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)

# child_key: set of fields identifying child model
# parent_key: set of fields identifying parent model

# 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 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

    # 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
    has n, :gse_gsms, "GSEGSM", :child_key => [:gse], :parent_key => [:gse]
    has n, :gsm_objects, "GSM", :through => :gse_gsm
    has n, :_fields, "GSEField", :child_key => [:gse], :parent_key => [:gse]

  end

  class GSEField < GEO
    storage_names[:expr_geo] = "gse"
    belongs_to :gse_object, "GSE", :child_key => [:gse], :parent_key => [:gse], :key => true
    property :field, String, :key => true
    property :value, String
  end

  class GSEGSM < GEO
    storage_names[:expr_geo] = "gse_gsm"
    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, :_fields, "GSMField", :child_key => [:gsm], :parent_key => [:gsm]
    # a sample may be associated with more than one series.
    has n, :gse_gsm, "GSEGSM", :child_key => [:gsm], :parent_key => [:gsm]
    has n, :gse_object, "GSE", :through => :gse_gsm

    # key is apparently optional here.
    #    has n, :measurements, "GSMGeneData", :child_key => [:gsm],
    #    :parent_key => [:gsm]#, :key => true
    # this is incorrect syntax.
    #    has n, :platforms, "GPL", :child_key => [:gsm], :parent_key => [:gsm], :through => :gsm_gpl
    # parent_key should be optional?
    #    has n, :gsm_gpls, "GSMGPL", :child_key => [:gsm]
  end

#  class GSMField < GEO
#    storage_names[:expr_geo] = "gsm"
#
#    belongs_to :gsm_object, "GSM", :child_key => [: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