initial version for quantitative features, some improvements suggested by david

19 files changed, 270 insertions, 389 deletions

diff --git a/application.rb b/application.rb
index 9f511e7..0bca96f 100644
--- a/application.rb
+++ b/application.rb
@@ -1,7 +1,7 @@
 ['rubygems', "haml", "sass", "rack-flash"].each do |lib|
 	require lib
 end
-gem "opentox-ruby-api-wrapper", "= 1.6.3"
+gem "opentox-ruby-api-wrapper", "= 1.6.4"
 require 'opentox-ruby-api-wrapper'
 gem 'sinatra-static-assets'
 require 'sinatra/static_assets'
@@ -49,21 +49,22 @@ end
 get '/model/:id/:view/?' do
   response['Content-Type'] = 'text/plain'
 	model = ToxCreateModel.get(params[:id])
-  model.process
-	model.save
 
   begin
+    model.process
+    model.save
     case params[:view]
       when "model"
 		    haml :model, :locals=>{:model=>model}, :layout => false
 		  when /validation/
-				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
+        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 d10b95f..99d6ab3 100644
--- a/model.rb
+++ b/model.rb
@@ -11,6 +11,18 @@ class ToxCreateModel
 	property :validation_report_uri, String, :length => 255
 	property :warnings, Text, :length => 2**32-1 
 	property :nr_compounds, Integer
+	property :nr_predictions, Integer
+	property :true_positives, Integer
+	property :false_positives, Integer
+	property :true_negatives, Integer
+	property :false_negatives, Integer
+	property :correct_predictions, Integer
+	property :weighted_area_under_roc, Float
+	property :sensitivity, Float
+	property :specificity, Float
+	property :r_square, Float
+	property :root_mean_squared_error, Float
+	property :mean_absolute_error, Float
 	property :type, String
 	property :created_at, DateTime
 
@@ -62,6 +74,7 @@ class ToxCreateModel
 		end
 	end
 
+=begin
 	def classification_validation
 		begin
 			uri = File.join(@validation_uri, 'statistics')
@@ -83,17 +96,21 @@ class ToxCreateModel
 					n += fp
 				end
 			end
-			{
-				:n => n,
-				:tp => tp,
-				:fp => fp,
-				:tn => tn,
-				:fn => fn, 
-				: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))
-			}
+      @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
@@ -104,10 +121,16 @@ class ToxCreateModel
 			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
 
@@ -129,6 +152,42 @@ class ToxCreateModel
 				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}"
+        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
+          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
+          update :nr_predictions => n
+          update :true_positives => tp
+          update :false_positives => fp
+          update :true_negatives => tn
+          update :false_negatives => fn
+          update :correct_predictions => 100*(tp+tn).to_f/n
+          update :weighted_area_under_roc => v[:classification_statistics][:weighted_area_under_roc].to_f
+          update :sensitivity => tp.to_f/(tp+fn)
+          update :specificity => tn.to_f/(tn+fp)
+        when "regression"
+          update :nr_predictions => v[:num_instances] - v[:num_unpredicted]
+          update :r_square => v[:regression_statistics][:r_square]
+          update :root_mean_squared_error => v[:regression_statistics][:root_mean_squared_error]
+          update :mean_absolute_error => v[:regression_statistics][:mean_absolute_error]
+        end
 			rescue
 				LOGGER.warn "Cannot create Validation Report Task #{@validation_report_task_uri} for  Validation URI #{@validation_uri} from Task #{@validation_task_uri}"
 			end
diff --git a/parser.rb b/parser.rb
index 8754531..8468cea 100644
--- a/parser.rb
+++ b/parser.rb
@@ -93,7 +93,7 @@ class Parser
 
