some commenting, reordering, creating examples without restclient

12 files changed, 161 insertions, 206 deletions

diff --git a/application.rb b/application.rb
index 55a7598..3625833 100644
--- a/application.rb
+++ b/application.rb
@@ -11,16 +11,19 @@ end
 require "example.rb"
 
 get '/examples/?' do
+  LOGGER.info "list examples"
   content_type "text/plain"
   Example.transform_example
 end
 
 get '/prepare_examples/?' do
+  LOGGER.info "prepare examples"
   content_type "text/plain"
   Example.prepare_example_resources
 end
 
 get '/test_examples/?' do
+  LOGGER.info "test examples"
   content_type "text/plain"
   Example.test_examples
 end
@@ -28,7 +31,6 @@ end
 # order is important, first add example methods and reports, than validation 
 # (otherwise sinatra will try to locate a validation with name examples or report)
 
-
 require "report/report_application.rb"
 require "validation/validation_application.rb"
 
diff --git a/example.rb b/example.rb
index 1e27077..f9a5529 100644
--- a/example.rb
+++ b/example.rb
@@ -12,6 +12,7 @@ class Example
   
   @@summary=""
   
+  # replaces placeholdes ( in <> brackets ) in EXAMPLE file with uris and ids
   def self.transform_example
   
     file = File.new("EXAMPLES", "r")
@@ -41,61 +42,45 @@ class Example
     res
   end
   
-  def self.delete_all(uri_list_service)
-    uri_list = OpenTox::RestClientWrapper.get(uri_list_service)
-    uri_list.split("\n").each do |uri|
-      OpenTox::RestClientWrapper.delete(uri)
-    end
-  end
-  
-  def self.log(log_string)
-    LOGGER.debug log_string
-    @@summary += log_string+"\n"
-  end
-  
+  # creates the resources that are requested by the examples
   def self.prepare_example_resources
     
     @@summary = ""
     delete_all(@@config[:services]["opentox-dataset"])
     
+    log "upload dataset"
     data = File.read(@@file.path)
     data_uri = OpenTox::RestClientWrapper.post @@config[:services]["opentox-dataset"], data, :content_type => "application/rdf+xml"
-    log "uploaded dataset "+data_uri
-    raise "failed to prepare demo" unless data_uri==@@data
-    
+
+    log "train-test-validation"
     Lib::Validation.auto_migrate!
     delete_all(@@config[:services]["opentox-model"])
-    vali_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-validation"],'/training_test_split'), { :dataset_uri => data_uri,
-                                                         :algorithm_uri => @@alg,
-                                                         :prediction_feature => @@feature,
-                                                         :algorithm_params => @@alg_params }
-    log "created validation via training test split "+vali_uri
-    raise "failed to prepare demo" unless vali_uri==File.join(@@config[:services]["opentox-validation"],'/1')
+    split_params = Validation::Util.train_test_dataset_split(data_uri, 0.9, 1)
+    v = Validation::Validation.new :training_dataset_uri => split_params[:training_dataset_uri], 
+                   :test_dataset_uri => split_params[:test_dataset_uri],
+                   :prediction_feature => @@feature
+    v.validate_algorithm( @@alg, @@alg_params) 
     
+    log "crossvalidation"
     Lib::Crossvalidation.auto_migrate!
-    cv_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-validation"],'/crossvalidation'), { :dataset_uri => data_uri,
-                                                         :algorithm_uri => @@alg,
-                                                         :prediction_feature => @@feature,
-                                                         :algorithm_params => @@alg_params,
-                                                         :num_folds => 5, :stratified => false }
-    log "created crossvalidation "+cv_uri
-    raise "failed to prepare demo" unless cv_uri==File.join(@@config[:services]["opentox-validation"],'/crossvalidation/1')
+    cv = Validation::Crossvalidation.new({ :dataset_uri => data_uri, :algorithm_uri => @@alg, :num_folds => 5, :stratified => false })
+    cv.create_cv_datasets( @@feature )
+    cv.perform_cv( @@alg_params )
+    
+    log "create validation report"
+    rep = Reports::ReportService.new(File.join(@@config[:services]["opentox-validation"],"report"))
+    rep.delete_all_reports("validation")
+    rep.create_report("validation",v.uri)
     
