new branch val_exp

3 files changed, 92 insertions, 16 deletions

diff --git a/validation/validation_application.rb b/validation/validation_application.rb
index 1bc55f6..89f47e0 100755
--- a/validation/validation_application.rb
+++ b/validation/validation_application.rb
@@ -9,8 +9,8 @@ require 'validation/validation_service.rb'
 helpers do
   def check_stratified(params)
     params[:stratified] = "false" unless params[:stratified]
-    raise OpenTox::BadRequestError.new "stratified != true|false|super, is #{params[:stratified]}" unless
-      params[:stratified]=~/true|false|super/
+    raise OpenTox::BadRequestError.new "stratified != true|false|super|anti, is #{params[:stratified]}" unless
+      params[:stratified]=~/true|false|super|anti/
   end
 end
 
@@ -22,7 +22,7 @@ get '/crossvalidation/?' do
     params[:algorithm] = model.metadata[OT.algorithm]
     params[:dataset] = model.metadata[OT.trainingDataset]
   end
-  uri_list = Lib::OhmUtil.find( Validation::Crossvalidation, params ).sort.collect{|v| v.crossvalidation_uri}.join("\n") + "\n"
+  uri_list = Lib::OhmUtil.find( Validation::Crossvalidation, params ).sort.delete_if{|v| !v.finished}.collect{|v| v.crossvalidation_uri}.join("\n") + "\n"
   if request.env['HTTP_ACCEPT'] =~ /text\/html/
     related_links = 
       "Single validations:             "+url_for("/",:full)+"\n"+
@@ -204,6 +204,18 @@ get '/crossvalidation/:id/statistics' do
   end
 end
 
+get '/crossvalidation/:id/statistics/uri' do
+  uri = Validation::Validation.find( :crossvalidation_id => params[:id], :validation_type => "crossvalidation_statistics" ).first.validation_uri
+  case request.env['HTTP_ACCEPT'].to_s
+  when /text\/html/
+    content_type "text/html"
+    OpenTox.text_to_html uri
+  else
+    content_type "text/uri-list"
+    uri
+  end  
+end
+
 get '/crossvalidation/:id/statistics/probabilities' do
   
   LOGGER.info "get crossvalidation statistics for crossvalidation with id "+params[:id].to_s
@@ -273,7 +285,7 @@ end
 get '/?' do
   
   LOGGER.info "list all validations, params: "+params.inspect
-  uri_list = Lib::OhmUtil.find( Validation::Validation, params ).sort.collect{|v| v.validation_uri}.join("\n") + "\n"
+  uri_list = Lib::OhmUtil.find( Validation::Validation, params ).sort.delete_if{|v| !v.finished}.collect{|v| v.validation_uri}.join("\n") + "\n"
   if request.env['HTTP_ACCEPT'] =~ /text\/html/
     related_links = 
       "To perform a validation:\n"+
@@ -619,6 +631,58 @@ get '/:id/probabilities' do
 end 
 
 
+get '/:id/viz' do
+  
+  begin
+    validation = Validation::Validation.get(params[:id])
+  rescue ActiveRecord::RecordNotFound => ex
+    raise OpenTox::NotFoundError.new("Validation '#{params[:id]}' not found.")
+  end
+  
+  m = OpenTox::Model::Generic.find(validation.model_uri)
+  predicted_feature = m.predicted_variable(nil)
+  actual_feature = validation.prediction_feature
+  
+  d = OpenTox::Dataset.create
+  
+  test = OpenTox::Dataset.find(validation.test_dataset_uri)
+  training = OpenTox::Dataset.find(validation.training_dataset_uri)
+  prediction = OpenTox::Dataset.find(validation.prediction_dataset_uri)
+  
+  dataset_feature = "http://dataset"
+  d.add_feature(dataset_feature)
+  correct_classified_feature = "http://correct-classified"
+  d.add_feature(correct_classified_feature)
+  predicted_nice_feature = "http://predicted"
+  d.add_feature(predicted_nice_feature)
+    
+  [training, test].each do |data|
+    data.compounds.each do |c|
+      d.add_compound(c)
+      d.add(c,dataset_feature,data==training ? "training" : "test")
+      data.features.each do |f,m|
+        d.add_feature(f,m)
+        data.data_entries[c][f].each do |v|
+          d.add(c,f,v)
+        end if data.data_entries[c][f]
+      end
+    end
+  end
+  
+  prediction.compounds.each do |c|
+    if prediction.data_entries[c][predicted_feature]
+      p = prediction.data_entries[c][predicted_feature]
+      a = d.data_entries[c][actual_feature]
+      [p,a].each do |v|
+        raise p.class.to_s+" "+p.inspect unless p.is_a?(Array) and p.size==1
+      end
+      d.add(c,predicted_nice_feature,p[0])
+      d.add(c,correct_classified_feature,p[0]==a[0] ? "correct" : "miss")
+    end 
+  end
+  d.to_csv
+end
+
 #get '/:id/predictions' do
 #  LOGGER.info "get validation predictions "+params.inspect
 #  begin
diff --git a/validation/validation_service.rb b/validation/validation_service.rb
index 8c8b11f..d30c7d2 100755
--- a/validation/validation_service.rb
+++ b/validation/validation_service.rb
@@ -446,6 +446,8 @@ module Validation
       
