lazar-gui 1.3.1 → 1.4.0.pre.0

data/task.rb

@@ -0,0 +1,68 @@
+DEFAULT_TASK_MAX_DURATION = 36000
+
+module OpenTox
+
+  class Task
+
+    include OpenTox
+    include Mongoid::Document
+    include Mongoid::Timestamps
+    store_in collection: "tasks"
+    field :pid, type: Integer
+    field :percent, type: Float, default: 0
+    field :predictions, type: Hash, default:{}
+    field :csv, type: String
+    field :dataset_id, type: BSON::ObjectId
+    field :model_id, type: BSON::ObjectId
+    field :subTasks, type: Array, default:[]
+
+    attr_accessor :pid, :percent, :predictions, :csv, :dataset_id, :model_id, :subTasks
+
+    def pid
+      self[:pid]
+    end
+    
+    def percent
+      self[:percent]
+    end
+    
+    def predictions
+      self[:predictions]
+    end
+
+    def csv
+      self[:csv]
+    end
+    
+    def dataset_id
+      self[:dataset_id]
+    end
+    
+    def model_id
+      self[:model_id]
+    end
+    
+    def subTasks
+      self[:subTasks]
+    end
+
+    def update_percent(percent)
+      self[:percent] = percent
+      save
+    end
+
+    def self.run
+      task = Task.new #uri
+      pid = fork do
+        yield
+      end
+      Process.detach(pid)
+      task[:pid] = pid
+      task.save
+      task
+    end
+
+  end
+
+end
+

data/unicorn.rb

@@ -1,2 +1 @@
-worker_processes 4
 timeout 6000

data/views/batch.haml

@@ -1,109 +1,50 @@
-%div.well
-  %a.btn.btn-warning{:href => to('/predict')}
-    %span.glyphicon.glyphicon-menu-left{:aria=>{:hidden=>"true"}}
+:javascript
+  // kill task pid if page is reloaded, `false` makes the request synchronous
+  window.addEventListener('unload', ktpid, false);
+  function ktpid() {
+    var client = new XMLHttpRequest();
+    client.open("GET", '//#{$host_with_port}/prediction/task?ktpid=#{@pid}', false);
+    client.setRequestHeader("Content-Type", "application/json");
+    client.send(null);
+  };
+%div.card
+  %a.btn.btn-outline-info{:href => "//#{$host_with_port}/predict?tpid=#{@pid}"}
+    %span.fa.fa-caret-left{:aria=>{:hidden=>"true"}}
     New Prediction
-  %a.btn.btn-success{:id => "downbutton", :href=>"#{to("/predict/#{@tmppath}/#{@filename}")}", :title=>"download"}
-    %span.glyphicon.glyphicon-download-alt
-    Download CSV
+%div.card.bg-light
+  %div.card-body
+    %h3.card-title="Batch prediction results for: #{@filename}"
+
+    // prepare variable values for javascript
+    // increase timer interval for large datasets
+    - timer = 10000#((@compounds_size/1000) == 0 ? 1000 : ((@compounds_size/1000)*1000))
+    // process batch predictions
+    - @models.each_with_index do |model,idx|
+      - m = Model::Validation.find model
+      - task = @tasks[idx].id
+      #result.card.bg-light{:id=>idx}
+        %div.card-body
+          %div.row
+            %div.col-6
+              %h5.card-title="#{m.endpoint} (#{m.species})"
+              #pager{:id=>idx}
+            %div.col-6
+              %a.btn.btn-outline-info.btn-sm.disabled{:id => "detailsbutton_#{idx}", :data=>{:toggle=>"collapse"}, :href=>"javascript:void(0)", :onclick=>"pagePredictions('//#{$host_with_port}/prediction/task/?predictions=#{task}','#{model}','#{idx}','#{@compounds_size}')"}
+                %span.fa.fa-caret-right
+                Details
+              %a.btn.btn-outline-info.btn-sm.disabled{:id => "downbutton_#{idx}", :href=>"//#{$host_with_port}/predict/batch/download?tid=#{task}", :title=>"download"}
+                %span.fa.fa-download
+                CSV
+          %p{:id=>"est_#{idx}"}
+            waiting ...
+          %img.h2{:src=>"/images/wait30trans.gif", :id=>"circle_#{idx}", :class=>"circle", :alt=>"wait", :style=>"display:none;"}
+          :javascript
+            $(document).ready(function() {
+              taskProgress('#{idx}','#{timer}','//#{$host_with_port}/prediction/task/?turi=#{task}');
+            });
+          #data-container.card.d-none.table-responsive{:id=>idx}
+    :javascript
+%div.modal.fade{:id=>"details", :tabindex=>"-1", :role=>"dialog"}
+  %div.modal-dialog.modal-lg{:role=>"document"}
+    %div.modal-content
 