-    delete_all(File.join(@@config[:services]["opentox-validation"],"/report/validation"))
-    val_report_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-validation"],'/report/validation'), { :validation_uris => vali_uri }
-    log "created validation report: "+val_report_uri
-    raise "failed to prepare demo" unless val_report_uri==File.join(@@config[:services]["opentox-validation"],'/report/validation/1')
+    log "create crossvalidation report"
+    rep.delete_all_reports("crossvalidation")
+    rep.create_report("crossvalidation",cv.uri)
     
-    delete_all(File.join(@@config[:services]["opentox-validation"],"/report/crossvalidation"))
-    cv_report_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-validation"],'/report/crossvalidation'), { :validation_uris => cv_uri }
-    log "created crossvalidation report: "+cv_report_uri
-    raise "failed to prepare demo" unless cv_report_uri==File.join(@@config[:services]["opentox-validation"],'/report/crossvalidation/1')
     log "done"
-
     @@summary
   end
   
-  
+  # performs all curl calls listed in examples after ">>>", next line is added if line ends with "\"
   def self.test_examples
     lines = transform_example.split("\n")
     curl_call = false
@@ -146,4 +131,19 @@ class Example
     @@summary  
   end
   
+  private
+  # deletes resources listed by service
+  def self.delete_all(uri_list_service)
+    uri_list = OpenTox::RestClientWrapper.get(uri_list_service)
+    uri_list.split("\n").each do |uri|
+      OpenTox::RestClientWrapper.delete(uri)
+    end
+  end
+  
+  # logs string and and adds to summary
+  def self.log(log_string)
+    LOGGER.info log_string
+    @@summary += log_string+"\n"
+  end
+  
 end
diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index f1930cc..aaa5d6f 100644
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -78,7 +78,7 @@ module Lib
           index += 1
         end
 
-        super(predicted_values, actual_values, confidence_values, prediction_feature, is_classification, class_values)
+        super(predicted_values, actual_values, confidence_values, is_classification, class_values)
         raise "illegal num compounds "+num_info if  @compounds.size != @predicted_values.size
     end
     
diff --git a/lib/predictions.rb b/lib/predictions.rb
index 9e6356e..1d53ab9 100644
--- a/lib/predictions.rb
+++ b/lib/predictions.rb
@@ -25,14 +25,12 @@ module Lib
     def initialize( predicted_values, 
                     actual_values, 
                     confidence_values, 
-                    prediction_feature, 
                     is_classification, 
                     prediction_feature_values=nil )
       
       @predicted_values = predicted_values
       @actual_values = actual_values
       @confidence_values = confidence_values
-      @prediction_feature = prediction_feature
       @is_classification = is_classification
       @prediction_feature_values = prediction_feature_values
       @num_classes = 1
@@ -61,7 +59,7 @@ module Lib
         end
       end
       
-      init_stats
+      init_stats()
       (0..@predicted_values.size-1).each do |i|
         update_stats( @predicted_values[i], @actual_values[i], @confidence_values[i] )
       end
@@ -175,6 +173,9 @@ module Lib
       return @num_unpredicted
     end
     
+    # internal structure of confusion matrix:
+    # hash with keys: hash{ :confusion_matrix_actual => <class_value>, :confusion_matrix_predicted => <class_value> }
+    #     and values: <int-value>
     def confusion_matrix
       raise "no classification" unless @is_classification
       res = {}
@@ -187,8 +188,6 @@ module Lib
       return res
     end
     
-
-    
     def area_under_roc(class_index=nil)
       return prediction_feature_value_map( lambda{ |i| area_under_roc(i) } ) if class_index==nil
       
@@ -361,7 +360,7 @@ module Lib
     end
     
     
-    ########################################################################################
+    # regression #######################################################################################
     
     def root_mean_squared_error
       Math.sqrt(@sum_squared_error / (@num_with_actual_value - @num_unpredicted).to_f)
@@ -375,7 +374,7 @@ module Lib
       return @variance_predicted / @variance_actual
     end
     
-    ########################################################################################
+    # data for roc-plots ###################################################################################
     
     def roc_confidence_values(class_value)
       class_index = @prediction_feature_values.index(class_value)
diff --git a/lib/validation_db.rb b/lib/validation_db.rb
index 30a0bda..5811f6c 100644
--- a/lib/validation_db.rb
+++ b/lib/validation_db.rb
@@ -3,7 +3,6 @@
   require lib
 end
 
