run.py

#!/usr/bin/env python3
"""
Cancer@Home v2 - Main Entry Point
Quick start script for the entire application
"""

import sys
import time
import subprocess
import webbrowser
from pathlib import Path
from rich.console import Console
from rich.panel import Panel
from rich.progress import Progress, SpinnerColumn, TextColumn
import yaml

console = Console()

def load_config():
    """Load configuration"""
    with open('config.yml', 'r') as f:
        return yaml.safe_load(f)

def check_docker():
    """Check if Docker is running"""
    try:
        subprocess.run(['docker', 'ps'], capture_output=True, check=True)
        return True
    except:
        return False

def setup_directories():
    """Create necessary directories"""
    dirs = [
        'data/gdc',
        'data/boinc',
        'data/processed/fastq',
        'data/processed/blast',
        'data/processed/variants',
        'data/cache',
        'logs'
    ]
    for dir_path in dirs:
        Path(dir_path).mkdir(parents=True, exist_ok=True)

def start_neo4j():
    """Start Neo4j container"""
    console.print("[cyan]Starting Neo4j database...[/cyan]")
    subprocess.run(['docker-compose', 'up', '-d'], check=True)
    
    # Wait for Neo4j to be ready
    console.print("[yellow]Waiting for Neo4j to be ready...[/yellow]")
    time.sleep(10)

def initialize_database():
    """Initialize Neo4j database schema"""
    from backend.neo4j.db_manager import DatabaseManager
    
    console.print("[cyan]Initializing database schema...[/cyan]")
    db = DatabaseManager()
    db.initialize_schema()
    console.print("[green]✓ Database initialized[/green]")

def start_backend():
    """Start FastAPI backend"""
    console.print("[cyan]Starting backend server...[/cyan]")
    import uvicorn
    from backend.api.main import app
    
    config = load_config()
    
    # Run in background
    import threading
    def run_server():
        uvicorn.run(
            app,
            host=config['app']['host'],
            port=config['app']['port'],
            log_level="info"
        )
    
    thread = threading.Thread(target=run_server, daemon=True)
    thread.start()
    time.sleep(3)

def open_browser():
    """Open browser to application"""
    config = load_config()
    url = f"http://{config['app']['host']}:{config['app']['port']}"
    console.print(f"[green]✓ Opening browser at {url}[/green]")
    time.sleep(2)
    webbrowser.open(url)

def main():
    """Main entry point"""
    console.clear()
    
    # Display banner
    banner = """
    ╔═══════════════════════════════════════════╗
    ║         Cancer@Home v2.0                  ║
    ║  Distributed Cancer Genomics Research     ║
    ╚═══════════════════════════════════════════╝
    """
    console.print(Panel(banner, style="bold blue"))
    
    try:
        with Progress(
            SpinnerColumn(),
            TextColumn("[progress.description]{task.description}"),
            console=console
        ) as progress:
            
            # Setup
            task = progress.add_task("[cyan]Setting up directories...", total=None)
            setup_directories()
            progress.update(task, completed=True)
            
            # Check Docker
            task = progress.add_task("[cyan]Checking Docker...", total=None)
            if not check_docker():
                console.print("[red]✗ Docker is not running. Please start Docker Desktop.[/red]")
                sys.exit(1)
            progress.update(task, completed=True)
            
            # Start Neo4j
            task = progress.add_task("[cyan]Starting Neo4j...", total=None)
            start_neo4j()
            progress.update(task, completed=True)
            
            # Initialize database
            task = progress.add_task("[cyan]Initializing database...", total=None)
            initialize_database()
            progress.update(task, completed=True)
            
            # Start backend
            task = progress.add_task("[cyan]Starting backend server...", total=None)
            start_backend()
            progress.update(task, completed=True)
        
        console.print("\n[bold green]✓ Cancer@Home is running![/bold green]\n")
        
        config = load_config()
        console.print(f"[cyan]→ Application:[/cyan] http://{config['app']['host']}:{config['app']['port']}")
        console.print(f"[cyan]→ Neo4j Browser:[/cyan] http://localhost:7474")
        console.print(f"[cyan]→ API Docs:[/cyan] http://{config['app']['host']}:{config['app']['port']}/docs")
        console.print(f"[cyan]→ GraphQL:[/cyan] http://{config['app']['host']}:{config['app']['port']}/graphql\n")
        
        console.print("[yellow]Press Ctrl+C to stop the server[/yellow]\n")
        
        # Open browser
        open_browser()
        
        # Keep running
        while True:
            time.sleep(1)
            
    except KeyboardInterrupt:
        console.print("\n[yellow]Shutting down...[/yellow]")
        subprocess.run(['docker-compose', 'down'])
        console.print("[green]✓ Goodbye![/green]")
        sys.exit(0)
    except Exception as e:
        console.print(f"[red]✗ Error: {e}[/red]")
        sys.exit(1)

if __name__ == "__main__":
    main()