merge from development -> lazar-gui

7 files changed, 67 insertions, 96 deletions

diff --git a/application.rb b/application.rb
index ee851d9..104003e 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
@@ -31,7 +32,7 @@ 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 +50,25 @@ 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
@@ -81,7 +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 = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : ""
+  subjectstring = @subjectid ? "?subjectid=#{CGI.escape(@subjectid)}" : ""
   haml :models, :locals=>{:models=>@models, :subjectstring => subjectstring}
 end
 
@@ -145,7 +156,7 @@ 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 +210,7 @@ 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 +229,16 @@ 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 +247,33 @@ 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 +285,7 @@ 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 +306,7 @@ 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))
@@ -306,12 +315,12 @@ 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)
           @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 
@@ -332,9 +341,9 @@ 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
@@ -353,14 +362,14 @@ 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."
     redirect url_for('/predict')
   end
   begin
-    @compound = OpenTox::Compound.from_name(params[:identifier])
+    @compound = OpenTox::Compound.from_smiles(params[:identifier])
   rescue
     flash[:notice] = "Could not find a structure for '#{@identifier}'. Please try again."
     redirect url_for('/predict')
@@ -372,15 +381,15 @@ 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 +397,7 @@ 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 +427,14 @@ 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
@@ -453,18 +462,10 @@ 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')
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])
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
diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index a5dc44c..ee783ce 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -77,8 +77,7 @@ $(function() {
         if (progress == "100") return -1;         
         
         $("div#model_" + id + "_progress").progressbar("value", parseInt(progress)); 
-        $("div#model_" + id + "_progress").attr({title: parseInt(progress) + "%", alt: parseInt(progress) + "%"});
-        //$("div#model_" + id + "_progress").attr("alt", parseInt(progress) + "%");
+        $("div#model_" + id + "_progress").attr({title: parseInt(progress) + "%"});
       },
       error: function(data) {
         id = -1;
@@ -208,6 +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,
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
diff --git a/views/help.haml b/views/help.haml
index 2b39d6c..f602dff 100644
--- a/views/help.haml
+++ b/views/help.haml
@@ -87,13 +87,13 @@
 
 %p
   Excel examples for download:
-  %ul
-    %li
-      = link_to "hamster_carcinogenicity.xls", "/hamster_carcinogenicity.xls"
-      (classification)
-    %li
-      = link_to "EPAFHM.xls", "/EPAFHM.xls"
-      (regression)
+%ul
+  %li
+    = link_to "hamster_carcinogenicity.xls", "/hamster_carcinogenicity.xls"
+    (classification)
+  %li
+    = link_to "EPAFHM.xls", "/EPAFHM.xls"
+    (regression)
 
 %h3 CSV example
 
@@ -113,13 +113,13 @@
 
 %p
   CSV examples for download:
-  %ul
-    %li
-      = link_to "hamster_carcinogenicity.csv", "/hamster_carcinogenicity.csv"
-      (classification)
-    %li
-      = link_to "EPAFHM.csv", "/EPAFHM.csv"
-      (regression)
+%ul
+  %li
+    = link_to "hamster_carcinogenicity.csv", "/hamster_carcinogenicity.csv"
+    (classification)
+  %li
+    = link_to "EPAFHM.csv", "/EPAFHM.csv"
+    (regression)
 
 %p You can create CSV files in Excel: Create a sheet with two columns and export them as CSV file with the "Save As" option from the menu, selecting the CSV (comma delimited) format.
 
diff --git a/views/model.haml b/views/model.haml
index 899bb6a..266fe19 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -24,7 +24,7 @@
                 #{js}
               });
               
-            %div{:id => "model_#{model.id}_progress", :class => "model_progress", :title => "#{percentage_completed}%", :alt => "#{percentage_completed}%"}
+            %div{:id => "model_#{model.id}_progress", :class => "model_progress", :title => "#{percentage_completed}%"}
               //= haml :model_progress, :locals=>{:percentage_completed=>percentage_completed}, :layout => false        
        
         %span
@@ -41,7 +41,7 @@
       - if CONFIG[:logger]=="debug"
         %dt Task:
         %dd
-          %a{:href => "#{model.task_uri}", :rel => "external"}
+          %a{:href => "#{model.task_uri}", :id => "model_#{model.id}_task_link", :rel => "external"}
             = model.task_uri
       - if model.warnings
         %dt Warnings: