From 347d49d5a0697cba6c8644914f51feb9ff4ecf35 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 17 Aug 2011 14:12:16 +0200
Subject: add subjectids where missing and some code cleanup

---
 application.rb | 52 +++++++++++++++++++++++++---------------------------
 1 file changed, 25 insertions(+), 27 deletions(-)

diff --git a/application.rb b/application.rb
index 3b88700..a60e597 100644
--- a/application.rb
+++ b/application.rb
@@ -81,7 +81,7 @@ end
 get '/models/?' do
   @models = ToxCreateModel.all.sort(:order => "DESC")
   @models.each{|m| raise "internal redis error: model is nil" unless m}
-  subjectstring = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : ""
+  subjectstring = @subjectid ? "?subjectid=#{CGI.escape(@subjectid)}" : ""
   haml :models, :locals=>{:models=>@models, :subjectstring => subjectstring}
 end
 
@@ -145,7 +145,7 @@ end
 get '/model/:id/:view/?' do
   response['Content-Type'] = 'text/plain'
   model = ToxCreateModel.get(params[:id])
-  subjectstring = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : ""
+  subjectstring = @subjectid ? "?subjectid=#{CGI.escape(@subjectid)}" : ""
   begin
     case params[:view]
       when "model"
@@ -199,7 +199,7 @@ end
 post '/feature' do
   session[:dataset] = params[:dataset]
   @features = []
-  OpenTox::Dataset.new(params[:dataset]).load_features.each do |uri,metadata|
+  OpenTox::Dataset.new(params[:dataset], @subjectid).load_features(@subjectid).each do |uri,metadata|
     @features << OpenTox::Feature.find(uri, @subjectid) if metadata[OWL.sameAs].match(/#{session[:echa]}/)
   end
   haml :feature
@@ -218,18 +218,16 @@ post '/models' do # 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],subjectid)
+    @dataset = OpenTox::Dataset.new(params[:dataset], @subjectid)
     name = @dataset.load_metadata[DC.title]
-    @prediction_feature = OpenTox::Feature.find params[:prediction_feature], subjectid
+    @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 => name, :subjectid => subjectid)
+  @model = ToxCreateModel.create(:name => name, :subjectid => @subjectid)
   @model.update :web_uri => url_for("/model/#{@model.id}", :full), :warnings => ""
   task = OpenTox::Task.create("Toxcreate Task - Uploading dataset and creating lazar model",url_for("/models",:full)) do |task|
 
@@ -238,33 +236,33 @@ post '/models' do # create a new model
 
     unless params[:dataset] and params[:prediction_feature]
       begin
-        @dataset = OpenTox::Dataset.create(nil, subjectid)
+        @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)
+          @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)
+          @dataset.load_spreadsheet(Excel.new excel_file, @subjectid)
           if @dataset.metadata[OT.Errors]
             raise "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} formats."
           end
         when ".sdf"
           sdf = params[:file][:tempfile].read
-          @dataset.load_sdf(sdf, subjectid)
+          @dataset.load_sdf(sdf, @subjectid)
         else
           raise "#{params[:file][:filename]} has an unsupported file type."
         end
-        @dataset.save(subjectid)
+        @dataset.save(@subjectid)
       rescue => e
         error "Dataset creation failed '#{e.message}'",e
       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)
+        @prediction_feature = OpenTox::Feature.find(@dataset.features.keys.first,@subjectid)
       end
     end
 
@@ -276,7 +274,7 @@ post '/models' do # create a new model
     @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.uri, :subjectid => subjectid}, 
+      lazar = OpenTox::Model::Lazar.create( {:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature.uri, :subjectid => @subjectid}, 
         OpenTox::SubTask.new(task,15,25))
     rescue => e
       error "Model creation failed",e # Please check if the input file is in a valid #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} format."
@@ -297,7 +295,7 @@ post '/models' do # create a new model
         crossvalidation = OpenTox::Crossvalidation.create( {
             :algorithm_uri => lazar.metadata[OT.algorithm],
             :dataset_uri => lazar.parameter("dataset_uri"),
-            :subjectid => subjectid,
+            :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))
@@ -306,7 +304,7 @@ post '/models' do # create a new model
         LOGGER.debug "Validation URI: #{@model.validation_uri}"
 
         # create summary
-        validation = crossvalidation.statistics(subjectid)
+        validation = crossvalidation.statistics(@subjectid)
         @model.update(:nr_predictions => validation.metadata[OT.numInstances].to_i - validation.metadata[OT.numUnpredicted].to_i)
         if validation.metadata[OT.classificationStatistics]
           @model.update(:correct_predictions => validation.metadata[OT.classificationStatistics][OT.percentCorrect].to_f)
@@ -332,9 +330,9 @@ post '/models' do # create a new model
     
       begin
         @model.update :status => "Creating validation report"
-        validation_report_uri = crossvalidation.find_or_create_report(subjectid, OpenTox::SubTask.new(task,80,90)) #unless @model.dirty?
+        validation_report_uri = crossvalidation.find_or_create_report(@subjectid, OpenTox::SubTask.new(task,80,90)) #unless @model.dirty?
         @model.update :validation_report_uri => validation_report_uri, :status => "Creating QMRF report"
-        qmrf_report = OpenTox::Crossvalidation::QMRFReport.create(@model.uri, subjectid, OpenTox::SubTask.new(task,90,99))
+        qmrf_report = OpenTox::Crossvalidation::QMRFReport.create(@model.uri, @subjectid, OpenTox::SubTask.new(task,90,99))
         @model.update(:validation_qmrf_uri => qmrf_report.uri, :status => "Completed")
       rescue => e
         error "Model report creation failed",e
@@ -353,7 +351,7 @@ post '/models' do # create a new model
 end
 
