* replace load with require (to avoid loading resources twice)

* adjust to new api
* move validation constants from wrapper to lib in validation
* accept header parsing in validation
* rdf-support in validation

6 files changed, 39 insertions, 32 deletions

diff --git a/report/environment.rb b/report/environment.rb
index 7420e80..c1c7cd6 100644
--- a/report/environment.rb
+++ b/report/environment.rb
@@ -13,21 +13,21 @@ require 'mime/types'
 module Reports
 end
 
-load "report/r_plot_factory.rb"
-load "report/plot_factory.rb"
-load "report/xml_report.rb"
-load "report/xml_report_util.rb"
-load "report/report_persistance.rb"
-load "report/report_factory.rb"
-load "report/report_service.rb"
-load "report/report_format.rb"
-load "report/validation_access.rb"
-load "report/validation_data.rb"
-load "report/predictions.rb"
-load "report/util.rb"
-load "report/external/mimeparse.rb"
+require "report/r_plot_factory.rb"
+require "report/plot_factory.rb"
+require "report/xml_report.rb"
+require "report/xml_report_util.rb"
+require "report/report_persistance.rb"
+require "report/report_factory.rb"
+require "report/report_service.rb"
+require "report/report_format.rb"
+require "report/validation_access.rb"
+require "report/validation_data.rb"
+require "report/prediction_util.rb"
+require "report/util.rb"
+require "report/external/mimeparse.rb"
 
-load "lib/ot_predictions.rb"
+require "lib/ot_predictions.rb"
 
 unless(defined? LOGGER)
   LOGGER = Logger.new(STDOUT)
diff --git a/report/report_application.rb b/report/report_application.rb
index de8a88e..3ff3c24 100644
--- a/report/report_application.rb
+++ b/report/report_application.rb
@@ -1,4 +1,4 @@
-load "report/environment.rb"
+require "report/environment.rb"
 
 def perform
   begin
diff --git a/report/report_factory.rb b/report/report_factory.rb
index 4b3d18e..8b14e0a 100644
--- a/report/report_factory.rb
+++ b/report/report_factory.rb
@@ -59,7 +59,7 @@ module Reports::ReportFactory
       report.add_section_result(validation_set, VAL_ATTR_TRAIN_TEST + VAL_ATTR_REGR, "Results", "Results")
     end
     
-    report.add_section_result(validation_set, OpenTox::Validation::ALL_PROPS, "All Results", "All Results")
+    report.add_section_result(validation_set, Lib::ALL_PROPS, "All Results", "All Results")
     report.add_section_predictions( validation_set ) 
     return report
   end
@@ -92,7 +92,7 @@ module Reports::ReportFactory
       report.add_section_result(validation_set, VAL_ATTR_CV+VAL_ATTR_REGR-[:num_folds], "Results","Results")
     end
       
-    report.add_section_result(validation_set, OpenTox::Validation::ALL_PROPS, "All Results", "All Results")
+    report.add_section_result(validation_set, Lib::ALL_PROPS, "All Results", "All Results")
     report.add_section_predictions( validation_set, [:crossvalidation_fold] ) 
     return report
   end
@@ -216,14 +216,21 @@ class Reports::ReportContent
   end
 
   def add_section_roc_plot( validation_set,
-                            class_value,
+                            class_value = nil,
                             split_set_attribute = nil,
                             plot_file_name="roc-plot.svg", 
                             section_title="Roc Plot",
                             section_text="This section contains the roc plot.",
                             image_title=nil,
                             image_caption=nil)
-    image_title = "Roc Plot for class-value '"+class_value+"'" unless image_title
+    unless image_title
+      if class_value
+        image_title = "Roc Plot for class-value '"+class_value+"'"
+      else
+        image_title = "Roc Plot for all classes"
+      end
+    end
+    
     
     section_roc = @xml_report.add_section(@xml_report.get_root_element, section_title)
     if validation_set.first.get_predictions
diff --git a/report/report_test.rb b/report/report_test.rb
index 1a4a5f5..6ac8810 100644
--- a/report/report_test.rb
+++ b/report/report_test.rb
@@ -5,7 +5,7 @@ require 'report/report_application.rb'
 require 'test/unit'
 require 'rack/test'
 
-load 'lib/test_util.rb'
+require "'lib/test_util.rb"
 
 
 #class Reports::ApplicationTest < Test::Unit::TestCase
@@ -151,7 +151,7 @@ class Reports::ReportServiceTest < Test::Unit::TestCase
         :algorithm_uri => ws_class_alg, 
         :split_ratio=>0.7,
         :prediction_feature => "classification",}
-    val_params[:feature_service_uri] = ws_feat_alg if ws_feat_alg
+    val_params[:feature_generation_uri] = ws_feat_alg if ws_feat_alg
     begin
       RestClient.post WS_VAL+"/validation/training_test_split", val_params
     rescue => ex
@@ -162,7 +162,7 @@ class Reports::ReportServiceTest < Test::Unit::TestCase
   def create_cross_validation(data_uri, ws_class_alg=WS_CLASS_ALG, ws_feat_alg=WS_FEATURE_ALG)
     puts "cross-validating"
     ext("curl -X POST -d num_folds=3 -d dataset_uri="+data_uri+" -d algorithm_uri="+ws_class_alg+" -d prediction_feature=classification"+
-        (ws_feat_alg ? " -d feature_service_uri="+ws_feat_alg : "")+
+        (ws_feat_alg ? " -d feature_generation_uri="+ws_feat_alg : "")+
         " "+WS_VAL+"/crossvalidation",nil)
   end
   
diff --git a/report/validation_access.rb b/report/validation_access.rb
index 4396624..2526e01 100644
--- a/report/validation_access.rb
+++ b/report/validation_access.rb
@@ -1,5 +1,5 @@
 
