Update mcp/cbio.py

mcp/cbio.py

@@ -1,22 +1,36 @@
-# mcp/cbio.py
+import logging
 
-from pybioportal import PyBioPortal
-import asyncio
+# Try to import the official pybioportal client; if it isn't installed, we'll disable cBio queries.
+try:
+    from pybioportal import fetch_muts_in_multiple_mol_profs, fetch_molecular_profiles
+    _CBIO_ENABLED = True
+except ImportError:
+    logging.warning("pybioportal package not available; disabling cBioPortal integration")
+    _CBIO_ENABLED = False
 
-async def fetch_cbio_variants(gene_symbol: str) -> list[dict]:
+async def fetch_cbio(gene: str) -> list:
     """
-    Fetches mutation/variant data for a specific gene symbol
-    from the default cBioPortal study (e.g. 'brca_mskcc_2020').
+    Fetch cancer variant data for the given gene from cBioPortal.
+    Returns an empty list if pybioportal isn't installed or on any error.
     """
-    base_url = "https://www.cbioportal.org"
-    client = PyBioPortal(base_url)
+    if not _CBIO_ENABLED:
+        return []
 
-    # Build the query path for mutations in the gene
-    query_path = f"/mutation?gene={gene_symbol}&studyId=brca_mskcc_2020"
-    loop = asyncio.get_event_loop()
-    df = await loop.run_in_executor(
-        None,
-        lambda: client.get_data_frame(query_path)
-    )
-    # Convert DataFrame rows to dicts for JSON serialization
-    return df.to_dict(orient="records")
+    try:
+        # 1) Grab all molecular profiles (you can restrict to particular studies if you like)
+        profiles = fetch_molecular_profiles()  # returns list of dicts with 'molecular_profile_id', etc.
+
+        # 2) For each profile, fetch the mutations for our gene
+        variants = []
+        for prof in profiles:
+            mpid = prof.get("molecular_profile_id")
+            if mpid:
+                # fetch_muts_in_multiple_mol_profs returns a list of mutation dicts
+                muts = fetch_muts_in_multiple_mol_profs([mpid], gene=gene)
+                variants.extend(muts or [])
+
+        return variants
+
+    except Exception as e:
+        logging.warning("cBioPortal variant fetch failed: %s", e)
+        return []