-
 module Lib
 
   VAL_PROPS = [ :id, :uri, :model_uri, :training_dataset_uri, :prediction_feature,
@@ -43,7 +42,6 @@ module Lib
     property :finished, Boolean, :default => false
     property :created_at, DateTime
     property :real_runtime, Float
-    #property :cpu_runtime, Float
     
     property :num_instances, Integer
     property :num_without_class, Integer
diff --git a/lib/wrapper.rb b/lib/wrapper.rb
index 40df0e5..cff9b2f 100644
--- a/lib/wrapper.rb
+++ b/lib/wrapper.rb
@@ -10,6 +10,13 @@ module OpenTox
    module Model
     class PredictionModel
       
+      attr_reader :uri
+      
+      def self.build( algorithm_uri, algorithm_parms )
+        uri = OpenTox::RestClientWrapper.post algorithm_uri,algorithm_parms
+        PredictionModel.new(uri)
+      end
+      
       def self.find( uri )
         begin
           RestClient.get uri,:accept => "application/rdf+xml"
diff --git a/report/report_service.rb b/report/report_service.rb
index 5c75ae4..36bd176 100644
--- a/report/report_service.rb
+++ b/report/report_service.rb
@@ -102,6 +102,13 @@ module Reports
       @persistance.delete_report(type, id)
     end
     
+    def delete_all_reports( type )
+      
+      LOGGER.info "deleteing all reports of ype '"+type.to_s+"'"
+      check_report_type(type)
+      @persistance.list_reports(type).each{ |id| @persistance.delete_report(type, id) }
+    end
+    
     def parse_type( report_uri )
       
       raise "invalid uri" unless report_uri.to_s =~/^#{@home_uri}.*/
diff --git a/test.rb b/test.rb
deleted file mode 100644
index 2265fb2..0000000
--- a/test.rb
+++ /dev/null
@@ -1,4 +0,0 @@
-
-require "validation/validation_test.rb"
-
-#require "report/report_test.rb"
\ No newline at end of file
diff --git a/validation/validation_application.rb b/validation/validation_application.rb
index 2c5806e..beb16ab 100644
--- a/validation/validation_application.rb
+++ b/validation/validation_application.rb
@@ -9,20 +9,22 @@ require 'validation/validation_service.rb'
 # hack: store self in $sinatra to make url_for method accessible in validation_service
 # (before is executed in every rest call, problem is that the request object is not set, until the first rest-call )
 before {$sinatra = self unless $sinatra}
+
 unless(defined? LOGGER)
   LOGGER = Logger.new(STDOUT)
   LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
 end
 
+
 class Sinatra::Base
-  # logging halts (!= 202)
+  # overwriting halt to log halts (!= 202)
   def halt(status,msg)
     LOGGER.error "halt "+status.to_s+" "+msg.to_s if (status != 202)
     throw :halt, [status, msg] 
   end
 end
 
-## REST API
+
 get '/crossvalidation/?' do
   LOGGER.info "list all crossvalidations"
   
diff --git a/validation/validation_format.rb b/validation/validation_format.rb
index 748271f..ed5c7b1 100644
--- a/validation/validation_format.rb
+++ b/validation/validation_format.rb
@@ -1,14 +1,18 @@
 
-module Validation
+require "lib/rdf_provider.rb"
 
+module Validation
+  
+  
   # adding to_yaml and to_rdf functionality to validation
   class Validation < Lib::Validation
+    include Lib::RDFProvider
   
-    # get_content is the basis for to_yaml and to_rdf
+    # get_content_as_hash is the basis for to_yaml and to_rdf
     # the idea is that everything is stored in a hash structure
-    # the hash is directly printed in to_yaml, while the has_keys can be used to resolve 
-    # the right properties, classes
-    def get_content
+    # the hash is directly printed in to_yaml, whereas the has_keys can be used to resolve 
+    # the right properties, classes for to_rdf
+    def get_content_as_hash
       
       h = {}
       Lib::VAL_PROPS.each{|p| h[p] = self.send(p)}
@@ -55,22 +59,75 @@ module Validation
       return h  
     end
     
