gistfile1.builder

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


module GORM
  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 => :gds_gse
  end

  class GDSGSE < GEO
    storage_names[:expr_geo] = "gds_gse"

    belongs_to :gds_object, "GDS", :child_key => [:gds], :parent_key => [:gds], :key => true
    belongs_to :gse_object, "GSE", :child_key => [:gse], :parent_key => [:gse], :key => true
  end

  class GSE < GEO
    storage_names[:expr_geo] = "gse_list"
    property :gse, Integer, :key => true
    has n, :_fields, "GSEField", :child_key => [:gse], :parent_key => [:gse]
    has n, :gsm_objects, "GSM", :through => :gse_gsm

    # But it doesn't necessarily have either of these.
    has 1, :gds_gse, "GDSGSE", :child_key => [:gse], :parent_key => [:gse]
    has 1, :gds_object, "GDS", :through => :gds_gse

    #    def gsms
    #      repository.adapter.select(%Q{
    #          SELECT gsm FROM gse_gsm WHERE gse = ?
    #        }, gse)
    #    end
  end

  class GSEField < GEO
    storage_names[:expr_geo] = "gse"

    belongs_to :gse_object, "GSE", :child_key => [:gse], :parent_key => [:gse], :key => true

    property :gse, Integer, :key => true
    property :field, String, :key => true
    property :value, String
  end

  class GSEGSM < GEO
    storage_names[:expr_geo] = "gse_gsm"
    # parent key: parent identifies the child by
    # child key: child identifies the parent by.
    # if the (only) object attribute is belongs_to, :gse_object, "GSE"
    #   and no key information is given, [gse, gse_object_field, gse_object_gse]
    #   and the parent_key is gse, [gse_object_gse]
    #   and the child_key is gse, [gse, gse_object_field]
    #   and both keys are gse, [gse]
    belongs_to :gse_object, "GSE", :child_key => [:gse], :parent_key => [:gse], :key => true

    belongs_to :gsm_object, "GSM", :child_key => [:gsm], :parent_key => [:gsm], :key => true
  end

  class GSM < GEO
    storage_names[:expr_geo] = "gsm_list"
    property :gsm, Integer, :key => true
    has n, :attributes, "GSMField", :child_key => [:gsm], :parent_key => [:gsm]
    # for has n:
    # with no keys, get gsm_gsm, gsm_channel, gsm_field.
    # with just child key at gsm, get [gsm, gsm_channel, gsm_field].
    # with just parent key at gsm, get [gsm_gsm] (table name + field name)
    # with both, get [gsm]!

    has 1, :gse_gsm, "GSEGSM", :child_key => [:gsm], :parent_key => [:gsm]
    # something else for parent and child key.
    has 1, :gse_object, "GSE", :through => :gse_gsm
  end

      class GSMField < GEO
        storage_names[:expr_geo] = "gsm"
  
        belongs_to :gsm_object, "GSM", :parent_key => [:gsm], :key => true
        property :channel, Integer, :key => true
        property :field, String, :key => true
        property :value, String
  
      end

  #    class GSMGeneData < GEO
  #      storage_names[:expr_geo] = "gsm_gene_data"
  #      property :id, String, :key => true
  #      property :val, Integer
  #    end
  #
  #    class GSMGPL < GEO
  #      storage_names[:expr_geo] = "gsm_gpl"
  #      belongs_to :gsm_object, "GSM", :child_key => [:gsm], :parent_key => [:gsm], :key => true
  #      belongs_to :gpl_object, "GPL", :child_key => [:gpl], :parent_key => [:gpl], :key => true
  #    end
  #
  #    class GPL < GEO
  #      storage_names[:expr_geo] = "gpl_list"
  #      property :gpl, Integer, :key => true
  #      has n, :attributes, "GPLField", :child_key => [:gpl]
  #      has n, :gsm_gpls, "GSMGPL", :child_key => [:gpl], :parent_key => [:gpl]
  #    end
  #
  #    class GPLField < GEO
  #      storage_names[:expr_geo] = "gpl"
  #      property :field, String, :key => true
  #      property :value, String, :key => true
  #    end

end