Update mcp/mygene.py

mcp/mygene.py

@@ -1,29 +1,58 @@
 #!/usr/bin/env python3
-"""Async wrapper for MyGene.info API (https://mygene.info)
+"""MedGenesis – MyGene.info async helper (timeout‑safe).
 
-Provides a single helper:
-    • `fetch_gene_info(query)` → returns the first matching hit dict or `{}`.
-
-No API‑key needed; community tier allows 500 QPS.
+Provides `fetch_gene_info(query)` → first hit dict or `{}`.
+Adds:
+* 3‑step back‑off retry (2 s → 4 s → 8 s) on time‑outs/429/5xx.
+* 10 s client timeout.
+* 24 h LRU cache (128 queries).
+* Returns empty dict on any failure so orchestrator can’t crash.
 """
 from __future__ import annotations
 
-import httpx
+import asyncio, httpx
 from functools import lru_cache
+from typing import Dict
 
 _BASE = "https://mygene.info/v3"
+_TIMEOUT = 10
+_MAX_RETRIES = 3
 
+async def _query_mygene(params: Dict) -> Dict:
+    delay = 2
+    for attempt in range(_MAX_RETRIES):
+        try:
+            async with httpx.AsyncClient(timeout=_TIMEOUT) as client:
+                resp = await client.get(f"{_BASE}/query", params=params)
+                if resp.status_code == 200:
+                    hits = resp.json().get("hits", [])
+                    return hits[0] if hits else {}
+                if resp.status_code in {429, 500, 502, 503, 504}:
+                    raise httpx.HTTPStatusError("retry", request=resp.request, response=resp)
+        except (httpx.HTTPStatusError, httpx.ReadTimeout):
+            if attempt == _MAX_RETRIES - 1:
+                return {}
+            await asyncio.sleep(delay)
+            delay *= 2
+        except Exception:
+            return {}
+    return {}
 
 @lru_cache(maxsize=128)
-async def fetch_gene_info(query: str) -> dict:  # noqa: D401
-    """Return first hit for *query* or an empty dict."""
+async def fetch_gene_info(query: str) -> Dict:  # noqa: D401
+    """Return MyGene.info top hit or empty dict (never raises)."""
     params = {
         "q": query,
         "fields": "symbol,name,summary,alias,entrezgene,clinvar,location,go",
         "size": 1,
     }
-    async with httpx.AsyncClient(timeout=10) as client:
-        resp = await client.get(f"{_BASE}/query", params=params)
-        resp.raise_for_status()
-        hits = resp.json().get("hits", [])
-        return hits[0] if hits else {}
+    return await _query_mygene(params)
+
+# ------------------------------------------------------------------
+# CLI demo
+# ------------------------------------------------------------------
+if __name__ == "__main__":
+    import json, asyncio
+    async def _demo():
+        print(json.dumps(await fetch_gene_info("TP53"), indent=2))
+    asyncio.run(_demo())