cdm-mcp-server 0.2.0

Develop MCP Servers for automate the work processes of the Clinical Data Manager.

Clinical Data Management MCP Server

A unified MCP (Model Context Protocol) server for automating Clinical Data Manager (CDM) workflows. Provides Excel comparison, Google Calendar integration, and more through any MCP-compatible AI agent.

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Available Tools

Excel & DB Spec Engine

• compare_common_excel: Compares specific sheets of two Excel files and generates a difference report (comparison_result.xlsx). Requires specifying the primary key column.
• compare_db_spec: Compares full CDM DB Spec workbooks. Automatically detects header positions and updates the Revision History sheet.

Calendar CSV Generator

• make_google_calendar_csv: Extracts key schedules from a Timeline/Schedule Excel file and converts them into a CSV formatted for Google Calendar. The output file can be imported manually via Google Calendar > Settings > Import/Export.

Blank eCRF PDF Comparison

• compare_ecrf_pdf_single: Compares two Blank eCRF PDF files and produces a single side-by-side comparison PDF. Changed pages are shown with Before (left) and After (right) layouts. Annotations use color coding: red = deleted, green = added, yellow = modified. Adjacent annotations of the same color are automatically merged.

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Installation

Step 1. Install uv

uv is a fast Python package manager. Installing it also gives you uvx, which runs packages without a separate Python installation.

Mac / Linux

curl -LsSf https://astral.sh/uv/install.sh | sh

Windows

powershell -c "irm https://astral.sh/uv/install.ps1 | iex"

Step 2. Register the MCP Server

Choose the AI client you use and run the corresponding command once. This registers the server globally so it's available from any directory.

Claude Code

claude mcp add --scope user cdm-server uvx cdm-mcp-server

Claude Desktop

Add the following to your Claude Desktop config file:

• Mac: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "cdm-server": {
      "command": "uvx",
      "args": ["cdm-mcp-server"]
    }
  }
}

Then restart Claude Desktop.

Gemini CLI

gemini mcp add cdm-server "uvx cdm-mcp-server" --scope user

Step 3. Verify the Connection

Claude Code

claude mcp list

Gemini CLI

gemini mcp list

You should see cdm-server: ✓ Connected.

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Usage

Once connected, simply describe what you need in natural language:

"Compare the previous and current DB Spec files and generate a difference report. Also extract the schedule from the Timeline sheet and create a CSV for Google Calendar."

The AI agent will automatically select and call the appropriate tool.

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Project Structure

src/
└── cdm_mcp_server/
    ├── __init__.py
    ├── server.py              # MCP server entry point
    └── modules/
        ├── excel_compare.py      # Excel & DB Spec comparison engine
        ├── calendar_maker.py     # Timeline parsing & Calendar CSV generator
        └── pdf_ecrf_compare.py   # Blank eCRF PDF comparison engine