add feature dataset test and computation of single cdk feature value (e.g. Cdk.ALOGP.AMR instead of Cdk.ALOGP) to lazar-phsychem test

1 files changed, 36 insertions, 9 deletions

diff --git a/test/lazar-physchem-long.rb b/test/lazar-physchem-long.rb
index 0b2820d..a4cb0b3 100644
--- a/test/lazar-physchem-long.rb
+++ b/test/lazar-physchem-long.rb
@@ -15,38 +15,65 @@ class LazarPhyschemDescriptorTest < MiniTest::Test
     assert_equal 111,sum
 
     # select descriptors for test
+    num_features_offset = 0
     desc.keep_if{|x| x=~/^Openbabel\./}
+    desc.delete("Openbabel.L5") # TODO Openbabel.L5 does not work, investigate!!!
     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"]
+      # A CDK descriptor can calculate serveral values, e.g., ALOGP produces ALOGP.ALogP, ALOGP.ALogp2, ALOGP.AMR
+      # both is accepted (and tested here): Cdk.ALOGP (produces 3 features), or ALOGP.AMR (produces only 1 feature)
+      desc += ["Cdk.ALOGP.AMR", "Cdk.WienerNumbers", "Joelib.LogP", "Joelib.count.HeteroCycles"]
+      num_features_offset = 1 # Cdk.WienerNumbers produces 2 (instead of 1) features
     end
-    puts "descriptors for modeling: #{desc}"
+    puts "Descriptors: #{desc}"
 
+    # UPLOAD DATA
     dataset = OpenTox::Dataset.new 
     dataset.upload File.join(DATA_DIR,"EPAFHM.medi.csv")
     assert_equal dataset.uri.uri?, true
-    puts dataset.uri
+    puts "Dataset: "+dataset.uri
 
+    # BUILD MODEL
     model_uri = OpenTox::Model::Lazar.create :dataset_uri => dataset.uri, :feature_generation_uri => File.join($algorithm[:uri],"descriptor","physchem"), :descriptors => desc
-    puts model_uri
+    puts "Model: "+model_uri
     model = OpenTox::Model::Lazar.new model_uri
     assert_equal model_uri.uri?, true
-    puts model.predicted_variable
+    puts "Predicted variable: "+model.predicted_variable
+    
+    # CHECK FEATURE DATASET
+    feature_dataset_uri = model.metadata[RDF::OT.featureDataset].first
+    puts "Feature dataset: #{feature_dataset_uri}"
+    features = OpenTox::Dataset.new(feature_dataset_uri).features
+    feature_titles = features.collect{|f| f.title}
+    desc.each do |d|
+      if (d=~/^Cdk\./ and d.count(".")==1) # CDK descriptors (e.g. Cdk.ALOG are included as Cdk.ALOGP.ALogP, Cdk.ALOGP.ALogp2 ..)
+        match = false
+        feature_titles.each do |f|
+          match = true if f=~/d/
+        end
+        assert match,"feature not found #{d} in feature dataset #{feature_titles.inspect}"
+      else
+        assert feature_titles.include?(d),"feature not found #{d} in feature dataset #{feature_titles.inspect}"
+      end
+    end
+    assert_equal (desc.size+num_features_offset),features.size,"wrong num features in feature dataset"
 
+    # predict compound
     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
-
+    puts "Prediction "+prediction.uri
+    
+    # check prediction
     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
+    puts "Predicted value: #{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