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 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 => :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]
    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]
    end
    
    class GSEField < GEO
      storage_names[:expr_geo] = "gse"
        
      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, :fields, "GSMField", :child_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]!
        
      # 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"
        
      property :gsm, Integer, :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, :fields, "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
end