test/rbbt/sources/test_biomart.rb in rbbt-sources-0.2.2 vs test/rbbt/sources/test_biomart.rb in rbbt-sources-0.3.1

@@ -2,29 +2,30 @@
 require 'rbbt/sources/biomart'
 require 'test/unit'
 
 class TestBioMart < Test::Unit::TestCase
 
-  def _test_get
+  def test_get
     assert_raise BioMart::QueryError do 
       BioMart.get('scerevisiae_gene_ensembl','entrezgene', ['protein_id'],['with_unknownattr'])
     end
 
-    data = BioMart.get('scerevisiae_gene_ensembl','entrezgene', ['protein_id'],[], nil, :nocache => false, :wget_options => { :quiet => false})
-    assert(data['852236']['protein_id'].include? 'CAA84864')
+    data = BioMart.get('scerevisiae_gene_ensembl','entrezgene', ['protein_id'],[], nil, :nocache => false, :merge => true, :wget_options => {:quiet => false})
+    tsv = TSV.new data, :double, :merge => true
+    assert(tsv['852236'][0].include? 'CAA84864')
 
     data = BioMart.get('scerevisiae_gene_ensembl','entrezgene', ['external_gene_id'],[], data, :nocache => false, :wget_options => { :quiet => false} )
-    assert(data['852236']['protein_id'].include? 'CAA84864')
-    assert(data['852236']['external_gene_id'].include? 'YBL044W')
+    tsv = TSV.new data, :double, :merge => true
+    assert(tsv['852236'][1].include? 'YBL044W')
   end
 
   def test_query
     data = BioMart.query('scerevisiae_gene_ensembl','entrezgene', ['protein_id','refseq_peptide','external_gene_id','ensembl_gene_id'], [], nil, :nocache => false, :wget_options => { :quiet => false})
 
     assert(data['852236']['external_gene_id'].include? 'YBL044W')
   end
 
-  def _test_tsv
+  def test_tsv
     data = BioMart.tsv('scerevisiae_gene_ensembl',['Entrez Gene', 'entrezgene'], [['Protein ID', 'protein_id'],['RefSeq Peptide','refseq_peptide']], [], nil, :nocache => false, :wget_options => { :quiet => false})
 
     assert(data['852236']['Protein ID'].include? 'CAA84864')
     assert_equal 'Entrez Gene', data.key_field
     assert_equal ['Protein ID', 'RefSeq Peptide'], data.fields