add regression plot, rescue not found errors, ..

11 files changed, 124 insertions, 34 deletions

diff --git a/application.rb b/application.rb
index 3b0dc71..236280c 100644
--- a/application.rb
+++ b/application.rb
@@ -4,15 +4,6 @@ gem 'opentox-ruby-api-wrapper', '= 1.4.4.4'
   require lib
 end
 
-require 'active_record'
-ActiveRecord::Base.establish_connection(  
-   :adapter => @@config[:database][:adapter],
-   :host => @@config[:database][:host],
-   :database => @@config[:database][:database],
-   :username => @@config[:database][:username],
-   :password => @@config[:database][:password]
-) 
-       
 #unless(defined? LOGGER)
   #LOGGER = Logger.new(STDOUT)
   #LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
diff --git a/lib/predictions.rb b/lib/predictions.rb
index c01dcdc..a183534 100644
--- a/lib/predictions.rb
+++ b/lib/predictions.rb
@@ -456,6 +456,10 @@ module Lib
     def num_instances
       return @predicted_values.size
     end
+    
+    def predicted_values
+      @predicted_values
+    end
   
     def predicted_value(instance_index)
       if @is_classification
@@ -465,6 +469,10 @@ module Lib
       end
     end
     
+    def actual_values
+      @actual_values
+    end
+    
     def actual_value(instance_index)
       if @is_classification
         @actual_values[instance_index]==nil ? nil : @prediction_feature_values[@actual_values[instance_index]]
diff --git a/lib/validation_db.rb b/lib/validation_db.rb
index 17e8f74..a3c9593 100644
--- a/lib/validation_db.rb
+++ b/lib/validation_db.rb
@@ -5,6 +5,15 @@ end
 
 require "lib/merge.rb"
 
+require 'active_record'
+ActiveRecord::Base.establish_connection(  
+   :adapter => @@config[:database][:adapter],
+   :host => @@config[:database][:host],
+   :database => @@config[:database][:database],
+   :username => @@config[:database][:username],
+   :password => @@config[:database][:password]
+) 
+
 module Lib
 
   VAL_PROPS_GENERAL = [ :id, :uri, :model_uri, :algorithm_uri, :training_dataset_uri, :prediction_feature,
@@ -39,7 +48,7 @@ module Lib
   VAL_REGR_PROPS = [ :root_mean_squared_error, :mean_absolute_error, :r_square, :target_variance_actual, :target_variance_predicted ]
   
   CROSS_VAL_PROPS = [:dataset_uri, :num_folds, :stratified, :random_seed]
-  CROSS_VAL_PROPS_REDUNDANT = [:algorithm_uri] + CROSS_VAL_PROPS 
+  CROSS_VAL_PROPS_REDUNDANT = [:algorithm_uri, :created_at] + CROSS_VAL_PROPS 
   
   ALL_PROPS = VAL_PROPS + VAL_CV_PROPS + VAL_CLASS_PROPS_EXTENDED + VAL_REGR_PROPS + CROSS_VAL_PROPS
 
diff --git a/report/environment.rb b/report/environment.rb
index 2cb03a6..c64d40d 100644
--- a/report/environment.rb
+++ b/report/environment.rb
@@ -11,6 +11,8 @@ require 'fileutils'
 require 'mime/types'
 require 'ruby-plot'
 
+gem 'ruby-plot', '= 0.0.2'
+
 module Reports
 end
 
diff --git a/report/plot_factory.rb b/report/plot_factory.rb
index e1fefeb..daaba52 100644
--- a/report/plot_factory.rb
+++ b/report/plot_factory.rb
@@ -13,7 +13,23 @@ end
 
 module Reports
   
-  module PlotFactory 
+  module PlotFactory
+    
+    def self.create_regression_plot( out_file, validation_set )
+      
+      LOGGER.debug "Creating regression plot, out-file:"+out_file.to_s
+      
+      names = []
+      x = []
+      y = []
+      validation_set.validations.each do |v|
+        names << v.algorithm_uri
+        x << v.get_predictions.predicted_values
+        y << v.get_predictions.actual_values
+      end
+      
+      RubyPlot::plot_points(out_file, "Regression plot", "Predicted values", "Actual values", names, x, y )
+    end
     
