Update mcp/cbio.py

mcp/cbio.py

@@ -1,43 +1,45 @@
 """
-cBioPortal helper · REST v4 · zero-crash
+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)                  
 
-* 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 []
+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.
 """
 
-from __future__ import annotations
-import os, asyncio, httpx
+# ───────────────────────── 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.
+"""
+import os, httpx
 from functools import lru_cache
 from typing import List, Dict
 
-_TOKEN = os.getenv("CBIO_KEY")          # optional
-_HDR   = {"Accept": "application/json"}
-if _TOKEN:
-    _HDR["Authorization"] = f"Bearer {_TOKEN}"
-
-_URL = ("https://www.cbioportal.org/api"
-        "/molecular-profiles/{profile}/genes/{gene}/mutations?projection=SUMMARY"
-        )                               # swagger ref :contentReference[oaicite:2]{index=2}
+_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}"
 
 @lru_cache(maxsize=256)
-async def fetch_cbio(
-    gene    : str,
-    profile : str = "brca_tcga_pan_can_atlas_2018_mutations"
+async def fetch_cbio_variants(
+    gene_symbol: str,
+    study: str = "brca_tcga_pan_can_atlas_2018",
+    *,
+    timeout: float = 15.0,
 ) -> 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:
-                return []               # gene absent
-            r.raise_for_status()
-            return r.json()
-
-    try:
-        return await _hit()
-    except (httpx.HTTPStatusError, httpx.ReadTimeout):
-        await asyncio.sleep(0.5)        # one back-off
-        try:
-            return await _hit()
-        except Exception:
-            return []                   # graceful fallback
+    """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()