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require_relative "setup.rb"
class LazarFminerTest < MiniTest::Test
def test_lazar_fminer
dataset = OpenTox::Dataset.new
dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv")
assert_equal dataset.uri.uri?, true
model_uri = OpenTox::Model::Lazar.create :dataset_uri => dataset.uri, :feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc")
assert_equal model_uri.uri?, true
model = OpenTox::Model::Lazar.new model_uri
assert_equal model.uri.uri?, true
feature_dataset_uri = model[RDF::OT.featureDataset]
feature_dataset = OpenTox::Dataset.new feature_dataset_uri
assert_equal dataset.compounds.size, feature_dataset.compounds.size
assert_equal 54, feature_dataset.features.size
assert_equal '[#6&A]-[#6&A]-[#6&A]=[#6&A]', OpenTox::Feature.new(feature_dataset.features.first.uri).title
[ {
:compound => OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"),
:prediction => "false",
:confidence => 0.25281385281385277
},{
:compound => OpenTox::Compound.from_smiles("c1ccccc1NN"),
:prediction => "false",
:confidence => 0.3639589577089577
} ].each do |example|
prediction_uri = model.predict :compound_uri => example[:compound].uri
#puts prediction_uri
prediction_dataset = OpenTox::Dataset.new prediction_uri
assert_equal prediction_dataset.uri.uri?, true
prediction = prediction_dataset.predictions.select{|p| p[:compound].uri == example[:compound].uri}.first
assert_equal example[:prediction], prediction[:value]
assert_equal example[:confidence], prediction[:confidence]
prediction_dataset.delete
end
# make a dataset prediction
compound_dataset = OpenTox::Dataset.new
compound_dataset.upload File.join(DATA_DIR,"EPAFHM.mini.csv")
assert_equal compound_dataset.uri.uri?, true
prediction_uri = model.predict :dataset_uri => dataset.uri
prediction = OpenTox::Dataset.new prediction_uri
assert_equal prediction.uri.uri?, true
# cleanup
[dataset,model,feature_dataset,compound_dataset].each{|o| o.delete}
end
end
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