From 4524aab585f88156058b6335c6e52f53947327c4 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Mon, 14 Mar 2011 16:01:41 +0100
Subject: minor fixes

---
 helper.rb        | 4 +++-
 views/model.haml | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/helper.rb b/helper.rb
index 0813fff..8e1f787 100644
--- a/helper.rb
+++ b/helper.rb
@@ -31,8 +31,10 @@ helpers do
   end
 
   def is_authorized(uri, action)
-    if session[:subjectid] != nil
+    if OpenTox::Authorization.server && session[:subjectid] != nil
       return OpenTox::Authorization.authorize(uri, action, session[:subjectid])
+    else
+      return true
     end
     return false
   end
diff --git a/views/model.haml b/views/model.haml
index 5addcb0..76a2f31 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}
-- 
cgit v1.2.3


From 37b3ecfa4bb27b2eb9ffe8efa7bf8a4d32cf1dca Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Mon, 14 Mar 2011 17:07:09 +0100
Subject: fix progress bar

---
 application.rb    | 2 +-
 views/models.haml | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/application.rb b/application.rb
index f6e03cc..1ab6576 100644
--- a/application.rb
+++ b/application.rb
@@ -192,7 +192,7 @@ post '/models' do # create a new model
   task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do |task|
 
     task.progress(5)
-    @model.update :status => "Uploading and saving dataset"
+    @model.update  :task_uri => task.uri, :status => "Uploading and saving dataset"
     begin
       @dataset = OpenTox::Dataset.create(nil, subjectid)
       # check format by extension - not all browsers provide correct content-type]) 
diff --git a/views/models.haml b/views/models.haml
index a99144a..77ea376 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -17,5 +17,6 @@
 = haml :classification, :layout => false
 = haml :regression, :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 
-- 
cgit v1.2.3


From a6ee4587bfcb565e87ab597b4e1156467ab67152 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Tue, 15 Mar 2011 12:14:14 +0100
Subject: sorting of models, created_at automation, ohm::callback

---
 application.rb                     |  4 ++--
 model.rb                           |  7 ++++++-
 public/progressbar/progressbar.css | 23 ++++++-----------------
 views/model.haml                   |  4 ++--
 4 files changed, 16 insertions(+), 22 deletions(-)

diff --git a/application.rb b/application.rb
index 1ab6576..243333c 100644
--- a/application.rb
+++ b/application.rb
@@ -70,7 +70,7 @@ get '/login' do
 end
 
 get '/models/?' do
-  @models = ToxCreateModel.all#.to_a.reverse
+  @models = ToxCreateModel.all.sort.reverse
   subjectstring = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : ""
   haml :models, :locals=>{:models=>@models, :subjectstring => subjectstring}
 end
@@ -192,7 +192,7 @@ post '/models' do # create a new model
   task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do |task|
 
     task.progress(5)
-    @model.update  :task_uri => task.uri, :status => "Uploading and saving dataset"
+    @model.update :status => "Uploading and saving dataset", :task_uri => task.uri
     begin
       @dataset = OpenTox::Dataset.create(nil, subjectid)
       # check format by extension - not all browsers provide correct content-type]) 
diff --git a/model.rb b/model.rb
index 7b91bab..7e33a67 100644
--- a/model.rb
+++ b/model.rb
@@ -1,4 +1,5 @@
 require 'ohm'
+require 'ohm/contrib'
 #require 'redis/objects'
 #@@redis = Redis.new(:thread_safe=>true)#(:host => '127.0.0.1', :port => 6379)
 
@@ -7,12 +8,16 @@ class ToxCreateModel < Ohm::Model
   #include Redis::Objects
 	#include DataMapper::Resource
 	#attribute :id
+  include Ohm::Callbacks
+  include Ohm::Typecast
+  include Ohm::Timestamping  
+
 	attribute :name
 	attribute :warnings
 	attribute :error_messages
 	attribute :type
   attribute :status
-	attribute :created_at
+	attribute :created_at, Date
 
 	attribute :task_uri
 	attribute :uri
diff --git a/public/progressbar/progressbar.css b/public/progressbar/progressbar.css
index 92e3f82..962abbc 100644
--- a/public/progressbar/progressbar.css
+++ b/public/progressbar/progressbar.css
@@ -11,7 +11,7 @@
 /* Layout helpers
 ----------------------------------*/
 .ui-helper-hidden { display: none; }
-.ui-helper-hidden-accessible { position: absolute !important; clip: rect(1px 1px 1px 1px); clip: rect(1px,1px,1px,1px); }
+.ui-helper-hidden-accessible { position: absolute !important; clip: rect(1px, 1px, 1px, 1px); clip: rect(1px,1px,1px,1px); }
 .ui-helper-reset { margin: 0; padding: 0; border: 0; outline: 0; line-height: 1.3; text-decoration: none; font-size: 100%; list-style: none; }
 .ui-helper-clearfix:after { content: "."; display: block; height: 0; clear: both; visibility: hidden; }
 .ui-helper-clearfix { display: inline-block; }
@@ -19,7 +19,7 @@
 * html .ui-helper-clearfix { height:1%; }
 .ui-helper-clearfix { display:block; }
 /* end clearfix */
-.ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: absolute; opacity: 0; filter:Alpha(Opacity=0); }
+.ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: absolute; }
 
 
 /* Interaction Cues
@@ -82,8 +82,8 @@
 .ui-state-error a, .ui-widget-content .ui-state-error a, .ui-widget-header .ui-state-error a { color: #cd0a0a; }
 .ui-state-error-text, .ui-widget-content .ui-state-error-text, .ui-widget-header .ui-state-error-text { color: #cd0a0a; }
 .ui-priority-primary, .ui-widget-content .ui-priority-primary, .ui-widget-header .ui-priority-primary { font-weight: bold; }
-.ui-priority-secondary, .ui-widget-content .ui-priority-secondary,  .ui-widget-header .ui-priority-secondary { opacity: .7; filter:Alpha(Opacity=70); font-weight: normal; }
-.ui-state-disabled, .ui-widget-content .ui-state-disabled, .ui-widget-header .ui-state-disabled { opacity: .35; filter:Alpha(Opacity=35); background-image: none; }
+.ui-priority-secondary, .ui-widget-content .ui-priority-secondary,  .ui-widget-header .ui-priority-secondary { font-weight: normal; }
+.ui-state-disabled, .ui-widget-content .ui-state-disabled, .ui-widget-header .ui-state-disabled { background-image: none; }
 
 /* Icons
 ----------------------------------*/
@@ -279,20 +279,9 @@
 /* Misc visuals
 ----------------------------------*/
 
-/* Corner radius */
-.ui-corner-tl { -moz-border-radius-topleft: 5px; -webkit-border-top-left-radius: 5px; border-top-left-radius: 5px; }
-.ui-corner-tr { -moz-border-radius-topright: 5px; -webkit-border-top-right-radius: 5px; border-top-right-radius: 5px; }
-.ui-corner-bl { -moz-border-radius-bottomleft: 5px; -webkit-border-bottom-left-radius: 5px; border-bottom-left-radius: 5px; }
-.ui-corner-br { -moz-border-radius-bottomright: 5px; -webkit-border-bottom-right-radius: 5px; border-bottom-right-radius: 5px; }
-.ui-corner-top { -moz-border-radius-topleft: 5px; -webkit-border-top-left-radius: 5px; border-top-left-radius: 5px; -moz-border-radius-topright: 5px; -webkit-border-top-right-radius: 5px; border-top-right-radius: 5px; }
-.ui-corner-bottom { -moz-border-radius-bottomleft: 5px; -webkit-border-bottom-left-radius: 5px; border-bottom-left-radius: 5px; -moz-border-radius-bottomright: 5px; -webkit-border-bottom-right-radius: 5px; border-bottom-right-radius: 5px; }
-.ui-corner-right {  -moz-border-radius-topright: 5px; -webkit-border-top-right-radius: 5px; border-top-right-radius: 5px; -moz-border-radius-bottomright: 5px; -webkit-border-bottom-right-radius: 5px; border-bottom-right-radius: 5px; }
-.ui-corner-left { -moz-border-radius-topleft: 5px; -webkit-border-top-left-radius: 5px; border-top-left-radius: 5px; -moz-border-radius-bottomleft: 5px; -webkit-border-bottom-left-radius: 5px; border-bottom-left-radius: 5px; }
-.ui-corner-all { -moz-border-radius: 5px; -webkit-border-radius: 5px; border-radius: 5px; }
-
 /* Overlays */
-.ui-widget-overlay { background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; opacity: .30;filter:Alpha(Opacity=30); }
-.ui-widget-shadow { margin: -8px 0 0 -8px; padding: 8px; background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; opacity: .30;filter:Alpha(Opacity=30); -moz-border-radius: 8px; -webkit-border-radius: 8px; border-radius: 8px; }/*
+.ui-widget-overlay { background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; }
+.ui-widget-shadow { margin: -8px 0 0 -8px; padding: 8px; background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x;}/*
  * jQuery UI Progressbar 1.8.9
  *
  * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
diff --git a/views/model.haml b/views/model.haml
index 76a2f31..5ecc86b 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -35,8 +35,8 @@
         %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 
-- 
cgit v1.2.3


From 422a5abc6c56f237d0bc84bce613e688867d0e16 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Tue, 15 Mar 2011 16:33:15 +0100
Subject: clean toxcreate.js, fix cancel edit modelname

---
 application.rb                  |  2 +-
 public/javascripts/toxcreate.js | 50 ++++++++++++++++++++++-------------------
 views/model_name_edit.haml      |  7 +++---
 views/models.haml               |  5 +++--
 4 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/application.rb b/application.rb
index 243333c..d11dad4 100644
--- a/application.rb
+++ b/application.rb
@@ -282,7 +282,7 @@ post '/models' do # create a new model
     #@model.warnings += "<p>Duplicated structures (all structures/activities used for model building, please  make sure, that the results were obtained from <em>independent</em> experiments):</p>" + duplicate_warnings unless duplicate_warnings.empty?
     lazar.uri
   end
-  @model.update(:task_uri => task.uri)
+  @model.update :task_uri => task.uri
 
   flash[:notice] = "Model creation and validation started - this may last up to several hours depending on the number and size of the training compounds."
   redirect url_for('/models')
diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index 94d944d..aea46f1 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -86,8 +86,6 @@ $(function() {
     });
     return id;
   };    
-  
-  
 
   loadModel = function(id, view) {
     if(id == "") return -1; 
@@ -111,27 +109,6 @@ $(function() {
     return false;
   };
 
-  checkValidation = function() {
-    var reload_id = "";
-    $("input.model_validation_report").each(function(){
-        if(!$(this).val().match(/Completed|Error/)) {
-          reload_id = this.id.replace("model_validation_report_","");
-          if(/^\d+$/.test(reload_id)) loadModel(reload_id, 'validation');
-        };
-    });
-//<<<<<<< HEAD
-    //var validationCheck = setTimeout('checkValidation()',15000);
-    //var validationCheck = setTimeout('checkValidation()',5000);
-//=======
-    $("input.model_validation_qmrf").each(function(){
-        if(!$(this).val().match(/Completed|Error/)) {
-          reload_id = this.id.replace("model_validation_qmrf_","");
-          if(/^\d+$/.test(reload_id)) loadModel(reload_id, 'model');
-        };
-    });
-    var validationCheck = setTimeout('checkValidation()',15000);
-//>>>>>>> d1ad229730f6e6043fe6e7a150e05ffa41e3cec2
-  }
 });
 
 jQuery.fn.editModel = function(type, options) {
@@ -161,6 +138,33 @@ jQuery.fn.editModel = function(type, options) {
   });
 };
 
+jQuery.fn.cancelEdit = function(type, options) {
+  var defaults = {
+    method: 'get',
+    action: 'model/' + options.id + '/name?mode=show',
+    trigger_on: 'click'
+  };
+  var opts = $.extend(defaults, options);
+  
+  this.bind(opts.trigger_on, function() { 
+    $.ajax({
+         type: opts.method,
+         url:  opts.action,
+         dataType: 'html',
+         data: {
+           '_method': 'get'
+         },
+         success: function(data) {         
+           $("div#model_" + opts.id + "_name").html(data);
+         },
+         error: function(data) {
+           alert("model cancel error!");
+         }
+       });
+    return false;
+  });
+};
+
 jQuery.fn.saveModel = function(type, options) {
   var defaults = {
     method: 'put',
diff --git a/views/model_name_edit.haml b/views/model_name_edit.haml
index aec59fc..a038996 100644
--- a/views/model_name_edit.haml
+++ b/views/model_name_edit.haml
@@ -1,5 +1,5 @@
-- js = "$('#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('GET', {id: '#{model.id}', mode: 'show'});\n  "
+- js += "$('#save_#{model.id}').saveModel('POST', {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 77ea376..268cda2 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -6,16 +6,17 @@
       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. This page is 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 :significant_fragments, :layout => false
+= haml :similarity, :layout => false
 
 - if @models
   - @models.each do |model|
-- 
cgit v1.2.3


From d8d49429f3d913fea56a631ac0a5b61c80916424 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Tue, 15 Mar 2011 16:39:22 +0100
Subject: clean toxcreate.js, fix cancel edit modelname / pt2

---
 public/javascripts/toxcreate.js | 6 +++---
 views/model_name.haml           | 2 +-
 views/model_name_edit.haml      | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index aea46f1..3f243fe 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -111,7 +111,7 @@ $(function() {
 
 });
 
-jQuery.fn.editModel = function(type, options) {
+jQuery.fn.editModel = function(options) {
   var defaults = {
     method: 'get',
     action: this.attr('href'),
@@ -138,7 +138,7 @@ jQuery.fn.editModel = function(type, options) {
   });
 };
 
-jQuery.fn.cancelEdit = function(type, options) {
+jQuery.fn.cancelEdit = function(options) {
   var defaults = {
     method: 'get',
     action: 'model/' + options.id + '/name?mode=show',
@@ -165,7 +165,7 @@ jQuery.fn.cancelEdit = function(type, options) {
   });
 };
 
-jQuery.fn.saveModel = function(type, options) {
+jQuery.fn.saveModel = function(options) {
   var defaults = {
     method: 'put',
     action: 'model/' + options.id,
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
   $(function() {
     #{js}
diff --git a/views/model_name_edit.haml b/views/model_name_edit.haml
index a038996..d92c68a 100644
--- a/views/model_name_edit.haml
+++ b/views/model_name_edit.haml
@@ -1,5 +1,5 @@
-- js = "$('#cancel_#{model.id}').cancelEdit('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}
-- 
cgit v1.2.3


From 592f509ec22dd3f742ee530c7b1692b1af05e528 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Thu, 24 Mar 2011 13:57:07 +0100
Subject: external links with rel='external' for w3c compliance

---
 public/javascripts/toxcreate.js  | 12 ++++++++++++
 views/create.haml                |  2 +-
 views/feature_table.haml         |  4 ++--
 views/help.haml                  |  8 ++++----
 views/layout.haml                |  6 +++---
 views/lazar.haml                 | 10 +++++-----
 views/lazar_algorithm.haml       |  4 ++--
 views/lazar_description.haml     |  4 ++--
 views/login.haml                 | 12 ++++++------
 views/model.haml                 |  2 +-
 views/regression_validation.haml |  6 +++---
 views/significant_fragments.haml |  2 +-
 views/unit.haml                  |  2 +-
 13 files changed, 43 insertions(+), 31 deletions(-)

diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index 3f243fe..d9946c4 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -226,3 +226,15 @@ jQuery.fn.deleteModel = function(type, options) {
      return false;
    });
 };
+
+$(document).ready(function() {
+  $('A[rel="external"]').each(function() {
+    $(this).attr('alt', 'Link opens in new window.');
+    $(this).attr('title', 'Link opens in new window.');
+  });
+  $('A[rel="external"]').click(function() {
+    window.open($(this).attr('href'));
+    return false;
+  });
+});
+
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 d9d7783..2a96636 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/opentox-toxmodel/issues'} issue tracker.
+          %a{:href => 'http://github.com/opentox/toxcreate/issues', :rel => "external"} issue tracker.
 
