several fixes; works with lazar tree e111369ce5564f159b3f5f85c92afdd22352eaa1

9 files changed, 127 insertions, 107 deletions

diff --git a/views/details.haml b/views/details.haml
index 8a57440..bb8250d 100644
--- a/views/details.haml
+++ b/views/details.haml
@@ -19,6 +19,6 @@
   %hr
   %p{:style=>"padding-left:0.5em;"}
     / pubchem link
-    %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :target=>"_blank"} PubChem read across 
+    %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :rel=>"external"} PubChem read across 
     %i (experimental)
   %br
diff --git a/views/layout.haml b/views/layout.haml
index a40b68c..dddf854 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -15,7 +15,7 @@
     %script{:src=>"/javascripts/bootstrap.min.js"}
     %script{:src=>"/javascripts/jquery.tablesorter.min.js"}
     %script{:src=>"/javascripts/jquery.tablesorter.widgets.js"}
-    %script{ :src=>"/javascripts/lazar-gui.js"}
+    %script{:src=>"/javascripts/lazar-gui.js"}
   %body
     %noscript
       %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"}
@@ -26,7 +26,7 @@
           %a{:href=> to("/predict")}
             %img.media-object{:src=>"/images/IST_logo_s.png", :alt=>"logo", :width=>"150px", :heigth=>"150px", :style=>"margin:0 3em 0 2em;"}
         %div.col-md-8
-          %h1.media-heading{:style=>"margin: 0 0 0 2em;"}
+          %h1.media-heading
             lazar toxicity predictions
         %div.col-md-2
           %h1.media-heading
@@ -55,7 +55,7 @@
               %img.share{:src=>"/images/Facebook.png"}
         %div.row
         Previous version:
-        %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old
+        %a{:href=>"http://lazar-old.in-silico.ch", :rel => "external"} lazar-old
       :javascript
         $(document).ready(function(){
           $("#back-top").hide();
@@ -79,15 +79,17 @@
             %p.text-muted
               © 
               %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
+              |
+              %a{:href => to("/license"), :rel => "external"} GPL3 License
           %supporters.col-md-12
-            %p Financial support:
-            %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"}
+            %p Financial support by
+            %a{:href=>"http://www.bfr.bund.de/de/start.html", :rel=>"external"}
               %img{:src=>"/images/bfr_logo.gif"}
-            %a{:href=>"http://www.opentox.org/", :target=>"_blank"}
+            %a{:href=>"http://www.opentox.org/", :rel=>"external"}
               %img{:src=>"/images/ot_logo.png"}
-            %a{:href=>"https://enanomapper.net/", :target=>"_blank"}
+            %a{:href=>"https://enanomapper.net/", :rel=>"external"}
               %img{:src=>"/images/enm_logo.png"}
-            %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"}
+            %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :rel=>"external"}
               %img{:src=>"/images/nestec.jpg"}
     
 
diff --git a/views/license.haml b/views/license.haml
new file mode 100644
index 0000000..2813220
--- /dev/null
+++ b/views/license.haml
@@ -0,0 +1 @@
+= @license
diff --git a/views/model_details.haml b/views/model_details.haml
index 1be75e7..7646471 100644
--- a/views/model_details.haml
+++ b/views/model_details.haml
@@ -1,26 +1,39 @@
 %b Model:
 %br
 Source:
-%a{:href=>model.source, :target=>"external"}
+%a{:href=>model.source, :rel=>"external"}
   = model.source
 %br
 - model.classification? ? type = "Classification" : type = "Regression"
 = "Type:\t"
 = type
 %br
-- training_dataset = OpenTox::Dataset.find model.training_dataset.id
+- training_dataset = OpenTox::Dataset.find model.model.training_dataset_id
 = "Training compounds:\t"
 = training_dataset.compounds.size
-
+%br
+%b Algorithms:
+%br
+Similarity:
+%a{:href=> "http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["similarity"]["method"].sub("::", "%2F")}", :rel=>"external"}
+  = model.model.algorithms["similarity"]["method"]
+= ", min: #{model.model.algorithms["similarity"]["min"]}"
+%br
+Prediction:
+%a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"}
+  = model.model.algorithms["prediction"]["method"]
+%br
+Descriptors:
+= model.model.algorithms["descriptors"]["method"]+","
+= model.model.algorithms["descriptors"]["type"]
 %p
 - if type == "Classification"
   %b Independent crossvalidations:
 - else
   %b Independent crossvalidations (-log10 transformed):
 %div.row{:id=>"validations#{model.id}", :style=>"background-color:#f5f5f5;"}
-  - model.crossvalidations.each do |crossvalidation|
+  - crossvalidations.each do |cv|
     %span.col-xs-4.col-sm-4.col-md-4.col-lg-4
-      - cv = OpenTox::CrossValidation.find crossvalidation.id
       = "Num folds:\t"
       = cv.folds
       %br
@@ -34,76 +47,81 @@ Source:
         = "Accuracy:\t"
         = cv.accuracy.round(3) if cv.accuracy
         %br
+        = "Weighted accuracy:\t"
+        = cv.weighted_accuracy.round(3) if cv.weighted_accuracy
+        %br
         = "True positive rate:\t"
-        = cv.true_rate["active"].round(3) if cv.true_rate["active"]
+        = cv.true_rate["active"].round(3) if cv.true_rate
         %br
         = "True negative rate:\t"
-        = cv.true_rate["inactive"].round(3) if cv.true_rate["inactive"]
+        = cv.true_rate["inactive"].round(3) if cv.true_rate
         %br 
         = "Positive predictive value:\t"
-        = cv.predictivity["active"].round(3) if cv.predictivity["active"]
+        = cv.predictivity["active"].round(3) if cv.predictivity
         %br
         = "Negative predictive value:\t"
-        = cv.predictivity["inactive"].round(3) if cv.predictivity["inactive"]
+        = cv.predictivity["inactive"].round(3) if cv.predictivity
         %p
-        %b Confusion Matrix:
