Merge branch 'development' of github.com:opentox/test into development

1 files changed, 51 insertions, 5 deletions

diff --git a/lazar.rb b/lazar.rb
index 59ec9ca..a88801d 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -25,20 +25,38 @@ class LazarTest < Test::Unit::TestCase
 =end
   def test_create_regression_model
     model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@regression_training_dataset.uri, :subjectid => @@subjectid}).to_s
-    puts model_uri
+    #puts model_uri
     validate_owl model_uri,@@subjectid
     lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
     @models << lazar
-    assert_equal 185, lazar.features.size
+    assert_equal 219, lazar.features.size
     compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
     prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid).to_s
     prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
     @predictions << prediction
-    assert_equal prediction.value(compound).round_to(3),0.2849.round_to(3)
-    assert_equal prediction.confidence(compound).round_to(3), 0.3223.round_to(3)
+    assert_equal prediction.value(compound).round_to(3),0.378.round_to(3)
+    assert_equal prediction.confidence(compound).round_to(3), 0.276.round_to(3)
     #assert_equal prediction.value(compound).round_to(4), 0.2847.round_to(4)
     #assert_equal prediction.confidence(compound).round_to(4), 0.3223.round_to(4)
-    assert_equal prediction.neighbors(compound).size, 73
+    assert_equal prediction.neighbors(compound).size, 61
+  end
+
+  def test_create_regression_prop_model
+    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@regression_training_dataset.uri, :subjectid => @@subjectid, :local_svm_kernel => "propositionalized"}).to_s
+    #puts model_uri
+    validate_owl model_uri,@@subjectid
+    lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
+    @models << lazar
+    assert_equal 219, lazar.features.size
+    compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid).to_s
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
+    @predictions << prediction
+    assert_equal prediction.value(compound).round_to(1),0.1.round_to(1)
+    assert_equal prediction.confidence(compound).round_to(3), 0.276.round_to(3)
+    #assert_equal prediction.value(compound).round_to(4), 0.2847.round_to(4)
+    #assert_equal prediction.confidence(compound).round_to(4), 0.3223.round_to(4)
+    assert_equal prediction.neighbors(compound).size, 61
   end
 
   def test_classification_model
@@ -104,6 +122,34 @@ class LazarTest < Test::Unit::TestCase
     compound = OpenTox::Compound.from_smiles "CC(=Nc1ccc2c(c1)Cc1ccccc21)O"
     assert_equal prediction.value(compound), nil
     assert_equal prediction.measured_activities(compound).first, true
+ end
+
+  def test_classification_svm_prop_model
+
+
+    # create model
+    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@classification_training_dataset.uri, :subjectid => @@subjectid, :prediction_algorithm => "local_svm_classification", :local_svm_kernel => "propositionalized"}).to_s
+    lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
+    @models << lazar
+    assert_equal lazar.features.size, 52
+
+    # single prediction
+    compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
+    @predictions << prediction
+    assert_equal prediction.value(compound), false
+    assert_equal prediction.confidence(compound).round_to(4), 0.4131.round_to(4)
+    assert_equal prediction.neighbors(compound).size, 14
+
+    # dataset prediction
+    test_dataset = OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid)
+    prediction = OpenTox::LazarPrediction.find lazar.run(:dataset_uri => test_dataset.uri, :subjectid => @@subjectid), @@subjectid
+    @predictions << prediction
+    assert_equal prediction.compounds.size, 4
+    compound = OpenTox::Compound.from_smiles "CC(=Nc1ccc2c(c1)Cc1ccccc21)O"
+    assert_equal prediction.value(compound), nil
+    assert_equal prediction.measured_activities(compound).first, true
 
   end