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nicomathieu

DocFill Agent MCP Server

by nicomathieu
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DocFill Agent

An LLM agent that reads, understands, and fills DOCX templates — preserving bold labels, fonts, and structure.

Built on Agno + FastMCP + python-docx.

What it does

Paste meeting notes or raw clinical data into the agent. It:

  1. Parses the DOCX template into a structured AST (headings, paragraphs, table cells — each with a stable element_id and its run-level formatting)

  2. Exposes 5 MCP tools the agent can call: upload_document, get_session_documents, load_document_ast, edit_document, validate_document_state

  3. The LLM reads the AST, matches fields to content, and calls edit_document with the right element_id

  4. A run-level formatter re-applies the template's bold/italic labels around the new plain-text values — automatically

No HTML conversion. No regex scraping. Pure AST surgery.

Architecture

┌─────────────────────────────────────────────────────────┐
│                    Agno Agent (Claude)                  │
│   system prompt: 5-step workflow                        │
│   tool calls ──────────────────────────────────────┐    │
└────────────────────────────────────────────────────│────┘
                                                     │ HTTP/MCP
┌────────────────────────────────────────────────────▼────┐
│                  FastMCP Server  (:8000)                 │
│                                                         │
│  upload_document ──► converter.build_ast()              │
│  load_document_ast ─► LocalDocumentStore.get_ast()      │
│  edit_document ─────► converter.apply_cell_edit()       │
│                        + run_formatter.create_runs()    │
│  validate_document_state ──► build_ast() comparison     │
└─────────────────────────────────────────────────────────┘
         │ python-docx read/write
┌────────▼────────────────────┐
│   DOCX template on disk     │
│   + AST JSON (local store)  │
└─────────────────────────────┘

Run-level formatting preservation

The core algorithmic challenge: the template has cells like

[bold] "Study Title: " [/bold][plain] "" [/plain]

The LLM produces "A Phase III randomised trial of Zetaribumab".
The formatter:

  1. Finds the longest common prefix between the new text and the original template text

  2. Maps that prefix to template runs (preserving bold)

  3. For remaining text, scans for known bold-label fragments and applies their formatting

  4. LLM-generated values always end up plain — no false bold

Quick start

# 1. Install
pip install -e ".[dev]"

# 2. Configure
cp .env.example .env
# → edit .env, add ANTHROPIC_API_KEY=sk-ant-...

# 3. Create the CSR template
python examples/csr_demo/create_template.py

# 4. Start the MCP server
uvicorn docfill.mcp.server:app --port 8000

# 5. Run the demo notebook
jupyter notebook examples/csr_demo/csr_fill_demo.ipynb

Project structure

docfill-agent/
├── src/
│   └── docfill/
│       ├── ast/
│       │   ├── models.py          # DocumentAST, TextRun, TableCellElement, …
│       │   ├── converter.py       # build_ast(), apply_cell_edit(), apply_heading_edit()
│       │   └── run_formatter.py   # create_runs_from_template() — the formatting engine
│       ├── storage/
│       │   ├── local.py           # LocalDocumentStore (filesystem-backed)
│       │   └── session.py         # SessionRegistry (in-memory)
│       └── mcp/
│           └── server.py          # FastMCP server — 5 tools
├── examples/
│   └── csr_demo/
│       ├── create_template.py     # Generates the fictional CSR DOCX template
│       ├── csr_fill_demo.ipynb    # End-to-end demo notebook
│       └── templates/             # csr_template.docx (generated by create_template.py)
├── pyproject.toml
├── .env.example
└── README.md

MCP tools

Tool

Args

Description

upload_document

file_path, file_id?

Parse DOCX → AST, register in session

get_session_documents

include_metadata?

List uploaded documents

load_document_ast

file_id

Return full element list with element_id, text, runs

edit_document

file_id, edits

Apply cell/heading edits with formatting preservation

validate_document_state

file_id, create_new_version?

Verify AST integrity, bump version

edit_document edit format:

[
  {
    "type": "table_cell",
    "element_id": "cell-t0-r1-c1",
    "changes": { "text": "A Phase III randomised trial of Zetaribumab 150 mg SC Q4W" }
  }
]

Replacing the LLM provider

The agent uses Agno's model abstraction. To switch providers:

# Anthropic (default)
from agno.models.anthropic import Claude
model = Claude(id="claude-sonnet-5")

# OpenAI
from agno.models.openai import OpenAIChat
model = OpenAIChat(id="gpt-4o")

# Any LiteLLM-compatible endpoint
from agno.models.litellm import LiteLLM
model = LiteLLM(id="bedrock/anthropic.claude-sonnet-4-5", api_key="...")

Extending to cloud storage

LocalDocumentStore mirrors the interface of an S3-backed store. To switch:

  1. Implement store_file, store_ast, get_file, get_ast with boto3

  2. Pass the new store instance into server.py

No changes to the converter or formatter needed.

Limitations & known gaps

  • apply_cell_edit rebuilds paragraphs from scratch — complex nested tables with merged cells may lose merge state. (Works for standard clinical templates.)

  • The formatter heuristic works well for Label: value patterns. Multi-column mixed formatting may need manual tuning.

  • The MCP server is single-process; the SessionRegistry is in-memory and not shared across workers.

License

MIT

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