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Reported issues for tooluniverse

Pod holds 19 of 24 problems reported by people outside the maintainer team. Issues filed by the project's own owners, members and collaborators are excluded entirely — a maintainer's release checklist is not a warning to a prospective user.

Back to tooluniverse.

Most discussed

Claude Desktop MCP extension (tooluniverse 1.0.16) fails to start due to yanked fitz dep — please cut a new extension release once #516 lands

Summary

The Claude Desktop extension bundle (tooluniverse v1.0.16, internal package tooluniverse-mcp-native 1.0.15) no longer starts: its bundled pyproject.toml declares fitz>=0.0.1.dev2, and since that version was yanked from PyPI, uv cannot resolve the environment. The server process exits before completing the MCP handshake, and Claude Desktop reports the extension as disconnected.

PR #516 fixes this in the main repo (fitz → pymupdf), but the Desktop extension ships its o

Read the thread · 2026-08-12 · open · external user · 4 comments

[Feature request] GEANT4 mcp integration

From simulation side a GEANT4 MCP integration like this one would be extremely usefull!

Read the thread · 2026-06-10 · open · external user · 2 comments

MCPB manifest invalid: server.type 'uv' violates spec enum (python|node|binary)

Problem

The MCPB bundle published at the GitHub Release asset URL

https://github.com/mims-harvard/ToolUniverse/releases/download/mcpb/tooluniverse.mcpb

fails MCPB-manifest validation in Claude Code 2.1.150 with:

MCPB manifest invalid at https://github.com/mims-harvard/ToolUniverse/releases/download/mcpb/tooluniverse.mcpb:
  Invalid manifest: server: Invalid enum value. Expected 'python' | 'node' | 'binary', received 'uv'

This surfaces on every claude /doctor invocation for an

Read the thread · 2026-05-26 · closed · external user · 2 comments

MCPB manifest fails Claude Code validation: server: "uv" not in allowed enum

The MCPB bundle published at https://github.com/mims-harvard/ToolUniverse/releases/download/mcpb/tooluniverse.mcpb fails to load in Claude Code's plugin system. /doctor reports:

Plugin (tooluniverse @ tooluniverse@life-sciences): MCPB manifest invalid at
https://github.com/mims-harvard/ToolUniverse/releases/download/mcpb/tooluniverse.mcpb:
Invalid manifest: server: Invalid enum value.
Expected 'python' | 'node' | 'binary', received 'uv'

Cause

The MCPB manifest schema (used by C

Read the thread · 2026-05-14 · closed · external user · 2 comments

MCPB manifest uses invalid server type 'uv' - should be 'python'

Description

The MCPB manifest at https://github.com/mims-harvard/ToolUniverse/releases/download/mcpb/tooluniverse.mcpb specifies an invalid server type, causing installation to fail.

Error Message

MCPB manifest invalid at https://github.com/mims-harvard/ToolUniverse/releases/download/mcpb/tooluniverse.mcpb: 
Invalid manifest: server: Invalid enum value. Expected 'python' | 'node' | 'binary', received 'uv'

Root Cause

The MCPB specification only allows three valid values

Read the thread · 2026-02-01 · closed · external user · 2 comments

Tool call in Claude Code crashes when ToolUniverse tool name is > 45 characters long

Description

The MCP standard specifies that tool names must be maximum 64 characters long (link). When the tool name is > 64 characters long, the tool call fails and puts Claude Code in an error loop that requires to exit or clear the session context.

Claude Code tool names are constructed using this template mcp__{mcp_server_name}__{tool_name}. Here the prefix is mcp__tooluniverse__ so th

Read the thread · 2026-01-26 · closed · external user · 5 comments

Could not connect to MCP server tooluniverse

Hi, I have followed the install instructions for Claude Desktop, but when I try and restart Claude three errors are produced:

Could not connect to MCP server tooluniverse MCP tooluniverse: spawn uv ENOENT MCP tooluniverse: Server disconnected. For troubleshooting guidance, please visit our debugging documentation

Any idea how these can be fixed?

Thanks, Ryan

Read the thread · 2025-11-07 · closed · external user · 4 comments

tools name too long

I tried to deploy the Tooluniverse MCP on claude and it worked. But claude failed to run the tool when i sent a query on chat window.

