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require_relative "setup.rb"
class LazarClassificationTest < MiniTest::Test
def test_lazar_classification
training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
model = Model::LazarClassification.create training_dataset.features.first, training_dataset
[ {
:compound => OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"),
:prediction => "false",
},{
:compound => OpenTox::Compound.from_smiles("c1ccccc1NN"),
:prediction => "false",
} ].each do |example|
prediction = model.predict example[:compound]
assert_equal example[:prediction], prediction[:value]
end
compound = Compound.from_smiles "CCO"
prediction = model.predict compound
assert_equal "true", prediction[:value]
assert_equal ["false"], prediction[:database_activities]
# make a dataset prediction
compound_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini_log10.csv")
prediction_dataset = model.predict compound_dataset
assert_equal compound_dataset.compounds, prediction_dataset.compounds
cid = prediction_dataset.compounds[7].id.to_s
assert_equal "Could not find similar compounds with experimental data in the training dataset.", prediction_dataset.predictions[cid][:warning]
prediction_dataset.predictions.each do |cid,pred|
assert_equal "Could not find similar compounds with experimental data in the training dataset.", pred[:warning] if pred[:value].nil?
end
cid = Compound.from_smiles("CCOC(=O)N").id.to_s
assert_equal "1 compounds have been removed from neighbors, because they have the same structure as the query compound.", prediction_dataset.predictions[cid][:warning]
# cleanup
[training_dataset,model,compound_dataset,prediction_dataset].each{|o| o.delete}
end
def test_lazar_kazius
t = Time.now
dataset = Dataset.from_csv_file File.join(DATA_DIR,"kazius.csv")
t = Time.now
model = Model::LazarClassification.create(dataset.features.first,dataset)
t = Time.now
2.times do
compound = Compound.from_smiles("Clc1ccccc1NN")
prediction = model.predict compound
assert_equal "1", prediction[:value]
#assert_in_delta 0.019858401199860445, prediction[:confidence], 0.001
end
dataset.delete
end
end
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