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require_relative "setup.rb"
class UseCasesTest < MiniTest::Test
def test_PA
# TODO add assertions
skip "This test ist very time consuming, enable on demand."
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 model_validation.crossvalidations.first.predictions.select{|cid,p| !p["warnings"].empty?}
#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
# TODO add assertions
skip "This test ist very time consuming, enable on demand."
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"
#model_validation = Model::Validation.find '5bd9b210ca62696be39ab74d'
#model_validation.crossvalidations.each do |cv|
#p cv
#end
#p model_validation.crossvalidations.first.predictions.select{|cid,p| !p["warnings"].empty?}
end
def test_download_public_models
Download.public_data
end
def test_import_public_models
skip
Import.public_data
end
end
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