The filesystem server stopped working with the OpenAI Agent SDK.

[buehler]

Describe the bug
It has been working with an old version of the filesystem server. However, after upgrading the server, openAI (and also the model context protocol inspector) throw errors when trying to list the tools.

To Reproduce
Either:

1. use npx -y @modelcontextprotocol/inspector npx @modelcontextprotocol/server-filesystem ./
2. try to "list tools"
3. get the following error:

[
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      0,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      1,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      2,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      3,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      4,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      5,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      6,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      7,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      8,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      9,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      10,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      11,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      12,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  }
]

Or:

1. use openai sdk to start the MCP server
2. when trying to interact with it
3. get the following error:

openai.BadRequestError: Error code: 400 - {'error': {'message': 'Invalid schema for function \'read_file\': schema must be a JSON Schema of \'type: "object"\', got \'type: "None"\'.', 'type': 'invalid_request_error', 'param': 'tools[0].parameters', 'code': 'invalid_function_parameters'}}

Expected behavior
The MCP server should work :)

Logs
Provided in the steps to reproduce

Additional context
Currently uses:
node 24
openai sdk 0.6.1
filesystem server latest

[buehler]

I try to find out in which version this happened. But it seems to be an issue deeply hidden. The published versions do not have this issue and when I download the main branch and run it, it works until the result is parsed where openAI agent sdk throws a different error about return types.

[buehler]

Addition: apparently it is a combination of several factors. The upgrade of "zod" and the upgrade of the MCP SDK.

Zod4 breaks somehow, and using zod3 with the "registerTool" method of the SDK also breaks.

Current working version for me:

  "dependencies": {
    "@modelcontextprotocol/sdk": "^1",
    "zod": "^3"
  }

and inside the mcp server use server.tool instead of server.registerTool. With this, I can run the server without issues.

[buehler]

finally got it working. but not with zod4. there is some issue with zod4 and the sdk I guess.

[vincentjames501]

@buehler , do you happen to know which version it broke for? Even as I start navigating backwards via npx -y @modelcontextprotocol/inspector@0.16.8 npx @modelcontextprotocol/server-filesystem@2025.1.14 ./data it is still failing for me?

[olaservo]

cc @domdomegg - looks like there was an issue with the filesystem refactor, I started looking into it but if you get a chance wanted to make sure you saw this too.

[badspider7]

i get the same issue

[buehler]

Hey @vincentjames501, I think it is more related to zod and the mcp-sdk. I did go back in time and installed all versions of the fileserver and somehow no version worked.

I tried around with sdk / zod versions locally and managed to get an implmementation running:

import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
import { readFile } from 'fs/promises';
import { z } from 'zod';

const log = (...params) => console.error(...params);

const server = new McpServer({
  name: 'filesystemserver',
  version: '1.0.0',
  capabilities: {
    resources: {},
    tools: {},
  },
});

server.registerTool(
  'read_file',
  {
    title: 'Read File',
    description: 'Read the content of a file and return it as text.',
    inputSchema: {
      path: z.string(),
    },
    outputSchema: {
      content: z.string().nullable(),
      error: z.string().optional(),
    },
  },
  async ({ path }) => {
    try {
      log('Reading file at path:', path);
      const content = (await readFile(path)).toString('utf8');
      return {
        content: [],
        structuredContent: {
          content,
        },
      };
    } catch (e) {
      log('Error reading file:', e);
      return {
        content: [],
        structuredContent: {
          content: null,
          error: `${e}`,
        },
      };
    }
  }
);

package json:

{
  "name": "filesystem_mcp_server",
  "private": true,
  "type": "module",
  "dependencies": {
    "@modelcontextprotocol/sdk": "^1",
    "zod": "^3"
  }
}

So finally, I think it may not be related to the code of fileserver, but more to the SDK in combination with Zod.

EDIT: note that this code does work with the openAI agent sdk, HOWEVER: you need to set use_structured_content=True in the MCPServerStdio class when instantiating the mcp server.

[Wo1framalpha]

The latest main branch source code no longer has this issue. It appears to have been fixed in recent commits, but the npm package has not been updated yet.

[Wo1framalpha]

In the August 23rd version, the "inputSchema" was generated via the zodToJsonSchema method from "zod-to-json-schema" package. However, it appears this method was used incorrectly, resulting in all tool‘s "inputSchemas" being {"$schema":"http://json-schema.org/draft-07/schema#"}. and failed validation by the MCP SDK.

[olaservo]

Thanks all for the sleuthing, it does seem like the issue is that this hasn't been published to npm in a while. Will update here once that gets sorted out.

[domdomegg]

it does seem like the issue is that this hasn't been published to npm in a while

Is that the filesystem server, or the OpenAI / inspector? I can try to chase around internally to get the filesystem server release approved.

[olaservo]

@domdomegg its the filesystem server: https://www.npmjs.com/package/@modelcontextprotocol/server-filesystem

Looks like this is the latest release awaiting approval: https://github.com/modelcontextprotocol/servers/actions/runs/19665766137