ * @property string|null $trajectory
+ * @property string|null $log_file
+ * @property array<array-key, mixed>|null $analysis
+ * @property string $force_field
+ * @property float $temperature
+ * @property float $simulation_time_ns
+ * @property int $box_size
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property-read \App\Models\User $user
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereAnalysis($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereBoxSize($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereErrorMessage($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereForceField($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereLigand($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereLogFile($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereProgress($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereProtein($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereSimulationTimeNs($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereStatus($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereTemperature($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereTrajectory($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|Simulation whereUserId($value)
+ */
+	class Simulation extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property int $user_id
+
+ * @property string $status
+
+ * @property array<array-key, mixed> $input
+ * @property array<array-key, mixed>|null $output
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property string $status
+ * @property-read \App\Models\User $user
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|TargetLookup newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|TargetLookup newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|TargetLookup query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|TargetLookup whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|TargetLookup whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|TargetLookup whereInput($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|TargetLookup whereOutput($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|TargetLookup whereStatus($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|TargetLookup whereUpdatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|TargetLookup whereUserId($value)
+ */
+	class TargetLookup extends \Eloquent {}
+}
+
+namespace App\Models{
+/**
+ * @property int $id
+ * @property string $name
+ * @property string $email
+ * @property \Illuminate\Support\Carbon|null $email_verified_at
+ * @property \Illuminate\Support\Carbon|null $last_otp_sent_at
+ * @property string $password
+ * @property string $role
+ * @property string|null $remember_token
+ * @property string|null $stripe_customer_id
+ * @property \Illuminate\Support\Carbon|null $created_at
+ * @property \Illuminate\Support\Carbon|null $updated_at
+ * @property string|null $email_verification_otp
+ * @property \Illuminate\Support\Carbon|null $email_verification_otp_expires_at
+ * @property bool $is_verified
+ * @property string|null $password_reset_otp
+ * @property \Illuminate\Support\Carbon|null $password_reset_otp_expires_at
+ * @property int|null $current_plan_id
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \App\Models\AiJob> $aiJobs
+ * @property-read int|null $ai_jobs_count
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \App\Models\ChemistryAnalysis> $chemistryAnalyses
+ * @property-read int|null $chemistry_analyses_count
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \App\Models\ChemistryCsvJob> $chemistryCsvJobs
+ * @property-read int|null $chemistry_csv_jobs_count
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \App\Models\ChemistryThread> $chemistryThreads
+ * @property-read int|null $chemistry_threads_count
+ * @property-read \Illuminate\Notifications\DatabaseNotificationCollection<int, \Illuminate\Notifications\DatabaseNotification> $notifications
+ * @property-read int|null $notifications_count
+ * @property-read \App\Models\Researcher|null $researcher
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \App\Models\Simulation> $simulations
+ * @property-read int|null $simulations_count
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \Laravel\Cashier\Subscription> $subscriptions
+ * @property-read int|null $subscriptions_count
+ * @property-read \Illuminate\Database\Eloquent\Collection<int, \Laravel\Sanctum\PersonalAccessToken> $tokens
+ * @property-read int|null $tokens_count
+ * @method static \Database\Factories\UserFactory factory($count = null, $state = [])
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User hasExpiredGenericTrial()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User newModelQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User newQuery()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User onGenericTrial()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User query()
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereCreatedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereCurrentPlanId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereEmail($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereEmailVerificationOtp($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereEmailVerificationOtpExpiresAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereEmailVerifiedAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereIsVerified($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereLastOtpSentAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereName($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User wherePassword($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User wherePasswordResetOtp($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User wherePasswordResetOtpExpiresAt($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereRememberToken($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereRole($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereStripeCustomerId($value)
+ * @method static \Illuminate\Database\Eloquent\Builder<static>|User whereUpdatedAt($value)
+ */
+	class User extends \Eloquent {}
+}
+

