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require_relative "setup.rb"
class UseCasesTest < MiniTest::Test
def test_PA
#kazius = Dataset.from_sdf_file "#{DATA_DIR}/cas_4337.sdf"
#hansen = Dataset.from_csv_file "#{DATA_DIR}/hansen.csv"
#efsa = Dataset.from_csv_file "#{DATA_DIR}/efsa.csv"
#datasets = [kazius,hansen,efsa]
#map = {"1" => "mutagen", "0" => "nonmutagen"}
#p "merging"
#training_dataset = Dataset.merge datasets: datasets, features: datasets.collect{|d| d.bioactivity_features.first}, value_maps: [nil,map,map], keep_original_features: false, remove_duplicates: true
#assert_equal 8281, training_dataset.compounds.size
#p training_dataset.features.size
#p training_dataset.id
#training_dataset = Dataset.find('5bd8ac8fca62695d767fca6b')
#training_dataset = Dataset.find('5bd8bbadca62695f69e7a33b')
#puts training_dataset.to_csv
p "create model_validation"
#model_validation = Model::Validation.from_dataset training_dataset: training_dataset, prediction_feature: training_dataset.merged_features.first, species: "Salmonella typhimurium", endpoint: "Mutagenicity"
#p model_validation.id
#model_validation = Model::Validation.find '5bd8df47ca6269604590ab38'
#p "predict"
#pa = Dataset.from_sdf_file "#{DATA_DIR}/PA.sdf"
#prediction_dataset = model_validation.predict pa
#p prediction_dataset.id
prediction_dataset = Dataset.find('5bd98b88ca6269609aab79f4')
puts prediction_dataset.to_csv
end
def test_tox21
training_dataset = Dataset.from_pubchem_aid 743122
p training_dataset.id
#'5bd9a1dbca626969d97fb421'
File.open("AID743122.csv","w+"){|f| f.puts training_dataset.to_csv}
model = Model::Lazar.create training_dataset: training_dataset
p model.id
#p Model::Lazar.find('5bd9a70bca626969d97fc9df')
model_validation = Model::Validation.from_dataset training_dataset: training_dataset, prediction_feature: training_dataset.bioactivity_features.first, species: "Human HG2L7.5c1 cell line", endpoint: "aryl hydrocarbon receptor (AhR) signaling pathway activation"
p model_validation.id
end
def test_public_models
skip
=begin
#classification
aids = [
1205, #Rodents (multiple species/sites)
1208, # rat carc
1199 # mouse
# Mutagenicity
1195 #MRDD
1188 #FHM
1208, # rat carc td50
1199 # mouse td50
# daphnia
# Blood Brain Barrier Penetration
# Lowest observed adverse effect level (LOAEL)
# 1204 estrogen receptor
# 1259408, # GENE-TOX
# 1159563 HepG2 cytotoxicity assay
# 588209 hepatotoxicity
# 1259333 cytotoxicity
# 1159569 HepG2 cytotoxicity counterscreen Measured in Cell-Based System Using Plate Reader - 2153-03_Inhibitor_Dose_DryPowder_Activity
# 2122 HTS Counterscreen for Detection of Compound Cytotoxicity in MIN6 Cells
# 116724 Acute toxicity determined after intravenal administration in mice
# 1148549 Toxicity in po dosed mouse assessed as mortality after 7 days
=end
end
end
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