-  / show file name
-  %topline
-    %div.row
-      %div.col-md-4
-        %h3 Batch Prediction Results:
-      %div.col-md-8
-        %h3= @filename
-  
-  / displays all prediction result in one table
-  %div.table-responsive
-    %table.table.table-bordered{:id=>"batch", :style=>"background-color:white;"}
-      %tbody
-        - if @warnings
-          - @warnings.each do |warning|
-            %tr
-              %td
-                %b Warning
-              %td
-                = warning.sub(/\b(tmp\/)\b/,"")
-        - @view.each do |compound, array|
-          %tr
-            %td{:style=>"vertical-align:top;"}
-              %p= compound.svg
-              %p= compound.smiles
-            - array.each do |model,prediction|
-              %td{:style=>"vertical-align:top;white-space:nowrap;"}
-                - model.model.class.to_s.match("Classification") ? type = "Classification" : type = "Regression"
-                - unit = model.unit
-                
-                %b{:class => "title"}
-                  = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
-                    
-                / check for prediction
-                - if prediction[:value]
-                  %p
-                  / show model type (classification|regression)
-                  %b Type:
-                  = type
-                  %p 
-                  / check for database hit
-                  - if prediction[:info] =~ /\b(identical)\b/i
-                    
-                    / 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(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements]
-                    
-                    
-                  / show prediction
-                  %p
-                    %b Prediction:
-                    %br
-                    = (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
-                    - if type == "Regression"
-                      %b 95% Prediction interval:
-                      - interval = (prediction[:prediction_interval].nil? ? nil : prediction[: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(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
-                    - else
-                      %b Probability:
-                      - unless prediction[:probabilities].nil?
-                        - probabilities = ""
-                        - prediction[:probabilities].each{|k,v| probabilities += "#{k}: #{v.signif(3)}<br>"}
-                        %br
-                        = probabilities
-                  / show warnings
-                  %p
-                  - if !prediction[:info].blank?
-                    %b Info:
-                    %br
-                    %p=prediction[:info].sub(/\'.*\'/,"").sub(/,/, ",<br>")
-                  - if !prediction[:warnings].blank?
-                    %b Warnings:
-                    - prediction[:warnings].uniq.each do |warning|
-                      %br
-                      %p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
-                        
-                  / no prediction  
-                - else
-                  %br
-                  - if !prediction[:info].blank?
-                    %b Info:
-                    %br
-                    %p=prediction[:info].sub(/\'.*\'/,"").sub(/,/, ",<br>")
-                  - if !prediction[:warnings].blank?
-                    %b Warnings:
-                    - prediction[:warnings].uniq.each do |warning|
-                      %br
-                      %p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
-            %tr

data/views/details.haml

@@ -6,7 +6,7 @@
   %button.close{ :type=>" button", data: { dismiss:"modal"}} ×
   %h3
     Names and synonyms:
-  %p= @compound.svg
+  %p= embedded_svg(@compound.svg, :title=>"x")
   %p
   %b="SMILES:"
   %p= @smiles
@@ -14,6 +14,11 @@
   %b="InChI:"
   %p= @inchi
   %br
+  - cid = @compound.cid
+  - if cid
+    %b="CID:"
+    %p= cid
+    %br
   %b="Names:"
   %p{:style=>"padding-left:0.5em;"}
   - if @names !~ /^no names/i
@@ -23,6 +28,9 @@
   %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", :rel=>"external"} PubChem read across 
+    - if cid
+      %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/cid/#{cid}", :title=>"Link opens in new window.", :alt=>"pubchem read across", :rel=>"external"} PubChem read across 
+    - else
+      %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/error.haml

