fix validation to rdf, add nightly

5 files changed, 62 insertions, 25 deletions

diff --git a/lib/rdf_provider.rb b/lib/rdf_provider.rb
index d630e7a..a0a09cf 100644
--- a/lib/rdf_provider.rb
+++ b/lib/rdf_provider.rb
@@ -59,7 +59,7 @@ module Lib
   
     def add_content( rdf_provider ) 
       @rdf_provider = rdf_provider
-      recursiv_add_content( @rdf_provider.get_content_as_hash, @model.subject(RDF['type'],rdf_provider.rdf_title) )
+      recursiv_add_content( @rdf_provider.get_content_as_hash, @owl.root_node )
     end
     
     def rdf
@@ -74,7 +74,10 @@ module Lib
     
     def recursiv_add_content( output, node )
       output.each do |k,v|
-        raise "null value: "+k.to_s if v==nil
+        if v==nil
+          LOGGER.warn "skipping nil value: "+k.to_s
+          next
+        end
         if v.is_a?(Hash)
           new_node = add_class( k, node )
           recursiv_add_content( v, new_node )
@@ -113,7 +116,7 @@ module Lib
         @model.delete node, @rdf_provider.literal_name(property), l
       rescue
       end
-      @model.add node, @rdf_provider.literal_name(property), value.to_s
+      @model.add node, @rdf_provider.literal_name(property), Redland::Literal.create(value)
     end
     
     def add_object_property(property, value, node )
diff --git a/nightly/nightly.rb b/nightly/nightly.rb
index 716dad4..2be2a5b 100644
--- a/nightly/nightly.rb
+++ b/nightly/nightly.rb
@@ -23,6 +23,7 @@ class Nightly
                      HamsterCrossvalidationBenchmark.new, 
                      MiniRegressionBenchmark.new,
                      CacoModelsRegressionBenchmark.new,
+                     CacoAlgsRegressionBenchmark.new,
                      #FatheadRegressionBenchmark.new,
                      ]
       
@@ -141,6 +142,7 @@ class Nightly
   class ValidationBenchmark < AbstractBenchmark
 
     def info_table
+      raise "no comparables" unless @comparables
       t = []
       t << ["param", "uri"]
       params.each do |k,v|
@@ -286,7 +288,7 @@ class Nightly
     end
     
     def validate(index)
-      Util.validate_model(@test_data, @test_class_data, @models[index]).to_s
+      Util.validate_model(@test_data, @test_class_data, @models[index])
     end
     
     def build_report(index)
@@ -324,7 +326,7 @@ class Nightly
     
     def validate(index)
       Util.validate_alg(@train_data, @test_data, @test_class_data,
-              @algs[index], @pred_feature, @alg_params[index]).to_s
+              @algs[index], @pred_feature, @alg_params[index])
     end
     
     def build_report(index)
@@ -361,7 +363,7 @@ class Nightly
     
     def validate(index)
       Util.cross_validate_alg(@data, @algs[index], @pred_feature, 
-              @num_folds, @random_seed, @stratified, @alg_params[index]).to_s
+              @num_folds, @random_seed, @stratified, @alg_params[index])
     end
     
     def build_report(index)
@@ -398,12 +400,16 @@ class Nightly
       @algs = [
         File.join(@@config[:services]["opentox-majority"],["/class/algorithm"]),
         File.join(@@lazar_server,"lazar"),
-        #"http://188.40.32.88/algorithm/lazar",
+        "http://188.40.32.88/algorithm/lazar",
+        #File.join(@@config[:services]["opentox-majority"],["/class/algorithm"]),
+        #File.join(@@config[:services]["opentox-majority"],["/class/algorithm"]),
         ]
       @alg_params = [
         nil,
         "feature_generation_uri="+File.join(@@lazar_server,"fminer"),
-        "feature_generation_uri=http://188.40.32.88/algorithm/fminer",
+        #"feature_generation_uri=http://188.40.32.88/algorithm/fminer",
+        nil,
+        nil
         ]
       @pred_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
 
@@ -440,13 +446,13 @@ class Nightly
         "feature_generation_uri="+File.join(@@lazar_server,"fminer"),
         "feature_generation_uri=http://188.40.32.88/algorithm/fminer",
         ]
-      @pred_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
-
+      
       LOGGER.debug "prepare hamster datasets"
       
-      #@test_class_data = Util.upload_dataset(@@dataset_service, @@file, @@file_type).chomp("\n")
-      @pred_feature = "http://188.40.32.88/toxcreate/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
-      @test_class_data = "http://188.40.32.88/dataset/57"
+      @pred_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+      @test_class_data = Util.upload_dataset(@@dataset_service, @@file, @@file_type).chomp("\n")
+      #@pred_feature = "http://188.40.32.88/toxcreate/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+      #@test_class_data = "http://188.40.32.88/dataset/57"
       
       split = Util.split_dataset(@test_class_data, @pred_feature, 0.9, 1)
       @train_data = split[0].to_s
@@ -482,6 +488,31 @@ class Nightly
     end
   end
   
+  class CacoAlgsRegressionBenchmark < TrainingTestValidationBenchmark
+    
+    def title
+      "Training test set validation, regression, caco dataset"
+    end
+    
+    def info
+      res = [ "Training test set validation on caco2 dataset." ] + super
+      return res
+    end
+    
+    def build()
+      @algs = [ 
+        "http://opentox.ntua.gr:3003/algorithm/mlr",
+        "http://ambit.uni-plovdiv.bg:8080/ambit2/algorithm/LR",
+        ]
+      @alg_params = [ nil, nil]
+      @train_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R7798"
+      @test_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R8353"
+      @pred_feature = "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/255510"
+      super
+    end
+  end
+
+  
   class CacoModelsRegressionBenchmark < TestModelValidationBenchmark
     
     def title
@@ -498,7 +529,8 @@ class Nightly
         "http://ambit.uni-plovdiv.bg:8080/ambit2/model/259260",
         "http://opentox.ntua.gr:3003/model/195",
         ]
-      @test_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R7798"
+      #@test_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R7798"
+      @test_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R8353"
       super
     end
   end
@@ -541,7 +573,7 @@ class Nightly
       data = File.read(file.path)
       data_uri = OpenTox::RestClientWrapper.post dataset_service, {:content_type => file_type}, data
       #data_uri = OpenTox::Task.find(data_uri).wait_for_resource.to_s if OpenTox::Utils.task_uri?(data_uri)
-      return data_uri
+      return data_uri.to_s
     end
     
     def self.split_dataset(data_uri, feature, split_ratio, random_seed)
@@ -556,13 +588,13 @@ class Nightly
       #LOGGER.info "waiting for validation "+uri.to_s
       #uri = OpenTox::Task.find(uri).wait_for_resource.to_s if OpenTox::Utils.task_uri?(uri)
       #LOGGER.info "validaiton done "+uri.to_s
-      return uri
+      return uri.to_s
     end
     
     def self.validate_model(test_data, test_class_data, model)
       uri = OpenTox::RestClientWrapper.post @@validation_service, { :test_dataset_uri => test_data, 
         :test_target_dataset_uri => test_class_data, :model_uri => model }
-      return uri
+      return uri.to_s
     end    
     
     def self.cross_validate_alg(data, alg, feature, folds, seed, stratified, alg_params)
@@ -572,19 +604,19 @@ class Nightly
       #LOGGER.info "waiting for validation "+uri.to_s
       #uri = OpenTox::Task.find(uri).wait_for_resource.to_s if OpenTox::Utils.task_uri?(uri)
       #LOGGER.info "validaiton done "+uri.to_s
-      return uri
+      return uri.to_s
     end
     
     def self.create_report(validation, type="validation")
       uri = OpenTox::RestClientWrapper.post File.join(@@validation_service,"report/"+type.to_s), { :validation_uris => validation }
       #uri = OpenTox::Task.find(uri).wait_for_resource.to_s if OpenTox::Utils.task_uri?(uri)
-      return uri
+      return uri.to_s
     end
     
