test/rbbt/knowledge_base/test_registry.rb in rbbt-util-5.14.34 vs test/rbbt/knowledge_base/test_registry.rb in rbbt-util-5.14.35

@@ -27,10 +27,12 @@
 
   KNOWLEDGE_BASE = KnowledgeBase.new '/tmp/kb.foo2'
 
   KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup
 
+  KNOWLEDGE_BASE.register :pina, datafile_test('pina'), :source => "UniProt/SwissProt Accession", :target => "Interactor UniProt/SwissProt Accession=~UniProt/SwissProt Accession", :undirected => true
+
   def test_database
     assert_equal "Associated Gene Name", KNOWLEDGE_BASE.get_database(:effects, :source_format => "Associated Gene Name").key_field
   end
 
   def test_index
@@ -39,14 +41,41 @@
 
   def test_index_persist
     assert KNOWLEDGE_BASE.get_index(:effects, :source_format => "Associated Gene Name", :target_format => "Ensembl Gene ID", :persist => true).include? "MDM2~ENSG00000141510"
   end
 
-
   def test_index_flat
     require 'rbbt/sources/tfacts'
     file = TFacts.regulators
     KNOWLEDGE_BASE.register :tfacts, file,  :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true
     assert KNOWLEDGE_BASE.subset(:tfacts, :source => ["TP53"], :target => :all).length > 10
+  end
+
+  def test_pina
+    index = KNOWLEDGE_BASE.get_index(:pina, :persist => false, :source_format => "Associated Gene Name", :target_format => "Associated Gene Name")
+    assert index["TP53~ARID1A"]
+    assert index["ARID1A~TP53"]
+    assert_equal index["ARID1A~TP53"], index["TP53~ARID1A"]
+
+    index = KNOWLEDGE_BASE.get_index(:pina, :persist => false, :source_format => "Associated Gene Name", :target_format => "Associated Gene Name", :undirected => false)
+    count = 0
+    index.through do |k,values|
+      split_values = values.collect{|v| v.split ";;" }
+      count += 1 if Misc.zip_fields(split_values).uniq != Misc.zip_fields(split_values)
+    end
+
+    index = KNOWLEDGE_BASE.get_index(:pina, :persist => false, :source_format => "Associated Gene Name", :target_format => "Associated Gene Name", :undirected => true)
+    count2 = 0
+    index.through do |k,values|
+      split_values = values.collect{|v| v.split ";;" }
+      count2 += 1 if Misc.zip_fields(split_values).uniq != Misc.zip_fields(split_values)
+    end
+
+    assert_equal count, count2
+  end
+
+
+  def test_pina2
+    index = KNOWLEDGE_BASE.get_index(:pina, :persist => true, :source_format => "Ensembl Gene ID", :target_format => "Ensembl Gene ID", :undirected => true)
   end
 end