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# File 'lib/rbbt/entity/identifiers.rb', line 10
def self.included(base)
base.annotation :format
base.annotation :organism
class << base
attr_accessor :identifier_files, :formats, :default_format, :name_format, :description_format
end
base.module_eval do
def identity_type
self.annotation_types.select{|m| m.include? Entity::Identified }.last
end
def identifier_files
files = identity_type.identifier_files.dup
files.collect!{|f| f.annotate f.gsub(/\bNAMESPACE\b/, organism) } if annotations.include? :organism and self.organism
if files.select{|f| f =~ /\bNAMESPACE\b/ }.any?
Log.warn "Rejecting some identifier files for lack of 'organism': " << files.select{|f| f =~ /\bNAMESPACE\b/ } * ", "
end
files.reject!{|f| f =~ /\bNAMESPACE\b/ }
files
end
def identifier_index(format = nil, source = nil)
Persist.memory("Entity index #{identity_type}: #{format} (from #{source || "All"})", :persist => true, :format => format, :source => source) do
source ||= self.respond_to?(:format)? self.format : nil
begin
index = TSV.translation_index(identifier_files, format, source, :persist => true)
raise "No index from #{ Misc.fingerprint source } to #{ Misc.fingerprint format }: #{Misc.fingerprint identifier_files}" if index.nil?
index.unnamed = true
index
rescue
raise $! if source.nil?
source = nil
retry
end
end
end
end
base.property :to => :both do |target_format|
target_format = case target_format
when :name
identity_type.name_format
when :default
identity_type.default_format
when :ensembl
identity_type.formats.select{|f| f =~ /Ensembl/}.first
else
target_format
end
return self if target_format == format
if Array === self
self.annotate(identifier_index(target_format, self.format).values_at(*self))
else
self.annotate(identifier_index(target_format, self.format)[self])
end.tap{|o| o.format = target_format unless o.nil? }
end
base.property :name => :both do
to(:name)
end
base.property :default => :both do
to(:default)
end
base.property :ensembl => :both do
to(:ensembl)
end
end
|