lazar-gui 1.1.3 → 1.3.1

data/views/neighbors.haml

@@ -2,7 +2,7 @@
   %h3 Neighbors:
   / tabs div
   #tabs
-    %ul.nav.nav-tabs.nav-justified{:id=>"neighborTabs", :role=>"tablist"}
+    %ul.nav.nav-tabs.nav-justified{:id=>"neighborTabs", :role=>"tablist", :style=>"width:100%;overflow-x:auto;"}
       - @models.each_with_index do |model,i|
         / get predictionFeature type
         - m = Model::Lazar.find model.model_id.to_s
@@ -68,7 +68,7 @@
                         = (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]
+                          = (type == "Regression") ? "#{neighbor[:measurement].delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(neighbor[:measurement].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : neighbor[:measurement]
                     / Similarity = tanimoto
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       = neighbor[:similarity].round(3)

data/views/predict.haml

@@ -126,12 +126,11 @@
       %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
       %p
       -#%label{:for=>"fileselect"}
-        or upload a CSV file for batch predictions (disabled in public version)
+        or upload a CSV file for batch predictions:
       -#%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"}
+      %span.btn.btn-default.btn-file{:style=>"display:none;"}
+        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled", :type=>"hidden"}
 
   %fieldset#middle.well
     %h2 2. Select one or more endpoints
@@ -140,19 +139,26 @@
         %div{:id=>endpoint.gsub(/\s+/, "_")}
           %h4.head-back=endpoint
           - @models.select{|m| m.endpoint == endpoint}.each do |model|
-            %div.row{:id => model.id}
-              %span.col-sm-4
+            %div.row{:id => model.id,:style=>"margin-bottom:1em;"}
+              %span.col-lg-4.col-md-4.col-sm-4.col-xs-4
                 %input{:type => "checkbox", :name => "selection[#{model.id}]", :id => "selection[#{model.species.gsub(/\s+/, "_")}]", :value => true, :disabled => false}
                 %label{:for => "selection[#{model.species.gsub(/\s+/, "_")}]"}
                   = model.species
-              %span.col-sm-8
+              %span.col-lg-8.col-md-8.col-sm-8.col-xs-8
                 %a.btn.btn-default.btn-xs{:data=>{:toggle=>"collapse"}, :href=>"#details#{model.id}", :onclick=>"load#{model.id}Details('#{model}')", :id => "link#{model.id}", :style=>"font-size:small;"}
+                  %span.glyphicon.glyphicon-menu-right
                   Details | Validation
                 %img.h2{:src=>"/images/wait30trans.gif", :id=>"circle#{model.id}", :class=>"circle#{model.id}", :alt=>"wait", :style=>"display:none;"}
             %div.panel-collapse.collapse{:id=>"details#{model.id}", :style=>"margin-left:1em;"}
             :javascript
               function load#{model.id}Details(model) {
                 button = document.getElementById("link#{model.id}");
+                span = button.childNodes[1];
+                if (span.className == "glyphicon glyphicon-menu-right"){
+                  span.className = "glyphicon glyphicon-menu-down";
+                } else if (span.className = "glyphicon glyphicon-menu-down"){
+                  span.className = "glyphicon glyphicon-menu-right";
+                };
                 image = document.getElementById("circle#{model.id}");
                 if ($('modeldetails#{model.id}').length == 0) {
                   $(button).hide();
@@ -170,9 +176,10 @@
               }
   %fieldset#bottom.well
     %div.row
-      %div.col-md-2
+      %div.col-lg-2.col-md-2.col-sm-2.col-xs-2
         %h2
           3. Predict
-      %div.col-md-10
-        %input.btn.btn-warning.h2{ :type => "submit", :id => "submit", :value=>">>", :onclick => "getsmiles()"}
+      %div.col-lg-10.col-md-10.col-sm-10.col-xs-10
+        %button.has-feedback.btn.btn-warning.h2{:type => "submit", :id => "submit", :value=>"", :onclick => "getsmiles()"}
+          %span.glyphicon.glyphicon-play
         %img.h2{:src=>"/images/wait30trans.gif", :id=>"circle", :class=>"circle", :alt=>"wait", :style=>"display:none;"}

data/views/prediction.haml

@@ -1,3 +1,11 @@
+: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
@@ -8,7 +16,7 @@
     %table.table.table-bordered{:id=>"overview"}
       %tbody
         %tr
-          %td{:id=>"compound", :style=>"vertical-align:top;"}
+          %td{:id=>"compound", :style=>"vertical-align:top;text-align:center;"}
             %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
@@ -23,7 +31,6 @@
                 = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})"
               
