bio-chembl 0.1.1
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- data/.document +5 -0
- data/.project +11 -0
- data/.travis.yml +12 -0
- data/Gemfile +17 -0
- data/Gemfile.lock +33 -0
- data/LICENSE.txt +20 -0
- data/README.md +79 -0
- data/Rakefile +45 -0
- data/VERSION +1 -0
- data/bio-chembl.gemspec +94 -0
- data/lib/bio-chembl.rb +12 -0
- data/lib/bio-chembl/assay.rb +96 -0
- data/lib/bio-chembl/bioactivity.rb +113 -0
- data/lib/bio-chembl/chembl.rb +30 -0
- data/lib/bio-chembl/chemblid.rb +102 -0
- data/lib/bio-chembl/compound.rb +157 -0
- data/lib/bio-chembl/datamodel.rb +25 -0
- data/lib/bio-chembl/rest_api_server.rb +40 -0
- data/lib/bio-chembl/rest_client.rb +264 -0
- data/lib/bio-chembl/target.rb +103 -0
- data/test/helper.rb +18 -0
- data/test/test_bio-chembl-assay.rb +152 -0
- data/test/test_bio-chembl-assay.sh +3 -0
- data/test/test_bio-chembl-chemblid.rb +36 -0
- data/test/test_bio-chembl-chemblid.sh +3 -0
- data/test/test_bio-chembl-compound.rb +125 -0
- data/test/test_bio-chembl-compound.sh +3 -0
- data/test/test_bio-chembl-rest-client.rb +188 -0
- data/test/test_bio-chembl-rest-client.sh +3 -0
- data/test/test_bio-chembl-target.rb +114 -0
- data/test/test_bio-chembl-target.sh +3 -0
- data/test/test_bio-chembl.rb +9 -0
- data/test/test_bio-chembl.sh +3 -0
- metadata +210 -0
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require 'helper'
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require 'bio-chembl/chembl.rb'
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class TestBioChemblURI < Test::Unit::TestCase
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def setup
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@obj = BioChEMBL::REST::ChEMBL_URI
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end
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def test_status
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assert_equal(@obj.status,
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"https://www.ebi.ac.uk/chemblws/status/")
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end
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def test_compounds
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assert_equal(@obj.compounds('CHEMBL1'),
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'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL1')
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end
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def test_compounds_image
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assert_equal(@obj.compounds('CHEMBL192', 'image'),
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'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image')
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end
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def test_compounds_image_params
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assert_equal(@obj.compounds('CHEMBL192', 'image', {:dimensions => 200}),
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'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image?dimensions=200')
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end
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def test_compounds_bioactivities
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assert_equal(@obj.compounds('CHEMBL1', 'bioactivities'),
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'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL1/bioactivities')
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end
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def test_compounds_stdinchikey
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assert_equal(@obj.compounds_stdinchikey("QFFGVLORLPOAEC-SNVBAGLBSA-N"),
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'https://www.ebi.ac.uk/chemblws/compounds/stdinchikey/QFFGVLORLPOAEC-SNVBAGLBSA-N')
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end
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def test_compounds_smiles
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assert_equal(@obj.compounds_smiles("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56"),
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'https://www.ebi.ac.uk/chemblws/compounds/smiles/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56')
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end
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def test_compounds_substructure
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assert_equal(@obj.compounds_substructure("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56"),
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'https://www.ebi.ac.uk/chemblws/compounds/substructure/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56')
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end
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def test_compounds_similarity
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assert_equal(@obj.compounds_similarity("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/70"),
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'https://www.ebi.ac.uk/chemblws/compounds/similarity/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/70')
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end
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def test_targets_id
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assert_equal(@obj.targets("CHEMBL2477"),
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'https://www.ebi.ac.uk/chemblws/targets/CHEMBL2477')
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end
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def test_targets_bioactivities
