several updates in code; validation integrated, probability for classification; updated call for more details for smarts view

7 files changed, 54 insertions, 27 deletions

diff --git a/application.rb b/application.rb
index 2cb16bb..e566211 100644
--- a/application.rb
+++ b/application.rb
@@ -10,8 +10,9 @@ helpers do
   @@models = []
   models = `curl -k GET -H accept:text/uri-list #{$model[:uri]}`.split("\n")
   .collect{|m| model = OpenTox::Model::Lazar.find m; @@models << model if model.type.flatten.to_s =~ /PredictionModel/}
-  @@cv = []
-  `curl -k GET -H accept:text/uri-list #{$validation[:uri]}/crossvalidation`.split("\n").each{|cv| x = OpenTox::Validation.find cv; @@cv << x}
+  #@@cv = []
+  #`curl -k GET -H accept:text/uri-list #{$validation[:uri]}/crossvalidation`.split("\n").each{|cv| x = OpenTox::Validation.find cv+"/statistics" if cv =~ /7/; @@cv << x}
+  #@@cv = OpenTox::Validation.find "https://dg.in-silico.ch/validation/crossvalidation/7/statistics"
 end
 
 get '/?' do
@@ -22,7 +23,7 @@ get '/predict/?' do
   # sort models by endpoint alphabetically
   $size = 0
   @models = @@models.sort!{|a, b| a.type.select{|e| e =~ /endpoint/i} <=> b.type.select{|e| e =~ /endpoint/i}}
-  @cv = @@cv.collect{|cv| cv.metadata.select{|x| x =~ /predictionFeature/}}
+  #@cv = @@cv#.collect{|cv| cv.metadata.select{|x| x =~ /predictionFeature/}}
   @models.size <= 0 ? (haml :info) : (haml :predict)
 end
 
@@ -200,7 +201,7 @@ post '/predict/?' do
     @predictions = []
     @model_type = []
     # get selected models
-    #TODO compare if model is selected by uri not title
+    # compare selected model by uri
     params[:selection].each do |model|
       # selected model = model[0]
       # compare selected with all models
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 32554d6..603f920 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -108,7 +108,6 @@
                   %td
                     = p.data_entries[count][3] != nil ? p.data_entries[count][3].round(3) : "Not enough similar compounds in training dataset." 
                   %td
-                    %br
                     - if @type =~ /classification/i
                       - if p.data_entries[count][3] != nil 
                         %a{:href => to("/prediction/#{CGI.escape(@model_uri)}/#{@type}/#{CGI.escape(neighbor_compound.uri)}/significant_fragments"), :id=>"link#{count_rs}#{count}sf", :target=>"details"} Significant fragments
diff --git a/views/predict.haml b/views/predict.haml
index 62fe93c..e9d222f 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -112,6 +112,7 @@
           %p{:style=>"display:inline;"} Algorithm:
           %code{:style=>"font-size:x-large;"} lazar
           - model.type.to_s =~ /regression/i ? type = "regression" : type = "classification"
+          - @model_type = type
           %p= "Type: "+type
           - training_dataset = OpenTox::Dataset.new "#{model[RDF::OT.trainingDataset]}"
           - training_compounds = training_dataset.compounds.size.to_s
@@ -123,26 +124,24 @@
             %a{:href=>"http://www.maunz.de/libfminer2-bbrc-doc/", :title=>"link opens in new window.", :target=>"_blank"} Fminer backbone refinement classes
           %br
           %br
-          %p{:style=>"display:inline"}= "Training Dataset: "
-          %a{:href=>"#{to("/predict/#{CGI.escape(model[RDF::OT.trainingDataset])}")}", :title=>"link opens in new window."} download rdf
+          %p{:style=>"display:inline"}= "Model: "
+          %a{:href=>"#{to("/predict/#{CGI.escape(model.uri)}")}", :title=>"download"} rdf
           %br
           %br
           %p{:style=>"display:inline"}= "Feature Dataset: "
-          %a{:href=>"#{to("/predict/#{CGI.escape(model[RDF::OT.featureDataset])}")}", :title=>"download"} download rdf
+          %a{:href=>"#{to("/predict/#{CGI.escape(model[RDF::OT.featureDataset])}")}", :title=>"download"} rdf
           %br
           %br
-          %p{:style=>"display:inline"}= "Model: "
-          %a{:href=>"#{to("/predict/#{CGI.escape(model.uri)}")}", :title=>"download"} download rdf
+          %p{:style=>"display:inline"}= "Training Dataset: "
+          %a{:href=>"#{to("/predict/#{CGI.escape(model[RDF::OT.trainingDataset])}")}", :title=>"link opens in new window."} rdf
           %br
-          %h3 Validation:
-          -#%p= @cv.inspect
-          %a{:href => "#"} 
-            Detailed report link
-          %p Number of predictions: integer
-          %p Correct predictions: %
-
-
-      //%br
+          - unless model.metadata[RDF::OT.crossValidation].nil?
+            %h3 Validation:
+            %a{:href => "#{model.metadata[RDF::OT.crossValidation][0]}", :title=>"link opens in new window.", :target=>"_blank"} 
+              Detailed report link
+            %br
+            - @cv = OpenTox::Validation.find "#{model.metadata[RDF::OT.crossValidation][0]+"/statistics"}"
+            = haml :validation, :layout => false, :validation => @cv, :model_type => @model_type
 
   .arrow
     %img{:src=>"/images/arrow_down_float.png", :alt=>"v", :class=> "arrow"}
diff --git a/views/prediction.haml b/views/prediction.haml
index 3cd2f3f..dfc7009 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -14,7 +14,7 @@
 
