Merge branch 'release/v3.2.0'HEADv4.0.0master

5 files changed, 47 insertions, 27 deletions

diff --git a/report/plot_factory.rb b/report/plot_factory.rb
index f114dd3..6e90dbc 100644
--- a/report/plot_factory.rb
+++ b/report/plot_factory.rb
@@ -4,7 +4,8 @@ ENV['RANK_PLOTTER_JAR'] = "RankPlotter/RankPlotter.jar" unless ENV['RANK_PLOTTER
 
 CONF_PLOT_RANGE = { :accuracy => [0.45,1.05], :true_positive_rate => [0.45,1.05],:true_negative_rate => [0.45,1.05],
   :false_positive_rate => [0.45,1.05], :false_negative_rate => [0.45,1.05], :positive_predictive_value => [0.45,1.05],
-  :negative_predictive_value => [0.45,1.05], :r_square => [0, 1.05],  :sample_correlation_coefficient => [0, 1.05] }
+  :negative_predictive_value => [0.45,1.05], :r_square => [0, 1.05],  :sample_correlation_coefficient => [0, 1.05],
+  :concordance_correlation_coefficient => [0, 1.05] }
 
 class Array
   def swap!(i,j)
@@ -124,7 +125,7 @@ module Reports
       else
         Reports::r_util.feature_value_plot(out_files, validation_set.validations[0].training_feature_dataset_uri,
           validation_set.validations[0].test_feature_dataset_uri, "Training Data", "Test Data",
-          nil, true, validation_set.validations[0].subjectid, waiting_task )
+          nil, validation_set.validations[0].subjectid, waiting_task )
       end
     end
     
diff --git a/report/report_content.rb b/report/report_content.rb
index 80473c5..033b367 100755
--- a/report/report_content.rb
+++ b/report/report_content.rb
@@ -63,20 +63,17 @@ class Reports::ReportContent
     end
   end
   
-  def add_predictions( validation_set, 
-                        validation_attributes=[],
+  def add_predictions( validation_set,
+                        add_validation_uris,   
                         section_title="Predictions",
                         section_text=nil,
                         table_title="Predictions")
-
-    #PENING
-    raise "validation attributes not implemented in get prediction array" if  validation_attributes.size>0
-    
     section_table = @xml_report.add_section(@current_section, section_title)
     if validation_set.validations[0].get_predictions
       @xml_report.add_paragraph(section_table, section_text) if section_text
+      v_uris = validation_set.validations.collect{|v| Array.new(v.num_instances.to_i,v.validation_uri)} if add_validation_uris
       @xml_report.add_table(section_table, table_title, Lib::OTPredictions.to_array(validation_set.validations.collect{|v| v.get_predictions}, 
-        true, true))
+        true, true, v_uris))
     else
       @xml_report.add_paragraph(section_table, "No prediction info available.")
     end
diff --git a/report/report_factory.rb b/report/report_factory.rb
index 2bb74ee..f73ffd9 100755
--- a/report/report_factory.rb
+++ b/report/report_factory.rb
@@ -9,7 +9,7 @@ VAL_ATTR_CLASS = [ :num_instances, :num_unpredicted, :accuracy, :weighted_accura
   :area_under_roc, :f_measure, :true_positive_rate, :true_negative_rate, :positive_predictive_value, :negative_predictive_value ]
 VAL_ATTR_REGR = [ :num_instances, :num_unpredicted, :root_mean_squared_error, 
   :weighted_root_mean_squared_error, :mean_absolute_error, :weighted_mean_absolute_error, :r_square, :weighted_r_square,
-  :sample_correlation_coefficient ]
+  :sample_correlation_coefficient, :concordance_correlation_coefficient ]
 
 #VAL_ATTR_BOX_PLOT_CLASS = [ :accuracy, :average_area_under_roc, 
 #  :area_under_roc, :f_measure, :true_positive_rate, :true_negative_rate ]
@@ -113,6 +113,9 @@ module Reports::ReportFactory
       report.add_confidence_plot(validation_set, :root_mean_squared_error, nil)
       report.add_confidence_plot(validation_set, :r_square, nil)
       report.align_last_two_images "Confidence Plots"
+      report.add_confidence_plot(validation_set, :sample_correlation_coefficient, nil)
+      report.add_confidence_plot(validation_set, :concordance_correlation_coefficient, nil)
+      report.align_last_two_images "More Confidence Plots"
     end
     task.progress(70) if task
     report.add_train_test_plot( validation_set, false, OpenTox::SubTask.create(task,70,80) )
@@ -121,7 +124,7 @@ module Reports::ReportFactory
     report.end_section
 
