template.py

import os
import shutil
from pathlib import Path

def create_directory_structure():
    """Create the initial directory structure for the Research Co-pilot project."""
    
    # Define the base directory structure
    directories = [
        "research_copilot/api",
        "research_copilot/api/routes",
        "research_copilot/core",
        "research_copilot/core/pdf_processing",
        "research_copilot/core/embedding",
        "research_copilot/core/citation",
        "research_copilot/core/rag",
        "research_copilot/database",
        "research_copilot/database/vector_store",
        "research_copilot/database/graph_store",
        "research_copilot/tasks",
        "research_copilot/utils",
        "research_copilot/config",
        "tests/unit",
        "tests/integration",
        "frontend/src",
        "frontend/public",
        "deployment",
        "docs",
    ]

    # Create directories
    for directory in directories:
        Path(directory).mkdir(parents=True, exist_ok=True)

def create_initial_files():
    """Create initial template files with basic structure."""
    
    files = {
        "research_copilot/__init__.py": """
# Research Co-pilot System
__version__ = '0.1.0'
""",
        "research_copilot/api/__init__.py": "",
        "research_copilot/api/app.py": """
from flask import Flask
from flask_cors import CORS

def create_app(config_object=None):
    app = Flask(__name__)
    CORS(app)
    
    if config_object:
        app.config.from_object(config_object)
    
    # Register blueprints here
    
    return app
""",
        "research_copilot/core/pdf_processing/extractor.py": """
from typing import Dict, Any

class PDFExtractor:
    def __init__(self):
        self.supported_formats = ['pdf']
    
    def extract_text(self, file_path: str) -> Dict[str, Any]:
        '''Extract text and metadata from PDF'''
        raise NotImplementedError
    
    def extract_figures(self, file_path: str) -> Dict[str, Any]:
        '''Extract figures and tables from PDF'''
        raise NotImplementedError
""",
        "research_copilot/core/rag/engine.py": """
from typing import List, Dict, Any

class RAGEngine:
    def __init__(self, vector_store, citation_store):
        self.vector_store = vector_store
        self.citation_store = citation_store
    
    async def process_query(self, query: str) -> Dict[str, Any]:
        '''Process user query and return enhanced response'''
        raise NotImplementedError
""",
        "research_copilot/config/settings.py": """
import os
from dotenv import load_dotenv

load_dotenv()

class Config:
    # Flask settings
    SECRET_KEY = os.getenv('SECRET_KEY', 'your-secret-key')
    
    # Database settings
    POSTGRES_URI = os.getenv('POSTGRES_URI', 'postgresql://localhost:5432/research_copilot')
    NEO4J_URI = os.getenv('NEO4J_URI', 'bolt://localhost:7687')
    QDRANT_HOST = os.getenv('QDRANT_HOST', 'localhost')
    QDRANT_PORT = os.getenv('QDRANT_PORT', 6333)
    
    # OpenAI settings
    OPENAI_API_KEY = os.getenv('OPENAI_API_KEY')
    
    # Redis settings
    REDIS_URL = os.getenv('REDIS_URL', 'redis://localhost:6379/0')
    
    # Celery settings
    CELERY_BROKER_URL = REDIS_URL
    CELERY_RESULT_BACKEND = REDIS_URL
""",
        ".env.example": """
SECRET_KEY=your-secret-key
POSTGRES_URI=postgresql://localhost:5432/research_copilot
NEO4J_URI=bolt://localhost:7687
QDRANT_HOST=localhost
QDRANT_PORT=6333
OPENAI_API_KEY=your-openai-api-key
REDIS_URL=redis://localhost:6379/0
""",
        "README.md": """
# Research Paper Co-pilot System

A sophisticated research assistance system that combines RAG (Retrieval-Augmented Generation) with citation network analysis to enhance academic research workflows.

## Features

- PDF processing and text extraction
- Citation network analysis
- RAG-powered query understanding
- Interactive visualizations
- Collaborative workspace

## Installation

```bash
pip install -e '.[dev]'
```

## Development Setup

1. Clone the repository
2. Create and activate a virtual environment
3. Install dependencies
4. Copy .env.example to .env and configure
5. Run the development server

## Usage

[Documentation in progress]
""",
        "docker-compose.yml": """
version: '3.8'

services:
  web:
    build: .
    ports:
      - "5000:5000"
    environment:
      - FLASK_ENV=development
    depends_on:
      - postgres
      - redis
      - neo4j
      - qdrant

  postgres:
    image: postgres:latest
    environment:
      POSTGRES_DB: research_copilot
      POSTGRES_USER: postgres
      POSTGRES_PASSWORD: postgres
    ports:
      - "5432:5432"

  redis:
    image: redis:latest
    ports:
      - "6379:6379"

  neo4j:
    image: neo4j:latest
    environment:
      NEO4J_AUTH: neo4j/password
    ports:
      - "7474:7474"
      - "7687:7687"

  qdrant:
    image: qdrant/qdrant:latest
    ports:
      - "6333:6333"
""",
        "Dockerfile": """
FROM python:3.11-slim

WORKDIR /app

COPY requirements.txt .
RUN pip install --no-cache-dir -r requirements.txt

COPY . .

CMD ["gunicorn", "--bind", "0.0.0.0:5000", "research_copilot.api.app:create_app()"]
"""
    }

    for file_path, content in files.items():
        with open(file_path, 'w') as f:
            f.write(content.strip())

def main():
    """Main function to generate the project template."""
    print("Generating Research Co-pilot project structure...")
    
    create_directory_structure()
    create_initial_files()
    
    print("\nProject structure created successfully!")
    print("\nNext steps:")
    print("1. Create and activate a virtual environment")
    print("2. Run: pip install -e '.[dev]'")
    print("3. Copy .env.example to .env and configure your environment variables")
    print("4. Start developing!")

if __name__ == "__main__":
    main()