set cookie in reports, hack for ambit, new examples

4 files changed, 36 insertions, 30 deletions

diff --git a/EXAMPLES b/EXAMPLES
index 7a617d6..a27e33b 100755
--- a/EXAMPLES
+++ b/EXAMPLES
@@ -17,7 +17,7 @@ get list of available validations
 
 >>> curl <validation_service>
 
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -31,7 +31,7 @@ get validation
 
 >>> curl <validation_service>/<validation_id>
 
-supported accept-headers: "text/x-yaml" and "application/rdf-xml"			
+supported accept-headers: "text/x-yaml" and "application/rdf+xml"			
 	
 	
 validate model on test-dateset
@@ -45,7 +45,7 @@ validate model on test-dateset
 optional params:
 test_target_dataset_uri, default is test_dataset_uri
 	
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -67,7 +67,7 @@ optional params:
 algorithm_params, default is empty
 test_target_dataset_uri, default is test_dataset_uri
 	
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -90,7 +90,7 @@ algorithm_params, default is empty
 split_ratio, default is 0.67
 random_seed, default is 1
 	
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -111,7 +111,7 @@ optional params:
 algorithm_params, default is empty
 random_seed, default is 1
 	
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -123,7 +123,7 @@ get list of available crossvalidations
 
 >>> curl <validation_service>/crossvalidation
 
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -137,7 +137,7 @@ get crossvalidation
 
 >>> curl <validation_service>/crossvalidation/<crossvalidation_id>
 
-supported accept-headers: "text/x-yaml" and "application/rdf-xml"			
+supported accept-headers: "text/x-yaml" and "application/rdf+xml"			
 	
 
 validate an algorithm on a dataset via crossvalidation
@@ -159,7 +159,7 @@ num_folds, default is 10
 random_seed, default is 1
 stratified, default is false
 	
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -176,7 +176,7 @@ get list of available report types
 
 >>> curl <validation_service>/report
 
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -190,7 +190,7 @@ get list of available reports of type validation
 
 >>> curl <validation_service>/report/validation
 
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -219,7 +219,7 @@ create validation report from validation
 >>> curl -X POST -d validation_uris="<validation_service>/<validation_id>" \
  <validation_service>/report/validation
 
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -231,7 +231,7 @@ get list of available reports of type crossvalidation
 
 >>> curl <validation_service>/report/crossvalidation
 
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -260,7 +260,7 @@ create crossvalidation report from crossvalidation
 >>> curl -X POST -d validation_uris="<validation_service>/crossvalidation/<crossvalidation_id>" \
  <validation_service>/report/crossvalidation
 
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -275,7 +275,7 @@ manually format html report
 
 This explicity invokes the report convertion to html, with css-style-sheet as parameter. 
 
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -319,7 +319,7 @@ get list of available qmrf report
 
 >>> curl <validation_service>/reach_report/qmrf
 
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
@@ -334,7 +334,7 @@ create a QMRF from a model
 >>> curl -X POST -d model_uri="<model_uri>" \
  <validation_service>/reach_report/qmrf
  
-result example (accept-header: application/rdf-xml)			
+result example (accept-header: application/rdf+xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index 537f0b8..9b1ee51 100755
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -55,7 +55,7 @@ module Lib
         @compounds = test_dataset.compounds
         LOGGER.debug "test dataset size: "+@compounds.size.to_s
         raise "test dataset is empty "+test_dataset_uri.to_s unless @compounds.size>0
-        class_values = feature_type=="classification" ? OpenTox::Feature.new(prediction_feature).domain : nil
+        class_values = feature_type=="classification" ? OpenTox::Feature.find(prediction_feature, subjectid).domain : nil
         
         actual_values = []
         @compounds.each do |c|
@@ -147,12 +147,13 @@ module Lib
     def classification_value(dataset, compound, feature, class_values)
       v = value(dataset, compound, feature)
       i = class_values.index(v)
-      raise "illegal class_value of predicted value "+v.to_s+" class: "+v.class.to_s unless v==nil or i!=nil
+      raise "illegal class_value of prediction (value is '"+v.to_s+"', class is '"+v.class.to_s+"'), possible values are "+
+        class_values.inspect unless v==nil or i!=nil
       i
     end
     
     def value(dataset, compound, feature)
-      
+      return nil if dataset.data_entries[compound]==nil
       if feature==nil
         v = dataset.data_entries[compound].values[0]
       else
diff --git a/report/report_application.rb b/report/report_application.rb
index 1a4504d..ab3d91b 100755
--- a/report/report_application.rb
+++ b/report/report_application.rb
@@ -76,7 +76,6 @@ end
 
 
 get '/report/:type/:id' do
-  
   perform do |rs| 
     
     accept_header = request.env['HTTP_ACCEPT']
@@ -90,6 +89,8 @@ get '/report/:type/:id' do
       result = body(File.new(report))
     end
   end
+
+  response.set_cookie("subjectid", @subjectid)
 end
 
 #OpenTox::Authorization.whitelist( Regexp.new("/report/.*/[0-9]+/.*"),"GET")
diff --git a/validation/validation_service.rb b/validation/validation_service.rb
index 944bed6..d917a96 100755
--- a/validation/validation_service.rb
+++ b/validation/validation_service.rb
@@ -138,16 +138,20 @@ module Validation
         self.algorithm_uri = model.metadata[OT.algorithm]
       end
       
-      dependentVariables = model.metadata[OT.dependentVariables]
-      if self.prediction_feature
-        raise OpenTox::NotFoundError.new "error validating model: model.dependent_variable != validation.prediction_feature ("+
-          dependentVariables.to_s+" != "+self.prediction_feature+"), model-metadata is "+model.metadata.inspect if self.prediction_feature!=dependentVariables
+      if self.prediction_feature and model.uri=~/ambit2\/model/
+        LOGGER.warn "REMOVE AMBIT HACK TO __NOT__ RELY ON DEPENDENT VARIABLE"        
       else
-        raise OpenTox::NotFoundError.new "model has no dependentVariables specified, please give prediction feature for model validation" unless dependentVariables
-        #self.attributes = { :prediction_feature => model.dependentVariables }
-        #self.save!
-        #self.update :prediction_feature => model.dependentVariables
-        self.prediction_feature = model.metadata[OT.dependentVariables]
+        dependentVariables = model.metadata[OT.dependentVariables]
+        if self.prediction_feature
+          raise OpenTox::NotFoundError.new "error validating model: model.dependent_variable != validation.prediction_feature ("+
+            dependentVariables.to_s+" != "+self.prediction_feature+"), model-metadata is "+model.metadata.inspect if self.prediction_feature!=dependentVariables
+        else
+          raise OpenTox::NotFoundError.new "model has no dependentVariables specified, please give prediction feature for model validation" unless dependentVariables
+          #self.attributes = { :prediction_feature => model.dependentVariables }
+          #self.save!
+          #self.update :prediction_feature => model.dependentVariables
+          self.prediction_feature = model.metadata[OT.dependentVariables]
+        end
       end
       
       prediction_dataset_uri = ""