 	def validate(smiles, act, row)
 		compound = OpenTox::Compound.new(:smiles => smiles)
-		if compound.inchi == ""
+		if compound.nil? or compound.inchi.nil? or compound.inchi == ""
 			@smiles_errors << "Row #{row}: " + [smiles,act].join(", ") 
 			return false
 		end
diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index 048bd46..d1ed490 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -80,7 +80,7 @@ $(function() {
   checkValidation = function() {
     var reload_id = "";
     $("input.model_validation_report").each(function(){
-        if($(this).val() != "Completed") {
+        if(!$(this).val().match(/Completed|Error/)) {
           reload_id = this.id.replace("model_validation_report_","");
           if(/^\d+$/.test(reload_id)) loadModel(reload_id, 'validation');
         };
diff --git a/views/classification.haml b/views/classification.haml
new file mode 100644
index 0000000..5c739cf
--- /dev/null
+++ b/views/classification.haml
@@ -0,0 +1,11 @@
+%dl#classification{ :style => "display: none;" }
+  %dt
+    Classification
+    (
+    = hide_link "#classification"
+    )
+  %dd 
+    Prediction of
+    %em qualitative
+    properties, e.g. to distinguish between toxic and non-toxic compounds
+
diff --git a/views/classification_validation.haml b/views/classification_validation.haml
index 26f0617..4a2d689 100644
--- a/views/classification_validation.haml
+++ b/views/classification_validation.haml
@@ -1,54 +1,33 @@
-%dl{:id => "model_validation_#{model.id}"}
-  %dt
-    Validation:
-    %input{ :id => "model_validation_report_#{model.id}", :type => "hidden", :value => "#{model.validation_report_status}", :class => "model_validation_report" }
-    - if model.validation_report_uri
-      %a{:href => model.validation_report_uri, :target => "_blank"} (more details)
-  %dd
-    - if model.validation_uri
-      - v = model.classification_validation
-      - if v == "Service offline"
-        = v
-      - else
-        %dl
-          %dt Number of predictions:
-          %dd= v[:n]
-          %dt Correct predictions:
-          %dd
-            = v[:correct_predictions]
-            = '%'
-          %dt
-            %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :target => "_blank"} Weighted area under ROC:
-          %dd 
-            = v[:weighted_area_under_roc]
-          %dt
-            %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :target => "_blank"} Specificity:
-          %dd= v[:specificity]
-          %dt
-            %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :target => "_blank"} Sensitivity:
-          %dd= v[:sensitivity]
-          %dt
-            %a{:href => "http://en.wikipedia.org/wiki/Confusion_matrix", :target => "_blank"} Confusion Matrix:
-          %dd
-            %table
-              %tr
-                %td{:colspan => 2, :rowspan => 2}
-                -#%td
-                %th{:colspan => 2} Measured
-              %tr
-                -#%td{:colspan => 2}
-                -#%th Predicted
-                %th{:bgcolor => "#CCD2DC"} active
-                %th{:bgcolor => "#CCD2DC"} inactive
-              %tr
-                %th{:rowspan => 2} Predicted
-                %th{:bgcolor => "#CCD2DC"} active
-                %td= v[:tp]
-                %td= v[:fp]
-              %tr
-                %th{:bgcolor => "#CCD2DC"} inactive
-                %td= v[:fn]
-                %td= v[:tn]
-    - else
-      = image_tag("/snake_transparent.gif") if model.validation_status == "Running"
-      %a{:href => model.validation_task_uri} #{model.validation_status}
+%dt Correct predictions:
+%dd
+  = sprintf("%.2f", model.correct_predictions)
+  = '%'
+%dt
+  %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :target => "_blank"} Weighted area under ROC:
+%dd 
+  = sprintf("%.3f", model.weighted_area_under_roc)
+%dt
+  %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :target => "_blank"} Specificity:
+%dd= sprintf("%.3f", model.specificity)
+%dt
+  %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :target => "_blank"} Sensitivity:
+%dd= sprintf("%.3f", model.sensitivity)
+%dt
+  %a{:href => "http://en.wikipedia.org/wiki/Confusion_matrix", :target => "_blank"} Confusion Matrix:
+%dd
+  %table
+    %tr
+      %td{:colspan => 2, :rowspan => 2}
+      %th{:colspan => 2} Measured
+    %tr
+      %th{:bgcolor => "#CCD2DC"} active
+      %th{:bgcolor => "#CCD2DC"} inactive
+    %tr
+      %th{:rowspan => 2} Predicted
+      %th{:bgcolor => "#CCD2DC"} active
+      %td= model.true_positives
+      %td= model.false_positives
+    %tr
+      %th{:bgcolor => "#CCD2DC"} inactive
+      %td= model.false_negatives
+      %td= model.true_negatives
diff --git a/views/create.haml b/views/create.haml
index 3cf05c1..20de401 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -4,13 +4,13 @@
     This service creates 
     %ul
       %li
-        %a{:href => 'http://lazar.in-silico.de'} lazar
-        %em classification
-        models (i.e. models that discriminate between toxic/nontoxic compounds) and
+        = toggle_link("#lazar_description","lazar")
+        %em= toggle_link("#classification","classification")
+        models and
       %li
-        %a{:href => 'http://lazar.in-silico.de'} lazar
-        %em regression
-        models (i.e. models that predict quantitative values, e.g. LC50's)
+        = toggle_link("#lazar_description","lazar")
+        %em= toggle_link("#regression","regression")
+        models 
     from your uploaded datasets. Further modelling algorithms will be added in future versions.
  
