O.M. Health AI — Medical RAG Assistant

A production-ready AI-powered medical assistant built on a full-stack RAG (Retrieval-Augmented Generation) architecture. The backend runs on Azure Container Apps, the frontend is deployed on Vercel. Designed for reliability, security, and a polished end-user experience.

🌐 Live Demo (Frontend): https://om-health-ai.vercel.app

⚙️ Backend API (Azure): https://rag-mcp-azure.redsand-f0795bb6.francecentral.azurecontainerapps.io

⚠️ Notice: The backend API is currently deployed using an Azure Free Tier allocation. If the live demo is unresponsive due to expired cloud credits, please check out the Demo Video or follow the Quick Start instructions below to run the architecture locally in seconds using Docker.

🎯 Project Overview

What it does:

• Answers medical questions in natural language using the MedQuAD dataset (16,000+ validated Q&A pairs from the NIH)

• Retrieves the most relevant medical context from a FAISS vector index using MMR search (Maximal Marginal Relevance)

• Synthesizes a clear, professional answer via Claude Haiku (Anthropic) through OpenRouter — entirely server-side

• Exposes a clean chat UI with dark mode, suggestion chips, and Markdown rendering

• Also exposes a MCP (Model Context Protocol) endpoint for agentic AI integrations

Architecture philosophy:

• Security by design: the LLM API key never reaches the browser — all synthesis happens in the backend

• Privacy by design: zero client-side storage of sensitive data, stateless request processing

• Lightweight: CPU-only, no GPU, no heavy vector database — optimized for cost-effective cloud deployment

• Production-ready: automated CI/CD, tested endpoints, verified MCP integration

Related MCP server: RAG-MCP

📊 Tech Stack

🏛️ Architecture

┌─────────────────────────────────────────────────────────────────┐
│                        USER BROWSER                             │
│              frontend/ (HTML + CSS + JS)                        │
│              Hosted on Vercel (static)                          │
└──────────────────────────┬──────────────────────────────────────┘
                           │  POST /chat  { query }
                           ▼
┌─────────────────────────────────────────────────────────────────┐
│              AZURE CONTAINER APPS (Backend)                     │
│                                                                 │
│  ┌─────────────────────────────────────────────────────────┐   │
│  │  FastAPI  app/main.py                                   │   │
│  │                                                         │   │
│  │  POST /chat ──► rag_engine.search() (MMR, k=3)         │   │
│  │                        │                               │   │
│  │                        ▼                               │   │
│  │              FAISS index (in-memory)                   │   │
│  │              MedQuAD Q&A embeddings                    │   │
│  │                        │                               │   │
│  │                        ▼                               │   │
│  │         httpx ──► OpenRouter API                       │   │
│  │                  Claude Haiku 4.5                      │   │
│  │                  (OPENROUTER_API_KEY — secret Azure)   │   │
│  │                        │                               │   │
│  │                        ▼                               │   │
│  │              { "answer": "..." }                       │   │
│  └─────────────────────────────────────────────────────────┘   │
│                                                                 │
│  Also exposes: /query (raw context), /reindex, /upload, /mcp   │
└─────────────────────────────────────────────────────────────────┘
                           │
                           ▼
              Azure Blob Storage
              (FAISS index files: index.faiss + index.pkl)

Key security boundary: the OPENROUTER_API_KEY is stored as an Azure Container Apps secret and injected at runtime. It is never sent to the browser, never committed to source, and never logged.

🏗️ Project Structure

rag-mcp-azure/
├── app/
│   ├── data/                    # PDF fallback for local dev
│   ├── main.py                  # FastAPI app: /chat, /query, /reindex, /upload, MCP mount
│   └── rag_engine.py            # RAG pipeline: MMR search, Blob/local ingestion, FAISS
├── frontend/
│   ├── index.html               # Full-page UI: navbar, hero, chat card, features, FAQ
│   ├── style.css                # Design system: CSS variables, dark mode, responsive
│   └── app.js                   # Chat logic: POST /chat, Markdown rendering, dark mode toggle
├── scripts/
│   ├── build_index_offline.py   # Build FAISS index from medquad.csv locally
│   ├── upload_index_to_blob.py  # Upload index files to Azure Blob Storage
│   └── deploy-aca.sh            # Manual Azure deployment script
├── tests/
│   ├── test_api.py              # REST endpoint tests (CI)
│   └── test_mcp_integration.py  # MCP client tests (manual, live server)
├── .github/workflows/deploy.yml # CI/CD pipeline
├── medquad.csv                  # Source dataset (NIH MedQuAD)
├── Dockerfile
├── requirements.txt
└── README.md

🧠 RAG Engine — Key Design Decisions

Dataset: MedQuAD

The knowledge base is built from the MedQuAD (Medical Question Answering Dataset) published by the NIH. It contains over 16,000 question-answer pairs covering diseases, symptoms, treatments, and diagnostics across dozens of medical specialties.

Unlike a pure document ingestion pipeline, the FAISS index here embeds both the question and the answer text, giving the retrieval step richer semantic context to match against user queries.

