Update mcp/cbio.py

mcp/cbio.py

@@ -1,45 +1,63 @@
+# mcp/cbio.py – lightweight async wrapper for cBioPortal REST v3
+
 """
-MedGenesis v2 – core modules synchronised with the new helper API clients.
-Contains three top‑level files:
-    • mcp/cbio.py         – cancer cohort variants via cBioPortal REST v3
-    • mcp/orchestrator.py – async pipeline coordinator
-    • app.py              – Streamlit UI (CPU‑only)                  
-
-All modules assume the new helper files (mygene.py, ensembl.py, opentargets.py,
-drugcentral_ext.py, pubchem_ext.py, gene_hub.py, clinicaltrials.py, etc.) are
-present in the mcp package as created earlier in the conversation.
-"""
+Fetch mutation summaries for a gene from a chosen study / molecular profile
+using the public cBioPortal instance (or a private instance via token).
 
-# ───────────────────────── mcp/cbio.py ────────────────────────────────
-"""cBioPortal REST helper – returns detailed mutation calls for a gene.
-The public instance does **not** require an API‑key; however, if you have a
-personal or GENIE instance token set as CBIO_KEY, it will be used.
+* 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.
 """
-import os, httpx
+
+from __future__ import annotations
+
+import os
+import httpx
 from functools import lru_cache
 from typing import List, Dict
 
-_CBIO_BASE   = os.getenv("CBIO_BASE_URL", "https://www.cbioportal.org/api")
-_CBIO_TOKEN  = os.getenv("CBIO_KEY")
-_HEADERS     = {"accept": "application/json"}
-if _CBIO_TOKEN:
-    _HEADERS["Authorization"] = f"Bearer {_CBIO_TOKEN}"
+__all__ = ["fetch_cbio"]
+
+# ---------------------------------------------------------------------------
+# Configuration – overridable via env‑vars to support private portals
+# ---------------------------------------------------------------------------
+_BASE = os.getenv("CBIO_BASE", "https://www.cbioportal.org/api")
+_TOKEN = os.getenv("CBIO_KEY")
 
+_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_variants(
-    gene_symbol: str,
-    study: str = "brca_tcga_pan_can_atlas_2018",
-    *,
-    timeout: float = 15.0,
+async def fetch_cbio(
+    gene: str,
+    profile: str = "brca_tcga_pan_can_atlas_2018_mutations",
 ) -> List[Dict]:
-    """Return list of variant dicts (DETAILED projection)."""
-    profile = f"{study}_mutations"
-    url     = (
-        f"{_CBIO_BASE}/molecular-profiles/{profile}/genes/{gene_symbol}/"
-        "mutations"
-    )
-    params  = {"projection": "DETAILED"}
-    async with httpx.AsyncClient(timeout=timeout, headers=_HEADERS, follow_redirects=True) as client:
-        r = await client.get(url, params=params)
-        r.raise_for_status()
-        return r.json()
+    """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 []