Class: BioRuby::MCP::Server::KEGGPathwayTool

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

Overview

KEGG pathway information tool

Constant Summary collapse

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

Class Method Summary collapse

Class Method Details

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



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# File 'lib/bioruby/mcp/server/kegg_tools.rb', line 28

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

  # Parse the pathway data using BioRuby
  pathway = Bio::KEGG::PATHWAY.new(pathway_data)
  
  result = []
  result << {
    type: 'text',
    text: "KEGG Pathway: #{pathway_id}\n" \
          "Name: #{pathway.name}\n" \
          "Description: #{pathway.description}\n" \
          "Class: #{pathway.pathway_class}\n" \
          "Genes: #{pathway.genes&.length || 0} genes\n" \
          "Compounds: #{pathway.compounds&.length || 0} compounds"
  }
  
  if pathway.genes && !pathway.genes.empty?
    gene_list = pathway.genes.first(10).map { |gene_id, name| "#{gene_id}: #{name}" }
    result << {
      type: 'text',
      text: "Sample genes (first 10):\n#{gene_list.join("\n")}"
    }
  end

  ::MCP::Tool::Response.new(result)
rescue => e
  ::MCP::Tool::Response.new([{
    type: 'text',
    text: "Error retrieving pathway info: #{e.message}"
  }])
end