diff options
Diffstat (limited to 'lib/fminer.rb')
| -rw-r--r-- | lib/fminer.rb | 22 |
1 files changed, 13 insertions, 9 deletions
diff --git a/lib/fminer.rb b/lib/fminer.rb index 8023bdd..3333517 100644 --- a/lib/fminer.rb +++ b/lib/fminer.rb @@ -1,3 +1,4 @@ +require_relative 'bbrc' =begin * Name: fminer.rb * Description: Fminer library @@ -10,6 +11,7 @@ module OpenTox # Fminer algorithms (https://github.com/amaunz/fminer2) class Fminer + include OpenTox attr_accessor :prediction_feature, :training_dataset, :minfreq, :compounds, :db_class_sizes, :all_activities, :smi @@ -19,15 +21,16 @@ module OpenTox # @param[Integer] per-mil value for min frequency 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]}" + bad_request_error "Please submit a dataset." unless params[:dataset] and !params[:dataset].nil? + @training_dataset = OpenTox::Dataset.new + @training_dataset = params[:dataset] 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 + params[:prediction_feature] = @training_dataset.features.first end - @prediction_feature = OpenTox::Feature.find params[:prediction_feature] - resource_not_found_error "No feature '#{params[:prediction_feature]}' in dataset '#{params[:dataset_uri]}'" unless - @training_dataset.find_feature_uri( params[:prediction_feature] ) + @prediction_feature = params[:prediction_feature] + resource_not_found_error "No feature '#{params[:prediction_feature]}' in dataset '#{params[:dataset]}'" unless + @training_dataset.features.include?( params[:prediction_feature] ) unless params[:min_frequency].nil? # check for percentage if params[:min_frequency].include? "pc" @@ -58,7 +61,8 @@ module OpenTox end if @minfreq.nil? @minfreq=min_frequency(@training_dataset,@prediction_feature,per_mil) - $logger.debug "min_frequency #{@minfreq} (input was #{per_mil} per-mil)" + p "min_frequency #{@minfreq} (input was #{per_mil} per-mil)" + #$logger.debug "min_frequency #{@minfreq} (input was #{per_mil} per-mil)" end end @@ -109,7 +113,7 @@ module OpenTox end if compound_activities.nil? - $logger.warn "No activity for '#{compound.uri}' and feature '#{@prediction_feature.uri}'" + $logger.warn "No activity for '#{compound.inchi}' and feature '#{@prediction_feature.title}'" else if @prediction_feature.feature_type == "classification" activity= value_map.invert[compound_activities].to_i # activities are mapped to 1..n @@ -178,7 +182,7 @@ module OpenTox # return [Integer] min-frequency def min_frequency(training_dataset,prediction_feature,per_mil) nr_labeled_cmpds=0 - f_idx=training_dataset.features.collect{|f| f.uri}.index prediction_feature.uri + f_idx=training_dataset.features.index prediction_feature training_dataset.compounds.each_with_index { |cmpd, c_idx| if ( training_dataset.data_entries[c_idx] ) unless training_dataset.data_entries[c_idx][f_idx].nil? |