     report.add_result(validation_set, Validation::ALL_PROPS, "All Results", "All Results")
-    report.add_predictions( validation_set )
+    report.add_predictions( validation_set, false )
     task.progress(100) if task
     report
   end
@@ -175,7 +178,8 @@ module Reports::ReportFactory
       report.end_section
       report.add_result(validation_set, 
         [:validation_uri, :validation_report_uri]+VAL_ATTR_CV+VAL_ATTR_CLASS-[:num_folds, :dataset_uri, :algorithm_uri],
-        "Results","Results")
+        "Results","Results") if 
+        (cv_set.unique_value(:num_folds).to_i < cv_set.unique_value(:num_instances).to_i)
     when "regression"
       report.add_result(cv_set, [:crossvalidation_uri]+VAL_ATTR_CV+VAL_ATTR_REGR-[:crossvalidation_fold],res_titel, res_titel, res_text)
       report.add_section("Plots")
@@ -189,12 +193,14 @@ module Reports::ReportFactory
       report.end_section
       report.add_result(validation_set, 
         [:validation_uri, :validation_report_uri]+VAL_ATTR_CV+VAL_ATTR_REGR-[:num_folds, :dataset_uri, :algorithm_uri], 
-        "Results","Results")
+        "Results","Results") if 
+        (cv_set.unique_value(:num_folds).to_i < cv_set.unique_value(:num_instances).to_i)
     end
     task.progress(90) if task
       
-    report.add_result(validation_set, Validation::ALL_PROPS, "All Results", "All Results")
-    report.add_predictions( validation_set ) #, [:crossvalidation_fold] )
+    report.add_result(validation_set, Validation::ALL_PROPS, "All Results", "All Results") if
+      (cv_set.unique_value(:num_folds).to_i < cv_set.unique_value(:num_instances).to_i)
+    report.add_predictions( validation_set, true )
     task.progress(100) if task
     report
   end
diff --git a/report/report_persistance.rb b/report/report_persistance.rb
index e02387f..ccdebad 100755
--- a/report/report_persistance.rb
+++ b/report/report_persistance.rb
@@ -200,6 +200,7 @@ module Reports
     index :report_type
     index :validation_uris
     index :crossvalidation_uris
+    index :algorithm_uris
     
     attr_accessor :subjectid
     
diff --git a/report/validation_access.rb b/report/validation_access.rb
index aaa7bdc..e2a3978 100755
--- a/report/validation_access.rb
+++ b/report/validation_access.rb
@@ -145,20 +145,35 @@ class Reports::ValidationDB
   end
 
   def test_feature_dataset_uri(validation, subjectid)
-    m = OpenTox::Model::Generic.find(validation.model_uri, subjectid)
-    feat_gen = nil
-    m.metadata[OT.parameters].each do |h|
-      if h[DC.title] and h[DC.title]=~/feature_generation/ and h[OT.paramValue]
-        feat_gen = h[OT.paramValue]
+    training_features = Lib::DatasetCache.find( training_feature_dataset_uri(validation,subjectid), subjectid )
+    test_dataset = Lib::DatasetCache.find( validation.test_dataset_uri, subjectid )
+    features_found = true 
+    training_features.features.keys.each do |f|
+      unless test_dataset.features.keys.include?(f)
+        features_found = false
+        LOGGER.debug "training-feature are not in test-datset #{f}"
         break
       end
-    end if m  and m.metadata[OT.parameters]
-    raise "no feature creation alg found" unless feat_gen
-    feat_gen = File.join(feat_gen,"match") if feat_gen=~/fminer/
-    uri = OpenTox::RestClientWrapper.post(feat_gen,{:subjectid => subjectid,
-      :feature_dataset_uri=>training_feature_dataset_uri(validation,subjectid),
-      :dataset_uri=>validation.test_dataset_uri})
-    @@tmp_resources << uri
+    end
+    if features_found
+      LOGGER.debug "all training-features found in test-datset"
+      uri = test_dataset.uri
+    else
+      m = OpenTox::Model::Generic.find(validation.model_uri, subjectid)
+      feat_gen = nil
+      m.metadata[OT.parameters].each do |h|
+        if h[DC.title] and h[DC.title]=~/feature_generation/ and h[OT.paramValue]
+          feat_gen = h[OT.paramValue]
+          break
+        end
+      end if m  and m.metadata[OT.parameters]
+      raise "no feature creation alg found" unless feat_gen
+      feat_gen = File.join(feat_gen,"match") if feat_gen=~/fminer/
+      uri = OpenTox::RestClientWrapper.post(feat_gen,{:subjectid => subjectid,
+        :feature_dataset_uri=>training_feature_dataset_uri(validation,subjectid),
+        :dataset_uri=>validation.test_dataset_uri})
+      @@tmp_resources << uri
+    end
     uri
   end