Merge branch 'hotfix/v1.0.2'v1.0.2

11 files changed, 69 insertions, 210 deletions

diff --git a/application.rb b/application.rb
index f6e03cc..fc21414 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 :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..5332629 100644
--- a/model.rb
+++ b/model.rb
@@ -1,12 +1,7 @@
 require 'ohm'
-#require 'redis/objects'
-#@@redis = Redis.new(:thread_safe=>true)#(:host => '127.0.0.1', :port => 6379)
 
 class ToxCreateModel < Ohm::Model
 
-  #include Redis::Objects
-	#include DataMapper::Resource
-	#attribute :id
 	attribute :name
 	attribute :warnings
 	attribute :error_messages
@@ -49,45 +44,6 @@ class ToxCreateModel < Ohm::Model
 
   #after :save, :check_policy
 
-=begin
-  attr_accessor :id, :name, :warnings, :error_messages, :type, :status, :created_at, :task_uri, :uri, :training_dataset, :feature_dataset, :validation_task_uri, :validation_uri, :validation_report_task_uri, :validation_report_uri, :validation_qmrf_task_uri, :validation_qmrf_uri, :nr_compounds, :nr_predictions, :true_positives, :false_positives, :true_negatives, :false_negatives, :correct_predictions, :weighted_area_under_roc, :sensitivity, :specificity, :r_square, :root_mean_squared_error, :mean_absolute_error, :web_uri
-
-  def self.all
-  end
-
-  def self.get(id)
-  end
-  
-  def self.create(params)
-    @id = @@redis.incr "toxcreate"
-    params.each { |k,v| @@redis.hset "toxcreate:#{@id}", k, v }
-    self.get(@id)
-  end
-
-  def update(params)
-  end
-
-  def method_missing
-    begin
-    rescue
-      raise "Unknown method"
-    end
-  end
-
-  attr_accessor :subjectid
-  @subjectid = nil
-
-  after :save, :check_policy
-
-def status
-		#begin
-			RestClient.get(File.join(@task_uri, 'hasStatus')).body
-		#rescue
-		#	"Service offline"
-		#end
-	end
-=end
-
 	def validation_status
 		begin
 			RestClient.get(File.join(@validation_task_uri, 'hasStatus')).body
@@ -112,115 +68,6 @@ def status
 		end
 	end
 
-	def algorithm
-		begin
-			RestClient.get(File.join(@uri, 'algorithm')).body
-		rescue
-			""
-		end
-	end
-
-	def training_dataset
-		begin
-			RestClient.get(File.join(@uri, 'trainingDataset')).body
-		rescue
-			""
-		end
-	end
-
-	def feature_dataset
-		begin
-			RestClient.get(File.join(@uri, 'feature_dataset')).body
-		rescue
-			""
-		end
-	end
-
-=begin
-  def process
-
-    LOGGER.debug self.to_yaml
-
-    if @uri.nil? and status == "Completed"
-			#update :uri => RestClient.get(File.join(@task_uri, 'resultURI')).body
-			#lazar = YAML.load(RestClient.get(@uri, :accept => "application/x-yaml").body)
-
-		elsif @validation_uri.nil? and validation_status == "Completed"
-			begin
-
-				#update :validation_uri => RestClient.get(File.join(@validation_task_uri, 'resultURI')).body
-				#LOGGER.debug "Validation URI: #{@validation_uri}"
-
-				#update :validation_report_task_uri => RestClient.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"), :validation_uris => @validation_uri).body
-				#LOGGER.debug "Validation Report Task URI: #{@validation_report_task_uri}"
-
-				#update :validation_qmrf_task_uri => RestClient.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"), :model_uri => @uri).body
-				#LOGGER.debug "QMRF Report Task URI: #{@validation_qmrf_task_uri}"
-
-        uri = File.join(@validation_uri, 'statistics')
-        yaml = RestClient.get(uri).body
-        v = YAML.load(yaml)
-
-        case type
-        when "classification"
-          tp=0; tn=0; fp=0; fn=0; n=0
-          v[:classification_statistics][:confusion_matrix][:confusion_matrix_cell].each do |cell|
-            if cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "true"
-              tp = cell[:confusion_matrix_value]
-              n += tp
-            elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "false"
-              tn = cell[:confusion_matrix_value]
-              n += tn
-            elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "true"
-              fn = cell[:confusion_matrix_value]
-              n += fn
-            elsif cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "false"
-              fp = cell[:confusion_matrix_value]
-              n += fp
-            end
-          end
-          update :nr_predictions => n
-          update :true_positives => tp
-          update :false_positives => fp
-          update :true_negatives => tn
-          update :false_negatives => fn
-          update :correct_predictions => 100*(tp+tn).to_f/n
-          update :weighted_area_under_roc => v[:classification_statistics][:weighted_area_under_roc].to_f
-          update :sensitivity => tp.to_f/(tp+fn)
-          update :specificity => tn.to_f/(tn+fp)
-        when "regression"
-          update :nr_predictions => v[:num_instances] - v[:num_unpredicted]
-          update :r_square => v[:regression_statistics][:r_square]
-          update :root_mean_squared_error => v[:regression_statistics][:root_mean_squared_error]
-          update :mean_absolute_error => v[:regression_statistics][:mean_absolute_error]
-        end
-			rescue
-				LOGGER.warn "Cannot create Validation Report Task #{@validation_report_task_uri} for  Validation URI #{@validation_uri} from Task #{@validation_task_uri}"
-			end
-
-		else
-
-      if @validation_report_uri.nil? and validation_report_status == "Completed"
-        begin
-          update :validation_report_uri => RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
-        rescue
-          LOGGER.warn "Cannot create Validation Report for  Task URI #{@validation_report_task_uri} "
-        end
-      end
-
-      if @validation_qmrf_uri.nil? and validation_qmrf_status == "Completed"
-        begin
-          update :validation_qmrf_uri => RestClient.get(File.join(@validation_qmrf_task_uri, 'resultURI')).body
-        rescue
-          LOGGER.warn "Cannot create QMRF Report for  Task URI #{@validation_qmrf_task_uri} "
-        end
-      end
-
-    end
-
-  end
-=end
-
   private
   def check_policy
     OpenTox::Authorization.check_policy(web_uri, subjectid)
@@ -228,4 +75,3 @@ def status
 
