agroportal-mcp

An MCP server that exposes the AgroPortal / OntoPortal API as tools for LLM clients (Claude Desktop, Claude Code, …). It is a thin wrapper around the ontologies_api_client Ruby gem, served with the official mcp gem over stdio (for local clients) or Streamable HTTP / SSE (for remote deployment).

Tools

More tools (e.g. search_ontologies, mappings, notes) can be added under lib/agroportal_mcp/tools/ and registered in TOOLS (lib/agroportal_mcp.rb).

Related MCP server: OMOPHub MCP Server

Requirements

• Ruby ≥ 2.7 (this project was set up with Homebrew Ruby at /usr/local/opt/ruby/bin/ruby).

• A checkout of ontologies_api_ruby_client as a sibling directory (the Gemfile references it via path: '../ontologies_api_ruby_client').

• An AgroPortal API key (create one from your AgroPortal account page).

Install

export PATH="/usr/local/opt/ruby/bin:$PATH"
cd ontologies_api_mcp
bundle install

Configuration

The server reads its connection settings from the environment:

Smoke test

You can drive the stdio protocol by hand:

export AGROPORTAL_API_KEY=your_key
printf '%s\n' \
  '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"smoke","version":"0"}}}' \
  '{"jsonrpc":"2.0","method":"notifications/initialized"}' \
  '{"jsonrpc":"2.0","id":2,"method":"tools/list"}' \
  '{"jsonrpc":"2.0","id":3,"method":"tools/call","params":{"name":"search_classes","arguments":{"query":"wheat","pagesize":3}}}' \
  | /usr/local/opt/ruby/bin/ruby bin/agroportal_mcp

Register with an MCP client

Claude Code (CLI)

claude mcp add agroportal \
  --env AGROPORTAL_API_KEY=your_key \
  -- /usr/local/opt/ruby/bin/ruby \
     /Users/maboukerfa/code/agroportal/ontologies_api_mcp/bin/agroportal_mcp

Claude Desktop (claude_desktop_config.json)

{
  "mcpServers": {
    "agroportal": {
      "command": "/usr/local/opt/ruby/bin/ruby",
      "args": [
        "/Users/maboukerfa/code/agroportal/ontologies_api_mcp/bin/agroportal_mcp"
      ],
      "env": {
        "AGROPORTAL_API_KEY": "your_key",
        "AGROPORTAL_REST_URL": "https://data.agroportal.eu"
      }
    }
  }
}

The entrypoint pins BUNDLE_GEMFILE to this project, so it can be launched from any working directory.

Remote deployment (Streamable HTTP / SSE)

To serve the same tools to remote clients, run the MCP Streamable HTTP transport instead of stdio. It uses SSE (text/event-stream) for streaming server responses, and replaces the deprecated standalone HTTP+SSE transport. config.ru mounts the server as a Rack app; install the http group (bundle install does this by default) and run it under Puma:

export AGROPORTAL_API_KEY=your_key
export AGROPORTAL_MCP_BEARER_TOKEN=$(openssl rand -hex 32)   # recommended
bundle exec puma config.ru -p 9292

The endpoint serves JSON-RPC at the root path. Smoke-test the handshake (drop the Authorization header if you left the token unset):

# 1) initialize — capture the Mcp-Session-Id from the response headers
curl -sN -i -X POST http://127.0.0.1:9292/ \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json, text/event-stream' \
  -H "Authorization: Bearer $AGROPORTAL_MCP_BEARER_TOKEN" \
  -d '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2025-11-25","capabilities":{},"clientInfo":{"name":"smoke","version":"0"}}}'

# 2) tools/list — reuse the session id from step 1 (response streams back as SSE)
curl -sN -X POST http://127.0.0.1:9292/ \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json, text/event-stream' \
  -H "Authorization: Bearer $AGROPORTAL_MCP_BEARER_TOKEN" \
  -H 'Mcp-Session-Id: <id-from-step-1>' \
  -H 'MCP-Protocol-Version: 2025-11-25' \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/list"}'

Operational notes:

• Terminate TLS in front. Run it behind a reverse proxy (nginx/Caddy) or load balancer that handles HTTPS — the bearer token is only as safe as the transport.

• Don't expose it unauthenticated. With AGROPORTAL_MCP_BEARER_TOKEN unset the endpoint is open (and warns at boot). Set it, or front it with an authenticating proxy.

• Concurrency. In the default stateful mode each connected client holds a long-lived SSE stream open, which ties up a Puma thread; size --threads (or set AGROPORTAL_MCP_STATELESS=true) to match expected concurrency. For many concurrent SSE streams, Falcon (fiber-based) scales better and serves the same config.ru — add gem 'falcon' to the :http group, then bundle exec falcon serve -b http://0.0.0.0:9292.

Register the remote server with Claude Code:

claude mcp add --transport http agroportal https://your-host.example/ \
  --header "Authorization: Bearer your_token"

Multi-tenant: per-user API keys

Host one shared instance and let each user authenticate with their own AgroPortal key. The server uses its own AGROPORTAL_API_KEY as the base credential and forwards each caller's key as userapikey, so the API attributes requests — permissions, rate limits, private ontologies — to that user.

export AGROPORTAL_API_KEY=server_app_key          # must be allowed to use userapikey (see below)
export AGROPORTAL_MCP_REQUIRE_USER_APIKEY=true     # reject requests with no user key
export AGROPORTAL_MCP_STATELESS=true               # recommended for multi-tenant
bundle exec puma config.ru -p 9292

Each user registers with their own key in the X-Agroportal-User-Apikey header:

claude mcp add --transport http agroportal https://mcp.agroportal.eu/ \
  --header "X-Agroportal-User-Apikey: <their_personal_key>"

The key is read per request and forwarded by the client's user_apikey middleware, producing Authorization: apikey token=<server>&userapikey=<user>. Thread#[] is fiber-local, so requests stay isolated under both Puma and Falcon.

Requirements and notes:

• The server's AGROPORTAL_API_KEY must be permitted to use userapikey — an admin/app account, not an ordinary user key. (You run AgroPortal, so you can mint one; confirm your API honours userapikey for it.)

• HTTPS is mandatory — users send their personal key on every request.

• Keep the client cache off (the default). A shared cache could serve one user's results, including private ontologies, to another.

• Without AGROPORTAL_MCP_REQUIRE_USER_APIKEY, a request that omits the header falls back to the server key; set it to reject those instead.

• The optional AGROPORTAL_MCP_BEARER_TOKEN gate is independent and can be layered on top for a deployment-wide secret.

Layout

bin/agroportal_mcp                     # executable stdio entrypoint (local clients)
config.ru                              # Rack entrypoint: Streamable HTTP / SSE (remote)
lib/agroportal_mcp.rb                  # build_server + run (stdio) / http_transport (SSE)
lib/agroportal_mcp/middleware.rb       # Rack middlewares: bearer gate + per-user apikey
lib/agroportal_mcp/client_setup.rb     # env -> LinkedData::Client config (+ Rails.cache shim)
lib/agroportal_mcp/tools/              # one file per MCP tool
  search_classes.rb