cdisc-mcp

curl -fsSL https://raw.githubusercontent.com/Teninq/cdisc-mcp/main/install.md

# Runtime only
pip install -e .

# With dev dependencies
pip install -e ".[dev]"

# With web explorer
pip install -e ".[web]"

# Linux / macOS
export CDISC_API_KEY=your_key_here

# Windows — Command Prompt
set CDISC_API_KEY=your_key_here

# Windows — PowerShell
$env:CDISC_API_KEY = "your_key_here"

# Start MCP server (for AI assistant integration)
cdisc-mcp

# OR: Start Web Explorer (quick interactive testing)
python web/app.py

# 1. Install web dependencies
pip install -e ".[web]"

# 2. Set your API key
export CDISC_API_KEY=your_key_here   # Linux/macOS
set CDISC_API_KEY=your_key_here      # Windows CMD
$env:CDISC_API_KEY = "your_key_here" # Windows PowerShell

# 3. Start the bridge server
python web/app.py

# 4. Open in browser
#    → http://localhost:8080

{
  "mcpServers": {
    "cdisc": {
      "command": "cdisc-mcp",
      "env": {
        "CDISC_API_KEY": "your_key_here"
      }
    }
  }
}

{
  "servers": {
    "cdisc": {
      "command": "cdisc-mcp",
      "env": {
        "CDISC_API_KEY": "your_key_here"
      }
    }
  }
}

# Add globally (available in all projects)
claude mcp add cdisc-mcp -e CDISC_API_KEY=your_key_here -- python -m cdisc_mcp.server

# Add for the current project only
claude mcp add cdisc-mcp --scope project -e CDISC_API_KEY=your_key_here -- python -m cdisc_mcp.server

# Verify the server was registered
claude mcp list

{
  "mcpServers": {
    "cdisc-mcp": {
      "command": "python",
      "args": ["-m", "cdisc_mcp.server"],
      "env": {
        "CDISC_API_KEY": "your_key_here"
      }
    }
  }
}

User: What SDTM domains are defined in version 3.4?
Claude: [calls get_sdtm_domains with version="3-4"] ...

pip install mcp

import asyncio
import os
from mcp import ClientSession, StdioServerParameters
from mcp.client.stdio import stdio_client

SERVER = StdioServerParameters(
    command="python",
    args=["-m", "cdisc_mcp.server"],
    env={"CDISC_API_KEY": os.environ["CDISC_API_KEY"]},
)

async def main():
    async with stdio_client(SERVER) as (read, write):
        async with ClientSession(read, write) as session:
            await session.initialize()

            # List all available tools
            tools = await session.list_tools()
            print([t.name for t in tools.tools])

            # Call a tool
            result = await session.call_tool(
                "get_sdtm_domains",
                arguments={"version": "3-4"},
            )
            print(result.content[0].text)

asyncio.run(main())

import asyncio, os, json
from contextlib import asynccontextmanager
from mcp import ClientSession, StdioServerParameters
from mcp.client.stdio import stdio_client

_SERVER = StdioServerParameters(
    command="python",
    args=["-m", "cdisc_mcp.server"],
    env={"CDISC_API_KEY": os.environ["CDISC_API_KEY"]},
)

@asynccontextmanager
async def cdisc_session():
    """Async context manager that yields an initialised MCP session."""
    async with stdio_client(_SERVER) as (read, write):
        async with ClientSession(read, write) as session:
            await session.initialize()
            yield session

async def call(tool: str, **kwargs) -> dict:
    async with cdisc_session() as s:
        result = await s.call_tool(tool, arguments=kwargs)
        return json.loads(result.content[0].text)

# --- Usage examples ---
async def demo():
    # Fetch SDTM domains
    domains = await call("get_sdtm_domains", version="3-4")

    # Fetch all variables in the AE domain
    variables = await call("get_sdtm_domain_variables", version="3-4", domain="AE")

    # Look up a single variable
    aeterm = await call("get_sdtm_variable", version="3-4", domain="AE", variable="AETERM")

    print(aeterm)

asyncio.run(demo())

# Products / versions
await session.call_tool("list_products", {})

# SDTM
await session.call_tool("get_sdtm_domains",          {"version": "3-4"})
await session.call_tool("get_sdtm_domain_variables", {"version": "3-4", "domain": "AE"})
await session.call_tool("get_sdtm_variable",         {"version": "3-4", "domain": "AE", "variable": "AETERM"})

# ADaM
await session.call_tool("get_adam_datastructures",   {"version": "1-3"})
await session.call_tool("get_adam_variable",         {"version": "1-3", "data_structure": "ADSL", "variable": "USUBJID"})

# CDASH
await session.call_tool("get_cdash_domains",         {"version": "2-0"})
await session.call_tool("get_cdash_domain_fields",   {"version": "2-0", "domain": "AE"})

# Controlled Terminology
await session.call_tool("list_ct_packages",          {})
await session.call_tool("get_codelist",              {"package_id": "sdtmct-2024-03-29", "codelist_id": "C66781"})
await session.call_tool("get_codelist_terms",        {"package_id": "sdtmct-2024-03-29", "codelist_id": "AGEU"})

MCP Client (Claude / VS Code / Cursor)
        │
        │  MCP protocol (stdio)
        ▼
   server.py  ──── FastMCP tool registration
        │
        ▼
   tools/  ──────── domain functions (sdtm, adam, cdash, terminology, search)
        │
        ▼
   client.py  ───── CDISCClient (async HTTP · TTL cache · retry)
        │
        │  HTTPS
        ▼
   library.cdisc.org/api  ──── CDISC Library REST API

# Full suite with coverage (≥80% required)
pytest

# Specific modules
pytest tests/test_tools.py tests/test_client.py -v

# Single test
pytest tests/test_tools.py::test_list_products -v

ruff check src/ tests/    # Linting
mypy src/                 # Type checking

src/cdisc_mcp/
├── server.py              # FastMCP server + tool registration
├── client.py              # Async HTTP client (cache, retry)
├── config.py              # Config dataclass + env loader
├── errors.py              # AuthenticationError, ResourceNotFoundError, RateLimitError
├── response_formatter.py  # HAL response normalization
└── tools/
    ├── search.py          # list_products (product catalog)
    ├── sdtm.py            # SDTM domain/variable tools
    ├── adam.py            # ADaM datastructure/variable tools
    ├── cdash.py           # CDASH domain/field tools
    ├── terminology.py     # CT package/codelist tools
    └── _validators.py     # Path traversal guards
web/
├── app.py                 # FastAPI bridge server
└── index.html             # Single-file browser explorer
tests/
├── test_config.py
├── test_client.py
├── test_response_formatter.py
├── test_tools.py
├── test_errors.py
└── test_server.py