 post '/predict/?' do # post chemical name to model
-  subjectid = session[:subjectid] ? session[:subjectid] : nil
+  
   @identifier = params[:identifier]
   unless params[:selection] and params[:identifier] != ''
     flash[:notice] = "Please enter a compound identifier and select an endpoint from the list."
@@ -372,15 +370,15 @@ post '/predict/?' do # post chemical name to model
     confidence = nil
     title = nil
     db_activities = []
-    lazar = OpenTox::Model::Lazar.find model.uri
-    prediction_dataset_uri = lazar.run({:compound_uri => @compound.uri, :subjectid => subjectid})
+    lazar = OpenTox::Model::Lazar.find model.uri, @subjectid
+    prediction_dataset_uri = lazar.run({:compound_uri => @compound.uri, :subjectid => @subjectid})
     LOGGER.debug "Prediction dataset_uri: #{prediction_dataset_uri}"
     if lazar.value_map
       @value_map = lazar.value_map
     else
       @value_map = nil
     end
-    prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri, subjectid)
+    prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri, @subjectid)
     if prediction_dataset.metadata[OT.hasSource].match(/dataset/)
       @predictions << {
         :title => model.name,
@@ -388,7 +386,7 @@ post '/predict/?' do # post chemical name to model
       }
     else
       predicted_feature = prediction_dataset.metadata[OT.dependentVariables]
-      prediction = OpenTox::Feature.find(predicted_feature, subjectid)
+      prediction = OpenTox::Feature.find(predicted_feature, @subjectid)
       if prediction.metadata[OT.error]
         @predictions << {
           :title => model.name,
@@ -418,14 +416,14 @@ post "/lazar/?" do # get detailed prediction
   @page = 0
   @page = params[:page].to_i if params[:page]
   @model_uri = params[:model_uri]
-  lazar = OpenTox::Model::Lazar.find @model_uri
-  prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => session[:subjectid])
+  lazar = OpenTox::Model::Lazar.find @model_uri, @subjectid
+  prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => @subjectid)
   if lazar.value_map
     @value_map = lazar.value_map
   else
     @value_map = nil
   end
-  @prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri, session[:subjectid])
+  @prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri, @subjectid)
   @compound = OpenTox::Compound.new(params[:compound_uri])
   haml :lazar
 end
-- 
cgit v1.2.3


From 69fd5215ea35842fa8c8d8d9e8a767eae2f2c577 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 17 Aug 2011 14:40:11 +0200
Subject: remove delete link when deleting

---
 public/javascripts/toxcreate.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index 91789f8..ee783ce 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -207,6 +207,7 @@ jQuery.fn.deleteModel = function(type, options) {
     if(confirm(opts.confirm_message)) {
       $("div#model_" + opts.id).fadeTo("slow",0.5);
       $("span#model_" + opts.id + "_status").html("Deleting");
+      $("a#delete_" + opts.id).html("");
       $.ajax({
          type: opts.method,
          url:  opts.action,
-- 
cgit v1.2.3


From 282ca3f261897df3324ecdf7040d1a7b1c37edd9 Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Thu, 18 Aug 2011 10:47:06 +0200
Subject: replace weighted_auc with average_auc

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

diff --git a/model.rb b/model.rb
index e433893..bab5bde 100644
--- a/model.rb
+++ b/model.rb
@@ -31,7 +31,7 @@ class ToxCreateModel < Ohm::Model
 	attribute :nr_compounds
   attribute :nr_predictions
   attribute :correct_predictions
-	attribute :weighted_area_under_roc
+	attribute :average_area_under_roc
 	attribute :sensitivity
 	attribute :specificity
 	attribute :r_square
-- 
cgit v1.2.3


From 12b3295738445c941b03b15c34ec9e7f2fb56816 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Thu, 18 Aug 2011 13:06:04 +0200
Subject: optimize ToxCreateModel deletion

---
 application.rb | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/application.rb b/application.rb
index a60e597..8ace27c 100644
--- a/application.rb
+++ b/application.rb
@@ -31,7 +31,7 @@ helpers do
 
   private 
   def delete_model(model, subjectid=nil)
-    task = OpenTox::Task.create("Deleting model: #{model.uri}",url_for("/delete",:full)) do |task|
+    task = OpenTox::Task.create("Deleting model: #{model.web_uri}", url_for("/delete",:full)) do |task|
       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
@@ -49,15 +49,25 @@ helpers do
       if model.feature_dataset
         delete_dependent(model.feature_dataset, subjectid) if model.feature_dataset.match(CONFIG[:services]["opentox-dataset"])
       end
+      task.progress(95)
+      model.delete
+      unless ToxCreateModel.get(model.id)
+      begin
+        aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, @subjectid)
+        LOGGER.debug "Policy deleted for ToxCreateModel URI: #{model.web_uri} with result: #{aa}"
+      rescue
+        LOGGER.warn "Policy delete error for ToxCreateModel URI: #{model.web_uri}"
+      end
+    end
       task.progress(100)
-      ""
+      url_for("/models",:full)
     end
   end
 
   def delete_dependent(uri, subjectid=nil)
     begin
-      RestClient.delete(uri, :subjectid => subjectid) if subjectid
-      RestClient.delete(uri) if !subjectid
+      OpenTox::RestClientWrapper.delete(uri, :subjectid => subjectid) if subjectid
+      OpenTox::RestClientWrapper.delete(uri) if !subjectid
     rescue
       LOGGER.warn "Can not delete uri: #{uri}"
     end
@@ -451,18 +461,10 @@ delete '/model/:id/?' do
   model = ToxCreateModel.get(params[:id])
   raise OpenTox::NotFoundError.new("Model with id: #{params[:id]} not found!") unless model
   begin
-    delete_model(model, @subjectid)   
-    model.delete
-    unless ToxCreateModel.get(params[:id])
-      begin
-        aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, @subjectid)
-        LOGGER.debug "Policy deleted for Dataset URI: #{uri} with result: #{aa}"
-      rescue
-        LOGGER.warn "Policy delete error for Dataset URI: #{uri}"
-      end
-    end
+    delete_model(model, @subjectid)
     flash[:notice] = "#{model.name} model deleted."
   rescue
+    LOGGER.error "#{model.name} model delete error."
     flash[:notice] = "#{model.name} model delete error."
   end
   redirect url_for('/models')
-- 
cgit v1.2.3


From b41552185b21f706e7f507020925f3253c38321d Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Mon, 22 Aug 2011 11:25:06 +0200
Subject: unify cookies

---
 application.rb |  5 +++--
 helper.rb      | 30 ------------------------------
 2 files changed, 3 insertions(+), 32 deletions(-)

diff --git a/application.rb b/application.rb
index a60e597..ac19da5 100644
--- a/application.rb
+++ b/application.rb
@@ -9,8 +9,9 @@ require 'ftools'
 require File.join(File.dirname(__FILE__),'model.rb')
 require File.join(File.dirname(__FILE__),'helper.rb')
 