app.py

@@ -1,736 +0,0 @@
-import json
-import os
-import subprocess
-from pathlib import Path
-import uuid
-from datetime import datetime
-
-import gradio as gr
-import pandas as pd
-from huggingface_hub import snapshot_download
-from rdkit import Chem
-from rdkit.Chem import Descriptors, Crippen, Lipinski, rdMolDescriptors, QED, AllChem
-
-
-# Prefer setting these in Hugging Face Space settings:
-# Secret:   HF_TOKEN
-# Variable: BUNDLE_REPO = Ailixir-AI-Team/egfr-ai-bundle
-BUNDLE_REPO = os.getenv("BUNDLE_REPO", "Ailixir-AI-Team/egfr-ai-bundle")
-HF_TOKEN = os.getenv("HF_TOKEN")
-
-CACHE_DIR = Path("bundle_cache")
-EXAMPLE_JSON = None
-API_SPEC_TEXT = None
-BACKEND_CONTRACT_TEXT = None
-BUNDLE_ROOT = None
-
-
-def download_bundle_light():
-    """Download only the light docs/examples/config needed by the Space."""
-    global EXAMPLE_JSON, API_SPEC_TEXT, BACKEND_CONTRACT_TEXT, BUNDLE_ROOT
-
-    try:
-        local_dir = snapshot_download(
-            repo_id=BUNDLE_REPO,
-            repo_type="dataset",
-            token=HF_TOKEN,
-            allow_patterns=[
-                "examples/generate_response.example.json",
-                "docs/API_RESPONSE_SPEC.md",
-                "configs/backend_contract.json",
-                "configs/sampling_model.bundle.toml",
-                "models/generator/egfr_generator.chkpt",
-                "README.md",
-            ],
-            local_dir=str(CACHE_DIR),
-        )
-
-        root = Path(local_dir)
-        BUNDLE_ROOT = root
-
-        example_path = root / "examples" / "generate_response.example.json"
-        spec_path = root / "docs" / "API_RESPONSE_SPEC.md"
-        contract_path = root / "configs" / "backend_contract.json"
-
-        if example_path.exists():
-            EXAMPLE_JSON = json.loads(example_path.read_text(encoding="utf-8"))
-
-        if spec_path.exists():
-            API_SPEC_TEXT = spec_path.read_text(encoding="utf-8")
-
-        if contract_path.exists():
-            BACKEND_CONTRACT_TEXT = contract_path.read_text(encoding="utf-8")
-
-        return True, f"Loaded docs/examples from {BUNDLE_REPO}"
-
-    except Exception as e:
-        return False, f"Could not load private bundle. Check HF_TOKEN secret and BUNDLE_REPO variable. Error: {e}"
-
-
-def canonicalize(smiles: str):
-    mol = Chem.MolFromSmiles(str(smiles).strip())
-    if mol is None:
-        return None, None
-    return mol, Chem.MolToSmiles(mol, isomericSmiles=True)
-
-
-def try_sa_score(mol):
-    try:
-        from rdkit.Contrib.SA_Score import sascorer
-        return round(float(sascorer.calculateScore(mol)), 4)
-    except Exception:
-        return None
-
-
-def compute_row(smiles: str):
-    mol, can = canonicalize(smiles)
-
-    if mol is None:
-        return {
-            "SMILES": smiles,
-            "valid": False,
-            "canonical_smiles": None,
-            "mw": None,
-            "logp": None,
-            "tpsa": None,
-            "hbd": None,
-            "hba": None,
-            "rot_bonds": None,
-            "qed": None,
-            "sa_score": None,
-            "pred_pAff_mean": None,
-            "docking_score": None,
-            "docking_status": "not_run",
-            "docking_pose_file": None,
-            "ligand_3d_file": None,
-            "note": "Invalid SMILES",
-        }
-
-    return {
-        "SMILES": smiles,
-        "valid": True,
-        "canonical_smiles": can,
-        "mw": round(float(Descriptors.MolWt(mol)), 4),
-        "logp": round(float(Crippen.MolLogP(mol)), 4),
-        "tpsa": round(float(rdMolDescriptors.CalcTPSA(mol)), 4),
-        "hbd": int(Lipinski.NumHDonors(mol)),
-        "hba": int(Lipinski.NumHAcceptors(mol)),
-        "rot_bonds": int(Lipinski.NumRotatableBonds(mol)),
-        "qed": round(float(QED.qed(mol)), 4),
-        "sa_score": try_sa_score(mol),
-        "pred_pAff_mean": None,
-        "docking_score": None,
-        "docking_status": "not_run",
-        "docking_pose_file": None,
-        "ligand_3d_file": None,
-        "note": "CPU demo: DeepPurpose and real docking are disabled in this Space.",
-    }
-
-
-def add_ligand_ids_to_rows(rows, prefix="lig"):
-    output = []
-    for i, row in enumerate(rows, start=1):
-        clean = dict(row)
-        if not clean.get("ligand_id"):
-            clean["ligand_id"] = f"{prefix}_{i:04d}"
-        output.append(clean)
-    return output
-
-
-def add_ligand_ids_to_df(df: pd.DataFrame, prefix="lig"):
-    df = df.copy()
-    if "ligand_id" not in df.columns:
-        df.insert(0, "ligand_id", [f"{prefix}_{i:04d}" for i in range(1, len(df) + 1)])
-    return df
-
-
-def clean_records_from_df(df: pd.DataFrame):
-    if df is None or df.empty:
-        return []
-    clean_df = df.astype(object).where(pd.notnull(df), None)
-    return clean_df.to_dict(orient="records")
-
-
-def write_results_csv(df: pd.DataFrame, filename: str = "score_smiles_results.csv"):
-    out_dir = Path("outputs")
-    out_dir.mkdir(parents=True, exist_ok=True)
-    out_path = out_dir / filename
-    df.to_csv(out_path, index=False)
-    return str(out_path)
-
-
-def score_smiles(smiles_text):
-    smiles_list = []
-    for part in str(smiles_text).replace(",", "\n").splitlines():
-        part = part.strip()
-        if part:
-            smiles_list.append(part)
-
-    if not smiles_list:
-        return pd.DataFrame(), {
-            "status": "error",
-            "message": "Please enter at least one SMILES.",
-        }, None
-
-    rows = add_ligand_ids_to_rows([compute_row(s) for s in smiles_list])
-    df = pd.DataFrame(rows)
-
-    csv_path = write_results_csv(df)
-    response = {
-        "status": "completed",
-        "mode": "score_smiles_cpu_demo",
-        "docking_mode": "off",
-        "summary": {
-            "num_input": len(smiles_list),
-            "num_valid": int(df["valid"].sum()) if "valid" in df.columns else 0,
-            "num_returned": int(len(df)),
-        },
-        "columns": list(df.columns),
-        "results": clean_records_from_df(df),
-        "download_csv_file": csv_path,
-        "warnings": [
-            "This Space is a CPU demo.",
-            "DeepPurpose pred_pAff_mean is not computed in this Space version.",
-            "Real docking is not run in this CPU Space; docking_status is not_run.",
-            "Outputs are computational predictions only.",
-        ],
-    }
-
-    return df, response, csv_path
-
-
-def get_api_spec():
-    return API_SPEC_TEXT or "API_RESPONSE_SPEC.md not loaded. Check HF_TOKEN secret or BUNDLE_REPO variable."
-
-
-def get_contract():
-    if BACKEND_CONTRACT_TEXT:
-        try:
-            return json.loads(BACKEND_CONTRACT_TEXT)
-        except Exception:
-            return {"raw": BACKEND_CONTRACT_TEXT}
-
-    return {
-        "status": "not_loaded",
-        "message": "backend_contract.json not loaded. Check HF_TOKEN secret or BUNDLE_REPO variable.",
-    }
-
-
-def _write_reinvent_sampling_config(job_id, num_molecules):
-    if BUNDLE_ROOT is None:
-        raise RuntimeError("Bundle root is not loaded. Check HF_TOKEN and BUNDLE_REPO.")
-
-    checkpoint = Path(BUNDLE_ROOT) / "models" / "generator" / "egfr_generator.chkpt"
-    if not checkpoint.exists():
-        raise FileNotFoundError(f"Generator checkpoint not found: {checkpoint}")
-
-    output_dir = Path("outputs")
-    output_dir.mkdir(exist_ok=True)
-
-    raw_csv = output_dir / f"{job_id}_raw_sampling.csv"
-    log_file = output_dir / f"{job_id}_reinvent.log"
-    resolved_json = output_dir / f"{job_id}_sampling_resolved.json"
-    config_path = output_dir / f"{job_id}_sampling.toml"
-
-    config_text = f"""
-run_type = "sampling"
-device = "cpu"
-
-json_out_config = "{resolved_json.resolve()}"
-
-[parameters]
-model_file = "{checkpoint.resolve()}"
-output_file = "{raw_csv.resolve()}"
-
-num_smiles = {int(num_molecules)}
-unique_molecules = true
-randomize_smiles = true
-"""
-
-    config_path.write_text(config_text.strip() + "\n", encoding="utf-8")
-    return config_path, raw_csv, log_file
-
-
-def _run_reinvent_sampling(job_id, num_molecules):
-    config_path, raw_csv, log_file = _write_reinvent_sampling_config(job_id, num_molecules)
-
-    cmd = [
-        "reinvent",
-        "-l",
-        str(log_file.resolve()),
-        str(config_path.resolve()),
-    ]
-
-    proc = subprocess.run(
-        cmd,
-        text=True,
-        stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
-        timeout=300,
-    )
-
-    if proc.returncode != 0:
-        raise RuntimeError(
-            "REINVENT sampling failed.\n"
-            f"Command: {' '.join(cmd)}\n"
-            f"Output:\n{proc.stdout[-4000:]}"
-        )
-
-    if not raw_csv.exists():
-        raise RuntimeError(f"REINVENT finished but output CSV was not found: {raw_csv}")
-
-    return raw_csv, log_file
-
-
-def _enrich_reinvent_csv(raw_csv, return_top_k):
-    raw_df = pd.read_csv(raw_csv)
-
-    if "SMILES" not in raw_df.columns:
-        raise ValueError(f"REINVENT output missing SMILES column. Columns: {list(raw_df.columns)}")
-
-    rows = []
-    for _, r in raw_df.iterrows():
-        row = compute_row(str(r["SMILES"]))
-
-        if "SMILES_state" in raw_df.columns:
-            try:
-                row["SMILES_state"] = int(r["SMILES_state"])
-            except Exception:
-                row["SMILES_state"] = None
-        else:
-            row["SMILES_state"] = None
-
-        if "NLL" in raw_df.columns:
-            try:
-                row["NLL"] = float(r["NLL"])
-            except Exception:
-                row["NLL"] = None
-        else:
-            row["NLL"] = None
-
-        rows.append(row)
-
-    rows = add_ligand_ids_to_rows(rows)
-    df = pd.DataFrame(rows)
-
-    preferred_cols = [
-        "ligand_id",
-        "SMILES",
-        "SMILES_state",
-        "NLL",
-        "valid",
-        "canonical_smiles",
-        "mw",
-        "logp",
-        "tpsa",
-        "hbd",
-        "hba",
-        "rot_bonds",
-        "qed",
-        "sa_score",
-        "pred_pAff_mean",
-        "docking_score",
-        "docking_status",
-        "docking_pose_file",
-        "ligand_3d_file",
-        "note",
-    ]
-
-    cols = [c for c in preferred_cols if c in df.columns] + [c for c in df.columns if c not in preferred_cols]
-    df = df[cols]
-
-    return_top_k = int(return_top_k)
-    if return_top_k > 0:
-        df = df.head(return_top_k)
-
-    return df
-
-
-def generate_job_demo(num_molecules, return_top_k, docking_mode, generation_backend):
-    """
-    Generation endpoint for the Space.
-
-    demo_rows: uses packaged example rows for stable demo.
-    live_reinvent_cpu: tries to run real REINVENT CPU sampling if available.
-    """
-    job_id = f"gen_{uuid.uuid4().hex[:8]}"
-    created_at = datetime.utcnow().isoformat() + "Z"
-    num_molecules = int(num_molecules)
-    return_top_k = int(return_top_k)
-
-    warnings = []
-
-    try:
-        if generation_backend == "live_reinvent_cpu":
-            raw_csv, _log_file = _run_reinvent_sampling(job_id, num_molecules)
-            df = _enrich_reinvent_csv(raw_csv, return_top_k)
-            mode = "live_reinvent_cpu_sampling"
-            status = "completed"
-            warnings.extend([
-                "Live REINVENT CPU sampling was executed in this Space.",
-                "DeepPurpose scoring is not enabled in this Space version; pred_pAff_mean is null.",
-                "Real docking is not run in this CPU Space; docking_status is not_run.",
-            ])
-
-        else:
-            if EXAMPLE_JSON and "results" in EXAMPLE_JSON:
-                rows = EXAMPLE_JSON["results"]
-            else:
-                rows = [compute_row("CCO"), compute_row("c1ccccc1")]
-
-            selected = rows[: max(1, min(return_top_k, len(rows)))]
-
-            clean_rows = []
-            for row in selected:
-                clean = dict(row)
-                clean["docking_score"] = None
-                clean["docking_status"] = "not_run"
-                clean["docking_pose_file"] = None
-                clean["ligand_3d_file"] = clean.get("ligand_3d_file", None)
-                if "pred_pAff_mean" not in clean:
-                    clean["pred_pAff_mean"] = None
-                clean_rows.append(clean)
-
-            clean_rows = add_ligand_ids_to_rows(clean_rows)
-            df = pd.DataFrame(clean_rows)
-            mode = "generate_job_cpu_demo"
-            status = "completed"
-            warnings.extend([
-                "This is a CPU demo generation response.",
-                "Live REINVENT generation was not executed because demo_rows was selected.",
-                "The response shape matches the planned backend contract.",
-                "Real docking is not run in this CPU Space; docking_status is not_run.",
-            ])
-
-    except Exception as e:
-        df = pd.DataFrame()
-        mode = "live_reinvent_cpu_sampling"
-        status = "failed"
-        warnings.append(str(e))
-
-    df = add_ligand_ids_to_df(df)
-
-    output_dir = Path("outputs")
-    output_dir.mkdir(exist_ok=True)
-    csv_path = output_dir / f"{job_id}_results.csv"
-    df.to_csv(csv_path, index=False)
-
-    job_summary = {
-        "job_id": job_id,
-        "status": status,
-        "mode": mode,
-        "created_at": created_at,
-        "preset": "egfr_generator",
-        "docking_mode": docking_mode,
-        "num_requested": num_molecules,
-        "num_returned": int(len(df)),
-        "download_csv_file": str(csv_path),
-        "live_generation": generation_backend == "live_reinvent_cpu",
-    }
-
-    response = {
-        "job_id": job_id,
-        "status": status,
-        "mode": mode,
-        "created_at": created_at,
-        "preset": "egfr_generator",
-        "docking_mode": docking_mode,
-        "summary": {
-            "num_requested": num_molecules,
-            "num_returned": int(len(df)),
-        },
-        "columns": list(df.columns),
-        "results": clean_records_from_df(df),
-        "download_csv_file": str(csv_path),
-        "warnings": warnings,
-    }
-
-    return job_summary, df, response, str(csv_path)
-
-
-def smiles_to_3d_file(smiles: str, file_format: str = "sdf"):
-    smiles = str(smiles).strip()
-    file_format = str(file_format).lower().strip()
-
-    if file_format not in ["sdf", "mol", "pdb"]:
-        return None, {
-            "status": "error",
-            "message": "Unsupported format. Choose sdf, mol, or pdb.",
-        }
-
-    mol = Chem.MolFromSmiles(smiles)
-    if mol is None:
-        return None, {
-            "status": "error",
-            "input_smiles": smiles,
-            "message": "Invalid SMILES.",
-        }
-
-    canonical_smiles = Chem.MolToSmiles(mol, isomericSmiles=True)
-
-    mol = Chem.AddHs(mol)
-
-    params = AllChem.ETKDGv3()
-    params.randomSeed = 42
-
-    embed_status = AllChem.EmbedMolecule(mol, params)
-    if embed_status != 0:
-        return None, {
-            "status": "error",
-            "input_smiles": smiles,
-            "canonical_smiles": canonical_smiles,
-            "message": "3D embedding failed.",
-        }
-
-    try:
-        AllChem.UFFOptimizeMolecule(mol, maxIters=500)
-        optimization_status = "UFF optimized"
-    except Exception as e:
-        optimization_status = f"UFF optimization failed, using embedded geometry only: {e}"
-
-    out_dir = Path("outputs/ligands")
-    out_dir.mkdir(parents=True, exist_ok=True)
-
-    safe_name = "ligand_3d"
-    out_path = out_dir / f"{safe_name}.{file_format}"
-
-    if file_format == "sdf":
-        writer = Chem.SDWriter(str(out_path))
-        writer.write(mol)
-        writer.close()
-    elif file_format == "mol":
-        Chem.MolToMolFile(mol, str(out_path))
-    elif file_format == "pdb":
-        Chem.MolToPDBFile(mol, str(out_path))
-
-    meta = {
-        "status": "completed",
-        "input_smiles": smiles,
-        "canonical_smiles": canonical_smiles,
-        "file_format": file_format,
-        "file_path": str(out_path),
-        "optimization_status": optimization_status,
-        "note": "This is a generated 3D conformer from SMILES, not a docked protein-ligand pose.",
-    }
-
-    return str(out_path), meta
-
-
-loaded_ok, loaded_msg = download_bundle_light()
-
-
-with gr.Blocks(title="EGFR AI Demo") as demo:
-    gr.Markdown(
-        """
-# EGFR AI Demo
-
-Private CPU demo for the EGFR AI backend workflow.
-
-This demo focuses on the 3 things needed by filters, backend, and frontend:
-
-1. Generated ligands returned as a list of objects.
-2. CSV download for generated/scored ligands.
-3. SMILES to downloadable 3D ligand file.
-
-Real AutoDock-GPU docking is disabled in this CPU Space, but docking fields are kept in the response schema.
-"""
-    )
-
-    gr.Markdown(f"**Bundle load status:** {loaded_msg}")
-
-    with gr.Tab("Generate Ligands"):
-        gr.Markdown(
-            """
-## Generate Ligands
-
-This tab returns generated ligands as `results`, a list of ligand objects.
-
-Each ligand object contains properties, affinity/docking placeholders, and stable IDs for filters/frontend.
-"""
-        )
-
-        generation_backend = gr.Dropdown(
-            label="generation_backend",
-            choices=["demo_rows", "live_reinvent_cpu"],
-            value="demo_rows",
-            info="Use demo_rows for stable demo. live_reinvent_cpu tries REINVENT CPU sampling if available.",
-        )
-
-        gen_num_molecules = gr.Number(
-            label="num_molecules",
-            value=20,
-            precision=0,
-        )
-
-        gen_return_top_k = gr.Number(
-            label="return_top_k",
-            value=20,
-            precision=0,
-        )
-
-        gen_docking_mode = gr.Dropdown(
-            label="docking_mode",
-            choices=["off", "top_k", "all"],
-            value="off",
-            info="CPU Space does not run real docking. This field is included for backend/frontend contract.",
-        )
-
-        gen_btn = gr.Button("Run Generate Job")
-
-        gen_summary = gr.JSON(label="Job summary")
-        gen_table = gr.Dataframe(label="Generated ligand objects table")
-        gen_json = gr.JSON(label="Backend-style JSON response")
-        gen_file = gr.File(label="Download CSV")
-
-        gen_btn.click(
-            generate_job_demo,
-            inputs=[gen_num_molecules, gen_return_top_k, gen_docking_mode, generation_backend],
-            outputs=[gen_summary, gen_table, gen_json, gen_file],
-        )
-
-    with gr.Tab("Score SMILES & 3D File"):
-        gr.Markdown(
-            """
-## Score SMILES
-
-Paste one or more SMILES. The response returns a list of ligand objects and a downloadable CSV file.
-"""
-        )
-
-        smiles_input = gr.Textbox(
-            label="SMILES input",
-            value="CCO\nc1ccccc1",
-            lines=5,
-        )
-
-        score_btn = gr.Button("Score SMILES")
-        score_table = gr.Dataframe(label="Ligand objects table")
-        score_json = gr.JSON(label="Backend-style JSON response")
-        score_csv = gr.File(label="Download CSV")
-
-        score_btn.click(
-            score_smiles,
-            inputs=smiles_input,
-            outputs=[score_table, score_json, score_csv],
-        )
-
-        gr.Markdown(
-            """
----
-
-## SMILES to 3D Ligand File
-
-Send one SMILES and download a generated 3D ligand file.
-
-Supported formats:
-- SDF
-- MOL
-- PDB
-
-Important: this creates a 3D conformer from SMILES. It is not a docked pose inside the EGFR binding pocket.
-"""
-        )
-
-        smiles_3d_input = gr.Textbox(
-            label="SMILES for 3D file",
-            value="CNCCC(=O)Nc1ccc2nncc(-c3ccc4cncnc4c3)c2c1",
-            lines=2,
-        )
-
-        format_input = gr.Radio(
-            choices=["sdf", "mol", "pdb"],
-            value="sdf",
-            label="Output file format",
-        )
-
-        make_3d_btn = gr.Button("Generate 3D ligand file")
-        ligand_file = gr.File(label="Download 3D ligand file")
-        ligand_meta = gr.JSON(label="3D file metadata")
-
-        make_3d_btn.click(
-            smiles_to_3d_file,
-            inputs=[smiles_3d_input, format_input],
-            outputs=[ligand_file, ligand_meta],
-        )
-
-    with gr.Tab("Contract & Notes"):
-        gr.Markdown(
-            """
-## Backend / Filters Contract
-
-### Main response shape
-
-The important part is:
-
-```json
-{
-  "results": [
-    {
-      "ligand_id": "lig_0001",
-      "SMILES": "...",
-      "canonical_smiles": "...",
-      "mw": 358.405,
-      "logp": 2.788,
-      "tpsa": 92.69,
-      "hbd": 2,
-      "hba": 6,
-      "rot_bonds": 5,
-      "qed": 0.5698,
-      "sa_score": 2.5204,
-      "pred_pAff_mean": null,
-      "docking_score": null,
-      "docking_status": "not_run",
-      "docking_pose_file": null,
-      "ligand_3d_file": null
-    }
-  ]
-}
-```
-
-### CSV
-
-Each Generate or Score action returns a downloadable CSV file.
-
-### 3D ligand file
-
-The SMILES to 3D tool returns a downloadable SDF/MOL/PDB file.
-
-### Docking modes in the full backend
-
-- `off`
-- `top_k`
-- `all`
-
-In this CPU Space:
-- `docking_score = null`
-- `docking_status = not_run`
-- `docking_pose_file = null`
-
-### Recommended DB columns
-
-- `docking_score FLOAT NULL`
-- `docking_status VARCHAR(30) DEFAULT 'not_run'`
-- `docking_pose_file TEXT NULL`
-- `docking_mode VARCHAR(20) DEFAULT 'off'`
-- `docking_error TEXT NULL`
-"""
-        )
-
-        contract_btn = gr.Button("Load backend_contract.json")
-        contract_json = gr.JSON(label="backend_contract.json")
-
-        contract_btn.click(
-            get_contract,
-            outputs=contract_json,
-        )
-
-        spec_btn = gr.Button("Load API_RESPONSE_SPEC.md")
-        spec_output = gr.Markdown(label="API_RESPONSE_SPEC.md")
-
-        spec_btn.click(
-            get_api_spec,
-            outputs=spec_output,
-        )
-
-
-demo.launch()

