Custom headers are not passed to the /tool/call

[NatiSayada]

What happened?

We have a multi-user environment, and we implement an MCP with user base auth.
For better token management, we wanted to use the custom header feature to track the user and the tokens.
We can see that the headers are passed to every /message request but not when the API is calling the tool.

the message request looks like this:

Request: POST /mcp/messages/

All request headers:
Headers({'host': 'localhost:8000', 'connection': 'keep-alive', 'content-type': 'application/json', 'lib-user-id': '6818cef5c03978714d1576dc', 'lib-user-name': 'user-name', 'accept': '*/*', 'accept-language': '*', 'sec-fetch-mode': 'cors', 'user-agent': 'node', 'accept-encoding': 'gzip, deflate', 'content-length': '54'})

Lib-User-ID header: 6818cef5c03978714d1576dc

when calling the tools:

Request: GET /status

All request headers:
Headers({'host': 'apiserver', 'accept': '*/*', 'accept-encoding': 'gzip, deflate', 'connection': 'keep-alive', 'user-agent': 'python-httpx/0.28.1'})

Lib-User-ID header: Not found
Incoming request headers to /status endpoint:
Headers({'host': 'apiserver', 'accept': '*/*', 'accept-encoding': 'gzip, deflate', 'connection': 'keep-alive', 'user-agent': 'python-httpx/0.28.1'})
  host: apiserver
  accept: */*
  accept-encoding: gzip, deflate
  connection: keep-alive
  user-agent: python-httpx/0.28.1

Version Information

ghcr.io/danny-avila/librechat-dev:latest

Steps to Reproduce

1. Enable custom headers
2. add some middleware to monitor the request headers

What browsers are you seeing the problem on?

Chrome

Relevant log output

2025-05-15T08:34:34.290Z debug: [MCP][User: 6818cef5c03978714d1576dc] Updated last activity timestamp: 2025-05-15T08:34:34.290Z
2025-05-15T08:34:34.290Z debug: [MCP][User: 6818cef5c03978714d1576dc][atlassian] Transport sending: {"method":"tools/call","params":{"name":"status","arguments":{}},"jsonrpc"... [truncated]
2025-05-15T08:34:34.301Z debug: [MCP][User: 6818cef5c03978714d1576dc] Updated last activity timestamp: 2025-05-15T08:34:34.301Z
2025-05-15T08:34:37.050Z debug: [MCP][User: 6818cef5c03978714d1576dc][atlassian] Transport sending: {"jsonrpc":"2.0","method":"notifications/cancelled","params":{"requestId":... [truncated]

Screenshots

No response

Code of Conduct

• I agree to follow this project's Code of Conduct

[danny-avila]

I'm not seeing this on my end, using an MCP Server with SSE transport.

MCP Server logs (mock server)
https://github.com/danny-avila/mock_confluence_mcp

2025-05-15 11:15:42,712 - __main__ - DEBUG - Request headers:
2025-05-15 11:15:42,712 - __main__ - DEBUG -   host: localhost:8002
2025-05-15 11:15:42,712 - __main__ - DEBUG -   connection: keep-alive
2025-05-15 11:15:42,712 - __main__ - DEBUG -   authorization: Bearer test
2025-05-15 11:15:42,713 - __main__ - DEBUG -   x-user-id: 68096bee4375901e7d0f24d6
2025-05-15 11:15:42,713 - __main__ - DEBUG -   content-type: application/json
2025-05-15 11:15:42,713 - __main__ - DEBUG -   accept: */*
2025-05-15 11:15:42,713 - __main__ - DEBUG -   accept-language: *
2025-05-15 11:15:42,713 - __main__ - DEBUG -   sec-fetch-mode: cors
2025-05-15 11:15:42,713 - __main__ - DEBUG -   user-agent: node
2025-05-15 11:15:42,713 - __main__ - DEBUG -   accept-encoding: gzip, deflate
2025-05-15 11:15:42,713 - __main__ - DEBUG -   content-length: 127
2025-05-15 11:15:42,713 - mcp.server.sse - DEBUG - Handling POST message
2025-05-15 11:15:42,713 - mcp.server.sse - DEBUG - Parsed session ID: 3bf4c8d4-1028-4331-b21e-69e20b258676
2025-05-15 11:15:42,713 - mcp.server.sse - DEBUG - Received JSON: b'{"jsonrpc":"2.0","method":"notifications/cancelled","params":{"requestId":1,"reason":"AbortError: This operation was aborted"}}'
2025-05-15 11:15:42,713 - mcp.server.sse - DEBUG - Validated client message: root=JSONRPCNotification(method='notifications/cancelled', params={'requestId': 1, 'reason': 'AbortError: This operation was aborted'}, jsonrpc='2.0')
2025-05-15 11:15:42,713 - mcp.server.sse - DEBUG - Sending session message to writer: SessionMessage(message=JSONRPCMessage(root=JSONRPCNotification(method='notifications/cancelled', params={'requestId': 1, 'reason': 'AbortError: This operation was aborted'}, jsonrpc='2.0')), metadata=None)
2025-05-15 11:15:42,713 - __main__ - DEBUG - Response: 202
2025-05-15 11:15:42,713 - __main__ - DEBUG - Response headers:
2025-05-15 11:15:42,713 - __main__ - DEBUG -   content-length: 8
INFO:     127.0.0.1:50502 - "POST /messages/?session_id=3bf4c8d410284331b21e69e20b258676 HTTP/1.1" 202 Accepted

LibreChat debugging:

[danny-avila]

More info would be needed about your MCP server, also I'm using the latest version of LibreChat.

[NatiSayada]

I think there was a problem with my implementation of fastapi_mcp.
The message endpoint was working ok, but any other endpoint on the MCP server was not getting any session data.

iv converted back to mcp lib, and now I can see the headers.

thanks @danny-avila