@@ -1,7 +1,6 @@
-%div.well
-  %a.btn.btn-warning{:href => to('/predict')}
-    %i.glyphicon.glyphicon-menu-left
+%div.card
+  %a.btn.btn-warning{:href => "//#{$host_with_port}/predict"}
+    %i.fa.fa-caret-left
     Back
-  %hr
-  %div.well{:style=>"width:100%;margin-bottom:2em;"}
+  %div.card-body
     = @error

data/views/faq.haml

@@ -1,2 +1,6 @@
-%div.well.faq
-  = @faq
+%div.card
+  %a.btn.btn-warning{:href => "//#{$host_with_port}/predict"}
+    %i.fa.fa-caret-left
+    Back
+  %div.card-body
+    = @faq

data/views/help.haml

@@ -0,0 +1,68 @@
+%div.card.bg-light
+  %div.card-body
+    %h3 How to use batch prediction
+
+    %p
+      You have two options to format your comma or tab sperated spreadsheet for batch predictions:
+
+    %br
+    %p
+      %div.row
+        %div.col-md-6
+          %strong Option 1:
+          %br
+          A spreadsheet with a single column and a header. The header should specify the input format (SMILES or InChI are accepted).
+        %div.col-md-6
+          %table.help
+            %tr.row
+              %th.col-md-12
+                SMILES
+            %tr.row
+              %td.col-md-12
+                C1ccccc1NN
+            %tr.row
+              %td.col-md-12
+                Cc1ccc(cc1\N=C=O)/N=C=O
+            %tr.row
+              %td.col-md-12
+                OC(=O)c1ccc(cc1)C(=O)O
+            %tr.row
+              %td.col-md-12
+                ="..."
+    %br
+    %p
+      %div.row
+        %div.col-md-6
+          %strong Option 2:
+          %br
+          A spreadsheet with two columns and a header. The first column may contain an arbitrary ID, 
+          the second column the compound structure (as SMILES or InChI).  
+          The header consists of "ID" followed by the input format (SMILES or InChI).
+        %div.col-md-6
+          %table.help
+            %tr.row
+              %th.col-md-4
+                ID
+              %th.col-md-8
+                SMILES
+            %tr.row
+              %td.col-md-4
+                2735
+              %td.col-md-8
+                C1ccccc1NN
+            %tr.row
+              %td.col-md-4
+                A2
+              %td.col-md-8
+                O=C(OCCCC)C1=CC=CC=C1C(OCCCC)=O
+            %tr.row
+              %td.col-md-4
+                82 B-6 304663
+              %td.col-md-8
+                CC(C)(C)C1=CC2(C=C(C1=O)C(C)(C)C)CCC(=O)O2
+            %tr.row
+              %td.col-md-4
+                ="..."
+              %td.col-md-8
+                ="..."
+    %br

data/views/info.haml

@@ -1,2 +1,3 @@
-%div.info
-  We are rebuilding the models. It will take a while, please be patient and reload the page in some time.
+%div.card.border-warning.mb-3
+  %div.card-body
+    We are rebuilding our models. It will take a while, please be patient and reload the page later.