-use Rack::Session::Cookie, :expire_after => 28800, 
-                           :secret => "ui6vaiNi-change_me"
+#moved to wrapper->environment
+#use Rack::Session::Cookie, :expire_after => 28800, 
+#                           :secret => "ui6vaiNi-change_me"
 use Rack::Flash
 
 set :lock, true
diff --git a/helper.rb b/helper.rb
index 698fd3e..80707c3 100644
--- a/helper.rb
+++ b/helper.rb
@@ -1,35 +1,5 @@
 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
-    if session[:subjectid] != nil
-      session[:username] = username
-      return true
-    else
-      session[:username] = ""
-      return false
-    end
-  end
-
-  def logout
-    if session[:subjectid] != nil
-      session[:subjectid] = nil
-      session[:username] = ""
-      return true
-    end
-    return false
-  end
-
-  def logged_in()
-    return true if !AA_SERVER
-    if session[:subjectid] != nil
-      return OpenTox::Authorization.is_token_valid(session[:subjectid])
-    end
-    return false
-  end
-
   def is_authorized(uri, action)
     if OpenTox::Authorization.server && session[:subjectid] != nil
       return OpenTox::Authorization.authorized?(uri, action, session[:subjectid])
-- 
cgit v1.2.3


From a4b6e68acf76949a1765177b6d5b8c454990cb8a Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Mon, 22 Aug 2011 12:20:12 +0200
Subject: replace weighted_auc with average_auc [2]

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

diff --git a/application.rb b/application.rb
index d2ee131..eb86916 100644
--- a/application.rb
+++ b/application.rb
@@ -320,7 +320,7 @@ post '/models' do # create a new model
         if validation.metadata[OT.classificationStatistics]
           @model.update(:correct_predictions => validation.metadata[OT.classificationStatistics][OT.percentCorrect].to_f)
           @model.update(:confusion_matrix => validation.confusion_matrix.to_yaml)
-          @model.update(:weighted_area_under_roc => validation.metadata[OT.classificationStatistics][OT.weightedAreaUnderRoc].to_f)
+          @model.update(:average_area_under_roc => validation.metadata[OT.classificationStatistics][OT.averageAreaUnderRoc].to_f)
           validation.metadata[OT.classificationStatistics][OT.classValueStatistics].each do |m|
             if m[OT.classValue] =~ TRUE_REGEXP
               #HACK: estimate true feature value correctly 
diff --git a/views/classification_validation.haml b/views/classification_validation.haml
index f25a321..9f5c2c9 100644
--- a/views/classification_validation.haml
+++ b/views/classification_validation.haml
@@ -3,9 +3,9 @@
   = sprintf("%.2f", model.correct_predictions.to_f) if model.correct_predictions
   = '%'
 %dt
-  %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :rel => "external"} Weighted area under ROC:
+  %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :rel => "external"} Average area under ROC:
 %dd 
-  = sprintf("%.3f", model.weighted_area_under_roc.to_f) if model.weighted_area_under_roc
+  = sprintf("%.3f", model.average_area_under_roc.to_f) if model.average_area_under_roc
 %dt
   %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :rel => "external"} Specificity:
 %dd= sprintf("%.3f", model.specificity.to_f) if model.specificity
-- 
cgit v1.2.3


From 3b7a80f1af7e8b68f2f8bc9fd137ec9be5658c20 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 22 Aug 2011 11:09:28 +0000
Subject: integers in confusion matrix, average area under roc

---
 application.rb                       |  3 ++-
 views/classification_validation.haml | 12 ++++++------
 views/model.haml                     |  4 ++--
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/application.rb b/application.rb
index 8ace27c..9eafcbe 100644
--- a/application.rb
+++ b/application.rb
@@ -319,7 +319,8 @@ post '/models' do # create a new model
         if validation.metadata[OT.classificationStatistics]
           @model.update(:correct_predictions => validation.metadata[OT.classificationStatistics][OT.percentCorrect].to_f)
           @model.update(:confusion_matrix => validation.confusion_matrix.to_yaml)
-          @model.update(:weighted_area_under_roc => validation.metadata[OT.classificationStatistics][OT.weightedAreaUnderRoc].to_f)
+          #@model.update(:weighted_area_under_roc => validation.metadata[OT.classificationStatistics][OT.weightedAreaUnderRoc].to_f)
+          @model.update(:weighted_area_under_roc => validation.metadata[OT.classificationStatistics][OT.averageAreaUnderRoc].to_f)
           validation.metadata[OT.classificationStatistics][OT.classValueStatistics].each do |m|
             if m[OT.classValue] =~ TRUE_REGEXP
               #HACK: estimate true feature value correctly 
diff --git a/views/classification_validation.haml b/views/classification_validation.haml
index f25a321..dd2a7ae 100644
--- a/views/classification_validation.haml
+++ b/views/classification_validation.haml
@@ -3,7 +3,7 @@
   = sprintf("%.2f", model.correct_predictions.to_f) if model.correct_predictions
   = '%'
 %dt
-  %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :rel => "external"} Weighted area under ROC:
+  %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :rel => "external"} Average area under ROC:
 %dd 
   = sprintf("%.3f", model.weighted_area_under_roc.to_f) if model.weighted_area_under_roc
 %dt
@@ -24,21 +24,21 @@
       %tr
         - (1..cm[0].size-1).each do |i|
           %th{:bgcolor => "#CCD2DC"}
-            = cm[0][i]
+            = cm[0][i].to_i
       %tr
         %th{:rowspan => (cm.size - 1)} Predicted
         - (0..cm[1].size-1).each do |i|
           - if i == 0
             %th{:bgcolor => "#CCD2DC"}
-              = cm[1][i]
+              = cm[1][i].to_i
           - else
-            %td= cm[1][i]
+            %td= cm[1][i].to_i
       - if cm.size > 2
         - (2..cm.size-1).each do |i|
           %tr
             - (0..cm[i].size-1).each do |j|
               - if j == 0
                 %th{:bgcolor => "#CCD2DC"}
-                  = cm[i][j]
+                  = cm[i][j].to_i
               - else
-                %td= cm[i][j]
+                %td= cm[i][j].to_i
diff --git a/views/model.haml b/views/model.haml
index e688ae9..f0fd660 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -29,9 +29,9 @@
         - 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|Error|Cancelled/ 
-              (delete)
+              &nbsp;(delete)
             - else
-              (stop)
+              &nbsp;(stop)
         %span
           %br
         
-- 
cgit v1.2.3


From 8656f259932b03c3ddf7f5eff755d70ab7fbe3eb Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 22 Aug 2011 12:54:35 +0000
Subject: confusion matrix class names fixed

