INSTALLATION.md

BioChat Installation Guide

This guide will help you install and set up BioChat for various use cases.

Prerequisites

• Python 3.8 or higher
• pip (Python package installer)
• API keys for:
  • OpenAI (for GPT-4 access)
  • NCBI E-utilities
  • BioGRID (optional)

Basic Installation

Install from PyPI

pip install biochat

Install from Source

git clone https://github.com/yourusername/biochat.git
cd biochat
pip install -e .

Set up Environment Variables

Create a .env file in your project root:

OPENAI_API_KEY=your_openai_api_key
NCBI_API_KEY=your_ncbi_api_key
CONTACT_EMAIL=your_email@example.com
BIOGRID_ACCESS_KEY=your_biogrid_api_key  # Optional

Integration with FastAPI

Installation

pip install biochat fastapi uvicorn

Quick Start

Create a file named main.py:

from fastapi import FastAPI, HTTPException, Depends
from pydantic import BaseModel
from typing import Dict
import os
from dotenv import load_dotenv

from biochat import BioChatOrchestrator

# Load environment variables
load_dotenv()

# FastAPI app
app = FastAPI(title="BioChat API")

# Pydantic model
class Query(BaseModel):
    text: str

# Dependency
def get_orchestrator():
    return BioChatOrchestrator(
        openai_api_key=os.getenv("OPENAI_API_KEY"),
        ncbi_api_key=os.getenv("NCBI_API_KEY"),
        biogrid_access_key=os.getenv("BIOGRID_ACCESS_KEY"),
        tool_name="BioChat_FastAPI",
        email=os.getenv("CONTACT_EMAIL")
    )

@app.post("/query")
async def process_query(
    query: Query,
    orchestrator: BioChatOrchestrator = Depends(get_orchestrator)
) -> Dict:
    try:
        response = await orchestrator.process_query(query.text)
        return {"response": response}
    except Exception as e:
        raise HTTPException(status_code=500, detail=str(e))

if __name__ == "__main__":
    import uvicorn
    uvicorn.run(app, host="0.0.0.0", port=8000)

Run the server:

python main.py

Or with uvicorn directly:

uvicorn main:app --reload

Integration with Django

Installation

pip install biochat django

1. Create a Django app

python manage.py startapp biochat_api

2. Add to INSTALLED_APPS

In your settings.py:

INSTALLED_APPS = [
    # ... existing apps
    'biochat_api',
]

# BioChat settings
OPENAI_API_KEY = os.environ.get('OPENAI_API_KEY')
NCBI_API_KEY = os.environ.get('NCBI_API_KEY')
CONTACT_EMAIL = os.environ.get('CONTACT_EMAIL')
BIOGRID_ACCESS_KEY = os.environ.get('BIOGRID_ACCESS_KEY')

3. Create models and views

Create biochat_api/models.py, biochat_api/views.py, and other files as shown in the examples.

4. Add URLs to your project

In your project's urls.py:

from django.urls import path, include

urlpatterns = [
    # ... existing patterns
    path('api/biochat/', include('biochat_api.urls')),
]

5. Run migrations

python manage.py makemigrations biochat_api
python manage.py migrate

Troubleshooting

API Keys

If you encounter authentication errors, check that your API keys are correctly set in environment variables or passed to the BioChatOrchestrator constructor.

Dependency Issues

If you encounter dependency conflicts, try creating a virtual environment:

python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate
pip install biochat

CORS Issues (for web applications)

If you're building a web application and encounter CORS issues, ensure you've added CORS middleware to your FastAPI or Django application.

For FastAPI, add:

from fastapi.middleware.cors import CORSMiddleware

app.add_middleware(
    CORSMiddleware,
    allow_origins=["*"],  # Modify this in production
    allow_credentials=True,
    allow_methods=["*"],
    allow_headers=["*"],
)

For Django, install django-cors-headers:

pip install django-cors-headers

And add to your settings.py:

INSTALLED_APPS = [
    # ... existing apps
    'corsheaders',
]

MIDDLEWARE = [
    'corsheaders.middleware.CorsMiddleware',
    # ... other middleware
]

CORS_ALLOW_ALL_ORIGINS = True  # Modify this in production