lazar-gui 1.0.0

data/views/prediction.haml

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+: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
+    New Prediction
+  / displays all prediction result in first table
+  %h3 Prediction Results:
+  %div.table-responsive
+    %table.table.table-bordered{:id=>"overview"}
+      %tbody
+        %tr
+          %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|
+            - type = @models[i].model.class.to_s.match("Classification") ? "Classification" : "Regression"
+            - @model_types[i] = type
+            - unit = @models[i].unit
+            %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
+                %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)
+                %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."}}
+                - 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."}}
+                %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
+                %p
+              - else
+                - @dbhit[i] = false
+                %p
+                  = "Not enough similar compounds </br>in training dataset."
+
+  / always show the neighbors table, message is given there  
+  = haml :neighbors, :layout => false, :model_type => @model_types, :dbhit => @dbhit
+

data/views/significant_fragments.haml

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+%div.modal-body{:style=>"padding:10px;"}
+  %button.close{ :type=>" button", data: { dismiss:"modal"}} ×
+  - if @type =~ /classification/i
+    %div.row
+      %div.col-md-4
+        %h3{:style=>"margin-left:8px;"}
+          Significant fragments:
+        %img{:src=>"#{@compound.uri}/image", :alt=>"#{@compound.smiles}", :title=>"#{@compound.smiles}", :width=>"300px", :heigth=>"300px"}
+      - if !@significant_fragments.empty?
+        %div.col-md-8
+          %table{:id => "sf"}
+            %tr
+              / @value_map => hash; interpret the effect
+              %th{:style=>"border:2px solid #E6E6E6;"}
+                Predominantly in compounds with activity "inactive"
+              %th{:style=>"border:2px solid #E6E6E6;"}
+                p value
+              - @significant_fragments.each do |fragments|
+                / fragments == [effect, smarts, pValue]
+                / fragments[0] = effect
+                /- $logger.debug "effect:\t#{fragments[0]}\n"
+                - if fragments[0] == @value_map.index("inactive")
+                  %tr
+                    %td
+                      / fragments[1] = smarts 
+                      = fragments[1]
+                      -#%img{:src => "http://smartsview.de/smartsview/auto/png/1/both/#{CGI.escape(fragments[1])}", :class => "smarts"}
+                    %td
+                      /fragments[2] = pValue
+                      = fragments[2]
+            %tr
+              %th{:style=>"border:2px solid #E6E6E6;"}
+                Predominantly in compounds with activity "active"   
+              %th{:style=>"border:2px solid #E6E6E6;"}
+                p value
+              - @significant_fragments.each do |fragments|
+                / fragments == [effect, smarts, pValue]
+                - if fragments[0] == @value_map.index("active")
+                  %tr
+                    %td
+                      -#%img{:src => "http://smartsview.de/smartsview/auto/png/1/both/#{CGI.escape(fragments[1])}", :class => "smarts"}
+                      = fragments[1]
+                    %td
+                      = fragments[2]
+    %br
+  - if @type =~ /regression/i
+    %div.row
+      %div.col-md-4
+        %h3
+          Descriptors:
+        %img{:src=>"#{@compound.uri}/image", :alt=>"#{@compound.smiles}", :title=>"#{@compound.smiles}", :width=>"300px", :heigth=>"300px"}
+      - if !@significant_fragments.empty?
+        %div.col-md-8
+          %table{:id =>"de"}
+            %tr
+              %th{:style=>"border:2px solid #E6E6E6;"}
+                Descriptor
+              %th{:style=>"border:2px solid #E6E6E6;"}
+                value
+              - @significant_fragments.each do |fragments|
+                %tr
+                  %td
+                    = fragments[0]
+                  %td
+                    = fragments[1][0].round(3)
+    %br

data/views/style.scss

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+body {
+  background-color:#E7E7E7;
+}
+table.table-borderless tbody tr td{
+  border-top: none;
+}
+h4.head-back, h5.head-back{
+  background-color: #E7E7E7;
+}
+.nav-tabs {
+  background-color: #E7E7E7;
+  margin-bottom: 0;
+
+  li.active a:hover {
+    background-color: #f5f5f5;
+  }
+
+  li a {
+    height: 5em;
+  }
+}
+img {
+  max-width: 100%;
+  max-height: 100%;
+}
+
+.plot {
+  height: 300px;
+  width: 300px;
+}
+.faq {
+  text-align: block;
+  margin-left:15%;
+  margin-right:15%;
+  margin-top:2%;
+}
+.faq h1 {
+  text-align: center;
+}
+.tablesorter-bootstrap thead .sorter-false {
+  cursor: default;
+}
+ul.share-buttons{
+  list-style: none;
+}
+.dropdown-menu {
+  min-width: 0px !important;
+  width:60px;
+}
+.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;
+
+  img{
+    width: 200px;
+    margin-right: 1em;
+  }
+}