+    # build hash structure and return with to_yaml
     def to_yaml
-      get_content.to_yaml
+      get_content_as_hash.to_yaml
+    end
+    
+    def rdf_title
+      "Validation"
+    end
+    
+    def uri
+      @uri
+    end
+    
+    @@literals = [ :created_at, :real_runtime, :num_instances, :num_without_class,
+                   :percent_without_class, :num_unpredicted, :percent_unpredicted, 
+                   :crossvalidation_fold, :crossvalidation_id,
+                   :num_correct, :num_incorrect, :percent_correct, :percent_incorrect,
+                   :area_under_roc, :false_negative_rate, :false_positive_rate,
+                   :f_measure, :num_false_positives, :num_false_negatives, 
+                   :num_true_positives, :num_true_negatives, :precision, 
+                   :recall, :true_negative_rate, :true_positive_rate,
+                   :confusion_matrix_value ]
+    # created at -> date
+    #      owl.set_literal(OT['numInstances'],validation.num_instances)
+    #      owl.set_literal(OT['numWithoutClass'],validation.num_without_class)
+    #      owl.set_literal(OT['percentWithoutClass'],validation.percent_without_class)
+    #      owl.set_literal(OT['numUnpredicted'],validation.num_unpredicted)
+    #      owl.set_literal(OT['percentUnpredicted'],validation.percent_unpredicted)
+                 
+                 
+    @@object_properties = { :model_uri => OT['validationModel'], :training_dataset_uri => OT['validationTrainingDataset'], 
+                     :prediction_feature => OT['predictedFeature'], :test_dataset_uri => OT['validationTestDataset'], 
+                     :prediction_dataset_uri => OT['validationPredictionDataset'], :crossvalidation_info => OT['hasValidationInfo'],
+                     :classification_statistics => OT['hasValidationInfo'],
+                     :class_value_statistics => OT['classValueStatistics'], :confusion_matrix => OT['confusionMatrix'],
+                     :confusion_matrix_cell => OT['confusionMatrixCell'], :class_value => OT['class_value'], 
+                     :confusion_matrix_actual => OT['confusionMatrixActual'], :confusion_matrix_predicted => OT['confusionMatrixPredicted'] } 
+                     
+    @@classes = { :crossvalidation_info => OT['CrossvalidationInfo'], :classification_statistics => OT['ClassificationStatistics'],
+                 :class_value_statistics => OT['ClassValueStatistics'],
+                 :confusion_matrix => OT['ConfusionMatrix'], :confusion_matrix_cell => OT['ConfusionMatrixCell']}  
+    
+    def literal?( prop )
+      @@literals.index( prop ) != nil
     end
     
-    def to_rdf
-      owl = ValidationOwl.new()
-      owl.title = "Validation"
-      owl.uri = uri
-      owl.add_content( ValidationToRDF.new, get_content, "Validation" )
-      owl.rdf
+    def literal_name( prop )
+      #PENDING
+      return OT[prop.to_s]
+    end
+    
+    def object_property?( prop )
+      @@object_properties.has_key?( prop )
     end
-   end
+    
+    def object_property_name( prop )
+      return @@object_properties[ prop ]
+    end
+  
+    def class_name( prop )
+      return @@classes[ prop ]
+    end
+    
+  end
     
   class Crossvalidation < Lib::Crossvalidation
+    include Lib::RDFProvider
     
-    def get_content
+    def get_content_as_hash
       h = {}
       Lib::CROSS_VAL_PROPS.each{|p| h[p] = self.send(p)}
       
@@ -83,91 +140,24 @@ module Validation
     end
     
     def to_yaml
-      get_content.to_yaml
+      get_content_as_hash.to_yaml
     end
     
-    def to_rdf
-      owl = ValidationOwl.new()
-      owl.title = "Crossvalidation"
-      owl.uri = uri
-      owl.add_content( CrossvalidationToRDF.new, get_content, "Crossvalidation" )
-      owl.rdf
+    def rdf_title
+      "Crossvalidation"
     end
     
-  end
-    
-  
-  class ValidationOwl
-    include OpenTox::Owl
-   
-    def initialize
-      super
-    end 
-    
-    def add_content( content_to_rdf, output, clazz ) 
-      @content_to_rdf = content_to_rdf
-      recursiv_add_content( output, @model.subject(RDF['type'],OT[clazz]) )
-    end
-    
-    private
-    def recursiv_add_content( output, node )
-      output.each do |k,v|
-        raise "null value: "+k.to_s if v==nil
-        if v.is_a?(Hash)
-          new_node = add_class( k, node )
-          recursiv_add_content( v, new_node )
-        elsif v.is_a?(Array)
-          v.each do |value|
-            new_node = add_class( k, node )
-            recursiv_add_content( value, new_node )
-          end
-        elsif @content_to_rdf.literal?(k)
-          set_literal( k, v, node)
-        elsif @content_to_rdf.object_property?(k)
-          add_object_property( k, v, node)
-        elsif [ :uri, :id, :finished ].index(k)!=nil
-          #skip
-        else
-          raise "illegal value k:"+k.to_s+" v:"+v.to_s
-        end
-      end
-    end
-  
-    def add_class( property, node )
-      raise "no object prop: "+property.to_s unless @content_to_rdf.object_property?(property)
-      raise "no class name: "+property.to_s unless @content_to_rdf.class_name(property) 
-      res = @model.create_resource
-      @model.add res, RDF['type'], @content_to_rdf.class_name(property)
-      @model.add res, DC['title'], @content_to_rdf.class_name(property)
-      @model.add node, @content_to_rdf.object_property_name(property), res
-      return res
-    end
-    
-    def set_literal(property, value, node )
-      raise "empty literal value "+property.to_s if value==nil || value.to_s.size==0
-      raise "no literal name "+propety.to_s unless @content_to_rdf.literal_name(property)
-      begin
-        l = @model.object(subject, @content_to_rdf.literal_name(property))
-        @model.delete node, @content_to_rdf.literal_name(property), l
-      rescue
-      end
-      @model.add node, @content_to_rdf.literal_name(property), value.to_s
+    def uri
+      @uri
     end
     