MMR Search (Maximal Marginal Relevance)

The search() method in rag_engine.py uses MMR instead of plain cosine similarity:

results = self.vector_store.max_marginal_relevance_search(query, k=3, fetch_k=20)

• fetch_k=20: retrieve the top 20 candidates by similarity

• k=3: from those 20, select the 3 most diverse results

This prevents the top-3 results from being near-duplicate chunks (a common failure mode when multiple similar Q&A pairs exist in the dataset), and ensures the LLM receives varied, complementary context.

Pre-built Index Loading

In production, the FAISS index is pre-built offline from medquad.csv and stored in Azure Blob Storage (INDEX_CONTAINER_NAME). On startup, the engine downloads index.faiss + index.pkl directly — no re-embedding at boot time, which keeps cold start under 30 seconds on 0.5 CPU.

🔐 Security Architecture

API Key — Server-Side Only

The most important security change from the initial prototype: the OpenRouter API key never leaves the server.

The key is injected at deploy time:

az containerapp secret set --name rag-mcp-azure --resource-group rg-rag-mcp-azure `
  --secrets "openrouter-api-key=sk-or-v1-..."

az containerapp update --name rag-mcp-azure --resource-group rg-rag-mcp-azure `
  --set-env-vars "OPENROUTER_API_KEY=secretref:openrouter-api-key"

Full Security Checklist

• ✅ OPENROUTER_API_KEY — Azure Container Apps secret, never in source or env plaintext

• ✅ BLOB_CONNECTION_STRING — Azure Container Apps secret, re-applied on every CI deploy

• ✅ GitHub Secrets — Azure, ACR, and Blob credentials stored as Actions secrets

• ✅ Service Principal — deployment uses a scoped Azure AD SP, not the subscription owner

• ✅ Pydantic validation — all request bodies validated before processing

• ✅ MCP DNS rebinding protection — TransportSecuritySettings scoped to known hosts

• ✅ CORS — open for public demo (MedQuAD is public data); restrict for production use

• ✅ Key rotation practiced — Blob Storage key was rotated after accidental log exposure during early debugging

🖥️ Frontend — UI/UX

The frontend is a static single-page application (HTML + CSS + JS, no framework) deployed on Vercel.

Features

• Full-page layout — navbar, hero section (2-column: pitch + live chat), features grid, security section, FAQ

• Functional chat card — real-time POST to /chat, typing indicator, timestamped messages

• Markdown rendering — bot responses rendered with headers, bold, lists, blockquotes (custom lightweight parser, no library)

• Lucide Icons — SVG icon library replacing all native emojis for consistent cross-platform rendering

• Dark mode — toggled via a settings dropdown in the navbar, persisted in localStorage, applied via body[data-theme="dark"] CSS variable overrides with smooth transition

• Suggestion chips — pre-filled question shortcuts that disappear after first use

• Privacy by design — zero sessionStorage/localStorage usage for sensitive data; no API key ever stored client-side

Dark Mode Implementation

/* Light (default) */
:root {
    --bg-color: #fdfdfd;
    --text-main: #111827;
    --white: #ffffff;
    --bot-bg: #f3f4f6;
    /* ... */
}

/* Dark */
body[data-theme="dark"] {
    --bg-color: #111827;
    --text-main: #f3f4f6;
    --white: #1f2937;
    --bot-bg: #374151;
    /* ... */
}

All colors in style.css use CSS variables — no hardcoded hex values for interface elements — ensuring the dark mode applies globally and consistently.

📡 API Endpoints

POST /chat ⭐ Primary endpoint

Full RAG + LLM pipeline. Retrieves context from FAISS, calls Claude Haiku via OpenRouter server-side, returns a synthesized medical answer.

Request:

{ "query": "What are the symptoms of hypertension?" }

Response:

{ "answer": "Hypertension is often called the 'silent killer' because..." }

POST /query

Returns raw FAISS context chunks without LLM synthesis. Used internally and for debugging/testing.

Response:

{
  "query": "...",
  "context_extrait": "Extrait 1:\n...\n\nExtrait 2:\n..."
}

GET /health

{ "status": "ok" }

POST /reindex

Rebuilds the FAISS index from Blob Storage (or local files). Call after uploading new documents.

POST /upload

Uploads a PDF and adds it to the in-memory index (ephemeral — lost on restart or /reindex).

MCP /mcp-server/mcp

See MCP Protocol Integration below.

🔌 MCP Protocol Integration

Model Context Protocol (MCP) is an open standard for connecting AI agents to external tools. O.M. Health AI exposes a search_documents tool over Streamable HTTP, allowing any MCP-compatible agent (Claude Desktop, custom agents) to query the medical knowledge base directly.

