add subjectid to several .new calls

5 files changed, 13 insertions, 13 deletions

diff --git a/descriptor.rb b/descriptor.rb
index 96599d6..25ec4f3 100644
--- a/descriptor.rb
+++ b/descriptor.rb
@@ -156,7 +156,7 @@ module OpenTox
 
     before '/descriptor/?*' do
       if request.get?
-        @algorithm = OpenTox::Algorithm.new @uri
+        @algorithm = OpenTox::Algorithm.new @uri, @subjectid
         @algorithm.parameters = [ 
           { RDF::DC.description => "Dataset URI", 
             RDF::OT.paramScope => "optional", 
@@ -233,7 +233,7 @@ module OpenTox
         if params[:compound_uri]
           compounds = [ Compound.new(params[:compound_uri], @subjectid) ]
         elsif params[:dataset_uri]
-          compounds = Dataset.new(params[:dataset_uri]).compounds
+          compounds = Dataset.new(params[:dataset_uri], @subjectid).compounds
         end
         [:openbabel, :cdk, :joelib].each{ |lib| send lib, compounds, descriptors[lib] }
         @feature_dataset.put
diff --git a/lib/dataset.rb b/lib/dataset.rb
index a42356b..4f51e41 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -13,7 +13,7 @@ module OpenTox
     # @return [Object] activity Database activity, or nil
     def database_activity(params)
       f=Feature.new params[:prediction_feature_uri], @subjectid
-      db_act = values(Compound.new(params[:compound_uri]), f)
+      db_act = values(Compound.new(params[:compound_uri], @subjectid), f)
       if !db_act.empty?
         if f.feature_type == "classification"
           db_act = db_act.to_scale.mode.dup
diff --git a/lib/lazar.rb b/lib/lazar.rb
index 3b8621c..ad0a406 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -24,7 +24,7 @@ module OpenTox
         instance_variable_set("@#{k}", [])
       }
 
-      @prediction_feature = OpenTox::Feature.new(@prediction_feature_uri,@subjectid)
+      @prediction_feature = OpenTox::Feature.new @prediction_feature_uri, @subjectid
       @predicted_variable = OpenTox::Feature.new @predicted_variable_uri, @subjectid
       @predicted_confidence = OpenTox::Feature.new @predicted_confidence_uri, @subjectid
       #@prediction_dataset.metadata = {
@@ -113,7 +113,7 @@ module OpenTox
       