-    def add_object_property(property, value, node )
-      raise "empty object property value "+property.to_s if value==nil || value.to_s.size==0
-      raise "no object property name "+propety.to_s unless @content_to_rdf.object_property_name(property)
-      @model.add node, @content_to_rdf.object_property_name(property), Redland::Uri.new(value) # untyped individual comes from this line, why??
-      #@model.add Redland::Uri.new(value), RDF['type'], type
-    end
-    
-  end
-  
-  
-  class ContentToRDF
+    @@literals = [ :stratified, :num_folds, :random_seed ]
+    @@object_properties = { :dataset_uri => OT['crossvalidationDataset'], :algorithm_uri => OT['crossvalidationAlgorithm'],
+                           :validation_uri => OT['crossvalidationValidation'], :validations => OT['crossvalidationValidations'] } 
+    @@classes = { :validations => OT['CrossvalidationValidations'] }
     
     def literal?( prop )
-      @literals.index( prop ) != nil
+      @@literals.index( prop ) != nil
     end
     
     def literal_name( prop )
@@ -176,62 +166,15 @@ module Validation
     end
     
     def object_property?( prop )
-      @object_properties.has_key?( prop )
+      @@object_properties.has_key?( prop )
     end
     
     def object_property_name( prop )
-      return @object_properties[ prop ]
+      return @@object_properties[ prop ]
     end
   
     def class_name( prop )
-      return @classes[ prop ]
+      return @@classes[ prop ]
     end
-    
-  end
-  
-  
-  class CrossvalidationToRDF < ContentToRDF
-    
-    def initialize()
-      @literals = [ :stratified, :num_folds, :random_seed ]
-      @object_properties = { :dataset_uri => OT['crossvalidationDataset'], :algorithm_uri => OT['crossvalidationAlgorithm'],
-                             :validation_uri => OT['crossvalidationValidation'], :validations => OT['crossvalidationValidations'] } 
-      @classes = { :validations => OT['CrossvalidationValidations'] }
-    end
-  end
-  
-  class ValidationToRDF < ContentToRDF
-  
-    def initialize()
-      @literals = [ :created_at, :real_runtime, :num_instances, :num_without_class,
-                   :percent_without_class, :num_unpredicted, :percent_unpredicted, 
-                   :crossvalidation_fold, :crossvalidation_id,
-                   :num_correct, :num_incorrect, :percent_correct, :percent_incorrect,
-                   :area_under_roc, :false_negative_rate, :false_positive_rate,
-                   :f_measure, :num_false_positives, :num_false_negatives, 
-                   :num_true_positives, :num_true_negatives, :precision, 
-                   :recall, :true_negative_rate, :true_positive_rate,
-                   :confusion_matrix_value ]
-      # created at -> date
-      #      owl.set_literal(OT['numInstances'],validation.num_instances)
-      #      owl.set_literal(OT['numWithoutClass'],validation.num_without_class)
-      #      owl.set_literal(OT['percentWithoutClass'],validation.percent_without_class)
-      #      owl.set_literal(OT['numUnpredicted'],validation.num_unpredicted)
-      #      owl.set_literal(OT['percentUnpredicted'],validation.percent_unpredicted)
-                   
-                   
-      @object_properties = { :model_uri => OT['validationModel'], :training_dataset_uri => OT['validationTrainingDataset'], 
-                       :prediction_feature => OT['predictedFeature'], :test_dataset_uri => OT['validationTestDataset'], 
-                       :prediction_dataset_uri => OT['validationPredictionDataset'], :crossvalidation_info => OT['hasValidationInfo'],
-                       :classification_statistics => OT['hasValidationInfo'],
-                       :class_value_statistics => OT['classValueStatistics'], :confusion_matrix => OT['confusionMatrix'],
-                       :confusion_matrix_cell => OT['confusionMatrixCell'], :class_value => OT['class_value'], 
-                       :confusion_matrix_actual => OT['confusionMatrixActual'], :confusion_matrix_predicted => OT['confusionMatrixPredicted'] } 
-                       
-      @classes = { :crossvalidation_info => OT['CrossvalidationInfo'], :classification_statistics => OT['ClassificationStatistics'],
-                   :class_value_statistics => OT['ClassValueStatistics'],
-                   :confusion_matrix => OT['ConfusionMatrix'], :confusion_matrix_cell => OT['ConfusionMatrixCell']}  
-    end
-  
   end
 end
diff --git a/validation/validation_service.rb b/validation/validation_service.rb
index 3231676..05f4b93 100644
--- a/validation/validation_service.rb
+++ b/validation/validation_service.rb
@@ -41,6 +41,7 @@ module Validation
       raise "do not set id manually" if params[:id]
       raise "do not set uri manually" if params[:uri]
       super params
+      # hack to overcome datamapper bug: save to set id
       save unless attribute_dirty?("id")
       raise "internal error, id not set "+to_yaml unless @id
       update :uri => $sinatra.url_for("/"+@id.to_s, :full)
@@ -77,14 +78,13 @@ module Validation
       end
       LOGGER.debug "building model '"+algorithm_uri.to_s+"' "+params.inspect
       
