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SETUP.md

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BrainRoute Database - Neon PostgreSQL Setup

This application now uses Neon PostgreSQL as the database backend instead of Google Sheets, with a secure API layer.

Architecture

  • Frontend: React app (port 3000)
  • Backend: Express API server (port 5000)
  • Database: Neon PostgreSQL (cloud-hosted)

Security Features

✅ Database credentials never exposed to frontend
✅ API layer with Helmet security headers
✅ CORS protection
✅ SSL connection to Neon database
✅ Environment variable isolation

Setup Instructions

1. Environment Configuration

The .env file contains:

  • DATABASE_URL: Neon PostgreSQL connection string (backend only)
  • REACT_APP_API_URL: API endpoint for frontend
  • PORT: Backend server port (default: 5000)
  • FRONTEND_URL: Frontend URL for CORS

Important: Only variables prefixed with REACT_APP_ are accessible to the frontend.

2. Database Setup

Run the schema creation script in your Neon dashboard SQL editor:

-- See server/schema.sql for the complete schema

Or connect via psql:

psql "postgresql://username:password@host/database?sslmode=require&channel_binding=require"

3. Install Dependencies

npm install

4. Running the Application

Development (Frontend + Backend together):

npm run dev

Production:

Terminal 1 - Backend:

npm run server

Terminal 2 - Frontend:

npm start

API Endpoints

GET /api/health

Health check endpoint

GET /api/molecules

Fetch all molecules from database

Response:

{
  "success": true,
  "data": [
    {
      "id": "MOL-001",
      "name": "Aspirin",
      "smiles": "CC(=O)OC1=CC=CC=C1C(=O)O",
      "weight": 180.158,
      "formula": "C9H8O4",
      "prediction": "BBB-",
      "confidence": 87.5,
      "mw": 180.158,
      "logp": 1.19,
      "hbd": 1,
      "hba": 4,
      "tpsa": 63.6,
      "rotatable_bonds": 3,
      "heavy_atoms": 13
    }
  ]
}

GET /api/molecules/:id

Fetch a single molecule by ID

Database Schema

CREATE TABLE molecules_and_predictions (
id INTEGER PRIMARY KEY GENERATED ALWAYS AS IDENTITY,
Smiles TEXT UNIQUE,
Name TEXT,
Prediction SMALLINT,
Confidence NUMERIC,
mw NUMERIC,
logp NUMERIC,
hbd INTEGER,
hba INTEGER,
tpsa INTEGER,
rotatable_bonds INTEGER,
heavy_atoms INTEGER,
formula TEXT

);

Deployment

Backend Deployment (e.g., Heroku, Railway, Render)

The backend must be hosted publicly to be accessible by the live frontend.

  1. Push code to GitHub.
  2. Create a new Web Service on Render.
  3. Connect your repository.
  4. Set Build Command: npm install
  5. Set Start Command: node server/index.js
  6. Add Environment Variables in Render Dashboard:
    • DATABASE_URL: Your Neon connection string
    • SERVER_PORT: 5000
  7. Deploy anf Copy your new backend URL (e.g., https://brainroutedb-api.onrender.com).

Frontend Deployment (e.g., Vercel, Netlify, GitHub Pages)

  1. Update your local .env file with the live backend URL: 
    REACT_APP_API_URL=https://your-backend-app.onrender.com
  2. Deploy the frontend: 
    npm run deploy
    This command builds the app and pushes it to the gh-pages branch.

Security Best Practices

  1. Never commit .env file - Use .env.example template instead
  2. Rotate credentials regularly - Update Neon password periodically
  3. Use HTTPS in production - Ensure SSL/TLS for API communication
  4. Implement rate limiting - Protect API from abuse
  5. Add authentication - Implement JWT or OAuth if needed

Troubleshooting

Connection Issues

  • Verify DATABASE_URL is correct
  • Check Neon database is running
  • Ensure SSL is enabled

CORS Errors

  • Check FRONTEND_URL in .env
  • Verify CORS settings in server/index.js

API Not Responding

  • Check backend server is running on correct port
  • Verify REACT_APP_API_URL matches backend URL

License

© 2026 BrainRoute-DB. All rights reserved.