Suf newfeature

README.md

@@ -1,4 +1,4 @@
-# <img src="docs/_static/logo.png" alt="ToolUniverse Logo" height="28" style="vertical-align: middle; margin-right: 8px;" /> ToolUniverse: Democratizing AI scientists
+# <img src="docs/_static/logo.png" alt="ToolUniverse Logo" height="28" style="vertical-align: middle; margin-right: 8px;" /> ToolUniverse: Democratizing AI scientists
 
 [![Paper](https://img.shields.io/badge/Paper-Arxiv-blue)](https://arxiv.org/abs/2509.23426)
 [![PyPI version](https://badge.fury.io/py/tooluniverse.svg)](https://badge.fury.io/py/tooluniverse)
@@ -232,6 +232,26 @@ Our comprehensive documentation covers everything from quick start to advanced w
 - **[Adding Tools Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/addtools/Adding_Tools_Tutorial.html)**: Step-by-step tool addition guide
 - **[MCP Tool Registration](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/addtools/mcp_tool_registration_en.html)**: Register tools via MCP
 
+### MedTok + MedLog Integrations
+
+ToolUniverse now ships with first-class support for the MedTok tokenizer service and the MedLog reference collector/FHIR bridge.
+
+- **MedTok REST tools** (`tool_type=["medtok"]`) expose `/tokenize`, `/embed`, `/nearest_neighbors`, `/map_text_to_code`, `/search_text`, and `/codes/{system}/{code}`. Point them at a running service by setting `MEDTOK_BASE_URL` (defaults to `http://localhost:8000`).
+- **MedTok MCP auto-loader** (`tool_type=["medtok_mcp_auto_loader"]`) can register tools from the FastMCP wrapper. Set `MEDTOK_MCP_SERVER_HOST` to the host running the `medtok_tool.py` MCP server.
+- **MedLog collector + FHIR tools** (`tool_type=["medlog"]`) wrap the reference implementation's REST APIs. Configure the collectors' endpoints with `MEDLOG_COLLECTOR_BASE_URL` (default `http://localhost:7001`) and `MEDLOG_FHIR_BASE_URL` (default `http://localhost:7003`).
+
+See `tests/integration/test_medtok_medlog_tools.py` for end-to-end examples that start the services, invoke the tools, and validate responses.
+
+### End-to-End Demo Script
+
+To launch the reference services and exercise the toolchain automatically, run:
+
+```bash
+python scripts/run_full_demo.py          # adds -h for options
+```
+
+The script starts MedTok + MedLog locally, runs representative tool calls (including optional external APIs like InterPro, KEGG, IUCN, JASPAR, MarineSpecies, cBioPortal, and Phenome Jax), and prints a success/failure summary.
+
 ### 📚 API Reference
 - **[API Directory](https://zitniklab.hms.harvard.edu/ToolUniverse/api/modules.html)**: Complete module listing
 - **[Core Modules](https://zitniklab.hms.harvard.edu/ToolUniverse/api/tooluniverse.html)**: Main ToolUniverse class and utilities

scripts/medlog_stub_server.py

@@ -0,0 +1,151 @@
+#!/usr/bin/env python
+"""
+Lightweight MedLog stub servers for local demos.
+
+Run the collector:
+    python scripts/medlog_stub_server.py --mode collector --host 127.0.0.1 --port 8911
+
+Run the FHIR bridge:
+    python scripts/medlog_stub_server.py --mode fhir --host 127.0.0.1 --port 8912
+"""
+
+from __future__ import annotations
+
+import argparse
+import os
+import threading
+import time
+from typing import Dict
+
+import uvicorn
+from fastapi import FastAPI, HTTPException
+
+
+STORE: Dict[str, Dict] = {}
+STORE_LOCK = threading.Lock()
+
+
+def build_collector_app() -> FastAPI:
+    app = FastAPI(title="MedLog Collector (Stub)", version="0.1.0")
+
+    @app.post("/medlog/events/init")
+    def init(payload: dict):
+        header = payload.get("header") or {}
+        event_id = header.get("event_id")
+        if not event_id:
+            raise HTTPException(400, "event_id required")
+        record = {
+            "header": header,
+            "model_instance": payload.get("model_instance", {}),
+            "user_identity": payload.get("user_identity", {}),
+            "target_identity": payload.get("target_identity"),
+            "inputs": payload.get("inputs"),
+            "retention_tier": payload.get("retention_tier", "steady"),
+            "fragments": [],
+        }
+        with STORE_LOCK:
+            STORE[event_id] = record
+        return {"status": "ok", "event_id": event_id}
+
+    @app.post("/medlog/events/{event_id}/append")
+    def append(event_id: str, fragment: dict):
+        with STORE_LOCK:
+            record = STORE.get(event_id)
+            if record is None:
+                raise HTTPException(404, "event not found")
+            record["fragments"].append(fragment)
+        return {"status": "ok", "event_id": event_id}
+
+    @app.get("/medlog/events/{event_id}/prov")
+    def prov(event_id: str):
+        with STORE_LOCK:
+            record = STORE.get(event_id)
+            if record is None:
+                raise HTTPException(404, "event not found")
+            header = record["header"]
+        return {"event_id": event_id, "provenance": {"header": header}}
+
+    @app.post("/query")
+    def query(body: dict):
+        run_id = body.get("run_id")
+        event_id = body.get("event_id")
+        limit = body.get("limit", 50)
+        results = []
+        with STORE_LOCK:
+            for eid, record in STORE.items():
+                header = record["header"]
+                if event_id and event_id != eid:
+                    continue
+                if run_id and header.get("run_id") != run_id:
+                    continue
+                results.append({"event_id": eid, "header": header})
+                if len(results) >= limit:
+                    break
+        return {"count": len(results), "results": results}
+
+    @app.post("/export/parquet")
+    def export():
+        return {"status": "ok", "outdir": "/tmp/parquet"}
+
+    return app
+
+
+def build_fhir_app() -> FastAPI:
+    app = FastAPI(title="MedLog FHIR Stub", version="0.1.0")
+
+    def bundle(records):
+        return {
+            "resourceType": "Bundle",
+            "type": "collection",
+            "entry": [
+                {
+                    "resource": {
+                        "resourceType": "Observation",
+                        "id": record["header"]["event_id"],
+                        "status": "final",
+                    }
+                }
+                for record in records
+            ],
+        }
+
+    @app.get("/bundle/{event_id}")
+    def bundle_event(event_id: str):
+        with STORE_LOCK:
+            record = STORE.get(event_id)
+        if record is None:
+            raise HTTPException(404, "event not found")
+        return bundle([record])
+
+    @app.get("/bundle/run/{run_id}")
+    def bundle_run(run_id: str):
+        with STORE_LOCK:
+            records = [
+                record
+                for record in STORE.values()
+                if record["header"].get("run_id") == run_id
+            ]
+        if not records:
+            raise HTTPException(404, "run not found")
+        return bundle(records)
+
+    return app
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--mode", choices=["collector", "fhir"], required=True)
+    parser.add_argument("--host", default=os.getenv("MEDLOG_HOST", "127.0.0.1"))
+    parser.add_argument("--port", type=int, default=int(os.getenv("MEDLOG_PORT", 0)) or 0)
+    args = parser.parse_args()
+
+    if args.port == 0:
+        args.port = 8911 if args.mode == "collector" else 8912
+
+    app = build_collector_app() if args.mode == "collector" else build_fhir_app()
+    print(f"Starting MedLog {args.mode} stub on {args.host}:{args.port}")
+    uvicorn.run(app, host=args.host, port=args.port, log_level="info")
+
+
+if __name__ == "__main__":
+    main()