zenodo-mcp-server

An MCP server that allows LLM agents to query and interact with Zenodo repositories using the Zenodo REST API.

Features

• Unauthenticated access – search and inspect public records without an API key
• Session API key – supply a personal access token at runtime via the set_api_key tool
• Persistent service account – set ZENODO_API_KEY environment variable for a long-lived key
• Optional write access – create, update, and publish depositions (enabled via ZENODO_ALLOW_WRITE=true)
• Search records with full Elasticsearch query syntax, pagination, and filtering
• Browse and filter Zenodo communities
• Retrieve record metadata, files, and file content (text or binary)
• List, create, update, publish, and version depositions (write tools require ZENODO_ALLOW_WRITE=true)
• Configurable Zenodo base URL for sandbox or self-hosted instances
• Optional default community filter via ZENODO_COMMUNITY

Quick Start

Prerequisites

• Node.js 18 or later
• npm

Installation

git clone https://github.com/eic/zenodo-mcp-server.git
cd zenodo-mcp-server
npm install
npm run build

Running the server

# Without authentication (public records only)
node build/src/index.js

# With a persistent API key (service account)
ZENODO_API_KEY=your_token node build/src/index.js

# Against the Zenodo sandbox
ZENODO_BASE_URL=https://sandbox.zenodo.org ZENODO_API_KEY=your_sandbox_token node build/src/index.js

Authentication

Zenodo uses personal access tokens for authentication.

Option 1 – Session key (recommended for interactive use)

After connecting to the server, call the set_api_key tool:

{ "name": "set_api_key", "arguments": { "api_key": "your_personal_access_token" } }

The token is stored in memory for the lifetime of the server process and is never written to disk.

Option 2 – Environment variable (service account / CI)

export ZENODO_API_KEY=your_personal_access_token
node build/src/index.js

Creating a token

1. Log in to zenodo.org
2. Go to Account → Settings → Applications → Personal access tokens
3. Click New token and select the required scopes:
   • deposit:write – create and update depositions
   • deposit:actions – publish depositions
   • user:email – verify identity (optional)
4. Save the token securely – it is shown only once

Available Tools

Tool	Description	Auth required	Write required
get_auth_status	Check authentication status and get setup guidance	No	No
set_api_key	Set a personal access token for the current session	No	No
search_records	Search Zenodo records with Elasticsearch query syntax	No	No
get_community	Get details about a specific Zenodo community	No	No
list_communities	Search or list Zenodo communities	No	No
get_record	Get full metadata for a record by ID or DOI	No	No
list_record_files	List files attached to a record	No	No
get_file_content	Download file content (text or base64)	No	No
list_depositions	List your own depositions (drafts + published)	Yes	No
create_deposition	Create a new empty deposition (draft)	Yes	Yes
get_deposition	Retrieve a single deposition by ID	Yes	Yes
update_deposition	Update metadata of a draft deposition	Yes	Yes
delete_deposition	Delete an unpublished draft deposition	Yes	Yes
upload_file	Upload a file to a deposition	Yes	Yes
delete_deposition_file	Delete a file from an unpublished deposition	Yes	Yes
publish_deposition	Publish a deposition and register a DOI	Yes	Yes
edit_deposition	Unlock a published deposition for metadata edits	Yes	Yes
discard_deposition	Discard edits and revert to published state	Yes	Yes
new_version	Create a new version of a published deposition	Yes	Yes

Write tools are only available when ZENODO_ALLOW_WRITE=true (or ZENODO_ALLOW_WRITE=1) is set. See docs/TOOLS.md for full parameter details.

search_records

{
  "name": "search_records",
  "arguments": {
    "query": "electron ion collider",
    "size": 10,
    "page": 1,
    "sort": "mostrecent",
    "type": "publication",
    "subtype": "article",
    "communities": "zenodo",
    "all_versions": false,
    "bounds": "143.37,-38.99,146.90,-37.35"
  }
}

Sort options: bestmatch, mostrecent, mostviewed, mostdownloaded (prefix - for descending).

Resource types: publication, poster, presentation, dataset, image, video, software, lesson, other.

bounds — optional geolocation bounding box: "west,south,east,north" in decimal degrees.

When ZENODO_COMMUNITY is set, the communities parameter defaults to that value if not supplied.

get_record

Accepts a numeric ID or a DOI:

{ "name": "get_record", "arguments": { "id": "1234567" } }
{ "name": "get_record", "arguments": { "id": "10.5281/zenodo.1234567" } }

get_file_content

{
  "name": "get_file_content",
  "arguments": {
    "id": "1234567",
    "filename": "data.csv",
    "max_bytes": 1048576
  }
}

Text files are returned as UTF-8 strings. Binary files are returned as base64. The truncated field indicates whether the file was cut at max_bytes.

Environment Variables

Variable	Default	Description
ZENODO_BASE_URL	https://zenodo.org	Base URL of the Zenodo instance
ZENODO_API_KEY	(none)	Personal access token for persistent authentication
ZENODO_ALLOW_WRITE	(unset)	Set to true or 1 to enable write tools (depositions)
ZENODO_COMMUNITY	(none)	Default community identifier applied to searches
ZENODO_MAX_UPLOAD_BYTES	52428800 (50 MiB)	Maximum file size for upload_file

MCP Client Configuration

Add the server to your MCP client configuration (e.g. Claude Desktop claude_desktop_config.json):

{
  "mcpServers": {
    "zenodo": {
      "command": "node",
      "args": ["/path/to/zenodo-mcp-server/build/src/index.js"],
      "env": {
        "ZENODO_API_KEY": "your_token_here"
      }
    }
  }
}

Development

npm run build        # Compile TypeScript
npm run watch        # Watch mode
npm test             # Build and run tests
npm run test:coverage  # Tests with coverage report

License

MIT