Merge branch 'development' into feature/ambit-datasets

16 files changed, 45 insertions, 43 deletions

diff --git a/views/create.haml b/views/create.haml
index 82f48d0..2149f3d 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -45,5 +45,5 @@
       and your models can be modified or deleted by other guests. Please
       = link_to "log in", "/login"
       with your
-      %a{:href => "www.opentox.org"} OpenTox
+      %a{:href => "http://www.opentox.org", :rel => "external"} OpenTox
       account to control your model permissions.
diff --git a/views/feature_table.haml b/views/feature_table.haml
index 4fa927c..a8a153f 100644
--- a/views/feature_table.haml
+++ b/views/feature_table.haml
@@ -4,7 +4,7 @@
       %th
         activating 
         (
-        %a{:href => "http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html"} SMARTS
+        %a{:href => "http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html", :rel => "external"} SMARTS
         )
       %th p value
     - if features[:activating]
@@ -17,7 +17,7 @@
       %th
         deactivating
         (
-        %a{:href => "http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html"} SMARTS
+        %a{:href => "http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html", :rel => "external"} SMARTS
         )
       %th p value
     - if features[:deactivating]
diff --git a/views/help.haml b/views/help.haml
index da6495e..3d39641 100644
--- a/views/help.haml
+++ b/views/help.haml
@@ -1,7 +1,7 @@
 = link_to "Back to model creation", '/create'
 %p
   Input files have two columns. Enter in the first column the chemical structure in
-  %a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification"} SMILES
+  %a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification", :rel => "external"} SMILES
   format, in the second column the toxic activity. The first line contains a description of the columns and is ignored.
 %dl
   %dt Classification datasets 
@@ -12,15 +12,15 @@
     %ul
       %li
         use
-        %a{:href => "http://en.wikipedia.org/wiki/Molar_(concentration)"} molar
+        %a{:href => "http://en.wikipedia.org/wiki/Molar_(concentration)", :rel => "external"} molar
         units
       %li enter non-logarithmic values (logarithms are taken internally)
       %li avoid 0 activities (will be ignored)
 %p 
   Input files are accepted in 
-  %a{:href => "http://en.wikipedia.org/wiki/Microsoft_Excel"} Excel
+  %a{:href => "http://en.wikipedia.org/wiki/Microsoft_Excel", :rel => "external"} Excel
   and
-  %a{:href => "http://en.wikipedia.org/wiki/Comma-separated_values"} CSV
+  %a{:href => "http://en.wikipedia.org/wiki/Comma-separated_values", :rel => "external"} CSV
   formats.
 
 %h3 Excel example
diff --git a/views/layout.haml b/views/layout.haml
index cdabe43..c849dec 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -37,7 +37,7 @@
       - if `hostname`.match(/ot-test/)
         .notice 
           This service is for testing purposes only - once a week all models will be deleted. Please send bug reports and feature requests to our 
-          %a{:href => 'http://github.com/opentox/toxcreate/issues'} issue tracker.
+          %a{:href => 'http://github.com/opentox/toxcreate/issues', :rel => "external"} issue tracker.
 
       - if flash[:notice]
         %p
@@ -48,6 +48,6 @@
 
     .footer
       ©
-      %a{:href => 'http://www.in-silico.ch'} in silico toxicology
+      %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico toxicology
       2009-2010, powered by
-      %a{:href => 'http://www.opentox.org'} <span style="color:#5D308A;font-family:arial,sans-serif,helvetica;letter-spacing:-1px;">Open</span><span style="color:#000;font-family:arial,sans-serif,helvetica;font-weight:bold;letter-spacing:-1px;position:relative;">Tox</span>
+      %a{:href => 'http://www.opentox.org', :rel => "external"} <span style="color:#5D308A;font-family:arial,sans-serif,helvetica;letter-spacing:-1px;">Open</span><span style="color:#000;font-family:arial,sans-serif,helvetica;font-weight:bold;letter-spacing:-1px;">Tox</span>
diff --git a/views/lazar.haml b/views/lazar.haml
index 3de7400..deb0c18 100644
--- a/views/lazar.haml
+++ b/views/lazar.haml
@@ -36,12 +36,12 @@
             %li= toggle_link("#fragments","Significant fragments")

             -# This does not work, ask nina/vedrin

             -# %li

-              %a{:href => "http://ambit.uni-plovdiv.bg:8080/ambit2/query/structure/?search=#{@compound.smiles}"} Ambit data

+              %a{:href => "http://ambit.uni-plovdiv.bg:8080/ambit2/query/structure/?search=#{@compound.smiles}", :rel => "external"} Ambit data

             -# %li

-              %a{:href => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pccompound&term=#{URI.encode('"'+@compound.inchi+'"[InChI]')}"}  PubChem data

-              (external)

+              %a{:href => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pccompound&term=#{URI.encode('"'+@compound.inchi+'"[InChI]')}", :rel => "external"}  PubChem data

+                (external)
             -# %li

-              %a{:href => "http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&inchi=#{URI.encode @compound.inchi}"} ToxNet data