-        %table.table.table-condensed.table-borderless{:style=>"width:20%;"}
-          %tbody
-            %tr
-              %td
-              %td
-              %td 
-                %b actual
-              %td
-              %td
-            %tr
-              %td
-              %td
-              %td active
-              %td inactive
-              -#%td total
-            %tr
-              %td 
-                %b predicted
-              %td active
-              %td 
-                =cv.confusion_matrix[0][0]
-              %td 
-                =cv.confusion_matrix[0][1]
-              -#%td 
-                =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1]
-            %tr
-              %td
-              %td inactive
-              %td 
-                =cv.confusion_matrix[1][0]
-              %td 
-                =cv.confusion_matrix[1][1]
-              -#%td 
-                =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1]
-            -#%tr
-              %td
-              %td total
-              %td
-                =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0]
-              %td
-                =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1]
-              %td
-                -#= "Confusion Matrix:\t"
-                -#= cv.confusion_matrix
+        - ["confusion_matrix", "weighted_confusion_matrix"].each_with_index do |matrix,idx|
+          %b= (idx == 0 ? "Confusion Matrix" : "Weighted Confusion Matrix")
+          %table.table.table-condensed.table-borderless{:style=>"width:20%;"}
+            %tbody
+              %tr
+                %td
+                %td
+                %td 
+                  %b actual
+                %td
+                %td
+              %tr
+                %td
+                %td
+                %td active
+                %td inactive
+                -#%td total
+              %tr
+                %td 
+                  %b predicted
+                %td active
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[0][0].round(3) : cv.send(matrix)[0][0])
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[0][1].round(3) : cv.send(matrix)[0][1])
+                -#%td 
+                  =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1]
+              %tr
+                %td
+                %td inactive
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[1][0].round(3) : cv.send(matrix)[1][0])
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[1][1].round(3) : cv.send(matrix)[1][1])
+                -#%td 
+                  =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1]
+              -#%tr
+                %td
+                %td total
+                %td
+                  =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0]
+                %td
+                  =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1]
+                %td
+                  -#= "Confusion Matrix:\t"
+                  -#= cv.confusion_matrix
+              %br
         %br
         /= "Confidence plot:"
         /%p.plot
         /  %img{:src=>"confp#{cv.id}.svg"}
       - if model.regression?
         %br
-        = "Root mean squared error:\t"
+        %a.ht5{:href=>"https://en.wikipedia.org/wiki/Root-mean-square_deviation", :rel=>"external"} RMSE:
         = cv.rmse.round(3) if cv.rmse
         %br
-        = "Mean absolute error:\t"
+        %a.ht5{:href=>"https://en.wikipedia.org/wiki/Mean_absolute_error", :rel=>"external"} MAE:
         = cv.mae.round(3) if cv.mae
         %br 
-        = "R square:\t"
+        %a.ht5{:href=>"https://en.wikipedia.org/wiki/Coefficient_of_determination", :rel=>"external"}= "R"+"<sup>2</sup>"+":"
         = cv.r_squared.round(3) if cv.r_squared
         %br
         /= "Confidence plot:"
@@ -113,5 +131,5 @@ Source:
         /= "Correlation plot"
         /%p.plot
         /  %img{:src=>"/corrp#{cv.id}.svg"}
-        
+          
 %br
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 096e432..d9f2796 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -79,20 +79,19 @@
                 - prediction[:neighbors].uniq.each_with_index do |neighbor,count|
                   %tr
                     / Compound
-                    - c = Compound.find(neighbor["_id"])
+                    - c = Compound.find(neighbor)
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"}
                       /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor["_id"])}/details"), :id=>"link#{j+1}#{count}"}}
                       %p= c.svg
                       %p= c.smiles
-                    - mw = c.molecular_weight
-                    / Measured Activity = compound.features
+                    / Measured Activity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
-                      - features = c.features.collect{|k,v| v if k == predictionFeature[j]["id"] }.compact.flatten
-                      = (predictionFeature[j]["type"] == "numeric") ? features.collect{|v| weight = c.mmol_to_mg(v); '%.2e' % v + " (#{@models[j].unit})"+" , #{'%.2e' % weight} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : features.join("</br>")
+                      = (type == "Regression" ? "#{neighbor[:measurement].delog10}" + " (#{unit})" : neighbor[:measurement])
+                      %br
+                      = "#{c.mmol_to_mg(neighbor[:measurement].delog10)}" + " (#{(unit =~ /\b(mol\/L)\b/) ? "mg/L" : "mg/kg_bw/day"})" if type == "Regression"
                     / Similarity = tanimoto
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
-                      / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
-                      = neighbor[:tanimoto] != nil ? neighbor[:tanimoto].to_f.round(3) : "Not enough similar compounds </br>in training dataset."
