adjust to new ruby api wrapper version

1 files changed, 35 insertions, 53 deletions

diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index 2098ab1..d81bd29 100644
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -5,6 +5,8 @@ module Lib
   
   class OTPredictions < Predictions
   
+    CHECK_VALUES = ENV['RACK_ENV']=="test"
+  
     def identifier(instance_index)
       return compound(instance_index)
     end
@@ -26,26 +28,31 @@ module Lib
         prediction_dataset = OpenTox::Dataset.find prediction_dataset_uri
         raise "test dataset not found: '"+test_dataset_uri.to_s+"'" unless test_dataset
         raise "prediction dataset not found: '"+prediction_dataset_uri.to_s+"'" unless prediction_dataset
+        raise "test dataset feature not found: '"+prediction_feature+"', available features: "+test_dataset.features.inspect if test_dataset.features.index(prediction_feature)==nil
+        raise "prediction dataset feature not found: '"+predicted_variable+"', available features: "+prediction_dataset.features.inspect if prediction_dataset.features.index(predicted_variable)==nil
+        
+        class_values = OpenTox::Feature.domain(prediction_feature)
+        
+        @compounds = test_dataset.compounds
+        raise "test dataset is empty" unless @compounds.size>0
+        raise "more predicted than test compounds test:"+@compounds.size.to_s+" < prediction:"+
+          prediction_dataset.compounds.size.to_s if @compounds.size < prediction_dataset.compounds.size
         
-        class_values = OpenTox::Feature.range(prediction_feature)
+        if CHECK_VALUES
+          prediction_dataset.compounds.each do |c| 
+            raise "predicted compound not found in test dataset" if @compounds.index(c)==nil
+          end
+        end
         
         actual_values = []
-        @compounds = []
-        test_dataset.data.each do |compound,featuresValues|
+        @compounds.each do |c|
           
-          @compounds.push compound
-          #@compounds << (OpenTox::Compound.new :uri=>compound.to_s).smiles
-          
-          value = nil
-          LOGGER.warn "value is hash, but no feature value '"+prediction_feature.to_s+
-            "', hash: '"+featuresValues.inspect+"'" if featuresValues.is_a?(Hash) and !featuresValues.has_key?(prediction_feature)
-          value = featuresValues[prediction_feature] if featuresValues.is_a?(Hash)
-          value = value[0] if value.is_a?(Array) and value.length == 1
-          value = nil if value.to_s.size==0  # PENDING: hack to avoid illegal boolean values
+          value = test_dataset.get_value(c, prediction_feature)
           
           if is_classification
             value = value.to_s unless value==nil
-            raise "illegal class_value of actual value "+value.to_s+" class: "+value.class.to_s unless value==nil or class_values.index(value)!=nil
+            raise "illegal class_value of actual value "+value.to_s+" class: "+
+              value.class.to_s unless value==nil or class_values.index(value)!=nil
             actual_values.push class_values.index(value) 
           else
             begin
@@ -58,50 +65,25 @@ module Lib
           end
         end
         
-        raise "test dataset is empty" unless @compounds.size>0
-        
-        predicted_values = Array.new(actual_values.size)
-        confidence_values = Array.new(actual_values.size)
-        
-        prediction_dataset.data.each do |compound,featuresValues|
-      
-          index = @compounds.index(compound)
-          raise "compound "+compound.to_s+" not found in\n"+@compounds.inspect if index==nil
-    
-          value = nil
-          LOGGER.warn "value is hash, but no feature value '"+predicted_variable.to_s+
-            "', hash: '"+featuresValues.inspect+"'" if featuresValues.is_a?(Hash) and !featuresValues.has_key?(predicted_variable)
-          value = featuresValues[predicted_variable] if featuresValues.is_a?(Hash)
-          value = value[0] if value.is_a?(Array) and value.length == 1
-          value = nil if value.to_s.size==0
-
-          if is_classification
-            
-            ### PENDING ####
-            confidence = nil
-            if value.is_a?(Hash)
-              confidence = value["confidence"].to_f.abs if value.has_key?("confidence")
-              value = value["classification"].to_s if value.has_key?("classification")
-            else
-              value = value.to_s unless value==nil # PENDING: hack to avoid illegal boolean values
-            end
-            ################
-            
-            raise "illegal class_value of predicted value "+value.to_s+" class: "+value.class.to_s unless value==nil or class_values.index(value)!=nil
-            predicted_values[index] = class_values.index(value) 
-            confidence_values[index] = confidence if confidence!=nil
+        predicted_values = []
+        confidence_values = []
+        @compounds.each do |c|
+          if prediction_dataset.compounds.index(c)==nil
+            predicted_values << nil
+            confidence_values << nil
           else
-            begin
-              value = value.to_f unless value==nil or value.is_a?(Numeric)
-            rescue
-              LOGGER.warn "no numeric value for regression: '"+value.to_s+"'"
-              value = nil
+            if is_classification
+              value = prediction_dataset.get_predicted_class(c, predicted_variable)
+              value = value.to_s unless value==nil
+              raise "illegal class_value of predicted value "+value.to_s+" class: "+value.class.to_s unless value==nil or class_values.index(value)!=nil
+              predicted_values << class_values.index(value)
+              confidence_values << prediction_dataset.get_prediction_confidence(c, predicted_variable)
+            else
+              raise "TODO regression"
             end
-            predicted_values[index] = value
           end
-          index += 1
         end
-
+        
         super(predicted_values, actual_values, confidence_values, is_classification, class_values)
         raise "illegal num compounds "+num_info if  @compounds.size != @predicted_values.size
     end