   %p
@@ -20,7 +20,7 @@
 
   %form{ :action => url_for('/upload'), :method => "post", :enctype => "multipart/form-data" }
     %fieldset
-      %label{:for => 'endpoint'} 1. Enter endpoint name and unit (for regression):
+      %label{:for => 'endpoint'} 1. Enter #{toggle_link("#endpoint_description","endpoint")} name and #{toggle_link("#unit","unit")} (for #{toggle_link("#regression","regression")}):
       %input{:type => 'text', :name => 'endpoint', :id => 'endpoint', :size => '50'}
       %br
       %label{:for => 'file'}
@@ -33,3 +33,9 @@
     %input{ :type => "submit", :value => "Create model"}
     = link_to "Cancel", '/create'
 
+  -# explanations
+  = haml :lazar_description, :layout => false
+  = haml :classification, :layout => false
+  = haml :regression, :layout => false
+  = haml :endpoint, :layout => false
+  = haml :unit, :layout => false
diff --git a/views/endpoint.haml b/views/endpoint.haml
new file mode 100644
index 0000000..af06b80
--- /dev/null
+++ b/views/endpoint.haml
@@ -0,0 +1,12 @@
+%dl#endpoint_description{ :style => "display: none;" }
+  %dt
+    Endpoint
+    (
+    = hide_link "#endpoint_description"
+    )
+  %dd 
+    Toxic effect that constitutes the outcome of an
+    %em in-vitro,
+    or
+    %em in-vivo
+    expriment, clinical trial or epidemiological study
diff --git a/views/help.haml b/views/help.haml
index 52339ce..eabf978 100644
--- a/views/help.haml
+++ b/views/help.haml
@@ -10,7 +10,10 @@
   %dd
     Enter a quantitative value. For optimal performance you should
     %ul
-      %li use molar units
+      %li
+        use
+        %a{:href => "http://en.wikipedia.org/wiki/Molar_(concentration)"} molar
+        units
       %li enter non-logarithmic values (logarithms are taken internally)
       %li avoid 0 activities (will be ignored)
 %p 
diff --git a/views/layout.haml b/views/layout.haml
index 6c9202b..a3db5e9 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -9,7 +9,9 @@
     %link{:rel=>'stylesheet', :href=>'stylesheets/style.css', :type => "text/css"}      
 
