Merge branch 'development' into reg_min_max

3 files changed, 11 insertions, 6 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 092205b..0ba6a83 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -52,11 +52,11 @@ module OpenTox
       include Algorithm
       attr_accessor :prediction_feature, :training_dataset, :minfreq, :compounds, :db_class_sizes, :all_activities, :smi
       
-      def check_params(params,per_mil)
+      def check_params(params,per_mil,subjectid=nil)
         raise OpenTox::NotFoundError.new "Please submit a dataset_uri." unless params[:dataset_uri] and  !params[:dataset_uri].nil?
         raise OpenTox::NotFoundError.new "Please submit a prediction_feature." unless params[:prediction_feature] and  !params[:prediction_feature].nil?
-        @prediction_feature = OpenTox::Feature.find params[:prediction_feature], @subjectid
-        @training_dataset = OpenTox::Dataset.find "#{params[:dataset_uri]}", @subjectid
+        @prediction_feature = OpenTox::Feature.find params[:prediction_feature], subjectid
+        @training_dataset = OpenTox::Dataset.find "#{params[:dataset_uri]}", subjectid
         raise OpenTox::NotFoundError.new "No feature #{params[:prediction_feature]} in dataset #{params[:dataset_uri]}" unless @training_dataset.features and @training_dataset.features.include?(params[:prediction_feature])
 
         unless params[:min_frequency].nil? 
diff --git a/lib/model.rb b/lib/model.rb
index d69a827..ff0ce0e 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -73,7 +73,7 @@ module OpenTox
               if use_confidence
                 conf_index = -1
                 predictedVariables.size.times do |i|
-                  f = OpenTox::Feature.find(predictedVariables[i])
+                  f = OpenTox::Feature.find(predictedVariables[i], subjectid)
                   conf_index = i if f.metadata[DC.title]=~/(?i)confidence/
                 end
                 raise "could not estimate predicted variable from model: '"+uri.to_s+
@@ -182,6 +182,7 @@ module OpenTox
       # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
       # @return [OpenTox::Dataset] Dataset with predictions
       def predict_dataset(dataset_uri, subjectid=nil, waiting_task=nil)
+      
         @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
         @prediction_dataset.add_metadata({
           OT.hasSource => @uri,
@@ -253,7 +254,7 @@ module OpenTox
           @prediction_dataset.metadata[OT.dependentVariables] = @metadata[OT.dependentVariables] unless @prediction_dataset.metadata[OT.dependentVariables] 
           @prediction_dataset.metadata[OT.predictedVariables] = [value_feature_uri, confidence_feature_uri] unless @prediction_dataset.metadata[OT.predictedVariables] 
 
-          if OpenTox::Feature.find(metadata[OT.dependentVariables]).feature_type == "classification"
+          if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "classification"
             @prediction_dataset.add @compound.uri, value_feature_uri, @value_map[prediction[:prediction]]
           else
             @prediction_dataset.add @compound.uri, value_feature_uri, prediction[:prediction]
diff --git a/lib/task.rb b/lib/task.rb
index 146a756..00499fa 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -169,6 +169,10 @@ module OpenTox
       @metadata[OT.hasStatus] == 'Running'
     end
 
+    def queued?
+      @metadata[OT.hasStatus] == 'Queued'
+    end
+
     def completed?
       @metadata[OT.hasStatus] == 'Completed'
     end
@@ -286,7 +290,7 @@ module OpenTox
         raise "illegal task state, task is completed, resultURI is no URI: '"+@metadata[OT.resultURI].to_s+
             "'" unless @metadata[OT.resultURI] and @metadata[OT.resultURI].to_s.uri? if completed?
         if @http_code == 202
-          raise "#{@uri}: illegal task state, code is 202, but hasStatus is not Running: '"+@metadata[OT.hasStatus]+"'" unless running?
+          raise "#{@uri}: illegal task state, code is 202, but hasStatus is not Running or Queued: '"+@metadata[OT.hasStatus]+"'" unless running? or queued?
         elsif @http_code == 201
           # ignore hasStatus
           # raise "#{@uri}: illegal task state, code is 201, but hasStatus is not Completed: '"+@metadata[OT.hasStatus]+"'" unless completed?