diff options
Diffstat (limited to 'test/model-nanoparticle.rb')
| -rw-r--r-- | test/model-nanoparticle.rb | 98 |
1 files changed, 94 insertions, 4 deletions
diff --git a/test/model-nanoparticle.rb b/test/model-nanoparticle.rb index 7244a29..8dc6830 100644 --- a/test/model-nanoparticle.rb +++ b/test/model-nanoparticle.rb @@ -5,10 +5,6 @@ class NanoparticleModelTest < MiniTest::Test def setup @training_dataset = Dataset.where(:name => "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles").first - unless @training_dataset - Import::Enanomapper.import File.join(File.dirname(__FILE__),"data","enm") - @training_dataset = Dataset.where(name: "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles").first - end @prediction_feature = @training_dataset.features.select{|f| f["name"] == 'log2(Net cell association)'}.first end @@ -31,6 +27,100 @@ class NanoparticleModelTest < MiniTest::Test 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 |