     # creates a roc plot (result is plotted into out_file)
     # * if (split_set_attributes == nil?)
diff --git a/report/report_factory.rb b/report/report_factory.rb
index dcc7b13..f62803d 100644
--- a/report/report_factory.rb
+++ b/report/report_factory.rb
@@ -61,6 +61,7 @@ module Reports::ReportFactory
       report.add_section_confusion_matrix(val)
     else #regression
       report.add_section_result(validation_set, VAL_ATTR_TRAIN_TEST + VAL_ATTR_REGR, "Results", "Results")
+      report.add_section_regression_plot(validation_set)
     end
     
     report.add_section_result(validation_set, Lib::ALL_PROPS, "All Results", "All Results")
@@ -154,6 +155,7 @@ module Reports::ReportFactory
           #regression
           report.add_section_result(validation_set,[:algorithm_uri]+VAL_ATTR_REGR,"Results","Results")
           report.add_section_bar_plot(validation_set,nil,:algorithm_uri,VAL_ATTR_BAR_PLOT_REGR, "bar-plot.svg")
+          report.add_section_regression_plot(validation_set)
           
           #report.add_section_result(merged, VAL_ATTR_CV+VAL_ATTR_REGR-[:crossvalidation_fold],"Mean Results","Mean Results")
           #report.add_section_result(validation_set, VAL_ATTR_CV+VAL_ATTR_REGR-[:num_folds], "Results","Results")
@@ -275,6 +277,39 @@ class Reports::ReportContent
     @xml_report.add_table(section_confusion, table_title, 
       Reports::XMLReportUtil::create_confusion_matrix( validation.confusion_matrix ), false)
   end
+  
+  def add_section_regression_plot( validation_set,
+                            split_set_attribute = nil,
+                            plot_file_name="regression-plot.svg", 
+                            section_title="Regression Plot",
+                            section_text=nil,
+                            image_title=nil,
+                            image_caption=nil)
+                            
+    section_text = "This section contains the regression plot." unless section_text
+    image_title = "Regression plot" unless image_title
+    
+    section_regr = @xml_report.add_section(@xml_report.get_root_element, section_title)
+    prediction_set = validation_set.collect{ |v| v.get_predictions }
+        
+    if prediction_set.size>0
+      
+      section_text += "\nWARNING: regression plot information not available for all validation results" if prediction_set.size!=validation_set.size
+      @xml_report.add_paragraph(section_regr, section_text) if section_text
+      begin
+        plot_file_path = add_tmp_file(plot_file_name)
+        Reports::PlotFactory.create_regression_plot( plot_file_path, prediction_set )
+        @xml_report.add_imagefigure(section_regr, image_title, plot_file_name, "SVG", image_caption)
+      rescue RuntimeError => ex
+        LOGGER.error("Could not create regression plot: "+ex.message)
+        rm_tmp_file(plot_file_name)
+        @xml_report.add_paragraph(section_regr, "could not create regression plot: "+ex.message)
+      end  
+    else
+      @xml_report.add_paragraph(section_regr, "No prediction info for regression available.")
+    end
+    
+  end
 
   def add_section_roc_plot( validation_set,
                             class_value = nil,
diff --git a/report/report_test.rb b/report/report_test.rb
index d580045..872bed0 100644
--- a/report/report_test.rb
+++ b/report/report_test.rb
@@ -38,13 +38,13 @@ class Reports::ApplicationTest < Test::Unit::TestCase
     #post 'http://ot.validation.de/report/crossvalidation',:validation_uris=>"http://ot.validation.de/crossvalidation/1"
     #uri = last_response.body.to_s
     
-    val_uris = ["http://ot.validation.de/crossvalidation/32"] #,"http://ot.validation.de/crossvalidation/8" ]
+    val_uris = ["http://localhost/validation/64","http://localhost/validation/65" ]
     
