bio-ucsc-api 0.2.0 → 0.2.1

data/spec/dp3_spec.rb

@@ -0,0 +1,617 @@
+require "bio-ucsc"
+require "pp"
+
+describe "Bio::Ucsc::Dp3" do
+
+  before(:all) do
+    Bio::Ucsc::Dp3::DBConnection.connect
+  end
+
+  describe "Bio::Ucsc::Dp3::All_est" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::All_est.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::All_mrna" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::All_mrna.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Author" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Author.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::BlastDm2FB" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::BlastDm2FB.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Cds" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Cds.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Cell" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Cell.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::ChainDm3" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chr2:1-10,000,000")
+        result = Bio::Ucsc::Dp3::ChainDm3.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::ChainDm3Link" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chr2:1-10,000,000")
+        result = Bio::Ucsc::Dp3::ChainDm3Link.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::ChromInfo" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::ChromInfo.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Description" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Description.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Development" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Development.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Est" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chr2:1-10,000,000")
+        result = Bio::Ucsc::Dp3::Est.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end
+
+  describe "Bio::Ucsc::Dp3::EstOrientInfo" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::EstOrientInfo.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::FbGenscan" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::FbGenscan.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::FlyBase2004Xref" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::FlyBase2004Xref.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::FlyBaseGene" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::FlyBaseGene.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::FlyBasePep" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::FlyBasePep.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Gap" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chr2:1-10,000,000")
+        result = Bio::Ucsc::Dp3::Gap.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GbCdnaInfo" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GbCdnaInfo.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GbDelete_tmp" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GbDelete_tmp.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GbExtFile" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GbExtFile.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GbLoaded" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GbLoaded.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GbMiscDiff" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GbMiscDiff.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GbSeq" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GbSeq.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GbStatus" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GbStatus.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GbWarn" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GbWarn.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GcPercent" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GcPercent.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GeneName" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GeneName.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Geneid" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Geneid.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Genewise" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Genewise.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Genscan" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Genscan.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::GenscanPep" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::GenscanPep.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Grp" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Grp.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::HgFindSpec" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::HgFindSpec.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::History" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::History.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::ImageClone" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::ImageClone.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::IntronEst" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chr2:1-10,000,000")
+        result = Bio::Ucsc::Dp3::IntronEst.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Keyword" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Keyword.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Library" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Library.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Mrna" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chr2:1-10,000,000")
+        result = Bio::Ucsc::Dp3::Mrna.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::MrnaClone" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::MrnaClone.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::MrnaOrientInfo" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::MrnaOrientInfo.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::NetDm3" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::NetDm3.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Organism" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Organism.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::ProductName" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::ProductName.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::RefLink" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::RefLink.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::RefSeqStatus" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::RefSeqStatus.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::RefSeqSummary" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::RefSeqSummary.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Rmsk" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chr2:1-10,000,000")
+        result = Bio::Ucsc::Dp3::Rmsk.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Sex" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Sex.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::SimpleRepeat" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::SimpleRepeat.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Source" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Source.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::TableDescriptions" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::TableDescriptions.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Tissue" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Tissue.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::TrackDb" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::TrackDb.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::Twinscan" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::Twinscan.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::XenoMrna" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::XenoMrna.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::XenoRefFlat" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::XenoRefFlat.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::XenoRefGene" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::XenoRefGene.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Dp3::XenoRefSeqAli" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Dp3::XenoRefSeqAli.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+end