   %body
-    .logo= image_tag "/ToxCreate_rgb_72.png", :alt => 'ToxCreate', :align => "right"
+    .logo
+      = image_tag "/ToxCreate_rgb_72.png", :alt => 'ToxCreate', :align => 'right'
+      %br Create and evaluate models to predict toxicity
     .index
       %ul
         %li{:class => ("selected" if /\/create/ =~ request.path )}
diff --git a/views/lazar_algorithm.haml b/views/lazar_algorithm.haml
index 6322b17..b83de6b 100644
--- a/views/lazar_algorithm.haml
+++ b/views/lazar_algorithm.haml
@@ -19,9 +19,15 @@
         %li
           a majority vote (weighted by compound similarity) for
           %em classification
+          (
+          %a{:href => "http://www.in-silico.de/articles/modi020905.pdf"} original publication
+          )
         %li
           a local QSAR model based on neighbors for
           %em regression
+          (
+          %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf"} original publication
+          )
 
     %p
       = toggle_link "#significant_fragments", "Significant fragments"
diff --git a/views/lazar_description.haml b/views/lazar_description.haml
new file mode 100644
index 0000000..d870425
--- /dev/null
+++ b/views/lazar_description.haml
@@ -0,0 +1,29 @@
+%dl#lazar_description{ :style => "display: none;" }
+  %dt
+    %code lazar
+    (
+    = hide_link "#lazar_description"
+    )
+  %dd 
+    %p
+      %code lazar
+      searches the training dataset for  
+      = toggle_link "#similarity", "similar"
+      compounds 
+      %em (neighbors)
+      and calculates the prediction from their measured activities.
+      %code lazar
+      calculates predictions using
+      %ul
+        %li
+          a majority vote (weighted by compound similarity) for
+          %em= toggle_link("#classification","classification")
+          (
+          %a{:href => "http://www.in-silico.de/articles/modi020905.pdf"} original publication
+          )
+        %li
+          a local QSAR model based on neighbors for
+          %em= toggle_link("#regression","regression")
+          (
+          %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf"} original publication
+          )
diff --git a/views/model.haml b/views/model.haml
index 234dcc6..454423a 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -8,6 +8,7 @@
 %div{:id => "model_#{model.id}"}  
   %h2
     = model.name
+
   .model
     %dl
       %dt Status:
@@ -31,9 +32,9 @@
       - if model.status == 'Completed'
         %dt Algorithm:
         %dd
-          %a{:href => "http://www.in-silico.de/articles/modi020905.pdf"} #{File.basename model.algorithm}
+          = toggle_link("#lazar_description","lazar")
         %dt Type:
-        %dd= model.type
+        %dd= toggle_link("##{model.type}","#{model.type}")
         %dt Descriptors:
         %dd
           %a{:href => 'http://www.maunz.de/libfminer2-bbrc-doc/'} Fminer backbone refinement classes
@@ -56,10 +57,5 @@
           %a{:href => "#{model.uri}.rdf"} RDF/XML
           ,
           %a{:href => "#{model.uri}.yaml"} YAML
-          %em  (experts, models cannot be exported in Excel)
-        - case model.type
-        - when "classification"
-          = haml :classification_validation, :locals=>{:model=>model}, :layout => false     
-        -when "regression"
-          = haml :regression_validation, :locals=>{:model=>model}, :layout => false     
-          
+          %em  (experts, models cannot be represented in Excel)
+        = haml :validation, :locals=>{:model=>model}, :layout => false     
diff --git a/views/models.haml b/views/models.haml
index 806a935..6712e3d 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -10,5 +10,11 @@
   });
 
