Merge branch 'development' into numeric

Conflicts:
	lazar.rb

1 files changed, 30 insertions, 92 deletions

diff --git a/lazar.rb b/lazar.rb
index 424716e..6cdca99 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -60,6 +60,26 @@ class LazarTest < Test::Unit::TestCase
     @model.delete(@@subjectid)
   end
 
+=begin
+=end
+  def test_create_regression_model
+    create_model :dataset_uri => @@regression_training_dataset.uri
+    predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN")
+    assert_in_delta @predictions.first.value(@compounds.first), 1.095, 0.01
+    assert_equal 0.453.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
+    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
+    cleanup
+  end
+
+  def test_create_regression_prop_model
+    create_model :dataset_uri => @@regression_training_dataset.uri, :local_svm_kernel => "propositionalized"
+    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
+    assert_equal 0.453.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
+    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
+    assert_equal 131, @model.features.size
+    cleanup
+  end
+
   def test_classification_model
     create_model :dataset_uri => @@classification_training_dataset.uri
     # single prediction
@@ -124,115 +144,33 @@ class LazarTest < Test::Unit::TestCase
     cleanup
   end
 
-  def test_classification_default_nr_hits_true
-    create_model :dataset_uri => @@classification_training_dataset.uri, :nr_hits => "true"
-    predict_compound OpenTox::Compound.from_smiles("c1c[c+](O)ccc1NN")
-    assert_equal "true", @predictions.first.value(@compounds.first)
-    assert_equal 0.0749, @predictions.first.confidence(@compounds.first).round_to(4)
-    assert_equal 18, @predictions.first.neighbors(@compounds.first).size
-    assert_equal 41, @model.features.size
-    cleanup
-  end
-
-  def test_classification_default_nr_hits_false
-    create_model :dataset_uri => @@classification_training_dataset.uri, :nr_hits => "false"
-    predict_compound OpenTox::Compound.from_smiles("NNc1cccc1")
-    assert_equal "true", @predictions.first.value(@compounds.first)
-    assert_equal 0.1339, @predictions.first.confidence(@compounds.first).round_to(4)
-    assert_equal 26, @predictions.first.neighbors(@compounds.first).size
-    assert_equal 41, @model.features.size
-    cleanup
-  end
-
-  def test_create_regression_model
-    create_model :dataset_uri => @@regression_training_dataset.uri
-    predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN")
-    assert_equal 0.93.round_to(2), @predictions.first.value(@compounds.first).round_to(2)#1.09
-    assert_equal 0.154.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
-    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
-    assert_equal 131, @model.features.size
-    cleanup
-  end
-
-  def test_create_regression_prop_model
-    create_model :dataset_uri => @@regression_training_dataset.uri, :local_svm_kernel => "propositionalized"
-    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
-    assert 0.5 || 0.6, @predictions.first.value(@compounds.first).round_to(1)
-    assert_equal 0.154, @predictions.first.confidence(@compounds.first).round_to(3)
-    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
-    assert_equal 131, @model.features.size
-    cleanup
-  end
-
-  def test_create_regression_svm_conf_and_nr_false
-    create_model :dataset_uri => @@regression_training_dataset.uri,:prediction_algorithm => "local_svm_regression", :nr_hits => false, :conf_stdev => false
-    predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN")
-    assert_equal 0.42, @predictions.first.value(@compounds.first).round_to(2)#1.09.round_to(2), @predictions.first.value(@compounds.first).round_to(2)
-    assert_equal 0.262, @predictions.first.confidence(@compounds.first).round_to(3)
-    assert_equal 123, @predictions.first.neighbors(@compounds.first).size
-    assert_equal 131, @model.features.size
-    cleanup
-  end
-
-#  def test_regression_mlr_prop_default
+# def test_regression_mlr_prop_model
 #    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop"
 #    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
-#    assert_equal 0.154, @predictions.first.confidence(@compounds.first).round_to(3)
+#    assert_equal 0.453, @predictions.first.confidence(@compounds.first).round_to(3)
 #    assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3)
 #    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
 #    assert_equal 131, @model.features.size
-#    cleanup
-#  end
+# end
 #
-#  def test_regression_mlr_prop_conf_stdev_true
+# def test_regression_mlr_prop_conf_stdev
 #    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :conf_stdev => "true"
 #    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
 #    assert_equal 0.154, @predictions.first.confidence(@compounds.first).round_to(3)
 #    assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3)
 #    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
-#    assert 132 || 131, @model.features.size
-#    cleanup
-#  end
+#    assert_equal 131, @model.features.size
+# end
 #
-#  def test_regression_mlr_prop_conf_stdev_false
-#    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :conf_stdev => "false"
+#
+# def test_regression_mlr_prop_weighted_model
+#    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :nr_hits => "true"
 #    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
 #    assert_equal 0.453, @predictions.first.confidence(@compounds.first).round_to(3)
 #    assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3)
 #    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
 #    assert_equal 131, @model.features.size
-#    cleanup
-#  end
-#
-#  def test_regression_mlr_prop_nr_hits_true
-#    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :nr_hits => "true"
-#    predict_compound  OpenTox::Compound.from_smiles("c1c[c+](O)ccc1NN")
-#    assert_equal 0.028, @predictions.first.confidence(@compounds.first).round_to(3)
-#    assert_equal 0.741, @predictions.first.value(@compounds.first).round_to(3)
-#    assert_equal 12, @predictions.first.neighbors(@compounds.first).size
-#    assert_equal 131, @model.features.size
-#    cleanup
-#  end
-#
-#  def test_regression_mlr_prop_nr_hits_false
-#    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :nr_hits => "false"
-#    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
-#    assert_equal 0.056, @predictions.first.confidence(@compounds.first).round_to(3)
-#    assert_equal 0.168, @predictions.first.value(@compounds.first).round_to(3)
-#    assert_equal 123, @predictions.first.neighbors(@compounds.first).size
-#    assert_equal 131, @model.features.size
-#    cleanup
-#  end
-#
-#  def test_regression_mlr_prop_conf_stdev_and_nr_hits_false
-#    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :nr_hits => "false", :conf_stdev => "false"
-#    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
-#    assert_equal 0.262, @predictions.first.confidence(@compounds.first).round_to(3)
-#    assert_equal 0.168, @predictions.first.value(@compounds.first).round_to(3)
-#    assert_equal 123, @predictions.first.neighbors(@compounds.first).size
-#    assert_equal 131, @model.features.size
-#    cleanup
-#  end
+# end
 
   def test_conf_stdev
     params = {:sims => [0.6,0.72,0.8], :acts => [1,1,1], :neighbors => [1,1,1], :conf_stdev => true}