app.py.backup_before_final_ui

@@ -1,754 +0,0 @@
-import json
-import os
-import subprocess
-from pathlib import Path
-import uuid
-from datetime import datetime
-import gradio as gr
-import pandas as pd
-from huggingface_hub import snapshot_download
-from rdkit import Chem
-from rdkit.Chem import Descriptors, Crippen, Lipinski, rdMolDescriptors, QED, AllChem
-
-
-BUNDLE_REPO = os.getenv("BUNDLE_REPO", "abdullahsamra/egfr-ai-bundle")
-HF_TOKEN = os.getenv("HF_TOKEN")
-
-CACHE_DIR = Path("bundle_cache")
-EXAMPLE_JSON = None
-API_SPEC_TEXT = None
-BACKEND_CONTRACT_TEXT = None
-BUNDLE_ROOT = None
-
-
-def download_bundle_light():
-    global EXAMPLE_JSON, API_SPEC_TEXT, BACKEND_CONTRACT_TEXT, BUNDLE_ROOT
-
-    try:
-        local_dir = snapshot_download(
-            repo_id=BUNDLE_REPO,
-            repo_type="dataset",
-            token=HF_TOKEN,
-            allow_patterns=[
-                "examples/generate_response.example.json",
-                "docs/API_RESPONSE_SPEC.md",
-                "configs/backend_contract.json",
-                "configs/sampling_model.bundle.toml",
-                "models/generator/egfr_generator.chkpt",
-                "README.md",
-            ],
-            local_dir=str(CACHE_DIR),
-        )
-
-        root = Path(local_dir)
-        BUNDLE_ROOT = root
-
-        example_path = root / "examples" / "generate_response.example.json"
-        spec_path = root / "docs" / "API_RESPONSE_SPEC.md"
-        contract_path = root / "configs" / "backend_contract.json"
-
-        if example_path.exists():
-            EXAMPLE_JSON = json.loads(example_path.read_text(encoding="utf-8"))
-
-        if spec_path.exists():
-            API_SPEC_TEXT = spec_path.read_text(encoding="utf-8")
-
-        if contract_path.exists():
-            BACKEND_CONTRACT_TEXT = contract_path.read_text(encoding="utf-8")
-
-        return True, f"Loaded docs/examples from {BUNDLE_REPO}"
-
-    except Exception as e:
-        return False, f"Could not load private bundle. Check HF_TOKEN secret and BUNDLE_REPO variable. Error: {e}"
-
-
-def canonicalize(smiles: str):
-    mol = Chem.MolFromSmiles(str(smiles).strip())
-    if mol is None:
-        return None, None
-    return mol, Chem.MolToSmiles(mol, isomericSmiles=True)
-
-
-def try_sa_score(mol):
-    try:
-        from rdkit.Contrib.SA_Score import sascorer
-        return round(float(sascorer.calculateScore(mol)), 4)
-    except Exception:
-        return None
-
-
-def compute_row(smiles: str):
-    mol, can = canonicalize(smiles)
-
-    if mol is None:
-        return {
-            "SMILES": smiles,
-            "valid": False,
-            "canonical_smiles": None,
-            "mw": None,
-            "logp": None,
-            "tpsa": None,
-            "hbd": None,
-            "hba": None,
-            "rot_bonds": None,
-            "qed": None,
-            "sa_score": None,
-            "pred_pAff_mean": None,
-            "docking_score": None,
-            "docking_status": "not_run",
-            "docking_pose_file": None,
-            "note": "Invalid SMILES",
-        }
-
-    return {
-        "SMILES": smiles,
-        "valid": True,
-        "canonical_smiles": can,
-        "mw": round(float(Descriptors.MolWt(mol)), 4),
-        "logp": round(float(Crippen.MolLogP(mol)), 4),
-        "tpsa": round(float(rdMolDescriptors.CalcTPSA(mol)), 4),
-        "hbd": int(Lipinski.NumHDonors(mol)),
-        "hba": int(Lipinski.NumHAcceptors(mol)),
-        "rot_bonds": int(Lipinski.NumRotatableBonds(mol)),
-        "qed": round(float(QED.qed(mol)), 4),
-        "sa_score": try_sa_score(mol),
-        "pred_pAff_mean": None,
-        "docking_score": None,
-        "docking_status": "not_run",
-        "docking_pose_file": None,
-        "note": "CPU demo: DeepPurpose and real docking are disabled in this Space.",
-    }
-
-
-
-def add_ligand_ids_to_rows(rows, prefix="lig"):
-    output = []
-    for i, row in enumerate(rows, start=1):
-        clean = dict(row)
-        if not clean.get("ligand_id"):
-            clean["ligand_id"] = f"{prefix}_{i:04d}"
-        output.append(clean)
-    return output
-
-
-def add_ligand_ids_to_df(df, prefix="lig"):
-    df = df.copy()
-    if "ligand_id" not in df.columns:
-        df.insert(0, "ligand_id", [f"{prefix}_{i:04d}" for i in range(1, len(df) + 1)])
-    return df
-
-def score_smiles(smiles_text):
-    smiles_list = []
-    for part in str(smiles_text).replace(",", "\n").splitlines():
-        part = part.strip()
-        if part:
-            smiles_list.append(part)
-
-    if not smiles_list:
-        return pd.DataFrame(), {
-            "status": "error",
-            "message": "Please enter at least one SMILES.",
-        }
-
-    rows = add_ligand_ids_to_rows([compute_row(s) for s in smiles_list])
-    df = pd.DataFrame(rows)
-
-    response = {
-        "status": "completed",
-        "mode": "score_smiles_cpu_demo",
-        "docking_mode": "off",
-        "summary": {
-            "num_input": len(smiles_list),
-            "num_valid": int(df["valid"].sum()),
-            "num_returned": len(df),
-        },
-        "columns": list(df.columns),
-        "results": rows,
-        "warnings": [
-            "This Space is a CPU demo.",
-            "DeepPurpose pred_pAff_mean is not computed in this Space version.",
-            "Real docking is not run in this CPU Space; docking_status is not_run.",
-            "Outputs are computational predictions only.",
-        ],
-    }
-    csv_path = write_results_csv(df)
-    response["download_csv_file"] = csv_path
-    return df, response, csv_path
-
-
-def get_example_table():
-    if EXAMPLE_JSON and "results" in EXAMPLE_JSON:
-        return pd.DataFrame(EXAMPLE_JSON["results"])
-    return pd.DataFrame([
-        {"message": "Example response not loaded. Check HF_TOKEN secret or BUNDLE_REPO variable."}
-    ])
-
-
-def get_example_json():
-    if EXAMPLE_JSON:
-        return EXAMPLE_JSON
-    return {
-        "status": "not_loaded",
-        "message": "Example response not loaded. Check HF_TOKEN secret or BUNDLE_REPO variable.",
-    }
-
-
-def get_api_spec():
-    return API_SPEC_TEXT or "API_RESPONSE_SPEC.md not loaded. Check HF_TOKEN secret or BUNDLE_REPO variable."
-
-
-def get_contract():
-    if BACKEND_CONTRACT_TEXT:
-        try:
-            return json.loads(BACKEND_CONTRACT_TEXT)
-        except Exception:
-            return {"raw": BACKEND_CONTRACT_TEXT}
-
-    return {
-        "status": "not_loaded",
-        "message": "backend_contract.json not loaded. Check HF_TOKEN secret or BUNDLE_REPO variable.",
-    }
-
-def _write_reinvent_sampling_config(job_id, num_molecules):
-    if BUNDLE_ROOT is None:
-        raise RuntimeError("Bundle root is not loaded. Check HF_TOKEN and BUNDLE_REPO.")
-
-    checkpoint = Path(BUNDLE_ROOT) / "models" / "generator" / "egfr_generator.chkpt"
-    if not checkpoint.exists():
-        raise FileNotFoundError(f"Generator checkpoint not found: {checkpoint}")
-
-    output_dir = Path("outputs")
-    output_dir.mkdir(exist_ok=True)
-
-    raw_csv = output_dir / f"{job_id}_raw_sampling.csv"
-    log_file = output_dir / f"{job_id}_reinvent.log"
-    resolved_json = output_dir / f"{job_id}_sampling_resolved.json"
-    config_path = output_dir / f"{job_id}_sampling.toml"
-
-    config_text = f"""
-run_type = "sampling"
-device = "cpu"
-
-json_out_config = "{resolved_json.resolve()}"
-
-[parameters]
-model_file = "{checkpoint.resolve()}"
-output_file = "{raw_csv.resolve()}"
-
-num_smiles = {int(num_molecules)}
-unique_molecules = true
-randomize_smiles = true
-"""
-
-    config_path.write_text(config_text.strip() + "\n", encoding="utf-8")
-    return config_path, raw_csv, log_file
-
-
-def _run_reinvent_sampling(job_id, num_molecules):
-    config_path, raw_csv, log_file = _write_reinvent_sampling_config(job_id, num_molecules)
-
-    cmd = [
-        "reinvent",
-        "-l",
-        str(log_file.resolve()),
-        str(config_path.resolve()),
-    ]
-
-    proc = subprocess.run(
-        cmd,
-        text=True,
-        stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
-        timeout=300,
-    )
-
-    if proc.returncode != 0:
-        raise RuntimeError(
-            "REINVENT sampling failed.\n"
-            f"Command: {' '.join(cmd)}\n"
-            f"Output:\n{proc.stdout[-4000:]}"
-        )
-
-    if not raw_csv.exists():
-        raise RuntimeError(f"REINVENT finished but output CSV was not found: {raw_csv}")
-
-    return raw_csv, log_file
-
-
-def _enrich_reinvent_csv(raw_csv, return_top_k):
-    raw_df = pd.read_csv(raw_csv)
-
-    if "SMILES" not in raw_df.columns:
-        raise ValueError(f"REINVENT output missing SMILES column. Columns: {list(raw_df.columns)}")
-
-    rows = []
-    for _, r in raw_df.iterrows():
-        row = compute_row(str(r["SMILES"]))
-
-        if "SMILES_state" in raw_df.columns:
-            try:
-                row["SMILES_state"] = int(r["SMILES_state"])
-            except Exception:
-                row["SMILES_state"] = None
-        else:
-            row["SMILES_state"] = None
-
-        if "NLL" in raw_df.columns:
-            try:
-                row["NLL"] = float(r["NLL"])
-            except Exception:
-                row["NLL"] = None
-        else:
-            row["NLL"] = None
-
-        # Keep these stable for frontend/backend filters.
-        row["pred_pAff_mean"] = None
-        row["docking_score"] = None
-        row["docking_status"] = "not_run"
-        row["docking_pose_file"] = None
-
-        rows.append(row)
-
-    df = pd.DataFrame(rows)
-
-    preferred_cols = [
-        "SMILES",
-        "SMILES_state",
-        "NLL",
-        "valid",
-        "canonical_smiles",
-        "mw",
-        "logp",
-        "tpsa",
-        "hbd",
-        "hba",
-        "rot_bonds",
-        "qed",
-        "sa_score",
-        "pred_pAff_mean",
-        "docking_score",
-        "docking_status",
-        "docking_pose_file",
-        "note",
-    ]
-
-    cols = [c for c in preferred_cols if c in df.columns] + [c for c in df.columns if c not in preferred_cols]
-    df = df[cols]
-
-    return_top_k = int(return_top_k)
-    if return_top_k > 0:
-        df = df.head(return_top_k)
-
-    return df
-
-
-def generate_job_demo(num_molecules, return_top_k, docking_mode, generation_backend):
-    """
-    Generation endpoint for the Space.
-
-    Demo mode uses packaged example rows.
-    Live mode tries to run REINVENT CPU sampling from the packaged checkpoint.
-    """
-    job_id = f"gen_{uuid.uuid4().hex[:8]}"
-    created_at = datetime.utcnow().isoformat() + "Z"
-    num_molecules = int(num_molecules)
-    return_top_k = int(return_top_k)
-
-    warnings = []
-
-    try:
-        if generation_backend == "live_reinvent_cpu":
-            raw_csv, log_file = _run_reinvent_sampling(job_id, num_molecules)
-            df = _enrich_reinvent_csv(raw_csv, return_top_k)
-            mode = "live_reinvent_cpu_sampling"
-            status = "completed"
-            warnings.extend([
-                "Live REINVENT CPU sampling was executed in this Space.",
-                "DeepPurpose scoring is not enabled in this Space version; pred_pAff_mean is null.",
-                "Real docking is not run in this CPU Space; docking_status is not_run.",
-            ])
-
-        else:
-            if EXAMPLE_JSON and "results" in EXAMPLE_JSON:
-                rows = EXAMPLE_JSON["results"]
-            else:
-                rows = [compute_row("CCO"), compute_row("c1ccccc1")]
-
-            selected = rows[: max(1, min(return_top_k, len(rows)))]
-
-            clean_rows = []
-            for row in selected:
-                clean = dict(row)
-                clean["docking_score"] = None
-                clean["docking_status"] = "not_run"
-                clean["docking_pose_file"] = None
-                if "pred_pAff_mean" not in clean:
-                    clean["pred_pAff_mean"] = None
-                clean_rows.append(clean)
-
-            df = pd.DataFrame(clean_rows)
-            mode = "generate_job_cpu_demo"
-            status = "completed"
-            warnings.extend([
-                "This is a CPU demo generation response.",
-                "Live REINVENT generation was not executed because demo mode was selected.",
-                "The response shape matches the planned backend contract.",
-                "Real docking is not run in this CPU Space; docking_status is not_run.",
-            ])
-
-    except Exception as e:
-        df = pd.DataFrame()
-        mode = "live_reinvent_cpu_sampling"
-        status = "failed"
-        warnings.append(str(e))
-
-    df = add_ligand_ids_to_df(df)
-
-    output_dir = Path("outputs")
-    output_dir.mkdir(exist_ok=True)
-    csv_path = output_dir / f"{job_id}_results.csv"
-    df.to_csv(csv_path, index=False)
-
-    job_summary = {
-        "job_id": job_id,
-        "status": status,
-        "mode": mode,
-        "created_at": created_at,
-        "preset": "egfr_generator",
-        "docking_mode": docking_mode,
-        "num_requested": num_molecules,
-        "num_returned": int(len(df)),
-        "download_csv_file": str(csv_path),
-        "live_generation": generation_backend == "live_reinvent_cpu",
-    }
-
-    response = {
-        "job_id": job_id,
-        "status": status,
-        "mode": mode,
-        "created_at": created_at,
-        "preset": "egfr_generator",
-        "docking_mode": docking_mode,
-        "summary": {
-            "num_requested": num_molecules,
-            "num_returned": int(len(df)),
-        },
-        "columns": list(df.columns),
-        "results": df.to_dict(orient="records"),
-        "download_csv_file": str(csv_path),
-        "warnings": warnings,
-    }
-
-    return job_summary, df, response, str(csv_path)
-
-
-def write_results_csv(df: pd.DataFrame, filename: str = "score_smiles_results.csv"):
-    out_dir = Path("outputs")
-    out_dir.mkdir(parents=True, exist_ok=True)
-    out_path = out_dir / filename
-    df.to_csv(out_path, index=False)
-    return str(out_path)
-
-
-def smiles_to_3d_file(smiles: str, file_format: str = "sdf"):
-    smiles = str(smiles).strip()
-    file_format = str(file_format).lower().strip()
-
-    if file_format not in ["sdf", "mol", "pdb"]:
-        return None, {
-            "status": "error",
-            "message": "Unsupported format. Choose sdf, mol, or pdb.",
-        }
-
-    mol = Chem.MolFromSmiles(smiles)
-    if mol is None:
-        return None, {
-            "status": "error",
-            "input_smiles": smiles,
-            "message": "Invalid SMILES.",
-        }
-
-    canonical_smiles = Chem.MolToSmiles(mol, isomericSmiles=True)
-
-    mol = Chem.AddHs(mol)
-
-    params = AllChem.ETKDGv3()
-    params.randomSeed = 42
-
-    embed_status = AllChem.EmbedMolecule(mol, params)
-    if embed_status != 0:
-        return None, {
-            "status": "error",
-            "input_smiles": smiles,
-            "canonical_smiles": canonical_smiles,
-            "message": "3D embedding failed.",
-        }
-
-    try:
-        AllChem.UFFOptimizeMolecule(mol, maxIters=500)
-        optimization_status = "UFF optimized"
-    except Exception as e:
-        optimization_status = f"UFF optimization failed, using embedded geometry only: {e}"
-
-    out_dir = Path("outputs/ligands")
-    out_dir.mkdir(parents=True, exist_ok=True)
-
-    safe_name = "ligand_3d"
-    out_path = out_dir / f"{safe_name}.{file_format}"
-
-    if file_format == "sdf":
-        writer = Chem.SDWriter(str(out_path))
-        writer.write(mol)
-        writer.close()
-    elif file_format == "mol":
-        Chem.MolToMolFile(mol, str(out_path))
-    elif file_format == "pdb":
-        Chem.MolToPDBFile(mol, str(out_path))
-
-    meta = {
-        "status": "completed",
-        "input_smiles": smiles,
-        "canonical_smiles": canonical_smiles,
-        "file_format": file_format,
-        "file_path": str(out_path),
-        "optimization_status": optimization_status,
-        "note": "This is a generated 3D conformer from SMILES, not a docked protein-ligand pose.",
-    }
-
-    return str(out_path), meta
-
-loaded_ok, loaded_msg = download_bundle_light()
-
-
-with gr.Blocks(title="EGFR AI Demo") as demo:
-    gr.Markdown(
-        """
-# EGFR AI Demo
-
-Private CPU demo for the EGFR AI backend workflow.
-
-This demo shows the backend response shape for generation, scoring, filtering, and docking integration.
-
-Real AutoDock-GPU docking is disabled in this CPU Space, but docking fields are present so backend/frontend teams can implement database columns and filters.
-"""
-    )
-
-    gr.Markdown(f"Bundle load status: {loaded_msg}")
-
-    with gr.Tab("Score SMILES"):
-        gr.Markdown(
-            """
-Enter one or more SMILES.
-
-This CPU demo calculates molecular properties and returns the same response columns expected by the backend.
-
-Important:
-- pred_pAff_mean is an integration field in this Space version.
-- real docking is disabled in this CPU Space.
-- docking_status is returned as not_run.
-"""
-        )
-
-        smiles_input = gr.Textbox(
-            label="SMILES input",
-            value="CCO\nc1ccccc1",
-            lines=5,
-        )
-
-        score_btn = gr.Button("Score SMILES")
-        score_table = gr.Dataframe(label="Results table")
-        score_json = gr.JSON(label="Backend-style JSON response")
-        score_csv = gr.File(label="Download CSV")
-
-
-        score_btn.click(
-            score_smiles,
-            inputs=smiles_input,
-            outputs=[score_table, score_json, score_csv],
-        )
-    with gr.Tab("Generate Job Demo"):
-        gr.Markdown(
-            """
-This tab demonstrates generation job behavior.
-
-Generation backend options:
-
-- demo_rows: uses packaged example rows. Fast and stable.
-- live_reinvent_cpu: tries to run real REINVENT sampling from the packaged checkpoint on CPU.
-
-The output is split into:
-
-1. Job summary: job_id, status, preset, mode, and metadata.
-2. Generated molecule results table.
-3. Full backend-style generation JSON.
-4. Download CSV.
-
-Notes:
-- DeepPurpose live scoring is not enabled yet in this Space version.
-- Real docking is disabled in this CPU Space, so docking_status is returned as not_run.
-"""
-        )
-
-        generation_backend = gr.Dropdown(
-            label="generation_backend",
-            choices=["demo_rows", "live_reinvent_cpu"],
-            value="demo_rows",
-        )
-
-        gen_num_molecules = gr.Number(
-            label="num_molecules",
-            value=20,
-            precision=0,
-        )
-
-        gen_return_top_k = gr.Number(
-            label="return_top_k",
-            value=20,
-            precision=0,
-        )
-
-        gen_docking_mode = gr.Dropdown(
-            label="docking_mode",
-            choices=["off", "top_k", "all"],
-            value="off",
-        )
-
-        gen_btn = gr.Button("Run Generation Job")
-
-        gen_summary = gr.JSON(label="Job summary")
-        gen_table = gr.Dataframe(label="Generated molecule results table")
-        gen_json = gr.JSON(label="Full backend-style generation JSON")
-        gen_file = gr.File(label="Download CSV")
-
-        gen_btn.click(
-            generate_job_demo,
-            inputs=[gen_num_molecules, gen_return_top_k, gen_docking_mode, generation_backend],
-            outputs=[gen_summary, gen_table, gen_json, gen_file],
-        )
-
-
-    with gr.Tab("Example Generate Response"):
-        gr.Markdown(
-            """
-This example is loaded from the private Hugging Face Dataset bundle.
-
-It shows the expected response shape after:
-
-Generate -> Enrich -> Optional Docking
-"""
-        )
-
-        example_btn = gr.Button("Load example response")
-        example_table = gr.Dataframe(label="Example results table")
-        example_json = gr.JSON(label="Example JSON response")
-
-        example_btn.click(
-            lambda: (get_example_table(), get_example_json()),
-            outputs=[example_table, example_json],
-        )
-
-        with gr.Tab("SMILES to 3D File"):
-            gr.Markdown(
-            """
-Convert a SMILES string into a downloadable 3D ligand file.
-
-Supported formats:
-
-- SDF
-- MOL
-- PDB
-
-Important: this creates a 3D conformer from SMILES. It is not a docked pose inside the EGFR binding pocket.
-"""
-        )
-
-        smiles_3d_input = gr.Textbox(
-            label="SMILES",
-            value="CCO",
-            lines=2,
-        )
-
-        format_input = gr.Radio(
-            choices=["sdf", "mol", "pdb"],
-            value="sdf",
-            label="Output file format",
-        )
-
-        make_3d_btn = gr.Button("Generate 3D ligand file")
-        ligand_file = gr.File(label="Download 3D ligand file")
-        ligand_meta = gr.JSON(label="3D file metadata")
-
-        make_3d_btn.click(
-            smiles_to_3d_file,
-            inputs=[smiles_3d_input, format_input],
-            outputs=[ligand_file, ligand_meta],
-        )
-        
-    with gr.Tab("Docking Contract"):
-        gr.Markdown(
-            """
-## Docking modes
-
-The full backend supports:
-
-- off
-- top_k
-- all
-
-In this CPU Space, real AutoDock-GPU docking is disabled.
-
-Returned docking fields in CPU demo:
-
-- docking_score: null
-- docking_status: not_run
-- docking_pose_file: null
-
-Recommended database columns:
-
-- docking_score FLOAT NULL
-- docking_status VARCHAR(30) DEFAULT 'not_run'
-- docking_pose_file TEXT NULL
-- docking_mode VARCHAR(20) DEFAULT 'off'
-- docking_error TEXT NULL
-
-Recommended frontend and filter behavior:
-
-- Show all valid molecules: valid == true
-- Show docked only: docking_status == completed
-- Show not-yet-docked molecules: docking_status == not_run
-- Sort docking results ascending, because more negative docking scores are usually better
-"""
-        )
-
-        contract_btn = gr.Button("Load backend contract")
-        contract_json = gr.JSON(label="backend_contract.json")
-
-        contract_btn.click(
-            get_contract,
-            outputs=contract_json,
-        )
-
-    with gr.Tab("API Spec"):
-        gr.Markdown(
-            """
-This tab loads the API response specification from the private artifact bundle.
-
-It explains the expected backend/frontend response format for:
-
-- generated molecules
-- scored SMILES
-- docking fields
-- frontend filters
-"""
-        )
-
-        spec_btn = gr.Button("Load API response spec")
-        spec_output = gr.Markdown(label="API_RESPONSE_SPEC.md")
-
-        spec_btn.click(
-            get_api_spec,
-            outputs=spec_output,
-        )
-
-
-demo.launch()