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assert_equal(@obj.targets("CHEMBL2477", 'bioactivities'),
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'https://www.ebi.ac.uk/chemblws/targets/CHEMBL2477/bioactivities')
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end
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def test_targets
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# targets
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assert_equal(@obj.targets,
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'https://www.ebi.ac.uk/chemblws/targets')
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end
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def test_targets_uniprot
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assert_equal(@obj.targets_uniprot("Q13936"),
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'https://www.ebi.ac.uk/chemblws/targets/uniprot/Q13936')
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end
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def test_targets_refseq
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assert_equal(@obj.targets_refseq("NP_001128722"),
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'https://www.ebi.ac.uk/chemblws/targets/refseq/NP_001128722')
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end
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def test_assays
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assert_equal(@obj.assays("CHEMBL1217643"),
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'https://www.ebi.ac.uk/chemblws/assays/CHEMBL1217643')
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end
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def test_assays_bioactivities
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assert_equal(@obj.assays("CHEMBL1217643", 'bioactivities'),
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'https://www.ebi.ac.uk/chemblws/assays/CHEMBL1217643/bioactivities')
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end
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end
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class TestBioChembl < Test::Unit::TestCase
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def setup
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@obj = BioChEMBL::REST.new
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end
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def test_new
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assert(@obj)
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end
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def test_uri_status
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assert_equal(@obj.uri.status,
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'https://www.ebi.ac.uk/chemblws/status/')
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end
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def test_status
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assert_equal(@obj.status, 'UP')
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end
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def test_compounds
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doc = @obj.compounds('CHEMBL1')
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assert_equal(doc,
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'<compound><chemblId>CHEMBL1</chemblId><knownDrug>No</knownDrug><medChemFriendly>Yes</medChemFriendly><passesRuleOfThree>No</passesRuleOfThree><molecularFormula>C32H32O8</molecularFormula><smiles>COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56</smiles><stdInChiKey>GHBOEFUAGSHXPO-XZOTUCIWSA-N</stdInChiKey><numRo5Violations>1</numRo5Violations><rotatableBonds>2</rotatableBonds><molecularWeight>544.59167</molecularWeight><alogp>3.627</alogp><acdLogp>7.669</acdLogp><acdLogd>7.669</acdLogd></compound>')
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end
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def test_compounds_image
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# assert_equal(@obj.compounds('CHEMBL192', 'image'),
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# '') # \x89PNG
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end
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def test_compounds_image_params
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# assert_equal(@obj.compounds('CHEMBL192', 'image', {:dimensions => 200}),
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# '')
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end
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def test_compounds_bioactivities
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doc = @obj.compounds('CHEMBL1', 'bioactivities')
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assert(doc =~ /<list><bioactivity><parent__cmpd__chemblid>CHEMBL1/)
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end
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def test_compounds_stdinchikey
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doc = @obj.compounds_stdinchikey("QFFGVLORLPOAEC-SNVBAGLBSA-N")
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assert(doc =~ /<compound><chemblId>CHEMBL1201760/)
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end
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def test_compounds_smiles
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doc = @obj.compounds_smiles("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56")
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assert(doc =~ /<list><compound><chemblId>CHEMBL1/)
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end