       - if flash[:notice]
         %p
@@ -48,6 +48,6 @@
 
     .footer
       &copy;
-      %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;position:relative;">Tox</span>
diff --git a/views/lazar.haml b/views/lazar.haml
index 3de7400..d52a645 100644
--- a/views/lazar.haml
+++ b/views/lazar.haml
@@ -36,13 +36,13 @@
             %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
-            -#http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&regno=000143157
+              %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;" }
         %td{:colspan => '4'}
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 7b63975..cd87757 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -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/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/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.
-- 
cgit v1.2.3


From 0559ff4159064118292ddc9ef0dbb032afbb6aef Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 30 Mar 2011 12:57:57 +0200
Subject: icon for external links

---
 public/external.gif | Bin 0 -> 212 bytes
 views/layout.haml   |   2 +-
 views/lazar.haml    |   4 ++--
 views/style.sass    |   3 +++
 4 files changed, 6 insertions(+), 3 deletions(-)
 create mode 100644 public/external.gif

diff --git a/public/external.gif b/public/external.gif
new file mode 100644
index 0000000..6114959
Binary files /dev/null and b/public/external.gif differ
diff --git a/views/layout.haml b/views/layout.haml
index 2a96636..c849dec 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -50,4 +50,4 @@
       &copy;
       %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico toxicology
       2009-2010, powered by
-      %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;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 d52a645..deb0c18 100644
--- a/views/lazar.haml
+++ b/views/lazar.haml
@@ -39,10 +39,10 @@
               %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]')}", :rel => "external"}  PubChem data
-      (external)
+                (external)
             -# %li
               %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
+            -#http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&regno=000143157
 
       %tr#names{ :style => "display: none;" }
         %td{:colspan => '4'}
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
-- 
cgit v1.2.3


From ec743296fe370e8557acc338ae6559733c2e298d Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 30 Mar 2011 13:25:26 +0200
Subject: create default policy after save

---
 application.rb   | 1 -
 model.rb         | 2 +-
 views/model.haml | 2 +-
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/application.rb b/application.rb
index d11dad4..a74fb47 100644
--- a/application.rb
+++ b/application.rb
@@ -252,7 +252,6 @@ post '/models' do # create a new model
 
         # create summary
         validation.summary(subjectid).each do |k,v|
-          #LOGGER.debug "mr ::: k: #{k.inspect} - v: #{v.inspect}" 
           begin
             eval "@model.update :#{k.to_s} => v" if v
           rescue
diff --git a/model.rb b/model.rb
index 2b71eaa..58eeecf 100644
--- a/model.rb
+++ b/model.rb
@@ -49,7 +49,7 @@ class ToxCreateModel < Ohm::Model
   attr_accessor :subjectid
   @subjectid = nil
 
-  #after :save, :check_policy
+  after :save, :check_policy
 
 	def validation_status
 		begin
diff --git a/views/model.haml b/views/model.haml
index cd87757..4933cdb 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -28,7 +28,7 @@
               //= 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)
-- 
cgit v1.2.3


From dcc070e630d7864f0ea735fe45b0b8304276424a Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Thu, 31 Mar 2011 13:16:42 +0200
Subject: clean merge with rautenberg

---
 model.rb | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/model.rb b/model.rb
index 58eeecf..5b1f4f5 100644
--- a/model.rb
+++ b/model.rb
@@ -1,7 +1,5 @@
 require 'ohm'
 require 'ohm/contrib'
-#require 'redis/objects'
-#@@redis = Redis.new(:thread_safe=>true)#(:host => '127.0.0.1', :port => 6379)
 
 class ToxCreateModel < Ohm::Model
 
@@ -80,5 +78,4 @@ class ToxCreateModel < Ohm::Model
     OpenTox::Authorization.check_policy(web_uri, subjectid)
   end
 
-end
-
+end
\ No newline at end of file
-- 
cgit v1.2.3


From f57103720c82700f7e43d54707e9381668f0fb67 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 31 Mar 2011 13:47:34 +0200
Subject: ambit endpint selection started

---
 application.rb       |  6 ++++++
 views/endpoints.haml | 10 ++++++++++
 2 files changed, 16 insertions(+)
 create mode 100644 views/endpoints.haml

diff --git a/application.rb b/application.rb
index 44adf89..9583411 100644
--- a/application.rb
+++ b/application.rb
@@ -175,6 +175,12 @@ get %r{/compound/(.*)} do |inchi|
   OpenTox::Compound.from_inchi(inchi).to_names.join(', ')
 end
 
+get '/endpoints' do
+  #@endpoint = params[:endpoint]
+  @endpoints = OpenTox::Ontology::Echa.endpoints#(params[:endpoint])
+  haml :endpoints
+end
+
 post '/models' do # create a new model
   unless params[:file] and params[:file][:tempfile] #params[:endpoint] and 
     flash[:notice] = "Please upload a Excel or CSV file."
diff --git a/views/endpoints.haml b/views/endpoints.haml
new file mode 100644
index 0000000..fc41190
--- /dev/null
+++ b/views/endpoints.haml
@@ -0,0 +1,10 @@
+%form{ :action => url_for('/endpoints'), :method => "get" }
+
+  - @endpoints.each do |endpoint,datasets|
+    %h2= endpoint.split('#').last + " " + datasets.size.to_s
+    - datasets.each do |dataset|
+      %br
+        %input{:type=>'radio', :name => "dataset", :value => dataset} #{dataset}
+
+  %p
+    %input{:type => 'submit'}
-- 
cgit v1.2.3


From 7dbcfb7b0df30c55d79574d5133f9ba9cf135a9f Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 31 Mar 2011 14:27:35 +0200
Subject: validation skipped for locahost installations

---
 application.rb | 27 ++++++++++++---------------
 1 file changed, 12 insertions(+), 15 deletions(-)

diff --git a/application.rb b/application.rb
index 400109b..7ada4ce 100644
--- a/application.rb
+++ b/application.rb
@@ -239,16 +239,20 @@ post '/models' do # create a new model
     end
     @model.update :type => type, :feature_dataset => lazar.metadata[OT.featureDataset], :uri => lazar.uri
 
-    unless url_for("",:full).match(/localhost/)
+    if url_for("",:full).match(/localhost/)
+      @model.update(:status => "Completed") #, :warnings => @model.warnings + "\nValidation service cannot be accessed from localhost.")
+      task.progress(100)
+    else
       @model.update :status => "Validating model"
       begin
-        validation = OpenTox::Crossvalidation.create(
-          {:algorithm_uri => lazar.metadata[OT.algorithm],
-          :dataset_uri => lazar.parameter("dataset_uri"),
-          :subjectid => subjectid,
-          :prediction_feature => lazar.parameter("prediction_feature"),
-          :algorithm_params => "feature_generation_uri=#{lazar.parameter("feature_generation_uri")}"},
-         nil, OpenTox::SubTask.new(task,25,80))
+        validation = OpenTox::Crossvalidation.create( {
+            :algorithm_uri => lazar.metadata[OT.algorithm],
+            :dataset_uri => lazar.parameter("dataset_uri"),
+            :subjectid => subjectid,
+            :prediction_feature => lazar.parameter("prediction_feature"),
+            :algorithm_params => "feature_generation_uri=#{lazar.parameter("feature_generation_uri")}" },
+            nil, OpenTox::SubTask.new(task,25,80))
+
         @model.update(:validation_uri => validation.uri)
         LOGGER.debug "Validation URI: #{@model.validation_uri}"
 