Endpoint

Exposed Tool

Python client example (verified end-to-end)

import asyncio
from mcp.client.streamable_http import streamable_http_client
from mcp import ClientSession

async def main():
    url = "https://rag-mcp-azure.redsand-f0795bb6.francecentral.azurecontainerapps.io/mcp-server/mcp"
    async with streamable_http_client(url) as (read, write):
        async with ClientSession(read, write) as session:
            await session.initialize()
            result = await session.call_tool("search_documents", {"query": "symptoms of diabetes"})
            for content in result.content:
                if hasattr(content, "text"):
                    print(content.text)

asyncio.run(main())

Claude Desktop config

{
  "mcpServers": {
    "om-health-ai": {
      "url": "https://rag-mcp-azure.redsand-f0795bb6.francecentral.azurecontainerapps.io/mcp-server/mcp"
    }
  }
}

DNS Rebinding Protection

The MCP SDK restricts the Host header to localhost by default. TransportSecuritySettings in app/main.py explicitly allow-lists the production Azure hostname — without this, requests return 421 Misdirected Request.

🚀 Quick Start

Local Development

git clone https://github.com/oumniya03/rag-mcp-azure.git
cd rag-mcp-azure
python -m venv .venv
.venv\Scripts\Activate        # Windows
# source .venv/bin/activate   # macOS/Linux
pip install -r requirements.txt

Set environment variables (create a .env or export directly):

# Required for LLM synthesis
export OPENROUTER_API_KEY=sk-or-v1-...

# Optional: load FAISS index from Blob Storage instead of local medquad_index/
export INDEX_CONTAINER_NAME=medquad-index
export BLOB_CONTAINER_URL=<your-connection-string>

Run the backend:

python -m uvicorn app.main:app --host 0.0.0.0 --port 8000

Open frontend/index.html directly in a browser, or serve it locally:

cd frontend && python -m http.server 3000

Test the chat endpoint:

curl -X POST http://localhost:8000/chat \
  -H "Content-Type: application/json" \
  -d '{"query": "What are the symptoms of high blood pressure?"}'

🐳 Docker

# Build
docker build -t om-health-ai:latest .

# Run (pass the API key at runtime)
docker run --rm -p 8000:8000 \
  -e OPENROUTER_API_KEY=sk-or-v1-... \
  om-health-ai:latest

Image profile: python:3.12-slim base, CPU-only torch wheel, ~500 MB compressed on ACR.

☁️ Azure Deployment

Production Resources

Required GitHub Secrets

CI/CD Pipeline (.github/workflows/deploy.yml)

On every push to main:

1. Install dependencies

2. Run REST tests (pytest tests/ -v -m "not integration")

3. Login to Azure (service principal)

4. Build & push Docker image to ACR

5. Idempotent deploy: az containerapp update if exists, az containerapp create otherwise

6. Re-apply both secrets (blob-connection-string, openrouter-api-key) on every deploy

git push origin main  # triggers the full pipeline

Blob Storage — FAISS Index

The pre-built FAISS index is stored in Blob Storage and loaded at startup (no re-embedding on cold start):

# Upload index files
az storage blob upload-batch `
  --destination medquad-index `
  --source medquad_index/ `
  --account-name ragmcpstorage26 `
  --auth-mode key

# Set the index container env var
az containerapp update --name rag-mcp-azure --resource-group rg-rag-mcp-azure `
  --set-env-vars "INDEX_CONTAINER_NAME=medquad-index"

🧪 Testing

Automated (CI)

pytest tests/ -v -m "not integration"

Covers /health, /query, /reindex, /upload — runs on every push to main.

MCP Integration (manual, requires live server)

pytest tests/test_mcp_integration.py -v

# Against local instance:
$env:MCP_TEST_URL="http://localhost:8000/mcp-server/mcp"
pytest tests/test_mcp_integration.py -v

Quick production smoke test

# Health
Invoke-RestMethod -Uri "https://rag-mcp-azure.redsand-f0795bb6.francecentral.azurecontainerapps.io/health"

# Chat
$body = @{query="What is hypertension?"} | ConvertTo-Json
Invoke-RestMethod -Method Post `
  -Uri "https://rag-mcp-azure.redsand-f0795bb6.francecentral.azurecontainerapps.io/chat" `
  -ContentType "application/json" -Body $body

🔧 Configuration Reference

Local tweaks (app/rag_engine.py):

• chunk_size / chunk_overlap — text splitter parameters (default: 500 / 50)

• k / fetch_k — MMR search parameters (default: k=3, fetch_k=20)

• Embedding model — HuggingFaceEmbeddings(model_name=...)

⚙️ Troubleshooting

📈 Performance Profile

🛣️ Roadmap

• MedQuAD medical knowledge base

• MMR search for diverse, non-redundant context

• Server-side LLM synthesis (/chat endpoint)

• API key security — backend-only, Azure secret

• Full-page frontend with dark mode and Lucide icons

• MCP Streamable HTTP endpoint (verified end-to-end)

• Pre-built FAISS index loaded from Blob Storage

• Automated CI/CD with GitHub Actions

• OIDC federated auth for CI/CD (replace ACR admin credentials)

• Rate limiting on /chat

• API key authentication for /chat and /upload

• Azure Application Insights (latency, error rate, usage)

• Persist /upload documents to Blob Storage

• Multi-language support

📝 License

Provided as-is for educational and portfolio purposes.

👤 Author

Oumniya Moutaouakil — AI Engineer, LLM / Agentic AI & RAG Systems.

Project status: ✅ Production-ready — backend on Azure Container Apps, frontend on Vercel, REST + MCP endpoints verified end-to-end.