subjectids partially removed

4 files changed, 10 insertions, 17 deletions

diff --git a/descriptor.rb b/descriptor.rb
index ce3ec54..2f313fc 100644
--- a/descriptor.rb
+++ b/descriptor.rb
@@ -9,7 +9,7 @@ module OpenTox
 
     before '/descriptor/:method/?' do
       if request.get?
-        @algorithm = OpenTox::Algorithm::Descriptor.new @uri
+        @algorithm = OpenTox::Algorithm::Descriptor.new @uri, @subjectid
         @algorithm.parameters = [ {
           RDF::DC.description => "Dataset URI", 
           RDF::OT.paramScope => "optional", 
@@ -92,9 +92,9 @@ module OpenTox
         Hash[result.map {|compound, v| [compound.uri, v] }].to_json
       elsif params[:dataset_uri] # return dataset
         task = OpenTox::Task.run("Calculating #{params[:method]} descriptors for dataset #{params[:dataset_uri]}.", @uri, @subjectid) do |task|
-          @compounds = OpenTox::Dataset.new(params[:dataset_uri], SUBJECTID).compounds
+          @compounds = OpenTox::Dataset.new(params[:dataset_uri],@subjectid).compounds
           result = OpenTox::Algorithm::Descriptor.send(params[:method].to_sym, @compounds, params[:descriptors])
-          dataset = OpenTox::Dataset.new nil, SUBJECTID
+          dataset = OpenTox::Dataset.new nil, @subjectid
           dataset.metadata = {
             RDF::DC.title => "Physico-chemical descriptors",
             RDF::DC.creator => @uri,
@@ -111,7 +111,7 @@ module OpenTox
                 RDF::DC.title => name,
                 RDF.type => [RDF::OT.Feature, feature_type],
                 RDF::DC.description => OpenTox::Algorithm::Descriptor.description(name)
-              }, SUBJECTID)
+              })
             }
             @features.each do |feature|
               value = result[compound][feature.title]
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 4f51e41..a42356b 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], @subjectid), f)
+      db_act = values(Compound.new(params[:compound_uri]), f)
       if !db_act.empty?
         if f.feature_type == "classification"
           db_act = db_act.to_scale.mode.dup
diff --git a/lib/fminer.rb b/lib/fminer.rb
index 6b21ce8..4cb3455 100644
--- a/lib/fminer.rb
+++ b/lib/fminer.rb
@@ -9,17 +9,10 @@ module OpenTox
   module Algorithm
 
     # Fminer algorithms (https://github.com/amaunz/fminer2)
-    class Fminer #< Algorithm
+    class Fminer 
       
       attr_accessor :prediction_feature, :training_dataset, :minfreq, :compounds, :db_class_sizes, :all_activities, :smi
 
-      def initialize(uri, subjectid=nil)
-        @uri = uri
-        @subjectid = subjectid
-        #super(uri, subjectid)
-      end
-
-
       # Check parameters of a fminer call
       # Sets training dataset, prediction feature, and minfreq instance variables
       # @param[Hash] parameters of the REST call
@@ -27,12 +20,12 @@ module OpenTox
       
       def check_params(params,per_mil)
         bad_request_error "Please submit a dataset_uri." unless params[:dataset_uri] and  !params[:dataset_uri].nil?
-        @training_dataset = OpenTox::Dataset.new "#{params[:dataset_uri]}", @subjectid 
+        @training_dataset = OpenTox::Dataset.new "#{params[:dataset_uri]}", @subjectid
         unless params[:prediction_feature] # try to read prediction_feature from dataset
           resource_not_found_error "Please provide a prediction_feature parameter" unless @training_dataset.features.size == 1
           params[:prediction_feature] = @training_dataset.features.first.uri
         end
-        @prediction_feature = OpenTox::Feature.find params[:prediction_feature], @subjectid 
+        @prediction_feature = OpenTox::Feature.find params[:prediction_feature], @subjectid
         resource_not_found_error "No feature '#{params[:prediction_feature]}' in dataset '#{params[:dataset_uri]}'" unless 
           @training_dataset.find_feature_uri( params[:prediction_feature] ) 
         unless params[:min_frequency].nil? 
diff --git a/test.rb b/test.rb
index dc5ac9f..08043c6 100644
--- a/test.rb
+++ b/test.rb
@@ -4,9 +4,9 @@ module OpenTox
   class Application < Service
     
     post '/test/wait_for_error_in_task/?' do
-      task = OpenTox::Task.run("wait_for_error_in_task",@uri,@subjectid) do |task|
+      task = OpenTox::Task.run("wait_for_error_in_task",@uri) do |task|
         sleep 1
-        uri = OpenTox::Dataset.new(File.join($dataset[:uri],'test/error_in_task'), @subjectid).post
+        uri = OpenTox::Dataset.new(File.join($dataset[:uri],'test/error_in_task')).post
       end
       response['Content-Type'] = 'text/uri-list'
       halt 202,task.uri.to_s+"\n"