diff options
Diffstat (limited to 'test')
-rw-r--r-- | test/model-classification.rb (renamed from test/classification.rb) | 16 | ||||
-rw-r--r-- | test/model.rb | 7 | ||||
-rw-r--r-- | test/nanoparticles.rb | 13 |
3 files changed, 22 insertions, 14 deletions
diff --git a/test/classification.rb b/test/model-classification.rb index c670bb5..1424f6a 100644 --- a/test/classification.rb +++ b/test/model-classification.rb @@ -4,7 +4,10 @@ class LazarClassificationTest < MiniTest::Test def test_classification_default algorithms = { - :descriptors => [ "MP2D" ], + :descriptors => { + :method => "fingerprint", + :type => "MP2D" + }, :similarity => { :method => "Algorithm::Similarity.tanimoto", :min => 0.1 @@ -55,7 +58,10 @@ class LazarClassificationTest < MiniTest::Test def test_classification_parameters algorithms = { - :descriptors => ['MACCS'], + :descriptors => { + :method => "fingerprint", + :type => "MACCS" + }, :similarity => { :min => 0.4 }, @@ -86,7 +92,11 @@ class LazarClassificationTest < MiniTest::Test training_dataset.delete end - def test_fingerprint_feature_selection + def test_caret_classification + skip + end + + def test_fingerprint_chisq_feature_selection skip end diff --git a/test/model.rb b/test/model.rb index 322ad90..027efe4 100644 --- a/test/model.rb +++ b/test/model.rb @@ -49,7 +49,10 @@ class ModelTest < MiniTest::Test def test_physchem_regression algorithms = { - :descriptors => [PhysChem::OPENBABEL], + :descriptors => { + :method => "calculate_properties", + :features => PhysChem.openbabel_descriptors, + }, :similarity => { :method => "Algorithm::Similarity.cosine", } @@ -60,9 +63,9 @@ class ModelTest < MiniTest::Test assert_equal "Algorithm::Caret.pls", model.algorithms[:prediction][:method] assert_equal "Algorithm::Similarity.cosine", model.algorithms[:similarity][:method] assert_equal 0.1, model.algorithms[:similarity][:min] + algorithms[:descriptors].delete :features assert_equal algorithms[:descriptors], model.algorithms[:descriptors] prediction = model.predict training_dataset.substances[10] - p prediction refute_nil prediction[:value] # TODO test predictin end diff --git a/test/nanoparticles.rb b/test/nanoparticles.rb index c489cb7..9a67e63 100644 --- a/test/nanoparticles.rb +++ b/test/nanoparticles.rb @@ -1,6 +1,5 @@ require_relative "setup.rb" - class NanoparticleTest < MiniTest::Test include OpenTox::Validation @@ -13,7 +12,7 @@ class NanoparticleTest < MiniTest::Test @prediction_feature = @training_dataset.features.select{|f| f["name"] == 'log2(Net cell association)'}.first end - def test_create_model + def test_nanoparticle_model model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature nanoparticle = @training_dataset.nanoparticles[-34] prediction = model.predict nanoparticle @@ -23,6 +22,8 @@ class NanoparticleTest < MiniTest::Test model.delete end + # validations + def test_validate_default_nanoparticle_model model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature cv = CrossValidation.create model @@ -77,15 +78,9 @@ class NanoparticleTest < MiniTest::Test refute_nil cv.rmse end - def test_export - skip - Dataset.all.each do |d| - puts d.to_csv - end - end def test_import_ld - skip + skip # Ambit JSON-LD export defunct dataset_ids = Import::Enanomapper.import_ld end end |