rename token_id to subjectid

8 files changed, 29 insertions, 29 deletions

diff --git a/application.rb b/application.rb
index 30458bc..2790076 100644
--- a/application.rb
+++ b/application.rb
@@ -118,14 +118,14 @@ post '/models' do # create a new model
     redirect url_for('/create')
   end
 
-  @model = ToxCreateModel.create(:name => params[:file][:filename].sub(/\..*$/,""), :token_id => session[:token_id])
+  @model = ToxCreateModel.create(:name => params[:file][:filename].sub(/\..*$/,""), :subjectid => session[:subjectid])
   @model.update :web_uri => url_for("/model/#{@model.id}", :full)
   @model.save
   task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do
 
     @model.update :status => "Uploading and saving dataset"
     begin
-      @dataset = OpenTox::Dataset.create(nil, session[:token_id])
+      @dataset = OpenTox::Dataset.create(nil, session[:subjectid])
       # check format by extension - not all browsers provide correct content-type]) 
       case File.extname(params[:file][:filename])
       when ".csv"
@@ -140,8 +140,8 @@ post '/models' do # create a new model
     rescue => e
       error "Dataset creation failed with #{e.message}"
     end
-    token_id = session[:token_id] if session[:token_id]
-    @dataset.save(token_id)
+    subjectid = session[:subjectid] if session[:subjectid]
+    @dataset.save(subjectid)
     if @dataset.compounds.size < 10
       error "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/excel_format"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets."
     end
@@ -158,7 +158,7 @@ post '/models' do # create a new model
 
     @model.update :status => "Creating prediction model"
     begin
-      lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :token_id => session[:token_id])
+      lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :subjectid => session[:subjectid])
     rescue => e
       error "Model creation failed with '#{e.message}'. Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format."
     end
@@ -181,7 +181,7 @@ post '/models' do # create a new model
         validation = OpenTox::Validation.create_crossvalidation(
           :algorithm_uri => OpenTox::Algorithm::Lazar.uri,
           :dataset_uri => lazar.parameter("dataset_uri"),
-          :token_id => session[:token_id],
+          :subjectid => session[:subjectid],
           :prediction_feature => lazar.parameter("prediction_feature"),
           :algorithm_params => "feature_generation_uri=#{lazar.parameter("feature_generation_uri")}"
         )
@@ -254,7 +254,7 @@ post '/predict/?' do # post chemical name to model
     title = nil
     db_activities = []
     lazar = OpenTox::Model::Lazar.new model.uri
-    prediction_dataset_uri = lazar.run(:compound_uri => @compound.uri, :token_id => session[:token_id])
+    prediction_dataset_uri = lazar.run(:compound_uri => @compound.uri, :subjectid => session[:subjectid])
     prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri)
     if prediction_dataset.metadata[OT.hasSource].match(/dataset/)
       @predictions << {
@@ -321,7 +321,7 @@ post "/lazar/?" do # get detailed prediction
   @page = params[:page].to_i if params[:page]
   @model_uri = params[:model_uri]
   lazar = OpenTox::Model::Lazar.new @model_uri
-  prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :token_id => params[:token_id])
+  prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => params[:subjectid])
   @prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri)
   @compound = OpenTox::Compound.new(params[:compound_uri])
   #@title = prediction.metadata[DC.title]
@@ -352,7 +352,7 @@ post "/lazar/?" do # get detailed prediction
 end
 
 post '/login' do
-  if session[:token_id] != nil
+  if session[:subjectid] != nil
     flash[:notice] = "You are already logged in as user: #{session[:username]}. Please log out first."
     redirect url_for('/login')
   end
@@ -376,12 +376,12 @@ end
 delete '/model/:id/?' do
   model = ToxCreateModel.get(params[:id])
   begin
-    RestClient.delete(model.uri, :token_id => session[:token_id]) if model.uri
+    RestClient.delete(model.uri, :subjectid => session[:subjectid]) if model.uri
     RestClient.delete model.task_uri if model.task_uri
     model.destroy
     unless ToxCreateModel.get(params[:id])
       begin
-        aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, session[:token_id])
+        aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, session[:subjectid])
         LOGGER.debug "Policy deleted for Dataset URI: #{uri} with result: #{aa}"
       rescue
         LOGGER.warn "Policy delete error for Dataset URI: #{uri}"
diff --git a/helper.rb b/helper.rb
index a660cc2..e892669 100644
--- a/helper.rb
+++ b/helper.rb
@@ -1,9 +1,9 @@
 helpers do
 
