issue fixes;added faq

4 files changed, 16 insertions, 75 deletions

diff --git a/views/faq_layout.haml b/views/faq_layout.haml
deleted file mode 100644
index a9b6664..0000000
--- a/views/faq_layout.haml
+++ /dev/null
@@ -1,67 +0,0 @@
-!!!
-%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"}
-  %head
-    %meta{'charset'=>"utf-8"}
-    %meta{'http-equiv'=>"X-UA-Compatible", :content=>"IE=edge"}
-    %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"}
-    %title Lazar GUI FAQ
-    %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/lazar-gui.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-2
-          %a{:href=> to("/predict")}
-            %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"}
-        %div.col-md-10
-          %h1.media-heading{:style=>"margin: 0 0 0 1em;display:inline;"} Lazar GUI
-          A Graphical User Interface for the <a href="http://github.com/opentox/lazar">Lazar</a> framework
-    
-    %div.container-fluid
-      :javascript
-        $(document).ready(function(){
-          $("#back-top").hide();
-          $(".blind").error(function(){
-            $(this).attr('src', '/images/blind.png');
-          });
-        });
-          
-      = yield
-    
-    %footer.footer
-      %div.container-fluid
-        %p.text-muted
-          &copy; 
-          %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}
-
-    #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;"}
-    :javascript
-      $("#back-top").hide();
-      $(function () {
-        $(window).scroll(function () {
-          if ($(this).scrollTop() > 600) {
-            $('#back-top').fadeIn();
-          } else {
-            $('#back-top').fadeOut();
-          }
-        });
-        // scroll body to 0px on click
-        $('#back-top a').click(function () {
-          $('body,html').animate({
-            scrollTop: 0
-          }, 500);
-          return false;
-        });
-      });
diff --git a/views/layout.haml b/views/layout.haml
index 62a224b..dc83956 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -36,15 +36,16 @@
     %div.container-fluid
       %topline
         %div.row
-          %div.col-md-8
+          %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
-            or send us an email.
-            %a{ :href=>"mailto:info@in-silico.ch", :target=>"_top"}
+            , 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
-          %div.col-md-2
+          %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+"}
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 2f0b3d7..18c23f8 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -3,6 +3,11 @@
 / align single prediction to endpoint ;
 / display preordered in table view ;
 
+:javascript
+  $(document).ready(function(){
+    addExternalLinks();
+  });
+
 %div.results
   %h3 Neighbors:
   / tabs div
@@ -35,6 +40,7 @@
           / presort by similarity ;
           :javascript
             $(document).ready(function(){
+              addExternalLinks();
               $("table##{j+1}").tablesorter({
                 debug: false,
                 theme: "bootstrap",
@@ -70,7 +76,7 @@
                       %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
                     %th.sorter-false{:style =>"vertical-align:middle;"}
                       Similarity
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"<a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
                     / %th{:style =>"vertical-align:middle;"}
                     / Supporting Information
                 %tbody
diff --git a/views/predict.haml b/views/predict.haml
index b7a4087..59630d0 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -111,7 +111,7 @@
   };
 
 // whole site content needs to be in one form. Input and checkboxes are proofed by js functions. 
-%form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return  !!(showcircle())" }
+%form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return !!(showcircle())" }
   %fieldset#top.well
     %h2 1. Draw a chemical structure
     #insert
@@ -130,7 +130,8 @@
       -#%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=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"}
+      %input{:type=>"hidden", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"}
 
   %fieldset#middle.well
     %h2 2. Select one or more endpoints