-load "lib/validation_db.rb"
+require "lib/validation_db.rb"
 
 # = Reports::ValidationAccess
 # 
@@ -53,7 +53,7 @@ class Reports::ValidationDB < Reports::ValidationAccess
     v = Lib::Validation.get(validation_id)
     raise Reports::BadRequest.new "no validation found with id "+validation_id.to_s unless v
     
-    (OpenTox::Validation::VAL_PROPS + OpenTox::Validation::VAL_CV_PROPS).each do |p|
+    (Lib::VAL_PROPS + Lib::VAL_CV_PROPS).each do |p|
       validation.send("#{p.to_s}=".to_sym, v[p])
     end
     
@@ -61,8 +61,8 @@ class Reports::ValidationDB < Reports::ValidationAccess
     #raise "cannot access model '"+v[:model_uri].to_s+"'" unless model
     #validation.prediction_feature = model.get_prediction_feature
     
-    {OpenTox::Validation::VAL_CLASS_PROP => OpenTox::Validation::VAL_CLASS_PROPS, 
-     OpenTox::Validation::VAL_REGR_PROP => OpenTox::Validation::VAL_REGR_PROPS}.each do |subset_name,subset_props|
+    {Lib::VAL_CLASS_PROP => Lib::VAL_CLASS_PROPS, 
+     Lib::VAL_REGR_PROP => Lib::VAL_REGR_PROPS}.each do |subset_name,subset_props|
       subset = v[subset_name]
       subset_props.each{ |prop| validation.send("#{prop.to_s}=".to_sym, subset[prop]) } if subset
     end
@@ -73,7 +73,7 @@ class Reports::ValidationDB < Reports::ValidationAccess
     cv = Lib::Crossvalidation.get(validation.crossvalidation_id)
     raise Reports::BadRequest.new "no crossvalidation found with id "+validation.crossvalidation_id.to_s unless cv
     
-    OpenTox::Validation::CROSS_VAL_PROPS.each do |p|
+    Lib::CROSS_VAL_PROPS.each do |p|
       validation.send("#{p.to_s}=".to_sym, cv[p])        
     end
   end
@@ -119,7 +119,7 @@ class Reports::ValidationWebservice < Reports::ValidationAccess
       raise Reports::BadRequest.new "cannot get validation at '"+uri.to_s+"', error msg: "+ex.message
     end
   
-    OpenTox::Validation::VAL_PROPS.each do |p|
+    Lib::VAL_PROPS.each do |p|
       validation.send("#{p}=".to_sym, data[p])        
     end
     
@@ -127,8 +127,8 @@ class Reports::ValidationWebservice < Reports::ValidationAccess
     #raise "cannot access model '"+v[:model_uri].to_s+"'" unless model
     #validation.prediction_feature = model.get_prediction_feature
     
-    {OpenTox::Validation::VAL_CV_PROP => OpenTox::Validation::VAL_CV_PROPS,
-     OpenTox::Validation::VAL_CLASS_PROP => OpenTox::Validation::VAL_CLASS_PROPS}.each do |subset_name,subset_props|
+    {Lib::VAL_CV_PROP => Lib::VAL_CV_PROPS,
+     Lib::VAL_CLASS_PROP => Lib::VAL_CLASS_PROPS}.each do |subset_name,subset_props|
       subset = data[subset_name]
       subset_props.each{ |prop| validation.send("#{prop}=".to_sym, subset[prop]) } if subset
     end
@@ -145,7 +145,7 @@ class Reports::ValidationWebservice < Reports::ValidationAccess
       raise Reports::BadRequest.new "cannot get crossvalidation at '"+cv_uri.to_s+"', error msg: "+ex.message
     end
     
-    OpenTox::Validation::CROSS_VAL_PROPS.each do |p|
+    Lib::CROSS_VAL_PROPS.each do |p|
       validation.send("#{p.to_s}=".to_sym, data[p])        
     end
   end
diff --git a/report/validation_data.rb b/report/validation_data.rb
index 99ec761..8a98542 100644
--- a/report/validation_data.rb
+++ b/report/validation_data.rb
@@ -58,7 +58,7 @@ module Reports
   #
   class Validation
     
-    @@validation_attributes = OpenTox::Validation::ALL_PROPS + 
+    @@validation_attributes = Lib::ALL_PROPS + 
       VAL_ATTR_VARIANCE.collect{ |a| (a.to_s+"_variance").to_sym } +
       VAL_ATTR_RANKING.collect{ |a| (a.to_s+"_ranking").to_sym }