Python: MCPStdioTool.call_tool hangs when MCP server sends resource notifications during tool execution

[manjunathshiva]

Environment

• agent-framework-core: 1.0.0rc5
• mcp (Python SDK): latest
• MCP server: mongodb-mcp-server@1.9.0 (via npx -y mongodb-mcp-server)
• Python: 3.14
• OS: Windows 11

Description

MCPStdioTool.call_tool hangs indefinitely when the MCP server sends a resources/updated notification alongside the
tool result. The underlying mcp Python SDK (ClientSession.call_tool) completes successfully with the same server and
arguments.

Steps to Reproduce

import asyncio
import os
from agent_framework import MCPStdioTool
from dotenv import load_dotenv

load_dotenv(override=False)

async def main():
env = dict(os.environ)
env["MDB_MCP_CONNECTION_STRING"] = os.getenv("MDB_MCP_CONNECTION_STRING")

  mcp = MCPStdioTool(
      name="MongoDB",
      command="npx",
      args=["-y", "mongodb-mcp-server"],
      env=env,
      load_prompts=False,
      request_timeout=30,
  )

  async with mcp:
      print(f"Connected, {len(mcp.functions)} tools available")
      tool = {fn.name: fn for fn in mcp.functions}["list-collections"]
      # This hangs indefinitely:
      result = await tool.invoke(arguments={"database": "sample_mflix"})
      print(result)

asyncio.run(main())

Expected Behavior

list-collections returns the result within the request_timeout window.

Actual Behavior

The call hangs indefinitely. Logs show the server responds and sends a resource notification, but the framework never
returns:

INFO:agent_framework._mcp:[server]: Detected a MongoDB connection string in the configuration, trying to connect...
INFO:agent_framework._mcp:[server]: Server with version 1.9.0 started with transport StdioServerTransport
INFO:agent_framework:Function name: list-collections
INFO:agent_framework._mcp:[resources]: Resource updated: debug://mongodb

Workaround

Using the mcp SDK directly (which agent-framework depends on) works without issue:

from mcp.client.session import ClientSession
from mcp.client.stdio import StdioServerParameters, stdio_client

async with stdio_client(server=StdioServerParameters(...)) as transport:
async with ClientSession(read_stream=transport[0], write_stream=transport[1]) as session:
await session.initialize()
result = await session.call_tool("list-collections", {"database": "sample_mflix"})
# Returns immediately with correct result

Analysis

The mongodb-mcp-server sends a resources/updated notification (debug://mongodb) during tool execution. The framework's
call_tool method (_mcp.py:1031) or the result parsing pipeline appears to not complete when these interleaved
notifications arrive, even though the underlying ClientSession handles them correctly.

[manjunathshiva]

Raised a fix for this: #4898