Corrected: CSV download, fminer prediction f detect

CSV: order of rows in order of compounds
fminer check_params: auto-detecting prediction feature in case of a
single feature in the dataset

3 files changed, 25 insertions, 8 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 948d4b7..4f18d89 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -56,9 +56,15 @@ module OpenTox
 
       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
+
+        unless params[:prediction_feature] # try to read prediction_feature from dataset
+          raise OpenTox::NotFoundError.new "Please provide a prediction_feature parameter" unless @training_dataset.features.size == 1
+          prediction_feature = OpenTox::Feature.find(@training_dataset.features.keys.first,@subjectid)
+          params[:prediction_feature] = prediction_feature.uri
+        end
+        @prediction_feature = OpenTox::Feature.find params[:prediction_feature], 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/serializer.rb b/lib/serializer.rb
index 2205ade..d3616ce 100644
--- a/lib/serializer.rb
+++ b/lib/serializer.rb
@@ -459,21 +459,32 @@ module OpenTox
       def initialize(dataset)
         @rows = []
         @rows << ["SMILES"]
+
         features = dataset.features.keys
 
+        # prepare for subgraphs
+        have_substructures = features.collect{ |id| dataset.features[id][RDF.type].include? OT.Substructure}.compact.uniq
+        if have_substructures.size == 1 && have_substructures[0] 
+          features_smarts = features.collect{ |id| "'" + dataset.features[id][OT.smarts] + "'" }
+          dataset.complete_data_entries
+        end
+      
+        # gather missing features
         delete_features = []
-        features.each{ |fn|
-          dataset.features[fn][RDF.type].each { |typestr|
+        features.each{ |id|
+          dataset.features[id][RDF.type].each { |typestr|
             if typestr.include? "MissingFeature"
-              delete_features << fn 
+              delete_features << id 
             end
           }
         }
+
         features = features - delete_features
+        features_smarts && @rows.first << features_smarts || @rows.first << features
 
-        @rows.first << features
         @rows.first.flatten!
-        dataset.data_entries.each do |compound,entries|
+        dataset.compounds.each do |compound|
+          entries=dataset.data_entries[compound]
           cmpd = Compound.new(compound)
           smiles = cmpd.to_smiles
           inchi = URI.encode_www_form_component(cmpd.to_inchi)
diff --git a/lib/utils.rb b/lib/utils.rb
index 0ad0d92..a3f8161 100644
--- a/lib/utils.rb
+++ b/lib/utils.rb
@@ -119,7 +119,7 @@ module OpenTox
 
         ds.save
       else
-        raise "No descriptors matching your criteria found."
+        raise OpenTox::BadRequestError.new "No descriptors matching your criteria found."
       end
 
     end