adjust to new A&A for GET, remove old Report-Errorreporting

2 files changed, 41 insertions, 23 deletions

diff --git a/validation/validation_service.rb b/validation/validation_service.rb
index eb9ecff..fa638cf 100755
--- a/validation/validation_service.rb
+++ b/validation/validation_service.rb
@@ -129,7 +129,7 @@ module Validation
       
       #model = OpenTox::Model::PredictionModel.find(self.model_uri)
       #raise OpenTox::NotFoundError.new "model not found: "+self.model_uri.to_s unless model
-      model = OpenTox::Model::Generic.find(self.model_uri)
+      model = OpenTox::Model::Generic.find(self.model_uri, self.subjectid)
       raise OpenTox::NotFoundError.new "model not found: "+self.model_uri.to_s unless model
       
       unless self.algorithm_uri
@@ -173,7 +173,7 @@ module Validation
       
       #model = OpenTox::Model::PredictionModel.find(self.model_uri) if model==nil and self.model_uri
       #raise OpenTox::NotFoundError.new "model not found: "+self.model_uri.to_s unless model
-      model = OpenTox::Model::Generic.find(self.model_uri) if model==nil and self.model_uri
+      model = OpenTox::Model::Generic.find(self.model_uri, self.subjectid) if model==nil and self.model_uri
       raise OpenTox::NotFoundError.new "model not found: "+self.model_uri.to_s unless model
       
       dependentVariables = model.metadata[OT.dependentVariables]
@@ -198,7 +198,7 @@ module Validation
       LOGGER.debug "computing prediction stats"
       prediction = Lib::OTPredictions.new( feature_type, 
         self.test_dataset_uri, self.test_target_dataset_uri, self.prediction_feature, 
-        self.prediction_dataset_uri, predicted_feature, OpenTox::SubTask.create(task, 0, 80) )
+        self.prediction_dataset_uri, predicted_feature, self.subjectid, OpenTox::SubTask.create(task, 0, 80) )
       #reading datasets and computing the main stats is 80% the work 
       
       unless dry_run
@@ -338,7 +338,7 @@ module Validation
       
       raise "random seed not set "+self.inspect unless self.random_seed
       LOGGER.debug "creating datasets for crossvalidation"
-      orig_dataset = OpenTox::Dataset.find(self.dataset_uri)
+      orig_dataset = OpenTox::Dataset.find(self.dataset_uri,self.subjectid)
       raise OpenTox::NotFoundError.new "Dataset not found: "+self.dataset_uri.to_s unless orig_dataset
       
       shuffled_compounds = orig_dataset.compounds.shuffle( self.random_seed )
@@ -448,7 +448,7 @@ module Validation
       
       random_seed=1 unless random_seed
       
-      orig_dataset = OpenTox::Dataset.find orig_dataset_uri
+      orig_dataset = OpenTox::Dataset.find orig_dataset_uri,subjectid
       orig_dataset.load_all
       raise OpenTox::NotFoundError.new "Dataset not found: "+orig_dataset_uri.to_s unless orig_dataset
       if prediction_feature
@@ -513,7 +513,7 @@ module Validation
       task.progress(100) if task
       
       if ENV['RACK_ENV'] =~ /test|debug/
-        training_dataset = OpenTox::Dataset.find result[:training_dataset_uri]
+        training_dataset = OpenTox::Dataset.find result[:training_dataset_uri],subjectid
         raise OpenTox::NotFoundError.new "Training dataset not found: '"+result[:training_dataset_uri].to_s+"'" unless training_dataset
         training_dataset.load_all
         value_count = 0
@@ -521,7 +521,8 @@ module Validation
           value_count += training_dataset.data_entries[c][prediction_feature].size
         end
         raise  "training compounds error" unless value_count==training_compounds.size
-        raise OpenTox::NotFoundError.new "Test dataset not found: '"+result[:test_dataset_uri].to_s+"'" unless OpenTox::Dataset.find result[:test_dataset_uri]
+        raise OpenTox::NotFoundError.new "Test dataset not found: '"+result[:test_dataset_uri].to_s+"'" unless 
+          OpenTox::Dataset.find result[:test_dataset_uri], subjectid
       end
       LOGGER.debug "bootstrapping done, training dataset: '"+result[:training_dataset_uri].to_s+"', test dataset: '"+result[:test_dataset_uri].to_s+"'"
       
@@ -535,8 +536,8 @@ module Validation
       split_ratio=0.67 unless split_ratio
       random_seed=1 unless random_seed
       