 %p Get an overview about ToxCreate models. This page is refreshed every 15 seconds to update the model status.
+
+-# explanations
+= haml :lazar_description, :layout => false
+= haml :classification, :layout => false
+= haml :regression, :layout => false
+
 - @models.each do |model|
   = haml :model, :locals=>{:model=>model}, :layout => false 
diff --git a/views/regression.haml b/views/regression.haml
new file mode 100644
index 0000000..4866b08
--- /dev/null
+++ b/views/regression.haml
@@ -0,0 +1,11 @@
+%dl#regression{ :style => "display: none;" }
+  %dt
+    Regression
+    (
+    = hide_link "#regression"
+    )
+  %dd 
+    Prediction of
+    %em quantitative
+    properties, e.g. LC50 values
+
diff --git a/views/regression_validation.haml b/views/regression_validation.haml
index ac45307..00267a9 100644
--- a/views/regression_validation.haml
+++ b/views/regression_validation.haml
@@ -1,27 +1,9 @@
-%dl{:id => "model_validation_#{model.id}"}
-  %dt
-    Validation:
-    %input{ :id => "model_validation_report_#{model.id}", :type => "hidden", :value => "#{model.validation_report_status}", :class => "model_validation_report" }
-    - if model.validation_report_uri
-      %a{:href => model.validation_report_uri, :target => "_blank"} (more details)
-  %dd
-    - if model.validation_uri
-      - v = model.regression_validation
-      - if v == "Service offline"
-        = v
-      - else
-        %dl
-          %dt Number of predictions
-          %dd= v[:num_instances] - v[:num_unpredicted]
-          %dt
-            %a{:href => "http://en.wikipedia.org/wiki/R-squared"} R-squared
-          %dd= sprintf '%.03g', v[:regression_statistics][:r_square]
-          %dt
-            %a{:href => "http://en.wikipedia.org/wiki/Root_mean_square_deviation"} Root Mean Square Error
-          %dd= sprintf '%.03g', v[:regression_statistics][:root_mean_squared_error]
-          %dt
-            %a{:href => "http://en.wikipedia.org/wiki/Mean_absolute_error"} Mean Absolute Error
-          %dd= sprintf '%.03g', v[:regression_statistics][:mean_absolute_error]
-    - else
-      = image_tag("/snake_transparent.gif") if model.validation_status == "Running"
-      %a{:href => model.validation_task_uri} #{model.validation_status}
+%dt
+  %a{:href => "http://en.wikipedia.org/wiki/R-squared"} R-squared
+%dd= sprintf '%.03g', model.r_square
+%dt
+  %a{:href => "http://en.wikipedia.org/wiki/Root_mean_square_deviation"} Root Mean Square Error
+%dd= sprintf '%.03g', model.root_mean_squared_error
+%dt
+  %a{:href => "http://en.wikipedia.org/wiki/Mean_absolute_error"} Mean Absolute Error
+%dd= sprintf '%.03g', model.mean_absolute_error
diff --git a/views/style.sass b/views/style.sass
index 4977da1..44917cc 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -19,9 +19,14 @@ body
   a:hover
     color: black
 
-  .headline
-    .logo
-      float: right
+  .logo
+    float: right
+    br
+      clear: both
+      //border-right: 90px
+    img
+      margin: 0
+      padding: 0
 
   .index
     clear: both
@@ -85,7 +90,7 @@ body
           font-weight: bold
           color: $fg_color
         label
-          width: 25em
+          width: 30em
           display: block
           float: left
         br
diff --git a/views/unit.haml b/views/unit.haml
new file mode 100644
index 0000000..a352599
--- /dev/null
+++ b/views/unit.haml
@@ -0,0 +1,10 @@
+%dl#unit{ :style => "display: none;" }
+  %dt
+    Unit
+    (
+    = hide_link "#unit"
+    )
+  %dd 
+    Unit of measurement, e.g. mmol or mmol/kg-bodyweight.  For optimal performance you should use 
+    %a{:href => "http://en.wikipedia.org/wiki/Molar_(concentration)"} molar
+    units.
diff --git a/views/validation.haml b/views/validation.haml
index d1af379..90150d1 100644
--- a/views/validation.haml
+++ b/views/validation.haml
@@ -1,264 +1,27 @@
-= "-> "
-%a{ :href => "/validation/#{params[:id]}" } Validation
+%dl{:id => "model_validation_#{model.id}"}
+  %dt
+    Validation:
+    %input{ :id => "model_validation_report_#{model.id}", :type => "hidden", :value => "#{model.validation_report_status}", :class => "model_validation_report" }
+  %dd
+    - if model.validation_uri
+      %dl
+        %dt
+          Detailed report:
+        %dd
+          - if model.validation_report_uri
+            %a{:href => model.validation_report_uri, :target => "_blank"} show
+          - else
+            = image_tag("/snake_transparent.gif") if model.validation_report_status == "Running"
+            %a{:href => model.validation_report_task_uri} #{model.validation_report_status}
+        %dt Number of predictions
+        %dd= model.nr_predictions
+        - case model.type
+        - when "classification"
+          = haml :classification_validation, :locals=>{:model=>model}, :layout => false     
+        - when "regression"
+          = haml :regression_validation, :locals=>{:model=>model}, :layout => false     
+    - else
+      = image_tag("/snake_transparent.gif") if model.validation_status == "Running"
+      %a{:href => model.validation_task_uri} #{model.validation_status}
+          
 
