adding weighted_accuracy, change accuracy computation, some minor changes

14 files changed, 221 insertions, 77 deletions

diff --git a/application.rb b/application.rb
index 319a95d..c18b05e 100755
--- a/application.rb
+++ b/application.rb
@@ -13,8 +13,6 @@ end
 
 require "example.rb"
 
-# this allows GET access to all validation URIS that do NOT end with /<number> or /<number>/
-OpenTox::Authorization.whitelist( /\/[0-9]+(\/?)$/, "GET", true )
 
 get '/examples/?' do
   LOGGER.info "list examples"
diff --git a/example.rb b/example.rb
index 3cced72..07151a8 100755
--- a/example.rb
+++ b/example.rb
@@ -124,7 +124,7 @@ class Example
       log "done"
       @@summary
     end
-    task.uri
+    return_task(task)
   end
   
   # performs all curl calls listed in examples after ">>>", next line is added if line ends with "\"
diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index e28f35b..b0e9720 100755
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -165,7 +165,9 @@ module Lib
       end
       raise "no array" unless v.is_a?(Array)
       if v.size>1
-        raise "multiple values"
+        v.uniq!
+        raise "not yet implemented: multiple non-equal values "+compound.to_s+" "+v.inspect if v.size>1
+        v = v[0]
       elsif v.size==1
         v = v[0]
       else
diff --git a/lib/predictions.rb b/lib/predictions.rb
index e73dda6..5850024 100755
--- a/lib/predictions.rb
+++ b/lib/predictions.rb
@@ -163,19 +163,36 @@ module Lib
     def percent_correct
       raise "no classification" unless @feature_type=="classification"
       return 0 if @num_with_actual_value==0
-      return 100 * @num_correct / @num_with_actual_value.to_f
+      return 100 * @num_correct / (@num_with_actual_value - @num_unpredicted).to_f
     end
     
     def percent_incorrect
       raise "no classification" unless @feature_type=="classification"
       return 0 if @num_with_actual_value==0
-      return 100 * @num_incorrect / @num_with_actual_value.to_f
+      return 100 * @num_incorrect / (@num_with_actual_value - @num_unpredicted).to_f
     end
     
     def accuracy
       return percent_correct / 100.0
     end
     
+    def weighted_accuracy
+      raise "no classification" unless @feature_type=="classification"
+      total = 0
+      correct = 0
+      (0..@predicted_values.size-1).each do |i|
+        if @predicted_values[i]!=nil
+          total += @confidence_values[i]
+          correct += @confidence_values[i] if @actual_values[i]==@predicted_values[i]
+        end
+      end
+      if total==0 || correct == 0
+        return 0  
+      else
+        return correct / total 
+      end
+    end
+
     def percent_unpredicted
       return 0 if @num_with_actual_value==0
       return 100 * @num_unpredicted / @num_with_actual_value.to_f
diff --git a/lib/validation_db.rb b/lib/validation_db.rb
index 4b852f9..c4cb2a2 100755
--- a/lib/validation_db.rb
+++ b/lib/validation_db.rb
@@ -18,10 +18,9 @@ module Lib
   # :classification_statistics
   VAL_CLASS_PROPS_SINGLE_SUM = [ :num_correct, :num_incorrect, :confusion_matrix  ]
   VAL_CLASS_PROPS_SINGLE_AVG = [ :percent_correct, :percent_incorrect, 
-    :weighted_area_under_roc, :accuracy ] 
+    :weighted_area_under_roc, :accuracy, :weighted_accuracy ] 
   VAL_CLASS_PROPS_SINGLE = VAL_CLASS_PROPS_SINGLE_SUM + VAL_CLASS_PROPS_SINGLE_AVG
   
-  
   # :class_value_statistics
   VAL_CLASS_PROPS_PER_CLASS_SUM = [ :num_false_positives, :num_false_negatives, 
                                 :num_true_positives, :num_true_negatives ]
diff --git a/reach_reports/reach_service.rb b/reach_reports/reach_service.rb
index 5e11dc1..f5b4b12 100755
--- a/reach_reports/reach_service.rb
+++ b/reach_reports/reach_service.rb
@@ -132,10 +132,12 @@ module ReachReports
     val_datasets = []
     
     if algorithm
-      cvs = Lib::Crossvalidation.find_all_uniq({:algorithm_uri => algorithm.uri})
+      cvs = Lib::Crossvalidation.find_all_uniq({:algorithm_uri => algorithm.uri, :finished => true})
       # PENDING: cv classification/regression hack
       cvs = cvs.delete_if do |cv|
-        val = Validation::Validation.first( :all, :conditions => { :crossvalidation_id => cv.id } )
+        #val = Validation::Validation.first( :all, :conditions => { :crossvalidation_id => cv.id } )
+        val = Validation::Validation.first( :crossvalidation_id => cv.id )
+        raise "should not happen: no validations found for crossvalidation "+cv.id.to_s unless val
         (val.classification_statistics!=nil) != (feature_type=="classification")
       end
       
