Update mcp/cbio.py

mcp/cbio.py

@@ -1,41 +1,43 @@
 """
-cBioPortal async helper – returns cohort-level mutation summary.
+cBioPortal helper · REST v4 · zero-crash
 
-• Works for ANY public molecular-profile ID
-• One retry on 5xx, returns [] on 404/timeout
-• Optional CBIO_KEY (JWT) for private studies
+* Public instance needs **no** API-key  :contentReference[oaicite:0]{index=0}
+* Optional Bearer token (`CBIO_KEY`) for private portals (e.g. GENIE) :contentReference[oaicite:1]{index=1}
+* One retry on 5xx / ReadTimeout, else returns []
 """
 
-from functools import lru_cache
+from __future__ import annotations
 import os, asyncio, httpx
+from functools import lru_cache
+from typing import List, Dict
 
-_BASE = "https://www.cbioportal.org/api"
-_URL  = _BASE + (
-    "/molecular-profiles/{profile}/genes/{gene}/mutations?projection=SUMMARY"
-)
-_KEY  = os.getenv("CBIO_KEY")            # optional
+_TOKEN = os.getenv("CBIO_KEY")          # optional
+_HDR   = {"Accept": "application/json"}
+if _TOKEN:
+    _HDR["Authorization"] = f"Bearer {_TOKEN}"
 
-@lru_cache(maxsize=256)
-async def fetch_cbio(gene: str,
-                     profile: str = "brca_tcga_pan_can_atlas_2018_mutations"
-                    ) -> list[dict]:
-    hdr = {"Accept": "application/json"}
-    if _KEY:
-        hdr["Authorization"] = f"Bearer {_KEY}"
+_URL = ("https://www.cbioportal.org/api"
+        "/molecular-profiles/{profile}/genes/{gene}/mutations?projection=SUMMARY"
+        )                               # swagger ref :contentReference[oaicite:2]{index=2}
 
-    async def _once() -> list[dict]:
-        async with httpx.AsyncClient(timeout=10, headers=hdr) as c:
+@lru_cache(maxsize=256)
+async def fetch_cbio(
+    gene    : str,
+    profile : str = "brca_tcga_pan_can_atlas_2018_mutations"
+) -> List[Dict]:
+    async def _hit() -> List[Dict]:
+        async with httpx.AsyncClient(timeout=10, headers=_HDR) as c:
             r = await c.get(_URL.format(profile=profile, gene=gene))
-            if r.status_code == 404:        # gene not present
-                return []
+            if r.status_code == 404:
+                return []               # gene absent
             r.raise_for_status()
             return r.json()
 
     try:
-        return await _once()
-    except httpx.HTTPStatusError:
-        await asyncio.sleep(0.4)            # back-off then retry
+        return await _hit()
+    except (httpx.HTTPStatusError, httpx.ReadTimeout):
+        await asyncio.sleep(0.5)        # one back-off
         try:
-            return await _once()
-        except Exception:                   # still bad → empty payload
-            return []
+            return await _hit()
+        except Exception:
+            return []                   # graceful fallback