-%h1
-  = @model['name'].capitalize.gsub(/_/,' ')
-  validation
-
-Created on 
-= @model['created_at']
-by
-= @model['user']
-(
-%a{ :href => @model['validation']['details_uri'] } Prediction details
-)
-
-%h3 Predictions weighted by confidence index
-%p
-  %em Best indication of the overall performance
-
-%table
-  %tr
-    %th
-      True positive predictions
-    %td
-      tp
-    %td
-      = sprintf("%0.2f",@summary[:weighted][:tp].to_f)
-  %tr
-    %th
-      True negative predictions
-    %td
-      tn
-    %td
-      = sprintf("%0.2f",@summary[:weighted][:tn].to_f)
-  %tr
-    %th
-      False positive predictions
-    %td
-      fp
-    %td
-      = sprintf("%0.2f",@summary[:weighted][:fp].to_f)
-  %tr
-    %th
-      False negative predictions
-    %td
-      fn
-    %td
-      = sprintf("%0.2f",@summary[:weighted][:fn].to_f)
-  %tr
-    %th
-      Sensitivity (true positive rate)
-    %td
-      tp/(tp+fn)
-    %td
-      = (100*@summary[:weighted][:tp].to_f/(@summary[:weighted][:tp].to_f+@summary[:weighted][:fn].to_f)).round/100.00
-  %tr
-    %th
-      Specificity (true negative rate)
-    %td
-      tn/(tn+fp)
-    %td
-      = (100*@summary[:weighted][:tn].to_f/(@summary[:weighted][:tn].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
-  %tr
-    %th
-      Positive predictivity
-    %td
-      tp/(tp+fp)
-    %td
-      = (100*@summary[:weighted][:tp].to_f/(@summary[:weighted][:tp].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
-  %tr
-    %th
-      Negative predictivity
-    %td
-      tn/(tn+fn)
-    %td
-      = (100*@summary[:weighted][:tn].to_f/(@summary[:weighted][:tn].to_f+@summary[:weighted][:fn].to_f).to_f).round/100.00
-  %tr
-    %th
-      False positive rate
-    %td
-      fp/(tp+fn)
-    %td
-      = (100*@summary[:weighted][:fp].to_f/(@summary[:weighted][:tp].to_f+@summary[:weighted][:fn].to_f).to_f).round/100.00
-  %tr
-    %th
-      False negative rate
-    %td
-      fn/(tn+fp)
-    %td
-      = (100*@summary[:weighted][:fn].to_f/(@summary[:weighted][:tn].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
-  %tr
-    %th
-      Accuracy (concordance)
-    %td
-      (tp+tn)/(tp+fp+tn+fn)
-    %th
-      = (100*(@summary[:weighted][:tp].to_f+@summary[:weighted][:tn].to_f)/(@summary[:weighted][:tp].to_f+@summary[:weighted][:tn].to_f+@summary[:weighted][:fn].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
-
-
-%h3 Predictions within the applicability domain
-%p
-  %em Hard cutoff at confidence > 0.025
-
-%table
-  %tr
-    %th
-      True positive predictions
-    %td
-      tp
-    %td
-      = @summary[:within_ad][:tp].to_i
-  %tr
-    %th
-      True negative predictions
-    %td
-      tn
-    %td
-      = @summary[:within_ad][:tn].to_i
-  %tr
-    %th
-      False positive predictions
-    %td
-      fp
-    %td
-      = @summary[:within_ad][:fp].to_i
-  %tr
-    %th
-      False negative predictions
-    %td
-      fn
-    %td
-      = @summary[:within_ad][:fn].to_i
-  %tr
-    %th
-      Sensitivity (true positive rate)
-    %td
-      tp/(tp+fn)
-    %td
-      = (100*@summary[:within_ad][:tp].to_i/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      Specificity (true negative rate)
