intermediary commit

2 files changed, 54 insertions, 26 deletions

diff --git a/test/lazar-physchem-long.rb b/test/lazar-physchem-long.rb
index 39e353e..280184d 100644
--- a/test/lazar-physchem-long.rb
+++ b/test/lazar-physchem-long.rb
@@ -23,7 +23,7 @@ class LazarPhyschemDescriptorTest < MiniTest::Test
     puts "Descriptors: #{@descriptors}"
 
     # UPLOAD DATA
-    @dataset = OpenTox::MeasuredDataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi.csv")
+    @dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi.csv")
     puts "Dataset: "+@dataset.id
 
     @compound_smiles = "CC(C)(C)CN"
@@ -32,6 +32,9 @@ class LazarPhyschemDescriptorTest < MiniTest::Test
     prediction_a = build_model_and_predict(true)
     prediction_b = build_model_and_predict(false)
     
+    p prediction_a.data_entries
+    p prediction_b.data_entries
+    
     assert_equal prediction_a,prediction_b,"predicted value differs depending on calculation method"
     puts "Predicted value: #{prediction_a}"
     # the actual value (from the complete EPAFHM dataset) is 5.45, but it is predicted higher when tested
@@ -45,6 +48,7 @@ class LazarPhyschemDescriptorTest < MiniTest::Test
     model_params = {:dataset => @dataset}
     #feat_gen_uri = File.join($algorithm[:uri],"descriptor","physchem")
     
+=begin
     if precompute_feature_dataset
       # PRECOMPUTE FEATURES
       p = "/tmp/mergedfile.csv"
@@ -59,27 +63,28 @@ class LazarPhyschemDescriptorTest < MiniTest::Test
       model_params[:feature_generation_uri] = feat_gen_uri
       model_params[:descriptors] = @descriptors
     end
+=end
       
     # BUILD MODEL
 
     #p descriptors
-    feature_dataset = OpenTox::CalculatedDataset.new
-    feature_dataset.compounds = @dataset.compounds
-    feature_dataset.data_entries = descriptors
-    feature_dataset.features = @descriptors.collect{|d| OpenTox::Feature.find_or_create_by(:title => d)}
-    feature_dataset["inchis"].each do |inchi|
-      assert_kind_of String, inchi
+    feature_dataset = OpenTox::Algorithm::Descriptor.physchem(@dataset, @descriptors)
+    #feature_dataset = DescriptorDataset.new
+    #feature_dataset.compounds = @dataset.compounds
+    #feature_dataset.data_entries = descriptors
+    #feature_dataset.features = @descriptors.collect{|d| OpenTox::Feature.find_or_create_by(:title => d)}
+    feature_dataset.compounds.each do |compound|
+      assert_kind_of Compound, compound
     end
-    feature_dataset["feature_ids"].each do |id|
+    feature_dataset.feature_ids.each do |id|
       assert_kind_of BSON::ObjectId, id
     end
     feature_dataset.data_entries.each do |entry|
-      #p entry
       assert_kind_of Array, entry
-      entry.each do |e|
+      #entry.each do |e|
         #p e
-        assert_kind_of Float, e
-      end
+      #  assert_kind_of Float, e
+      #end
     end
     feature_dataset.save
     model = OpenTox::Model::Lazar.create @dataset, feature_dataset
@@ -93,7 +98,7 @@ class LazarPhyschemDescriptorTest < MiniTest::Test
     #feature_dataset = OpenTox::Dataset.new(feature_dataset_uri)
     assert_equal @dataset.compounds.size,feature_dataset.compounds.size,"Incorrect number of compounds in feature dataset"
     features = feature_dataset.features
-    feature_titles = features.collect{|f| f.title}
+    feature_titles = features.collect{|f| f.name}
     @descriptors.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
@@ -105,23 +110,22 @@ class LazarPhyschemDescriptorTest < MiniTest::Test
         assert feature_titles.include?(d),"feature not found #{d} in feature dataset #{feature_titles.inspect}"
       end
     end
-    assert_equal @descriptors.size,features.size,"Incorrect number of features in feature dataset"
-    #assert_equal (@descriptors.size+@num_features_offset),features.size,"wrong num features in feature dataset"
+    # Cdk.WienerNumbers returns 2 features
+    assert_equal (@descriptors.size+@num_features_offset),features.size,"wrong num features in feature dataset"
 
     # predict compound
-    compound_uri = "#{$compound[:uri]}/#{@compound_inchi}"
-    compound = OpenTox::Compound.new @compound_inchi
-    prediction = model.predict :compound => compound
-    p prediction
+    compound = OpenTox::Compound.from_inchi @compound_inchi
+    prediction = model.predict compound
+    prediction
     #prediction = OpenTox::Dataset.new prediction_uri
     #assert_equal prediction.uri.uri?, true
     #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"
-    prediction.data_entry_value(prediction.compound_indices(compound_uri).first,model.predicted_variable)
+    # TODO 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"
+    #prediction.data_entry_value(prediction.compound_indices(compound_uri).first,model.predicted_variable)
   end
 
 end
diff --git a/test/lazar-physchem-short.rb b/test/lazar-physchem-short.rb
index 5b00231..c9de60c 100644
--- a/test/lazar-physchem-short.rb
+++ b/test/lazar-physchem-short.rb
@@ -1,3 +1,27 @@
-$short_tests = true
+require_relative "setup.rb"
 
-require File.join(File.expand_path(File.dirname(__FILE__)),"lazar-physchem-long.rb")
+class LazarPhyschemDescriptorTest < MiniTest::Test
+  def test_epafhm
+    # check available descriptors
+    @descriptors = OpenTox::Algorithm::Descriptor::DESCRIPTORS.keys
+    assert_equal 111,@descriptors.size,"wrong number of physchem descriptors"
+    @descriptor_values = OpenTox::Algorithm::Descriptor::DESCRIPTOR_VALUES
+
+    # select descriptors for test
+    @num_features_offset = 0
+    @descriptors.keep_if{|x| x=~/^Openbabel\./}
+    @descriptors.delete("Openbabel.L5") # TODO Openbabel.L5 does not work, investigate!!!
+    puts "Descriptors: #{@descriptors}"
+
+    # UPLOAD DATA
+    training_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi.csv")
+    puts "Dataset: "+training_dataset.id
+    feature_dataset = Algorithm::Descriptor.physchem training_dataset, @descriptors
+    model = Model::Lazar.create training_dataset, feature_dataset
+    #p model
+    compound = Compound.from_smiles "CC(C)(C)CN"
+    prediction = model.predict compound
+    p prediction
+
+  end
+end