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require_relative "setup.rb"
class LazarModelTest < MiniTest::Test
MODELS = []
# test hamster
=begin
MODELS << {
:titel => "hamster_carcinogenicity",
:file => File.join(DATA_DIR,"hamster_carcinogenicity.csv"),
:type => "classification",
:feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"),
:min_frequency => 2,
:test_values => {
:feature_size => 54,
:first_feature => "[#6&A]-[#6&A]-[#6&A]=[#6&A]",
:prediction1 => [OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H").uri,"false",0.25281385281385277],
:prediction2 => [OpenTox::Compound.from_smiles("c1ccccc1NN").uri,"false",0.3639589577089577]
}
}
=end
# Hamster
MODELS << {
:titel => "DSSTox_Carcinogenic_Potency_DBS_v5d_Hamster",
:file => File.join(DATA_DIR,"CPDBAS_v5d_cleaned","DSSTox_Carcinogenic_Potency_DBS_Hamster.csv"),
:type => "classification",
:feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"),
:min_frequency => 2,
:test_values => {
:feature_size => 58,
:first_feature => '[#6&A]-[#6&A]-[#6&A]=[#6&A]',
:prediction1 => [OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H").uri,"inactive",0.23658008658008656],
:prediction2 => [OpenTox::Compound.from_smiles("c1ccccc1NN").uri,"inactive",0.34980297480297484]
}
}
=begin
# Mutagenicity
MODELS << {
:titel => "DSSTox_Carcinogenic_Potency_DBS_v5d_Mutagenicity",
:file => File.join(DATA_DIR,"CPDBAS_v5d_cleaned","DSSTox_Carcinogenic_Potency_DBS_Mutagenicity_no_duplicates.csv"),
:type => "classification",
:feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"),
:min_frequency => 8,
:test_values => {
:feature_size => 58,
:first_feature => '[#6&A]-[#6&A]-[#6&A]=[#6&A]',
:prediction1 => [OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H").uri,"inactive",0.23658008658008656],
:prediction2 => [OpenTox::Compound.from_smiles("c1ccccc1NN").uri,"inactive",0.34980297480297484]
}
}
# Mouse
MODELS << {
:titel => "DSSTox_Carcinogenic_Potency_DBS_v5d_Mouse",
:file => File.join(DATA_DIR,"CPDBAS_v5d_cleaned","DSSTox_Carcinogenic_Potency_DBS_Mouse.csv"),
:type => "classification",
:feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"),
:min_frequency => 10,
:test_values => {
:feature_size => 58,
:first_feature => '[#6&A]-[#6&A]-[#6&A]=[#6&A]',
:prediction1 => [OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H").uri,"inactive",0.23658008658008656],
:prediction2 => [OpenTox::Compound.from_smiles("c1ccccc1NN").uri,"inactive",0.34980297480297484]
}
}
# Rat
MODELS << {
:titel => "DSSTox_Carcinogenic_Potency_DBS_v5d_Rat",
:file => File.join(DATA_DIR,"CPDBAS_v5d_cleaned","DSSTox_Carcinogenic_Potency_DBS_Rat.csv"),
:type => "classification",
:feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"),
:min_frequency => 12,
:test_values => {
:feature_size => 58,
:first_feature => '[#6&A]-[#6&A]-[#6&A]=[#6&A]',
:prediction1 => [OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H").uri,"inactive",0.23658008658008656],
:prediction2 => [OpenTox::Compound.from_smiles("c1ccccc1NN").uri,"inactive",0.34980297480297484]
}
}
# MultiCellCall
MODELS << {
:titel => "DSSTox_Carcinogenic_Potency_DBS_v5d_MultiCellCall",
:file => File.join(DATA_DIR,"CPDBAS_v5d_cleaned","DSSTox_Carcinogenic_Potency_DBS_MultiCellCall_no_duplicates.csv"),
:type => "classification",
:feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"),
:min_frequency => 11,
:test_values => {
:feature_size => 58,
:first_feature => '[#6&A]-[#6&A]-[#6&A]=[#6&A]',
:prediction1 => [OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H").uri,"inactive",0.23658008658008656],
:prediction2 => [OpenTox::Compound.from_smiles("c1ccccc1NN").uri,"inactive",0.34980297480297484]
}
}
# SingleCellCall
MODELS << {
:titel => "DSSTox_Carcinogenic_Potency_DBS_v5d_SingleCellCall",
:file => File.join(DATA_DIR,"CPDBAS_v5d_cleaned","DSSTox_Carcinogenic_Potency_DBS_SingleCellCall.csv"),
:type => "classification",
:feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"),
:min_frequency => 15,
:test_values => {
:feature_size => 58,
:first_feature => '[#6&A]-[#6&A]-[#6&A]=[#6&A]',
:prediction1 => [OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H").uri,"inactive",0.23658008658008656],
:prediction2 => [OpenTox::Compound.from_smiles("c1ccccc1NN").uri,"inactive",0.34980297480297484]
}
}
=end
def test_lazar_models
MODELS.each do |model|
dataset = OpenTox::Dataset.new
dataset.upload model[:file]
assert_equal dataset.uri.uri?, true
# puts model[:file]
# puts dataset.uri
# puts
model_uri = OpenTox::Model::Lazar.create :dataset_uri => dataset.uri, :feature_generation_uri => model[:feature_generation_uri], :min_frequency => model[:min_frequency]
assert_equal model_uri.uri?, true
# puts "model_uri for '#{model[:titel]}': #{model_uri}"
this_model = OpenTox::Model::Lazar.new model_uri
assert_equal this_model.uri.uri?, true
feature_dataset_uri = this_model[RDF::OT.featureDataset]
feature_dataset = OpenTox::Dataset.new feature_dataset_uri
assert_equal dataset.compounds.size, feature_dataset.compounds.size
assert_equal model[:test_values][:feature_size], feature_dataset.features.size
# puts feature_dataset.features.size
assert_equal model[:test_values][:first_feature], OpenTox::Feature.new(feature_dataset.features.first.uri).title
# puts OpenTox::Feature.new(feature_dataset.features.first.uri).title
[ {
:compound => model[:test_values][:prediction1][0],
:prediction => model[:test_values][:prediction1][1],
:confidence => model[:test_values][:prediction1][2]
},{
:compound => model[:test_values][:prediction2][0],
:prediction => model[:test_values][:prediction2][1],
:confidence => model[:test_values][:prediction2][2]
} ].each do |example|
prediction_uri = this_model.predict :compound_uri => example[:compound]
# 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]}.first
assert_equal example[:prediction], prediction[:value]
# puts prediction[:value]
assert_equal example[:confidence], prediction[:confidence]
# puts prediction[:confidence]
# puts prediction_dataset.uri
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 = this_model.predict :dataset_uri => dataset.uri
prediction = OpenTox::Dataset.new prediction_uri
assert_equal prediction.uri.uri?, true
# puts prediction.uri
# cleanup
[dataset,this_model,feature_dataset,compound_dataset].each{|o| o.delete}
end
end
end
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