gistfile1.builder

require "dm-core"
require "dm-timestamps"

# Note, a GSE etc could have two of the same field (i.e. Pubmed so check for that
# and make an array instead)

# GDS
#   has 1 GSE
#   has n GDSSubsets
# GDSSubset
#   belongs_to GDS
#   has n samples (GDSSubsets)
# GDSSubsetMember
#   belongs_to GDSSubset
#   has 1 GSM
# GSE
#   # does not necessarily belong to a GDS
#   has n GSMs
# GSM
#   has 1 GPL
#   has n measurements (
# GPL
#   has n GSMs

module GEOAnnotator
  module ORM
    class GEO
      def self.inherited(subclass)
        subclass.class_eval do
          include DataMapper::Resource
          def self.default_repository_name; :expr_geo; end
        end
      end
    end
    
    class GDS < GEO
      storage_names[:expr_geo] = "gds"
        
      property :gds, Integer, :key => true
        
      property :channel, Integer
      property :gpl_organism, String
      property :feature, Integer
      property :pubmed, Integer
      property :sample_organism, String
      property :sample_type, String
      property :technology, String
      property :title, String
      property :type, String
      
      has 1, :gds_gse, "GDSGSE", :child_key => [:gds], :parent_key => [:gds]
      has 1, :gse_object, "GSE", :through => :gdsgse
    end 
    
    class GDSGSE < GEO
      storage_names[:expr_geo] = "gds_gse"
        
      belongs_to :gds_object, "GDS", :child_key => [:gds], 
                 :parent_key => [:gds], :key => true
                   
      # child_key is parent's key INTO the child, parent_key is child's key 
      # INTO the parent.
      belongs_to :gse_object, "GSE", :child_key => [:gse], 
                 :parent_key => [:gse]
    end
    
    class GSE < GEO
      storage_names[:expr_geo] = "gse"
        
      property :gse, Integer, :key => true
      property :field, String, :key => true
      property :value, String
      
      has n, :gsms, "GSM"
    end
    
    class GSM < GEO
      storage_names[:expr_geo] = "gsm"
        
      property :gsm, Integer, :key => true
      property :channel, Integer, :key => true
      property :field, String, :key => true
      property :value, String
      
      has n, :measurements, "GSMGeneData"
    end
    
    class GSMGeneData < GEO
      storage_names[:expr_geo] = "gsm_gene_data"
      property :id, String, :key => true
      property :value, Integer
    end

  end
end