---
 views/classification_validation.haml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/views/classification_validation.haml b/views/classification_validation.haml
index 362a76f..47e1f75 100644
--- a/views/classification_validation.haml
+++ b/views/classification_validation.haml
@@ -24,13 +24,13 @@
       %tr
         - (1..cm[0].size-1).each do |i|
           %th{:bgcolor => "#CCD2DC"}
-            = cm[0][i].to_i
+            = cm[0][i]
       %tr
         %th{:rowspan => (cm.size - 1)} Predicted
         - (0..cm[1].size-1).each do |i|
           - if i == 0
             %th{:bgcolor => "#CCD2DC"}
-              = cm[1][i].to_i
+              = cm[1][i]
           - else
             %td= cm[1][i].to_i
       - if cm.size > 2
@@ -39,6 +39,6 @@
             - (0..cm[i].size-1).each do |j|
               - if j == 0
                 %th{:bgcolor => "#CCD2DC"}
-                  = cm[i][j].to_i
+                  = cm[i][j]
               - else
                 %td= cm[i][j].to_i
-- 
cgit v1.2.3


From c71f69b610b270b9c25cf58e84a035078905fa46 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Mon, 22 Aug 2011 15:28:27 +0200
Subject: remove subjectidstring for unified cookies

---
 application.rb                  |  8 +++-----
 public/javascripts/toxcreate.js | 14 +++++++-------
 views/model.haml                | 18 +++++++++---------
 views/models.haml               |  6 +++---
 views/validation.haml           |  2 +-
 5 files changed, 23 insertions(+), 25 deletions(-)

diff --git a/application.rb b/application.rb
index eb86916..9ef50f8 100644
--- a/application.rb
+++ b/application.rb
@@ -92,8 +92,7 @@ end
 get '/models/?' do
   @models = ToxCreateModel.all.sort(:order => "DESC")
   @models.each{|m| raise "internal redis error: model is nil" unless m}
-  subjectstring = @subjectid ? "?subjectid=#{CGI.escape(@subjectid)}" : ""
-  haml :models, :locals=>{:models=>@models, :subjectstring => subjectstring}
+  haml :models, :locals=>{:models=>@models}
 end
 
 get '/model/:id/status/?' do
@@ -156,13 +155,12 @@ end
 get '/model/:id/:view/?' do
   response['Content-Type'] = 'text/plain'
   model = ToxCreateModel.get(params[:id])
-  subjectstring = @subjectid ? "?subjectid=#{CGI.escape(@subjectid)}" : ""
   begin
     case params[:view]
       when "model"
-        haml :model, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false
+        haml :model, :locals=>{:model=>model}, :layout => false
       when /validation/
-        haml :validation, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false
+        haml :validation, :locals=>{:model=>model}, :layout => false
       else
         return "unable to render model: id #{params[:id]}, view #{params[:view]}"
     end
diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index ee783ce..0e82040 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -18,20 +18,20 @@ $(function() {
     return this.replace(/^\s+|\s+$/g, '');
   }
 
-  checkStati = function(stati, subjectstr) {
+  checkStati = function(stati) {
     stati = stati.split(", ");
     $("body")
     var newstati = new Array;
     $.each(stati, function(){
-      checkProgress(this, subjectstr);
-      if(checkStatus(this, subjectstr) > 0) newstati.push(this);
+      checkProgress(this);
+      if(checkStatus(this) > 0) newstati.push(this);
     });  
-    if (newstati.length > 0) var statusCheck = setTimeout('checkStati("' + newstati.join(", ") + '", "' + subjectstr + '")',10000);
+    if (newstati.length > 0) var statusCheck = setTimeout('checkStati("' + newstati.join(", ") + '")',10000);
   };
   
-  checkStatus = function(id, subjectstr) {
+  checkStatus = function(id) {
     if(id == "") return -1; 
-    var opts = {method: 'get', action: 'model/' + id + '/status' + subjectstr, id: id};
+    var opts = {method: 'get', action: 'model/' + id + '/status', id: id};
     var status_changed = $.ajax({
       type: opts.method,
       url: opts.action,
@@ -62,7 +62,7 @@ $(function() {
   };
   
   
-  checkProgress = function(id, subjectstr) {
+  checkProgress = function(id) {
     var task = $("input#model_" + id + "_task").attr('value');
     var opts = {action: task + "/percentageCompleted" , id: id};
     var progress_changed = $.ajax({
diff --git a/views/model.haml b/views/model.haml
index e688ae9..670ba1a 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -65,26 +65,26 @@
         %dt Training dataset:
         %dd
           - if model.training_dataset.match(/ambit/i)
-            %a{:href => "#{model.training_dataset}#{subjectstring}", :rel => "external"} Ambit database
+            %a{:href => "#{model.training_dataset}", :rel => "external"} Ambit database
           - else
-            %a{:href => "#{model.training_dataset}.xls#{subjectstring}"} Excel sheet
+            %a{:href => "#{model.training_dataset}.xls"} Excel sheet
             ,
             -#%a{:href => "#{model.training_dataset}.rdf"} RDF/XML
             -#%em (experts) ,
-            %a{:href => "#{model.training_dataset}.sdf#{subjectstring}" } SDF
+            %a{:href => "#{model.training_dataset}.sdf" } SDF
             ,
-            %a{:href => "#{model.training_dataset}.yaml#{subjectstring}" } YAML
+            %a{:href => "#{model.training_dataset}.yaml" } YAML
             %em  (experts)
       - if model.feature_dataset
         %dt Feature dataset:
         %dd
           -#%a{:href => "#{model.feature_dataset}.rdf"} RDF/XML
           -#,
-          %a{:href => "#{model.feature_dataset}.xls#{subjectstring}"} Excel sheet
+          %a{:href => "#{model.feature_dataset}.xls"} Excel sheet
           ,
-          %a{:href => "#{model.feature_dataset}.sdf#{subjectstring}"} SDF
+          %a{:href => "#{model.feature_dataset}.sdf"} SDF
           ,
-          %a{:href => "#{model.feature_dataset}.yaml#{subjectstring}"} YAML
+          %a{:href => "#{model.feature_dataset}.yaml"} YAML
           %em  (experts)
       - if model.uri
         %dt Model:
@@ -94,7 +94,7 @@
           -#,
           - if model.validation_qmrf_uri
             %a{:href => File.join(model.validation_qmrf_uri,"editor")} QMRF Editor, 
-          %a{:href => "#{model.uri}.yaml#{subjectstring}"} YAML
+          %a{:href => "#{model.uri}.yaml"} YAML
           %em  (experts, models cannot be represented in Excel)
 