+              %a{:href => "http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&inchi=#{URI.encode @compound.inchi}", :rel => "external"} ToxNet data

             -#http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&regno=000143157

 

       %tr#names{ :style => "display: none;" }

diff --git a/views/lazar_algorithm.haml b/views/lazar_algorithm.haml
index b83de6b..85823b5 100644
--- a/views/lazar_algorithm.haml
+++ b/views/lazar_algorithm.haml
@@ -20,13 +20,13 @@
           a majority vote (weighted by compound similarity) for
           %em classification
           (
-          %a{:href => "http://www.in-silico.de/articles/modi020905.pdf"} original publication
+          %a{:href => "http://www.in-silico.de/articles/modi020905.pdf", :rel => "external"} original publication
           )
         %li
           a local QSAR model based on neighbors for
           %em regression
           (
-          %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf"} original publication
+          %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf", :rel => "external"} original publication
           )
 
     %p
diff --git a/views/lazar_description.haml b/views/lazar_description.haml
index d8e995d..3eee850 100644
--- a/views/lazar_description.haml
+++ b/views/lazar_description.haml
@@ -18,11 +18,11 @@
         a majority vote (weighted by compound similarity) for
         %em= toggle_link("#classification","classification")
         (
-        %a{:href => "http://www.in-silico.de/articles/modi020905.pdf"} original publication
+        %a{:href => "http://www.in-silico.de/articles/modi020905.pdf", :rel => "external"} original publication
         )
       %li
         a local QSAR model based on neighbors for
         %em= toggle_link("#regression","regression")
         (
-        %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf"} original publication
+        %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf", :rel => "external"} original publication
         )
diff --git a/views/login.haml b/views/login.haml
index 6d15bb7..1a74f12 100644
--- a/views/login.haml
+++ b/views/login.haml
@@ -7,15 +7,15 @@
       and your models can be modified or deleted by other guests.
       To control models permissions you can
       log in with your
-      %a{:href => "http://www.opentox.org"} OpenTox
-      username/password below. If have no 
-      %a{:href => "http://www.opentox.org"} OpenTox
-      account yet you can 
-      %a{:href => "http://www.opentox.org/join_form"} register here.
+      %a{:href => "http://www.opentox.org", :rel => "external"} OpenTox
+      username/password below. If you don't have an
+      %a{:href => "http://www.opentox.org", :rel => "external"} OpenTox
+      account yet you could  
+      %a{:href => "http://www.opentox.org/join_form", :rel => "external"} register here.
   - else
     %p
       Change
-      %a{:href => "http://www.opentox.org"} OpenTox
+      %a{:href => "http://www.opentox.org", :rel => "external"} OpenTox
       account:
 
   -# if !logged_in()
diff --git a/views/model.haml b/views/model.haml
index 91d7016..4933cdb 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -18,7 +18,7 @@
           - if (task = OpenTox::Task.exist?(model.task_uri))
             %input{:type => 'hidden', :id => "model_#{model.id}_task", :value => "#{model.task_uri}"}
             - percentage_completed = task.metadata[OT.percentageCompleted].to_i
-            - js = "$('#model_#{model.id}_progress').progressbar({ value: #{percentage_completed} })";
+            - js = "$('#model_#{model.id}_progress').progressbar({ value: #{percentage_completed} });"
             :javascript
               $(function() {
                 #{js}
@@ -28,15 +28,15 @@
               //= haml :model_progress, :locals=>{:percentage_completed=>percentage_completed}, :layout => false        
         - if is_authorized(model.web_uri, "DELETE")
           %a{:href => url_for("/model/#{model.id}"), :id => "delete_#{model.id}", :class => 'delete_link'} 
-            - if model.status == "Completed" 
+            - if model.status =~ /Completed|Error|Cancelled/ 
               (delete)
             - else
               (stop)
         %span
           %br
         