app.py.backup_old_tabs

@@ -1,754 +0,0 @@
-import json
-import os
-import subprocess
-from pathlib import Path
-import uuid
-from datetime import datetime
-import gradio as gr
-import pandas as pd
-from huggingface_hub import snapshot_download
-from rdkit import Chem
-from rdkit.Chem import Descriptors, Crippen, Lipinski, rdMolDescriptors, QED, AllChem
-
-
-BUNDLE_REPO = os.getenv("BUNDLE_REPO", "abdullahsamra/egfr-ai-bundle")
-HF_TOKEN = os.getenv("HF_TOKEN")
-
-CACHE_DIR = Path("bundle_cache")
-EXAMPLE_JSON = None
-API_SPEC_TEXT = None
-BACKEND_CONTRACT_TEXT = None
-BUNDLE_ROOT = None
-
-
-def download_bundle_light():
-    global EXAMPLE_JSON, API_SPEC_TEXT, BACKEND_CONTRACT_TEXT, BUNDLE_ROOT
-
-    try:
-        local_dir = snapshot_download(
-            repo_id=BUNDLE_REPO,
-            repo_type="dataset",
-            token=HF_TOKEN,
-            allow_patterns=[
-                "examples/generate_response.example.json",
-                "docs/API_RESPONSE_SPEC.md",
-                "configs/backend_contract.json",
-                "configs/sampling_model.bundle.toml",
-                "models/generator/egfr_generator.chkpt",
-                "README.md",
-            ],
-            local_dir=str(CACHE_DIR),
-        )
-
-        root = Path(local_dir)
-        BUNDLE_ROOT = root
-
-        example_path = root / "examples" / "generate_response.example.json"
-        spec_path = root / "docs" / "API_RESPONSE_SPEC.md"
-        contract_path = root / "configs" / "backend_contract.json"
-
-        if example_path.exists():
-            EXAMPLE_JSON = json.loads(example_path.read_text(encoding="utf-8"))
-
-        if spec_path.exists():
-            API_SPEC_TEXT = spec_path.read_text(encoding="utf-8")
-
-        if contract_path.exists():
-            BACKEND_CONTRACT_TEXT = contract_path.read_text(encoding="utf-8")
-
-        return True, f"Loaded docs/examples from {BUNDLE_REPO}"
-
-    except Exception as e:
-        return False, f"Could not load private bundle. Check HF_TOKEN secret and BUNDLE_REPO variable. Error: {e}"
-
-
-def canonicalize(smiles: str):
-    mol = Chem.MolFromSmiles(str(smiles).strip())
-    if mol is None:
-        return None, None
-    return mol, Chem.MolToSmiles(mol, isomericSmiles=True)
-
-
-def try_sa_score(mol):
-    try:
-        from rdkit.Contrib.SA_Score import sascorer
-        return round(float(sascorer.calculateScore(mol)), 4)
-    except Exception:
-        return None
-
-
-def compute_row(smiles: str):
-    mol, can = canonicalize(smiles)
-
-    if mol is None:
-        return {
-            "SMILES": smiles,
-            "valid": False,
-            "canonical_smiles": None,
-            "mw": None,
-            "logp": None,
-            "tpsa": None,
-            "hbd": None,
-            "hba": None,
-            "rot_bonds": None,
-            "qed": None,
-            "sa_score": None,
-            "pred_pAff_mean": None,
-            "docking_score": None,
-            "docking_status": "not_run",
-            "docking_pose_file": None,
-            "note": "Invalid SMILES",
-        }
-
-    return {
-        "SMILES": smiles,
-        "valid": True,
-        "canonical_smiles": can,
-        "mw": round(float(Descriptors.MolWt(mol)), 4),
-        "logp": round(float(Crippen.MolLogP(mol)), 4),
-        "tpsa": round(float(rdMolDescriptors.CalcTPSA(mol)), 4),
-        "hbd": int(Lipinski.NumHDonors(mol)),
-        "hba": int(Lipinski.NumHAcceptors(mol)),
-        "rot_bonds": int(Lipinski.NumRotatableBonds(mol)),
-        "qed": round(float(QED.qed(mol)), 4),
-        "sa_score": try_sa_score(mol),
-        "pred_pAff_mean": None,
-        "docking_score": None,
-        "docking_status": "not_run",
-        "docking_pose_file": None,
-        "note": "CPU demo: DeepPurpose and real docking are disabled in this Space.",
-    }
-
-
-
-def add_ligand_ids_to_rows(rows, prefix="lig"):
-    output = []
-    for i, row in enumerate(rows, start=1):
-        clean = dict(row)
-        if not clean.get("ligand_id"):
-            clean["ligand_id"] = f"{prefix}_{i:04d}"
-        output.append(clean)
-    return output
-
-
-def add_ligand_ids_to_df(df, prefix="lig"):
-    df = df.copy()
-    if "ligand_id" not in df.columns:
-        df.insert(0, "ligand_id", [f"{prefix}_{i:04d}" for i in range(1, len(df) + 1)])
-    return df
-
-def score_smiles(smiles_text):
-    smiles_list = []
-    for part in str(smiles_text).replace(",", "\n").splitlines():
-        part = part.strip()
-        if part:
-            smiles_list.append(part)
-
-    if not smiles_list:
-        return pd.DataFrame(), {
-            "status": "error",
-            "message": "Please enter at least one SMILES.",
-        }
-
-    rows = add_ligand_ids_to_rows([compute_row(s) for s in smiles_list])
-    df = pd.DataFrame(rows)
-
-    response = {
-        "status": "completed",
-        "mode": "score_smiles_cpu_demo",
-        "docking_mode": "off",
-        "summary": {
-            "num_input": len(smiles_list),
-            "num_valid": int(df["valid"].sum()),
-            "num_returned": len(df),
-        },
-        "columns": list(df.columns),
-        "results": rows,
-        "warnings": [
-            "This Space is a CPU demo.",
-            "DeepPurpose pred_pAff_mean is not computed in this Space version.",
-            "Real docking is not run in this CPU Space; docking_status is not_run.",
-            "Outputs are computational predictions only.",
-        ],
-    }
-    csv_path = write_results_csv(df)
-    response["download_csv_file"] = csv_path
-    return df, response, csv_path
-
-
-def get_example_table():
-    if EXAMPLE_JSON and "results" in EXAMPLE_JSON:
-        return pd.DataFrame(EXAMPLE_JSON["results"])
-    return pd.DataFrame([
-        {"message": "Example response not loaded. Check HF_TOKEN secret or BUNDLE_REPO variable."}
-    ])
-
-
-def get_example_json():
-    if EXAMPLE_JSON:
-        return EXAMPLE_JSON
-    return {
-        "status": "not_loaded",
-        "message": "Example response not loaded. Check HF_TOKEN secret or BUNDLE_REPO variable.",
-    }
-
-
-def get_api_spec():
-    return API_SPEC_TEXT or "API_RESPONSE_SPEC.md not loaded. Check HF_TOKEN secret or BUNDLE_REPO variable."
-
-
-def get_contract():
-    if BACKEND_CONTRACT_TEXT:
-        try:
-            return json.loads(BACKEND_CONTRACT_TEXT)
-        except Exception:
-            return {"raw": BACKEND_CONTRACT_TEXT}
-
-    return {
-        "status": "not_loaded",
-        "message": "backend_contract.json not loaded. Check HF_TOKEN secret or BUNDLE_REPO variable.",
-    }
-
-def _write_reinvent_sampling_config(job_id, num_molecules):
-    if BUNDLE_ROOT is None:
-        raise RuntimeError("Bundle root is not loaded. Check HF_TOKEN and BUNDLE_REPO.")
-
-    checkpoint = Path(BUNDLE_ROOT) / "models" / "generator" / "egfr_generator.chkpt"
-    if not checkpoint.exists():
-        raise FileNotFoundError(f"Generator checkpoint not found: {checkpoint}")
-
-    output_dir = Path("outputs")
-    output_dir.mkdir(exist_ok=True)
-
-    raw_csv = output_dir / f"{job_id}_raw_sampling.csv"
-    log_file = output_dir / f"{job_id}_reinvent.log"
-    resolved_json = output_dir / f"{job_id}_sampling_resolved.json"
-    config_path = output_dir / f"{job_id}_sampling.toml"
-
-    config_text = f"""
-run_type = "sampling"
-device = "cpu"
-
-json_out_config = "{resolved_json.resolve()}"
-
-[parameters]
-model_file = "{checkpoint.resolve()}"
-output_file = "{raw_csv.resolve()}"
-
-num_smiles = {int(num_molecules)}
-unique_molecules = true
-randomize_smiles = true
-"""
-
-    config_path.write_text(config_text.strip() + "\n", encoding="utf-8")
-    return config_path, raw_csv, log_file
-
-
-def _run_reinvent_sampling(job_id, num_molecules):
-    config_path, raw_csv, log_file = _write_reinvent_sampling_config(job_id, num_molecules)
-
-    cmd = [
-        "reinvent",
-        "-l",
-        str(log_file.resolve()),
-        str(config_path.resolve()),
-    ]
-
-    proc = subprocess.run(
-        cmd,
-        text=True,
-        stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
-        timeout=300,
-    )
-
-    if proc.returncode != 0:
-        raise RuntimeError(
-            "REINVENT sampling failed.\n"
-            f"Command: {' '.join(cmd)}\n"
-            f"Output:\n{proc.stdout[-4000:]}"
-        )
-
-    if not raw_csv.exists():
-        raise RuntimeError(f"REINVENT finished but output CSV was not found: {raw_csv}")
-
-    return raw_csv, log_file
-
-
-def _enrich_reinvent_csv(raw_csv, return_top_k):
-    raw_df = pd.read_csv(raw_csv)
-
-    if "SMILES" not in raw_df.columns:
-        raise ValueError(f"REINVENT output missing SMILES column. Columns: {list(raw_df.columns)}")
-
-    rows = []
-    for _, r in raw_df.iterrows():
-        row = compute_row(str(r["SMILES"]))
-
-        if "SMILES_state" in raw_df.columns:
-            try:
-                row["SMILES_state"] = int(r["SMILES_state"])
-            except Exception:
-                row["SMILES_state"] = None
-        else:
-            row["SMILES_state"] = None
-
-        if "NLL" in raw_df.columns:
-            try:
-                row["NLL"] = float(r["NLL"])
-            except Exception:
-                row["NLL"] = None
-        else:
-            row["NLL"] = None
-
-        # Keep these stable for frontend/backend filters.
-        row["pred_pAff_mean"] = None
-        row["docking_score"] = None
-        row["docking_status"] = "not_run"
-        row["docking_pose_file"] = None
-
-        rows.append(row)
-
-    df = pd.DataFrame(rows)
-
-    preferred_cols = [
-        "SMILES",
-        "SMILES_state",
-        "NLL",
-        "valid",
-        "canonical_smiles",
-        "mw",
-        "logp",
-        "tpsa",
-        "hbd",
-        "hba",
-        "rot_bonds",
-        "qed",
-        "sa_score",
-        "pred_pAff_mean",
-        "docking_score",
-        "docking_status",
-        "docking_pose_file",
-        "note",
-    ]
-
-    cols = [c for c in preferred_cols if c in df.columns] + [c for c in df.columns if c not in preferred_cols]
-    df = df[cols]
-
-    return_top_k = int(return_top_k)
-    if return_top_k > 0:
-        df = df.head(return_top_k)
-
-    return df
-
-
-def generate_job_demo(num_molecules, return_top_k, docking_mode, generation_backend):
-    """
-    Generation endpoint for the Space.
-
-    Demo mode uses packaged example rows.
-    Live mode tries to run REINVENT CPU sampling from the packaged checkpoint.
-    """
-    job_id = f"gen_{uuid.uuid4().hex[:8]}"
-    created_at = datetime.utcnow().isoformat() + "Z"
-    num_molecules = int(num_molecules)
-    return_top_k = int(return_top_k)
-
-    warnings = []
-
-    try:
-        if generation_backend == "live_reinvent_cpu":
-            raw_csv, log_file = _run_reinvent_sampling(job_id, num_molecules)
-            df = _enrich_reinvent_csv(raw_csv, return_top_k)
-            mode = "live_reinvent_cpu_sampling"
-            status = "completed"
-            warnings.extend([
-                "Live REINVENT CPU sampling was executed in this Space.",
-                "DeepPurpose scoring is not enabled in this Space version; pred_pAff_mean is null.",
-                "Real docking is not run in this CPU Space; docking_status is not_run.",
-            ])
-
-        else:
-            if EXAMPLE_JSON and "results" in EXAMPLE_JSON:
-                rows = EXAMPLE_JSON["results"]
-            else:
-                rows = [compute_row("CCO"), compute_row("c1ccccc1")]
-
-            selected = rows[: max(1, min(return_top_k, len(rows)))]
-
-            clean_rows = []
-            for row in selected:
-                clean = dict(row)
-                clean["docking_score"] = None
-                clean["docking_status"] = "not_run"
-                clean["docking_pose_file"] = None
-                if "pred_pAff_mean" not in clean:
-                    clean["pred_pAff_mean"] = None
-                clean_rows.append(clean)
-
-            df = pd.DataFrame(clean_rows)
-            mode = "generate_job_cpu_demo"
-            status = "completed"
-            warnings.extend([
-                "This is a CPU demo generation response.",
-                "Live REINVENT generation was not executed because demo mode was selected.",
-                "The response shape matches the planned backend contract.",
-                "Real docking is not run in this CPU Space; docking_status is not_run.",
-            ])
-
-    except Exception as e:
-        df = pd.DataFrame()
-        mode = "live_reinvent_cpu_sampling"
-        status = "failed"
-        warnings.append(str(e))
-
-    df = add_ligand_ids_to_df(df)
-
-    output_dir = Path("outputs")
-    output_dir.mkdir(exist_ok=True)
-    csv_path = output_dir / f"{job_id}_results.csv"
-    df.to_csv(csv_path, index=False)
-
-    job_summary = {
-        "job_id": job_id,
-        "status": status,
-        "mode": mode,
-        "created_at": created_at,
-        "preset": "egfr_generator",
-        "docking_mode": docking_mode,
-        "num_requested": num_molecules,
-        "num_returned": int(len(df)),
-        "download_csv_file": str(csv_path),
-        "live_generation": generation_backend == "live_reinvent_cpu",
-    }
-
-    response = {
-        "job_id": job_id,
-        "status": status,
-        "mode": mode,
-        "created_at": created_at,
-        "preset": "egfr_generator",
-        "docking_mode": docking_mode,
-        "summary": {
-            "num_requested": num_molecules,
-            "num_returned": int(len(df)),
-        },
-        "columns": list(df.columns),
-        "results": df.to_dict(orient="records"),
-        "download_csv_file": str(csv_path),
-        "warnings": warnings,
-    }
-
-    return job_summary, df, response, str(csv_path)
-
-
-def write_results_csv(df: pd.DataFrame, filename: str = "score_smiles_results.csv"):
-    out_dir = Path("outputs")
-    out_dir.mkdir(parents=True, exist_ok=True)
-    out_path = out_dir / filename
-    df.to_csv(out_path, index=False)
-    return str(out_path)
-
-
-def smiles_to_3d_file(smiles: str, file_format: str = "sdf"):
-    smiles = str(smiles).strip()
-    file_format = str(file_format).lower().strip()
-
-    if file_format not in ["sdf", "mol", "pdb"]:
-        return None, {
-            "status": "error",
-            "message": "Unsupported format. Choose sdf, mol, or pdb.",
-        }
-
-    mol = Chem.MolFromSmiles(smiles)
-    if mol is None:
-        return None, {
-            "status": "error",
-            "input_smiles": smiles,
-            "message": "Invalid SMILES.",
-        }
-
-    canonical_smiles = Chem.MolToSmiles(mol, isomericSmiles=True)
-
-    mol = Chem.AddHs(mol)
-
-    params = AllChem.ETKDGv3()
-    params.randomSeed = 42
-
-    embed_status = AllChem.EmbedMolecule(mol, params)
-    if embed_status != 0:
-        return None, {
-            "status": "error",
-            "input_smiles": smiles,
-            "canonical_smiles": canonical_smiles,
-            "message": "3D embedding failed.",
-        }
-
-    try:
-        AllChem.UFFOptimizeMolecule(mol, maxIters=500)
-        optimization_status = "UFF optimized"
-    except Exception as e:
-        optimization_status = f"UFF optimization failed, using embedded geometry only: {e}"
-
-    out_dir = Path("outputs/ligands")
-    out_dir.mkdir(parents=True, exist_ok=True)
-
-    safe_name = "ligand_3d"
-    out_path = out_dir / f"{safe_name}.{file_format}"
-
-    if file_format == "sdf":
-        writer = Chem.SDWriter(str(out_path))
-        writer.write(mol)
-        writer.close()
-    elif file_format == "mol":
-        Chem.MolToMolFile(mol, str(out_path))
-    elif file_format == "pdb":
-        Chem.MolToPDBFile(mol, str(out_path))
-
-    meta = {
-        "status": "completed",
-        "input_smiles": smiles,
-        "canonical_smiles": canonical_smiles,
-        "file_format": file_format,
-        "file_path": str(out_path),
-        "optimization_status": optimization_status,
-        "note": "This is a generated 3D conformer from SMILES, not a docked protein-ligand pose.",
-    }
-
-    return str(out_path), meta
-
-loaded_ok, loaded_msg = download_bundle_light()
-
-
-with gr.Blocks(title="EGFR AI Demo") as demo:
-    gr.Markdown(
-        """
-# EGFR AI Demo
-
-Private CPU demo for the EGFR AI backend workflow.
-
-This demo shows the backend response shape for generation, scoring, filtering, and docking integration.
-
-Real AutoDock-GPU docking is disabled in this CPU Space, but docking fields are present so backend/frontend teams can implement database columns and filters.
-"""
-    )
-
-    gr.Markdown(f"Bundle load status: {loaded_msg}")
-
-    with gr.Tab("Score SMILES"):
-        gr.Markdown(
-            """
-Enter one or more SMILES.
-
-This CPU demo calculates molecular properties and returns the same response columns expected by the backend.
-
-Important:
-- pred_pAff_mean is an integration field in this Space version.
-- real docking is disabled in this CPU Space.
-- docking_status is returned as not_run.
-"""
-        )
-
-        smiles_input = gr.Textbox(
-            label="SMILES input",
-            value="CCO\nc1ccccc1",
-            lines=5,
-        )
-
-        score_btn = gr.Button("Score SMILES")
-        score_table = gr.Dataframe(label="Results table")
-        score_json = gr.JSON(label="Backend-style JSON response")
-        score_csv = gr.File(label="Download CSV")
-
-
-        score_btn.click(
-            score_smiles,
-            inputs=smiles_input,
-            outputs=[score_table, score_json, score_csv],
-        )
-    with gr.Tab("Generate Job Demo"):
-        gr.Markdown(
-            """
-This tab demonstrates generation job behavior.
-
-Generation backend options:
-
-- demo_rows: uses packaged example rows. Fast and stable.
-- live_reinvent_cpu: tries to run real REINVENT sampling from the packaged checkpoint on CPU.
-
-The output is split into:
-
-1. Job summary: job_id, status, preset, mode, and metadata.
-2. Generated molecule results table.
-3. Full backend-style generation JSON.
-4. Download CSV.
-
-Notes:
-- DeepPurpose live scoring is not enabled yet in this Space version.
-- Real docking is disabled in this CPU Space, so docking_status is returned as not_run.
-"""
-        )
-
-        generation_backend = gr.Dropdown(
-            label="generation_backend",
-            choices=["demo_rows", "live_reinvent_cpu"],
-            value="demo_rows",
-        )
-
-        gen_num_molecules = gr.Number(
-            label="num_molecules",
-            value=20,
-            precision=0,
-        )
-
-        gen_return_top_k = gr.Number(
-            label="return_top_k",
-            value=20,
-            precision=0,
-        )
-
-        gen_docking_mode = gr.Dropdown(
-            label="docking_mode",
-            choices=["off", "top_k", "all"],
-            value="off",
-        )
-
-        gen_btn = gr.Button("Run Generation Job")
-
-        gen_summary = gr.JSON(label="Job summary")
-        gen_table = gr.Dataframe(label="Generated molecule results table")
-        gen_json = gr.JSON(label="Full backend-style generation JSON")
-        gen_file = gr.File(label="Download CSV")
-
-        gen_btn.click(
-            generate_job_demo,
-            inputs=[gen_num_molecules, gen_return_top_k, gen_docking_mode, generation_backend],
-            outputs=[gen_summary, gen_table, gen_json, gen_file],
-        )
-
-
-    with gr.Tab("Example Generate Response"):
-        gr.Markdown(
-            """
-This example is loaded from the private Hugging Face Dataset bundle.
-
-It shows the expected response shape after:
-
-Generate -> Enrich -> Optional Docking
-"""
-        )
-
-        example_btn = gr.Button("Load example response")
-        example_table = gr.Dataframe(label="Example results table")
-        example_json = gr.JSON(label="Example JSON response")
-
-        example_btn.click(
-            lambda: (get_example_table(), get_example_json()),
-            outputs=[example_table, example_json],
-        )
-
-        with gr.Tab("SMILES to 3D File"):
-            gr.Markdown(
-            """
-Convert a SMILES string into a downloadable 3D ligand file.
-
-Supported formats:
-
-- SDF
-- MOL
-- PDB
-
-Important: this creates a 3D conformer from SMILES. It is not a docked pose inside the EGFR binding pocket.
-"""
-        )
-
-        smiles_3d_input = gr.Textbox(
-            label="SMILES",
-            value="CCO",
-            lines=2,
-        )
-
-        format_input = gr.Radio(
-            choices=["sdf", "mol", "pdb"],
-            value="sdf",
-            label="Output file format",
-        )
-
-        make_3d_btn = gr.Button("Generate 3D ligand file")
-        ligand_file = gr.File(label="Download 3D ligand file")
-        ligand_meta = gr.JSON(label="3D file metadata")
-
-        make_3d_btn.click(
-            smiles_to_3d_file,
-            inputs=[smiles_3d_input, format_input],
-            outputs=[ligand_file, ligand_meta],
-        )
-        
-    with gr.Tab("Docking Contract"):
-        gr.Markdown(
-            """
-## Docking modes
-
-The full backend supports:
-
-- off
-- top_k
-- all
-
-In this CPU Space, real AutoDock-GPU docking is disabled.
-
-Returned docking fields in CPU demo:
-
-- docking_score: null
-- docking_status: not_run
-- docking_pose_file: null
-
-Recommended database columns:
-
-- docking_score FLOAT NULL
-- docking_status VARCHAR(30) DEFAULT 'not_run'
-- docking_pose_file TEXT NULL
-- docking_mode VARCHAR(20) DEFAULT 'off'
-- docking_error TEXT NULL
-
-Recommended frontend and filter behavior:
-
-- Show all valid molecules: valid == true
-- Show docked only: docking_status == completed
-- Show not-yet-docked molecules: docking_status == not_run
-- Sort docking results ascending, because more negative docking scores are usually better
-"""
-        )
-
-        contract_btn = gr.Button("Load backend contract")
-        contract_json = gr.JSON(label="backend_contract.json")
-
-        contract_btn.click(
-            get_contract,
-            outputs=contract_json,
-        )
-
-    with gr.Tab("API Spec"):
-        gr.Markdown(
-            """
-This tab loads the API response specification from the private artifact bundle.
-
-It explains the expected backend/frontend response format for:
-
-- generated molecules
-- scored SMILES
-- docking fields
-- frontend filters
-"""
-        )
-
-        spec_btn = gr.Button("Load API response spec")
-        spec_output = gr.Markdown(label="API_RESPONSE_SPEC.md")
-
-        spec_btn.click(
-            get_api_spec,
-            outputs=spec_output,
-        )
-
-
-demo.launch()

