Class: OpenTox::Parser::Table

Inherits:
Object
  • Object
show all
Defined in:
lib/parser.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Table

Returns a new instance of Table.



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# File 'lib/parser.rb', line 522

def initialize
  @data = {}
  @activity_errors = []
  @max_class_values = 3
end

Instance Attribute Details

#compounds ⇒ Object

Returns the value of attribute compounds.



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# File 'lib/parser.rb', line 520

def compounds
  @compounds
end

#data ⇒ Object

Returns the value of attribute data.



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# File 'lib/parser.rb', line 520

def data
  @data
end

#features ⇒ Object

Returns the value of attribute features.



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# File 'lib/parser.rb', line 520

def features
  @features
end

Instance Method Details

#add_to_dataset(dataset) ⇒ Object 



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# File 'lib/parser.rb', line 567

def add_to_dataset(dataset)
  features.each do |feature_name|
    feature_uri = File.join(dataset.uri,"feature",URI.encode(feature_name))
    dataset.add_feature(feature_uri,{DC.title => feature_name})
  end

  @data.each do |compound,row|
    unless row.empty?
      row.each do |feature,value|
        if OpenTox::Algorithm::numeric?(value)
          value = value.to_f
        elsif value.nil? or value.empty?
          value = nil
        else
          value = value.to_s
        end
        feature_uri = File.join(dataset.uri,"feature",URI.encode(feature))
        dataset.add(compound, feature_uri, value)
        #dataset.features[feature_uri][RDF.type] = feature_types(feature)
        #dataset.features[feature_uri][OT.acceptValue] = feature_values(feature)
        if feature_types(feature).include? OT.NumericFeature
          dataset.features[feature_uri][RDF.type] = [OT.NumericFeature]
        else
          dataset.features[feature_uri][RDF.type] = [OT.NominalFeature]
          dataset.features[feature_uri][OT.acceptValue] = feature_values(feature) 
        end
      end
    end
  end
end

#clean_features ⇒ Object 



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# File 'lib/parser.rb', line 540

def clean_features
  ignored_features = []
  features.each do |feature|
    if feature_values(feature).size > @max_class_values
      if feature_types(feature).size == 1 and feature_types(feature).first == OT.NumericFeature
        # REGRESSION
      elsif feature_types(feature).include? OT.NumericFeature
        @data.each{|c,row| row[feature] = nil unless OpenTox::Algorithm::numeric?(row[feature]) } # delete nominal features
        @activity_errors << "Nominal feature values of #{feature} ignored (using numeric features for regression models)."
      else
        @activity_errors << "Feature #{feature} ignored (more than #{@max_class_values} nominal feature values and no numeric values)."
        ignored_features << feature
        next
      end
    elsif feature_values(feature).size <= 1
        @activity_errors << "Feature #{feature} ignored (less than 2 feature values)."
        ignored_features << feature
    else
      # CLASSIFICATION
    end
  end
  ignored_features.each do |feature|
    @data.each{ |c,row| row.delete feature }
  end
  @activity_errors
end

#feature_types(feature) ⇒ Object 



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# File 'lib/parser.rb', line 532

def feature_types(feature)
  @data.collect{|c, row| feature_type(row[feature])}.uniq.compact
end

#feature_values(feature) ⇒ Object 



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# File 'lib/parser.rb', line 528

def feature_values(feature)
  @data.collect{|c, row| row[feature]}.uniq.compact
end