Zileo Docs

MCP (Model Context Protocol) server for indexing, semantic search, and generation of multi-format documents. Exposes 13 tools over JSON-RPC 2.0 so an LLM can search your local PDF, Excel, and Word files, and create or edit Excel and Word documents.

Developed by Assistance Micro Design

Built with Claude Code by Anthropic

---

Beta Warning

This project is in beta. Use at your own risk and review the trade-offs before relying on it.

Risk	Description
API Costs	Every index_document call triggers Mistral embeddings (and OCR for image pages). Indexing large PDFs can generate non-trivial billing.
Breaking Changes	The MCP tool surface evolves between minor versions. Version 0.3.0 split search_documents into search_hybrid and search_semantic; expect similar adjustments before 1.0.
Security	Designed for personal local use behind Docker. The author declines responsibility if exposed to the public internet without an additional auth layer.
Instability	Schemas validated with extra="forbid" since 0.4.0 — clients sending unknown fields now receive VALIDATION_ERROR instead of silent acceptance.
No SLA	No guaranteed availability, no support contract. File issues via GitHub.

Recommendation: Run behind a private network, set API_KEY, and pin the Docker image to a tagged version.

---

Description

Zileo Docs ingests heterogeneous office documents, extracts their content (native text or Mistral OCR), chunks the result while preserving Markdown structure, embeds each chunk with Mistral (1024-dim dense vectors plus BM25 sparse vectors), and stores them in Qdrant. An LLM connected over MCP can then search the indexed corpus, read full documents, and generate new Excel or Word files — all from natural-language tool calls.

Key Features

• 13 MCP tools over JSON-RPC 2.0 / HTTP (POST /mcp)
• Multi-format ingestion: PDF (native + OCR), Excel .xlsx/.xls, Word .docx
• Hybrid search (dense + BM25 RRF) with cosine relevance guard against off-domain results
• Semantic-only search with explicit score_threshold
• Excel and Word generation from structured input (data, formulas, styles, charts)
• Path traversal, formula-injection, and ZIP-bomb protections
• Per-endpoint rate limiting (slowapi) and API-key authentication
• Docker multi-stage image, non-root runtime, health-checked

---

Prerequisites

Dependency	Purpose	Installation
Docker Engine >= 24	Container runtime	https://docs.docker.com/engine/install/
Docker Compose v2	Service orchestration	Bundled with Docker Desktop or the docker compose CLI plugin
Mistral API key	Embeddings (1024d) + OCR	https://console.mistral.ai/

---

Build Requirements

Required only when developing outside Docker (the container ships everything else).

Tool	Min version	Verify
Python	3.11	python3 --version # >= 3.11
uv	0.9	uv --version # >= 0.9

---

Installation

git clone https://github.com/assistance-micro-design/zileo-docs.git
cd zileo-docs
cp .env.example .env

# Edit .env: set MISTRAL_API_KEY and DOCUMENTS_PATH
# Generate an API key to protect the server:
echo "API_KEY=$(openssl rand -hex 32)" >> .env

docker compose up -d

About API_KEY — Protects /api/v1/*, /mcp, and /health. Outside DEBUG=true, the server refuses to start with an empty key. See docs/mcp-client-setup.md for passing it to MCP clients.

Verify the server is up:

curl -H "X-API-Key: $API_KEY" http://localhost:8000/health
# {"status": "healthy", ...}

---

Tech Stack

Layer	Technology
Language	Python 3.11+
Web framework	FastAPI
MCP runtime	mcp SDK (JSON-RPC 2.0 over HTTP)
Dense embeddings	Mistral (mistral-embed, 1024 dim)
Sparse embeddings	fastembed (BM25)
Vector store	Qdrant 1.16.3
OCR	Mistral OCR API
PDF extraction	PyMuPDF + pymupdf4llm
Excel I/O	openpyxl, xlrd
Word I/O	docx2python, python-docx
Packaging	uv + Hatchling
Runtime	Docker Compose (multi-stage, non-root)

---

MCP Configuration

The MCP endpoint is POST /mcp (JSON-RPC 2.0 over HTTP).

Claude Desktop

Add to the Claude Desktop config:

OS	Path
Linux	~/.config/Claude/claude_desktop_config.json
macOS	~/Library/Application Support/Claude/claude_desktop_config.json
Windows	%APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "zileo-docs": {
      "url": "http://localhost:8000/mcp",
      "transport": "http",
      "headers": {
        "X-API-Key": "your_api_key_here"
      }
    }
  }
}

Replace your_api_key_here with the API_KEY from .env. Restart Claude Desktop after editing.

Zileo Chat

In Zileo Chat, open Settings → MCP → Add server and fill in the form:

Field	Value
Name	zileo-docs
Deployment method	HTTP
Arguments	the endpoint URL on the first line — http://localhost:8000/mcp
Authentication	API key
Header name	X-API-Key
API key value	the API_KEY from your .env

The API-key value is stored in your OS keychain — never written to the database in plain text, never exported. Only non-sensitive metadata (the header name) is persisted.

Set the endpoint URL according to where Zileo Chat runs relative to the server:

Scenario	Endpoint URL
Same host	http://localhost:8000/mcp
Zileo Chat in Docker, same host	http://zileo-docs:8000/mcp — join the zileo-docs_mcp-network network
Remote host (LAN)	http://<server-ip>:8000/mcp — enable the LAN access toggle at the top of the MCP settings first

Then Save. See docs/mcp-client-setup.md for details.

Other MCP clients

Any MCP-compatible client can connect over HTTP Streamable to http://localhost:8000/mcp. The server implements:

• initialize — Handshake and capabilities
• tools/list — Lists the 13 available tools
• tools/call — Invokes a tool

Transport is HTTP POST with JSON-RPC 2.0 payloads. No SSE, no WebSocket.

---

MCP Tools

Indexing and search

Tool	Description
index_document	Extract and index a PDF, Excel, or Word file into Qdrant
search_hybrid	Hybrid search (dense + BM25 RRF) with cosine relevance guard against off-domain hits
search_semantic	Pure semantic search (cosine, default threshold 0.7)
get_document	Fetch the metadata and chunks for a document
delete_document	Remove a document from the index (source file untouched)
list_indexed_documents	List documents already indexed
read_document_content	Read the reconstructed Markdown content of a document
get_excel_formulas	Fetch the formulas from an indexed Excel file

Generation and editing

Tool	Description
create_excel_document	Create an Excel file (.xlsx) with data, styles, and charts
edit_excel_document	Edit an existing Excel file (13 operations)
create_word_document	Create a Word file (.docx) from Markdown content

Utilities

Tool	Description
list_available_documents	List source files (two sources: documents, generated)
inspect_generated_file	Inspect the structure of a generated Excel file

---

Configuration

Main environment variables (see docs/configuration.md for the full list):

Variable	Required	Description
MISTRAL_API_KEY	Yes	Mistral API key (embeddings + OCR)
API_KEY	Yes (outside DEBUG)	Authentication key for protected endpoints. Generate via openssl rand -hex 32. Empty value accepted only when DEBUG=true.
DOCUMENTS_PATH	Yes	Local path to your source documents
OUTPUT_PATH	No	Output directory for generated files (default: /app/output)
QDRANT_HOST	No	Qdrant host (default: localhost, qdrant inside Docker)
DEBUG	No	Enables Swagger UI and CORS (default: false)

---

Local Development

uv sync --extra dev
docker compose up -d qdrant   # Qdrant only
uv run uvicorn src.main:app --reload

Tests

uv run pytest tests/unit/ -v          # Unit tests
uv run pytest tests/integration/ -v   # Requires Qdrant
uv run pytest tests/e2e/ -v           # Full pipeline

Validation

uv run ruff check src/ tests/
uv run ruff format --check src/ tests/
uv run mypy src/
uv run pytest --cov=src --cov-fail-under=80

RAG evaluation

Offline evaluation of search quality against the golden set (tests/eval/golden_questions.yml). Requires the server running with indexed documents.

uv run python3 scripts/eval_rag.py --tool search_hybrid    # or search_semantic
# Metrics: recall@1, recall@5, MRR, false-positive rate (off-domain), mean results

---

Architecture

src/
  main.py              # FastAPI app + /mcp endpoint
  core/                # Config, exceptions, logging
  api/routes/          # REST endpoints (health, documents, search)
  mcp/
    server.py          # JSON-RPC 2.0 router
    tools/             # 13 MCP tools
  services/
    pdf/               # Analysis, native extraction, Mistral OCR
    excel/             # Extraction + generation + editing
    word/              # docx2python extraction
    inspection/        # Generated-file inspection
    document/          # Multi-format router
    chunking/          # Chunk splitting
    embedding/         # Mistral embeddings (1024 dim)
    vector/            # Qdrant storage
  models/              # Pydantic schemas

---

Documentation

• MCP client setup — Claude Desktop, Zileo Chat, other clients
• Research guide — Indexing, hybrid search, reading
• Generation guide — Excel and Word options, design, examples
• API reference — REST endpoints and 13 MCP tools
• Architecture — Processing pipeline and components
• Configuration — Environment variables
• Deployment — Docker and local development
• Multi-format support — PDF, Excel, Word
• Code style — Conventions

---

Contributing

See CONTRIBUTING.md and .github/PULL_REQUEST_TEMPLATE.md.

Quick path:

1. Fork the repository
2. Create a feature branch (git checkout -b feat/your-feature)
3. Commit with a conventional message (git commit -m "feat(scope): summary")
4. Push and open a Pull Request against main
5. Ensure CI is green and the PR checklist is satisfied

---

Security

To report a vulnerability, see SECURITY.md. Do not open public issues for security reports.

---

License

Distributed under the GNU Affero General Public License v3.0 or later.

Copyright 2025-2026 Assistance Micro Design
Licensed under the GNU Affero General Public License v3.0 or later

This license is mandatory because the project depends on PyMuPDF and pymupdf4llm (Artifex Software, Inc.), both distributed under AGPL-3.0. See THIRD_PARTY_LICENSES.md for the complete inventory and NOTICE for attribution.

---

Acknowledgments

• Mistral AI — Embeddings and OCR
• Qdrant — Vector database
• PyMuPDF and pymupdf4llm — PDF extraction
• FastAPI — Web framework
• Model Context Protocol — Tool protocol
• Built with Claude Code by Anthropic

---

Assistance Micro Design | GitHub