bio-ensembl-rest 0.1.0

data/test/test-comparative-genomics.rb

@@ -0,0 +1,159 @@
+require_relative 'helper'
+
+class TestComparativeGenomics < Test::Unit::TestCase
+
+  context 'genetree_id' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      tree = ComparativeGenomics.genetree_id 'ENSGT00390000003602'
+      assert tree.index('Euteleostomi') && tree.index('Sarcopterygii')
+    end
+
+    should 'work with nh response type' do
+      tree1 = ComparativeGenomics.genetree_id 'ENSGT00390000003602',
+                response: 'nh',
+                nh_format: 'species_short_name'
+      tree2 = ComparativeGenomics.genetree_id 'ENSGT00390000003602',
+                response: 'nh',
+                nh_format: 'species'
+      assert tree1.size < tree2.size
+      assert tree1.index 'Xmac'
+      assert tree2.index 'xiphophorus_maculatus'
+    end
+
+    should 'return a Bio::PhyloXML object' do
+      tree = ComparativeGenomics.genetree_id 'ENSGT00390000003602',
+              response: 'ruby' 
+      assert_instance_of Bio::PhyloXML::Parser, tree
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'genetree_member_id' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      tree = ComparativeGenomics.genetree_member_id 'ENSG00000157764'
+      assert tree.index('Petromyzon marinus')
+    end
+
+    should 'return a Bio::PhyloXML object' do
+      tree = ComparativeGenomics.genetree_member_id'ENSG00000157764',
+              response: 'ruby' 
+      assert_instance_of Bio::PhyloXML::Parser, tree
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'genetree_member_symbol' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      tree = ComparativeGenomics.genetree_member_symbol 'homo_sapiens', 'BRCA2'
+      assert tree.index('BRCA2')
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'homology_id' do 
+
+    setup do
+      EnsemblRest.connect_db
+      require 'rexml/document'
+    end
+
+    should 'support a basic call and return the correct data' do
+      hom = ComparativeGenomics.homology_id 'ENSG00000157764'
+      assert hom.index 'Bilateria'
+      assert hom.index 'ENSG00000157764'
+      assert hom.index 'ENSG00000173327'
+    end
+
+    should 'return a json object' do
+      hom = ComparativeGenomics.homology_id 'ENSG00000157764',
+              response: 'json'
+      assert_nothing_raised { JSON.parse hom }
+    end
+
+    should 'return a xml object' do
+      hom = ComparativeGenomics.homology_id 'ENSG00000157764',
+              response: 'xml'      
+      assert_nothing_raised { REXML::Document.new hom }
+    end
+
+    should 'support the sequence parameter' do 
+      hom = ComparativeGenomics.homology_id 'ENSG00000157764', sequence: 'none'
+      hom2 = ComparativeGenomics.homology_id 'ENSG00000157764', sequence: 'protein'
+      assert hom.size < hom2.size
+    end
+
+    sleep(1)
+
+    should 'return a list of Homology objects' do 
+      homs = ComparativeGenomics.homology_id 'ENSG00000157764', 
+              response: 'ruby'
+      homs.each { |hom| assert_instance_of Homology, hom }
+      homs.each do |hom|
+        hom.bio_methods.each {|met| assert hom.respond_to? met}
+      end
+    end
+
+    should 'support the aligned parameter' do
+      al = ComparativeGenomics.homology_id 'ENSG00000157764'
+      nal = ComparativeGenomics.homology_id 'ENSG00000157764', aligned: false
+      assert al.size > nal.size
+    end
+
+    sleep(1)
+
+  end
+  
+
+  context 'homology_symbol' do
+
+    setup do
+      EnsemblRest.connect_db
+      require 'rexml/document'
+    end
+
+    should 'support a basic call and return the correct data' do
+      hom = ComparativeGenomics.homology_symbol 'human', 'BRCA2'
+      assert hom.index 'Homininae'
+      assert hom.index 'ENSG00000139618'
+    end
+
+
+    should 'return a list of Homology objects' do 
+      homs = ComparativeGenomics.homology_symbol 'human', 'BRCA2', 
+              response: 'ruby'
+      homs.each { |hom| assert_instance_of Homology, hom }
+      homs.each do |hom|
+        hom.bio_methods.each {|met| assert hom.respond_to? met}
+      end
+    end
+
+    sleep(1)
+
+  end
+
+
+end

