lazar-gui 1.0.2 → 1.1.3

data/views/details.haml

@@ -1,8 +1,12 @@
+:javascript
+  $(document).ready(function(){
+    addExternalLinks();
+  });
 %div.modal-body{:style=>"padding:10px;"}
   %button.close{ :type=>" button", data: { dismiss:"modal"}} ×
   %h3
     Names and synonyms:
-  %img.img-responsive{:src=>"#{@compound.uri}/image", :alt=>"Compound image not available", :width=>"300px", :heigth=>"300px", :style=>"float:left;"}
+  %p= @compound.svg
   %p
   %b="SMILES:"
   %p= @smiles
@@ -19,6 +23,6 @@
   %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

data/views/layout.haml

@@ -15,45 +15,52 @@
     %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"}
       Your web browser must have JavaScript enabled in order for this application to display correctly.
     %header.page-header
       %div.row
-        %div.col-md-2
+        %div.col-md-3
           %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;"}
+            %img.media-object{:src=>"/images/IST_logo_s.png", :alt=>"logo", :width=>"150px", :heigth=>"150px"}
+        %div.col-md-6
+          %h1.media-heading
             lazar toxicity predictions
-        %div.col-md-2
+        %div.col-md-3
           %h1.media-heading
             %small
-              %a{:href=>"https://nano-lazar.in-silico.ch"} nano-lazar
+              %a{:href=>"https://nano-lazar.in-silico.ch", :rel=>"external"} nano-lazar
 
     %div.container-fluid
-      %topline
+      %topline.alert
         %div.row
-          %div.col-md-8
+          %div.col-md-10
             Problems, bugs, ideas for improvements ? Please report at our
             %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker
-            or send us an email
-            %a{ :href=>"mailto:info@in-silico.ch", :target=>"_top"}
+            , check out the 
+            %a{:href=> to("/faq"), :rel => "external"} FAQ
+            page or send us an email.
+            %a{ :href=>"mailto:info@in-silico.ch?subject=[lazar v#{@version}]", :target=>"_top"}
               %img.share{:src=>"/images/Email.png"}
-            (version #{@version}).
-          %div.col-md-2
-          %div.col-md-2
-            %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"}
+            [version: #{@version}]
+          %div.col-md-2{:style=>"text-align:right;"}
+            %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Tweet"}
               %img.share{:src=>"/images/Twitter.png"}
-            %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"}
+            %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on Google+"}
               %img.share{:src=>"/images/Google+.png"}
-            %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on LinkedIn"}
+            %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on LinkedIn"}
               %img.share{:src=>"/images/LinkedIn.png"}
-            %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Facebook"}
+            %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on Facebook"}
               %img.share{:src=>"/images/Facebook.png"}
-              
+        %div.row
+          %div.col-md-12
+            Please cite
+            %a{ :href=>"https://doi.org/10.3389/fphar.2013.00038", :rel=>"external"}
+              %img{ :src=>"https://zenodo.org/badge/DOI/10.3389/zenodo.10.3389.svg", :alt=>"DOI"}
+            in scientific publications.
+      
       :javascript
         $(document).ready(function(){
           $("#back-top").hide();
@@ -77,17 +84,19 @@
             %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"}
-    
+ 
 
     #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"}
       %a{:href => "", :style=>"text:decoration:none;color:#ccc;"}

data/views/license.haml

@@ -0,0 +1 @@
+= @license

data/views/model_details.haml

@@ -1,26 +1,43 @@
 %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
-
+= training_dataset.data_entries.size
+%br
+= "Training dataset:\t"
+%a{:href=>"#{to("/predict/dataset/#{training_dataset.name}")}"}
+  = training_dataset.name
+%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 +51,83 @@ Source:
         = "Accuracy:\t"
         = cv.accuracy.round(3) if cv.accuracy
         %br
-        = "True positive rate:\t"
-        = cv.true_rate["active"].round(3) if cv.true_rate["active"]
-        %br
-        = "True negative rate:\t"
-        = cv.true_rate["inactive"].round(3) if cv.true_rate["inactive"]
-        %br 
-        = "Positive predictive value:\t"
-        = cv.predictivity["active"].round(3) if cv.predictivity["active"]
-        %br
-        = "Negative predictive value:\t"
-        = cv.predictivity["inactive"].round(3) if cv.predictivity["inactive"]
+        = "Weighted accuracy:\t"
+        = cv.weighted_accuracy.round(3) if cv.weighted_accuracy
+        - if cv.true_rate
+          %br
+          = "True positive rate:\t"
+          = cv.true_rate[cv.accept_values[0]].round(3)
+          %br
+          = "True negative rate:\t"
+          = cv.true_rate[cv.accept_values[1]].round(3)
+        - if cv.predictivity
+          %br 
+          = "Positive predictive value:\t"
+          = cv.predictivity[cv.accept_values[0]].round(3)
+          %br
+          = "Negative predictive value:\t"
+          = cv.predictivity[cv.accept_values[1]].round(3)
         %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 +137,5 @@ Source:
         /= "Correlation plot"
         /%p.plot
         /  %img{:src=>"/corrp#{cv.id}.svg"}
-        
-%br
+          
+%br 