data/views/validation.haml

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+- 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)} %"
+

metadata

@@ -0,0 +1,373 @@
+--- !ruby/object:Gem::Specification
+name: lazar-gui
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+platform: ruby
+authors:
+- Christoph Helma
+- Denis Gebele
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2016-06-08 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
+  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
+- !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
+  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
+- !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
+  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
+- !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
+  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
+- !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
+  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
+- !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
+  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
+- !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
+  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
+description: Graphical User Interface for Lazar Toxicology Predictions
+email:
+- helma@in-silico.ch
+- gebele@in-silico.ch
+executables:
+- lazar-start
+- lazar-stop
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- FAQ.md
+- Gemfile
+- README.md
+- VERSION
+- application.rb
+- bin/lazar-start
+- bin/lazar-start.sh
+- bin/lazar-stop
+- bin/lazar-stop.sh
+- config.ru
+- helper.rb
+- lazar-gui.gemspec
+- public/css/bootstrap-theme.min.css
+- public/css/bootstrap.min.css
+- public/css/images/black-asc.gif
+- public/css/images/black-desc.gif
+- public/css/images/black-unsorted.gif
+- public/css/images/bootstrap-black-unsorted.png
+- public/css/images/bootstrap-white-unsorted.png
+- public/css/images/dragtable-handle.png
+- public/css/images/dragtable-handle.svg
+- public/css/images/dropbox-asc-hovered.png
+- public/css/images/dropbox-asc.png
+- public/css/images/dropbox-desc-hovered.png
+- public/css/images/dropbox-desc.png
+- public/css/images/first.png
+- public/css/images/green-asc.gif
+- public/css/images/green-desc.gif
+- public/css/images/green-header.gif
+- public/css/images/green-unsorted.gif
+- public/css/images/ice-asc.gif
+- public/css/images/ice-desc.gif
+- public/css/images/ice-unsorted.gif
+- public/css/images/last.png
+- public/css/images/loading.gif
+- public/css/images/metro-black-asc.png
+- public/css/images/metro-black-desc.png
+- public/css/images/metro-loading.gif
+- public/css/images/metro-unsorted.png
+- public/css/images/metro-white-asc.png
+- public/css/images/metro-white-desc.png
+- public/css/images/next.png
+- public/css/images/prev.png
+- public/css/images/white-asc.gif
+- public/css/images/white-desc.gif
+- public/css/images/white-unsorted.gif
+- public/css/jquery-ui.css
+- public/css/jquery-ui.theme.min.css
+- public/css/theme.bootstrap.css
+- public/css/theme.bootstrap.min.css
+- public/css/theme.default.min.css
+- public/fonts/glyphicons-halflings-regular.eot
+- public/fonts/glyphicons-halflings-regular.svg
+- public/fonts/glyphicons-halflings-regular.ttf
+- public/fonts/glyphicons-halflings-regular.woff
+- public/fonts/glyphicons-halflings-regular.woff2
+- public/images/Email.png
+- public/images/Facebook.png
+- public/images/Google+.png
+- public/images/IST_logo_s.png
+- public/images/LinkedIn.png
+- public/images/OpenToxEuro2013_small.png
+- public/images/Twitter.png
+- public/images/arrow_down_float.png
+- public/images/arrow_left_float.png
+- public/images/arrow_right_float.png
+- public/images/arrow_up_float.png
+- public/images/asc.gif
+- public/images/bfr_logo.gif
+- public/images/bg.gif
+- public/images/blind.png
+- public/images/desc.gif
+- public/images/enm_logo.png
+- public/images/favicon.ico
+- public/images/gray_jean.png
+- public/images/info_white.png
+- public/images/ist_logo.png
+- public/images/nestec.jpg
+- public/images/ot_logo.png
+- public/images/wait30trans.gif
+- public/javascripts/bootstrap.min.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
+- public/javascripts/jquery.bpopup.min.js
+- public/javascripts/jquery.tablesorter.min.js
+- public/javascripts/jquery.tablesorter.widgets.js
+- public/javascripts/jquery.tools.min.js
+- public/javascripts/lazar-gui.js
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+- public/rect.png
+- public/stylesheets/jquery-ui.css
+- test/lazarweb.rb
+- test/setup.rb
+- unicorn.rb
+- views/batch.haml
+- views/details.haml
+- views/error.haml
+- views/faq.haml
+- views/faq_layout.haml
+- views/info.haml
+- views/jme_help.html
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+- views/layout.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
+metadata: {}
+post_install_message: "\n  Service cmds:\n    lazar-start &\n    lazar-stop\n  "
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: lazar-gui
+rubygems_version: 2.5.1
+signing_key: 
+specification_version: 4
+summary: lazar-gui
+test_files: []