Added test for current models.

2 files changed, 97 insertions, 5 deletions

diff --git a/test/lazar-fminer.rb b/test/lazar-fminer.rb
index ef17985..4f146c6 100644
--- a/test/lazar-fminer.rb
+++ b/test/lazar-fminer.rb
@@ -3,7 +3,7 @@ require_relative "setup.rb"
 class LazarFminerTest < MiniTest::Test
 
   def test_lazar_fminer
-    dataset = OpenTox::Dataset.new 
+    dataset = OpenTox::Dataset.new
     dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv")
     assert_equal dataset.uri.uri?, true
     model_uri = OpenTox::Model::Lazar.create :dataset_uri => dataset.uri, :feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc")
@@ -11,7 +11,7 @@ class LazarFminerTest < MiniTest::Test
     model = OpenTox::Model::Lazar.new model_uri
     assert_equal model.uri.uri?, true
     feature_dataset_uri = model[RDF::OT.featureDataset]
-    feature_dataset = OpenTox::Dataset.new feature_dataset_uri 
+    feature_dataset = OpenTox::Dataset.new feature_dataset_uri
     assert_equal dataset.compounds.size, feature_dataset.compounds.size
     assert_equal 54, feature_dataset.features.size
     assert_equal '[#6&A]-[#6&A]-[#6&A]=[#6&A]', OpenTox::Feature.new(feature_dataset.features.first.uri).title
@@ -21,13 +21,12 @@ class LazarFminerTest < MiniTest::Test
       :prediction => "false",
       :confidence => 0.25281385281385277
     },{
-      # lazar Parameter, min_frequency = 8
       :compound => OpenTox::Compound.from_smiles("c1ccccc1NN"),
       :prediction => "false",
       :confidence => 0.3639589577089577
     } ].each do |example|
       prediction_uri = model.predict :compound_uri => example[:compound].uri
-      puts prediction_uri
+      #puts prediction_uri
       prediction_dataset = OpenTox::Dataset.new prediction_uri
       assert_equal prediction_dataset.uri.uri?, true
       prediction = prediction_dataset.predictions.select{|p| p[:compound].uri == example[:compound].uri}.first
@@ -37,7 +36,7 @@ class LazarFminerTest < MiniTest::Test
     end
 
     # make a dataset prediction
-    compound_dataset = OpenTox::Dataset.new 
+    compound_dataset = OpenTox::Dataset.new
     compound_dataset.upload File.join(DATA_DIR,"EPAFHM.mini.csv")
     assert_equal compound_dataset.uri.uri?, true
     prediction_uri = model.predict :dataset_uri => dataset.uri
diff --git a/test/lazar-models.rb b/test/lazar-models.rb
new file mode 100644
index 0000000..df4e32a
--- /dev/null
+++ b/test/lazar-models.rb
@@ -0,0 +1,93 @@
+require_relative "setup.rb"
+
+class LazarModelTest < MiniTest::Test
+
+  MODELS = []
+  MODELS << {
+    :titel => "hamster_carcinogenicity",
+    :file => File.join(DATA_DIR,"hamster_carcinogenicity.csv"),
+    :type => "classification",
+    :feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"),
+    :min_frequency => 2,
+    :test_values => {
+      :feature_size => 54,
+      :first_feature => "[#6&A]-[#6&A]-[#6&A]=[#6&A]",
+      :prediction1 => [OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H").uri,"false",0.25281385281385277],
+      :prediction2 => [OpenTox::Compound.from_smiles("c1ccccc1NN").uri,"false",0.3639589577089577]
+    }
+  }
+  MODELS << {
+    :titel => "DSSTox_Carcinogenic_Potency_DBS_v5d_Hamster",
+    :file => File.join(DATA_DIR,"CPDBAS_v5d_cleaned","DSSTox_Carcinogenic_Potency_DBS_Hamster.csv"),
+    :type => "classification",
+    :feature_generation_uri => File.join($algorithm[:uri],"fminer","bbrc"),
+    :min_frequency => 2,
+    :test_values => {
+      :feature_size => 58,
+      :first_feature => '[#6&A]-[#6&A]-[#6&A]=[#6&A]',
+      :prediction1 => [OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H").uri,"inactive",0.23658008658008656],
+      :prediction2 => [OpenTox::Compound.from_smiles("c1ccccc1NN").uri,"inactive",0.34980297480297484]
+  }
+  }
+
+
+  #DSSTox_Carcinogenic_Potency_DBS_Mouse.csv
+  #DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv
+  #DSSTox_Carcinogenic_Potency_DBS_MultiCellCall_no_duplicates.csv
+  #DSSTox_Carcinogenic_Potency_DBS_Mutagenicity.csv
+  #DSSTox_Carcinogenic_Potency_DBS_Mutagenicity_no_duplicates.csv
+  #DSSTox_Carcinogenic_Potency_DBS_Rat.csv
+  #DSSTox_Carcinogenic_Potency_DBS_SingleCellCall.csv
+  def test_lazar_models
+    MODELS.each do |model|
+      dataset = OpenTox::Dataset.new
+      dataset.upload model[:file]
+      assert_equal dataset.uri.uri?, true
+      model_uri = OpenTox::Model::Lazar.create :dataset_uri => dataset.uri, :feature_generation_uri => model[:feature_generation_uri]
+      assert_equal model_uri.uri?, true
+      #puts "model_uri for '#{model[:titel]}': #{model_uri}"
+      this_model = OpenTox::Model::Lazar.new model_uri
+      assert_equal this_model.uri.uri?, true
+      feature_dataset_uri = this_model[RDF::OT.featureDataset]
+      feature_dataset = OpenTox::Dataset.new feature_dataset_uri
+      assert_equal dataset.compounds.size, feature_dataset.compounds.size
+      assert_equal model[:test_values][:feature_size], feature_dataset.features.size
+      #puts feature_dataset.features.size
+      assert_equal model[:test_values][:first_feature], OpenTox::Feature.new(feature_dataset.features.first.uri).title
+      #puts OpenTox::Feature.new(feature_dataset.features.first.uri).title
+
+      [ {
+        :compound => model[:test_values][:prediction1][0],
+        :prediction => model[:test_values][:prediction1][1],
+        :confidence => model[:test_values][:prediction1][2]
+      },{
+        :compound => model[:test_values][:prediction2][0],
+        :prediction => model[:test_values][:prediction2][1],
+        :confidence => model[:test_values][:prediction2][2]
+      } ].each do |example|
+        prediction_uri = this_model.predict :compound_uri => example[:compound]
+        #puts prediction_uri
+        prediction_dataset = OpenTox::Dataset.new prediction_uri
+        assert_equal prediction_dataset.uri.uri?, true
+        prediction = prediction_dataset.predictions.select{|p| p[:compound].uri == example[:compound]}.first
+        assert_equal example[:prediction], prediction[:value]
+        #puts prediction[:value]
+        assert_equal example[:confidence], prediction[:confidence]
+        #puts prediction[:confidence]
+        #puts prediction_dataset.uri
+        #prediction_dataset.delete
+      end
+
+      # make a dataset prediction
+      compound_dataset = OpenTox::Dataset.new
+      compound_dataset.upload File.join(DATA_DIR,"EPAFHM.mini.csv")
+      assert_equal compound_dataset.uri.uri?, true
+      prediction_uri = this_model.predict :dataset_uri => dataset.uri
+      prediction = OpenTox::Dataset.new prediction_uri
+      assert_equal prediction.uri.uri?, true
+
+      # cleanup
+      [dataset,this_model,feature_dataset,compound_dataset].each{|o| o.delete}
+    end
+  end
+end