 end
 
-#DataMapper.auto_upgrade!
diff --git a/public/progressbar/progressbar.css b/public/progressbar/progressbar.css
index 92e3f82..f3b4131 100644
--- a/public/progressbar/progressbar.css
+++ b/public/progressbar/progressbar.css
@@ -11,7 +11,9 @@
 /* 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-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; }
@@ -19,8 +21,9 @@
 * 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); }
-
+*/
 
 /* Interaction Cues
 ----------------------------------*/
@@ -40,7 +43,6 @@
 /* Overlays */
 .ui-widget-overlay { position: absolute; top: 0; left: 0; width: 100%; height: 100%; }
 
-
 /*
  * jQuery UI CSS Framework 1.8.9
  *
@@ -82,8 +84,10 @@
 .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; }
+*/
 
 /* Icons
 ----------------------------------*/
@@ -280,6 +284,7 @@
 ----------------------------------*/
 
 /* 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; }
@@ -289,10 +294,17 @@
 .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-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)
@@ -302,4 +314,4 @@
  * http://docs.jquery.com/UI/Progressbar#theming
  */
 .ui-progressbar { height:20px; text-align: left; }
-.ui-progressbar .ui-progressbar-value {margin: -1px; height:20px; }
\ No newline at end of file
+.ui-progressbar .ui-progressbar-value {margin: -1px; height:20px; }
diff --git a/views/create.haml b/views/create.haml
index c04f841..82f48d0 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -1,17 +1,16 @@
 .input
 
-  %p
-    This service creates 
-    %ul
-      %li
-        = toggle_link("#lazar_description","lazar")
-        %em= toggle_link("#classification","classification")
-        models and
-      %li
-        = toggle_link("#lazar_description","lazar")
-        %em= toggle_link("#regression","regression")
-        models 
-    from your uploaded datasets. Further modelling algorithms will be added in future versions.
+  This service creates 
+  %ul
+    %li
+      = toggle_link("#lazar_description","lazar")
+      %em= toggle_link("#classification","classification")
+      models and
+    %li
+      = toggle_link("#lazar_description","lazar")
+      %em= toggle_link("#regression","regression")
+      models 
+  from your uploaded datasets. Further modelling algorithms will be added in future versions.
  
   %p
     Please read the 
diff --git a/views/help.haml b/views/help.haml
index a8bbf4b..da6495e 100644
--- a/views/help.haml
+++ b/views/help.haml
@@ -2,7 +2,7 @@
 %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
-  format, in the second column the toxic activity.
+  format, in the second column the toxic activity. The first line contains a description of the columns and is ignored.
 %dl
   %dt Classification datasets 
   %dd Please use 1/0, active/inactive or true/false to indicate active/inactive compounds.
@@ -36,6 +36,11 @@
     %tr
       - n += 1
       %th= n
+      %td SMILES
+      %td Hamster Carcinogenicity
+    %tr
+      - n += 1
+      %th= n
       %td CC(=O)Nc1ccc(O)cc1
       %td 1  
     %tr
@@ -87,6 +92,7 @@
 
