MacOS Troubleshooting Guide¶

Prerequisites:

Ensure you have uv installed. Recommended method for macOS:
```
brew install uv
```
For other systems or methods, see the uv installation guide.
Ensure you have npx available (usually comes with Node.js/npm). Recommended method for macOS if needed:
```
brew install node
```

1. Testing the CLI Directly:

You can run biomcp commands directly without a full installation using uv:

Check the version:

uv run --with biomcp-python biomcp version
# Expected Output (version may vary): biomcp version: 0.1.0

Test a search command (e.g., trial search):

uv run --with biomcp-python biomcp trial search --condition NSCLC | head -n 5
# Expected Output (NCT ID and Title will vary):
# # Record 1
# Nct Number: NCT0XXXXXXX
# Study Title:
#   Some Title Related to NSCLC
# Study Url: https://clinicaltrials.gov/study/NCT0XXXXXXX

2. Testing the MCP Server with Inspector:

This verifies that the server starts correctly and the tools are available via the Model Context Protocol.

Run the inspector, telling it to start your server using the uv command:

npx @modelcontextprotocol/inspector uv run --with biomcp-python biomcp run

Open the MCP Inspector interface in your browser (usually http://127.0.0.1:6274).
You should see the list of available tools (e.g., article_searcher, trial_protocol, variant_searcher, etc.).
Try invoking a tool:
Select trial_searcher.

Enter valid JSON input matching the TrialQuery model, for example:

{
  "conditions": ["Melanoma"],
  "recruiting_status": "OPEN"
}

Click "Call Tool".
You should see a Markdown-formatted list of results in the "Output" section.