       %tbody
         %tr
-          %td{:id=>"compound", :style=>"width: 200px;padding:0.2em;"}
+          %td{:id=>"compound", :style=>"width: 200px;vertical-align:top;"}
             %a{:href => to("/prediction/#{CGI.escape(@compound.uri)}/details"), :id=>"linkCompound", :target=>"details_overview"}
               Names and synonyms
               %img{:src=>"#{@compound.uri}/image", :alt=>"Compound image not available", :title=>"#{@compound.smiles}", :width=>"150", :height=>"150"}
@@ -57,9 +57,13 @@
                   %b Result:
                   %b
                     - if c.class == String
-                      = (c != '' ? c : "No prediction result.")
+                      - result = (c != '' ? c : "No prediction result.")
+                      = result
                     - else
-                      = (c != '' ? c.round(3) : "No prediction result.")
+                      - result = (c != '' ? c.round(3) : "No prediction result.")
+                      = result
+                    - confidence = (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) ? p.data_entries[0][1].round(2) : "--"
+                  
                   / title must be empty for tooltip
                   %a{:href=>"#result", :title=>"", :id=>"result"}
                     %img{:src=>"/images/info_white.png"}
@@ -84,10 +88,16 @@
                         %a{:href=>"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract", :target=>"_blank"} original publication
                         )
                       Please keep in mind that predictions are based on the measured activities of neighbors.
+                  - @cv = OpenTox::Validation.find @prediction_models[count].metadata[RDF::OT.crossValidation][0]+"/statistics" unless @prediction_models[count].title.include?("Mutagenicity")
+                    - unless @model_type[count] == "regression"
+                    %b
+                      = "Probalitity: "
+                    - unless result == "No prediction result." or confidence == "--"
+                      = "#{@cv.probabilities( confidence, result )[:probs][result].round(3)*100} %"
                   %p
                   .confidence
                     %b Confidence:
-                    = (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) ? p.data_entries[0][1].round(3) : "--"
+                    = confidence
                     / title must be empty for tooltip
                     %a{:href=>"#confidence", :title=>"", :id=>"confidence"}
                       %img{:src=>"/images/info_white.png"}
@@ -101,6 +111,8 @@
                         Confidence values may take any value between 0 and 1.
                         For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between 
                         reliable and unreliable predictions.
+
+
                   %p
                   /TODO add tooltip for significant ftagments and descriptors
                   - if @model_type[count] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
diff --git a/views/significant_fragments.haml b/views/significant_fragments.haml
index 3004c89..b039804 100644
--- a/views/significant_fragments.haml
+++ b/views/significant_fragments.haml
@@ -1,7 +1,7 @@
 %link{ :href=>"/style.css", :media=>"screen, projection", :rel=>"stylesheet", :type=>"text/css"}
 .content{:style=>"margin-top:0;"}
   - if @type =~ /classification/i
-    .significant_fragments{:style=>"padding:0.7em;padding-bottom:5em;"}
+    .significant_fragments{:style=>"padding:0.7em;padding-bottom:10em;"}
       %button{:id=>"closebutton", :onclick=>"parent.$('#iframe_details').bPopup().close();parent.$('#iframe_overview').bPopup().close();"}
         X
       %h2{:style=>"margin-left:8px;"}
@@ -25,7 +25,7 @@
                   %td
                     / fragments[1] = smarts 
                     = fragments[1]
-                    %img{:src => "http://smartsview.de/smartsview/auto/png/2/none/#{CGI.escape(fragments[1])}", :class => "smarts"}
+                    %img{:src => "http://smartsview.de/smartsview/auto/png/1/both/#{CGI.escape(fragments[1])}", :class => "smarts"}
                   %td
                     /fragments[2] = pValue
                     = fragments[2]
@@ -42,7 +42,7 @@
               - if fragments[0] == @value_map.index("active")
                 %tr
                   %td
-                    %img{:src => "http://smartsview.de/smartsview/auto/png/2/none/#{CGI.escape(fragments[1])}", :class => "smarts"}
+                    %img{:src => "http://smartsview.de/smartsview/auto/png/1/both/#{CGI.escape(fragments[1])}", :class => "smarts"}
                     = fragments[1]
                   %td
                     = fragments[2]
diff --git a/views/style.scss b/views/style.scss
index caeef49..a068ab1 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -157,7 +157,7 @@ body {
     //float: left;
   }
   img.smarts:hover{
-    transform: scale(5);
+    transform: scale(4);
     border: solid 1px black;
   }
 
diff --git a/views/validation.haml b/views/validation.haml
new file mode 100644
index 0000000..fd63ea6
--- /dev/null
+++ b/views/validation.haml
@@ -0,0 +1,16 @@
+- case @model_type
+- when "classification"
+  - prediction = @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#numCorrect"] + @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#numIncorrect"]
+  %p= "Number of predictions: #{prediction}"
+  - percent = @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#percentCorrect"]
+  %p= "Correct predictions: #{percent.round(2)} %"
+- when "regression"
+  - prediction = @cv.metadata["http://www.opentox.org/api/1.2#numInstances"].to_i - @cv.metadata["http://www.opentox.org/api/1.2#numUnpredicted"].to_i
+  %p= "Number of predictions: #{prediction}"
+  - rSquare = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#rSquare"]
+  %p= "R-squared: #{rSquare.round(2)} %"
+  - rootMeanSquaredError = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#rootMeanSquaredError"]
+  %p= "Root Mean Square Error: #{rootMeanSquaredError.round(2)} %"
+  - meanAbsoluteError = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#meanAbsoluteError"]
+  %p= "Mean Absolute Error: #{meanAbsoluteError.round(2)} %"
+