-    post 'http://ot.validation.de/report/crossvalidation',:validation_uris=>val_uris.join("\n")
+    post '/report/algorithm_comparison',:validation_uris=>val_uris.join("\n")
     uri = wait_for_task(last_response.body.to_s)
     puts uri
     id = uri.squeeze("/").split("/")[-1]
-    get '/report/crossvalidation/'+id,nil,'HTTP_ACCEPT' => "text/html" 
+    get '/report/validation/'+id,nil,'HTTP_ACCEPT' => "text/html" 
     puts uri
     
     #rep = Reports::ReportService.new("http://some.location")
diff --git a/test/test_examples_util.rb b/test/test_examples_util.rb
index 49e0336..7fcb1ec 100644
--- a/test/test_examples_util.rb
+++ b/test/test_examples_util.rb
@@ -114,6 +114,7 @@ module ValidationExamples
         @validation_uri = Util.validation_post '/'+validation_type, get_params
       rescue => ex
         @validation_error = ex.message
+        LOGGER.error ex.message
       end
     end
     
diff --git a/validation/validation_application.rb b/validation/validation_application.rb
index 13dc26d..9abf2d4 100644
--- a/validation/validation_application.rb
+++ b/validation/validation_application.rb
@@ -23,7 +23,11 @@ end
 
 get '/crossvalidation/:id' do
   LOGGER.info "get crossvalidation with id "+params[:id].to_s
-  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.find(params[:id])
+  begin
+    crossvalidation = Validation::Crossvalidation.find(params[:id])
+  rescue ActiveRecord::RecordNotFound => ex
+    halt 404, "Crossvalidation '#{params[:id]}' not found."
+  end
   
   case request.env['HTTP_ACCEPT'].to_s
   when "application/rdf+xml"
@@ -41,28 +45,40 @@ end
 delete '/crossvalidation/:id/?' do
   LOGGER.info "delete crossvalidation with id "+params[:id].to_s
   content_type "text/plain"
-  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.find(params[:id])
-  crossvalidation.delete
+  begin
+    crossvalidation = Validation::Crossvalidation.find(params[:id])
+  rescue ActiveRecord::RecordNotFound => ex
+    halt 404, "Crossvalidation '#{params[:id]}' not found."
+  end
+  Validation::Crossvalidation.delete(params[:id])
 end
 
 get '/crossvalidation/:id/validations' do
   LOGGER.info "get all validations for crossvalidation with id "+params[:id].to_s
-  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.find(params[:id])
+  begin
+    crossvalidation = Validation::Crossvalidation.find(params[:id])
+  rescue ActiveRecord::RecordNotFound => ex
+    halt 404, "Crossvalidation '#{params[:id]}' not found."
+  end
   content_type "text/uri-list"
-  Validation::Validation.all(:crossvalidation_id => params[:id]).collect{ |v| v.uri.to_s }.join("\n")+"\n"
+  Validation::Validation.find( :all, :conditions => { :crossvalidation_id => params[:id] } ).collect{ |v| v.uri.to_s }.join("\n")+"\n"
 end
 
 
 get '/crossvalidation/:id/statistics' do
   LOGGER.info "get merged validation-result for crossvalidation with id "+params[:id].to_s
-  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Validation::Crossvalidation.find(params[:id])
+  begin
+    crossvalidation = Validation::Crossvalidation.find(params[:id])
+  rescue ActiveRecord::RecordNotFound => ex
+    halt 404, "Crossvalidation '#{params[:id]}' not found."
+  end
   
   Lib::MergeObjects.register_merge_attributes( Validation::Validation,
-    Lib::VAL_MERGE_AVG,Lib::VAL_MERGE_SUM,Lib::VAL_MERGE_GENERAL) unless 
+    Lib::VAL_MERGE_AVG,Lib::VAL_MERGE_SUM,Lib::VAL_MERGE_GENERAL-[:uri]) unless 
       Lib::MergeObjects.merge_attributes_registered?(Validation::Validation)
   