-    = haml :validation, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false     
+    = haml :validation, :locals=>{:model=>model}, :layout => false
diff --git a/views/models.haml b/views/models.haml
index 9ab2858..a1ef8ba 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -3,7 +3,7 @@
 :javascript
   $(function() {
     if(#{stati != 0}) { 
-      setTimeout('checkStati("#{stati_to_check}", "#{subjectstring}")',5000);
+      setTimeout('checkStati("#{stati_to_check}", "")',5000);
     }
     var reload_validation = true;
   });
@@ -20,6 +20,6 @@
 
 - if @models
   - @models.each do |model|
-    = haml :model, :locals=>{:model=>model,:subjectstring=>subjectstring}, :layout => false 
--if @models.size == 0 
+    = haml :model, :locals=>{:model=>model}, :layout => false
+-if @models.size == 0
   .notice There are currently no models. You have to create a model first.
diff --git a/views/validation.haml b/views/validation.haml
index b8a6eaa..0a094d6 100644
--- a/views/validation.haml
+++ b/views/validation.haml
@@ -7,7 +7,7 @@
         - if model.validation_report_uri
           %dt Detailed report:
           %dd
-            %a{:href => model.validation_report_uri + subjectstring, :target => "_blank"} show
+            %a{:href => model.validation_report_uri, :target => "_blank"} show
         %dt Number of predictions:
         %dd= model.nr_predictions.to_s
         - case model.type
-- 
cgit v1.2.3


From f5eccd4ce22acb2fa05e84fb80e8385cce235d51 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 22 Aug 2011 16:23:00 +0000
Subject: NA inserted if valdiation parameters missing

---
 views/classification_validation.haml | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/views/classification_validation.haml b/views/classification_validation.haml
index 47e1f75..e06cb65 100644
--- a/views/classification_validation.haml
+++ b/views/classification_validation.haml
@@ -5,13 +5,24 @@
 %dt
   %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :rel => "external"} Average area under ROC:
 %dd 
-  = sprintf("%.3f", model.average_area_under_roc.to_f) if model.average_area_under_roc
+  - if model.average_area_under_roc
+    = sprintf("%.3f", model.average_area_under_roc.to_f)
+  - else
+    = 'NA'
 %dt
   %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :rel => "external"} Specificity:
-%dd= sprintf("%.3f", model.specificity.to_f) if model.specificity
+%dd
+  - if model.specificity
+    = sprintf("%.3f", model.specificity.to_f)
+  - else
+    = 'NA'
 %dt
   %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :rel => "external"} Sensitivity:
-%dd= sprintf("%.3f", model.sensitivity.to_f) if model.sensitivity
+%dd
+  - if model.sensitivity
+    = sprintf("%.3f", model.sensitivity.to_f)
+  - else
+    = 'NA'
 %dt
   %a{:href => "http://en.wikipedia.org/wiki/Confusion_matrix", :rel => "external"} Confusion Matrix:
 - if model.confusion_matrix
-- 
cgit v1.2.3


From db81a67c87a4f048f297d60ee60a7632f4595854 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 24 Aug 2011 16:22:13 +0200
Subject: A&A do not show models without allow for GET request

---
 views/models.haml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/views/models.haml b/views/models.haml
index a1ef8ba..e4f35b6 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -20,6 +20,7 @@
 
 - if @models
   - @models.each do |model|
-    = haml :model, :locals=>{:model=>model}, :layout => false
+    - if is_authorized(model.web_uri, "GET")
+      = haml :model, :locals=>{:model=>model}, :layout => false
 -if @models.size == 0
   .notice There are currently no models. You have to create a model first.
-- 
cgit v1.2.3


From c242bfc291a7dab733c424968509709813e6e331 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Tue, 30 Aug 2011 17:07:56 +0200
Subject: add model sorting

---
 application.rb               | 15 ++++++++++-
 helper.rb                    |  5 ++++
 views/models.haml            |  8 +++---
 views/models_navigation.haml | 61 ++++++++++++++++++++++++++++++++++++++++++++
 views/style.sass             | 23 +++++++++++++++++
 5 files changed, 108 insertions(+), 4 deletions(-)
 create mode 100644 views/models_navigation.haml

diff --git a/application.rb b/application.rb
index 9ef50f8..c03915c 100644
--- a/application.rb
+++ b/application.rb
@@ -90,7 +90,20 @@ get '/login' do
 end
 
 get '/models/?' do
-  @models = ToxCreateModel.all.sort(:order => "DESC")
+  @page = params[:page] ? params[:page].to_i : 0
+  order = params["order"] == "ASC" ? "ASC" : "DESC"
+  params["order"] = order
+  sort_by = params["sort_by"]
+  if sort_by
+    case sort_by
+    when "name", "created_at", "type", "id"
+      @models = ToxCreateModel.all.sort_by(sort_by.to_sym, :order => "#{order} ALPHA")
+    end
+  else
+    params["sort_by"] = "id"
+  end
+
+  @models = ToxCreateModel.all.sort(:order => "DESC") unless @models
   @models.each{|m| raise "internal redis error: model is nil" unless m}
   haml :models, :locals=>{:models=>@models}
 end
diff --git a/helper.rb b/helper.rb
index 80707c3..799135b 100644
--- a/helper.rb
+++ b/helper.rb
@@ -91,5 +91,10 @@ helpers do
     haml :neighbors_navigation, :layout => false
   end
 
