rtirrell

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

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INFO = <<HERE
TABLES:
gds
  - key gds
gse
  - key gse

gds_gse
  - key gds
  - int gse

rtirrell

# workaround from
# http://stackoverflow.com/questions/1987386/foreign-key-name-in-datamapper-associations
field_naming_convention = lambda do |v|
  if v.name.to_s[0..0] == v.name.to_s[0..0].upcase
    v.name.to_s
  else
    DataMapper::NamingConventions::Field::Underscored.call(v)
  end
end

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field_naming_convention = lambda do |v|
  if v.name.to_s[0..0] == v.name[0..0].to_s.upcase
    DataMapper::NamingConventions::Field::Underscored(v) 
  else
    v.name.to_s
  end
end

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# file1.rb

USER_RPT_REPOSITORY_NAME = :user_rpt
class Gene
  include DataMapper::Resource
  def self.default_repository_name; USER_RPT_REPOSITORY_NAME; end

  belongs_to :gene_info, :child_key => [:GeneID], :parent_key => [:GeneID],
    :key => true, :repository => repository(:annot_gene)
  belongs_to :homologene, :child_key => [:HID], :parent_key => [:HID],

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class MRCONSO
  include DataMapper::Resource
  def self.default_repository_name; UMLS_REPOSITORY_NAME; end

#  storage_names[UMLS_REPOSITORY_NAME] = "MRCONSO"
  def self.storage_name(repository)
    "MRCONSO"
  end

  property :CUI, String

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r>> require 'orm'
ArgumentError: +name+ was :key, which cannot be used as a property name since it collides with an existing method
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/property.rb:787:in `initialize'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/property/numeric.rb:19:in `initialize'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/property/integer.rb:15:in `initialize'
	from /Library/Ruby/Gems/1.8/gems/dm-validations-1.0.0/lib/dm-validations.rb:41:in `new'
	from /Library/Ruby/Gems/1.8/gems/dm-validations-1.0.0/lib/dm-validations.rb:41:in `new'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/model/property.rb:84:in `property'
	from ./user_orm.rb:17
	from /Library/Ruby/Site/1.8/rubygems/custom_require.rb:31:in `gem_original_require'

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>> require 'orm'
NoMethodError: undefined method `name' for nil:NilClass
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/property_set.rb:161:in `initialize'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/property_set.rb:161:in `map'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/property_set.rb:161:in `initialize'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/associations/relationship.rb:256:in `new'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/associations/relationship.rb:256:in `parent_key'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/associations/many_to_one.rb:52:in `child_key'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core.rb:332:in `finalize_model'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core.rb:331:in `each'

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class Gene
  include DataMapper::Resource
  def self.default_repository_name; USER_RPT_REPOSITORY_NAME; end
    
  belongs_to :gene_info, :key => true, :child_key => [:GeneID], :parent_key => [:GeneID], 
             :repository => repository(:annot_gene)
  belongs_to :homologene, :child_key => [:HID], :parent_key => [:HID], 
             :repository => repository(:annot_gene)
  belongs_to :subset_comparison, :key => true, 
             :repository => repository(:nosology)

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# ERROR ONE
>> c = Cor.get(1060, :cid, :spearman)
 ~ (0.002499) SELECT `id`, `type`, `meth`, `cor`, `pval`, `pval_adj`, `perm_pval`, `len` FROM `cors` WHERE (`type` = 1 AND `meth` = 2 AND `id` = '1060') ORDER BY `id`, `type`, `meth` LIMIT 1
=> #<Cor @id="1060" @type=:cid @cor=0.0115675 @pval=0.315327 @pval_adj=nil @perm_pval=0.311 @meth=:spearman @len=7537>
>> c.update :pval_adj => 0.001
DataMapper::ImmutableError: Immutable resource cannot be modified
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/resource/state/immutable.rb:16:in `set'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/model/property.rb:269:in `pval_adj='
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/resource.rb:345:in `__send__'
	from /Library/Ruby/Gems/1.8/gems/dm-core-1.0.0/lib/dm-core/resource.rb:345:in `attributes='