data/views/layout.haml

@@ -6,77 +6,55 @@
     %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"}
     %title lazar Toxicity Predictions
     %link{:rel=>'icon', :type=>'image/x-icon', :href=>'/images/favicon.ico'}
-    %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"}
-    %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"}
-    %link{:rel=>'stylesheet', :href=>"#{'/css/theme.bootstrap.min.css'}"}
-    %link{ :href=>"/style.css", :rel=>"stylesheet"}
-    %link{ :href=>"/stylesheets/jquery-ui.css", :rel=>"stylesheet"}
-    %script{:src=>"/javascripts/jquery-1.11.2.min.js"}
-    %script{:src=>"/javascripts/bootstrap.min.js"}
-    %script{:src=>"/javascripts/jquery.tablesorter.min.js"}
-    %script{:src=>"/javascripts/jquery.tablesorter.widgets.js"}
+    %link{:href=>"/stylesheets/bootstrap.min.css", :rel=>"stylesheet"}
+    %link{:href=>"/stylesheets/font-awesome.min.css", :rel=>"stylesheet"}
+    %link{:href=>"/stylesheets/pagination.css", :rel=>"stylesheet"}
+    %link{:href=>"/style.css", :rel=>"stylesheet"}
+    %script{ :src=>"/javascripts/jquery.min.js"}
+    %script{ :src=>"/javascripts/popper.min.js"}
     %script{:src=>"/javascripts/lazar-gui.js"}
-    %script{:src=>"/javascripts/google_analytics_lazar.js"}
+    %script{ :src=>"/javascripts/bootstrap.js"}
+    %script{:src=>"/javascripts/pagination.min.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-3
-          %a{:href=> to("/predict")}
-            %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-3
-          %h1.media-heading
-            %small
-              %a.btn{:href=>"https://nano-lazar.in-silico.ch", :rel=>"external"}
-                nano-lazar
-                %span.glyphicon.glyphicon-new-window
-
+    %header.container-fluid.page-header
+      %div.row.align-items-center
+        %div.col-3
+          %a.card-link{:href=> "https://in-silico.ch/", :rel=>"external"}
+            %img{:src=>"/images/IST_logo_s.png", :alt=>"logo", :width=>"120px"}
+        %div.col-7
+          %h1 lazar toxicity predictions
+        %div.col-2
+          %h5
+            %a.text-right{:href=>"https://nano-lazar.in-silico.ch", :rel=>"external"}
+              nano-lazar
+              %span.fa.fa-xs.fa-external-link
     %div.container-fluid
       %topline.alert
-        %div.row
-          %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
-            , 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{: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", :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", :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", :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();
-          $(".blind").error(function(){
-            $(this).attr('src', '/images/blind.png');
-          });
-        });
-        $(document).ready(function(){
-          $('[data-toggle="popover"]').popover();
-          $('.modal').on('hidden.bs.modal', function () {
-            $(this).removeData('bs.modal');
-          });
-        });
+        %p
+          Problems, bugs, ideas for improvements ? Please report at our
+          %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker
+          , check out the 
+          %a{:href=> "//#{$host_with_port}/predict/faq"} FAQ
+          page or send us an email.
+          %a{ :href=>"mailto:info@in-silico.ch?subject=[lazar v#{@version}]", :target=>"_top"}
+            %span.fa.fa-envelope
+          [version: #{@version}]
+        %p
+          A graphical overview of the service API can be found
+          %a{:href => "//#{$host_with_port}/api", :rel => "external"} here.
+          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.
+          %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=https%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Tweet"}
+            %span.fa.fa-twitter-square
+          %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=https%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=https%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on LinkedIn"}
+            %span.fa.fa-linkedin-square
+          %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=https%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=https%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on Facebook"}
+            %span.fa.fa-facebook-square
           
       = yield
     
@@ -88,24 +66,24 @@
               © 
               %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
-            %div.panel.panel-default
+              %a{:href => "//#{$host_with_port}/predict/license", :rel => "external"} GPL3 License
+        %supporters.row
+          %div.card-body.text-center
+            %div.card-title
               Financial support by
-              %div.panel-body
-                %a{:href=>"http://www.bfr.bund.de/de/start.html", :rel=>"external"}
-                  %img{:src=>"/images/bfr_logo.gif"}
-                %a{:href=>"http://www.opentox.org/", :rel=>"external"}
-                  %img{:src=>"/images/ot_logo.png"}
-                %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", :rel=>"external"}
-                  %img{:src=>"/images/nestec.jpg"}
- 
+            %div.card-text
+              %a{:href=>"https://www.bfr.bund.de/de/start.html", :rel=>"external"}
+                %img{:src=>"/images/bfr_logo.gif"}
+              %a{:href=>"https://www.opentox.org/", :rel=>"external"}
+                %img{:src=>"/images/ot_logo.png"}
+              %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", :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;"}
-        %span.glyphicon.glyphicon-circle-arrow-up{:style => "font-size:3em;color:black;"}
+        %span.fa.fa-caret-up{:style => "font-size:3em;color:black;"}
     :javascript
       $("#back-top").hide();
       $(function () {
@@ -124,3 +102,15 @@
           return false;
         });
       });
+      $(document).ready(function(){
+        $("#back-top").hide();
+        $(".blind").on('error', function(){
+          $(this).attr('src', '/images/blind.png');
+        });
+      });
+      $(document).ready(function(){
+        //$('[data-toggle="popover"]').popover();
+        $('.modal').on('hidden.bs.modal', function () {
+          $(this).removeData('bs.modal');
+        });
+      });