+  def models_navigation
+    @page = 0 unless @page
+    haml :models_navigation, :layout => false
+  end
+
 end
 
diff --git a/views/models.haml b/views/models.haml
index a1ef8ba..d3ee8c0 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -17,9 +17,11 @@
 = haml :regression, :layout => false
 = haml :similarity, :layout => false
 = haml :significant_fragments, :layout => false
-
-- if @models
-  - @models.each do |model|
+- first = 5*@page
+- last = first+4
+= models_navigation
+- if @models[first..last]
+  - @models[first..last].each do |model|
     = haml :model, :locals=>{:model=>model}, :layout => false
 -if @models.size == 0
   .notice There are currently no models. You have to create a model first.
diff --git a/views/models_navigation.haml b/views/models_navigation.haml
new file mode 100644
index 0000000..fa5bd31
--- /dev/null
+++ b/views/models_navigation.haml
@@ -0,0 +1,61 @@
+.models_navigation
+
+  %form{:name => "nav", :action => url_for('/models'), :method => "get", :id => "nav"}
+    %input{:type => :hidden, :name => :sort_by, :id => "sort_by", :value => params[:sort_by]}
+    %input{:type => :hidden, :name => :order, :id => "order", :value => params[:order]}
+    %input{:type => :hidden, :name => :subjectid, :value => session[:subjectid]}    
+    %input{:type => :hidden, :name => :page, :id => "page", :value => params[:page]}
+
+    Models are sorted by:
+    - ["id","created_at","name","type"].each do |s|    
+      - idname = s == "created_at" ? "date" : s 
+      - if params[:sort_by] == s
+        %div{:id => idname, :class => "active"}
+          %span="#{idname}"
+          - if params[:order] == "ASC"
+            #up{:class => "link"}= "&dArr;"
+          - else
+            #down{:class => "link"}= "&uArr;"
+      - else
+        %div{:id => idname, :class => "link"}="#{idname}"
+    |
+    models:
+
+    #prev= "prev" unless @page.to_i == 0
+
+    - if @models.size < 5*@page+5
+      - last = @models.size 
+    - else 
+      - last = 5*@page+5
+
+    = "(#{5*@page+1}-#{last}/#{@models.size})" 
+
+    #next= "next" unless 5*@page.to_i+5 >= @models.size
+
+    - js = ""
+    - ["id","created_at","name","type"].each do |s|
+      - idname = s == "created_at" ? "date" : s
+      - js += "$('##{idname}').click(function() \{ \n "
+      - js += "  $('#sort_by').val('#{s}');\n "
+      - js += "  $('#nav').submit();\n "
+      - js += "});\n "
+
+    :javascript
+      $("#prev").click(function() {
+        $("#page").val(#{@page-1});
+        $("#nav").submit();
+      });
+      $("#next").click(function() {
+        $("#page").val(#{@page+1});
+        $("#nav").submit();
+      });
+      #{js}
+      $("#down").click(function() {
+        $("#order").val("ASC");
+        $("#nav").submit();
+      });
+      $("#up").click(function() {
+        $("#order").val("DESC");
+        $("#nav").submit();
+      });
+      
\ No newline at end of file
diff --git a/views/style.sass b/views/style.sass
index 15ae256..9f055e4 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -267,3 +267,26 @@ dl
   margin-left: 16px
   margin-right: 16px
   float: left
+
+.models_navigation
+  #prev
+    @extend a
+    display: inline
+    cursor: pointer
+  #next
+    @extend a
+    display: inline
+    cursor: pointer
+  .link
+    @extend a
+    display: inline
+    cursor: pointer
+  .active
+    display: inline
+    color: #000
+    font-weight: bold
+    padding: 0 1px
+  .thin
+    font-weight: 100
+  span
+    text-decoration: underline
-- 
cgit v1.2.3


From aeb03ab4a64353d51830d14dbd82f5d19c7254c6 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 31 Aug 2011 11:22:21 +0200
Subject: sorting for id

---
 application.rb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index c03915c..13bc02d 100644
--- a/application.rb
+++ b/application.rb
@@ -96,8 +96,10 @@ get '/models/?' do
   sort_by = params["sort_by"]
   if sort_by
     case sort_by
-    when "name", "created_at", "type", "id"
+    when "name", "created_at", "type"
       @models = ToxCreateModel.all.sort_by(sort_by.to_sym, :order => "#{order} ALPHA")
+    when "id"
+      @models = ToxCreateModel.all.sort(:order => "#{order}")
     end
   else
     params["sort_by"] = "id"
-- 
cgit v1.2.3


From c6e75e0028c8e3d45a236b8d79f3c0d15092da61 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 31 Aug 2011 12:47:42 +0200
Subject: optimize models navigation | put authorized to view model to
 application.rb

---
 application.rb               |   1 +
 public/arrow_down.png        | Bin 0 -> 411 bytes
 public/arrow_up.png          | Bin 0 -> 394 bytes
 views/models.haml            |   3 +--
 views/models_navigation.haml |   6 ++++--
 views/style.sass             |   2 --
 6 files changed, 6 insertions(+), 6 deletions(-)
 create mode 100644 public/arrow_down.png
 create mode 100644 public/arrow_up.png

diff --git a/application.rb b/application.rb
index 13bc02d..12784f0 100644
--- a/application.rb
+++ b/application.rb
@@ -107,6 +107,7 @@ get '/models/?' do
 
   @models = ToxCreateModel.all.sort(:order => "DESC") unless @models
   @models.each{|m| raise "internal redis error: model is nil" unless m}
+  @models.delete_if{|m| !is_authorized(m.web_uri, "GET")}
   haml :models, :locals=>{:models=>@models}
 end
 
diff --git a/public/arrow_down.png b/public/arrow_down.png
new file mode 100644
index 0000000..d298656
Binary files /dev/null and b/public/arrow_down.png differ
diff --git a/public/arrow_up.png b/public/arrow_up.png
new file mode 100644
index 0000000..70417dc
Binary files /dev/null and b/public/arrow_up.png differ
diff --git a/views/models.haml b/views/models.haml
index 6a181df..1419e37 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -17,11 +17,10 @@
 = haml :regression, :layout => false
 = haml :similarity, :layout => false
 = haml :significant_fragments, :layout => false
--# - if is_authorized(model.web_uri, "GET")
 
 - first = 5*@page
 - last = first+4
-= models_navigation
+= models_navigation if @models.size > 1
 - if @models[first..last]
   - @models[first..last].each do |model|
     = haml :model, :locals=>{:model=>model}, :layout => false
diff --git a/views/models_navigation.haml b/views/models_navigation.haml
index fa5bd31..d324fce 100644
--- a/views/models_navigation.haml
+++ b/views/models_navigation.haml
@@ -13,9 +13,11 @@
         %div{:id => idname, :class => "active"}
           %span="#{idname}"
           - if params[:order] == "ASC"
-            #up{:class => "link"}= "&dArr;"
+            #up{:class => "link"}
+              %img{:src => "arrow_down.png", :alt => 'in ascending order', :title => 'in ascending order'}/
           - else
-            #down{:class => "link"}= "&uArr;"
+            #down{:class => "link"}
+              %img{:src => "arrow_up.png", :alt => 'in descending order', :title => 'in descending order'}/
       - else
         %div{:id => idname, :class => "link"}="#{idname}"
     |
diff --git a/views/style.sass b/views/style.sass
index 9f055e4..56eee02 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -288,5 +288,3 @@ dl
     padding: 0 1px
   .thin
     font-weight: 100
-  span
-    text-decoration: underline
-- 
cgit v1.2.3


