RDF/XML download disabled, QMRF report generation enabled

4 files changed, 55 insertions, 85 deletions

diff --git a/application.rb b/application.rb
index 9616841..7a18fd5 100644
--- a/application.rb
+++ b/application.rb
@@ -58,13 +58,6 @@ get '/model/:id/:view/?' do
 		    haml :model, :locals=>{:model=>model}, :layout => false
 		  when /validation/
         haml :validation, :locals=>{:model=>model}, :layout => false
-				#if model.type == "classification"
-					#haml :classification_validation, :locals=>{:model=>model}, :layout => false
-				#elsif model.type == "regression"
-					#haml :regression_validation, :locals=>{:model=>model}, :layout => false
-				#else
-					#return "Unknown model type '#{model.type}'"
-				#end
 		  else
 				return "unable to render model: id #{params[:id]}, view #{params[:view]}"
 		end
diff --git a/model.rb b/model.rb
index 99d6ab3..da12f0b 100644
--- a/model.rb
+++ b/model.rb
@@ -1,15 +1,25 @@
 class ToxCreateModel
 
 	include DataMapper::Resource
+
 	property :id, Serial
 	property :name, String, :length => 255
-	property :uri, String, :length => 255
+	property :warnings, Text, :length => 2**32-1 
+	property :type, String
+	property :created_at, DateTime
+
 	property :task_uri, String, :length => 255
+	property :uri, String, :length => 255
+
 	property :validation_task_uri, String, :length => 255
 	property :validation_uri, String, :length => 255
+
 	property :validation_report_task_uri, String, :length => 255
 	property :validation_report_uri, String, :length => 255
-	property :warnings, Text, :length => 2**32-1 
+
+	property :validation_qmrf_task_uri, String, :length => 255
+	property :validation_qmrf_uri, String, :length => 255
+
 	property :nr_compounds, Integer
 	property :nr_predictions, Integer
 	property :true_positives, Integer
@@ -23,8 +33,6 @@ class ToxCreateModel
 	property :r_square, Float
 	property :root_mean_squared_error, Float
 	property :mean_absolute_error, Float
-	property :type, String
-	property :created_at, DateTime
 
 	def status
 		#begin
@@ -50,6 +58,14 @@ class ToxCreateModel
 		end
 	end
 
+	def validation_qmrf_status
+		begin
+			RestClient.get(File.join(@validation_qmrf_task_uri, 'hasStatus')).body
+		rescue
+			"Service offline"
+		end
+	end
+
 	def algorithm
 		begin
 			RestClient.get(File.join(@uri, 'algorithm')).body
@@ -74,64 +90,6 @@ class ToxCreateModel
 		end
 	end
 
-=begin
-	def classification_validation
-		begin
-			uri = File.join(@validation_uri, 'statistics')
-			yaml = RestClient.get(uri).body
-			v = YAML.load(yaml)
-			tp=0; tn=0; fp=0; fn=0; n=0
-			v[:classification_statistics][:confusion_matrix][:confusion_matrix_cell].each do |cell|
-				if cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "true"
-					tp = cell[:confusion_matrix_value]
-					n += tp
-				elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "false"
-					tn = cell[:confusion_matrix_value]
-					n += tn
-				elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "true"
-					fn = cell[:confusion_matrix_value]
-					n += fn
-				elsif cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "false"
-					fp = cell[:confusion_matrix_value]
-					n += fp
-				end
-			end
-      @nr_predictions = n
-      @true_positives = tp
-      @false_positives = fp
-      @true_negatives = tn
-      @false_negatives = fn
-      @correct_predictions = 100*(tp+tn).to_f/n
-      @weighted_area_under_roc = v[:classification_statistics][:weighted_area_under_roc].to_f
-      @sensitivity = tp.to_f/(tp+fn)
-      @specificity = tn.to_f/(tn+fp)
-      save
-				#:correct_predictions => sprintf("%.2f", 100*(tp+tn).to_f/n),
-				#:weighted_area_under_roc => sprintf("%.3f", v[:classification_statistics][:weighted_area_under_roc].to_f),
-				#:sensitivity => sprintf("%.3f", tp.to_f/(tp+fn)),
-				#:specificity => sprintf("%.3f", tn.to_f/(tn+fp))
-			#}
-		rescue
-			"Service offline"
-		end
-	end
-
-	def regression_validation
-		begin
-			uri = File.join(@validation_uri, 'statistics')
-			yaml = RestClient.get(uri).body
-			v = YAML.load(yaml)
-      @nr_predictions = v[:num_instances] - v[:num_unpredicted]
-      @r_square = v[:regression_statistics][:r_square]
-      @root_mean_squared_error = v[:regression_statistics][:root_mean_squared_error]
-      @mean_absolute_error = v[:regression_statistics][:mean_absolute_error]
-      save
-		rescue
-			"Service offline"
-		end
-	end
-=end
-
   def process
 
