rebuild code for public release;prepared to work with lazar v1.0.0;reintroduced compound details

5 files changed, 57 insertions, 24 deletions

diff --git a/views/details.haml b/views/details.haml
index bb8250d..be4948a 100644
--- a/views/details.haml
+++ b/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
diff --git a/views/layout.haml b/views/layout.haml
index 5ed63e8..62a224b 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -29,11 +29,30 @@
           %h1.media-heading
             lazar toxicity predictions
         %div.col-md-2
-          %h5
+          %h1.media-heading
             %small
-              [version: #{@version}]
+              %a{:href=>"https://nano-lazar.in-silico.ch", :rel=>"external"} nano-lazar
 
     %div.container-fluid
+      %topline
+        %div.row
+          %div.col-md-8
+            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"}
+              %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=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"}
       :javascript
         $(document).ready(function(){
           $("#back-top").hide();
@@ -57,7 +76,19 @@
             %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 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/", :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;"}
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 32b8389..a608c4d 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -81,8 +81,8 @@
                     / Compound
                     - 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
                     
                     / Measured Activity
diff --git a/views/predict.haml b/views/predict.haml
index 9a7d0d4..b7a4087 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -125,12 +125,12 @@
       %br
       %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
       %p
-      %label{:for=>"fileselect"}
-        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"}
+      -#%label{:for=>"fileselect"}
+        or upload a CSV file for batch predictions (disabled in public version)
+      -#%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"}
 
   %fieldset#middle.well
     %h2 2. Select one or more endpoints
diff --git a/views/prediction.haml b/views/prediction.haml
index b090be5..362f006 100644
--- a/views/prediction.haml
+++ b/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
@@ -16,7 +9,8 @@
       %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
           - @model_types = {}
           - @dbhit = {}
@@ -57,7 +51,7 @@
                 %p
                   %b Prediction:
                   / 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>."}}
+                  %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>."}}
                   %br
                   = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                   
@@ -67,20 +61,20 @@
                     %b 95% Prediction interval:
                     - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval])
                     / prediction interval 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."}}
+                    %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} - #{interval[0].delog10} (#{unit})"
                     %br
                     = "#{@compound.mmol_to_mg(interval[1].delog10)} - #{@compound.mmol_to_mg(interval[0].delog10)} #{(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=>"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."}}
                     - unless prediction[:probabilities].nil?
                       %br
                       = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}"
                       %br
                       = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}"
-                    / probability 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."}}
                 
                 / show warnings
                 %p
@@ -94,4 +88,8 @@
 
   / 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