@@ -274,13 +278,6 @@ post '/models' do # create a new model
       end
       
     end
-
-
-    #@model.warnings += "<p>Incorrect Smiles structures (ignored):</p>" + parser.smiles_errors.join("<br/>") unless parser.smiles_errors.empty?
-    #@model.warnings += "<p>Irregular activities (ignored):</p>" + parser.activity_errors.join("<br/>") unless parser.activity_errors.empty?
-    #duplicate_warnings = ''
-    #parser.duplicates.each {|inchi,lines| duplicate_warnings += "<p>#{lines.join('<br/>')}</p>" if lines.size > 1 }
-    #@model.warnings += "<p>Duplicated structures (all structures/activities used for model building, please  make sure, that the results were obtained from <em>independent</em> experiments):</p>" + duplicate_warnings unless duplicate_warnings.empty?
     lazar.uri
   end
   @model.update :task_uri => task.uri
-- 
cgit v1.2.3


From 29516a370a458915050eca3dca586b3ec3b6f877 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 31 Mar 2011 17:16:37 +0200
Subject: explicit prediction_feature, validation skipped if
 CONFIG[:services][opentox-validation] not set

---
 application.rb       | 79 +++++++++++++++++++++++++++++++---------------------
 views/endpoints.haml | 10 -------
 2 files changed, 48 insertions(+), 41 deletions(-)
 delete mode 100644 views/endpoints.haml

diff --git a/application.rb b/application.rb
index c5190ea..e7a2658 100644
--- a/application.rb
+++ b/application.rb
@@ -175,15 +175,16 @@ get %r{/compound/(.*)} do |inchi|
   OpenTox::Compound.from_inchi(inchi).to_names.join(', ')
 end
 
-get '/endpoints' do
+get '/ambit' do
   #@endpoint = params[:endpoint]
   @endpoints = OpenTox::Ontology::Echa.endpoints#(params[:endpoint])
-  haml :endpoints
+  haml :ambit
 end
 
 post '/models' do # create a new model
-  unless params[:file] and params[:file][:tempfile] #params[:endpoint] and 
-    flash[:notice] = "Please upload a Excel or CSV file."
+
+  unless (params[:dataset] and params[:prediction_feature]) or (params[:file] and params[:file][:tempfile]) #params[:endpoint] and 
+    flash[:notice] = "Please upload a Excel or CSV file or select an AMBIT dataset."
     redirect url_for('/create')
   end
 
@@ -192,46 +193,62 @@ post '/models' do # create a new model
     flash[:notice] = "Please login to create a new model."
     redirect url_for('/create')
   end
+
   subjectid = session[:subjectid] ? session[:subjectid] : nil
+
+  if params[:dataset] and params[:prediction_feature]
+    @dataset = OpenTox::Dataset.new(params[:dataset])
+    name = @dataset.load_metadata[DC.title]
+    @prediction_feature = params[:prediction_feature]
+  elsif params[:file][:filename]
+    name = params[:file][:filename].sub(/\..*$/,"")
+  end
+
   @model = ToxCreateModel.create(:name => params[:file][:filename].sub(/\..*$/,""), :subjectid => subjectid)
   @model.update :web_uri => url_for("/model/#{@model.id}", :full), :warnings => ""
   task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do |task|
 
     task.progress(5)
     @model.update :status => "Uploading and saving dataset", :task_uri => task.uri
-    begin
-      @dataset = OpenTox::Dataset.create(nil, subjectid)
-      # check format by extension - not all browsers provide correct content-type]) 
-      case File.extname(params[:file][:filename])
-      when ".csv"
-        csv = params[:file][:tempfile].read
-        @dataset.load_csv(csv, subjectid)
-      when ".xls", ".xlsx"
-        excel_file = params[:file][:tempfile].path + File.extname(params[:file][:filename])
-        File.rename(params[:file][:tempfile].path, excel_file) # add extension, spreadsheet does not read files without extensions
-        @dataset.load_spreadsheet(Excel.new excel_file, subjectid)
-      else
-        error "#{params[:file][:filename]} has a unsupported file type."
+
+    unless params[:dataset]
+      begin
+        @dataset = OpenTox::Dataset.create(nil, subjectid)
+        # check format by extension - not all browsers provide correct content-type]) 
+        case File.extname(params[:file][:filename])
+        when ".csv"
+          csv = params[:file][:tempfile].read
+          @dataset.load_csv(csv, subjectid)
+        when ".xls", ".xlsx"
+          excel_file = params[:file][:tempfile].path + File.extname(params[:file][:filename])
+          File.rename(params[:file][:tempfile].path, excel_file) # add extension, spreadsheet does not read files without extensions
+          @dataset.load_spreadsheet(Excel.new excel_file, subjectid)
+          if @dataset.metadata[OT.Errors]
+            error "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} formats."
+          end
+        else
+          error "#{params[:file][:filename]} has a unsupported file type."
+        end
+        if @dataset.features.keys.size != 1
+          error "More than one feature in dataset #{params[:file][:filename]}. Please delete irrelvant columns and try again."
+        else
+          @prediction_feature = @dataset.features.keys.first
+        end
+        @dataset.save(subjectid)
+      rescue => e
+        error "Dataset creation failed with #{e.message}"
       end
-    rescue => e
-      error "Dataset creation failed with #{e.message}"
     end
-    @dataset.save(subjectid)
+
     task.progress(10)
     if @dataset.compounds.size < 10
       error "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/excel_format"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets."
     end
-    if @dataset.features.keys.size != 1
-      error "More than one feature in dataset #{params[:file][:filename]}. Please delete irrelvant columns and try again."
-    end
-    if @dataset.metadata[OT.Errors]
-      error "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} formats."
-    end
     @model.update :training_dataset => @dataset.uri, :nr_compounds => @dataset.compounds.size, :status => "Creating prediction model"
     @model.update :warnings => @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings].empty?
     task.progress(15)
     begin
-      lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :subjectid => subjectid)
+      lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature, :subjectid => subjectid)
     rescue => e
       error "Model creation failed with '#{e.message}'. Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format."
     end
@@ -245,10 +262,7 @@ post '/models' do # create a new model
     end
     @model.update :type => type, :feature_dataset => lazar.metadata[OT.featureDataset], :uri => lazar.uri
 
-    if url_for("",:full).match(/localhost/)
-      @model.update(:status => "Completed") #, :warnings => @model.warnings + "\nValidation service cannot be accessed from localhost.")
-      task.progress(100)
-    else
+    if CONFIG[:services]["opentox-validation"]
       @model.update :status => "Validating model"
       begin
         validation = OpenTox::Crossvalidation.create( {
@@ -283,6 +297,9 @@ post '/models' do # create a new model
         @model.update :warnings => @model.warnings + "\nModel validation failed with #{e.message}.", :status => "Error", :error_messages => e.message
       end
       
+    else
+      @model.update(:status => "Completed") #, :warnings => @model.warnings + "\nValidation service cannot be accessed from localhost.")
+      task.progress(100)
     end
     lazar.uri
   end
diff --git a/views/endpoints.haml b/views/endpoints.haml
deleted file mode 100644
index fc41190..0000000
--- a/views/endpoints.haml
+++ /dev/null
@@ -1,10 +0,0 @@
-%form{ :action => url_for('/endpoints'), :method => "get" }
-
-  - @endpoints.each do |endpoint,datasets|
-    %h2= endpoint.split('#').last + " " + datasets.size.to_s
-    - datasets.each do |dataset|
-      %br
-        %input{:type=>'radio', :name => "dataset", :value => dataset} #{dataset}
-
-  %p
-    %input{:type => 'submit'}
-- 
cgit v1.2.3