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def test_compounds_substructure
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doc = @obj.compounds_substructure("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56")
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assert(doc, '<list/>')
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end
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def test_compounds_similarity
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doc = @obj.compounds_similarity("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/70")
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assert(doc =~ /<list><compound><chemblId>CHEMBL/)
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end
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def test_targets_id
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doc = @obj.targets("CHEMBL2477")
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assert(doc =~ /<target><chemblId>CHEMBL2477/)
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end
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def test_targets_bioactivities
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doc = @obj.targets("CHEMBL2477", 'bioactivities')
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assert(doc =~ /<list><bioactivity><parent__cmpd__chemblid>CHEMBL/)
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end
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def test_targets
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doc = @obj.targets
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assert(doc =~ /<list><target><chemblId>CHEMBL/)
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end
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def test_targets_uniprot
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doc = @obj.targets_uniprot("Q13936")
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assert_equal(doc, '<target><chemblId>CHEMBL1940</chemblId><targetType>PROTEIN</targetType><preferredName>Voltage-gated L-type calcium channel alpha-1C subunit</preferredName><proteinAccession>Q13936</proteinAccession><synonyms>Voltage-dependent L-type calcium channel subunit alpha-1C; Calcium channel, L type, alpha-1 polypeptide, isoform 1, cardiac muscle; Voltage-gated calcium channel subunit alpha Cav1.2</synonyms><organism>Homo sapiens</organism><description>Voltage-dependent L-type calcium channel subunit alpha-1C</description><geneNames>CACNA1C; CACH2; CACN2; CACNL1A1; CCHL1A1</geneNames></target>')
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end
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def test_targets_refseq_not_fount
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assert_raise(Exception) {
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@obj.targets_refseq("NP_001128722")
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}
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end
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def test_assays
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doc = @obj.assays("CHEMBL1217643")
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assert(doc =~ /<assay><chemblId>CHEMBL1217643/)
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end
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def test_assays_bioactivities
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doc = @obj.assays("CHEMBL1217643", 'bioactivities')
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assert(doc =~ /<list><bioactivity><parent__cmpd__chemblid>CHEMBL/)
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end
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end
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require 'helper'
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require 'bio-chembl/chembl.rb'
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class TestBioChemblTarget < Test::Unit::TestCase
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def setup
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@xml = "<target><chemblId>CHEMBL1785</chemblId><targetType>PROTEIN</targetType><preferredName>Endothelin receptor ET-B</preferredName><proteinAccession>P24530</proteinAccession><synonyms>Endothelin B receptor; Endothelin receptor non-selective type; ET-B; ET-BR</synonyms><organism>Homo sapiens</organism><description>Endothelin B receptor</description><geneNames>EDNRB; ETRB</geneNames></target>"
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@chemblId = "CHEMBL1785"
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end
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def test_target_parser_xml
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doc = BioChEMBL::Target.parse_xml(@xml)
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assert_equal(doc.chemblId, "CHEMBL1785")
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end
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def test_target_attributes
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doc = BioChEMBL::Target.parse_xml(@xml)
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assert_equal(doc.class, BioChEMBL::Target)
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end
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def test_target_attributes
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doc = BioChEMBL::Target.parse_xml(@xml)
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assert_equal("CHEMBL1785", doc.chemblId)
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assert_equal("PROTEIN", doc.targetType)
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assert_equal("Endothelin receptor ET-B", doc.preferredName)