-      -#%dt Started:
-      -#%dd= model.created_at.strftime("%m/%d/%Y - %I:%M:%S%p")
+      %dt Started:
+      %dd= Time.parse(model.created_at.to_s).strftime("%m/%d/%Y - %I:%M:%S%p") if model.created_at
       - if model.nr_compounds
         %dt Training compounds:
         %dd= model.nr_compounds 
@@ -54,7 +54,7 @@
         %dd= toggle_link("##{model.type}","#{model.type}")
       %dt Descriptors:
       %dd
-        %a{:href => 'http://www.maunz.de/libfminer2-bbrc-doc/'} Fminer backbone refinement classes
+        %a{:href => 'http://www.maunz.de/libfminer2-bbrc-doc/', :rel => "external"} Fminer backbone refinement classes
       - if model.training_dataset
         %dt Training dataset:
         %dd
diff --git a/views/model_name.haml b/views/model_name.haml
index b1f6f10..91516ce 100644
--- a/views/model_name.haml
+++ b/views/model_name.haml
@@ -1,4 +1,4 @@
-- js = "$('#edit_#{model.id}').editModel('PUT', {id: '#{model.id}', mode: 'edit'});\n  "
+- js = "$('#edit_#{model.id}').editModel({id: '#{model.id}', mode: 'edit'});\n  "
 :javascript
   $(function() {
     #{js}
diff --git a/views/model_name_edit.haml b/views/model_name_edit.haml
index aec59fc..d92c68a 100644
--- a/views/model_name_edit.haml
+++ b/views/model_name_edit.haml
@@ -1,5 +1,5 @@
-- js = "$('#cancel_#{model.id}').editModel('GET', {id: '#{model.id}', mode: 'show'});\n  "
-- js = "$('#save_#{model.id}').saveModel('POST', {id: '#{model.id}', mode: 'show'});\n  "
+- js = "$('#cancel_#{model.id}').cancelEdit({id: '#{model.id}', mode: 'show'});\n  "
+- js += "$('#save_#{model.id}').saveModel({id: '#{model.id}', mode: 'show'});\n  "
 :javascript
   $(function() {
     #{js}
@@ -10,5 +10,4 @@
   %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
   %input{ :type => "submit", :value => "Save", :id => "save_#{model.id}", :class => "edit_button"}
   %span{:class => "edit_button"}      
-    %a{:href => url_for("/model/#{model.id}/name?mode=show"), :id => "cancel_#{model.id}"} Cancel
-
+    %a{:href => "#", :id => "cancel_#{model.id}"} Cancel
diff --git a/views/models.haml b/views/models.haml
index 67c061c..6724807 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -6,18 +6,18 @@
       setTimeout('checkStati("#{stati_to_check}", "#{subjectstring}")',5000);
     }
     var reload_validation = true;
-    //if(reload_validation) setTimeout('checkValidation()',15000);
   });
 
 -# %p Get an overview about ToxCreate models. This page is refreshed every 15 seconds to update the model status.
 %p Get an overview about ToxCreate models. Parts of this page are refreshed every 5 seconds to update the model status.
 
 -# explanations
-= haml :lazar_description, :layout => false
 = haml :classification, :layout => false
+= haml :lazar_description, :layout => false
 = haml :regression, :layout => false
 = haml :similarity, :layout => false
 = haml :significant_fragments, :layout => false
 
-- @models.each do |model|
-  = haml :model, :locals=>{:model=>model,:subjectstring=>subjectstring}, :layout => false 
+- if @models
+  - @models.each do |model|
+    = haml :model, :locals=>{:model=>model,:subjectstring=>subjectstring}, :layout => false 
diff --git a/views/regression_validation.haml b/views/regression_validation.haml
index 00267a9..4dd4f6d 100644
--- a/views/regression_validation.haml
+++ b/views/regression_validation.haml
@@ -1,9 +1,9 @@
 %dt
-  %a{:href => "http://en.wikipedia.org/wiki/R-squared"} R-squared
+  %a{:href => "http://en.wikipedia.org/wiki/R-squared", :rel => "external"} R-squared
 %dd= sprintf '%.03g', model.r_square
 %dt
-  %a{:href => "http://en.wikipedia.org/wiki/Root_mean_square_deviation"} Root Mean Square Error
+  %a{:href => "http://en.wikipedia.org/wiki/Root_mean_square_deviation", :rel => "external"} Root Mean Square Error
 %dd= sprintf '%.03g', model.root_mean_squared_error
 %dt
-  %a{:href => "http://en.wikipedia.org/wiki/Mean_absolute_error"} Mean Absolute Error
+  %a{:href => "http://en.wikipedia.org/wiki/Mean_absolute_error", :rel => "external"} Mean Absolute Error
 %dd= sprintf '%.03g', model.mean_absolute_error
diff --git a/views/significant_fragments.haml b/views/significant_fragments.haml
index 87cb113..bd39826 100644
--- a/views/significant_fragments.haml
+++ b/views/significant_fragments.haml
@@ -6,5 +6,5 @@
     )
   %dd 
     Substructures that occur (statistically significant) more frequently in active or inactive compounds. Substuctures can take any shape (without cycles) and are determined with the 
-    %a{:href => "http://www.maunz.de/libfminer2-bbrc-doc/"} fminer
+    %a{:href => "http://www.maunz.de/libfminer2-bbrc-doc/", :rel => "external"} fminer
     algorithm.
diff --git a/views/style.sass b/views/style.sass
index db1f1bf..0588444 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -18,6 +18,9 @@ body
     color: $ot_purple
   a:hover
     color: black
+  a[rel="external"]
+    background: transparent url('../external.gif') center right no-repeat
+    padding-right: 15px
 
   .headline
     .logo
diff --git a/views/unit.haml b/views/unit.haml
index a352599..88433b5 100644
--- a/views/unit.haml
+++ b/views/unit.haml
@@ -6,5 +6,5 @@
     )
   %dd 
     Unit of measurement, e.g. mmol or mmol/kg-bodyweight.  For optimal performance you should use 
-    %a{:href => "http://en.wikipedia.org/wiki/Molar_(concentration)"} molar
+    %a{:href => "http://en.wikipedia.org/wiki/Molar_(concentration)", :rel => "external"} molar
     units.