From 2fadf0789c47b49e5c47997d6e392faa7da88230 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 31 Aug 2011 16:10:51 +0200
Subject: sorting functionality for models page

---
 public/arrow_left.png           | Bin 0 -> 374 bytes
 public/arrow_left_inactive.png  | Bin 0 -> 364 bytes
 public/arrow_right.png          | Bin 0 -> 386 bytes
 public/arrow_right_inactive.png | Bin 0 -> 400 bytes
 views/models_navigation.haml    |  31 ++++++++++++++++++-------------
 views/style.sass                |   1 -
 6 files changed, 18 insertions(+), 14 deletions(-)
 create mode 100644 public/arrow_left.png
 create mode 100644 public/arrow_left_inactive.png
 create mode 100644 public/arrow_right.png
 create mode 100644 public/arrow_right_inactive.png

diff --git a/public/arrow_left.png b/public/arrow_left.png
new file mode 100644
index 0000000..8d18c67
Binary files /dev/null and b/public/arrow_left.png differ
diff --git a/public/arrow_left_inactive.png b/public/arrow_left_inactive.png
new file mode 100644
index 0000000..52c11bf
Binary files /dev/null and b/public/arrow_left_inactive.png differ
diff --git a/public/arrow_right.png b/public/arrow_right.png
new file mode 100644
index 0000000..7fe64a8
Binary files /dev/null and b/public/arrow_right.png differ
diff --git a/public/arrow_right_inactive.png b/public/arrow_right_inactive.png
new file mode 100644
index 0000000..496f79e
Binary files /dev/null and b/public/arrow_right_inactive.png differ
diff --git a/views/models_navigation.haml b/views/models_navigation.haml
index d324fce..4b3ba2d 100644
--- a/views/models_navigation.haml
+++ b/views/models_navigation.haml
@@ -3,15 +3,14 @@
   %form{:name => "nav", :action => url_for('/models'), :method => "get", :id => "nav"}
     %input{:type => :hidden, :name => :sort_by, :id => "sort_by", :value => params[:sort_by]}
     %input{:type => :hidden, :name => :order, :id => "order", :value => params[:order]}
-    %input{:type => :hidden, :name => :subjectid, :value => session[:subjectid]}    
     %input{:type => :hidden, :name => :page, :id => "page", :value => params[:page]}
 
     Models are sorted by:
-    - ["id","created_at","name","type"].each do |s|    
-      - idname = s == "created_at" ? "date" : s 
+    - ["id","created_at","name","type"].each do |s|
+      - idname = s == "created_at" ? "date" : s
       - if params[:sort_by] == s
         %div{:id => idname, :class => "active"}
-          %span="#{idname}"
+          %span="#{idname.capitalize}"
           - if params[:order] == "ASC"
             #up{:class => "link"}
               %img{:src => "arrow_down.png", :alt => 'in ascending order', :title => 'in ascending order'}/
@@ -19,20 +18,26 @@
             #down{:class => "link"}
               %img{:src => "arrow_up.png", :alt => 'in descending order', :title => 'in descending order'}/
       - else
-        %div{:id => idname, :class => "link"}="#{idname}"
+        %div{:id => idname, :class => "link"}="#{idname.capitalize}&nbsp;"
     |
-    models:
-
-    #prev= "prev" unless @page.to_i == 0
+    Models:
+    - unless @page.to_i == 0
+      #prev
+        %img{:src => "arrow_left.png", :alt => 'previous', :title => 'previous'}/
+    -else
+      %img{:src => "arrow_left_inactive.png", :alt => '', :title => ''}/
 
     - if @models.size < 5*@page+5
-      - last = @models.size 
-    - else 
+      - last = @models.size
+    - else
       - last = 5*@page+5
 
-    = "(#{5*@page+1}-#{last}/#{@models.size})" 
-
-    #next= "next" unless 5*@page.to_i+5 >= @models.size
+    = "(#{5*@page+1}-#{last}/#{@models.size})"
+    - unless 5*@page.to_i+5 >= @models.size
+      #next
+        %img{:src => "arrow_right.png", :alt => 'next', :title => 'next'}/
+    -else
+      %img{:src => "arrow_right_inactive.png", :alt => '', :title => ''}/
 
     - js = ""
     - ["id","created_at","name","type"].each do |s|
diff --git a/views/style.sass b/views/style.sass
index 56eee02..23b157a 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -285,6 +285,5 @@ dl
     display: inline
     color: #000
     font-weight: bold
-    padding: 0 1px
   .thin
     font-weight: 100
-- 
cgit v1.2.3


From 7ec60be28a09f748ee624e8b44bdc2e936de71f9 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 31 Aug 2011 17:06:54 +0200
Subject: show pages only if more than 5 models

---
 views/models_navigation.haml | 40 +++++++++++++++++++++-------------------
 1 file changed, 21 insertions(+), 19 deletions(-)

diff --git a/views/models_navigation.haml b/views/models_navigation.haml
index 4b3ba2d..ed8b720 100644
--- a/views/models_navigation.haml
+++ b/views/models_navigation.haml
@@ -19,25 +19,27 @@
               %img{:src => "arrow_up.png", :alt => 'in descending order', :title => 'in descending order'}/
       - else
         %div{:id => idname, :class => "link"}="#{idname.capitalize}&nbsp;"
-    |
-    Models:
-    - unless @page.to_i == 0
-      #prev
-        %img{:src => "arrow_left.png", :alt => 'previous', :title => 'previous'}/
-    -else
-      %img{:src => "arrow_left_inactive.png", :alt => '', :title => ''}/
-
-    - if @models.size < 5*@page+5
-      - last = @models.size
-    - else
-      - last = 5*@page+5
-
-    = "(#{5*@page+1}-#{last}/#{@models.size})"
-    - unless 5*@page.to_i+5 >= @models.size
-      #next
-        %img{:src => "arrow_right.png", :alt => 'next', :title => 'next'}/
-    -else
-      %img{:src => "arrow_right_inactive.png", :alt => '', :title => ''}/
+    - if @models.size > 5
+      |
+      Models:
+      = "#{@models.size}"
+      - unless @page.to_i == 0
+        #prev
+          %img{:src => "arrow_left.png", :alt => 'previous', :title => 'previous'}/
+      -else
+        %img{:src => "arrow_left_inactive.png", :alt => '', :title => ''}/
+  
+      - if @models.size < 5*@page+5
+        - last = @models.size
+      - else
+        - last = 5*@page+5
+  
+      = "(#{5*@page+1}-#{last}/#{@models.size})"
+      - unless 5*@page.to_i+5 >= @models.size
+        #next
+          %img{:src => "arrow_right.png", :alt => 'next', :title => 'next'}/
+      -else
+        %img{:src => "arrow_right_inactive.png", :alt => '', :title => ''}/
 
