adding weighted_accuracy, change accuracy computation, some minor changes

2 files changed, 110 insertions, 32 deletions

diff --git a/test/test_examples.rb b/test/test_examples.rb
index 192f1a4..29fe8cd 100755
--- a/test/test_examples.rb
+++ b/test/test_examples.rb
@@ -355,17 +355,87 @@ module ValidationExamples
   end
   
   ########################################################################################################
- 
   
   class NtuaModel < ModelValidation
     def initialize
-      @model_uri = "http://opentox.ntua.gr:4000/model/0d8a9a27-3481-4450-bca1-d420a791de9d" 
+      @model_uri = "http://opentox.ntua.gr:4000/model/0d8a9a27-3481-4450-bca1-d420a791de9d"
       @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/54"
       #@prediction_feature=http://apps.ideaconsult.net:8080/ambit2/feature/22200
     end
   end
   
    ########################################################################################################
+   
+  class HamsterTrainingTest < TrainingTestValidation
+    def initialize
+#      @test_target_dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
+#      @training_dataset_file = File.new("data/hamster_carcinogenicity.train.yaml","r")
+#      @test_dataset_file = File.new("data/hamster_carcinogenicity.test.yaml","r")
+      
+      @test_target_dataset_file = File.new("data/hamster_carcinogenicity.csv","r")
+      @training_dataset_file = File.new("data/hamster_carcinogenicity.train.csv","r")
+      @test_dataset_file = File.new("data/hamster_carcinogenicity.test.csv","r")
+      
+      
+      #@prediction_feature = "http://local-ot/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+      #@prediction_feature = "http://local-ot/dataset/1/feature/hamster_carcinogenicity"
+    end
+  end
+  
+  class MajorityHamsterTrainingTest < HamsterTrainingTest
+    def initialize
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
+      super
+    end
+  end
+  
+  ########################################################################################################
+  
+  class RepdoseSplit < SplitTestValidation
+    def initialize
+      @dataset_file = File.new("data/repdose_classification.csv","r")
+    end
+  end
+  
+  class LazarRepdoseSplit < RepdoseSplit
+    def initialize
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
+      super
+    end
+  end
+  
+  class MajorityRepdoseSplit < RepdoseSplit
+    def initialize
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
+      super
+    end
+  end  
+  
+    ########################################################################################################
+  
+  class RepdoseCrossValidation < CrossValidation
+    def initialize
+      @dataset_file = File.new("data/repdose_classification.csv","r")
+    end
+  end
+  
+  class LazarRepdoseCrossValidation < RepdoseCrossValidation
+    def initialize
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+      @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
+      super
+    end
+  end
+  
+  class MajorityRepdoseCrossValidation < RepdoseCrossValidation
+    def initialize
+      @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
+      super
+    end
+  end  
+  
+   ########################################################################################################
   
   @@list = {
       "1" => [ LazarHamsterSplit, MajorityHamsterSplit ],
@@ -416,6 +486,14 @@ module ValidationExamples
       "14b" =>  [ MajorityEPAFHMCrossvalidation ],
       
       "15a" =>  [ NtuaModel ],
+      
+      "16" => [ LazarRepdoseSplit, MajorityRepdoseSplit ],
+      "16a" => [ LazarRepdoseSplit ],
+      "16b" => [ MajorityRepdoseSplit ],      
+      
+      "17" => [ LazarRepdoseCrossValidation, MajorityRepdoseCrossValidation ],
+      "17a" => [ LazarRepdoseCrossValidation ],
+      "17b" => [ MajorityRepdoseCrossValidation ],  
     }
   
   def self.list
diff --git a/test/test_examples_util.rb b/test/test_examples_util.rb
index 8344594..51cf4cc 100755
--- a/test/test_examples_util.rb
+++ b/test/test_examples_util.rb
@@ -47,11 +47,11 @@ module ValidationExamples
         to_compare << v.validation_uri if v.validation_uri and v.validation_error==nil
       end
       return nil if to_compare.size < 2
-      begin
+      #begin
         return validation_post "report/algorithm_comparison",{ :validation_uris => to_compare.join("\n") }, subjectid
-      rescue => ex
-        return "error creating comparison report "+ex.message
-      end
+      #rescue => ex
+        #return "error creating comparison report "+ex.message
+      #end
     end
     
     def self.validation_post(uri, params, subjectid )
@@ -92,9 +92,9 @@ module ValidationExamples
     def self.wait(uri)
       if uri.task_uri?
         task = OpenTox::Task.find(uri.to_s.chomp)
-        task.wait_for_completion nil,5
+        task.wait_for_completion
         #raise "task failed: "+uri.to_s+", description: '"+task.description.to_s+"'" if task.error?
-        LOGGER.error "task failed:\n"+task.errorReport.to_yaml if task.error?
+        LOGGER.error "task failed :\n"+task.to_yaml if task.error?
         uri = task.result_uri
       end
       uri
@@ -267,50 +267,50 @@ module ValidationExamples
     end
     
     def delete
-      begin
+      #begin
         if @validation_uri =~ /crossvalidation/
           cv = "crossvalidation/"
         else
           cv = ""
         end
         Util.validation_delete '/'+cv+@validation_uri.split('/')[-1] if @validation_uri
-      rescue => ex
-        puts "Could not delete validation: "+ex.message
-      end
-      begin
+      #rescue => ex
+        #puts "Could not delete validation: "+ex.message
+      #end
+      #begin
         Util.validation_delete '/report/'+report_type+'/'+@report_uri.split('/')[-1] if @report_uri
-      rescue => ex
-        puts "Could not delete report:' "+@report_uri+" "+ex.message
-      end
+      #rescue => ex
+        #puts "Could not delete report:' "+@report_uri+" "+ex.message
+      #end
       @uploaded_datasets.each do |d|
-        begin
+       # begin
           puts "deleting dataset "+d
           OpenTox::RestClientWrapper.delete(d,{:subjectid => SUBJECTID})
-        rescue => ex
-          puts "Could not delete dataset:' "+d+" "+ex.message
-        end
+#        rescue => ex
+          #puts "Could not delete dataset:' "+d+" "+ex.message
+        #end
       end
     end
     
     def report
-      begin
+      #begin
         @report_uri = Util.validation_post '/report/'+report_type,{:validation_uris => @validation_uri}, @subjectid if @validation_uri
         Util.validation_get "/report/"+report_uri.split("/")[-2]+"/"+report_uri.split("/")[-1], @subjectid if @report_uri
-      rescue => ex
-        puts "could not create report: "+ex.message
-        raise ex
-        @report_error = ex.message
-      end
+      #rescue => ex
+        #puts "could not create report: "+ex.message
+        #raise ex
+        #@report_error = ex.message
+      #end
     end
     
     def validate
-      begin
+      #begin
         @validation_uri = Util.validation_post '/'+validation_type, get_params, @subjectid
-      rescue => ex
-        puts "could not validate: "+ex.message
-        @validation_error = ex.message
-        LOGGER.error ex.message
-      end
+      #rescue => ex
+        #puts "could not validate: "+ex.message
+        #@validation_error = ex.message
+        #LOGGER.error ex.message
+      #end
     end
     
     def compare_yaml_vs_rdf