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assert_equal("P24530", doc.proteinAccession)
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assert_equal("Endothelin B receptor; Endothelin receptor non-selective type; ET-B; ET-BR", doc.synonyms)
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assert_equal("Homo sapiens", doc.organism)
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assert_equal("Endothelin B receptor", doc.description)
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assert_equal("EDNRB; ETRB", doc.geneNames)
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end
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def test_target_synonyms_to_array
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doc = BioChEMBL::Target.parse_xml(@xml)
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assert_equal("Endothelin B receptor; Endothelin receptor non-selective type; ET-B; ET-BR", doc.synonyms)
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synonyms = BioChEMBL.to_array(doc.synonyms)
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assert_equal(4, synonyms.size)
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assert_equal("Endothelin B receptor", synonyms[0])
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end
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def test_target_geneNames_to_array
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doc = BioChEMBL::Target.parse_xml(@xml)
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assert_equal("EDNRB; ETRB", doc.geneNames)
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geneNames = BioChEMBL.to_array(doc.geneNames)
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assert_equal(2, geneNames.size)
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assert_equal("EDNRB", geneNames[0])
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end
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def test_target_parse_json
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assert_raise(NotImplementedError) {
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BioChEMBL::Target.parse_json("")
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}
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end
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def test_target_parse_rdf
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assert_raise(NotImplementedError) {
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BioChEMBL::Target.parse_rdf("")
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}
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end
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def test_target_parse
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doc = BioChEMBL::Target.parse(@xml)
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assert_equal("CHEMBL1785", doc.chemblId)
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end
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def test_target_resolve
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doc = BioChEMBL::Target.new
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doc.chemblId = @chemblId
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assert_equal(doc.targetType, nil)
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doc.resolve
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assert_equal(doc.targetType, "PROTEIN")
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end
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end
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class TestBioChemblTargetClassMethods < Test::Unit::TestCase
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def setup
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@chemblId = "CHEMBL2477"
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@target = BioChEMBL::Target.find(@chemblId)
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@uniprot_id = "Q13936"
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@refseq_id = "NP_001128722"
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end
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def test_find
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assert_equal(@target.chemblId, "CHEMBL2477")
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assert_equal(@target.targetType, "PROTEIN")
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end
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def test_find_by_uniprot
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@target = BioChEMBL::Target.find_by_uniprot(@uniprot_id)
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assert_equal(@target.chemblId, "CHEMBL1940")
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assert_equal(@target.targetType, "PROTEIN")
|
97
|
+
end
|
98
|
+
|
99
|
+
def test_find_by_refseq
|
100
|
+
# @target = BioChEMBL::Target.find_by_refseq(@refseq_id)
|
101
|
+
# p @target
|
102
|
+
# assert_equal(@target.chemblId, "CHEMBL2477")
|
103
|
+
# assert_equal(@target.targetType, "PROTEIN")
|
104
|
+
end
|
105
|
+
|
106
|
+
def test_bioactivities
|
107
|
+
docs = @target.bioactivities
|
108
|
+
assert_equal(Array, docs.class)
|
109
|
+
assert_equal(BioChEMBL::Bioactivity, docs.first.class)
|
110
|
+
assert_equal("Homo sapiens", docs.first.organism)
|
111
|
+
assert_equal("Bioorg. Med. Chem. Lett., (1998) 8:13:1703", docs.first.reference)
|
112
|
+
end
|
113
|
+
|
114
|
+
end
|
metadata
ADDED
@@ -0,0 +1,210 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: bio-chembl
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
prerelease: false
|
5
|
+
segments:
|
6
|
+
- 0
|
7
|
+
- 1
|
8
|
+
- 1
|
9
|
+
version: 0.1.1
|
