| |
| """ |
| System Verification Script |
| Verifies all components are properly configured and working |
| |
| Run with: python verify_system.py |
| """ |
| import os |
| import sys |
| import json |
| from pathlib import Path |
|
|
| def check_file_exists(file_path: str, description: str = "") -> bool: |
| """Check if a file exists""" |
| desc = f" ({description})" if description else "" |
| if os.path.exists(file_path): |
| print(f" ✅ {file_path}{desc}") |
| return True |
| else: |
| print(f" ❌ {file_path}{desc} - NOT FOUND") |
| return False |
|
|
| def check_python_version() -> bool: |
| """Check Python version""" |
| print("\n📌 Python Version:") |
| version = f"{sys.version_info.major}.{sys.version_info.minor}" |
| if sys.version_info >= (3, 10): |
| print(f" ✅ Python {version} (requirement: 3.10+)") |
| return True |
| else: |
| print(f" ❌ Python {version} (requirement: 3.10+)") |
| return False |
|
|
| def check_virtual_env() -> bool: |
| """Check if in virtual environment""" |
| print("\n🔧 Virtual Environment:") |
| if hasattr(sys, 'real_prefix') or (hasattr(sys, 'base_prefix') and sys.base_prefix != sys.prefix): |
| print(f" ✅ Virtual environment detected") |
| return True |
| else: |
| print(f" ⚠️ Not in virtual environment (recommended for production)") |
| return False |
|
|
| def check_package(package_name: str, description: str = "") -> bool: |
| """Check if a package is installed""" |
| try: |
| __import__(package_name) |
| desc = f" - {description}" if description else "" |
| print(f" ✅ {package_name}{desc}") |
| return True |
| except ImportError: |
| desc = f" - {description}" if description else "" |
| print(f" ❌ {package_name}{desc} - NOT INSTALLED") |
| return False |
|
|
| def check_core_packages() -> bool: |
| """Check core dependencies""" |
| print("\n📦 Core Dependencies:") |
| core_packages = [ |
| ("fastapi", "FastAPI web framework"), |
| ("uvicorn", "ASGI server"), |
| ("pydantic", "Data validation"), |
| ("numpy", "Numerical computing"), |
| ("pandas", "Data processing"), |
| ("requests", "HTTP client"), |
| ("torch", "PyTorch deep learning"), |
| ] |
| |
| all_installed = True |
| for package, desc in core_packages: |
| if not check_package(package, desc): |
| all_installed = False |
| |
| return all_installed |
|
|
| def check_optional_packages() -> bool: |
| """Check optional but recommended packages""" |
| print("\n⭐ Optional Packages (recommended):") |
| optional_packages = [ |
| ("DeepPurpose", "AI prediction model"), |
| ("tdc", "Therapeutic Data Commons"), |
| ] |
| |
| all_installed = True |
| for package, desc in optional_packages: |
| result = check_package(package, desc) |
| if not result: |
| print(f" ℹ️ To install: pip install git+https://github.com/kexinhuang12345/{package}.git") |
| all_installed = False |
| |
| return all_installed |
|
|
| def check_gpu() -> bool: |
| """Check GPU availability""" |
| print("\n🎮 GPU Support:") |
| try: |
| import torch |
| if torch.cuda.is_available(): |
| print(f" ✅ GPU detected: {torch.cuda.get_device_name(0)}") |
| print(f" CUDA Version: {torch.version.cuda}") |
| print(f" Device Count: {torch.cuda.device_count()}") |
| return True |
| else: |
| print(f" ℹ️ No GPU detected - using CPU mode") |
| print(f" (System will still work, but predictions will be slower)") |
| return False |
| except ImportError: |
| print(f" ❌ PyTorch not installed") |
| return False |
|
|
| def check_project_structure() -> bool: |
| """Check project file structure""" |
| print("\n📂 Project Structure:") |
| |
| required_files = [ |
| ("app/main.py", "FastAPI application"), |
| ("app/config.py", "Configuration"), |
| ("app/models.py", "Data models"), |
| ("app/local_tdc.py", "Local drug database"), |
| ("app/pipelines/__init__.py", "Pipeline module"), |
