test_identifiers.rb in rbbt-util-5.43.0

- old
+ new
@@ -6,69 +6,29 @@
 module Gene
   extend Entity
 end
 
 class TestEntityIdentifiers < Test::Unit::TestCase
-  def setup
-    require 'rbbt/sources/kegg'
-    require 'rbbt/sources/organism'
-    Gene.add_identifiers Organism.identifiers("NAMESPACE"), "Ensembl Gene ID", "Associated Gene Name"
-    Gene.add_identifiers KEGG.identifiers
-    Gene.add_identifiers Organism.identifiers("NAMESPACE"), "Ensembl Gene ID", "Associated Gene Name"
-    Gene.add_identifiers KEGG.identifiers
 
-  end
   def test_name
     Gene.add_identifiers datafile_test('identifiers'), "Ensembl Gene ID", "Associated Gene Name"
     assert_equal "TP53", Gene.setup("ENSG00000141510").name
   end
 
   def test_name_organism
-    assert_equal "TP53", Gene.setup("ENSG00000141510", "Ensembl Gene ID", "Hsa/feb2014").name
+    keyword_test :organism do
+      require 'rbbt/sources/organism'
+      Gene.add_identifiers Organism.identifiers("NAMESPACE"), "Ensembl Gene ID", "Associated Gene Name"
+      assert_equal "TP53", Gene.setup("ENSG00000141510", "Ensembl Gene ID", "Hsa/feb2014").name
+    end
   end
 
   def test_identifier_files
+    Gene.add_identifiers datafile_test('identifiers'), "Ensembl Gene ID", "Associated Gene Name"
     assert Gene.identifier_files.any?
   end
 
   def test_Entity_identifier_files
+    Gene.add_identifiers datafile_test('identifiers'), "Ensembl Gene ID", "Associated Gene Name"
     assert Entity.identifier_files("Ensembl Gene ID").any?
-  end
-
-  def test_translate_kegg
-    assert_match "hsa", Gene.setup("ENSG00000141510", "Ensembl Gene ID", "Hsa/feb2014").to("KEGG Gene ID")
-    assert_match "TP53", Gene.setup("ENSG00000141510", "Ensembl Gene ID", "Hsa/feb2014").to("KEGG Gene ID").to(:name)
-  end
-
-  def ___test_complex
-
-    file = Path.setup('/home/mvazquezg/git/workflows/PanCancer/share/network/gene_sets/CORUM_protein_complexes.gmt')
-    name = File.basename(file).sub(/\.gmt$/,'')
-    organism = "Hsa/feb2014"
-    key_field = "#{ name } Pathway ID"
-    description_field = "#{name} Pathway Description"
-    description_file = file.find + '.identifiers'
-    tsv = TSV.open(file, :fix => Proc.new{|l| p=l.split"\t"; [p[0], p[1], p[2..-1]*"|"]*"\t"})
-    tsv.namespace = organism
-    tsv.unnamed = true
-    gene_field, count = Organism.guess_id(organism, tsv.values.collect{|l| l.last}.flatten.uniq )
-    tsv.key_field = key_field
-    tsv.fields = [description_field, gene_field]
-    descriptions = tsv.slice(description_field)
-    Open.write(description_file, descriptions.to_single.to_s) #unless File.exist? description_file
-    values = tsv.slice(gene_field)
-    values.identifiers = description_file
-
-    mod = Module.new
-    mod_name = Misc.camel_case(key_field.gsub(/\s+/,'_').sub(/_ID$/,''))
-    Object.const_set(mod_name, mod)
-    mod.instance_eval do
-      extend Entity
-      add_identifiers Path.setup(description_file), key_field, description_field
-
-      annotation :format
-    end
-    entity = "CORUM:6052"
-    mod.setup(entity, :format => key_field)
-    puts entity.name
   end
 end