Update mcp/cbio.py

mcp/cbio.py

@@ -1,63 +1,24 @@
-# mcp/cbio.py – lightweight async wrapper for cBioPortal REST v3
-
 """
-Fetch mutation summaries for a gene from a chosen study / molecular profile
-using the public cBioPortal instance (or a private instance via token).
-
-* Default public base URL: https://www.cbioportal.org/api
-* Optionally read `CBIO_BASE` and `CBIO_KEY` from environment variables to
-  switch instance and/or add an `Authorization: Bearer <TOKEN>` header.
-* Returns the JSON response directly (empty list on any 4xx/5xx).
-* Response caching: `@lru_cache` to avoid repeated round‑trips for the same
-  (gene, profile) pair during a session.
+cbio.py – cBioPortal REST helper (no API-key required for public portal).
+Returns variant summary rows for a gene / profile.
 """
-
-from __future__ import annotations
-
-import os
-import httpx
 from functools import lru_cache
-from typing import List, Dict
-
-__all__ = ["fetch_cbio"]
+import httpx, asyncio
 
-# ---------------------------------------------------------------------------
-# Configuration – overridable via env‑vars to support private portals
-# ---------------------------------------------------------------------------
-_BASE = os.getenv("CBIO_BASE", "https://www.cbioportal.org/api")
-_TOKEN = os.getenv("CBIO_KEY")
+_BASE = "https://www.cbioportal.org/api/molecular-profiles/{profile}/genes/{gene}/mutations"
+_HEADERS = {"Accept": "application/json"}
 
-_HEADERS: Dict[str, str] = {
-    "Accept": "application/json",
-}
-if _TOKEN:
-    _HEADERS["Authorization"] = f"Bearer {_TOKEN}"
-
-_URL_TEMPLATE = (
-    "{base}/molecular-profiles/{profile}/genes/{gene}/mutations?projection=SUMMARY"
-)
-
-# ---------------------------------------------------------------------------
-# Public helper
-# ---------------------------------------------------------------------------
 @lru_cache(maxsize=256)
 async def fetch_cbio(
     gene: str,
     profile: str = "brca_tcga_pan_can_atlas_2018_mutations",
-) -> List[Dict]:
-    """Return mutation summary list or an empty list on error/empty response."""
-
-    url = _URL_TEMPLATE.format(base=_BASE.rstrip("/"), profile=profile, gene=gene)
-
-    async with httpx.AsyncClient(timeout=15, headers=_HEADERS) as client:
-        try:
-            resp = await client.get(url)
-            # Treat 404/403 as empty but propagate other errors for logging
-            if resp.status_code == 200:
-                return resp.json()  # type: ignore[return-value]
-            elif resp.status_code in (404, 403):
-                return []
-            resp.raise_for_status()
-        except Exception:
-            # network issue, invalid JSON, etc. – keep UX smooth
-            return []
+) -> 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()