data/views/neighbors.haml

@@ -1,38 +1,17 @@
-/ unpacks multi prediction array ;
-/ prepare it for neighbors ;
-/ align single prediction to endpoint ;
-/ display preordered in table view ;
-
 %div.results
   %h3 Neighbors:
   / tabs div
   #tabs
     %ul.nav.nav-tabs.nav-justified{:id=>"neighborTabs", :role=>"tablist"}
-      / each model a tab head ;
-      / hash for predictionFeature
-      - predictionFeature = {}
       - @models.each_with_index do |model,i|
         / get predictionFeature type
         - m = Model::Lazar.find model.model_id.to_s
-        - predFeature = Feature.find m.prediction_feature_id.to_s
-        / define feature type (numeric : nominal)
-        - predFeatureType = (predFeature.numeric? ? "numeric" : "nominal")
-        / use prediction feature id for neighbor compound features
-        - predFeatureId = m.prediction_feature_id.to_s
-        - predictionFeature[i] = {"id" => predFeatureId, "type" => predFeatureType}
         %li{:class => ("active" if i == 0)}
           %a{:href => "#results_#{i+1}", :id => "linkTab#{i+1}", data: {toggle:"tab"}}
             = "#{model.endpoint} (#{model.species})"
     %div.tab-content
-      / unpack to single arrays
       - @predictions.each_with_index do |prediction,j|
-        / pass model type for significant fragments view
         #results.tab-pane{:id=>"#{j+1}", :class => ("active" if j == 0)}
-          / prepare dataset for neighbors table ;
-          / delete first array which contains prediction ;
-          / following arrays are the neighbor predictions ;
-          / call the tablesorter plugin ;
-          / presort by similarity ;
           :javascript
             $(document).ready(function(){
               $("table##{j+1}").tablesorter({
@@ -58,7 +37,7 @@
                 widthFixed: false
               });
             });
-          - if prediction[:neighbors].size > 0
+          - if prediction[:neighbors]
             %div.table-responsive
               %table{:id=>"#{j+1}", :style=>"border-style: solid;"}
                 %thead
@@ -67,32 +46,32 @@
                       Compound
                     %th.sorter-false{:style =>"vertical-align:middle;"}
                       Measured Activity
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
                     %th.sorter-false{:style =>"vertical-align:middle;"}
                       Similarity
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
-                    / %th{:style =>"vertical-align:middle;"}
-                    / Supporting Information
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"<a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
                 %tbody
                   - type = @model_types[j]
                   - unit = @models[j].unit
                 - 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
+                      %a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(c.id.to_s)}/details"), :id=>"link#{j+1}#{count}"}}
+                        = 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>")
+                      - if neighbor[:measurement].is_a?(Array)
+                        = (type == "Regression") ? neighbor[:measurement].collect{|value| "#{value.delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : neighbor[:measurement].join(", ")
+                      - else
+                        - if !neighbor[:measurement].nil?
+                          = (type == "Regression") ? "#{neighbor[:measurement].delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(neighbor[:measurement].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : neighbor[:measurement]
                     / 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

data/views/predict.haml

@@ -111,7 +111,7 @@
   };
 
 // whole site content needs to be in one form. Input and checkboxes are proofed by js functions. 
-%form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return  !!(showcircle())" }
+%form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return !!(showcircle())" }
   %fieldset#top.well
     %h2 1. Draw a chemical structure
     #insert
@@ -125,11 +125,13 @@
       %br
       %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
       %p
-      %label{:for=>"fileselect"}
+      -#%label{:for=>"fileselect"}
         or upload a CSV file for batch predictions (disabled in public version)
-      %br
-      %span.btn.btn-default.btn-file
-        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"}
+      -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"One column with compounds and keyword SMILES or InChI in the first row."}}
+      -#%br
+      -#%span.btn.btn-default.btn-file
+        -#%input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"}
+      %input{:type=>"hidden", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"}
 
   %fieldset#middle.well
     %h2 2. Select one or more endpoints
@@ -162,6 +164,7 @@
                     document.getElementById("details#{model.id}").appendChild(details);
                     $(button).show();
                     $(image).hide();
+                    addExternalLinks();
                   });
                 }
               }