@@ -166,11 +168,11 @@ module ReachReports
             val  = YAML.load( OpenTox::RestClientWrapper.get File.join(cv.crossvalidation_uri,"statistics") )
             case feature_type
             when "classification"
-              lmo << "percent_correct: "+val[:classification_statistics][:percent_correct].to_s
-              lmo << "weighted AUC: "+val[:classification_statistics][:weighted_area_under_roc].to_s
+              lmo << "percent_correct: "+val[OT.classificationStatistics][OT.percentCorrect].to_s
+              lmo << "weighted AUC: "+val[OT.classificationStatistics][OT.weightedAreaUnderRoc].to_s
             when "regression"
-              lmo << "root_mean_squared_error: "+val[:regression_statistics][:root_mean_squared_error].to_s
-              lmo << "r_square "+val[:regression_statistics][:r_square].to_s
+              lmo << "root_mean_squared_error: "+val[OT.regressionStatistics][OT.rootMeanSquaredError].to_s
+              lmo << "r_square "+val[OT.regressionStatistics][OT.rSquare].to_s
             end
             reports = OpenTox::RestClientWrapper.get File.join(CONFIG[:services]["opentox-validation"],"report/crossvalidation?crossvalidation_uris="+cv.crossvalidation_uri)
             if reports and reports.chomp.size>0
diff --git a/reach_reports/reach_test.rb b/reach_reports/reach_test.rb
index 4f7113b..9a354e7 100755
--- a/reach_reports/reach_test.rb
+++ b/reach_reports/reach_test.rb
@@ -115,7 +115,15 @@ class ReachTest < Test::Unit::TestCase
 #    puts last_response.body
     
     #model_uri = "http://ambit.uni-plovdiv.bg:8080/ambit2/model/173393"
-    model_uri = "http://local-ot/model/1"
+    
+    model_uri = "http://local-ot/majority/class/model/58"
+#    m = OpenTox::Model::Generic.find(model_uri)
+#    puts m.metadata[OT.algorithm] if m
+#    a = OpenTox::Algorithm::Generic.find(m.metadata[OT.algorithm])
+#    puts a.metadata.inspect
+#    exit
+    
+#    model_uri = "http://local-ot/model/1"
     #http://local-ot/majority/class/model/15
     #model_uri = "http://local-ot/majority/class/model/15"
    # model_uri = "http://local-ot/majority/class/model/91"
diff --git a/report/report_factory.rb b/report/report_factory.rb
index a5234a3..8fa185e 100755
--- a/report/report_factory.rb
+++ b/report/report_factory.rb
@@ -5,7 +5,7 @@ VAL_ATTR_TRAIN_TEST = [ :model_uri, :training_dataset_uri, :test_dataset_uri, :p
 VAL_ATTR_CV = [ :algorithm_uri, :dataset_uri, :num_folds, :crossvalidation_fold ]
 
 # selected attributes of interest when performing classification
-VAL_ATTR_CLASS = [ :percent_correct, :weighted_area_under_roc, 
+VAL_ATTR_CLASS = [ :accuracy, :weighted_accuracy, :weighted_area_under_roc, 
   :area_under_roc, :f_measure, :true_positive_rate, :true_negative_rate ]
 VAL_ATTR_REGR = [ :root_mean_squared_error, :mean_absolute_error, :r_square ]
 
diff --git a/report/validation_access.rb b/report/validation_access.rb
index 9c45165..03ec0e5 100755
--- a/report/validation_access.rb
+++ b/report/validation_access.rb
@@ -125,7 +125,6 @@ class Reports::ValidationDB < Reports::ValidationAccess
   end
   