Here is the error from claude: ''' tools.13.FrontendRemoteMcpToolDefinition.name: String shouldhave at most 64 characters '''

i asked the LLM and it told me that over 64 characters tools'name definition is not allowed in MCP Protocol and i run a .py to see if there do are over 64 characters tools'name. Here are some from fda_drug_labeling_tools.json: ''' tool #7

Read the thread · 2025-06-05 · closed · external user · 3 comments

Most recent

The Claude Desktop MCPB extension (ant.dir.gh.tooluniverse.tooluniverse-mcp) cannot start

The Claude Desktop MCPB extension (ant.dir.gh.tooluniverse.tooluniverse-mcp) cannot start. uv fails dependency resolution before Python ever launches, the pipe closes, and Claude Desktop retries in a tight loop — my mcp-server-ToolUniverse.log reached 15,888 lines (1.19 MB) from a single session.

The failure

Running the extension's exact command by hand:

× No solution found when resolving `--with` dependencies:
  ╰─▶ Because only fitz==0.0.0 is available and
      tooluniverse-mc

[Read the thread](https://github.com/mims-harvard/ToolUniverse/issues/528) · 2026-08-13 · closed · external user · 1 comment

### execute_tool's `arguments` parameter loses `type: object` in exposed MCP schema, causing clients to send it as a JSON string

While using the ToolUniverse MCP server (compact mode, stdio transport) from Claude Code, every call to `execute_tool` failed with:

1 validation error for call[execute_tool] arguments Input should be a valid dictionary [type=dict_type, input_value='{"query": "...", "limit": 3}', input_type=str]


The client (Claude Code) was sending `arguments` as a JSON-encoded **string** even though it was constructed as a proper object.

## Root cause

`execute_tool`'s schema declares `arguments` as

[Read the thread](https://github.com/mims-harvard/ToolUniverse/issues/253) · 2026-06-12 · closed · external user · 2 comments

### Gemini provider: `return_json` agentic tools fail; deterministic tools default to temp 1.0

[submited with claude-code]

**Version:** tooluniverse 1.2.4 (pip/uv)
**Provider under test:** Gemini (free tier), `gemini-flash-latest`
**Config:** `TOOLUNIVERSE_LLM_DEFAULT_PROVIDER=GEMINI`, `TOOLUNIVERSE_LLM_MODEL_DEFAULT=gemini-flash-latest`, `TOOLUNIVERSE_LLM_CONFIG_MODE=env_override`

I ran the full `agents`-category battery end to end on the Gemini provider (both the CLI `tu run` path and the MCP `execute_tool` path). Most tools work well. Two issues surfaced that specifically affect anyo

[Read the thread](https://github.com/mims-harvard/ToolUniverse/issues/247) · 2026-06-05 · closed · external user · 1 comment

### tu test reports return_schema mismatch on tools returning valid live data (UniProt, RCSB, ClinicalTrials) — v1.2.4

[Submitted via claude-code]

## Summary

Several tools report `return_schema mismatch` under `tu test` even though they successfully retrieve correct, well-formed live data. The declared `return_schema` for these tools appears narrower or staler than what the live upstream APIs now return, so `tu test` produces false negatives. `tu run` / MCP `execute_tool` are unaffected (they do not enforce `return_schema`), so this is a validation-metadata bug rather than a functional one, but it makes `tu te

[Read the thread](https://github.com/mims-harvard/ToolUniverse/issues/246) · 2026-06-05 · closed · external user · 1 comment

### `ClinicalTrials_search_studies` sends invalid `filter.studyType` param to CT.gov v2 API → 400 Bad Request

### Summary

`ClinicalTrials_search_studies` (and the underlying `ClinicalTrialsTool._run_search`) maps the `filter_study_type` argument to a query-string param `filter.studyType`, which is not a valid CT.gov v2 API parameter. Any call that passes `filter_study_type` hard-fails with HTTP 400 from CT.gov.

This appears to be a half-completed refactor: the same file already implements the correct `filter.advanced` AREA-expression handling for `filter_phase` (line 178: *"CTG API v2 uses filter.adva

[Read the thread](https://github.com/mims-harvard/ToolUniverse/issues/189) · 2026-05-22 · closed · external user · 0 comments

### MCP tool definitions fully injected into system prompt, causing massive token waste

Scenario: Connecting tooluniverse (2214 tools) via MCP. Every conversation round injects all tool names, descriptions, and parameter schemas into the system prompt.