From 3430ce8d28846a405d403b2c4a03bcab5a11f9e6 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 4 Apr 2011 18:44:44 +0200
Subject: Selection of AMBIT datasets added

---
 application.rb            |  56 ++++++++++++++--------
 helper.rb                 |   5 +-
 views/ambit.haml          |  15 ++++++
 views/compound_image.haml |   1 -
 views/create.haml         |  10 +++-
 views/echa.haml           |  13 ++++++
 views/feature.haml        |  26 +++++++++++
 views/layout.haml         |   4 +-
 views/lazar.haml          | 116 +++++++++++++++++++++++-----------------------
 views/model.haml          |  15 +++---
 10 files changed, 169 insertions(+), 92 deletions(-)
 create mode 100644 views/ambit.haml
 create mode 100644 views/echa.haml
 create mode 100644 views/feature.haml

diff --git a/application.rb b/application.rb
index e7a2658..24b7a56 100644
--- a/application.rb
+++ b/application.rb
@@ -56,7 +56,7 @@ helpers do
 end
 
 before do
-    if !logged_in and !( env['REQUEST_URI'] =~ /\/login$/ and env['REQUEST_METHOD'] == "POST" ) #or !AA_SERVER
+    if !logged_in and !( env['REQUEST_URI'] =~ /\/login$/ and env['REQUEST_METHOD'] == "POST" ) or !AA_SERVER
       login("guest","guest")
     end
 end
@@ -175,12 +175,26 @@ get %r{/compound/(.*)} do |inchi|
   OpenTox::Compound.from_inchi(inchi).to_names.join(', ')
 end
 
-get '/ambit' do
-  #@endpoint = params[:endpoint]
-  @endpoints = OpenTox::Ontology::Echa.endpoints#(params[:endpoint])
+get '/echa' do
+  @endpoints = OpenTox::Ontology::Echa.endpoints
+  haml :echa
+end
+
+post '/ambit' do
+  session[:echa] = params[:endpoint]
+  @datasets  = OpenTox::Ontology::Echa.datasets(params[:endpoint])
   haml :ambit
 end
 
+post '/feature' do
+  session[:dataset] = params[:dataset]
+  @features = []
+  OpenTox::Dataset.new(params[:dataset]).load_features.each do |uri,metadata|
+    @features << OpenTox::Feature.find(uri) if metadata[OWL.sameAs].match(/#{session[:echa]}/)
+  end
+  haml :feature
+end
+
 post '/models' do # create a new model
 
   unless (params[:dataset] and params[:prediction_feature]) or (params[:file] and params[:file][:tempfile]) #params[:endpoint] and 
@@ -197,21 +211,22 @@ post '/models' do # create a new model
   subjectid = session[:subjectid] ? session[:subjectid] : nil
 
   if params[:dataset] and params[:prediction_feature]
-    @dataset = OpenTox::Dataset.new(params[:dataset])
+    @dataset = OpenTox::Dataset.new(params[:dataset],subjectid)
     name = @dataset.load_metadata[DC.title]
-    @prediction_feature = params[:prediction_feature]
+    @prediction_feature = OpenTox::Feature.find params[:prediction_feature], subjectid
+    @dataset.load_compounds
   elsif params[:file][:filename]
     name = params[:file][:filename].sub(/\..*$/,"")
   end
 
-  @model = ToxCreateModel.create(:name => params[:file][:filename].sub(/\..*$/,""), :subjectid => subjectid)
+  @model = ToxCreateModel.create(:name => name, :subjectid => subjectid)
   @model.update :web_uri => url_for("/model/#{@model.id}", :full), :warnings => ""
   task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do |task|
 
     task.progress(5)
     @model.update :status => "Uploading and saving dataset", :task_uri => task.uri
 
-    unless params[:dataset]
+    unless params[:dataset] and params[:prediction_feature]
       begin
         @dataset = OpenTox::Dataset.create(nil, subjectid)
         # check format by extension - not all browsers provide correct content-type]) 
@@ -229,15 +244,15 @@ post '/models' do # create a new model
         else
           error "#{params[:file][:filename]} has a unsupported file type."
         end
-        if @dataset.features.keys.size != 1
-          error "More than one feature in dataset #{params[:file][:filename]}. Please delete irrelvant columns and try again."
-        else
-          @prediction_feature = @dataset.features.keys.first
-        end
         @dataset.save(subjectid)
       rescue => e
         error "Dataset creation failed with #{e.message}"
       end
+      if @dataset.features.keys.size != 1
+        error "More than one feature in dataset #{params[:file][:filename]}. Please delete irrelvant columns and try again."
+      else
+        @prediction_feature = OpenTox::Feature.find(@dataset.features.keys.first,subjectid)
+      end
     end
 
     task.progress(10)
@@ -245,22 +260,23 @@ post '/models' do # create a new model
       error "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/excel_format"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets."
     end
     @model.update :training_dataset => @dataset.uri, :nr_compounds => @dataset.compounds.size, :status => "Creating prediction model"
-    @model.update :warnings => @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings].empty?
+    @model.update :warnings => @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings] and @dataset.metadata[OT.Warnings].empty?
     task.progress(15)
     begin
-      lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature, :subjectid => subjectid)
+      lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature.uri, :subjectid => subjectid)
     rescue => e
-      error "Model creation failed with '#{e.message}'. Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format."
+      error "Model creation failed with '#{e.message}'."# Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format."
     end
     task.progress(25)
+=begin
     type = "unknown"
-    case lazar.metadata[OT.isA]
-    when /Classification/
+    if lazar.metadata[RDF.type].grep(/Classification/)
       type = "classification"
-    when /Regression/
+    elsif lazar.metadata[RDF.type].grep(/Regression/)
       type = "regression"
     end
-    @model.update :type => type, :feature_dataset => lazar.metadata[OT.featureDataset], :uri => lazar.uri
+=end
+    @model.update :type => @prediction_feature.feature_type, :feature_dataset => lazar.metadata[OT.featureDataset], :uri => lazar.uri
 
     if CONFIG[:services]["opentox-validation"]
       @model.update :status => "Validating model"
diff --git a/helper.rb b/helper.rb
index 7d7a856..2fe8785 100644
--- a/helper.rb
+++ b/helper.rb
@@ -3,7 +3,7 @@ helpers do
   def login(username, password)
     logout
     session[:subjectid] = OpenTox::Authorization.authenticate(username, password)
-    LOGGER.debug "ToxCreate login user #{username} with subjectid: " + session[:subjectid].to_s
+    #LOGGER.debug "ToxCreate login user #{username} with subjectid: " + session[:subjectid].to_s
     if session[:subjectid] != nil
       session[:username] = username
       return true
@@ -53,8 +53,7 @@ helpers do
 
   def sort(descriptors)
     features = {:activating => [], :deactivating => []}
-
-    descriptors.each { |d| LOGGER.debug d.inspect; features[d[OT.effect].to_sym] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} }
+    descriptors.each { |d| features[d[OT.effect].to_sym] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} }
     features
   end
 
diff --git a/views/ambit.haml b/views/ambit.haml
new file mode 100644
index 0000000..685c0dc
--- /dev/null
+++ b/views/ambit.haml
@@ -0,0 +1,15 @@
+%b Select:
+= session[:echa].split('#').last
+= "-&gt;"
+%b Dataset 
+%em= "-&gt; Prediction Feature"
+
+%form{ :action => url_for('/feature'), :method => "post" }
+  %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
+
+  - @datasets.each do |dataset|
+    %br
+      %input{:type=>'radio', :name => "dataset", :value => dataset} #{OpenTox::Dataset.new(dataset).load_metadata[DC.title]}
+
+  %p
+    %input{:type => 'submit', :value => 'Next'}
diff --git a/views/compound_image.haml b/views/compound_image.haml
index 18944dc..25e0dbf 100644
--- a/views/compound_image.haml
+++ b/views/compound_image.haml
@@ -1,2 +1 @@
 %img{:src => compound.matching_smarts_image_uri(features[:activating].collect{|f| f[:smarts]},features[:deactivating].collect{|f| f[:smarts]}), :alt => compound.to_smiles}
-
diff --git a/views/create.haml b/views/create.haml
index 2149f3d..48669f4 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -17,18 +17,24 @@
     = link_to "instructions for creating training datasets", '/help'
     before submitting.
 