-      model_uri = OpenTox::RestClientWrapper.post algorithm_uri,params
-      update :model_uri => model_uri
-      
+      model = OpenTox::Model::PredictionModel.build(algorithm_uri, params)
+      update :model_uri => model.uri
       validate_model
     end
     
     # validates a model
-    # PENDING: a new dataset is created to store the predictions, this should be optional: STORE predictions yes/no
+    # PENDING: a new dataset is created to store the predictions, this should be optional: delete predictions afterwards yes/no
     def validate_model
       
       LOGGER.debug "validating model '"+@model_uri+"'"
@@ -125,6 +125,7 @@ module Validation
       raise "do not set id manually" if params[:id]
       raise "do not set uri manually" if params[:uri]
       super params
+      # hack to overcome datamapper bug: save to set id
       save unless attribute_dirty?("id")
       raise "internal error, id not set" unless @id
       update :uri => $sinatra.url_for("/crossvalidation/"+@id.to_s, :full)
@@ -277,7 +278,8 @@ module Validation
   
   module Util
     
-    
+    # creates a new dataset from orig_dataset.data
+    # copies only features and compounds included in compounds array 
     def self.create_new_dataset( orig_dataset_data, compounds, title, source )
       
       dataset = OpenTox::Dataset.new
@@ -306,7 +308,6 @@ module Validation
       uri = dataset.save
       raise "no dataset uri" if uri==nil || uri.to_s.length<1
       return uri
-      
     end
     
   
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index f6a3e6a..72fabe6 100644
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -134,8 +134,8 @@ class ValidationTest < Test::Unit::TestCase
 #      #model_uri = "http://ot.model.de/12"
 #      #data_uri_test = "http://ot.dataset.de/67"
 #      
-#      model_uri = "http://ot.model.de/45" #trained with training split from hamster
-#      data_uri_test = "http://ot.dataset.de/367" #hamster test split
+#      model_uri = "http://ot.model.de/1" 
+#      data_uri_test = "http://ot.dataset.de/3"
 #      
 #      post '', {:test_dataset_uri => data_uri_test, :model_uri => model_uri, :prediction_feature => FEATURE_URI}
 #      verify_validation
@@ -185,13 +185,13 @@ class ValidationTest < Test::Unit::TestCase
     #get '/prepare_examples'
     get '/test_examples'
 
-    #get '/350',nil,'HTTP_ACCEPT' => "application/rdf+xml"
+    #get '/1',nil,'HTTP_ACCEPT' => "application/rdf+xml"
     #get '/350',nil,'HTTP_ACCEPT' => "text/x-yaml"
     
     #get '/crossvalidation/1',nil,'HTTP_ACCEPT' => "application/rdf+xml"
     #get '/crossvalidation/1',nil,'HTTP_ACCEPT' => "text/x-yaml"
     
-    #puts last_response.body
+    puts last_response.body
   end
   
   private