Added pc_type switch

2 files changed, 8 insertions, 5 deletions

diff --git a/lib/model.rb b/lib/model.rb
index d7a0516..21e33b5 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -102,7 +102,7 @@ module OpenTox
       include Algorithm
       include Model
 
-      attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim, :subjectid, :prop_kernel, :value_map, :nr_hits, :conf_stdev, :prediction_min_max
+      attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim, :subjectid, :prop_kernel, :value_map, :nr_hits, :conf_stdev, :prediction_min_max, :pc_type
 
       def initialize(uri=nil)
 
@@ -130,6 +130,7 @@ module OpenTox
         @min_sim = 0.3
         @prop_kernel = false
         @conf_stdev = false
+        @pc_type = "electronic"
 
       end
 
@@ -180,11 +181,12 @@ module OpenTox
         lazar.nr_hits = hash["nr_hits"] if hash["nr_hits"]
         lazar.conf_stdev = hash["conf_stdev"] if hash["conf_stdev"]
         lazar.prediction_min_max = hash["prediction_min_max"] if hash["prediction_min_max"]
+        lazar.pc_type = hash["pc_type"] if hash["pc_type"]
         lazar
       end
 
       def to_json
-        Yajl::Encoder.encode({:uri => @uri,:metadata => @metadata, :compound => @compound, :prediction_dataset => @prediction_dataset, :features => @features, :effects => @effects, :activities => @activities, :p_values => @p_values, :fingerprints => @fingerprints, :feature_calculation_algorithm => @feature_calculation_algorithm, :similarity_algorithm => @similarity_algorithm, :prediction_algorithm => @prediction_algorithm, :min_sim => @min_sim, :subjectid => @subjectid, :prop_kernel => @prop_kernel, :value_map => @value_map, :nr_hits => @nr_hits, :conf_stdev => @conf_stdev, :prediction_min_max => @prediction_min_max})
+        Yajl::Encoder.encode({:uri => @uri,:metadata => @metadata, :compound => @compound, :prediction_dataset => @prediction_dataset, :features => @features, :effects => @effects, :activities => @activities, :p_values => @p_values, :fingerprints => @fingerprints, :feature_calculation_algorithm => @feature_calculation_algorithm, :similarity_algorithm => @similarity_algorithm, :prediction_algorithm => @prediction_algorithm, :min_sim => @min_sim, :subjectid => @subjectid, :prop_kernel => @prop_kernel, :value_map => @value_map, :nr_hits => @nr_hits, :conf_stdev => @conf_stdev, :prediction_min_max => @prediction_min_max}, :pc_type => @pc_type)
       end
 
       def run( params, accept_header=nil, waiting_task=nil )
@@ -278,6 +280,7 @@ module OpenTox
                                                           :nr_hits => @nr_hits,
                                                           :conf_stdev => @conf_stdev,
                                                           :prediction_min_max => @prediction_min_max
+                                                          :pc_type => @pc_type
                                                          } ) ")
 
           value_feature_uri = File.join( @uri, "predicted", "value")
diff --git a/lib/utils.rb b/lib/utils.rb
index 44a3e2b..af517e9 100644
--- a/lib/utils.rb
+++ b/lib/utils.rb
@@ -150,16 +150,16 @@ module OpenTox
       # Calculate the propositionalization matrix (aka instantiation matrix) via physico-chemical descriptors.
       # Same for the vector describing the query compound.
       # The third argument takes a string from {"geometrical", "topological", "electronic", "constitutional", "hybrid" } as in ambit_descriptors.yaml
-      # @param[Hash] Required keys: :neighbors, :compound, :pc_group
+      # @param[Hash] Required keys: :neighbors, :compound, :pc_type
       # @return[Array, Array] Props, ids of surviving training compounds
 
       def self.get_props_pc(params)
         ambit_ds_service_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/"
         descs = YAML::load_file( File.join(ENV['HOME'], ".opentox", "config", "ambit_descriptors.yaml") )
         descs_uris = []
-        params[:pc_group] = "electronic" if params[:pc_group].nil?
+        params[:pc_type] = "electronic" if params[:pc_type].nil?
         descs.each { |uri, cat_name| 
-          if cat_name[:category] == params[:pc_group]
+          if cat_name[:category] == params[:pc_type]
             descs_uris << uri
           end
         }