   def login(username, password)
-    session[:token_id] = OpenTox::Authorization.authenticate(username, password)
-    LOGGER.debug "ToxCreate login user #{username} with token_id: " + session[:token_id].to_s
-    if session[:token_id] != nil
+    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
@@ -13,8 +13,8 @@ helpers do
   end
 
   def logout
-    if session[:token_id] != nil
-      session[:token_id] = nil
+    if session[:subjectid] != nil
+      session[:subjectid] = nil
       session[:username] = ""
       return true
     end
@@ -23,15 +23,15 @@ helpers do
 
   def logged_in()
     return true if !AA_SERVER
-    if session[:token_id] != nil
-      return OpenTox::Authorization.is_token_valid(session[:token_id])
+    if session[:subjectid] != nil
+      return OpenTox::Authorization.is_token_valid(session[:subjectid])
     end
     return false
   end
 
   def is_authorized(uri, action)
-    if session[:token_id] != nil
-      return OpenTox::Authorization.authorize(uri, action, session[:token_id])
+    if session[:subjectid] != nil
+      return OpenTox::Authorization.authorize(uri, action, session[:subjectid])
     end
     return false
   end
diff --git a/model.rb b/model.rb
index 82a0135..eb459b3 100644
--- a/model.rb
+++ b/model.rb
@@ -40,8 +40,8 @@ class ToxCreateModel
 
   property :web_uri, String, :length => 255
 
-  attr_accessor :token_id
-  @token_id = nil
+  attr_accessor :subjectid
+  @subjectid = nil
 
   after :save, :check_policy
 
@@ -190,7 +190,7 @@ def status
 
   private
   def check_policy
-    OpenTox::Authorization.check_policy(web_uri, token_id)
+    OpenTox::Authorization.check_policy(web_uri, subjectid)
   end
 
 end
diff --git a/views/create.haml b/views/create.haml
index d83d2b9..5aeac67 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -30,7 +30,7 @@
         = link_to "CSV", '/help'
         format:
       %input{:type => 'file', :name => 'file', :id => 'file', :size => '41'}
-      %input{:type => 'hidden', :name => 'token_id', :id => 'token_id', :value => session[:token_id]}
+      %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
     %input{ :type => "submit", :value => "Create model"}
     = link_to "Cancel", '/create'
 
diff --git a/views/fragment.haml b/views/fragment.haml
index eae786c..3b9f68b 100644
--- a/views/fragment.haml
+++ b/views/fragment.haml
@@ -2,7 +2,7 @@
   %input{:type => :hidden, :name => :compound_uri, :value => compound_uri}
   %input{:type => :hidden, :name => :model_uri, :value => model_uri}
   %input{:type => :hidden, :name => :highlight, :value => smarts}
-  %input{:type => :hidden, :name => :token_id, :value => session[:token_id]}
+  %input{:type => :hidden, :name => :subjectid, :value => session[:subjectid]}
   - if smarts.nil?
     %input{ :type => "submit", :value => "Reset"}
   - else
diff --git a/views/login.haml b/views/login.haml
index 4f45de3..747430e 100644
--- a/views/login.haml
+++ b/views/login.haml
@@ -26,7 +26,7 @@
         %b= session[:username]
         - if LOGGER.level == Logger::DEBUG        
           %br
-          = session[:token_id]
+          = session[:subjectid]
       %input{ :type => "submit", :value => "Logout"} 
       = link_to "Cancel", '/login'
-      
\ No newline at end of file
+      
diff --git a/views/predict.haml b/views/predict.haml
index 6337a5b..cd5c0d4 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -29,7 +29,7 @@
           %input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => model.id} 
           %br
 
-      %input{:type => 'hidden', :name => 'token_id', :id => 'token_id', :value => session[:token_id]}
+      %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
       %input{ :type => "submit", :value => "Predict", :onclick => "getsmiles();"}
       = link_to 'Cancel', '/predict' 
 
diff --git a/views/prediction.haml b/views/prediction.haml
index f0b48e8..9bb3f76 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -44,7 +44,7 @@
               %form{:name => "form", :action => url_for('/lazar'), :method => "post", :enctype => "multipart/form-data" }
                 %input{:type => :hidden, :name => :compound_uri, :value => @compound.uri}
                 %input{:type => :hidden, :name => :model_uri, :value => p[:model_uri]}
-                %input{:type => :hidden, :name => :token_id, :value => session[:token_id]}
+                %input{:type => :hidden, :name => :subjectid, :value => session[:subjectid]}
                 %input{ :type => "submit", :value => "Details"}
 
 = haml :confidence, :layout => false