     if @uri.nil? and status == "Completed"
@@ -148,13 +106,20 @@ class ToxCreateModel
 
 		elsif @validation_uri.nil? and validation_status == "Completed"
 			begin
+
 				update :validation_uri => RestClient.get(File.join(@validation_task_uri, 'resultURI')).body
 				LOGGER.debug "Validation URI: #{@validation_uri}"
+
 				update :validation_report_task_uri => RestClient.post(File.join(@@config[:services]["opentox-validation"],"/report/crossvalidation"), :validation_uris => @validation_uri).body
 				LOGGER.debug "Validation Report Task URI: #{@validation_report_task_uri}"
+
+				update :validation_qmrf_task_uri => RestClient.post(File.join(@@config[:services]["opentox-validation"],"/reach_report/qmrf"), :model_uri => @uri).body
+				LOGGER.debug "QMRF Report Task URI: #{@validation_qmrf_task_uri}"
+
         uri = File.join(@validation_uri, 'statistics')
         yaml = RestClient.get(uri).body
         v = YAML.load(yaml)
+
         case type
         when "classification"
           tp=0; tn=0; fp=0; fn=0; n=0
@@ -192,15 +157,25 @@ class ToxCreateModel
 				LOGGER.warn "Cannot create Validation Report Task #{@validation_report_task_uri} for  Validation URI #{@validation_uri} from Task #{@validation_task_uri}"
 			end
 
-		elsif @validation_report_uri.nil? and validation_report_status == "Completed"
-			begin
-				LOGGER.debug File.join(@validation_report_task_uri, 'resultURI')
-				LOGGER.debug "Report URI: "+RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
-				update :validation_report_uri => RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
-			rescue
-				LOGGER.warn "Cannot create Validation Report for  Task URI #{@validation_report_task_uri} "
-			end
-		end
+		else
+
+      if @validation_report_uri.nil? and validation_report_status == "Completed"
+        begin
+          update :validation_report_uri => RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
+        rescue
+          LOGGER.warn "Cannot create Validation Report for  Task URI #{@validation_report_task_uri} "
+        end
+      end
+
+      if @validation_qmrf_uri.nil? and validation_qmrf_status == "Completed"
+        begin
+          update :validation_qmrf_uri => RestClient.get(File.join(@validation_qmrf_task_uri, 'resultURI')).body
+        rescue
+          LOGGER.warn "Cannot create QMRF Report for  Task URI #{@validation_qmrf_task_uri} "
+        end
+      end
+
+    end
 
   end
 
diff --git a/views/model.haml b/views/model.haml
index 454423a..0c8ea8f 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -42,20 +42,22 @@
         %dd
           %a{:href => "#{model.training_dataset}.xls"} Excel sheet
           ,
-          %a{:href => "#{model.training_dataset}.rdf"} RDF/XML
-          %em (experts) ,
+          -#%a{:href => "#{model.training_dataset}.rdf"} RDF/XML
+          -#%em (experts) ,
           %a{:href => "#{model.training_dataset}.yaml"} YAML
           %em  (experts)
         %dt Feature dataset:
         %dd
-          %a{:href => "#{model.feature_dataset}.rdf"} RDF/XML
-          ,
+          -#%a{:href => "#{model.feature_dataset}.rdf"} RDF/XML
+          -#,
           %a{:href => "#{model.feature_dataset}.yaml"} YAML
           %em  (experts, dataset too large for Excel)
         %dt Model:
         %dd
-          %a{:href => "#{model.uri}.rdf"} RDF/XML
-          ,
+          -#%a{:href => "#{model.uri}.rdf"} RDF/XML
+          -#,
+          - unless model.validation_qmrf_uri.nil?
+            %a{:href => File.join(model.validation_qmrf_uri,"editor")} QMRF Editor, 
           %a{:href => "#{model.uri}.yaml"} YAML
           %em  (experts, models cannot be represented in Excel)
         = haml :validation, :locals=>{:model=>model}, :layout => false     
diff --git a/views/style.sass b/views/style.sass
index ea9e65a..5f362a3 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -85,7 +85,7 @@ body
           font-weight: bold
           color: $fg_color
         label
-          width: 25em
+          width: 28em
           display: block
           float: left
         br