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require_relative "setup.rb"
class NanoparticleModelTest < MiniTest::Test
include OpenTox::Validation
def setup
@training_dataset = Dataset.where(:name => "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles").first
@prediction_feature = @training_dataset.features.select{|f| f["name"] == 'log2(Net cell association)'}.first
end
def test_core_coating_source_uris
@training_dataset.nanoparticles.each do |np|
refute_nil np.core.source
np.coating.each{|c| refute_nil c.source}
end
end
def test_nanoparticle_model
assert true, @prediction_feature.measured
model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature
refute_empty model.dependent_variables
refute_empty model.descriptor_ids
refute_empty model.independent_variables
assert_equal "Algorithm::Caret.rf", model.algorithms[:prediction][:method]
assert_equal "Algorithm::Similarity.weighted_cosine", model.algorithms[:similarity][:method]
nanoparticle = @training_dataset.nanoparticles[-34]
assert_includes nanoparticle.dataset_ids, @training_dataset.id
prediction = model.predict nanoparticle
refute_nil prediction[:value]
assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions."
prediction = model.predict @training_dataset.substances[14]
refute_nil prediction[:value]
assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions."
model.delete
end
def test_nanoparticle_fingerprint_model
assert true, @prediction_feature.measured
algorithms = {
:descriptors => {
:method => "fingerprint",
:type => "MP2D",
},
:similarity => {
:method => "Algorithm::Similarity.tanimoto",
:min => 0.1
},
:feature_selection => nil
}
model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature, algorithms: algorithms
refute_empty model.dependent_variables
refute_empty model.descriptor_ids
refute_empty model.independent_variables
assert_equal "Algorithm::Caret.rf", model.algorithms[:prediction][:method]
assert_equal "Algorithm::Similarity.tanimoto", model.algorithms[:similarity][:method]
assert_nil model.algorithms[:descriptors][:categories]
nanoparticle = @training_dataset.nanoparticles[-34]
assert_includes nanoparticle.dataset_ids, @training_dataset.id
prediction = model.predict nanoparticle
refute_nil prediction[:value]
assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions."
prediction = model.predict @training_dataset.substances[14]
refute_nil prediction[:value]
assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions."
model.delete
end
def test_nanoparticle_fingerprint_model_with_feature_selection
assert true, @prediction_feature.measured
algorithms = {
:descriptors => {
:method => "fingerprint",
:type => "MP2D",
},
:similarity => {
:method => "Algorithm::Similarity.tanimoto",
:min => 0.1
},
}
model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature, algorithms: algorithms
refute_empty model.algorithms[:feature_selection]
refute_empty model.dependent_variables
refute_empty model.descriptor_ids
refute_empty model.independent_variables
assert_equal "Algorithm::Caret.rf", model.algorithms[:prediction][:method]
assert_equal "Algorithm::Similarity.tanimoto", model.algorithms[:similarity][:method]
nanoparticle = @training_dataset.nanoparticles[-34]
assert_includes nanoparticle.dataset_ids, @training_dataset.id
prediction = model.predict nanoparticle
refute_nil prediction[:value]
assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions."
prediction = model.predict @training_dataset.substances[14]
refute_nil prediction[:value]
assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions."
model.delete
end
def test_nanoparticle_calculated_properties_model
skip "Nanoparticle calculate_properties similarity not yet implemented"
assert true, @prediction_feature.measured
algorithms = {
:descriptors => {
:method => "calculate_properties",
:features => PhysChem.openbabel_descriptors,
},
:similarity => {
:method => "Algorithm::Similarity.weighted_cosine",
:min => 0.5
},
:prediction => {
:method => "Algorithm::Regression.weighted_average",
},
}
model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature, algorithms: algorithms
refute_empty model.dependent_variables
refute_empty model.descriptor_ids
refute_empty model.independent_variables
assert_equal "Algorithm::Caret.rf", model.algorithms[:prediction][:method]
assert_equal "Algorithm::Similarity.weighted", model.algorithms[:similarity][:method]
nanoparticle = @training_dataset.nanoparticles[-34]
assert_includes nanoparticle.dataset_ids, @training_dataset.id
prediction = model.predict nanoparticle
refute_nil prediction[:value]
assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions."
prediction = model.predict @training_dataset.substances[14]
refute_nil prediction[:value]
assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions."
model.delete
end
def test_import_ld
skip # Ambit JSON-LD export defunct
dataset_ids = Import::Enanomapper.import_ld
end
end
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