+
   %form{ :action => url_for('/models'), :method => "post", :enctype => "multipart/form-data" }
     %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
     %fieldset
       %label{:for => 'file'}
-        Select training data in
+        Upload training data in
         = link_to "Excel", '/help'
         or
         = link_to "CSV", '/help'
         format:
       %input{:type => 'file', :name => 'file', :id => 'file', :size => '41'}
     %input{ :type => "submit", :value => "Create model"}
-    = link_to "Cancel", '/create'
+    =# link_to "Cancel", '/create'
+
+  %p
+    or
+    %a{:href => "echa"} Select a AMBIT dataset
+    (experimental)
 
   -# explanations
   = haml :lazar_description, :layout => false
diff --git a/views/echa.haml b/views/echa.haml
new file mode 100644
index 0000000..1cabfa0
--- /dev/null
+++ b/views/echa.haml
@@ -0,0 +1,13 @@
+%b Select:
+%b ECHA Endpoint
+%em= "-&gt; Dataset -&gt; Prediction Feature"
+
+%form{ :action => url_for('/ambit'), :method => "post" }
+  %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
+
+  - @endpoints.each do |endpoint|
+    %br
+      %input{:type=>'radio', :name => "endpoint", :value => endpoint} #{endpoint.split('#').last}
+
+  %p
+    %input{:type => 'submit', :value => "Next"}
diff --git a/views/feature.haml b/views/feature.haml
new file mode 100644
index 0000000..c5b8293
--- /dev/null
+++ b/views/feature.haml
@@ -0,0 +1,26 @@
+%b Select:
+= session[:echa].split('#').last
+= "-&gt;"
+= OpenTox::Dataset.new(session[:dataset]).load_metadata[DC.title]
+= "-&gt;"
+%b Prediction feature
+
+%form{ :action => url_for('/models'), :method => "post" }
+
+  %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
+  %input{:type => 'hidden', :name => 'dataset', :id => 'dataset', :value => session[:dataset]}
+
+  - @features.each do |feature|
+    -# type = "unknown"
+    -# if feature.metadata[RDF.type].include?(OT.NominalFeature)
+      - type = "classification"
+    -# elsif feature.metadata[RDF.type].include?(OT.NumericFeature)
+      - type = "regression"
+
+    %br
+      %input{:type=>'radio', :name => "prediction_feature", :value => feature.uri} #{feature.metadata[DC.title]} (#{feature.feature_type}) 
+    %br
+      =# feature.inspect
+
+  %p
+    %input{:type => 'submit', :value => "Create model"}
diff --git a/views/layout.haml b/views/layout.haml
index c849dec..174db9f 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -17,7 +17,7 @@
       Create and evaluate models to predict toxicity
     .index
       %ul
-        %li{:class => ("selected" if /\/create/ =~ request.path )}
+        %li{:class => ("selected" if /\/create|echa|ambit|feature/ =~ request.path )}
           = link_to "Create", "/create"
         %li{:class => ("selected" if /models/ =~ request.path )}
           = link_to "Inspect", "/models"
@@ -49,5 +49,5 @@
     .footer
       &copy;
       %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico toxicology
-      2009-2010, powered by
+      2009-2011, powered by
       %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 deb0c18..6ae6b20 100644
--- a/views/lazar.haml
+++ b/views/lazar.haml
@@ -1,59 +1,59 @@
-%p= link_to "New prediction", "/predict"
-.lazar-predictions
-
-  -# explanations
-  = haml :lazar_algorithm, :layout => false
-  = haml :confidence, :layout => false
-  = haml :similarity, :layout => false
-  = haml :significant_fragments, :layout => false
-  = haml :training_data, :layout => false
-
-  %a{:name => "prediction"}
-  %table
-    %thead
-      %tr
-        %th= @prediction.title
-        %th= toggle_link("#lazar_algorithm","Prediction")
-        %th= toggle_link("#confidence","Confidence")
-        %th Supporting information
-
-      %tr
-        -# %td
-          %img{:src => @compound.to_image_uri, :alt => @compound.to_smiles}
-        %td.image= compound_image(@compound,@prediction.descriptors(@compound))
-        %td= activity_markup(@prediction.value(@compound))
-        %td= sprintf('%.03g', @prediction.confidence(@compound)) 
-        -#%td= @prediction.confidence(@compound)
-        %td
-          %ul
-            %li
-              %a{:href => "#prediction", :id => "show_names"} Names and synonyms
-              :javascript
-                $("a#show_names").click(function () {
-                  $("#compound_names").load("#{File.join("/compound",@compound.inchi)}");  
-                  $("tr#names").toggle();  
-                });
-            %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}", :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]')}", :rel => "external"}  PubChem data
+%p= link_to "New prediction", "/predict"
+.lazar-predictions
+
+  -# explanations
+  = haml :lazar_algorithm, :layout => false
+  = haml :confidence, :layout => false
+  = haml :similarity, :layout => false
+  = haml :significant_fragments, :layout => false
+  = haml :training_data, :layout => false
+
+  %a{:name => "prediction"}
+  %table
+    %thead
+      %tr
+        %th= @prediction.title
+        %th= toggle_link("#lazar_algorithm","Prediction")
+        %th= toggle_link("#confidence","Confidence")
+        %th Supporting information
+
+      %tr
+        -# %td
+          %img{:src => @compound.to_image_uri, :alt => @compound.to_smiles}
+        %td.image= compound_image(@compound,@prediction.descriptors(@compound))
+        %td= activity_markup(@prediction.value(@compound))
+        %td= sprintf('%.03g', @prediction.confidence(@compound)) 
+        -#%td= @prediction.confidence(@compound)
+        %td
+          %ul
+            %li
+              %a{:href => "#prediction", :id => "show_names"} Names and synonyms
+              :javascript
+                $("a#show_names").click(function () {
+                  $("#compound_names").load("#{File.join("/compound",@compound.inchi)}");  
+                  $("tr#names").toggle();  
+                });
+            %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}", :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]')}", :rel => "external"}  PubChem data
                 (external)
-            -# %li
-              %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;" }
-        %td{:colspan => '4'}
-          %a{:name => 'names'}
-          = hide_link('#names')
-          #compound_names
-      %tr#fragments{ :style => "display: none;" }
-        %td{:colspan => '4'}
-          = hide_link('#fragments')
-          = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(@compound))}, :layout => false
-
-    %tbody#neighbors
-      = haml :neighbors, :locals => {:neighbors => @prediction.neighbors(@compound), :page => @page},  :layout => false
-
+            -# %li
+              %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;" }
+        %td{:colspan => '4'}
+          %a{:name => 'names'}
+          = hide_link('#names')
+          #compound_names
+      %tr#fragments{ :style => "display: none;" }
+        %td{:colspan => '4'}
+          = hide_link('#fragments')
+          = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(@compound))}, :layout => false
+
+    %tbody#neighbors
+      = haml :neighbors, :locals => {:neighbors => @prediction.neighbors(@compound), :page => @page},  :layout => false
+
diff --git a/views/model.haml b/views/model.haml
index 4933cdb..b4b3c59 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -58,12 +58,15 @@
       - if model.training_dataset
         %dt Training dataset:
         %dd
-          %a{:href => "#{model.training_dataset}.xls#{subjectstring}"} Excel sheet
-          ,
-          -#%a{:href => "#{model.training_dataset}.rdf"} RDF/XML
-          -#%em (experts) ,
-          %a{:href => "#{model.training_dataset}.yaml#{subjectstring}" } YAML
-          %em  (experts)
+          - if model.training_dataset.match(/ambit/i)
+            %a{:href => "#{model.training_dataset}#{subjectstring}", :rel => "external"} Ambit database
+          - else
+            %a{:href => "#{model.training_dataset}.xls#{subjectstring}"} Excel sheet
+            ,
+            -#%a{:href => "#{model.training_dataset}.rdf"} RDF/XML
+            -#%em (experts) ,
+            %a{:href => "#{model.training_dataset}.yaml#{subjectstring}" } YAML
+            %em  (experts)
       - if model.feature_dataset
         %dt Feature dataset:
         %dd
-- 
cgit v1.2.3


