mcp-docqa-server

An MCP server that gives any AI client semantic search over a document corpus — the retrieval half of a RAG pipeline, shipped as reusable infrastructure. Point Claude Desktop (or any MCP host) at it and the model can search, read, and cite your documents autonomously; generation stays in the client, retrieval lives here.

"What does the corpus say about the hour-1 sepsis bundle?"
        │
        ▼                      MCP (stdio / HTTP)
┌──────────────┐   search_documents("hour-1 sepsis bundle", k=5)   ┌───────────────┐
│  Claude /    │ ────────────────────────────────────────────────► │ docqa server  │
│  any MCP     │ ◄──────────────────────────────────────────────── │ embed → ANN   │
│  host        │     top-k chunks + titles, urls, scores           │ search → rank │
└──────────────┘                                                   └──────┬────────┘
                                                                          │
                                                          SQLite (embedded, exact)
                                                          or Postgres + pgvector (HNSW)

Why this exists

Most RAG demos hard-wire retrieval into one chatbot. Exposing retrieval through MCP inverts that: index once, query from anywhere — Claude Desktop, an IDE agent, a CI job, your own client. The server is deliberately boring infrastructure: typed tools, two interchangeable storage backends, pluggable embeddings, an eval harness, and loud failures where silent ones usually live (see Design decisions).

Features

• Four typed MCP tools — search_documents, fetch_document, corpus_stats, ping — with docstrings written for the calling model, because tool descriptions are the interface.
• Two vector stores, one contract: embedded SQLite (zero infrastructure, exact brute-force cosine) and Postgres + pgvector (HNSW index, production posture). Both pass the same behavioral test battery.
• Pluggable embeddings: OpenAI text-embedding-3-small, or a deterministic keyless hashing embedder so a fresh clone works with no API key, no database, no network.
• Idempotent ingestion: per-document content hashes mean re-runs skip unchanged docs — nothing gets re-embedded (or re-billed) by accident.
• Corpus fetcher for PubMed abstracts via the keyless NCBI E-utilities API (rate-limit aware).
• Retrieval eval harness: recall@k and MRR against a labeled testset, usable as a CI quality gate (docqa-eval --min-recall5 0.9).
• stdio + Streamable HTTP transports, Dockerfile included.
• CI that means it: lint, unit tests, a real MCP client round-trip over stdio, and an integration job against a live pgvector service container that ends by gating on retrieval recall.

Quickstart — 60 seconds, no API key

git clone https://github.com/saivarun161/mcp-docqa-server.git
cd mcp-docqa-server
python3 -m venv .venv && source .venv/bin/activate
pip install -e ".[dev]"

docqa-ingest index --sample   # bundle of 12 healthcare docs -> SQLite index
docqa-eval                    # recall@1/3/5 + MRR against the bundled testset

You now have a working index at data/index.db. Talk to it over real MCP with the Inspector:

npx @modelcontextprotocol/inspector .venv/bin/docqa-server

Wire it into Claude Desktop

1. Open ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows).
2. Add the block from claude_desktop_config.example.json with absolute paths — hosts launch servers from their own working directory, so relative paths break.
3. Fully restart Claude Desktop and ask: "Search the docqa corpus: what counts as stage 2 hypertension?"

The model will call search_documents, read the chunks, and answer with sources.

A real corpus

Index a few hundred PubMed abstracts on any topic (keyless, public data):

docqa-ingest fetch --query "semaglutide cardiovascular outcomes" --max-docs 200
docqa-ingest index --corpus data/corpus.jsonl
docqa-ingest stats

Any JSONL with id, title, url, text fields works — swap PubMed for arXiv, EDGAR filings, or your own notes.

