1 files changed, 52 insertions, 0 deletions
diff --git a/test/lazar-physchem-long.rb b/test/lazar-physchem-long.rb
new file mode 100644
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+++ b/test/lazar-physchem-long.rb
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+require_relative "setup.rb"
+
+class LazarPhyschemDescriptorTest < MiniTest::Test
+
+  def test_lazar_pc_descriptors
+
+    # check available descriptors
+    desc = OpenTox::Algorithm::Descriptor.physchem_descriptors.keys
+    assert_equal 111,desc.size,"wrong num physchem descriptors"
+    sum = 0
+    {"Openbabel"=>16,"Cdk"=>50,"Joelib"=>45}.each do |k,v|
+      assert_equal v,desc.select{|x| x=~/^#{k}\./}.size,"wrong num #{k} descriptors"
+      sum += v
+    end
+    assert_equal 111,sum
+
+    # select descriptors for test
+    desc.keep_if{|x| x=~/^Openbabel\./}
+    unless defined?($short_tests)
+      # the actual descriptor calculation is rather fast, computing 3D structures takes time
+      desc += ["Cdk.XLogP", "Cdk.WienerNumbers", "Joelib.LogP", "Joelib.count.HeteroCycles"]
+    end
+    puts "descriptors for modeling: #{desc}"
+
+    dataset = OpenTox::Dataset.new 
+    dataset.upload File.join(DATA_DIR,"EPAFHM.medi.csv")
+    assert_equal dataset.uri.uri?, true
+    puts dataset.uri
+
+    model_uri = OpenTox::Model::Lazar.create :dataset_uri => dataset.uri, :feature_generation_uri => File.join($algorithm[:uri],"descriptor","physchem"), :descriptors => desc
+    puts model_uri
+    model = OpenTox::Model::Lazar.new model_uri
+    assert_equal model_uri.uri?, true
+    puts model.predicted_variable
+
+    compound_uri = "#{$compound[:uri]}/InChI=1S/C13H8Cl2O2/c14-12-5-4-11(7-13(12)15)17-10-3-1-2-9(6-10)8-16/h1-8H"
+    prediction_uri = model.predict :compound_uri => compound_uri
+    prediction = OpenTox::Dataset.new prediction_uri
+    assert_equal prediction.uri.uri?, true
+    puts prediction.uri
+
+    assert prediction.features.collect{|f| f.uri}.include?(model.predicted_variable),"prediction feature #{model.predicted_variable} not included prediction dataset #{prediction.features.collect{|f| f.uri}}"
+    assert prediction.compounds.collect{|c| c.uri}.include?(compound_uri),"compound #{compound_uri} not included in prediction dataset #{prediction.compounds.collect{|c| c.uri}}"
+    assert_equal 1,prediction.compound_indices(compound_uri).size,"compound should only be once in the dataset"
+
+    predicted_value = prediction.data_entry_value(prediction.compound_indices(compound_uri).first,model.predicted_variable)
+    puts predicted_value
+    assert predicted_value > 0.005,"predicted values should be above 0.005, is #{predicted_value}"
+    assert predicted_value < 0.1,"predicted values should be below 0.1, is #{predicted_value}"
+  end
+
+end