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

9 files changed, 9 insertions, 67 deletions

diff --git a/.gitignore b/.gitignore
index 6bd1177..58da13c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,4 @@ public/*.owl
 java/docs/*
 *.*~
 Gemfile.lock
+fminer_debug.txt
diff --git a/Gemfile b/Gemfile
index fb18710..1192d8b 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,4 +1,4 @@
-source :gemcutter
+source "https://rubygems.org"
 gemspec
 gem 'opentox-server', :path => "../opentox-server"
 gem "opentox-client", :path => "../opentox-client"
diff --git a/algorithm.gemspec b/algorithm.gemspec
index dc334b9..b9d3241 100644
--- a/algorithm.gemspec
+++ b/algorithm.gemspec
@@ -19,11 +19,11 @@ Gem::Specification.new do |s|
   # specify any dependencies here; for example:
   s.add_runtime_dependency "opentox-server"
   s.add_runtime_dependency "opentox-client"
-  s.add_runtime_dependency 'rinruby', "~>2.0.2"
-  s.add_runtime_dependency 'nokogiri', "~>1.4.4"
-  s.add_runtime_dependency 'statsample', "~>1.1"
-  s.add_runtime_dependency 'gsl', "~>1.14"
-  s.add_runtime_dependency "openbabel", "~>2.3.1.5"
-  s.add_runtime_dependency "rjb" ,"1.4.3" # error in 1.4.5
+  s.add_runtime_dependency 'rinruby'#, "~>2.0.2"
+  s.add_runtime_dependency 'nokogiri'#, "~>1.4.4"
+  s.add_runtime_dependency 'statsample'#, "~>1.1"
+  s.add_runtime_dependency 'gsl'#, "~>1.14"
+  s.add_runtime_dependency "openbabel"#, "~>2.3.1.5"
+  s.add_runtime_dependency "rjb" ,"1.4.6" # error in 1.4.5#,"1.4.3"
   s.post_install_message = "Please configure your service in ~/.opentox/config/algorithm.rb"
 end
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
 
diff --git a/webapp/fminer.rb b/webapp/fminer.rb
index 2d11dcb..4f9abfe 100644
--- a/webapp/fminer.rb
+++ b/webapp/fminer.rb
@@ -244,60 +244,22 @@ module OpenTox
         fminer_noact_compounds = fminer_compounds - @@fminer.compounds
 
         feature_dataset.features = features
-        if (params[:get_target] == "true")
-          puts "get_target TRUE"
-          feature_dataset.features = [ @@fminer.prediction_feature ] + feature_dataset.features
-        else
-          puts "get_target FALSE"
-        end
+        feature_dataset.features = [ @@fminer.prediction_feature ] + feature_dataset.features if params[:get_target] == "true"
         feature_dataset.compounds = fminer_compounds
         fminer_compounds.each_with_index { |c,idx|
-          #puts c.smiles
-          # TODO: fix here, insert with add_data_entry
-          #row = [ c ]
           # TODO: reenable option
           #if (params[:get_target] == "true")
             #row = row + [ prediction_feature_all_acts[idx] ]
           #end
           features.each { |f|
-            #m = c.match([f.title])[f.title]
-            #m = 0 unless m
             v = fminer_results[c][f.uri] if fminer_results[c] 
             unless fminer_noact_compounds.include? c
               v = 0 if v.nil?
             end
-            #unless m == v
-              #puts f.title
-              #puts m
-              #puts v
-            #end
             feature_dataset.add_data_entry c, f, v.to_i
-            #row << (fminer_results[c] ? fminer_results[c][f.uri] : nil)
           }
-          #row.collect! { |v| v ? v : 0 } unless fminer_noact_compounds.include? c
-          #feature_dataset << row
         }
 
-=begin
-CH: Ordering seems to be ok here
-        feature_dataset.compounds.each_with_index do |c,i|
-          feature_dataset.features.each_with_index do |f,j|
-            m = c.match([f.title])[f.title]
-            #puts c.smiles
-            #puts f.title
-            #puts m.inspect
-            v = feature_dataset.data_entries[i][j]
-            #puts v.inspect
-            unless m.to_i == v.to_i
-              puts f.title
-              puts m.to_i
-              puts v.to_i
-            end
-          end
-        end
-=end
-          
-        #puts feature_dataset.to_csv
         feature_dataset.put 
         feature_dataset.uri
 
diff --git a/webapp/lazar.rb b/webapp/lazar.rb
index 3700cd8..921b08e 100644
--- a/webapp/lazar.rb
+++ b/webapp/lazar.rb
@@ -28,7 +28,6 @@ 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]
@@ -62,8 +61,6 @@ module OpenTox
       task = OpenTox::Task.run("Apply lazar model",uri('/lazar/predict'), @subjectid) do |task|
 
         lazar = OpenTox::LazarPrediction.new params
-        puts "RESULT"
-        puts lazar.prediction_dataset.uri
         lazar.prediction_dataset.uri
 
       end