codeocean

This MCP server provides tools to search, run, and manage Code Ocean capsules and pipelines, along with handling associated data assets. The server is wired to the Code Ocean API via a domain and token, enabling authenticated interactions with your Code Ocean environment. Use MCP clients or tooling that supports the MCP protocol to connect to this server, and you’ll be able to discover available tools, execute capsules or pipelines, and transfer or reference data assets as part of your computational workflows. The AGENT_ID is used to identify the originating client in logs and dashboards.

To use the server in your environment, configure an MCP transport (e.g., uvx stdio transport) pointing to codeocean-mcp-server. Provide your Code Ocean domain and API token through environment variables. Once connected, you can browse the available MCP tools, call endpoints for running capsules or pipelines, and manage data assets associated with your Code Ocean projects. Local testing with MCP Inspector can help validate tool availability and request/response formats before integrating into automated workflows.

Prerequisites:

• Install uv (the Python/UV runtime) from Astral or via the UV project documentation.
• Install Python 3.10 or newer (via uv python install 3.10 or newer).
• Generate a Code Ocean access token from the Code Ocean user guide and keep it ready for configuration.

Installation steps:

1. Install UV/uvx runtime:
   • Follow instructions at the Astral uv deployment docs to install the uv runtime on your system.
2. Ensure Python 3.10+ is available through uv:
   • uv python install 3.10
3. Obtain your Code Ocean API token and note the domain you will connect to (e.g., https://codeocean.acme.com).
4. Start the MCP server using uvx with the proper server identifier:
   • uvx codeocean-mcp-server
5. Configure MCP clients to point at the server using the environment variables:
   • CODEOCEAN_DOMAIN=https://codeocean.acme.com
   • CODEOCEAN_TOKEN=<YOUR_API_KEY>
   • AGENT_ID=<Your_CLIENT_IDENTIFIER>

If you are integrating with specific tools (VS Code, Claude Desktop, Cline, Roo Code, Cursor, Windsurf), follow their respective gotchas for adding a new mcpServers entry that uses the same uvx transport and environment variables.

Tips and common considerations:

• The CODEOCEAN_DOMAIN and CODEOCEAN_TOKEN must be kept secure; avoid committing them to version control.
• AGENT_ID helps identify the source client in logs and UI dashboards.
• If you switch between environments (e.g., local testing vs. production Code Ocean), ensure the domain and token reflect the target environment.
• For debugging, you can use MCP Inspector to connect to uvx and inspect available tools and tool calls.
• If you encounter connection issues, verify that the uvx process is running and that the environment variables are correctly exported to the process.
• You can customize log formatting with the LOG_FORMAT environment variable if needed; missing LOG_FORMAT defaults to FastMCP’s standard logging.