app/Helpers/OtpHelper.php

@@ -0,0 +1,28 @@
+<?php
+
+namespace App\Helpers;
+
+use App\Models\User;
+use App\Services\OtpService;
+
+class OtpHelper
+{
+    /**
+     * Send OTP by type for a user email
+     *
+     * @param string $email
+     * @param string $type ('email_verification' or 'password_reset')
+     * @param OtpService $otpService
+     * @return array
+     */
+    public static function sendOtpByType(string $email, string $type, OtpService $otpService): array
+    {
+        $user = User::where('email', $email)->firstOrFail();
+
+        $otpService->resendOtp($user, $type);
+
+        return [
+            'email' => $user->email
+        ];
+    }
+}

app/Http/Controllers/Api/AdmetController.php

@@ -0,0 +1,29 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use Illuminate\Http\Request;
+use App\Services\AdmetService;
+
+class AdmetController extends BaseController
+{
+    public function predict(Request $request, AdmetService $admetService)
+    {
+        try {
+            if ($request->hasFile('file')) {
+                $file = $request->file('file');
+                $extension = $file->getClientOriginalExtension();
+                $content = file_get_contents($file->getRealPath());
+                $result = $admetService->predictFromFile($content, $extension);
+                return $this->successResponse('ADMET predictions generated successfully', $result);
+            } elseif ($request->has('smiles') && !empty($request->input('smiles'))) {
+                $result = $admetService->predictBatchFromString($request->input('smiles'));
+                return $this->successResponse('ADMET predictions generated successfully', $result);
+            } else {
+                return $this->errorResponse('Please provide either a file or SMILES string', 400);
+            }
+        } catch (\Exception $e) {
+            return $this->errorResponse('Failed to generate ADMET predictions: ' . $e->getMessage(), 500);
+        }
+    }
+}

app/Http/Controllers/Api/AiServicesIntegrationController.php

@@ -0,0 +1,121 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use Illuminate\Http\JsonResponse;
+use Illuminate\Http\Request;
+use Illuminate\Routing\Controller;
+use Illuminate\Support\Facades\Http;
+
+class AiServicesIntegrationController extends Controller
+{
+    public function health(): JsonResponse
+    {
+        $checks = [
+            'admet' => config('services.admet.url'),
+            'chemical_rag' => config('services.chemical_ai.url'),
+            'drug_repurposing' => config('services.drug_repurposing.url'),
+        ];
+
+        $results = [];
+
+        foreach ($checks as $name => $baseUrl) {
+            $results[$name] = $this->probeHealth($baseUrl);
+            usleep(200_000);
+        }
+
+        $allHealthy = collect($results)->every(
+            fn (array $result) => ($result['status'] ?? '') === 'healthy'
+        );
+
+        return response()->json([
+            'success' => $allHealthy,
+            'services' => $results,
+        ], $allHealthy ? 200 : 503);
+    }
+
+    public function testAdmet(Request $request): JsonResponse
+    {
+        $baseUrl = rtrim((string) config('services.admet.url'), '/');
+        $smiles = (string) $request->input('smiles', 'c1ccccc1');
+
+        $response = Http::timeout(180)->post("{$baseUrl}/predict", [
+            'smiles' => $smiles,
+        ]);
+
+        return $this->proxyResponse('admet', $response);
+    }
+
+    public function testChemicalSearch(Request $request): JsonResponse
+    {
+        $baseUrl = rtrim((string) config('services.chemical_ai.url'), '/');
+        $smiles = (string) $request->input('smiles', 'CCO');
+        $topK = (int) $request->input('top_k', 3);
+
+        $response = Http::timeout(180)->post("{$baseUrl}/search/retrieval-only", [
+            'smiles' => $smiles,
+            'top_k' => $topK,
+        ]);
+
+        return $this->proxyResponse('chemical_rag', $response);
+    }
+
+    public function testDrugRepurposing(): JsonResponse
+    {
+        $baseUrl = rtrim((string) config('services.drug_repurposing.url'), '/');
+
+        $health = Http::timeout(60)->retry(3, 500)->withUserAgent('AILIXIR-Internal/1.0')->get("{$baseUrl}/health");
+        usleep(200_000);
+        $modelStatus = Http::timeout(60)->retry(3, 500)->withUserAgent('AILIXIR-Internal/1.0')->get("{$baseUrl}/api/v1/model-status");
+
+        $success = $health->successful() && $modelStatus->successful();
+
+        return response()->json([
+            'success' => $success,
+            'service' => 'drug_repurposing',
+            'health' => [
+                'status' => $health->status(),
+                'body' => $health->json(),
+            ],
+            'model_status' => [
+                'status' => $modelStatus->status(),
+                'body' => $modelStatus->json(),
+            ],
+        ], $success ? 200 : 502);
+    }
+
+    private function probeHealth(?string $baseUrl): array
+    {
+        if (empty($baseUrl)) {
+            return [
+                'status' => 'misconfigured',
+                'error' => 'URL not configured',
+            ];
+        }
+
+        try {
+            $response = Http::timeout(60)->retry(3, 500)->withUserAgent('AILIXIR-Internal/1.0')->get(rtrim($baseUrl, '/').'/health');
+
+            return [
+                'status' => $response->successful() ? 'healthy' : 'unhealthy',
+                'http_status' => $response->status(),
+                'body' => $response->json() ?? $response->body(),
+            ];
+        } catch (\Throwable $e) {
+            return [
+                'status' => 'unreachable',
+                'error' => $e->getMessage(),
+            ];
+        }
+    }
+
+    private function proxyResponse(string $service, \Illuminate\Http\Client\Response $response): JsonResponse
+    {
+        return response()->json([
+            'success' => $response->successful(),
+            'service' => $service,
+            'upstream_status' => $response->status(),
+            'data' => $response->json(),
+        ], $response->successful() ? 200 : 502);
+    }
+}

app/Http/Controllers/Api/AuthController.php

@@ -0,0 +1,115 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use App\Http\Controllers\Api\BaseController;
+use App\Http\Requests\User\LoginRequest;
+use App\Http\Requests\User\RegisterRequest;
+use App\Http\Requests\User\LoginGoogleRequest;
+use App\Http\Requests\User\CheckEmailRequest;
+use Illuminate\Http\Request;
+use App\Services\UserService;
+use App\Services\OtpService;
+use App\Models\User;
+
+class AuthController extends BaseController
+{
+
+    protected $userService;
+    protected $otpService;
+
+    public function __construct(UserService $userService, OtpService $otpService)
+    {
+        $this->userService = $userService;
+        $this->otpService = $otpService;
+    }
+
+    /** ---------------- Register ---------------- */
+
+    public function register(RegisterRequest $request)
+    {
+        $user = $this->userService->registerUser($request->validated());
+
+        return $this->successResponse(
+            'Registered successfully. Please check your email for OTP verification code.',
+            ['email' => $user->email]
+        );
+    }
+
+
+    public function login(LoginRequest $request)
+    {
+        $result = $this->userService->loginUser($request->validated());
+
+        if (isset($result['error'])) {
+            return $this->errorResponse($result['error'], $result['code'] ?? 400);
+        }
+
+        return $this->successResponse('Login successful', [
+            'token' => $result['token'],
+            'user'  => $result['user']
+        ]);
+    }
+
+    /** ---------------- Forgot Password ---------------- */
+
+    public function forgotPassword(CheckEmailRequest $request)
+    {
+        $user = User::where('email', $request->email)->first();
+
+        $this->otpService->sendOtp($user, 'password_reset');
+
+        return $this->successResponse(
+            'Password reset OTP has been sent to your email.',
+            ['email' => $user->email]
+        );
+    }
+
+    /** ---------------- Resend OTP ---------------- */
+
+    public function resendOtp(Request $request)
+    {
+        $request->validate([
+            'email' => 'required|email|exists:users,email',
+            'type' => 'required|in:email_verification,password_reset'
+        ]);
+
+        $user = User::where('email', $request->email)->first();
+
+        try {
+            $this->otpService->resendOtp($user, $request->type);
+
+            return $this->successResponse(
+                'OTP has been resent to your email.',
+                ['email' => $user->email]
+            );
+        } catch (\Illuminate\Validation\ValidationException $e) {
+            return $this->errorResponse($e->getMessage(), 429);
+        }
+    }
+
+    public function logout(Request $request)
+    {
+        $request->user()->currentAccessToken()->delete();
+
+        return $this->successResponse('Logged out successfully');
+    }
+
+    /** ---------------- Google OAuth ---------------- */
+
+    public function handleGoogleCallback(LoginGoogleRequest $request)
+    {
+        $result = $this->userService->loginGoogleUser(
+            $request->validated()['access_token']
+        );
+
+        if (isset($result['error'])) {
+            return $this->errorResponse($result['error'], $result['code'] ?? 400);
+        }
+
+        return $this->successResponse('Google login successful', [
+            'token' => $result['token'],
+            'user'  => $result['user']
+        ]);
+    }
+}

app/Http/Controllers/Api/AwardController.php

@@ -0,0 +1,52 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use App\Http\Controllers\Api\BaseController;
+use App\Http\Resources\ScientistResource;
+use App\Http\Resources\AwardResource;
+use App\Services\AwardService;
+use Illuminate\Http\Request;
+
+class AwardController extends BaseController
+{
+    protected $service;
+
+    public function __construct(AwardService $service)
+    {
+        $this->service = $service;
+    }
+
+    public function index(Request $request)
+    {
+        $perPage = min(100, max(1, (int)$request->get('per_page', 10)));
+
+        $awards = $this->service->getAwards($perPage);
+
+        return $this->paginatedResponse(
+            'Awards retrieved successfully',
+            $awards->through(fn($award) => new AwardResource($award)),
+            $awards
+        );
+    }
+
+    public function show($id)
+    {
+        $award = $this->service->getAward($id);
+
+        return $this->successResponse(
+            'Award retrieved successfully',
+            new AwardResource($award)
+        );
+    }
+
+    public function getScientistsByAward($id)
+    {
+        $award = $this->service->getAward($id);
+
+        return $this->successResponse(
+            'Scientists retrieved successfully',
+            ScientistResource::collection($award->scientists)
+        );
+    }
+}

app/Http/Controllers/Api/BaseController.php

@@ -0,0 +1,13 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use Illuminate\Foundation\Auth\Access\AuthorizesRequests;
+use Illuminate\Foundation\Validation\ValidatesRequests;
+use Illuminate\Routing\Controller;
+use App\Traits\ApiResponseTrait;
+
+class BaseController extends Controller
+{
+    use AuthorizesRequests, ValidatesRequests, ApiResponseTrait;
+}

app/Http/Controllers/Api/ChemicalSearchController.php

@@ -0,0 +1,74 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use App\Http\Requests\ChemicalSearchRequest;
+use App\Services\ChemicalSearchService;
+use Illuminate\Http\JsonResponse;
+use Illuminate\Support\Facades\Auth;
+
+class ChemicalSearchController extends BaseController
+{
+    public function __construct(
+        private ChemicalSearchService $searchService
+    ) {}
+
+    /**
+     * POST /api/chemical-search
+     * Retrieval Only - Synchronous
+     */
+    public function store(ChemicalSearchRequest $request): JsonResponse
+    {
+        $user = Auth::user();
+
+        $result = $this->searchService->search(
+            smiles: $request->validated('smiles'),
+            topK: $request->input('top_k', 5),
+            userId: $user->id
+        );
+
+        if (!$result['success']) {
+            return response()->json([
+                'success' => false,
+                'message' => $result['error'] ?? 'Search failed',
+            ], 500);
+        }
+
+        return response()->json([
+            'success' => true,
+            'query' => [
+                'smiles' => $request->validated('smiles'),
+                'top_k' => $request->input('top_k', 5),
+            ],
+            'compounds' => $result['compounds'],
+            'metadata' => $result['metadata'],
+        ]);
+    }
+    public function fullRag(ChemicalSearchRequest $request): JsonResponse
+    {
+        $user = Auth::user();
+
+        $result = $this->searchService->fullRag(
+            smiles: $request->validated('smiles'),
+            topK: $request->input('top_k', 5),
+            userId: $user->id
+        );
+
+        if (!$result['success']) {
+            return response()->json([
+                'success' => false,
+                'message' => $result['error'] ?? 'Search failed',
+            ], 500);
+        }
+
+        return response()->json([
+            'success' => true,
+            'query' => [
+                'smiles' => $request->validated('smiles'),
+                'top_k' => $request->input('top_k', 5),
+            ],
+            'compounds' => $result['compounds'],
+            'metadata' => $result['metadata'],
+        ]);
+    }
+}