         if @compound_uri # add neighbors only for compound predictions
           @neighbors.each do |neighbor|
-            n =  OpenTox::Compound.new(neighbor[:compound])
+            n =  OpenTox::Compound.new(neighbor[:compound], @subjectid)
             @prediction_dataset.add_data_entry n, @prediction_feature, @prediction_feature.value_map[neighbor[:activity]]
             @prediction_dataset.add_data_entry n, @similarity_feature, neighbor[:similarity]
             #@prediction_dataset << [ n, @prediction_feature.value_map[neighbor[:activity]], nil, nil, neighbor[:similarity] ]
@@ -199,7 +199,7 @@ module OpenTox
         self[RDF::OT.featureDataset] = params["feature_dataset_uri"]
       else
         # run feature generation algorithm
-        feature_dataset_uri = OpenTox::Algorithm.new(params[:feature_generation_uri]).run(params)
+        feature_dataset_uri = OpenTox::Algorithm.new(params[:feature_generation_uri], @subjectid).run(params)
         @parameters << {RDF::DC.title => "feature_dataset_uri", RDF::OT.paramValue => feature_dataset_uri}
         self[RDF::OT.featureDataset] = feature_dataset_uri
       end
diff --git a/webapp/fminer.rb b/webapp/fminer.rb
index 4f9abfe..95d3621 100644
--- a/webapp/fminer.rb
+++ b/webapp/fminer.rb
@@ -33,7 +33,7 @@ module OpenTox
     # Get representation of BBRC algorithm
     # @return [String] Representation
     get "/fminer/bbrc/?" do
-      algorithm = OpenTox::Algorithm.new(to('/fminer/bbrc',:full))
+      algorithm = OpenTox::Algorithm.new(to('/fminer/bbrc',:full), @subjectid)
       algorithm.metadata = {
         RDF::DC.title => 'Backbone Refinement Class Representatives',
         RDF::DC.creator => "andreas@maunz.de",
@@ -55,7 +55,7 @@ module OpenTox
     # Get representation of BBRC-sample algorithm
     # @return [String] Representation
     get "/fminer/bbrc/sample/?" do
-      algorithm = OpenTox::Algorithm.new(to('/fminer/bbrc/sample',:full))
+      algorithm = OpenTox::Algorithm.new(to('/fminer/bbrc/sample',:full), @subjectid)
       algorithm.metadata = {
         RDF::DC.title => 'Backbone Refinement Class Representatives, obtained from samples of a dataset',
         RDF::DC.creator => "andreas@maunz.de",
@@ -77,7 +77,7 @@ module OpenTox
     # Get representation of fminer LAST-PM algorithm
     # @return [String] Representation
     get "/fminer/last/?" do
-      algorithm = OpenTox::Algorithm.new(to('/fminer/last',:full))
+      algorithm = OpenTox::Algorithm.new(to('/fminer/last',:full), @subjectid)
       algorithm.metadata = {
         RDF::DC.title => 'Latent Structure Pattern Mining descriptors',
         RDF::DC.creator => "andreas@maunz.de",
@@ -98,7 +98,7 @@ module OpenTox
     # Get representation of matching algorithm
     # @return [String] Representation
     get "/fminer/:method/match?" do
-      algorithm = OpenTox::Algorithm.new(to("/fminer/#{params[:method]}/match",:full))
+      algorithm = OpenTox::Algorithm.new(to("/fminer/#{params[:method]}/match",:full), @subjectid)
       algorithm.metadata = {
         RDF::DC.title => 'fminer feature matching',
         RDF::DC.creator => "mguetlein@gmail.com, andreas@maunz.de",
@@ -127,7 +127,7 @@ module OpenTox
     # @return [text/uri-list] Task URI
     post '/fminer/bbrc/?' do
     
-      @@fminer=OpenTox::Algorithm::Fminer.new(to('/fminer/bbrc',:full))
+      @@fminer=OpenTox::Algorithm::Fminer.new(to('/fminer/bbrc',:full), @subjectid)
       @@fminer.check_params(params,5)
     
       task = OpenTox::Task.run("Mining BBRC features", uri('/fminer/bbrc'), @subjectid) do |task|
@@ -283,7 +283,7 @@ module OpenTox
     # @return [text/uri-list] Task URI
     post '/fminer/last/?' do
     
-      @@fminer=OpenTox::Algorithm::Fminer.new(to('/fminer/last',:full))
+      @@fminer=OpenTox::Algorithm::Fminer.new(to('/fminer/last',:full), @subjectid)
       @@fminer.check_params(params,80)
     
       task = OpenTox::Task.run("Mining LAST features", uri('/fminer/last'), @subjectid) do |task|
diff --git a/webapp/test.rb b/webapp/test.rb
index 75044da..dc5ac9f 100644
--- a/webapp/test.rb
+++ b/webapp/test.rb
@@ -6,7 +6,7 @@ module OpenTox
     post '/test/wait_for_error_in_task/?' do
       task = OpenTox::Task.run("wait_for_error_in_task",@uri,@subjectid) do |task|
         sleep 1
-        uri = OpenTox::Dataset.new(File.join($dataset[:uri],'test/error_in_task')).post
+        uri = OpenTox::Dataset.new(File.join($dataset[:uri],'test/error_in_task'), @subjectid).post
       end
       response['Content-Type'] = 'text/uri-list'
       halt 202,task.uri.to_s+"\n"