   def feature_type( validation, subjectid=nil )
-    raise "subjectid is nil" unless subjectid
     OpenTox::Model::Generic.new(validation.model_uri).feature_type(subjectid)
     #get_model(validation).classification?
   end
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
diff --git a/validation/validation_application.rb b/validation/validation_application.rb
index b444b3f..9b517cf 100755
--- a/validation/validation_application.rb
+++ b/validation/validation_application.rb
@@ -549,11 +549,9 @@ get '/:id' do
       "All validations:                 "+url_for("/",:full)+"\n"+
       "All validation reports:          "+url_for("/report/validation",:full)
     OpenTox.text_to_html validation.to_yaml,related_links,description
-  when /application\/x-yaml|\*\/\*/ 
+  else #default is yaml 
     content_type "application/x-yaml"
     validation.to_yaml
-  else
-    raise OpenTox::BadRequestError.new "MIME type '"+request.env['HTTP_ACCEPT'].to_s+"' not supported, valid Accept-Headers: \"application/rdf+xml\", \"application/x-yaml\", \"text/html\"."
   end
 end
 
diff --git a/validation/validation_format.rb b/validation/validation_format.rb
index e72e7ec..f69ceac 100755
--- a/validation/validation_format.rb
+++ b/validation/validation_format.rb
@@ -10,8 +10,6 @@ module Validation
     # the hash is directly printed in to_yaml, or added to the owl-structure
     def get_content_as_hash()
       
-      LOGGER.debug self.validation_uri
-      
       h = {}
       (Lib::VAL_PROPS - [:validation_uri]).each do |p|
          h[p] = self.send(p)
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index 26f12e7..27fd6b1 100755
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -20,10 +20,10 @@ LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
 LOGGER.formatter = Logger::Formatter.new
 
 if AA_SERVER
-  #TEST_USER = "mgtest"
-  #TEST_PW = "mgpasswd"
-  TEST_USER = "guest"
-  TEST_PW = "guest"
+  TEST_USER = "mgtest"
+  TEST_PW = "mgpasswd"
+#  TEST_USER = "guest"
+#  TEST_PW = "guest"
   SUBJECTID = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
   raise "could not log in" unless SUBJECTID
   puts "logged in: "+SUBJECTID.to_s
@@ -60,6 +60,18 @@ class ValidationTest < Test::Unit::TestCase
     begin
       $test_case = self
       
+#      begin
+#        #OpenTox::RestClientWrapper.get "http://local-ot/validation/runtime-error",{:accept => "application/rdf+xml"}
+#        puts OpenTox::RestClientWrapper.post "http://opentox.ntua.gr:4000/model/0d8a9a27-3481-4450-bca1-d420a791de9d",
+#          {:dataset=>"http://apps.ideaconsult.net:8080/ambit2/dataset/54"},{:accept => "text/uri-list", :subjectid => SUBJECTID} 
+#        #puts OpenTox::RestClientWrapper.post "http://opentox.ntua.gr:4000/model/0d8a9a27-3481-4450-bca1-d420a791de9d",{},{:accept => "text/uri-list", :subjectid => "AQIC5wM2LY4SfcwUNX97nTvaSTdYJ+nTUqZsR0UitJ4+jlc=@AAJTSQACMDE=#"}
+#      rescue => err
+#        rep = OpenTox::ErrorReport.create(err, "")
+#         puts rep.to_yaml
+#      end  
+        
+        # "http://opentox.ntua.gr:4000/model/0d8a9a27-3481-4450-bca1-d420a791de9d"
+      
 #      get "/19999",nil,'HTTP_ACCEPT' => "text/html"
 #      exit
 #       
@@ -126,23 +138,41 @@ class ValidationTest < Test::Unit::TestCase
       # m = OpenTox::Model::Generic.find("http://local-ot/model/1323333")
       # puts m.to_yaml
   
-  #     post "/validate_datasets",{
-  #      :test_dataset_uri=>"http://local-ot/dataset/506",
-  #       :prediction_dataset_uri=>"http://local-ot/dataset/526",
-  #       :test_target_dataset_uri=>"http://local-ot/dataset/504",
-  #       :prediction_feature=>"http://local-ot/dataset/504/feature/LC50_mmol",
-  #       :model_uri=>"http://local-ot/model/48"}
-  #      #:regression=>"true"}
-  ##       :classification=>"true"}
-  #    puts last_response.body
-      
-      #run_test("13a","http://local-ot/validation/39",nil,false) #,"http://local-ot/validation/28")#,"http://local-ot/validation/394");
+#     post "/validate_datasets",{
+#         :test_dataset_uri=>"http://local-ot/dataset/390",
+#         :prediction_dataset_uri=>"http://local-ot/dataset/392",
+#         :test_target_dataset_uri=>"http://local-ot/dataset/388",
+#         :prediction_feature=>"http://local-ot/dataset/388/feature/repdose_classification",
+#         :model_uri=>"http://local-ot/model/31"}
+#        #:regression=>"true"}
+#  #       :classification=>"true"}
+#      uri = last_response.body
+#      val = wait_for_task(uri)
+#      puts val
+#      get "/"+val.split("/")[-1]
       
