validation tests ok

2 files changed, 19 insertions, 18 deletions

diff --git a/lib/lazar.rb b/lib/lazar.rb
index f731544..b85c13b 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -17,6 +17,7 @@ module OpenTox
       params.each {|k,v|
         self.class.class_eval { attr_accessor k.to_sym }
         instance_variable_set "@#{k}", v
+        puts "#{k} => #{v}"
         @prediction_dataset.parameters << {RDF::DC.title => k, RDF::OT.paramValue => v}
       }
       ["cmpds", "fps", "acts", "n_prop", "q_prop", "neighbors"].each {|k|
@@ -24,21 +25,26 @@ module OpenTox
         instance_variable_set("@#{k}", [])
       }
 
+      puts "Loading #{@prediction_feature_uri}"
       @prediction_feature = OpenTox::Feature.new(@prediction_feature_uri,@subjectid)
-      # TODO: set feature type
-      @predicted_variable = OpenTox::Feature.find_or_create({RDF::DC.title => "#{@prediction_feature.title} prediction", RDF.type => @prediction_feature[RDF.type]}, @subjectid)
-      @predicted_confidence = OpenTox::Feature.find_or_create({RDF::DC.title => "#{@prediction_feature.title} confidence", RDF.type => [RDF::OT.Feature, RDF::OT.NumericFeature]}, @subjectid)
-      
+      @predicted_variable = OpenTox::Feature.new @predicted_variable_uri, @subjectid
+      @predicted_confidence = OpenTox::Feature.new @predicted_confidence_uri, @subjectid
+      puts @predicted_variable.inspect
+      puts @predicted_confidence.inspect
+      puts "Setting metadata"
+      #@prediction_dataset.metadata = {
       @prediction_dataset.metadata = {
         RDF::DC.title => "Lazar prediction for #{@prediction_feature.title}",
         RDF::DC.creator => @model_uri,
         RDF::OT.hasSource => @model_uri,
         RDF::OT.dependentVariables => @prediction_feature_uri,
-        RDF::OT.predictedVariables => [@predicted_variable.uri,@predicted_confidence.uri]
+        RDF::OT.predictedVariables => [@predicted_variable_uri,@predicted_confidence_uri]
       }
 
+      puts "Loading #{@training_dataset_uri}"
       @training_dataset = OpenTox::Dataset.new(@training_dataset_uri,@subjectid)
 
+      puts "Loading #{@feature_dataset_uri}"
       @feature_dataset = OpenTox::Dataset.new(@feature_dataset_uri, @subjectid)
       bad_request_error "No features found in feature dataset #{@feature_dataset.uri}." if @feature_dataset.features.empty?
 
@@ -49,9 +55,10 @@ module OpenTox
       prediction_feature_pos = @training_dataset.features.collect{|f| f.uri}.index @prediction_feature.uri
 
       if @dataset_uri
-        compounds = OpenTox::Dataset.find(@dataset_uri).compounds
+        puts "Loading #{@dataset_uri}"
+        compounds = OpenTox::Dataset.new(@dataset_uri,@subjectid).compounds
       else
-        compounds = [ OpenTox::Compound.new(@compound_uri) ]
+        compounds = [ OpenTox::Compound.new(@compound_uri,@subjectid) ]
       end
       compounds.each do |compound|
           
@@ -77,20 +84,12 @@ module OpenTox
             #:lib => @model.lib
           }
           compound_fingerprints = OpenTox::Algorithm::FeatureValues.send( @feature_calculation_algorithm, compound_params, @subjectid )
-          puts compound_fingerprints.inspect
           @training_dataset.compounds.each_with_index { |cmpd, idx|
             act = @training_dataset.data_entries[idx][prediction_feature_pos]
             @acts << (@prediction_feature.feature_type=="classification" ? @prediction_feature.value_map.invert[act] : nil)
             @n_prop << @feature_dataset.data_entries[idx]#.collect.to_a
             @cmpds << cmpd.uri
           }
-          #puts "COMPOUNDS"
-          #puts @n_prop.inspect
-          puts @cmpds.inspect
-          puts @fps.inspect
-          puts @acts.inspect
-          puts @n_prop.inspect
-          puts @q_prop.inspect
 
           @q_prop = @feature_dataset.features.collect { |f| 
             val = compound_fingerprints[f.title]
@@ -119,8 +118,8 @@ module OpenTox
           
         end
 
-        @prediction_dataset.add_data_entry compound, @predicted_variable, predicted_value
-        @prediction_dataset.add_data_entry compound, @predicted_confidence, confidence_value
+        @prediction_dataset.add_data_entry compound, predicted_variable, predicted_value
+        @prediction_dataset.add_data_entry compound, predicted_confidence, confidence_value
       
         if @compound_uri # add neighbors only for compound predictions
           @neighbors.each do |neighbor|
@@ -158,6 +157,7 @@ module OpenTox
       end
       self[RDF::OT.trainingDataset] = training_dataset.uri
       prediction_feature = OpenTox::Feature.new(params[:prediction_feature], @subjectid) 
+      predicted_variable = OpenTox::Feature.find_or_create({RDF::DC.title => "#{prediction_feature.title} prediction", RDF.type => [RDF::OT.Feature, prediction_feature[RDF.type]]}, @subjectid)
       self[RDF::DC.title] = prediction_feature.title 
       @parameters << {RDF::DC.title => "prediction_feature_uri", RDF::OT.paramValue => prediction_feature.uri}
       self[RDF::OT.dependentVariables] = prediction_feature.uri
@@ -166,7 +166,7 @@ module OpenTox
       @parameters << {RDF::DC.title => "prediction_algorithm", RDF::OT.paramValue => params[:prediction_algorithm]} if params[:prediction_algorithm]
 
       confidence_feature = OpenTox::Feature.find_or_create({RDF::DC.title => "predicted_confidence", RDF.type => [RDF::OT.Feature, RDF::OT.NumericFeature]}, @subjectid)
-      self[RDF::OT.predictedVariables] = [ prediction_feature.uri, confidence_feature.uri ]
+      self[RDF::OT.predictedVariables] = [ predicted_variable.uri, confidence_feature.uri ]
       case prediction_feature.feature_type
       when "classification"
         @parameters << {RDF::DC.title => "prediction_algorithm", RDF::OT.paramValue => "weighted_majority_vote"} unless parameter_value "prediction_algorithm"
diff --git a/webapp/lazar.rb b/webapp/lazar.rb
index c40fc98..3700cd8 100644
--- a/webapp/lazar.rb
+++ b/webapp/lazar.rb
@@ -28,6 +28,7 @@ module OpenTox
     # @param [optional,String] - further parameters for the feature generation service 
     # @return [text/uri-list] Task URI 
     post '/lazar/?' do 
+      puts params.inspect
       resource_not_found_error "Please provide a dataset_uri parameter." unless params[:dataset_uri]
       resource_not_found_error "Dataset '#{params[:dataset_uri]}' not found." unless URI.accessible? params[:dataset_uri]
       bad_request_error "Please provide a feature_generation_uri parameter." unless params[:feature_generation_uri]