mesa-mcp¶

Repo: idss-mesa/mesa-mcp · Language: Python 3.11+ · Registered as: mesa-mcp

The flagship MESA server. It bridges the CyVerse Data Store (iRODS) with ontology-driven metadata management and exposes everything as MCP tools.

Tool groups¶

Prefix	What it does
`ds_*`	iRODS Data Store: list/read/write/move files, directories, AVUs, ACLs, tickets, rules, policies (drop-in compatible with irods-mcp-server)
`mesa_ols_*`	Browse OBO/OLS ontologies: search terms, fetch hierarchies, generate AVU templates
`mesa_avu_*`	Apply ontology terms and DataCite fields as AVUs (with the CURIE in the `unit` slot)
`mesa_datacite_*`	DataCite metadata: template, validate, export, apply
`mesa_ducklake_*`	Metadata history: init a project, snapshot, list history, time-travel, diff (backed by mesa-ducklake)

How MESA runs it¶

The installer creates a uv venv and installs mesa-mcp editable (alongside mesa-ducklake), then registers the stdio entry point:

~/.mesa/.venv/bin/mesa-mcp --transport stdio

It is registered under the name mesa-mcp with every detected client — see Claude Code, Codex CLI, Antigravity, or OpenCode for the exact registration each one gets.

The AVU contract¶

Metadata is written as (attribute, value, unit) triples, where unit is reserved for the ontology CURIE when the AVU came from OBO/OLS. Provenance (actor, source, ticket, rule) is recorded in DuckLake columns, never folded into the triple.

Configuration¶

Configuration precedence is CLI flag > environment variable > YAML file > defaults. The defaults target anonymous public CyVerse access. See Credentials and .env.example for the full set.

Full documentation lives in the repo under docs/ (user / dev / deploy guides).