mcp/cbio.py

"""
cbio.py – cBioPortal REST helper (no API-key required for public portal).
Returns variant summary rows for a gene / profile.
"""
from functools import lru_cache
import httpx, asyncio

_BASE = "https://www.cbioportal.org/api/molecular-profiles/{profile}/genes/{gene}/mutations"
_HEADERS = {"Accept": "application/json"}

@lru_cache(maxsize=256)
async def fetch_cbio(
    gene: str,
    profile: str = "brca_tcga_pan_can_atlas_2018_mutations",
) -> list[dict]:
    if not gene:
        return []
    url = _BASE.format(profile=profile, gene=gene)
    params = {"projection": "SUMMARY"}
    async with httpx.AsyncClient(timeout=10, headers=_HEADERS) as c:
        r = await c.get(url, params=params)
        if r.status_code >= 400:
            return []          # swallow 4xx/5xx → empty list
        return r.json()