     - js = ""
     - ["id","created_at","name","type"].each do |s|
-- 
cgit v1.2.3


From 9299e2d50ac9f63ef30b7d5ead662b8f2f2df78f Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 31 Aug 2011 17:23:27 +0200
Subject: make w3c valid

---
 views/create.haml  | 19 ++++++++++---------
 views/predict.haml |  2 +-
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/views/create.haml b/views/create.haml
index b706484..5dbd71d 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -47,15 +47,16 @@
     structure-activity models from your experimental data. The models can be used to predict toxicity of new chemicals (e.g. for 
     %a{:href => "http://ec.europa.eu/environment/chemicals/reach/reach_intro.htm", :rel => "external"} REACH
     purposes) and to reduce the need for animal testing.  The following methods are currently available:
-    %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 (experimental) 
+  %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 (experimental)
+  %p
     Further modelling algorithms may be added in future versions.
 
   .login_notice
diff --git a/views/predict.haml b/views/predict.haml
index 8aae7cf..670ca44 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -20,7 +20,7 @@
           %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> 
+            courtesy of Peter Ertl, Novartis 
         %br  
         -# %label{:for => 'identifier'} or enter a Name, InChI, Smiles, CAS, ...
         %label{:for => 'identifier'} or enter a Smiles string
-- 
cgit v1.2.3


From 038c4563032f65f935f38ef6bffe426b2dd14c0c Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 14 Sep 2011 10:05:47 +0200
Subject: Endpoint selection from ontology server with cache

---
 helper.rb             | 21 ++++++++++++++++++++-
 views/create.haml     |  2 ++
 views/endpoint.haml   |  2 +-
 views/model_echa.haml |  2 ++
 views/style.sass      | 10 ++++++++++
 5 files changed, 35 insertions(+), 2 deletions(-)
 create mode 100644 views/model_echa.haml

diff --git a/helper.rb b/helper.rb
index 799135b..9b47142 100644
--- a/helper.rb
+++ b/helper.rb
@@ -96,5 +96,24 @@ helpers do
     haml :models_navigation, :layout => false
   end
 
+  def endpoint_option_list(max_time=3600)
+    out = ""
+    tmpfile = File.join(TMP_DIR, "endpoint_option_list")
+    if File.exists? tmpfile
+      if Time.now-File.mtime(tmpfile) <= max_time
+        f = File.open(tmpfile, 'r+')
+        f.each{|line| out << line}
+        return out
+      else
+        File.unlink(tmpfile)
+      end
+    end
+    result = OpenTox::Ontology::Echa.endpoint_option_list()
+    if result.lines.count > 3
+      f = File.new(tmpfile,"w")
+      f.print result
+      f.close
+    end
+    return result
+  end
 end
-
diff --git a/views/create.haml b/views/create.haml
index 5dbd71d..da85382 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -24,6 +24,8 @@
         = link_to "SDF", '/help'
         format:
       %input{:type => 'file', :name => 'file', :id => 'file', :size => '41'}
+      %br
+      -# = haml :model_echa, :layout => false
     %input{ :type => "submit", :value => "Create model"}
     =# link_to "Cancel", '/create'
 
diff --git a/views/endpoint.haml b/views/endpoint.haml
index af06b80..9c250ca 100644
--- a/views/endpoint.haml
+++ b/views/endpoint.haml
@@ -9,4 +9,4 @@
     %em in-vitro,
     or
     %em in-vivo
-    expriment, clinical trial or epidemiological study
+    experiment, clinical trial or epidemiological study
diff --git a/views/model_echa.haml b/views/model_echa.haml
new file mode 100644
index 0000000..257a28a
--- /dev/null
+++ b/views/model_echa.haml
@@ -0,0 +1,2 @@
+Select an endpoint:
+= endpoint_option_list
\ No newline at end of file
diff --git a/views/style.sass b/views/style.sass
index 23b157a..c2a74cb 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -287,3 +287,13 @@ dl
     font-weight: bold
   .thin
     font-weight: 100
+
+.level_1
+  padding-left: 10px
+  font-weight: bold
+.level_2
+  padding-left: 20px
+.level_3
+  padding-left: 30px
+.level_4
+  padding-left: 40px
-- 
cgit v1.2.3


From e967ffe75370d39d0928e440a9023e2da6e35ae3 Mon Sep 17 00:00:00 2001
From: mr <mr@mrautenberg.de>
Date: Wed, 21 Sep 2011 11:16:28 +0200
Subject: remove id from sort tab

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

diff --git a/application.rb b/application.rb
index 12784f0..2b320e0 100644
--- a/application.rb
+++ b/application.rb
@@ -102,7 +102,7 @@ get '/models/?' do
       @models = ToxCreateModel.all.sort(:order => "#{order}")
     end
   else
-    params["sort_by"] = "id"
+    params["sort_by"] = "created_at"
   end
 
   @models = ToxCreateModel.all.sort(:order => "DESC") unless @models
diff --git a/views/models_navigation.haml b/views/models_navigation.haml
index ed8b720..b491cb5 100644
--- a/views/models_navigation.haml
+++ b/views/models_navigation.haml
@@ -5,8 +5,8 @@
     %input{:type => :hidden, :name => :order, :id => "order", :value => params[:order]}
     %input{:type => :hidden, :name => :page, :id => "page", :value => params[:page]}
 
-    Models are sorted by:
-    - ["id","created_at","name","type"].each do |s|
+    Sort by:
+    - ["created_at","name","type"].each do |s|
       - idname = s == "created_at" ? "date" : s
       - if params[:sort_by] == s
         %div{:id => idname, :class => "active"}
-- 
cgit v1.2.3