From 6322fbb063dab874b3d170c8b26d453c9e2f5160 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 6 Apr 2011 10:13:42 +0200
Subject: fix missing subjetid send to Lazar.create

---
 application.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index 400109b..14194ab 100644
--- a/application.rb
+++ b/application.rb
@@ -225,7 +225,7 @@ post '/models' do # create a new model
     @model.update :warnings => @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings].empty?
     task.progress(15)
     begin
-      lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :subjectid => subjectid)
+      lazar = OpenTox::Model::Lazar.create({:dataset_uri => @dataset.uri, :subjectid => subjectid})
     rescue => e
       error "Model creation failed with '#{e.message}'. Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format."
     end
-- 
cgit v1.2.3


From f86342d29cdc6e18b51a79712b3064eded7b4e67 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Tue, 19 Apr 2011 16:14:38 +0200
Subject: subjectid in several places

---
 application.rb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/application.rb b/application.rb
index 24b7a56..99a84c6 100644
--- a/application.rb
+++ b/application.rb
@@ -190,7 +190,7 @@ post '/feature' do
   session[:dataset] = params[:dataset]
   @features = []
   OpenTox::Dataset.new(params[:dataset]).load_features.each do |uri,metadata|
-    @features << OpenTox::Feature.find(uri) if metadata[OWL.sameAs].match(/#{session[:echa]}/)
+    @features << OpenTox::Feature.find(uri, @subjectid) if metadata[OWL.sameAs].match(/#{session[:echa]}/)
   end
   haml :feature
 end
@@ -356,7 +356,7 @@ post '/predict/?' do # post chemical name to model
       }
     else
       predicted_feature = prediction_dataset.metadata[OT.dependentVariables]
-      prediction = OpenTox::Feature.find(predicted_feature)
+      prediction = OpenTox::Feature.find(predicted_feature, subjectid)
       if prediction.metadata[OT.error]
         @predictions << {
           :title => model.name,
@@ -382,7 +382,7 @@ post "/lazar/?" do # get detailed prediction
   @page = params[:page].to_i if params[:page]
   @model_uri = params[:model_uri]
   lazar = OpenTox::Model::Lazar.new @model_uri
-  prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => params[:subjectid])
+  prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => session[:subjectid])
   @prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri, session[:subjectid])
   @compound = OpenTox::Compound.new(params[:compound_uri])
   haml :lazar
-- 
cgit v1.2.3


From 50a53447706ff6eedd56ca9beb136f1acaf5faf1 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 2 May 2011 14:34:48 +0200
Subject: first line added to example datasets

---
 public/hamster_carcinogenicity.csv |   1 +
 public/hamster_carcinogenicity.xls | Bin 57856 -> 11776 bytes
 2 files changed, 1 insertion(+)

diff --git a/public/hamster_carcinogenicity.csv b/public/hamster_carcinogenicity.csv
index e9ca269..f087233 100644
--- a/public/hamster_carcinogenicity.csv
+++ b/public/hamster_carcinogenicity.csv
@@ -1,3 +1,4 @@
+SMILES, hamster_carcinogenicity
 CC=O,1
 C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O,1
 O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1,1
diff --git a/public/hamster_carcinogenicity.xls b/public/hamster_carcinogenicity.xls
index 0015ac6..95e8fc4 100644
Binary files a/public/hamster_carcinogenicity.xls and b/public/hamster_carcinogenicity.xls differ
-- 
cgit v1.2.3


From 03329e15db879c12808e6a10f666a35d86459519 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Mon, 2 May 2011 15:36:53 +0200
Subject: link to excel csv help on upload error

---
 application.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index 99a84c6..e24a76a 100644
--- a/application.rb
+++ b/application.rb
@@ -239,7 +239,7 @@ post '/models' do # create a new model
           File.rename(params[:file][:tempfile].path, excel_file) # add extension, spreadsheet does not read files without extensions
           @dataset.load_spreadsheet(Excel.new excel_file, subjectid)
           if @dataset.metadata[OT.Errors]
-            error "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} formats."
+            error "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} formats."
           end
         else
           error "#{params[:file][:filename]} has a unsupported file type."
-- 
cgit v1.2.3


From f3c731bfbbc345867812a1b057f213895a196571 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Mon, 2 May 2011 16:26:19 +0200
Subject: link to excel csv help on upload error

---
 application.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/application.rb b/application.rb
index e24a76a..3d259fd 100644
--- a/application.rb
+++ b/application.rb
@@ -257,7 +257,7 @@ post '/models' do # create a new model
 
     task.progress(10)
     if @dataset.compounds.size < 10
-      error "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/excel_format"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets."
+      error "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/help"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets."
     end
     @model.update :training_dataset => @dataset.uri, :nr_compounds => @dataset.compounds.size, :status => "Creating prediction model"
     @model.update :warnings => @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings] and @dataset.metadata[OT.Warnings].empty?
@@ -265,7 +265,7 @@ post '/models' do # create a new model
     begin
       lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature.uri, :subjectid => subjectid)
     rescue => e
-      error "Model creation failed with '#{e.message}'."# Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format."
+      error "Model creation failed with '#{e.message}'."# Please check if the input file is in a valid #{link_to "Excel", "/help"} or #{link_to "CSV", "/csv_format"} format."
     end
     task.progress(25)
 =begin
-- 
cgit v1.2.3


From 676cc08edeb6c1d37a6e880b5d249499ca8e1223 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Mon, 2 May 2011 16:35:08 +0200
Subject: link to excel csv help on upload error

---
 application.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index 3d259fd..c261437 100644
--- a/application.rb
+++ b/application.rb
@@ -265,7 +265,7 @@ post '/models' do # create a new model
     begin
       lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature.uri, :subjectid => subjectid)
     rescue => e
-      error "Model creation failed with '#{e.message}'."# Please check if the input file is in a valid #{link_to "Excel", "/help"} or #{link_to "CSV", "/csv_format"} format."
+      error "Model creation failed with '#{e.message}'."# Please check if the input file is in a valid #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} format."
     end
     task.progress(25)
 =begin
-- 
cgit v1.2.3


From 422b6bd6a046479e2bb55bc168b3bc2af9ae98e3 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 4 May 2011 15:02:58 +0200
Subject: create view: regression models are experimental

---
 views/create.haml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/views/create.haml b/views/create.haml
index 48669f4..0b299f5 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -9,7 +9,7 @@
     %li
       = toggle_link("#lazar_description","lazar")
       %em= toggle_link("#regression","regression")
-      models 
+      models (experimental) 
   from your uploaded datasets. Further modelling algorithms will be added in future versions.
  