Problem: Even when only 1-2 tools are actually used, the full set of 2214 definitions consumes 50K-100K+ tokens per turn. In practice, nearly no user needs all tools simultaneously in a single project.

Suggestion: Could you add lazy loading or selective registration for type:local MCP servers? For example:

Group tools by category,

[Read the thread](https://github.com/mims-harvard/ToolUniverse/issues/185) · 2026-05-14 · closed · external user · 1 comment

### DisGeNET tool returns empty results due to outdated API endpoint/auth

The DisGeNET_search_gene and DisGeNET_search_disease tools always return empty results (count: 0, status: success) regardless of input.
Diagnosis: The tool description references disgenet.org (old domain), but DisGeNET has migrated to a commercial service at api.disgenet.com since 2024 with a new authentication scheme.
Confirmation: Direct testing of the new API works correctly:

curl -H "Authorization: Bearer $DISGENET_API_KEY" \
  "https://api.disgenet.com/api/v1/gda/summary?gene_ncbi_id=7157&

[Read the thread](https://github.com/mims-harvard/ToolUniverse/issues/175) · 2026-05-07 · closed · external user · 1 comment

### feat: add USPTO Open Data Portal tools (patent search, PTAB, office actions)

## Summary

Add tools for the USPTO Open Data Portal (ODP) API. Enables patent landscape analysis, competitive IP intelligence, and litigation risk assessment directly from ToolUniverse.

## API Reference

- **Base URL**: `https://api.uspto.gov/api/v1`
- **Auth**: `x-api-key` header (`USPTO_API_KEY` env var)
- **Docs**: https://data.uspto.gov/apis/api-syntax-examples
- **Rate limits**: https://data.uspto.gov/apis/api-rate-limits
- **Swagger**: https://data.uspto.gov/apis/swagger-ui

## Critical 

[Read the thread](https://github.com/mims-harvard/ToolUniverse/issues/159) · 2026-04-06 · closed · external user · 1 comment

### Add a description to improve Dispatch discoverability

Hi! Your Claude Code skill `devtu-github` has been discovered by [Dispatch](https://dispatch.visionairy.biz) — a Claude Code runtime that proactively recommends tools at task shifts and intercepts when Claude picks something suboptimal — helping developers discover the best plugins, skills, and MCPs for what they're working on.

Right now your skill has no description, which limits how effectively Dispatch can recommend it. A short 1–2 sentence description of what your skill does would significa

[Read the thread](https://github.com/mims-harvard/ToolUniverse/issues/155) · 2026-03-29 · closed · external user · 1 comment

### MCPB manifest invalid: server type 'uv' not supported by Claude Code plugin system

## Bug Report

**Plugin:** tooluniverse @ life-sciences  
**Version:** 1.0.0

## Error

When installing the plugin via Claude Code's plugin system, the following error appears:

MCPB manifest invalid at https://github.com/mims-harvard/ToolUniverse/releases/download/mcpb/tooluniverse.mcpb: Invalid manifest: server: Invalid enum value. Expected 'python' | 'node' | 'binary', received 'uv'


## Cause

The `.mcpb` manifest file declares `server: uv`, but Claude Code's plugin system only accept

[Read the thread](https://github.com/mims-harvard/ToolUniverse/issues/131) · 2026-03-13 · closed · external user · 1 comment

### cBioPortal_get_mutations tool returns 404 due to API changes

### Description

Trying to retrieve mutation data from cBioPortal causes a 404 (Not found) error.

### Example

get BRCA2 mutations in breast cancer from cBioPortal ... ... ⏺ tooluniverse - cBioPortal_get_mutations (MCP)(study_id: "brca_tcga", gene_list: "BRCA2") ⎿  { "status": "error", "error": "cBioPortal API error: 404 Client Error: for url: https://www.cbioportal.org/api/mutations?studyId=brca_tcga&geneList=BRCA2", "url": "https://www.cbioportal.org/api/mut

Read the thread · 2026-02-01 · closed · external user · 1 comment

The remaining reports are on the project's issue tracker.