data/test/test-cross-reference.rb

@@ -0,0 +1,81 @@
+require_relative 'helper'
+
+class TestCrossReference < Test::Unit::TestCase
+
+  context 'xrefs_id' do 
+
+    setup do       
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      ref = CrossReference.xrefs_id 'ENSG00000157764'
+      assert ref.index 'BRAF1'
+    end
+
+    should 'return a json object' do
+      ref = CrossReference.xrefs_id 'ENSG00000157764'
+      assert_nothing_raised { JSON.parse ref }
+    end
+
+    should 'return a ruby array' do
+      refs = CrossReference.xrefs_id 'ENSG00000157764', response: 'ruby'
+      assert_instance_of Array, refs
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'xrefs_name' do
+
+    setup do       
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      ref = CrossReference.xrefs_name 'Homo sapiens', 'BRCA2'
+      assert ref.index 'BRCA2'
+      assert ref.index 'BRCC2'
+      assert ref.index 'BROVCA2'
+    end
+
+    should 'return a JSON object' do
+      refs = CrossReference.xrefs_name 'human', 'BRCA2', response: 'json'
+      assert_nothing_raised { JSON.parse refs }
+    end
+
+    should 'return a ruby array' do
+      refs = CrossReference.xrefs_name 'human', 'BRCA2', response: 'ruby'
+      assert_instance_of Array, refs
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'xrefs_symbol' do
+
+    setup do       
+      EnsemblRest.connect_db
+      require 'rexml/document'
+    end
+
+    should 'support a basic call and return the correct data' do
+      ref = CrossReference.xrefs_symbol 'homo_sapiens', 'BRCA2'
+      assert ref.index 'ENSG00000139618'
+      assert ref.index 'ENST00000544455'
+    end
+
+    should 'return xml object' do
+      refs = CrossReference.xrefs_symbol 'homo_sapiens', 'BRCA2', response: 'xml'
+      assert_nothing_raised { REXML::Document.new refs }
+    end
+
+    sleep(1)
+
+  end
+
+end

data/test/test-features.rb

@@ -0,0 +1,76 @@
+require_relative 'helper'
+
+class TestFeatures < Test::Unit::TestCase
+
+  context 'feature_id' do 
+
+    setup do       
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      fts = Features.feature_id 'ENSG00000157764', %w(gene)
+      assert fts.index 'ENSG00000157764'      # gene ID
+      assert fts.index '140424943'            # gene starts here
+      assert fts.index '140624564'            # gene end here
+    end
+
+
+    should 'support multiple features' do 
+      assert_nothing_raised do 
+        Features.feature_id 'ENSG00000157764', %w(gene transcript exon), 
+          response: 'json'
+      end
+    end
+
+    should 'raise error if no feature is given' do 
+      assert_raises RuntimeError do 
+        Features.feature_id 'ENSG00000157764', response: 'json'
+      end
+    end
+
+    should 'return a ruby object' do 
+      fts = Features.feature_id 'ENSG00000157764', %w(gene), response: 'ruby'
+      assert_instance_of Array, fts 
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'feature_region' do 
+
+    setup do       
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      fts = Features.feature_region 'human', '7:140424943-140624564', %w(gene)
+      assert_nothing_raised { JSON.parse fts }
+      assert fts.index 'ENSG00000157764'   # gene ID
+      assert fts.index 'BRAF'              # gene name
+      assert fts.index '140424943'         # gene starts here
+      assert fts.index '140624564'         # gene end here
+    end
+
+    should 'support multiple features' do 
+      assert_nothing_raised do 
+        Features.feature_region 'human', '7:140424943-140624564',
+          %w(variation constrained regulatory),
+          response: 'json'
+      end
+    end
+
+    should 'raise error if no feature is given' do 
+      assert_raises RuntimeError do 
+        Features.feature_region 'human', '7:140424943-140624564', response: 'xml'
+      end
+    end
+
+    sleep(1)
+
+  end
+
+
+end

data/test/test-information.rb

@@ -0,0 +1,131 @@
+require_relative 'helper'
+
+class TestInformation < Test::Unit::TestCase
+
+  context 'assembly_info' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      info = Information.assembly_info 'homo_sapiens'
+      assert info =~ /GRCh\d{2}/       # check for GRC assembly code  
+      assert info.index 'X'            # check for X chromosome
+      assert info.index 'Y'            # check for Y chromosome
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'assembly_info_region' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      info = Information.assembly_info_region 'homo_sapiens', 'X'
+      assert info.index '155270560'         # the length of the X chromosome
+      assert info.index 'chromosome'        # coordinate_system should be this
+    end
+
+  end
+
+
+  context 'info_comparas' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      info = Information.info_comparas
+      assert info.index 'comparas'         
+      assert info.index 'name'         # we expect at least name and release 
+      assert info.index 'release'      # number of the databases
+    end
+
+  end
+
+
+  context 'info_data' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      info = Information.info_data       
+      assert info.index 'releases'         # we expect a release number
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'info_ping' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      info = Information.info_ping       
+      assert info.index 'ping'
+      assert info.index '1'            # so we know the server is alive
+    end
+
+  end
+
+
+  context 'info_rest' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      info = Information.info_rest      
+      assert info.index 'release'            # we expect a release number
+    end
+
+  end
+
+
+  context 'info_software' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      info = Information.info_software      
+      assert info.index 'release'            # we expect a release number
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'info_species' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      info = Information.info_species division: 'ensembl'      
+      assert info.index 'saccharomyces_cerevisiae'   # yeast! everyone has that
+      assert info.index 'vicugna pacos'              # ALPACA! everyone loves them
+    end
+
+  end
+
+
+
+end