lazar-gui 1.0.2 → 1.1.3

data/views/prediction.haml

@@ -1,10 +1,3 @@
-:javascript
-  $(document).ready(function(){
-    $('[data-toggle="popover"]').popover();
-    $('.modal').on('hidden.bs.modal', function () {
-      $(this).removeData('bs.modal');
-    });
-  });
 %div.well
   %a.btn.btn-warning{:href => to('/predict')}
     %i.glyphicon.glyphicon-menu-left
@@ -16,9 +9,9 @@
       %tbody
         %tr
           %td{:id=>"compound", :style=>"vertical-align:top;"}
-            %p= @compound.svg
+            %a.btn.btn-link{:href => "#details0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@compound.id.to_s)}/details"), :id=>"link01"}}
+              = @compound.svg
             %p= @compound.smiles
-          - mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -28,57 +21,92 @@
             %td{:style=>"vertical-align:top;white-space:nowrap;"}
               %b{:class => "title"}
                 = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})"
-              %p
-              - if prediction[:confidence] == "measured"
-                - @dbhit[i] = true
+              
+              / check for prediction
+              /- if prediction[:neighbors].size > 0
+              - if prediction[:neighbors] and !prediction[:value].nil?
                 %p
-                %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(", ")
-                - 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]
-                %p
-                  %b Compound is part of the training dataset
-              - elsif prediction[:neighbors].size > 0
-                %p
-                / model type (classification|regression)
+                / show model type (classification|regression)
                 %b Type:
                 = 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
-                - 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)"}"
-                  / 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."}}
+                %p 
+                / check for database hit
+                - if prediction[:info] =~ /\b(identical)\b/i
+                  - @dbhit[i] = true
+                  
+                  / show message about dbhit and measurements
+                  %p
+                    %b Compound is part of the training dataset
+                    %p
+                    %b Measured activity:
+                    %br
+                    - if prediction[:measurements].is_a?(Array)
+                      = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:measurements].join(", ")
+                    - else
+                      = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements]
+                
                 - 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."}}
+                  - @dbhit[i] = false
+                
+                / show prediction
                 %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)
-                / Significant fragments:
-                / %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments
-                / - if @model_type[i] =~ /regression/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
-                / Descriptors
-                / %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors
-                / %p
+                  %b Prediction:
+                  / prediction popover
+                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :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>.<hr></hr><a href=\"https://doi.org/10.3389/fphar.2013.00038\", target=\"_blank\"><img src=\"https://zenodo.org/badge/DOI/10.3389/zenodo.10.3389.svg\" alt=\"DOI\"></a>"}}
+                  %br
+                  = (type == "Regression") ? "#{prediction[:value].delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                  
+                  / show prediction interval or probability
+                  %p
+                  - if type == "Regression"
+                    %b 95% Prediction interval:
+                    - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval])
+                    / prediction interval popover
+                    %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :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.nil? ? "--" : "#{interval[1].delog10.signif(3)} - #{interval[0].delog10.signif(3)} (#{unit})"
+                    %br
+                    = "#{@compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{@compound.mmol_to_mg(interval[0].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
+                  - else
+                    %b Probability:
+                    / probability popover
+                    %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Pobability", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Probability that the prediction belongs to one of the given classes."}}
+                    - unless prediction[:probabilities].nil?
+                      %br
+                      = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0].signif(3)}"
+                      - if prediction[:probabilities].size == 2
+                        %br
+                        = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1].signif(3)}"
+                
+                / show warnings and info
                 %p
+                - if !prediction[:info].blank?
+                  %b info:
+                  %br
+                  %p=prediction[:info].sub(/excluded/, "excluded<br>")
+                - if !prediction[:warnings].blank?
+                  %b warnings:
+                  - prediction[:warnings].uniq.each do |warning|
+                    %br
+                    %p=warning
+                    %p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
               - else
+                %br
                 - @dbhit[i] = false
-                %p
-                  = "Not enough similar compounds </br>in training dataset."
+                - if !prediction[:info].blank?
+                  %b info:
+                  %br
+                  %p=prediction[:info].sub(/excluded/, "excluded<br>")
+                - if !prediction[:warnings].blank?
+                  %b warnings:
+                  - prediction[:warnings].uniq.each do |warning|
+                    %br
+                    %p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
 