| ("app/pipelines/disease_targets.py", "Disease targets"), |
| ("app/pipelines/protein_sequences.py", "Protein sequences"), |
| ("app/pipelines/drug_library.py", "Drug library"), |
| ("app/pipelines/ai_screening.py", "AI screening"), |
| ("app/pipelines/result_processing.py", "Result processing"), |
| ("requirements.txt", "Dependencies"), |
| ("start.bat", "Windows startup"), |
| ("start.sh", "Linux/Mac startup"), |
| ("test_api.py", "Tests"), |
| ("PRODUCTION_GUIDE.md", "Documentation"), |
| ] |
| |
| all_present = True |
| for file_path, description in required_files: |
| if not check_file_exists(file_path, description): |
| all_present = False |
| |
| return all_present |
|
|
| def check_config_files() -> bool: |
| """Check configuration values""" |
| print("\n⚙️ Configuration:") |
| |
| try: |
| from app.config import settings |
| print(f" ✅ Config loaded successfully") |
| print(f" Device: {settings.DEVICE}") |
| print(f" Max Drugs: {settings.MAX_DRUGS_FOR_DEMO}") |
| print(f" Batch Size: {settings.BATCH_SIZE}") |
| print(f" API Version: {settings.API_VERSION}") |
| return True |
| except Exception as e: |
| print(f" ❌ Config loading failed: {str(e)}") |
| return False |
|
|
| def check_data_models() -> bool: |
| """Check data models""" |
| print("\n📋 Data Models:") |
| |
| try: |
| from app.models import ( |
| ScreeningRequest, |
| ScreeningResponse, |
| DrugCandidate, |
| DiseaseSearchRequest, |
| ) |
| print(f" ✅ All data models loaded") |
| return True |
| except Exception as e: |
| print(f" ❌ Data models failed: {str(e)}") |
| return False |
|
|
| def check_pipelines() -> bool: |
| """Check pipeline modules""" |
| print("\n🔄 Pipeline Modules:") |
| |
| try: |
| from app.pipelines import ( |
| DiseaseTargetPipeline, |
| ProteinSequencePipeline, |
| DrugLibraryPipeline, |
| AIScreeningPipeline, |
| ResultProcessingPipeline, |
| ) |
| print(f" ✅ All pipelines loaded") |
| return True |
| except Exception as e: |
| print(f" ❌ Pipelines failed: {str(e)}") |
| return False |
|
|
| def main(): |
| """Run all checks""" |
| print("\n" + "="*70) |
| print(" 🧬 DRUG REPURPOSING SYSTEM - VERIFICATION") |
| print("="*70) |
| |
| checks = [] |
| |
| |
| checks.append(("Python Version", check_python_version())) |
| checks.append(("Virtual Environment", check_virtual_env())) |
| checks.append(("Core Dependencies", check_core_packages())) |
| checks.append(("Optional Dependencies", check_optional_packages())) |
| checks.append(("GPU Support", check_gpu())) |
| checks.append(("Project Structure", check_project_structure())) |
| checks.append(("Configuration", check_config_files())) |
| checks.append(("Data Models", check_data_models())) |
| checks.append(("Pipeline Modules", check_pipelines())) |
| |
| |
| print("\n" + "="*70) |
| print(" 📊 VERIFICATION SUMMARY") |
| print("="*70) |
| |
| passed = sum(1 for _, result in checks if result) |
| total = len(checks) |
| |
| for check_name, result in checks: |
| status = "✅ PASS" if result else "❌ FAIL" |
| print(f"{check_name:.<50} {status}") |
| |
| print("\n" + "="*70) |
| |
| if passed == total: |
| print("✅ ALL CHECKS PASSED - SYSTEM READY") |
| print("="*70) |
| print("\nNext steps:") |
| print(" 1. Start the API: python start.bat (Windows) or ./start.sh (Linux/Mac)") |
| print(" 2. Visit: http://localhost:8000/docs") |
| print(" 3. Test the /api/v1/screen endpoint") |
| print("\nFor help: See PRODUCTION_GUIDE.md or QUICK_START.md") |
| return 0 |
| else: |
| failures = total - passed |
| print(f"⚠️ {failures} CHECK(S) FAILED") |
| print("="*70) |
| print("\nSee above for details and recommendations.") |
| print("Missing packages can be installed with requirements.txt:") |
| print(" pip install -r requirements.txt") |
| return 1 |
|
|
| if __name__ == "__main__": |
| sys.exit(main()) |
|
|