     def self.create_alg_comparison_report(validations)
       uri = OpenTox::RestClientWrapper.post File.join(@@validation_service,"report/algorithm_comparison"), { :validation_uris => validations.join("\n") }
       #uri = OpenTox::Task.find(uri).wait_for_resource.to_s if OpenTox::Utils.task_uri?(uri)
-      return uri
+      return uri.to_s
     end
     
   end
diff --git a/report/prediction_util.rb b/report/prediction_util.rb
index 051022f..598f07d 100644
--- a/report/prediction_util.rb
+++ b/report/prediction_util.rb
@@ -19,7 +19,7 @@ module Reports::PredictionUtil
           a = []
           validation_attributes.each{ |att| a.push(v.send(att).to_s) }
           
-          a.push(v.get_predictions.identifier(i)[0,65]) #.gsub(/[-(),=]/, '')[0,10])
+          a.push(v.get_predictions.identifier(i)) #.gsub(/[-(),=]/, '')[0,10])
           #a.push(OpenTox::Compound.new(:uri=>v.get_predictions.compound(i)).smiles[0,65]) #.gsub(/[-(),=]/, '')[0,10])
           
           a.push(v.get_predictions.actual_value(i).to_nice_s) 
diff --git a/validation/validation_format.rb b/validation/validation_format.rb
index e740293..b61037f 100644
--- a/validation/validation_format.rb
+++ b/validation/validation_format.rb
@@ -83,7 +83,9 @@ module Validation
                    :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, :weighted_area_under_roc ]
+                   :confusion_matrix_value, :weighted_area_under_roc, 
+                   :target_variance_actual, :root_mean_squared_error,
+                   :target_variance_predicted, :mean_absolute_error, :r_square ]
     # created at -> date
     #      owl.set_literal(OT['numInstances'],validation.num_instances)
     #      owl.set_literal(OT['numWithoutClass'],validation.num_without_class)
@@ -95,13 +97,13 @@ module Validation
     @@object_properties = { :model_uri => OT['validationModel'], :training_dataset_uri => OT['validationTrainingDataset'], :algorithm_uri => OT['validationAlgorithm'],
                      :prediction_feature => OT['predictedFeature'], :test_dataset_uri => OT['validationTestDataset'], :test_target_dataset_uri => OT['validationTestClassDataset'],
                      :prediction_dataset_uri => OT['validationPredictionDataset'], :crossvalidation_info => OT['hasValidationInfo'],
-                     :classification_statistics => OT['hasValidationInfo'],
+                     :classification_statistics => OT['hasValidationInfo'], :regression_statistics => OT['hasValidationInfo'],
                      :class_value_statistics => OT['classValueStatistics'], :confusion_matrix => OT['confusionMatrix'],
                      :confusion_matrix_cell => OT['confusionMatrixCell'], :class_value => OT['classValue'], 
                      :confusion_matrix_actual => OT['confusionMatrixActual'], :confusion_matrix_predicted => OT['confusionMatrixPredicted'] } 
                      
     @@classes = { :crossvalidation_info => OT['CrossvalidationInfo'], :classification_statistics => OT['ClassificationStatistics'],
-                 :class_value_statistics => OT['ClassValueStatistics'],
+                  :regression_statistics => OT['RegresssionStatistics'], :class_value_statistics => OT['ClassValueStatistics'],
                  :confusion_matrix => OT['ConfusionMatrix'], :confusion_matrix_cell => OT['ConfusionMatrixCell']}  
     
     def literal?( prop )
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index cafd06a..3509a84 100644
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -22,7 +22,7 @@ class ValidationTest < Test::Unit::TestCase
       Nightly.build_nightly
       #get "/build_nightly" 
       #get "/nightly"  
-      #get '1',nil,'HTTP_ACCEPT' => "application/rdf+xml"     
+      #get '16',nil,'HTTP_ACCEPT' => "application/rdf+xml"     
       #puts last_response.body
       
       #prepare_examples