       meta = { DC.creator => self.crossvalidation_uri }
       case stratified
+      when "anti"
+         raise "anti-stratification not yet supported for cv"
       when "false"
         if self.loo=="true"
           shuffled_compounds = orig_dataset.compounds
@@ -631,16 +633,16 @@ module Validation
       meta = { DC.creator => $url_provider.url_for('/training_test_split',:full) }
       
       case stratified
-      when /true|super/
+      when /true|super|anti/
         if stratified=="true"
           raise OpenTox::BadRequestError.new "prediction feature required for stratified splits" unless prediction_feature
           features = [prediction_feature]
         else
-          LOGGER.warn "prediction feature is ignored for super-stratified splits" if prediction_feature
+          LOGGER.warn "prediction feature is ignored for super- or anti-stratified splits" if prediction_feature
           features = nil
         end
         r_util = OpenTox::RUtil.new 
-        train, test = r_util.stratified_split( orig_dataset, meta, "NA", split_ratio, @subjectid, random_seed, features )
+        train, test = r_util.stratified_split( orig_dataset, meta, "NA", split_ratio, @subjectid, random_seed, features, stratified=="anti" )
         r_util.quit_r
         result = {:training_dataset_uri => train.uri, :test_dataset_uri => test.uri}
       when "false"
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index 70f3ca4..0001076 100755
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -84,9 +84,14 @@ class ValidationTest < Test::Unit::TestCase
 #      post "/report/method_comparison",
 #        {:validation_uris=>"http://local-ot/validation/389,http://local-ot/validation/390,http://local-ot/validation/391,http://local-ot/validation/392",
 #         :identifier=>"split1,split1,split2,split2"}
-
-              
-      #post "/report/validation",{:validation_uris=>"http://local-ot/validation/171"}
+      
+      get '15709/viz'
+      puts last_response.body
+      exit
+        
+      post "/report/validation",{:validation_uris=>"http://local-ot/validation/15647"}
+      exit
+      
       #post "/report/validation",{:validation_uris=>"http://local-ot/validation/389"}
       
       #dataset_uri = OpenTox::Dataset.create_from_csv_file(File.new("data/EPAFHM.csv").path, nil).uri
@@ -94,9 +99,13 @@ class ValidationTest < Test::Unit::TestCase
       
 #      #dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/603306?feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/764036"
 #      #dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/603204"
-#      post "/plain_training_test_split",{:dataset_uri=>dataset_uri, :stratified=>"true", :split_ratio=>0.3}
-#      puts last_response.body
-#      uri = last_response.body
+      
+      dataset_uri = "http://local-ot/dataset/9264"
+      post "/plain_training_test_split",{:dataset_uri=>dataset_uri, :stratified=>"false", :split_ratio=>0.5}
+      puts last_response.body
+      uri = last_response.body
+      exit
+      
 #      rep = wait_for_task(uri)
 #      puts rep
       #OpenTox::RestClientWrapper.post("http://opentox.informatik.uni-freiburg.de/validation/plain_training_test_split",
@@ -131,7 +140,8 @@ class ValidationTest < Test::Unit::TestCase
       #get 'crossvalidation/189/statistics'
       #puts last_response.body
 
-      #run_test("13a")       
+      run_test("1a")
+      #run_test("13a",:validation_uri=>"http://local-ot/validation/1568")  
     #  run_test("1a",:validation_uri=>"http://local-ot/validation/513")
 
       #get '/crossvalidation/79/predictions',nil,'HTTP_ACCEPT' => "application/x-yaml"
@@ -178,8 +188,8 @@ class ValidationTest < Test::Unit::TestCase
       #  :random_seed => 1
       #  })
       
-      #run_test("23a")
-      run_test("23a",{:validation_uri=>"http://local-ot/validation/crossvalidation/53"})
+      #run_test("3a")
+      #run_test("23a",{:validation_uri=>"http://local-ot/validation/crossvalidation/56"})
       #run_test("23a",{:validation_uri=>"http://local-ot/validation/crossvalidation/47"})
       #23a loo {:validation_uri=>"http://local-ot/validation/crossvalidation/47"})        
       #loo mit datasets auf ortona {:validation_uri=>"http://local-ot/validation/crossvalidation/46"}