+      #run_test("17a") #,"http://local-ot/validation/39",nil,false) #,"http://local-ot/validation/28")#,"http://local-ot/validation/394");
+       
+#      p = {
+#        :dataset_uri=>"http://local-ot/dataset/388",
+#        :algorithm_uri => "http://local-ot/majority/class/algorithm",
+#        :prediction_feature=>"http://local-ot/dataset/388/feature/repdose_classification",
+#        :num_folds => 2 }
+      #cv = OpenTox::Crossvalidation.create(p)
+#      cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/14")
+#      puts cv.uri
+#      puts cv.find_or_create_report.uri
+#      puts cv.summary.inspect
+
       #puts OpenTox::Authorization.list_policy_uris(SUBJECTID).inspect
       
       #puts OpenTox::Authorization.list_policy_uris(SUBJECTID).inspect
 
-      run_test("15a",nil,nil,false) #,{:dataset_uri=>"http://local-ot/dataset/45", :prediction_feature => "http://local-ot/dataset/45/feature/Hamster%20Carcinogenicity"})
+      #run_test("1b") #,{:dataset_uri => "http://local-ot/dataset/313", :prediction_feature => "http://local-ot/dataset/313/feature/repdose_classification"})
+      
+      model = OpenTox::Model::Generic.find("http://local-ot/majority/class/model/58")
+      OpenTox::QMRFReport.create(model)
+      
       
       #get "/12123123123123123"
       #get "/chain"
@@ -176,9 +206,12 @@ class ValidationTest < Test::Unit::TestCase
       #prepare_examples
       #do_test_examples # USES CURL, DO NOT FORGET TO RESTART VALIDATION SERVICE
       #do_test_examples_ortona
-      
+    
+    rescue => ex
+      rep = OpenTox::ErrorReport.create(ex, "")
+      puts rep.to_yaml
     ensure
-      OpenTox::Authorization.logout(SUBJECTID) if AA_SERVER
+      #OpenTox::Authorization.logout(SUBJECTID) if AA_SERVER
     end
   end
 
@@ -186,7 +219,7 @@ class ValidationTest < Test::Unit::TestCase
     Sinatra::Application
   end
   
-  def run_test(select=nil, validation_uri=nil, report_uri=nil, delete=false, overwrite={})
+  def run_test(select=nil, overwrite={}, delete=false )
     
     if AA_SERVER && SUBJECTID && delete
       policies_before = OpenTox::Authorization.list_policy_uris(SUBJECTID)
@@ -199,7 +232,6 @@ class ValidationTest < Test::Unit::TestCase
         ex = v.new
         ex.subjectid = SUBJECTID
         
-        ex.validation_uri = validation_uri
         overwrite.each do |k,v|
           ex.send(k.to_s+"=",v)
         end
@@ -208,13 +240,26 @@ class ValidationTest < Test::Unit::TestCase
           ex.upload_files
           ex.check_requirements
           ex.validate
+            
           LOGGER.debug "validation done '"+ex.validation_uri.to_s+"'"
-          puts ex.validation_uri+"?subjectid="+CGI.escape(SUBJECTID) if SUBJECTID and !delete and ex.validation_uri
+          if !delete and ex.validation_uri
+            if SUBJECTID
+              puts ex.validation_uri+"?subjectid="+CGI.escape(SUBJECTID)
+            else
+              puts ex.validation_uri
+            end
+          end
+            
         end
-        ex.report_uri = report_uri
         unless ex.report_uri
           ex.report
-          puts ex.report_uri+"?subjectid="+CGI.escape(SUBJECTID)  if SUBJECTID and !delete and ex.report_uri
+          if !delete and ex.report_uri
+            if SUBJECTID  
+              puts ex.report_uri+"?subjectid="+CGI.escape(SUBJECTID)
+            else
+              puts ex.report_uri
+            end
+          end
         end
         ##ex.verify_yaml
         ##ex.compare_yaml_vs_rdf