validation statistic fixes

1 files changed, 0 insertions, 135 deletions

diff --git a/test/model-nanoparticle.rb b/test/model-nanoparticle.rb
deleted file mode 100644
index 67bbfdd..0000000
--- a/test/model-nanoparticle.rb
+++ /dev/null
@@ -1,135 +0,0 @@
-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