-      orig_dataset = OpenTox::Dataset.find orig_dataset_uri
-      orig_dataset.load_all
+      orig_dataset = OpenTox::Dataset.find orig_dataset_uri, subjectid
+      orig_dataset.load_all subjectid
       raise OpenTox::NotFoundError.new "Dataset not found: "+orig_dataset_uri.to_s unless orig_dataset
       raise OpenTox::NotFoundError.new "Split ratio invalid: "+split_ratio.to_s unless split_ratio and split_ratio=split_ratio.to_f
       raise OpenTox::NotFoundError.new "Split ratio not >0 and <1 :"+split_ratio.to_s unless split_ratio>0 && split_ratio<1
@@ -597,10 +598,11 @@ module Validation
       task.progress(100) if task  
       
       if ENV['RACK_ENV'] =~ /test|debug/
-        raise OpenTox::NotFoundError.new "Training dataset not found: '"+result[:training_dataset_uri].to_s+"'" unless OpenTox::Dataset.find result[:training_dataset_uri]
-        test_data = OpenTox::Dataset.find result[:test_dataset_uri]
+        raise OpenTox::NotFoundError.new "Training dataset not found: '"+result[:training_dataset_uri].to_s+"'" unless 
+          OpenTox::Dataset.find(result[:training_dataset_uri],subjectid)
+        test_data = OpenTox::Dataset.find result[:test_dataset_uri],subjectid
         raise OpenTox::NotFoundError.new "Test dataset not found: '"+result[:test_dataset_uri].to_s+"'" unless test_data 
-        test_data.load_compounds
+        test_data.load_compounds subjectid
         raise "Test dataset num coumpounds != "+(compounds.size-split-1).to_s+", instead: "+
           test_data.compounds.size.to_s+"\n"+test_data.to_yaml unless test_data.compounds.size==(compounds.size-1-split)
       end
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index 3138252..603b270 100755
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -26,11 +26,16 @@ if AA_SERVER
   raise "could not log in" unless SUBJECTID
   puts "logged in: "+SUBJECTID.to_s
 else
+  puts "AA disabled"
   SUBJECTID = nil
 end
 
 #Rack::Test::DEFAULT_HOST = "local-ot" #"/validation"
 module Sinatra
+  
+  set :raise_errors, false
+  set :show_exceptions, false
+
   module UrlForHelper
     BASE = "http://local-ot/validation"
     def url_for url_fragment, mode=:path_only
@@ -53,7 +58,8 @@ class ValidationTest < Test::Unit::TestCase
     begin
       $test_case = self
       
-      #get "/1",nil,'HTTP_ACCEPT' => "text/html" 
+#      get "/19999",nil,'HTTP_ACCEPT' => "text/html"
+#      exit
 #       
 #      get "/234234232341",nil,'HTTP_ACCEPT' => "application/x-yaml"
 #      puts last_response.body
@@ -131,13 +137,23 @@ class ValidationTest < Test::Unit::TestCase
       #run_test("13a","http://local-ot/validation/39",nil,false) #,"http://local-ot/validation/28")#,"http://local-ot/validation/394");
       
       #puts OpenTox::Authorization.list_policy_uris(SUBJECTID).inspect
+      
+      #puts OpenTox::Authorization.list_policy_uris(SUBJECTID).inspect
 
-      #run_test("1b",nil,nil,false,{:dataset_uri=>"http://local-ot/dataset/45", :prediction_feature => "http://local-ot/dataset/45/feature/Hamster%20Carcinogenicity"})
+      run_test("14a",nil,nil,false) #,{:dataset_uri=>"http://local-ot/dataset/45", :prediction_feature => "http://local-ot/dataset/45/feature/Hamster%20Carcinogenicity"})
       
       #get "/12123123123123123"
-      get "/chain"
-      #get "/examples"
-      puts last_response.body
+      #get "/chain"
+      
+      #OpenTox::RestClientWrapper.get("http://local-ot/validation/task-error")
+      #get "/error",nil,'HTTP_ACCEPT' => "application/rdf+xml"
+      #puts ""
+      #puts ""
+      #puts last_response.body 
+      #exit
+      
+#      get "/error"
+#      puts last_response.body
 
       #delete "/1",:subjectid=>SUBJECTID
       
@@ -170,7 +186,7 @@ class ValidationTest < Test::Unit::TestCase
   
   def run_test(select=nil, validation_uri=nil, report_uri=nil, delete=false, overwrite={})
     
-    if AA_SERVER && delete
+    if AA_SERVER && SUBJECTID && delete
       policies_before = OpenTox::Authorization.list_policy_uris(SUBJECTID)
     end
     
@@ -191,17 +207,17 @@ class ValidationTest < Test::Unit::TestCase
           ex.validate
           LOGGER.debug "validation done '"+ex.validation_uri.to_s+"'"
         end
-#        ex.report_uri = report_uri
-#        unless ex.report_uri
-#          ex.report
-#        end
+        ex.report_uri = report_uri
+        unless ex.report_uri
+          ex.report
+        end
         ##ex.verify_yaml
         ##ex.compare_yaml_vs_rdf
         ex.delete if delete
       end
     end
     
-    if AA_SERVER && delete
+    if AA_SERVER && SUBJECTID && delete
       policies_after= OpenTox::Authorization.list_policy_uris(SUBJECTID)
       diff = policies_after.size - policies_before.size
       if (diff != 0)