 .code
   %code
+    %br SMILES, Hamster Carcinogenicity
     %br CC(=O)Nc1ccc(O)cc1, 1  
     %br O=c1[nH]cnc2[nH]ncc12, 1  
     %br CCCCNc1cc(cc(c1Oc2ccccc2)S(=O)(=O)N)C(=O)O, 1  
diff --git a/views/layout.haml b/views/layout.haml
index d54b413..d9d7783 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -1,8 +1,8 @@
-!!!
+!!! 
 %html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"}
 
   %head
-    %meta{'http-equiv' => 'Content-Type', :content => 'text/html'}
+    %meta{'http-equiv' => 'Content-Type', :content => 'text/html; charset=UTF-8'}
     %title ToxCreate
     %script{:type => "text/javascript", :src  => "javascripts/jquery.js"}
     %script{:type => "text/javascript", :src  => "javascripts/toxcreate.js"}
@@ -12,7 +12,7 @@
 
   %body
     .logo
-      = image_tag "/ToxCreate_rgb_72.png", :alt => 'ToxCreate', :align => 'right'
+      %img{:src => "ToxCreate_rgb_72.png", :alt => 'ToxCreate', :align => 'right'}/
       %br
       Create and evaluate models to predict toxicity
     .index
@@ -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/helma/opentox-toxmodel/issues'} issue tracker.
+          %a{:href => 'http://github.com/opentox/opentox-toxmodel/issues'} issue tracker.
 
       - if flash[:notice]
         %p
diff --git a/views/lazar_description.haml b/views/lazar_description.haml
index d870425..d8e995d 100644
--- a/views/lazar_description.haml
+++ b/views/lazar_description.haml
@@ -5,25 +5,24 @@
     = hide_link "#lazar_description"
     )
   %dd 
-    %p
-      %code lazar
-      searches the training dataset for  
-      = toggle_link "#similarity", "similar"
-      compounds 
-      %em (neighbors)
-      and calculates the prediction from their measured activities.
-      %code lazar
-      calculates predictions using
-      %ul
-        %li
-          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
-          )
-        %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
-          )
+    %code lazar
+    searches the training dataset for  
+    = toggle_link "#similarity", "similar"
+    compounds 
+    %em (neighbors)
+    and calculates the prediction from their measured activities.
+    %code lazar
+    calculates predictions using
+    %ul
+      %li
+        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
+        )
+      %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
+        )
diff --git a/views/model.haml b/views/model.haml
index 5addcb0..91d7016 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -83,4 +83,5 @@
             %a{:href => File.join(model.validation_qmrf_uri,"editor")} QMRF Editor, 
           %a{:href => "#{model.uri}.yaml#{subjectstring}"} YAML
           %em  (experts, models cannot be represented in Excel)
-      = haml :validation, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false     
+
+    = haml :validation, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false     
diff --git a/views/models.haml b/views/models.haml
index a99144a..67c061c 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -10,12 +10,14 @@
   });
 
 -# %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.
+%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 :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 
diff --git a/views/predict.haml b/views/predict.haml
index 347592c..d8c34a2 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -16,7 +16,7 @@
         .jme
           %applet{:code => "JME.class",  :name => "JME", :archive => "JME.jar", :width => "500", :height => "360"}
             %param{ :name => "options", :value => "polarnitro"}
-              Please enable Java and JavaScript in your browser to use the JME editor. 
+            Please enable Java and JavaScript in your browser to use the JME editor. 
 
         %label{:for => 'identifier'} or enter a Name, InChI, Smiles, CAS, ...
         %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
@@ -24,10 +24,10 @@
         %legend
           Choose one or more prediction models
         - @models.each do |model|
-          %label{:for => model.id}
+          %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.id, :disabled => false} 
+          %input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => "model#{model.id}", :disabled => false} 
           %br
 
       %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
diff --git a/views/validation.haml b/views/validation.haml
index 06a57e7..b8a6eaa 100644
--- a/views/validation.haml
+++ b/views/validation.haml
@@ -2,22 +2,16 @@
   %dl{:id => "model_validation_#{model.id}"}
     %dt
       Validation:
-      -# %input{ :id => "model_validation_report_#{model.id}", :type => "hidden", :value => "#{model.validation_report_status}", :class => "model_validation_report" }
     %dd
       %dl
         - if model.validation_report_uri
           %dt Detailed report:
           %dd
             %a{:href => model.validation_report_uri + subjectstring, :target => "_blank"} show
-        %dt Number of predictions
+        %dt Number of predictions:
         %dd= model.nr_predictions.to_s
         - case model.type
         - when "classification"
           = haml :classification_validation, :locals=>{:model=>model}, :layout => false if model.correct_predictions
         - when "regression"
           = haml :regression_validation, :locals=>{:model=>model}, :layout => false     
--# else
-  = image_tag("/snake_transparent.gif") if model.validation_status == "Running"
-  %a{:href => model.validation_task_uri} #{model.validation_status}
-            
-