   %p
-- 
cgit v1.2.3


From 2de3bef8b5e29114961dfe2dbad9c379ebc359f6 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Thu, 5 May 2011 11:49:46 +0200
Subject: fix cancelling task on deletion

---
 application.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index 0123585..98d7fea 100644
--- a/application.rb
+++ b/application.rb
@@ -27,7 +27,7 @@ helpers do
   private 
   def delete_model(model, subjectid=nil)
     task = OpenTox::Task.create("Deleting model: #{model.uri}",url_for("/delete",:full)) do |task|
-      begin RestClient.put(File.join(model.task_uri, 'Cancelled'),subjectid) if model.task_uri rescue LOGGER.warn "Cannot cancel task #{model.task_uri}" end
+      begin OpenTox::RestClientWrapper.put(File.join(model.task_uri, "Cancelled"), "Cancelled",{:subjectid => subjectid}) if model.task_uri rescue LOGGER.warn "Cannot cancel task #{model.task_uri}" end
       task.progress(15)
       delete_dependent(model.uri, subjectid) if model.uri
       task.progress(30)
-- 
cgit v1.2.3


From d7f392b227060dc5f52a688b9d37000ba580aaf2 Mon Sep 17 00:00:00 2001
From: Denis Gebele <gebele@alfadeo.de>
Date: Mon, 9 May 2011 17:30:30 +0200
Subject: copyrights for JME, image fix for Safari browser

---
 views/predict.haml | 9 ++++++++-
 views/style.sass   | 4 +++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/views/predict.haml b/views/predict.haml
index d8c34a2..92e19e7 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -18,18 +18,25 @@
             %param{ :name => "options", :value => "polarnitro"}
             Please enable Java and JavaScript in your browser to use the JME editor. 
 
+          %jme_info
+            <span style="font-size:75%">&copy;
+            %a{:href => 'http://www.molinspiration.com/jme/index.html', :rel => "external"} JME Editor
+            courtesy of Peter Ertl, Novartis</span> 
+        %br  
         %label{:for => 'identifier'} or enter a Name, InChI, Smiles, CAS, ...
         %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
+      %br
       %fieldset
         %legend
           Choose one or more prediction models
+        %br
         - @models.each do |model|
           %label{:for => "model#{model.id}"}
             = model.name
           -#%input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => model.id, :disabled => !is_authorized(model.uri, "GET")} 
           %input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => "model#{model.id}", :disabled => false} 
           %br
-
+      %br
       %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
       %input{ :type => "submit", :value => "Predict", :onclick => "getsmiles();"}
       = link_to 'Cancel', '/predict' 
diff --git a/views/style.sass b/views/style.sass
index 0588444..dd7a843 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -130,7 +130,9 @@ body
           padding: 0.5em
         img
           padding: 0
-          height: 100%
+          //height: 100%
+          width: 150px
+          height: 150px
 
     .lazar-predictions
       clear: both
-- 
cgit v1.2.3


From 58337063969a7aee419b97c9b1c04124bbdcb1aa Mon Sep 17 00:00:00 2001
From: Denis Gebele <gebele@alfadeo.de>
Date: Wed, 11 May 2011 14:33:17 +0200
Subject: label cursor changes

---
 views/style.sass | 1 +
 1 file changed, 1 insertion(+)

diff --git a/views/style.sass b/views/style.sass
index dd7a843..ffae6a5 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -93,6 +93,7 @@ body
           font-weight: bold
           color: $fg_color
         label
+          cursor: pointer
           //width: 28em
           //display: block
           //float: left
-- 
cgit v1.2.3


From db1251962cc926312d1b5d06a06f95344130b537 Mon Sep 17 00:00:00 2001
From: Denis Gebele <gebele@alfadeo.de>
Date: Thu, 12 May 2011 10:49:33 +0200
Subject: checkboxes move to left

---
 views/predict.haml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/views/predict.haml b/views/predict.haml
index 92e19e7..ec667e6 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -31,10 +31,10 @@
           Choose one or more prediction models
         %br
         - @models.each do |model|
+          %input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => "model#{model.id}", :disabled => false}
           %label{:for => "model#{model.id}"}
             = model.name
-          -#%input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => model.id, :disabled => !is_authorized(model.uri, "GET")} 
-          %input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => "model#{model.id}", :disabled => false} 
+          -#%input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => model.id, :disabled => !is_authorized(model.uri, "GET")}            
           %br
       %br
       %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
-- 
cgit v1.2.3


From 2fa1764ffc79b1bcd751e57b4f4e71a264e3b168 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Fri, 13 May 2011 14:09:25 +0200
Subject: fix haml 3 error

---
 views/login.haml | 14 ++------------
 1 file changed, 2 insertions(+), 12 deletions(-)

diff --git a/views/login.haml b/views/login.haml
index 6d15bb7..3da552d 100644
--- a/views/login.haml
+++ b/views/login.haml
@@ -33,15 +33,5 @@
     %form{ :action => url_for('/login'), :method => "post" }
       %input{:type => 'hidden', :name => 'username', :id => 'username', :value => "guest"}
       %input{:type => 'hidden', :name => 'password', :id => 'password', :value => "guest"}
-      %input{ :type => "submit", :value => "Login as guest"}
-  -# else
-    %form{ :action => url_for('/logout'), :method => "post" }
-      -#%p 
-        You are logged in as: 
-        %b= session[:username]
-        -# if LOGGER.level == Logger::DEBUG        
-          %br
-          = session[:subjectid]
-      %input{ :type => "submit", :value => "Switch user"} 
-      = link_to "Cancel", '/login'
-      
+      %input{:type => "submit", :value => "Login as guest"}
+
-- 
cgit v1.2.3


From e9a1905129b84ce06925c08538b088697fbfa640 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Mon, 16 May 2011 14:01:44 +0200
Subject: haml error in lazar.haml

---
 views/lazar.haml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/views/lazar.haml b/views/lazar.haml
index 6ae6b20..8483cf5 100644
--- a/views/lazar.haml
+++ b/views/lazar.haml
@@ -38,8 +38,7 @@
             -# %li
               %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]')}", :rel => "external"}  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}", :rel => "external"} ToxNet data
             -#http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&regno=000143157
-- 
cgit v1.2.3


From b19f254428c46061a88dbe11b0298a48abf85648 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 16 May 2011 14:46:00 +0000
Subject: haml format error fixed in views/lazar.haml

---
 views/lazar.haml | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/views/lazar.haml b/views/lazar.haml
index 6ae6b20..3f1d030 100644
--- a/views/lazar.haml
+++ b/views/lazar.haml
@@ -18,12 +18,9 @@
         %th Supporting information
 
       %tr
-        -# %td
-          %img{:src => @compound.to_image_uri, :alt => @compound.to_smiles}
         %td.image= compound_image(@compound,@prediction.descriptors(@compound))
         %td= activity_markup(@prediction.value(@compound))
         %td= sprintf('%.03g', @prediction.confidence(@compound)) 
-        -#%td= @prediction.confidence(@compound)
         %td
           %ul
             %li
@@ -34,15 +31,6 @@
                   $("tr#names").toggle();  
                 });
             %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}", :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]')}", :rel => "external"}  PubChem data
-                (external)
-            -# %li
-              %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;" }
         %td{:colspan => '4'}
-- 
cgit v1.2.3


From cfa443a8e93bd6f0e574c7c96f4cb0895a17c6f4 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Mon, 23 May 2011 13:38:19 +0200
Subject: configure new version requested opentox-ruby gem

---
 application.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index 98d7fea..60d50cd 100644
--- a/application.rb
+++ b/application.rb
@@ -1,7 +1,7 @@
 ['rubygems', "haml", "sass", "rack-flash"].each do |lib|
   require lib
 end
-gem "opentox-ruby", "~> 1"
+gem "opentox-ruby", "~> 2"
 require 'opentox-ruby'
 gem 'sinatra-static-assets'
 require 'sinatra/static_assets'
-- 
cgit v1.2.3