Class: BioRuby::MCP::Server::KEGGOrganismTool

Inherits:
MCP::Tool
  • Object
show all
Defined in:
lib/bioruby/mcp/server/kegg_tools.rb

Overview

KEGG organism list tool

Constant Summary collapse

KEGG_REST_BASE = 
'http://rest.kegg.jp'

Class Method Summary collapse

Class Method Details

.call(filter: nil, server_context: nil) ⇒ Object 



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# File 'lib/bioruby/mcp/server/kegg_tools.rb', line 360

def call(filter: nil, server_context: nil)
  # Get list of organisms from KEGG REST API
  organism_data = kegg_list_entries('organism')
  
  if organism_data.nil? || organism_data.empty?
    return ::MCP::Tool::Response.new([{
      type: 'text',
      text: 'No organisms found'
    }])
  end

  organisms = organism_data.split("\n").map do |line|
    parts = line.split("\t")
    if parts.length >= 2
      org_code = parts[0]
      org_name = parts[1]
      { code: org_code, name: org_name }
    end
  end.compact

  # Apply filter if provided
  if filter
    organisms = organisms.select do |org|
      org[:name].downcase.include?(filter.downcase) ||
      org[:code].downcase.include?(filter.downcase)
    end
  end

  # Limit results and format
  organisms = organisms.first(50)
  formatted_list = organisms.map { |org| "#{org[:code]}: #{org[:name]}" }

  ::MCP::Tool::Response.new([{
    type: 'text',
    text: "KEGG Organisms#{filter ? " (filtered by '#{filter}')" : ''} (first 50):\n#{formatted_list.join("\n")}"
  }])
rescue => e
  ::MCP::Tool::Response.new([{
    type: 'text',
    text: "Error listing organisms: #{e.message}"
  }])
end