app/Http/Controllers/Api/ChemistryController.php

@@ -0,0 +1,524 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use App\Http\Controllers\Controller;
+use App\Http\Requests\ChemistryChatRequest;
+use App\Http\Requests\ChemistryCompareRequest;
+use App\Http\Requests\ChemistryDockingRequest;
+use App\Http\Resources\ChemistryResponseResource;
+use App\Models\ChemistryAnalysis;
+use App\Models\ChemistryCsvJob;
+use App\Models\ChemistryThread;
+use App\Services\ChemistryApiService;
+use Illuminate\Http\JsonResponse;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Storage;
+use Illuminate\Support\Facades\Auth;
+
+
+class ChemistryController extends BaseController
+{
+    public function __construct(
+        protected ChemistryApiService $chemistryService
+    ) {}
+
+    // ==================== Health ====================
+    public function health(): JsonResponse
+    {
+        $result = $this->chemistryService->healthCheck();
+        return response()->json(new ChemistryResponseResource($result));
+    }
+
+    // ==================== Threads ====================
+    public function createThread(): JsonResponse
+    {
+        $user = Auth::user();
+
+        $result = $this->chemistryService->createThread();
+
+        if (!$result['success']) {
+            return response()->json(new ChemistryResponseResource($result), 500);
+        }
+
+        $thread = ChemistryThread::create([
+            'user_id' => $user->id,
+            'thread_id' => $result['data']['thread_id'],
+            'title' => 'New Conversation',
+            'status' => 'active',
+            'last_used_at' => now(),
+        ]);
+
+        return response()->json([
+            'success' => true,
+            'data' => [
+                'thread_id' => $thread->thread_id,
+                'id' => $thread->id,
+                'created_at' => $thread->created_at,
+            ],
+        ]);
+    }
+
+    public function listThreads(): JsonResponse
+    {
+        $threads = Auth::user()->chemistryThreads()
+            ->where('status', 'active')
+            ->orderBy('last_used_at', 'desc')
+            ->get(['id', 'thread_id', 'title', 'last_used_at', 'created_at']);
+
+        return response()->json([
+            'success' => true,
+            'data' => $threads,
+        ]);
+    }
+
+    // ==================== Chat (معدل: title من أول سؤال) ====================
+    public function chat(ChemistryChatRequest $request): JsonResponse
+    {
+        $user = Auth::user();
+        $threadId = $request->input('thread_id');
+
+        if ($threadId) {
+            $thread = ChemistryThread::where('user_id', $user->id)
+                ->where('thread_id', $threadId)
+                ->first();
+
+            if (!$thread) {
+                return response()->json([
+                    'success' => false,
+                    'error' => 'Thread not found or access denied',
+                ], 403);
+            }
+
+            // ← لو الـ title لسه "New Conversation"، غيريه لأول سؤال
+            if ($thread->title === 'New Conversation') {
+                $message = $request->input('message');
+                $newTitle = mb_strlen($message) > 50
+                    ? mb_substr($message, 0, 50) . '...'
+                    : $message;
+
+                $thread->update([
+                    'title' => $newTitle,
+                    'last_used_at' => now(),
+                ]);
+            } else {
+                $thread->update(['last_used_at' => now()]);
+            }
+        }
+
+        $result = $this->chemistryService->chat(
+            $request->input('message'),
+            $threadId
+        );
+
+        if (!$result['success']) {
+            return response()->json(new ChemistryResponseResource($result), $result['status']);
+        }
+
+        ChemistryAnalysis::create([
+            'user_id' => $user->id,
+            'chemistry_thread_id' => $thread?->id,
+            'type' => 'chat',
+            'input_data' => $request->input('message'),
+            'response' => $result['data']['reply'] ?? null,
+            'processing_time_ms' => $result['data']['processing_time_ms'] ?? null,
+            'status' => 'success',
+        ]);
+
+        return response()->json(new ChemistryResponseResource($result));
+    }
+
+    // ==================== Analyze SMILES ====================
+    public function analyzeSmiles(Request $request): JsonResponse
+    {
+        $user = Auth::user();
+
+        $request->validate([
+            'smiles' => 'required|string|max:1000',
+            'thread_id' => 'nullable|string|max:255',
+        ]);
+
+        $threadId = $request->input('thread_id');
+        $thread = $this->validateThread($user->id, $threadId);
+
+        $smiles = $request->input('smiles');
+
+        $result = $this->chemistryService->analyzeSmiles($smiles, $threadId);
+
+        return $this->saveAndRespond($result, $user->id, 'smiles', $smiles, $thread?->id);
+    }
+
+    // ==================== Compare ====================
+    public function compare(ChemistryCompareRequest $request): JsonResponse
+    {
+        $user = Auth::user();
+        $threadId = $request->input('thread_id');
+        $thread = $this->validateThread($user->id, $threadId);
+
+        $result = $this->chemistryService->compareMolecules(
+            $request->input('smiles'),
+            $threadId
+        );
+
+        $input = implode(', ', $request->input('smiles'));
+        return $this->saveAndRespond($result, $user->id, 'compare', $input, $thread?->id);
+    }
+
+    // ==================== Docking ====================
+    public function docking(ChemistryDockingRequest $request): JsonResponse
+    {
+        $user = Auth::user();
+        $threadId = $request->input('thread_id');
+        $thread = $this->validateThread($user->id, $threadId);
+
+        $result = $this->chemistryService->analyzeDocking(
+            $request->input('docking_data'),
+            $threadId
+        );
+
+        return $this->saveAndRespond($result, $user->id, 'docking', $request->input('docking_data'), $thread?->id);
+    }
+
+    // ==================== CSV (معدل: required thread_id) ====================
+    public function uploadCsv(Request $request): JsonResponse
+    {
+        $user = Auth::user();
+
+        $request->validate([
+            'file' => 'required|file|mimes:csv,txt|max:2048',
+            'analysis_type' => 'nullable|in:full,quick,admet,classify',
+            'thread_id' => 'required|string|max:255',
+        ]);
+
+        $file = $request->file('file');
+        $analysisType = $request->input('analysis_type', 'full');
+        $threadId = $request->input('thread_id');
+
+        // Validate thread belongs to user
+        $thread = ChemistryThread::where('user_id', $user->id)
+            ->where('thread_id', $threadId)
+            ->first();
+
+        if (!$thread) {
+            return response()->json([
+                'success' => false,
+                'error' => 'Thread not found or access denied',
+            ], 403);
+        }
+
+        $result = $this->chemistryService->uploadCsv($file, $analysisType);
+
+        if (!$result['success']) {
+            return response()->json(new ChemistryResponseResource($result), $result['status']);
+        }
+
+        $apiJobId = $result['data']['job_id'] ?? null;
+        $totalRows = $result['data']['total_rows'] ?? 0;
+
+        if (!$apiJobId) {
+            return response()->json([
+                'success' => false,
+                'error' => 'Failed to get job ID from API',
+            ], 500);
+        }
+
+        $job = ChemistryCsvJob::create([
+            'user_id' => $user->id,
+            'chemistry_thread_id' => $thread->id,
+            'job_id' => $apiJobId,
+            'filename' => $file->getClientOriginalName(),
+            'analysis_type' => $analysisType,
+            'total_rows' => $totalRows,
+            'status' => 'queued',
+        ]);
+
+        // Update thread last_used_at
+        $thread->update(['last_used_at' => now()]);
+
+        return response()->json([
+            'success' => true,
+            'data' => [
+                'job_id' => $job->job_id,
+                'id' => $job->id,
+                'status' => $job->status,
+                'total_rows' => $job->total_rows,
+            ],
+        ]);
+    }
+
+    public function csvStatus(string $jobId): JsonResponse
+    {
+        $user = Auth::user();
+
+        $job = ChemistryCsvJob::where('user_id', $user->id)
+            ->where('job_id', $jobId)
+            ->first();
+
+        if (!$job) {
+            return response()->json([
+                'success' => false,
+                'error' => 'Job not found or access denied',
+            ], 404);
+        }
+
+        $result = $this->chemistryService->getCsvStatus($jobId);
+
+        if ($result['success'] && isset($result['data'])) {
+            $apiData = $result['data'];
+
+            $job->update([
+                'status' => $apiData['status'] ?? $job->status,
+                'completed_rows' => $apiData['completed'] ?? $job->completed_rows,
+                'failed_rows' => $apiData['failed_rows'] ?? $job->failed_rows,
+                'progress_percent' => $apiData['progress_percent'] ?? $job->progress_percent,
+            ]);
+
+            if ($apiData['status'] === 'done' && !$job->completed_at) {
+                $job->update(['completed_at' => now(), 'status' => 'done']);
+            }
+        }
+
+        return response()->json([
+            'success' => true,
+            'data' => [
+                'job_id' => $job->job_id,
+                'status' => $job->status,
+                'total' => $job->total_rows,
+                'completed' => $job->completed_rows,
+                'failed' => $job->failed_rows,
+                'progress_percent' => $job->progress_percent,
+            ],
+        ]);
+    }
+
+    public function csvResults(string $jobId)
+    {
+        $user = Auth::user();
+
+        $job = ChemistryCsvJob::where('user_id', $user->id)
+            ->where('job_id', $jobId)
+            ->first();
+
+        if (!$job) {
+            return response()->json([
+                'success' => false,
+                'error' => 'Job not found or access denied',
+            ], 404);
+        }
+
+        if ($job->status !== 'done') {
+            return response()->json([
+                'success' => false,
+                'error' => 'Job not completed yet',
+            ], 400);
+        }
+
+        // ← Return content from DB if available
+        if ($job->result_content) {
+            return response($job->result_content)
+                ->header('Content-Type', 'text/csv')
+                ->header('Content-Disposition', 'attachment; filename="results_' . $jobId . '.csv"');
+        }
+
+        $result = $this->chemistryService->getCsvResults($jobId);
+
+        if (is_string($result)) {
+            // ← Store content in DB instead of file path
+            $job->update([
+                'result_content' => $result,
+                'result_file_path' => null,
+            ]);
+
+            return response($result)
+                ->header('Content-Type', 'text/csv')
+                ->header('Content-Disposition', 'attachment; filename="results_' . $jobId . '.csv"');
+        }
+
+        return response()->json(new ChemistryResponseResource($result));
+    }
+
+    public function listJobs(Request $request): JsonResponse
+    {
+        $user = Auth::user();
+
+        $query = $user->chemistryCsvJobs()
+            ->orderBy('created_at', 'desc');
+
+        // Optional: filter by thread_id
+        if ($request->has('thread_id')) {
+            $thread = ChemistryThread::where('user_id', $user->id)
+                ->where('thread_id', $request->input('thread_id'))
+                ->first();
+
+            if ($thread) {
+                $query->where('chemistry_thread_id', $thread->id);
+            }
+        }
+
+        $jobs = $query->get([
+            'id',
+            'job_id',
+            'chemistry_thread_id',
+            'filename',
+            'analysis_type',
+            'status',
+            'total_rows',
+            'completed_rows',
+            'failed_rows',
+            'progress_percent',
+            'created_at'
+        ]);
+
+        return response()->json([
+            'success' => true,
+            'data' => $jobs,
+        ]);
+    }
+
+    public function deleteJob(string $jobId): JsonResponse
+    {
+        $user = Auth::user();
+
+        $job = ChemistryCsvJob::where('user_id', $user->id)
+            ->where('job_id', $jobId)
+            ->first();
+
+        if (!$job) {
+            return response()->json([
+                'success' => false,
+                'error' => 'Job not found or access denied',
+            ], 404);
+        }
+
+        $result = $this->chemistryService->deleteCsvJob($jobId);
+
+        if ($job->result_file_path && Storage::exists($job->result_file_path)) {
+            Storage::delete($job->result_file_path);
+        }
+
+        $job->delete();
+
+        return response()->json([
+            'success' => true,
+            'message' => 'Job deleted successfully',
+        ]);
+    }
+
+    // ==================== User History ====================
+    public function userHistory(Request $request): JsonResponse
+    {
+        $user = Auth::user();
+        $type = $request->input('type');
+
+        $query = $user->chemistryAnalyses()
+            ->with('thread:id,thread_id,title')
+            ->orderBy('created_at', 'desc');
+
+        if ($type) {
+            $query->where('type', $type);
+        }
+
+        $history = $query->paginate(20);
+
+        return response()->json([
+            'success' => true,
+            'data' => $history,
+        ]);
+    }
+
+    // ==================== Thread Messages (جديد) ====================
+    public function threadMessages(Request $request): JsonResponse
+    {
+        $user = Auth::user();
+
+        $request->validate([
+            'thread_id' => 'required|string|max:255',
+        ]);
+
+        $threadId = $request->input('thread_id');
+
+        $thread = ChemistryThread::where('user_id', $user->id)
+            ->where('thread_id', $threadId)
+            ->first();
+
+        if (!$thread) {
+            return response()->json([
+                'success' => false,
+                'error' => 'Thread not found or access denied',
+            ], 403);
+        }
+
+        // Chat/analysis messages
+        $messages = ChemistryAnalysis::where('user_id', $user->id)
+            ->where('chemistry_thread_id', $thread->id)
+            ->orderBy('created_at', 'asc')
+            ->get(['id', 'type', 'input_data', 'response', 'status', 'created_at']);
+
+        // CSV jobs related to this thread
+        $csvJobs = ChemistryCsvJob::where('user_id', $user->id)
+            ->where('chemistry_thread_id', $thread->id)
+            ->orderBy('created_at', 'asc')
+            ->get([
+                'id',
+                'job_id',
+                'filename',
+                'analysis_type',
+                'status',
+                'total_rows',
+                'completed_rows',
+                'failed_rows',
+                'progress_percent',
+                'result_content',
+                'created_at',
+                'completed_at'
+            ]);
+
+        return response()->json([
+            'success' => true,
+            'data' => [
+                'thread_id' => $thread->thread_id,
+                'title' => $thread->title,
+                'messages' => $messages,
+                'csv_jobs' => $csvJobs,
+            ],
+        ]);
+    }
+
+    // ==================== Helper Methods ====================
+    private function validateThread(int $userId, ?string $threadId): ?ChemistryThread
+    {
+        if (!$threadId) return null;
+
+        return ChemistryThread::where('user_id', $userId)
+            ->where('thread_id', $threadId)
+            ->first();
+    }
+
+    private function saveAndRespond(array $result, int $userId, string $type, string $input, ?int $threadId = null): JsonResponse
+    {
+        if (!$result['success']) {
+            ChemistryAnalysis::create([
+                'user_id' => $userId,
+                'chemistry_thread_id' => $threadId,
+                'type' => $type,
+                'input_data' => $input,
+                'status' => 'failed',
+                'error_message' => is_string($result['error']) ? $result['error'] : json_encode($result['error']),
+            ]);
+
+            return response()->json(new ChemistryResponseResource($result), $result['status']);
+        }
+
+        ChemistryAnalysis::create([
+            'user_id' => $userId,
+            'chemistry_thread_id' => $threadId,
+            'type' => $type,
+            'input_data' => $input,
+            'response' => $result['data']['reply'] ?? null,
+            'processing_time_ms' => $result['data']['processing_time_ms'] ?? null,
+            'status' => 'success',
+        ]);
+
+        return response()->json(new ChemistryResponseResource($result));
+    }
+}