-  v = Lib::MergeObjects.merge_array_objects( Validation::Validation.all(:crossvalidation_id => params[:id]) )
-  v.uri = nil
+  v = Lib::MergeObjects.merge_array_objects( Validation::Validation.find( :all, :conditions => { :crossvalidation_id => params[:id] } ) )
+  v.validation_uri = nil
   v.created_at = nil
   v.id = nil
   content_type "text/x-yaml"
@@ -104,8 +120,12 @@ end
 
 get '/:id' do
   LOGGER.info "get validation with id "+params[:id].to_s+" '"+request.env['HTTP_ACCEPT'].to_s+"'"
-  halt 404, "Validation '#{params[:id]}' not found." unless validation = Validation::Validation.find(params[:id])
-  
+  begin
+    validation = Validation::Validation.find(params[:id])
+  rescue ActiveRecord::RecordNotFound => ex
+    halt 404, "Validation '#{params[:id]}' not found."
+  end
+
   case request.env['HTTP_ACCEPT'].to_s
   when "application/rdf+xml"
     content_type "application/rdf+xml"
@@ -195,10 +215,13 @@ post '/create_validation' do
   halt 202,task_uri
 end
 
-
 get '/:id/:attribute' do
   LOGGER.info "access validation attribute "+params.inspect
-  halt 404, "Validation #{params[:id]} not found." unless validation = Validation::Validation.find(params[:id])
+  begin
+    validation = Validation::Validation.find(params[:id])
+  rescue ActiveRecord::RecordNotFound => ex
+    halt 404, "Validation '#{params[:id]}' not found."
+  end
   begin
     raise unless validation.attribute_loaded?(params[:attribute])
   rescue
@@ -210,7 +233,11 @@ end
 
 delete '/:id' do
   LOGGER.info "delete validation with id "+params[:id].to_s
-  halt 404, "Validation #{params[:id]} not found." unless validation = Validation::Validation.find(params[:id])
+  begin
+    validation = Validation::Validation.find(params[:id])
+  rescue ActiveRecord::RecordNotFound => ex
+    halt 404, "Validation '#{params[:id]}' not found."
+  end
   content_type "text/plain"
-  validation.delete
+  Validation::Validation.delete(params[:id])
 end
\ No newline at end of file
diff --git a/validation/validation_format.rb b/validation/validation_format.rb
index 357d96e..97d9eed 100644
--- a/validation/validation_format.rb
+++ b/validation/validation_format.rb
@@ -37,7 +37,7 @@ module Validation
         h[:crossvalidation_info] = cv
       end
       if classification_statistics 
-        class_stats = YAML.load(classification_statistics.to_s)
+        class_stats = ((classification_statistics.is_a?(Hash)) ? classification_statistics : YAML.load(classification_statistics.to_s))
         clazz = {}
         Lib::VAL_CLASS_PROPS_SINGLE.each{ |p| clazz[p] = class_stats[p] }
         
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index 1e3908a..3fa3056 100644
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -17,13 +17,13 @@ class ValidationTest < Test::Unit::TestCase
   def test_it
     $test_case = self
 
-    #get "/1"
-    #puts last_response.body
+   # get "/crossvalidation/1/statistics"
+   # puts last_response.body
     
 #    post "/test_validation",:select=>"6d" #,:report=>"yes,please"
 #    puts last_response.body
     
-    run_test("2b")
+    run_test("3a")
  
     #puts Nightly.build_nightly("1", false)
     
@@ -38,11 +38,12 @@ class ValidationTest < Test::Unit::TestCase
   def run_test(select)
     validationExamples = ValidationExamples.select(select)
     validationExamples.each do |vv|
-      vv.each do |v|  
+      vv.each do |v| 
         ex = v.new
         ex.upload_files
         ex.check_requirements
         ex.validate
+        LOGGER.debug "validation done "+ex.validation_uri.to_s
         ex.report
       end
     end