   / always show the neighbors table, message is given there  
   = haml :neighbors, :layout => false, :model_type => @model_types, :dbhit => @dbhit
+    
+%div.modal.fade{:id=>"details0", :role=>"dialog"}
+  %div.modal-dialog.modal-lg
+    %div.modal-content
 

data/views/style.scss

@@ -1,3 +1,29 @@
+@media (min-width: 320px){
+  .page-header{
+    img.media-object{
+      margin-left:0;
+    }
+    background-color: #fff;
+    padding:10px 0 10px 0;
+    margin: 0;
+    text-align:left;
+    //display:inline-block;
+    width:100%;
+  }
+}
+@media (min-width: 480px){
+  .page-header{
+    img.media-object{
+      margin-left:1em;
+    }
+    background-color: #fff;
+    padding:20px 0 20px 0;
+    margin: 0;
+    text-align:center;
+    //display:inline-block;
+    width:100%;
+  }
+}
 body {
   background-color:#E7E7E7;
 }
@@ -9,14 +35,14 @@ h4.head-back, h5.head-back{
 }
 .nav-tabs {
   background-color: #E7E7E7;
-  margin-bottom: 0;
+  //margin-bottom: 0;
 
   li.active a:hover {
     background-color: #f5f5f5;
   }
 
   li a {
-    height: 5em;
+    height: 7em;
   }
 }
 img {
@@ -40,6 +66,9 @@ img {
 .tablesorter-bootstrap thead .sorter-false {
   cursor: default;
 }
+.tablesorter-bootstrap thead {
+  background-color: #E7E7E7;
+}
 ul.share-buttons{
   list-style: none;
 }
@@ -50,21 +79,19 @@ ul.share-buttons{
 .dropdown-menu a {
   padding: 0 2px 1px 2px !important;
 }
-.page-header{
-  margin:20px 0 20px;
-  text-align:justify;
-  display:inline-block;
-  width:98.5%;
-}
 .share{
   width: 30px;
   padding-right: 5px;
 }
 supporters{
   background-color: white;
-
+  text-align:center;
   img{
     width: 200px;
     margin-right: 1em;
   }
 }
+
+.footer{
+  margin-top:3em;
+}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lazar-gui
 version: !ruby/object:Gem::Version
-  version: 1.0.2
+  version: 1.1.3
 platform: ruby
 authors:
 - Christoph Helma
@@ -9,148 +9,106 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-13 00:00:00.000000000 Z
+date: 2017-05-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: lazar
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 0.9.3
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.9.3
+        version: 1.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 0.9.3
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.9.3
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: gem-path
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 0.6.1
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.6.1
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 0.6.1
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.6.1
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: sinatra
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 1.4.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.0
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 1.4.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.0
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdiscount
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 2.1.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.1.0
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 2.1.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.1.0
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: haml
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 4.0.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.0
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 4.0.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.0
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: sass
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 3.4.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.4.0
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 3.4.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.4.0
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: unicorn
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 5.1.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 5.1.0
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 5.1.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 5.1.0
+        version: '0'
 description: Graphical User Interface for Lazar Toxicology Predictions
 email:
 - helma@in-silico.ch
@@ -164,6 +122,7 @@ files:
 - ".gitignore"
 - FAQ.md
 - Gemfile
+- LICENSE.md
 - README.md
 - VERSION
 - application.rb
@@ -176,6 +135,7 @@ files:
 - lazar-gui.gemspec
 - public/css/bootstrap-theme.min.css
 - public/css/bootstrap.min.css
+- public/css/bootstrap.vertical-tabs.min.css
 - public/css/images/black-asc.gif
 - public/css/images/black-desc.gif
 - public/css/images/black-unsorted.gif
@@ -251,42 +211,138 @@ files:
 - public/javascripts/jquery.tablesorter.widgets.js
 - public/javascripts/jquery.tools.min.js
 - public/javascripts/lazar-gui.js
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 - public/jsme/gwt/chrome/chrome_rtl.css
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 - public/jsme/gwt/chrome/mosaic.css
 - public/jsme/gwt/chrome/mosaic_rtl.css
-- public/jsme/hosted.html
 - public/jsme/jsa.css
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 - public/jsme/jsme.nocache.js
 - public/rect.png
 - public/stylesheets/jquery-ui.css
@@ -334,18 +390,17 @@ files:
 - views/details.haml
 - views/error.haml
 - views/faq.haml
-- views/faq_layout.haml
 - views/info.haml
 - views/jme_help.html
 - views/js_link.haml
 - views/layout.haml
+- views/license.haml
 - views/model_details.haml
 - views/neighbors.haml
 - views/predict.haml
 - views/prediction.haml
 - views/significant_fragments.haml
 - views/style.scss
-- views/validation.haml
 homepage: http://github.com/opentox/lazar-gui
 licenses:
 - GPL-3.0
@@ -366,7 +421,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: lazar-gui
-rubygems_version: 2.5.1
+rubygems_version: 2.5.2
 signing_key: 
 specification_version: 4
 summary: lazar-gui