app/Http/Controllers/Api/ConvertSmilesController.php

@@ -0,0 +1,180 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use App\Models\DockingJob;
+use App\Traits\ApiResponseTrait;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Log;
+use Illuminate\Support\Facades\Process;
+use Illuminate\Support\Facades\Validator;
+use Illuminate\Support\Str;
+
+class ConvertSmilesController
+{
+    use ApiResponseTrait;
+
+    public function convert(Request $request)
+    {
+        $validator = Validator::make($request->all(), [
+            'ligand_smiles' => 'required|string|max:2000',
+        ]);
+
+        if ($validator->fails()) {
+            return $this->errorResponse('Validation Error', 422, $validator->errors());
+        }
+
+        $conversion = $this->convertSmilesToPdbqt($request->ligand_smiles);
+
+        if ($conversion['status'] === 'error') {
+            return $this->errorResponse(
+                'SMILES conversion failed: ' . $conversion['message'],
+                422
+            );
+        }
+
+        // Create a completed job record scoped to SMILES-only conversions
+        $job = DockingJob::create([
+            'user_id'      => $request->user()->id,
+            'input_type'   => 'smiles',
+            'smiles'       => $request->ligand_smiles,
+            'protein_name' => null,
+            'ligand_name'  => 'generated_from_smiles.pdbqt',
+            'protein_path' => '',
+            'ligand_path'  => $conversion['output_file'],
+            'status'       => 'completed',
+            'result_data'  => [
+                'output_file' => $conversion['output_file'],
+                'smiles'      => $request->ligand_smiles,
+            ],
+        ]);
+
+        return $this->successResponse('SMILES converted to PDBQT successfully', [
+            'job_id'       => $job->id,
+            'download_url' => url('/api/convert-smiles/download/' . $job->id),
+            'smiles'       => $request->ligand_smiles,
+        ]);
+    }
+
+    /**
+     * Download the converted PDBQT file.
+     */
+    public function download(Request $request, $id)
+    {
+        $job = DockingJob::where('id', $id)
+            ->where('user_id', $request->user()->id)
+            ->where('input_type', 'smiles')
+            ->whereNull('protein_name')   // ensure it's a convert-only job
+            ->first();
+
+        if (! $job || $job->status !== 'completed') {
+            return $this->errorResponse('File not available or unauthorized', 404);
+        }
+
+        $filePath = $job->result_data['output_file'] ?? $job->ligand_path ?? null;
+
+        if (! $filePath || ! file_exists($filePath)) {
+            return $this->errorResponse('File not found on server', 404);
+        }
+
+        return response()->download($filePath, 'converted_ligand_' . $job->id . '.pdbqt');
+    }
+
+    /**
+     * List all SMILES conversion jobs for the authenticated user.
+     */
+    public function history(Request $request)
+    {
+        $perPage = min((int) $request->query('per_page', 15), 100);
+
+        $paginator = DockingJob::where('user_id', $request->user()->id)
+            ->where('input_type', 'smiles')
+            ->whereNull('protein_name')
+            ->orderBy('created_at', 'desc')
+            ->paginate($perPage);
+
+        $items = collect($paginator->items())->map(function ($job) {
+            $data = [
+                'job_id'     => $job->id,
+                'status'     => $job->status,
+                'smiles'     => $job->smiles,
+                'created_at' => $job->created_at->toIso8601String(),
+            ];
+
+            if ($job->status === 'completed' && $job->result_data) {
+                $data['results'] = [
+                    'download_url' => url('/api/convert-smiles/download/' . $job->id),
+                ];
+            }
+
+            return $data;
+        });
+
+        return $this->successResponse('Conversion history retrieved successfully', [
+            'items'      => $items,
+            'pagination' => [
+                'current_page' => $paginator->currentPage(),
+                'per_page'     => $paginator->perPage(),
+                'total'        => $paginator->total(),
+                'last_page'    => $paginator->lastPage(),
+                'has_more'     => $paginator->hasMorePages(),
+            ],
+        ]);
+    }
+
+    /**
+     * Internal helper: run the SMILES → PDBQT Python conversion.
+     *
+     * @return array{status: string, output_file?: string, message?: string}
+     */
+    private function convertSmilesToPdbqt(string $smiles): array
+    {
+        $pythonPath = env('DOCKING_PYTHON_PATH', base_path('vina_env/bin/python'));
+        $scriptPath = env('SMILES_SCRIPT_PATH', base_path('scripts/smiles_to_pdbqt.py'));
+
+        $outputFilename = Str::random(40) . '.pdbqt';
+        $outputDir      = storage_path('app/private/docking/generated');
+        $outputPath     = $outputDir . '/' . $outputFilename;
+
+        if (! is_dir($outputDir)) {
+            mkdir($outputDir, 0755, true);
+        }
+
+        $cmd = sprintf(
+            '%s %s %s %s',
+            escapeshellarg($pythonPath),
+            escapeshellarg($scriptPath),
+            escapeshellarg($smiles),
+            escapeshellarg($outputPath)
+        );
+
+        try {
+            $result     = Process::timeout(120)->run($cmd);
+            $fullOutput = $result->output();
+            $outputData = null;
+
+            if (preg_match('/\{"status":\s*"(success|error)".*\}/s', $fullOutput, $matches)) {
+                $outputData = json_decode($matches[0], true);
+            }
+
+            if (! $result->successful()) {
+                $errorMsg = $outputData['message'] ?? $result->errorOutput() ?: 'Unknown conversion error';
+                Log::error('SMILES conversion failed', ['smiles' => $smiles, 'error' => $errorMsg]);
+                return ['status' => 'error', 'message' => $errorMsg];
+            }
+
+            if ($outputData && $outputData['status'] === 'success') {
+                return $outputData;
+            }
+
+            if ($outputData && $outputData['status'] === 'error') {
+                return $outputData;
+            }
+
+            return ['status' => 'error', 'message' => 'Unexpected output from conversion script'];
+        } catch (\Exception $e) {
+            Log::error('SMILES conversion exception', ['smiles' => $smiles, 'error' => $e->getMessage()]);
+            return ['status' => 'error', 'message' => $e->getMessage()];
+        }
+    }
+}

app/Http/Controllers/Api/DockingController.php

@@ -0,0 +1,214 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use App\Http\Requests\Docking\SubmitDockingRequest;
+use App\Jobs\ConvertSmilesJob;
+use App\Jobs\RunDockingJob;
+use App\Models\DockingJob;
+use App\Traits\ApiResponseTrait;
+use Illuminate\Http\Request;
+use Illuminate\Http\UploadedFile;
+use Illuminate\Support\Facades\Log;
+use Illuminate\Support\Facades\Process;
+use Illuminate\Http\Exceptions\HttpResponseException;
+use Illuminate\Support\Str;
+use Laravel\Sanctum\PersonalAccessToken;
+use Symfony\Component\HttpFoundation\StreamedResponse;
+
+class DockingController
+{
+    use ApiResponseTrait;
+
+    public function submit(SubmitDockingRequest $request)
+    {
+        $isSmiles = $request->filled('ligand_smiles');
+
+        if ($isSmiles) {
+            $ligandPath = null;
+        } else {
+            $ligandPath = $this->storeAsPdbqt($request->file('ligand_file'), true);
+        }
+
+        $proteinPath = $this->storeAsPdbqt($request->file('protein_file'), false);
+
+        $job = DockingJob::create([
+            'user_id' => $request->user()->id,
+            'input_type' => $isSmiles ? 'smiles' : 'file',
+            'smiles' => $isSmiles ? $request->ligand_smiles : null,
+            'protein_name' => $request->protein_name,
+            'ligand_name' => $request->ligand_name,
+            'protein_path' => $proteinPath,
+            'ligand_path' => $ligandPath,
+            'status' => 'pending',
+        ]);
+
+        $params = [
+            'center_x' => $request->center_x,
+            'center_y' => $request->center_y,
+            'center_z' => $request->center_z,
+            'box_size_x' => $request->box_size_x,
+            'box_size_y' => $request->box_size_y,
+            'box_size_z' => $request->box_size_z,
+            'exhaustiveness' => $request->exhaustiveness ?? 8,
+            'n_poses' => $request->n_poses ?? 5,
+        ];
+
+        if ($isSmiles) {
+            ConvertSmilesJob::dispatch($job, $request->ligand_smiles, $params);
+        } else {
+            RunDockingJob::dispatch($job, $params);
+        }
+
+        return $this->successResponse('Docking Job Successfully Queued', [
+            'job_id' => $job->id,
+            'status' => $job->status,
+        ]);
+    }
+
+    public function history(Request $request)
+    {
+        $perPage = min((int) $request->query('per_page', 15), 100);
+
+        $paginator = DockingJob::dockingOnly()
+            ->where('user_id', $request->user()->id)
+            ->orderBy('created_at', 'desc')
+            ->paginate($perPage)
+            ->through(function ($job) {
+                return [
+                    'id' => $job->id,
+                    'status' => $job->status,
+                    'protein' => $job->protein_name,
+                    'ligand' => $job->ligand_name,
+                    'created_at' => $job->created_at->toIso8601String(),
+                    'download_url' => url('/api/docking/download/'.$job->id),
+                    'scores' => $job->vina_scores ?? [],
+                    'error' => $job->status === 'failed' ? ($job->result_data['error'] ?? null) : null,
+                ];
+            });
+
+        return $this->paginatedResponse('Docking history retrieved successfully', $paginator);
+    }
+
+    public function status(Request $request, $id)
+    {
+        $job = DockingJob::dockingOnly()
+            ->where('id', $id)
+            ->where('user_id', $request->user()->id)
+            ->first();
+
+        if (! $job) {
+            return $this->errorResponse('Docking job not found or unauthorized', 404);
+        }
+
+        return $this->successResponse('Job details retrieved successfully', [
+            'id' => $job->id,
+            'status' => $job->status,
+            'protein' => $job->protein_name,
+            'ligand' => $job->ligand_name,
+            'created_at' => $job->created_at->toIso8601String(),
+            'download_url' => url('/api/docking/download/'.$job->id),
+            'scores' => $job->vina_scores ?? [],
+            'error' => $job->status === 'failed' ? ($job->result_data['error'] ?? null) : null,
+        ]);
+    }
+
+    public function download(Request $request, $id)
+    {
+        $token = $request->bearerToken() ?? $request->query('token');
+
+        if (! $token) {
+            return $this->errorResponse('Unauthenticated', 401);
+        }
+
+        $accessToken = PersonalAccessToken::findToken($token);
+        if (! $accessToken || ! $accessToken->tokenable) {
+            return $this->errorResponse('Invalid token', 401);
+        }
+
+        $job = DockingJob::dockingOnly()
+            ->where('id', $id)
+            ->where('user_id', $accessToken->tokenable->id)
+            ->first();
+
+        if (! $job || $job->status !== 'completed') {
+            return $this->errorResponse('Docking file not available or unauthorized', 404);
+        }
+
+        $filePath = $job->result_data['output_file'] ?? null;
+
+        if (! $filePath || ! file_exists($filePath)) {
+            return $this->errorResponse('File not found on server', 404);
+        }
+
+        return new StreamedResponse(function () use ($filePath) {
+            $stream = fopen($filePath, 'rb');
+            if ($stream) {
+                fpassthru($stream);
+                fclose($stream);
+            }
+        }, 200, [
+            'Content-Type' => 'application/octet-stream',
+            'Content-Disposition' => 'attachment; filename="docking_result_'.$job->id.'.pdbqt"',
+            'Content-Length' => filesize($filePath),
+        ]);
+    }
+
+    private function storeAsPdbqt(UploadedFile $file, bool $isLigand): string
+    {
+        $ext = strtolower($file->getClientOriginalExtension());
+        $filename = Str::random(40).'.pdbqt';
+        $destPath = storage_path('app/private/docking/'.$filename);
+
+        if ($ext === 'pdbqt') {
+            $file->storeAs('docking', $filename);
+        } elseif ($ext === 'pdb') {
+            $this->convertPdbToPdbqt($file->getRealPath(), $destPath, $isLigand);
+        } else {
+            throw new HttpResponseException(
+                $this->errorResponse('Unsupported file format: .'.$ext.'. Only .pdb and .pdbqt files are accepted.', 422)
+            );
+        }
+
+        return $destPath;
+    }
+
+    private function convertPdbToPdbqt(string $source, string $dest, bool $isLigand): void
+    {
+        $pythonPath = env('DOCKING_PYTHON_PATH');
+        $obabel = $pythonPath ? dirname($pythonPath).'/obabel' : 'obabel';
+        if (! file_exists($obabel)) {
+            $obabel = 'obabel';
+        }
+
+        $result = Process::timeout(60)->run([
+            $obabel,
+            '-ipdb', $source,
+            '-opdbqt',
+            '-O', $dest,
+        ]);
+
+        if (! $result->successful()) {
+            Log::error('PDB-to-PDBQT conversion failed', [
+                'source' => $source,
+                'dest' => $dest,
+                'error' => $result->errorOutput(),
+            ]);
+            throw new HttpResponseException(
+                $this->errorResponse('Failed to convert PDB file to PDBQT format.', 500)
+            );
+        }
+
+        $content = file_get_contents($dest);
+        $lines = explode("\n", $content);
+
+        if ($isLigand) {
+            $lines = array_map(fn ($line) => str_starts_with($line, 'ATOM') ? 'HETATM'.substr($line, 6) : $line, $lines);
+        } else {
+            $lines = array_filter($lines, fn ($line) => preg_match('/^(ATOM|HETATM)/', $line));
+            $lines = array_values($lines);
+        }
+
+        file_put_contents($dest, implode("\n", $lines));
+    }
+}

app/Http/Controllers/Api/EmailVerificationController.php

@@ -0,0 +1,85 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use App\Http\Controllers\Controller;
+use App\Http\Requests\VerifyOtpRequest;
+use App\Services\OtpService;
+use App\Models\User;
+use Illuminate\Http\Request;
+
+class EmailVerificationController extends BaseController
+{
+    protected $otpService;
+
+    public function __construct(OtpService $otpService)
+    {
+        $this->otpService = $otpService;
+    }
+
+    /**
+     * Verify Email OTP
+     */
+    public function verify(Request $request)
+    {
+        $request->validate([
+            'email' => 'required|email|exists:users,email',
+            'otp' => 'required|digits:6',
+        ]);
+
+        $user = User::where('email', $request->email)->first();
+
+        try {
+            $this->otpService->verifyOtp($user, 'email_verification', $request->otp);
+
+            $user->update([
+                'is_verified' => true,
+                'email_verification_otp' => null,
+                'email_verification_otp_expires_at' => null,
+            ]);
+
+            $token = $user->createToken('auth_token')->plainTextToken;
+
+            return response()->json([
+                'success' => true,
+                'message' => 'Email verified successfully',
+                'data' => [
+                    'token' => $token,
+                    'user' => $user
+                ]
+            ]);
+        } catch (\Exception $e) {
+            return response()->json([
+                'success' => false,
+                'message' => $e->getMessage()
+            ], 400);
+        }
+    }
+
+    /**
+     * Resend OTP
+     */
+    public function resend(Request $request)
+    {
+        $request->validate([
+            'email' => 'required|email|exists:users,email'
+        ]);
+
+        $user = User::where('email', $request->email)->first();
+
+        try {
+            $this->otpService->resendOtp($user, 'email_verification');
+
+            return response()->json([
+                'success' => true,
+                'message' => 'OTP resent successfully',
+                'data' => ['email' => $user->email]
+            ]);
+        } catch (\Exception $e) {
+            return response()->json([
+                'success' => false,
+                'message' => $e->getMessage()
+            ], 400);
+        }
+    }
+}