debug messsages partially removed, gem depencies updated. tested with ruby 2.0.0p0

4 files changed, 0 insertions, 18 deletions

diff --git a/lib/algorithm/feature_values.rb b/lib/algorithm/feature_values.rb
index 62373e7..9a575a3 100644
--- a/lib/algorithm/feature_values.rb
+++ b/lib/algorithm/feature_values.rb
@@ -14,7 +14,6 @@ module OpenTox
       # @return [Array] Array with matching Smarts
       def self.match(params, subjectid)
         features = params[:feature_dataset].features.collect{ |f| f[RDF::DC.title] }
-        puts features.inspect
         params[:compound].match(features)
       end
 
diff --git a/lib/algorithm/similarity.rb b/lib/algorithm/similarity.rb
index 88eed35..22b4c28 100644
--- a/lib/algorithm/similarity.rb
+++ b/lib/algorithm/similarity.rb
@@ -15,8 +15,6 @@ module OpenTox
       # @param [Array] b fingerprints of second compound
       # @return [Float] Tanimoto similarity
       def self.tanimoto(a,b)
-        puts a.inspect
-        puts b.inspect
         common_p_sum = 0.0
         all_p_sum = 0.0
         size = [ a.size, b.size ].min
diff --git a/lib/algorithm/transform.rb b/lib/algorithm/transform.rb
index c851f73..b2f7e7e 100644
--- a/lib/algorithm/transform.rb
+++ b/lib/algorithm/transform.rb
@@ -334,13 +334,8 @@ module OpenTox
         # @param[Array] training_props Propositionalized data for this neighbor
         # @param[Integer] Index of neighbor
         def add_neighbor(training_props, idx)
-          puts idx
-          #puts training_props.inspect
-          #puts @q_prop.inspect
-          #puts @model.acts[idx].to_s
           unless @model.acts[idx].nil?
             sim = similarity(training_props)
-            puts sim
             if sim > @model.min_sim.to_f
                 @model.neighbors << {
                   :compound => @cmpds[idx],
diff --git a/lib/lazar.rb b/lib/lazar.rb
index b85c13b..3b8621c 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -17,7 +17,6 @@ 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|
@@ -25,13 +24,9 @@ module OpenTox
         instance_variable_set("@#{k}", [])
       }
 
-      puts "Loading #{@prediction_feature_uri}"
       @prediction_feature = OpenTox::Feature.new(@prediction_feature_uri,@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}",
@@ -41,10 +36,8 @@ module OpenTox
         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?
 
@@ -55,14 +48,12 @@ module OpenTox
       prediction_feature_pos = @training_dataset.features.collect{|f| f.uri}.index @prediction_feature.uri
 
       if @dataset_uri
-        puts "Loading #{@dataset_uri}"
         compounds = OpenTox::Dataset.new(@dataset_uri,@subjectid).compounds
       else
         compounds = [ OpenTox::Compound.new(@compound_uri,@subjectid) ]
       end
       compounds.each do |compound|
           
-        puts compound.smiles
         database_activity = @training_dataset.database_activity(params)
         if database_activity
           @prediction_dataset.add_data_entry compound, @prediction_feature, database_activity
@@ -108,7 +99,6 @@ module OpenTox
                 :min_train_performance => @min_train_performance
                 } )
          
-          puts prediction.inspect
           predicted_value = prediction[:prediction].to_f
           confidence_value = prediction[:confidence].to_f