               / check for prediction
-              /- if prediction[:neighbors].size > 0
               - if prediction[:neighbors] and !prediction[:value].nil?
                 %p
                 / show model type (classification|regression)
@@ -36,14 +43,17 @@
                   
                   / show message about dbhit and measurements
                   %p
-                    %b Compound is part of the training dataset
+                    :plain
+                      This compound was part of the training dataset. <i>All</i> information </br>
+                      from this compound was removed from the training data before the </br>
+                      prediction, to obtain unbiased results.
                     %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]
+                      = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements]
                 
                 - else
                   - @dbhit[i] = false
@@ -54,7 +64,7 @@
                   / 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]
+                  = (type == "Regression") ? "#{prediction[:value].delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                   
                   / show prediction interval or probability
                   %p
@@ -66,7 +76,7 @@
                     %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?
+                    = "#{@compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{@compound.mmol_to_mg(interval[0].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !interval.nil?
                   - else
                     %b Probability:
                     / probability popover
@@ -80,28 +90,26 @@
                 
                 / 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|
+                  - if !prediction[:info].blank?
+                    %b Info:
                     %br
-                    %p=warning
-                    %p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
+                    %p=prediction[:info].sub(/\'.*\'/,"").sub(/,/, ",<br>")
+                  - if !prediction[:warnings].blank?
+                    %b Warnings:
+                    - prediction[:warnings].uniq.each do |warning|
+                      %p=warning #.sub(/,/, ",<br>")
+                      /%p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
               - else
                 %br
-                - @dbhit[i] = false
                 - if !prediction[:info].blank?
-                  %b info:
+                  %b Info:
                   %br
-                  %p=prediction[:info].sub(/excluded/, "excluded<br>")
+                  %p=prediction[:info].sub(/\'.*\'/,"").sub(/,/, ",<br>")
                 - if !prediction[:warnings].blank?
-                  %b warnings:
+                  %b Warnings:
                   - prediction[:warnings].uniq.each do |warning|
                     %br
-                    %p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
+                    %p=warning.sub(/,/, ",<br>")
 
   / always show the neighbors table, message is given there  
   = haml :neighbors, :layout => false, :model_type => @model_types, :dbhit => @dbhit

data/views/style.scss

@@ -35,14 +35,13 @@ h4.head-back, h5.head-back{
 }
 .nav-tabs {
   background-color: #E7E7E7;
-  //margin-bottom: 0;
 
   li.active a:hover {
     background-color: #f5f5f5;
   }
 
   li a {
-    height: 7em;
+    //height: 7em;
   }
 }
 img {
@@ -84,11 +83,10 @@ ul.share-buttons{
   padding-right: 5px;
 }
 supporters{
-  background-color: white;
   text-align:center;
   img{
     width: 200px;
-    margin-right: 1em;
+    margin: 1em;
   }
 }
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lazar-gui
 version: !ruby/object:Gem::Version
-  version: 1.1.3
+  version: 1.3.1
 platform: ruby
 authors:
 - Christoph Helma
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-05-26 00:00:00.000000000 Z
+date: 2018-04-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: lazar
@@ -17,16 +17,16 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '0'
 - !ruby/object:Gem::Dependency
-  name: gem-path
+  name: sinatra
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -40,7 +40,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: sinatra
+  name: sinatra-reloader
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -109,6 +109,34 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: qsar-report
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: gem-path
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Graphical User Interface for Lazar Toxicology Predictions
 email:
 - helma@in-silico.ch
@@ -203,6 +231,7 @@ files:
 - public/images/ot_logo.png
 - public/images/wait30trans.gif
 - public/javascripts/bootstrap.min.js
+- public/javascripts/google_analytics_lazar.js
 - public/javascripts/jquery-1.11.2.min.js
 - public/javascripts/jquery-1.8.3.min.js
 - public/javascripts/jquery-ui-1.10.3.custom.min.js
@@ -383,8 +412,10 @@ files:
 - public/jsme/jsme.nocache.js
 - public/rect.png
 - public/stylesheets/jquery-ui.css
+- qmrf_report.rb
 - test/lazarweb.rb
 - test/setup.rb
+- tmp/.gitignore
 - unicorn.rb
 - views/batch.haml
 - views/details.haml
@@ -405,7 +436,7 @@ homepage: http://github.com/opentox/lazar-gui
 licenses:
 - GPL-3.0
 metadata: {}
-post_install_message: "\n  Service cmds:\n    lazar-start &\n    lazar-stop\n  "
+post_install_message: "\n  Service commands:\n    lazar-start\n    lazar-stop\n  "
 rdoc_options: []
 require_paths:
 - lib
@@ -421,7 +452,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: lazar-gui
-rubygems_version: 2.5.2
+rubygems_version: 2.6.8
 signing_key: 
 specification_version: 4
 summary: lazar-gui