Class: BioRuby::MCP::Server::KEGGPathwayFinderTool

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

Overview

KEGG pathway finder 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 293

def call(compound_id:, server_context: nil)
  # Clean up compound ID
  compound_id = compound_id.gsub(/^(cpd:|compound:)/, '')
  
  # Get compound info first to find associated pathways
  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

  compound = Bio::KEGG::COMPOUND.new(compound_data)
  
  if compound.pathways.nil? || compound.pathways.empty?
    return ::MCP::Tool::Response.new([{
      type: 'text',
      text: "No pathways found for compound: #{compound_id}"
    }])
  end

  pathway_list = compound.pathways.map do |pathway_id, pathway_name|
    "#{pathway_id}: #{pathway_name}"
  end

  ::MCP::Tool::Response.new([{
    type: 'text',
    text: "Pathways containing compound #{compound_id}:\n#{pathway_list.join("\n")}"
  }])
rescue => e
  ::MCP::Tool::Response.new([{
    type: 'text',
    text: "Error finding pathways: #{e.message}"
  }])
end