lib/rbbt/sources/organism.rb in rbbt-sources-0.2.2 vs lib/rbbt/sources/organism.rb in rbbt-sources-0.3.1

@@ -1,21 +1,41 @@
 require 'rbbt-util'
-require 'rbbt/util/data_module'
+require 'rbbt/util/resource'
 
 
 module Organism
+  extend Resource
+  relative_to Rbbt, "share/organisms"
+
   class OrganismNotProcessedError < StandardError; end
 
   def self.datadir(org)
     File.join(Rbbt.datadir, 'organisms', org)
   end 
 
-  def self.normalize(org, list, field = nil, others = nil, options = {})
+  def self.attach_translations(org, tsv, target = nil, fields = nil, options = {})
+    Log.high "Attaching Translations for #{ org.inspect }, target #{target.inspect}, fields #{fields.inspect}"
+    options = Misc.add_defaults options, :persistence => true, :case_insensitive => false
+
+    options.merge! :key    => target unless target.nil?
+    options.merge! :fields => fields unless fields.nil?
+
+    index = identifiers(org).tsv options
+
+    tsv.attach index, [:key]
+  end
+
+  def self.normalize(org, list, target = nil, fields = nil, options = {})
     return [] if list.nil? or list.empty?
     options = Misc.add_defaults options, :persistence => true, :case_insensitive => true, :double => false
     double = Misc.process_options options, :double
-    
+
+    options.merge! :target => target unless target.nil?
+    options.merge! :fields => fields unless fields.nil?
+
+    index = identifiers(org).index options
+
     if Array === list
       if double
         index.values_at *list
       else
         index.values_at(*list).collect{|e| Misc.first e}
@@ -34,23 +54,29 @@
     field_matches = identifiers.field_matches(values)
     field_matches.sort_by{|field, matches| matches.uniq.length}.last
   end
 
   def self.organisms
-    Dir.glob(File.join(PKGData.sharedir_for_file(__FILE__), 'install/Organism/*/Rakefile')).collect{|f| File.basename(File.dirname(f))}
+    Dir.glob(File.join(Rbbt.share.organisms.find, '*')).collect{|f| File.basename(f)}
   end
 
   def self.name(organism)
-    Open.read(Organism.scientific_name(organism)).strip
+    Organism.scientific_name(organism).read.strip
   end
 
   def self.organism(name)
     organisms.select{|organism|
       organism == name or Organism.name(organism) =~ /#{ name }/i
     }.first
   end
-  
-  extend DataModule
-  
-  Hsa = with_key('Hsa')
-  Sce = with_key('Sce')
+
+  ["Hsa", "Sce"].each do |organism|
+    rakefile = Rbbt["share/install/Organism/#{ organism }/Rakefile"]
+    rakefile.lib_dir = Resource.caller_lib_dir __FILE__
+    rakefile.pkgdir = 'phgx'
+    Organism[organism].define_as_rake rakefile
+    module_eval "#{ organism } = with_key '#{organism}'"
+  end
+
 end
+
+