-    %td
-      tn/(tn+fp)
-    %td
-      = (100*@summary[:within_ad][:tn].to_i/(@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Positive predictivity
-    %td
-      tp/(tp+fp)
-    %td
-      = (100*@summary[:within_ad][:tp].to_i/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Negative predictivity
-    %td
-      tn/(tn+fn)
-    %td
-      = (100*@summary[:within_ad][:tn].to_i/(@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      False positive rate
-    %td
-      fp/(tp+fn)
-    %td
-      = (100*@summary[:within_ad][:fp].to_i/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      False negative rate
-    %td
-      fn/(tn+fp)
-    %td
-      = (100*@summary[:within_ad][:fn].to_i/(@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Accuracy (concordance)
-    %td
-      (tp+tn)/(tp+fp+tn+fn)
-    %th
-      = (100*(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:tn].to_i)/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fn].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
-
-%h3 All predictions
-%p
-  %em Poor indication of the overall performance. Depends predominatly on the fraction of compounds within the applicability domain.
-
-%table
-  %tr
-    %th
-      True positive predictions
-    %td
-      tp
-    %td
-      = @summary[:all][:tp].to_i
-  %tr
-    %th
-      True negative predictions
-    %td
-      tn
-    %td
-      = @summary[:all][:tn].to_i
-  %tr
-    %th
-      False positive predictions
-    %td
-      fp
-    %td
-      = @summary[:all][:fp].to_i
-  %tr
-    %th
-      False negative predictions
-    %td
-      fn
-    %td
-      = @summary[:all][:fn].to_i
-  %tr
-    %th
-      Sensitivity (true positive rate)
-    %td
-      tp/(tp+fn)
-    %td
-      = (100*@summary[:all][:tp].to_i/(@summary[:all][:tp].to_i+@summary[:all][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      Specificity (true negative rate)
-    %td
-      tn/(tn+fp)
-    %td
-      = (100*@summary[:all][:tn].to_i/(@summary[:all][:tn].to_i+@summary[:all][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Positive predictivity
-    %td
-      tp/(tp+fp)
-    %td
-      = (100*@summary[:all][:tp].to_i/(@summary[:all][:tp].to_i+@summary[:all][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Negative predictivity
-    %td
-      tn/(tn+fn)
-    %td
-      = (100*@summary[:all][:tn].to_i/(@summary[:all][:tn].to_i+@summary[:all][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      False positive rate
-    %td
-      fp/(tp+fn)
-    %td
-      = (100*@summary[:all][:fp].to_i/(@summary[:all][:tp].to_i+@summary[:all][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      False negative rate
-    %td
-      fn/(tn+fp)
-    %td
-      = (100*@summary[:all][:fn].to_i/(@summary[:all][:tn].to_i+@summary[:all][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Accuracy (concordance)
-    %td
-      (tp+tn)/(tp+fp+tn+fn)
-    %th
-      = (100*(@summary[:all][:tp].to_i+@summary[:all][:tn].to_i)/(@summary[:all][:tp].to_i+@summary[:all][:tn].to_i+@summary[:all][:fn].to_i+@summary[:all][:fp].to_i).to_f).round/100.00