1) Support for progress (task), 2) force numeric feature type

1) utils.rb
2) parser.rb

2 files changed, 18 insertions, 9 deletions

diff --git a/lib/parser.rb b/lib/parser.rb
index 18c0ba7..4b56786 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -349,8 +349,10 @@ module OpenTox
 
       # Load CSV string (format specification: http://toxcreate.org/help)
       # @param [String] csv CSV representation of the dataset
+      # @param [Boolean] drop_missing Whether completely missing rows should be droppped
+      # @param [Boolean] all_numeric Whether all features should be treated as numeric
       # @return [OpenTox::Dataset] Dataset object with CSV data
-      def load_csv(csv, drop_missing=false)
+      def load_csv(csv, drop_missing=false, all_numeric=false)
         row = 0
         input = csv.split("\n")
         headers = split_row(input.shift)
@@ -362,7 +364,7 @@ module OpenTox
           row = split_row(row)
           value_maps = detect_new_values(row, value_maps)
           value_maps.each_with_index { |vm,j|
-            if vm.size > @max_class_values # max @max_class_values classes.
+            if (vm.size > @max_class_values) || all_numeric # max @max_class_values classes.
               regression_features[j]=true 
             else
               regression_features[j]=false
@@ -371,7 +373,7 @@ module OpenTox
         }
 
         input.each_with_index { |row, i| 
-          drop=false
+          drop = false
           row = split_row(row)
           raise "Entry has size #{row.size}, different from headers (#{headers.size})" if row.size != headers.size
           if row.include?("")
@@ -486,7 +488,7 @@ module OpenTox
 
             feature_idx += 1
   
-            if val != nil
+            if val != nil && !val.infinite? && !val.nan?
               @dataset.add(compound.uri, feature, val)
               if type != OT.NumericFeature
                 @dataset.features[feature][OT.acceptValue] = [] unless @dataset.features[feature][OT.acceptValue]
diff --git a/lib/utils.rb b/lib/utils.rb
index 705dd5d..709200b 100644
--- a/lib/utils.rb
+++ b/lib/utils.rb
@@ -22,14 +22,18 @@ module OpenTox
 
         # joelib via rjb
         types = params[:pc_type].split(",")
+
+        step= (1.0/types.size * 100).floor
         if types.size && types.include?("joelib")
           jl_master = get_jl_descriptors ( { :compounds => compounds, :rjb => params[:rjb] } )
           types.delete("joelib")
         end
+        params[:task].progress(step) if params[:task]
+
 
         # ambit via REST
         if types.size > 0
-          ambit_result_uri, smiles_to_inchi = get_ambit_descriptors( { :compounds => compounds, :pc_type => types.join(',') } )
+          ambit_result_uri, smiles_to_inchi = get_ambit_descriptors( { :compounds => compounds, :pc_type => types.join(','), :task => params[:task], :step => step } )
           LOGGER.debug "Ambit result uri for #{params.inspect}: '#{ambit_result_uri.to_yaml}'"
           ambit_master = load_ds_csv(ambit_result_uri, smiles_to_inchi)
         end
@@ -56,7 +60,7 @@ module OpenTox
         ds = OpenTox::Dataset.new
         ds.save
         parser.dataset = ds
-        ds = parser.load_csv(master.collect{|r| r.join(",")}.join("\n"))
+        ds = parser.load_csv(master.collect{|r| r.join(",")}.join("\n"),false,true)
         ds.save
 
       rescue Exception => e
@@ -73,7 +77,6 @@ module OpenTox
     def self.get_jl_descriptors(params)
 
       s = params[:rjb]
-      LOGGER.debug("------ AM #{s}")
       master = nil
       raise "No Java environment" unless s
 
@@ -162,13 +165,14 @@ module OpenTox
         ambit_mopac_model_uri = "http://apps.ideaconsult.net:8080/ambit2/model/69632"
         descs = YAML::load_file( File.join(ENV['HOME'], ".opentox", "config", "ambit_descriptors.yaml") )
         descs_uris = []
-        params[:pc_type] = "electronic,cpsa" if params[:pc_type].nil? # rescue missing pc_type
         types = params[:pc_type].split(",")
         descs.each { |uri, cat_name| 
           if types.include? cat_name[:category]
-            descs_uris << uri
+            descs_uris << "#{cat_name[:category]}:::#{uri}"
           end
         }
+        descs_uris.sort!
+        descs_uris.collect! { |uri| uri.split(":::").last }
         if descs_uris.size == 0
           raise "Error! Empty set of descriptors. Did you supply one of [geometrical, topological, electronic, constitutional, hybrid, cpsa] ?"
         end
@@ -209,7 +213,10 @@ module OpenTox
         ambit_result_uri = [] # 1st pos: base uri, then features
         ambit_result_uri << ambit_ds_uri + "?"
         ambit_result_uri << ("feature_uris[]=" + URI.encode_www_form_component(ambit_smiles_uri) + "&")
+        current_cat = ""
         descs_uris.each_with_index do |uri, i|
+          old_cat = current_cat; current_cat = descs[uri][:category]
+          params[:task].progress(params[:task].metadata[OT.percentageCompleted] + params[:step]) if params[:task] && params[:step] && old_cat != current_cat && old_cat != ""
           algorithm = Algorithm::Generic.new(uri)
           result_uri = algorithm.run({:dataset_uri => ambit_ds_uri})
           ambit_result_uri << result_uri.split("?")[1] + "&"