+                      = neighbor[:similarity].round(3)
 
           - else
             %span.btn.btn-default.disabled
diff --git a/views/predict.haml b/views/predict.haml
index 010ed12..8ae5684 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -162,6 +162,7 @@
                     document.getElementById("details#{model.id}").appendChild(details);
                     $(button).show();
                     $(image).hide();
+                    addExternalLinks();
                   });
                 }
               }
diff --git a/views/prediction.haml b/views/prediction.haml
index 0f3d57b..1aefe06 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,7 +18,6 @@
           %td{:id=>"compound", :style=>"vertical-align:top;"}
             %p= @compound.svg
             %p= @compound.smiles
-          - mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -29,17 +28,20 @@
               %b{:class => "title"}
                 = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})"
               %p
-              - if prediction[:confidence] == "measured"
+              - if prediction[:warning] =~ /\b(identical)\b/i
                 - @dbhit[i] = true
                 %p
+                /TODO combine with regular view, if prediction value is present
                 %b Measured activity:
                 - p prediction[:value]
                 - if prediction[:value].is_a?(Array)
-                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{unit})"+", #{'%.2e' % weight} #{unit == "mmol/L" ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ")
+                  = (type == "Regression") ? prediction[:value].collect{|value| "#{value} (#{unit}) , #{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ")
                 - else
-                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                  = (type == "Regression") ? "#{prediction[:value]} (#{unit}), #{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                 %p
                   %b Compound is part of the training dataset
+                  / warning popover
+                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"#{prediction[:warning]}"}}
               - elsif prediction[:neighbors].size > 0
                 %p
                 / model type (classification|regression)
@@ -47,23 +49,30 @@
                 = type
                 %br
                 %b Prediction:
-                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) , #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
-                / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
                 / prediction popover
                 %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
                 %br
+                = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
+                %br
                 - if type == "Regression"
                   %b 95% Prediction interval:
-                  - interval = prediction[:prediction_interval].nil? ? " - - " : prediction[:prediction_interval].collect{|i| i.round(2)}
-                  %br
-                  = "#{interval[0]} - #{interval[1]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"
+                  - interval = (prediction[:prediction_interval].nil? ? ["- -","- -"] : prediction[:prediction_interval])
                   / prediction intervall popover
                   %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
+                  %br
+                  = "#{interval[0].delog10} - #{interval[1].delog10} (#{unit})"
+                  %br
+                  = "#{@compound.mmol_to_mg(interval[0].delog10)} - #{@compound.mmol_to_mg(interval[1].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
                 - else
-                  %b Confidence:
-                  = prediction[:confidence].round(2) unless prediction[:confidence].nil?
-                  / confidence popover
-                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. 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."}}
+                  %b Probability:
+                  - unless prediction[:probabilities].nil?
+                    %br
+                    = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}"
+                    %br
+                    = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}"
+                  / probability popover
+                  -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. 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[i] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
diff --git a/views/style.scss b/views/style.scss
index 49e03ab..2c84781 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -51,10 +51,12 @@ ul.share-buttons{
   padding: 0 2px 1px 2px !important;
 }
 .page-header{
-  margin:20px 0 20px;
-  text-align:justify;
+  background-color: #fff;
+  padding:20px 0 20px 0;
+  margin: 0;
+  text-align:center;
   display:inline-block;
-  width:98.5%;
+  width:100%;
 }
 .share{
   width: 30px;
@@ -62,9 +64,13 @@ ul.share-buttons{
 }
 supporters{
   background-color: white;
-
+  text-align:center;
   img{
     width: 200px;
     margin-right: 1em;
   }
 }
+
+.footer{
+  margin-top:3em;
+}
diff --git a/views/validation.haml b/views/validation.haml
deleted file mode 100644
index fd63ea6..0000000
--- a/views/validation.haml
+++ /dev/null
@@ -1,16 +0,0 @@
-- 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)} %"
-