Class: BioRuby::MCP::Server::KEGGCompoundTool

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

Overview

KEGG compound information tool

Constant Summary collapse

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

Class Method Summary collapse

Class Method Details

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



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# File 'lib/bioruby/mcp/server/kegg_tools.rb', line 102

def call(compound_id:, server_context: nil)
  # Clean up compound ID if needed
  compound_id = compound_id.gsub(/^(cpd:|compound:)/, '')
  
  # Get compound entry from KEGG REST API
  compound_data = kegg_get_entry(compound_id)
  
  if compound_data.nil? || compound_data.empty?
    return ::MCP::Tool::Response.new([{
      type: 'text',
      text: "Compound not found: #{compound_id}"
    }])
  end

  # Parse the compound data using BioRuby
  compound = Bio::KEGG::COMPOUND.new(compound_data)
  
  ::MCP::Tool::Response.new([{
    type: 'text',
    text: "KEGG Compound: #{compound_id}\n" \
          "Name: #{compound.name}\n" \
          "Formula: #{compound.formula}\n" \
          "Mass: #{compound.mass}\n" \
          "Comment: #{compound.comment}\n" \
          "Pathways: #{compound.pathways&.length || 0} pathways\n" \
          "Enzymes: #{compound.enzymes&.length || 0} enzymes"
  }])
rescue => e
  ::MCP::Tool::Response.new([{
    type: 'text',
    text: "Error retrieving compound info: #{e.message}"
  }])
end