10
|
+
platform: ruby
|
11
|
+
authors:
|
12
|
+
- Mitsuteru Nakao
|
13
|
+
autorequire:
|
14
|
+
bindir: bin
|
15
|
+
cert_chain: []
|
16
|
+
|
17
|
+
date: 2012-07-22 00:00:00 +09:00
|
18
|
+
default_executable:
|
19
|
+
dependencies:
|
20
|
+
- !ruby/object:Gem::Dependency
|
21
|
+
name: shoulda
|
22
|
+
prerelease: false
|
23
|
+
requirement: &id001 !ruby/object:Gem::Requirement
|
24
|
+
none: false
|
25
|
+
requirements:
|
26
|
+
- - ">="
|
27
|
+
- !ruby/object:Gem::Version
|
28
|
+
segments:
|
29
|
+
- 0
|
30
|
+
version: "0"
|
31
|
+
type: :development
|
32
|
+
version_requirements: *id001
|
33
|
+
- !ruby/object:Gem::Dependency
|
34
|
+
name: rdoc
|
35
|
+
prerelease: false
|
36
|
+
requirement: &id002 !ruby/object:Gem::Requirement
|
37
|
+
none: false
|
38
|
+
requirements:
|
39
|
+
- - ~>
|
40
|
+
- !ruby/object:Gem::Version
|
41
|
+
segments:
|
42
|
+
- 3
|
43
|
+
- 12
|
44
|
+
version: "3.12"
|
45
|
+
type: :development
|
46
|
+
version_requirements: *id002
|
47
|
+
- !ruby/object:Gem::Dependency
|
48
|
+
name: bundler
|
49
|
+
prerelease: false
|
50
|
+
requirement: &id003 !ruby/object:Gem::Requirement
|
51
|
+
none: false
|
52
|
+
requirements:
|
53
|
+
- - ">="
|
54
|
+
- !ruby/object:Gem::Version
|
55
|
+
segments:
|
56
|
+
- 1
|
57
|
+
- 0
|
58
|
+
- 0
|
59
|
+
version: 1.0.0
|
60
|
+
type: :development
|
61
|
+
version_requirements: *id003
|
62
|
+
- !ruby/object:Gem::Dependency
|
63
|
+
name: jeweler
|
64
|
+
prerelease: false
|
65
|
+
requirement: &id004 !ruby/object:Gem::Requirement
|
66
|
+
none: false
|
67
|
+
requirements:
|
68
|
+
- - ~>
|
69
|
+
- !ruby/object:Gem::Version
|
70
|
+
segments:
|
71
|
+
- 1
|
72
|
+
- 8
|
73
|
+
- 3
|
74
|
+
version: 1.8.3
|
75
|
+
type: :development
|
76
|
+
version_requirements: *id004
|
77
|
+
- !ruby/object:Gem::Dependency
|
78
|
+
name: bio
|
79
|
+
prerelease: false
|
80
|
+
requirement: &id005 !ruby/object:Gem::Requirement
|
81
|
+
none: false
|
82
|
+
requirements:
|
83
|
+
- - ">="
|
84
|
+
- !ruby/object:Gem::Version
|
85
|
+
segments:
|
86
|
+
- 1
|
87
|
+
- 4
|
88
|
+
- 2
|
89
|
+
version: 1.4.2
|
90
|
+
type: :development
|
91
|
+
version_requirements: *id005
|
92
|
+
- !ruby/object:Gem::Dependency
|
93
|
+
name: rdoc
|
94
|
+
prerelease: false
|
95
|
+
requirement: &id006 !ruby/object:Gem::Requirement
|
96
|
+
none: false
|
97
|
+
requirements:
|
98
|
+
- - ~>
|
99
|
+
- !ruby/object:Gem::Version
|
100
|
+
segments:
|
101
|
+
- 3
|
102
|
+
- 12
|
103
|
+
version: "3.12"
|
104
|
+
type: :development
|
105
|
+
version_requirements: *id006
|
106
|
+
- !ruby/object:Gem::Dependency
|
107
|
+
name: curb
|
108
|
+
prerelease: false
|
109
|
+
requirement: &id007 !ruby/object:Gem::Requirement
|
110
|
+
none: false
|
111
|
+
requirements:
|
112
|
+
- - ">="
|
113
|
+
- !ruby/object:Gem::Version
|
114
|
+
segments:
|
115
|
+
- 0
|
116
|
+
version: "0"
|
117
|
+
type: :development
|
118
|
+
version_requirements: *id007
|
119
|
+
- !ruby/object:Gem::Dependency
|
120
|
+
name: nokogiri
|
121
|
+
prerelease: false
|
122
|
+
requirement: &id008 !ruby/object:Gem::Requirement
|
123
|
+
none: false
|
124
|
+
requirements:
|
125
|
+
- - ~>
|
126
|
+
- !ruby/object:Gem::Version
|
127
|
+
segments:
|
128
|
+
- 1
|
129
|
+
- 5
|
130
|
+
- 5
|
131
|
+
version: 1.5.5
|
132
|
+
type: :development
|
133
|
+
version_requirements: *id008
|
134
|
+
description: BioRuby plugin for ChEMBL REST API Client, Parser and Container classes
|
135
|
+
email: mitsuteru.nakao@gmail.com
|
136
|
+
executables: []
|
137
|
+
|
138
|
+
extensions: []
|
139
|
+
|
140
|
+
extra_rdoc_files:
|
141
|
+
- LICENSE.txt
|
142
|
+
- README.md
|
143
|
+
files:
|
144
|
+
- .document
|
145
|
+
- .project
|
146
|
+
- .travis.yml
|
147
|
+
- Gemfile
|
148
|
+
- Gemfile.lock
|
149
|
+
- LICENSE.txt
|
150
|
+
- README.md
|
151
|
+
- Rakefile
|
152
|
+
- VERSION
|
153
|
+
- bio-chembl.gemspec
|
154
|
+
- lib/bio-chembl.rb
|
155
|
+
- lib/bio-chembl/assay.rb
|
156
|
+
- lib/bio-chembl/bioactivity.rb
|
157
|
+
- lib/bio-chembl/chembl.rb
|
158
|
+
- lib/bio-chembl/chemblid.rb
|
159
|
+
- lib/bio-chembl/compound.rb
|
160
|
+
- lib/bio-chembl/datamodel.rb
|
161
|
+
- lib/bio-chembl/rest_api_server.rb
|
162
|
+
- lib/bio-chembl/rest_client.rb
|
163
|
+
- lib/bio-chembl/target.rb
|
164
|
+
- test/helper.rb
|
165
|
+
- test/test_bio-chembl-assay.rb
|
166
|
+
- test/test_bio-chembl-assay.sh
|
167
|
+
- test/test_bio-chembl-chemblid.rb
|
168
|
+
- test/test_bio-chembl-chemblid.sh
|
169
|
+
- test/test_bio-chembl-compound.rb
|
170
|
+
- test/test_bio-chembl-compound.sh
|
171
|
+
- test/test_bio-chembl-rest-client.rb
|
172
|
+
- test/test_bio-chembl-rest-client.sh
|
173
|
+
- test/test_bio-chembl-target.rb
|
174
|
+
- test/test_bio-chembl-target.sh
|
175
|
+
- test/test_bio-chembl.rb
|
176
|
+
- test/test_bio-chembl.sh
|
177
|
+
has_rdoc: true
|
178
|
+
homepage: http://github.com/nakao/bio-chembl
|
179
|
+
licenses:
|
180
|
+
- MIT
|
181
|
+
post_install_message:
|
182
|
+
rdoc_options: []
|
183
|
+
|
184
|
+
require_paths:
|
185
|
+
- lib
|
186
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
187
|
+
none: false
|
188
|
+
requirements:
|
189
|
+
- - ">="
|
190
|
+
- !ruby/object:Gem::Version
|
191
|
+
segments:
|
192
|
+
- 0
|
193
|
+
version: "0"
|
194
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
195
|
+
none: false
|
196
|
+
requirements:
|
197
|
+
- - ">="
|
198
|
+
- !ruby/object:Gem::Version
|
199
|
+
segments:
|
200
|
+
- 0
|
201
|
+
version: "0"
|
202
|
+
requirements: []
|
203
|
+
|
204
|
+
rubyforge_project:
|
205
|
+
rubygems_version: 1.3.7
|
206
|
+
signing_key:
|
207
|
+
specification_version: 3
|
208
|
+
summary: ChEMBL REST API Client, Parser and Container
|
209
|
+
test_files: []
|
210
|
+
|