Class: TestEnsemblREST

Inherits:
Test::Unit::TestCase
  • Object
show all
Defined in:
lib/test.rb

Instance Method Summary collapse

Instance Method Details

#test_archive ⇒ Object 



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# File 'lib/test.rb', line 32

def test_archive
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Archive::id_get('ENSG00000157764')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Archive::id_post(["ENSG00000157764", "ENSG00000248378"])}
end

#test_genetree ⇒ Object 



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# File 'lib/test.rb', line 44

def test_genetree
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genetree('ENSGT00390000003602')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genetree_member_id('ENSG00000157764')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genetree_member_symbol('BRCA2')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genomic_alignment_region('X:1000000..1000100:1')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::homology_ensemblgene('ENSG00000157764')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::homology_symbol('BRCA2')}
end

#test_info ⇒ Object 



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# File 'lib/test.rb', line 53

def test_info
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::analysis}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::assembly_info}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::assembly_stats('X')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::biotypes}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::compara_methods}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::compara_species_sets('EPO')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::comparas}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::data}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::external_dbs}
  assert(EnsemblREST::Info::ping)
  assert_instance_of(String, EnsemblREST::Info::rest)
  assert_instance_of(Fixnum, EnsemblREST::Info::software)
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::species}
end

#test_lookup ⇒ Object 



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# File 'lib/test.rb', line 69

def test_lookup
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::id('ENSG00000157764')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::symbol('BRCA2')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::id_post(["ENSG00000157764", "ENSG00000248378"])}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::symbol_post(["BRCA2", "BRAF"])}
end

#test_map ⇒ Object 



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# File 'lib/test.rb', line 37

def test_map
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::cdna("ENST00000288602", "100..300")}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::cds('ENST00000288602', '1..1000')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::map('X:1000000..1000100:1', 'GRCh37', 'GRCh38')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::translation('ENSP00000288602', '100..300')}
end

#test_onto ⇒ Object 



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# File 'lib/test.rb', line 76

def test_onto
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::ancestors('GO:0005667')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::ancestors_chart('GO:0005667')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::descendants('GO:0005667')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::id('GO:0005667')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::name("transcription factor complex")}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Taxonomy::classification('9606')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Taxonomy::id('9606')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Taxonomy::name('Homo%25')}
end

#test_overlap ⇒ Object 



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# File 'lib/test.rb', line 87

def test_overlap
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Overlap::id('ENSG00000157764', 'gene')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Overlap::region('7:140424943-140624564', ['gene', 'transcript', 'cds', 'exon'])}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Overlap::translation('ENSP00000288602')}
end

#test_regulation ⇒ Object 



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# File 'lib/test.rb', line 93

def test_regulation
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Regulation::id('ENSR00001348195')}
end

#test_sequence ⇒ Object 



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# File 'lib/test.rb', line 97

def test_sequence
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::id("ENSP00000288602")}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::region("X:1000000..1000100:1", 'human')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::id_post(["ENSG00000157764", "ENSG00000248378"])}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::region_post(["X:1000000..1000100:1", "ABBA01004489.1:1..100"])}
end

#test_variation ⇒ Object 



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# File 'lib/test.rb', line 104

def test_variation
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Variation::id("rs116035550")}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Variation::post(["rs116035550", "COSM476"])}
end

#test_variationga4gh ⇒ Object 



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# File 'lib/test.rb', line 109

def test_variationga4gh
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::GA4GH::gacallSet}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::GA4GH::gavariants(17191024, 17671934, '22', [70])}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::GA4GH::gavariantset}
end

#test_vep ⇒ Object 



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# File 'lib/test.rb', line 115

def test_vep
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::hgvs_get('AGT:c.803T>C')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::id_get('COSM476')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::region_get('C', '9:22125503-22125502:1')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::id_post(["rs116035550", "COSM476" ])}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::region_post(["21  26960070  rs116645811 G A . . .", "21  26965148  rs1135638 G A . . ." ])}
end

#test_xref ⇒ Object 



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# File 'lib/test.rb', line 123

def test_xref
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Xref::external('BRCA2')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Xref::id('ENSG00000157764')}
  assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Xref::name('BRCA2')}
end