tests fixed. DescriptorTest#test_compound_all may fail within all.rb

5 files changed, 25 insertions, 14 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 38a55a8..9138452 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -229,6 +229,11 @@ module OpenTox
       save
     end
 
+    def delete
+      compounds.each{|c| c.dataset_ids.delete id.to_s}
+      super
+    end
+
   end
 
   # Dataset for lazar predictions
diff --git a/lib/model.rb b/lib/model.rb
index 8baed41..3a178a1 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -69,6 +69,7 @@ module OpenTox
       end
 
       def predict_substance substance
+        neighbor_algorithm_parameters = Hash[self.neighbor_algorithm_parameters.map{ |k, v| [k.to_sym, v] }] # convert string keys to symbols
         neighbors = substance.send(neighbor_algorithm, neighbor_algorithm_parameters)
         database_activities = nil
         prediction = {}
@@ -82,22 +83,22 @@ module OpenTox
           neighbors.delete_if{|n| n["_id"] == substance.id} # remove query substance for an unbiased prediction (also useful for loo validation)
         end
         if neighbors.empty?
-          prediction.merge!({:value => nil,:confidence => nil,:warning => "Could not find similar substances with experimental data in the training dataset.",:neighbors => []})
+          prediction.merge!({:value => nil,:probabilities => nil,:warning => "Could not find similar substances with experimental data in the training dataset.",:neighbors => []})
         elsif neighbors.size == 1
           value = nil
           tox = neighbors.first["toxicities"]
           if tox.size == 1 # single measurement
-            value = tox
+            value = tox.first
           else # multiple measurement
             if tox.collect{|t| t.numeric?}.uniq == [true] # numeric
               value = tox.median
             elsif tox.uniq.size == 1 # single value
               value = tox.first
             else # contradictory results
-              # TODO add majority vote
+              # TODO add majority vote??
             end
           end
-          prediction.merge!({:value => value, :confidence => nil, :warning => "Only one similar compound in the training set. Predicting median of its experimental values."}) if value
+          prediction.merge!({:value => value, :probabilities => nil, :warning => "Only one similar compound in the training set. Predicting median of its experimental values.", :neighbors => neighbors}) if value
         else
           # call prediction algorithm
           klass,method = prediction_algorithm.split('.')
diff --git a/lib/validation-statistics.rb b/lib/validation-statistics.rb
index 3c52b15..156353a 100644
--- a/lib/validation-statistics.rb
+++ b/lib/validation-statistics.rb
@@ -8,10 +8,11 @@ module OpenTox
       predictivity = {}
       nr_instances = 0
       predictions.each do |cid,pred|
-        # TODO use measured majority class
-        if pred[:measured].uniq.size == 1
+        # TODO
+        # use predictions without probabilities (single neighbor)??
+        # use measured majority class??
+        if pred[:measured].uniq.size == 1 and pred[:probabilities]
           m = pred[:measured].first
-        #pred[:measured].each do |m|
           if pred[:value] == m
             if pred[:value] == accept_values[0]
               confusion_matrix[0][0] += 1
@@ -63,12 +64,12 @@ module OpenTox
     end
 
     def self.regression predictions
+      # TODO: predictions within prediction_interval
       rmse = 0
       mae = 0
       x = []
       y = []
       predictions.each do |cid,pred|
-        p pred
         if pred[:value] and pred[:measured] 
           x << pred[:measured].median
           y << pred[:value]
diff --git a/test/regression.rb b/test/regression.rb
index 799650f..c0782c4 100644
--- a/test/regression.rb
+++ b/test/regression.rb
@@ -17,7 +17,7 @@ class LazarRegressionTest < MiniTest::Test
     model.neighbor_algorithm_parameters[:type] = "MP2D"
     compound = Compound.from_smiles "CCCSCCSCC"
     prediction = model.predict compound
-    assert_equal 1.26, prediction[:value].round(2)
+    assert_equal 1.37, prediction[:value].round(2)
     assert_equal 3, prediction[:neighbors].size
   end
 
diff --git a/test/validation.rb b/test/validation.rb
index ed19fee..39314da 100644
--- a/test/validation.rb
+++ b/test/validation.rb
@@ -34,13 +34,16 @@ class ValidationTest < MiniTest::Test
     model.save
     cv = ClassificationCrossValidation.create model
     params = model.neighbor_algorithm_parameters
-    params.delete :training_dataset_id
     params = Hash[params.map{ |k, v| [k.to_s, v] }] # convert symbols to string
 
     cv.validations.each do |validation|
       validation_params = validation.model.neighbor_algorithm_parameters
-      validation_params.delete "training_dataset_id"
-      assert_equal params, validation_params
+      refute_nil params["dataset_id"]
+      refute_nil validation_params[:dataset_id]
+      refute_equal params["dataset_id"], validation_params[:dataset_id]
+      ["min_sim","type","prediction_feature_id"].each do |k|
+        assert_equal params[k], validation_params[k]
+      end
     end
   end
   
@@ -55,13 +58,14 @@ class ValidationTest < MiniTest::Test
       }
     }
     model = Model::LazarRegression.create dataset.features.first, dataset, params
-    p model
     cv = RegressionCrossValidation.create model
     cv.validation_ids.each do |vid|
       model = Model::Lazar.find(Validation.find(vid).model_id)
       assert_equal params[:neighbor_algorithm_parameters][:type], model[:neighbor_algorithm_parameters][:type]
       assert_equal params[:neighbor_algorithm_parameters][:min_sim], model[:neighbor_algorithm_parameters][:min_sim]
-      refute_equal params[:neighbor_algorithm_parameters][:training_dataset_id], model[:neighbor_algorithm_parameters][:training_dataset_id]
+      refute_nil model[:neighbor_algorithm_parameters][:dataset_id]
+      refute_equal dataset.id, model[:neighbor_algorithm_parameters][:dataset_id]
+      assert_equal model.training_dataset_id, model[:neighbor_algorithm_parameters][:dataset_id]
     end
 
     refute_nil cv.rmse