BioAnalyzer

#!/usr/bin/env python3
"""
BioAnalyzer Global Command - User-Friendly Entry Point

This script provides a global command interface for BioAnalyzer.
It can be installed system-wide or used as a standalone command.

Usage:
    BioAnalyzer help                    # Show help
    BioAnalyzer build                   # Build containers
    BioAnalyzer start                   # Start application
    BioAnalyzer analyze <pmid>          # Analyze single paper
    BioAnalyzer analyze <pmid1,pmid2>   # Analyze multiple papers
    BioAnalyzer fields                  # Show field information
    BioAnalyzer status                  # Check status
    BioAnalyzer stop                    # Stop application
"""

import sys
import os
from pathlib import Path

# Find the BioAnalyzer backend directory
def find_bioanalyzer_backend():
    """Find the BioAnalyzer backend directory."""
    # Try different possible locations
    possible_paths = [
        Path(__file__).parent,  # Current directory
        Path(__file__).parent / "BioAnalyzer-Backend",  # Adjacent directory
        Path.home() / "Desktop" / "BioAnalyzer-Backend",  # Desktop
        Path("/opt/bioanalyzer"),  # System installation
        Path("/usr/local/bin/bioanalyzer"),  # Local installation
    ]
    
    for path in possible_paths:
        cli_path = path / "cli.py"
        if cli_path.exists():
            return path
    
    return None

def main():
    """Main entry point for BioAnalyzer command."""
    # Find the backend directory
    backend_dir = find_bioanalyzer_backend()
    
    if not backend_dir:
        print("""
❌ Error: BioAnalyzer backend not found!

Please ensure BioAnalyzer-Backend is installed and accessible.

Possible solutions:
1. Run from the BioAnalyzer-Backend directory
2. Install BioAnalyzer system-wide: ./install.sh
3. Set BIOANALYZER_PATH environment variable

For help, visit: https://github.com/your-repo/bioanalyzer-backend
        """)
        sys.exit(1)
    
    # Add the backend directory to Python path
    sys.path.insert(0, str(backend_dir))
    
    # Change to the backend directory
    os.chdir(backend_dir)

    # Load .env from the backend directory if present so CLI and docker-run
    # receive the same environment variables developers place in .env.
    try:
        env_path = backend_dir / '.env'
        if env_path.exists():
            try:
                from dotenv import load_dotenv
                load_dotenv(str(env_path))
                print(f"Loaded environment variables from {env_path}")
            except Exception:
                # Fallback: parse the .env file manually if python-dotenv is not installed
                try:
                    with open(env_path, 'r', encoding='utf-8') as f:
                        for raw in f:
                            line = raw.strip()
                            if not line or line.startswith('#'):
                                continue
                            if '=' not in line:
                                continue
                            key, val = line.split('=', 1)
                            key = key.strip()
                            val = val.strip().strip('"').strip("'")
                            # Only set the env var if not already present in the environment
                            if key and val and os.environ.get(key) is None:
                                os.environ[key] = val
                    print(f"Loaded environment variables from {env_path} (fallback parser)")
                except Exception:
                    pass
    except Exception:
        pass
    
    # Import and run the CLI
    try:
        from cli import main as cli_main
        cli_main()
    except ImportError as e:
        print(f"""
❌ Error importing BioAnalyzer CLI: {e}

Please ensure all dependencies are installed:
   pip install -r config/requirements.txt

Or use Docker:
   ./docker-setup.sh
        """)
        sys.exit(1)
    except Exception as e:
        print(f"❌ Error running BioAnalyzer: {e}")
        sys.exit(1)

if __name__ == "__main__":
    main()