Production posture

Semantic embeddings — put an OpenAI key in .env (see .env.example) and re-index; DOCQA_EMBEDDINGS=auto picks it up:

pip install -e ".[openai]"
docqa-ingest index --corpus data/corpus.jsonl --force

Postgres + pgvector — vectors move into an HNSW-indexed table; search runs inside the database:

docker compose up -d        # pgvector/pgvector:pg16 with the extension enabled
export DOCQA_STORE=pgvector DATABASE_URL=postgresql://docqa:docqa@localhost:5432/docqa
pip install -e ".[pg]"
docqa-ingest index --sample

HTTP transport — for network-reachable deployments instead of stdio:

docqa-server --transport http --host 0.0.0.0 --port 8000
# or containerized:
docker build -t mcp-docqa-server . && docker run -p 8000:8000 mcp-docqa-server

MCP tools

Tool	Arguments	Returns
search_documents	query, k=5	top-k chunks with doc_id, title, url, text, score
fetch_document	doc_id	the full source document
corpus_stats	—	doc/chunk counts, backend, embedder that built the index
ping	—	"pong" (connectivity check)

Retrieval quality

docqa-eval retrieves for every testset question and reports where the expected document ranked:

Retrieval eval — 12 questions, k=5
store=sqlite  embedder=hash-v1-512

  [rank 1] What blood pressure reading counts as stage 2 hypertension?  (expects sample-001)
  ...
recall@1=1.00  recall@3=1.00  recall@5=1.00  MRR=1.00

The bundled corpus is small and topically distinct, so even the lexical fallback embedder scores perfectly — that run proves the plumbing. The interesting experiments start when you index a few hundred PubMed abstracts and compare hash vs openai embeddings on your own testset; CI runs the eval against a live pgvector container and fails the build if recall@5 drops below 0.9.

Design decisions

• Embedder identity is persisted and enforced. Vectors from different embedders live in unrelated spaces; querying an OpenAI-built index with hash vectors doesn't error mathematically — it just returns garbage. The store records which embedder built it and the retriever refuses a mismatch with an actionable message. Silent failure → loud failure.
• Brute force is a feature at SQLite scale. Exact cosine over a few thousand chunks is milliseconds with NumPy and has zero recall loss; ANN indexes buy speed at scale, not correctness. The pgvector backend adds HNSW when the corpus outgrows brute force.
• Chunks carry their title. Each chunk is prefixed with its document title before embedding, so a chunk ripped out of context still knows what it's about.
• One behavioral battery, two backends. The SQLite and pgvector stores pass the identical test suite (tests/store_suite.py), which is what "interchangeable" actually means.
• The MCP layer is tested with a real MCP client. CI spawns the server over stdio and drives it with an mcp.ClientSession — the same handshake Claude Desktop performs — not by calling Python functions directly.
• Public data only. PubMed abstracts and original sample docs. Never index proprietary or employer documents into a demo corpus.

Project structure

src/docqa/
├── server.py            # FastMCP server + tool definitions
├── retriever.py         # embed query -> store search, with embedder guard
├── embeddings.py        # OpenAIEmbedder | HashingEmbedder (keyless fallback)
├── chunking.py          # word windows with overlap
├── config.py            # env-driven settings (.env aware)
├── store/
│   ├── base.py          # VectorStore contract + embedder guard
│   ├── sqlite_store.py  # embedded, exact brute-force cosine
│   └── pgvector_store.py# Postgres + pgvector, HNSW
├── ingest/
│   ├── pubmed.py        # NCBI E-utilities fetcher (keyless, rate-limited)
│   ├── pipeline.py      # chunk -> embed -> upsert, content-hash idempotent
│   └── cli.py           # docqa-ingest fetch | index | stats
├── eval/run_eval.py     # recall@k + MRR, CI-gateable
└── data/                # bundled 12-doc sample corpus + labeled testset
tests/                   # unit + store battery + MCP stdio round-trip
.github/workflows/ci.yml # lint, tests, live pgvector integration + recall gate

Roadmap

• [x] MCP tools over stdio + Streamable HTTP
• [x] SQLite and pgvector backends behind one contract
• [x] Idempotent ingestion + PubMed fetcher
• [x] Eval harness with CI recall gate
• [ ] Hybrid retrieval (BM25 + vector, reciprocal rank fusion)
• [ ] Cross-encoder reranking stage
• [ ] More corpus adapters (arXiv, EDGAR)
• [ ] Bearer-token auth for the HTTP transport

License

MIT — see LICENSE.

Built by Varun Kammadanam — backend + GenAI engineer (Java, Python, AWS, RAG systems).