require 'rbbt'
require 'rbbt/resource'

module KEGG
  extend Resource
  self.pkgdir = "phgx"
  self.subdir = "share/kegg"


  KEGG.claim KEGG.root, :rake, Rbbt.share.install.KEGG.Rakefile.find(:lib)

  def self.names
    @@names ||= KEGG.pathways.tsv :fields => ["Pathway Name"], :persist => true, :type => :single, :unnamed => true
  end

  def self.descriptions
    @@descriptions ||= KEGG.pathways.tsv(:fields => ["Pathway Description"], :persist => true, :type => :single, :unnamed => true)
  end


  def self.index2genes
    @@index2genes ||= KEGG.gene_pathway.tsv(:key_field => "KEGG Pathway ID", :fields => ["KEGG Gene ID"], :persist => true, :type => :flat, :merge => true)
  end

  def self.index2ens
    @@index2ens ||= KEGG.identifiers.index(:persist => true)
  end

  def self.index2kegg
    @@index2kegg ||= KEGG.identifiers.index(:target => "KEGG Gene ID", :persist => true)
  end

  def self.id2name(id)
    names[id]
  end

  def self.name2id(name)
    names.select{|id,n| n.downcase.index(name.downcase) == 0}.collect{|id,n| id} rescue []
  end


  def self.description(id)
    descriptions[id]
  end
end

if defined? Entity 

  module KeggPathway
    extend Entity
    self.format = "KEGG Pathway ID"

    self.annotation :organism

    def self.filter(query, field = nil, options = nil, entity = nil)
      return true if query == entity

      return true if KeggPathway.setup(entity.dup, options.merge(:format => field)).name.index query

      false
    end

    property :name => :single2array do
      return nil if self.nil?
      name = KEGG.id2name(self)
      name.sub(/ - Homo.*/,'') unless name.nil?
    end

    property :description => :single2array do
      KEGG.description(self)
    end

    property :genes => :array2single do |*args|
      organism = args.first || self.organism
      KEGG.index2genes.values_at(*self).
        each{|gene| gene.organism = organism if gene.respond_to? :organism }
    end
  end

  if defined? Gene and Entity === Gene
    module Gene
      add_identifiers KEGG.identifiers

      #def to_kegg
      #  return self if format == "KEGG Gene ID"
      #  if Array === self
      #    Gene.setup(KEGG.index2kegg.values_at(*to("Ensembl Gene ID")), "KEGG Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
      #  else
      #    Gene.setup(KEGG.index2kegg[to("Ensembl Gene ID")], "KEGG Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
      #  end
      #end

      #def from_kegg
      #  return self unless format == "KEGG Gene ID"
      #  if Array === self
      #    Gene.setup(KEGG.index2ens.values_at(*self), "Ensembl Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
      #  else
      #    Gene.setup(KEGG.index2ens[self], "Ensembl Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
      #  end
      #end

      #property :to => :array2single do |new_format|
      #  case
      #  when format == new_format
      #    self 
      #  when format == "KEGG Gene ID"
      #    ensembl = from_kegg.clean_annotations
      #    Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => ensembl, :format => new_format).exec.chunked_values_at(ensembl), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
      #  when new_format == "KEGG Gene ID"
      #    to_kegg
      #  else
      #    Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => self, :format => new_format).exec.chunked_values_at(self), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
      #  end
      #end


      def self.gene_kegg_pathway_index
        @@gene_kegg_pathway_index ||= 
          KEGG.gene_pathway.tsv(:persist => true, :key_field => "KEGG Gene ID", :fields => ["KEGG Pathway ID"], :type => :flat, :merge => true)
      end

      property :kegg_pathways => :array2single do
        @kegg_pathways ||= Gene.gene_kegg_pathway_index.values_at(*self.to("KEGG Gene ID")).
          each{|pth| pth.organism = organism if pth.respond_to? :organism }.tap{|o| KeggPathway.setup(o, organism)}
      end
    end
  end
end