Class: Nimbus::Configuration

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

Overview

Nimbus configuration object.

This class reads every user file. Once the user’s config.yml file is loaded, a set of default and custom options is created and stored.

Nimbus::Configuration also reads the testing files and the data to create the training set to be passed to the Nimbus::Forest random forest generator and the Nimbus::Tree classes in it.

Constant Summary collapse

DEFAULTS = 
{
  forest_size:          300,
  tree_SNP_sample_size: 60,
  tree_SNP_total_count: 200,
  tree_node_min_size:   5,

  loss_function_discrete:   'majority_class',
  loss_function_continuous: 'average',

  training_file: 'training.data',
  testing_file:  'testing.data',
  forest_file:   'forest.yml',
  config_file:   'config.yml',

  output_forest_file:   'random_forest.yml',
  output_training_file: 'training_file_predictions.txt',
  output_testing_file:  'testing_file_predictions.txt',
  output_tree_errors_file: 'generalization_errors.txt',
  output_snp_importances_file: 'snp_importances.txt',

  silent: false
}

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Configuration

Initialize a Nimbus::Configuration object.

Set all options to their default values.



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# File 'lib/nimbus/configuration.rb', line 64

def initialize
  @do_training = false
  @do_testing  = false
  @do_importances = true

  @forest_size              = DEFAULTS[:forest_size]
  @tree_SNP_sample_size     = DEFAULTS[:tree_SNP_sample_size]
  @tree_SNP_total_count     = DEFAULTS[:tree_SNP_total_count]
  @tree_node_min_size       = DEFAULTS[:tree_node_min_size]
  @loss_function_discrete   = DEFAULTS[:loss_function_discrete]
  @loss_function_continuous = DEFAULTS[:loss_function_continuous]

  @output_forest_file   = File.expand_path(DEFAULTS[:output_forest_file], Dir.pwd)
  @output_training_file = File.expand_path(DEFAULTS[:output_training_file], Dir.pwd)
  @output_testing_file  = File.expand_path(DEFAULTS[:output_testing_file], Dir.pwd)
  @output_tree_errors_file  = File.expand_path(DEFAULTS[:output_tree_errors_file], Dir.pwd)
  @output_snp_importances_file = File.expand_path(DEFAULTS[:output_snp_importances_file], Dir.pwd)

  @silent = ENV['nimbus_test'] == 'running_nimbus_tests' ? true : DEFAULTS[:silent]
end

Instance Attribute Details

#classes ⇒ Object

Returns the value of attribute classes.



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# File 'lib/nimbus/configuration.rb', line 14

def classes
  @classes
end

#config_file ⇒ Object

Returns the value of attribute config_file.



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# File 'lib/nimbus/configuration.rb', line 14

def config_file
  @config_file
end

#do_importances ⇒ Object

Returns the value of attribute do_importances.



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# File 'lib/nimbus/configuration.rb', line 14

def do_importances
  @do_importances
end

#do_testing ⇒ Object

Returns the value of attribute do_testing.



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# File 'lib/nimbus/configuration.rb', line 14

def do_testing
  @do_testing
end

#do_training ⇒ Object

Returns the value of attribute do_training.



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# File 'lib/nimbus/configuration.rb', line 14

def do_training
  @do_training
end

#forest_file ⇒ Object

Returns the value of attribute forest_file.



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# File 'lib/nimbus/configuration.rb', line 14

def forest_file
  @forest_file
end

#forest_size ⇒ Object

Returns the value of attribute forest_size.



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# File 'lib/nimbus/configuration.rb', line 14

def forest_size
  @forest_size
end

#loss_function_continuous ⇒ Object

Returns the value of attribute loss_function_continuous.



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# File 'lib/nimbus/configuration.rb', line 14

def loss_function_continuous
  @loss_function_continuous
end

#loss_function_discrete ⇒ Object

Returns the value of attribute loss_function_discrete.



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# File 'lib/nimbus/configuration.rb', line 14

def loss_function_discrete
  @loss_function_discrete
end

#output_forest_file ⇒ Object

Returns the value of attribute output_forest_file.



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# File 'lib/nimbus/configuration.rb', line 14

def output_forest_file
  @output_forest_file
end

#output_snp_importances_file ⇒ Object

Returns the value of attribute output_snp_importances_file.



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# File 'lib/nimbus/configuration.rb', line 14

def output_snp_importances_file
  @output_snp_importances_file
end

#output_testing_file ⇒ Object

Returns the value of attribute output_testing_file.



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# File 'lib/nimbus/configuration.rb', line 14

def output_testing_file
  @output_testing_file
end

#output_training_file ⇒ Object

Returns the value of attribute output_training_file.



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# File 'lib/nimbus/configuration.rb', line 14

def output_training_file
  @output_training_file
end

#output_tree_errors_file ⇒ Object

Returns the value of attribute output_tree_errors_file.



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# File 'lib/nimbus/configuration.rb', line 14

def output_tree_errors_file
  @output_tree_errors_file
end

#silent ⇒ Object

Returns the value of attribute silent.



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# File 'lib/nimbus/configuration.rb', line 14

def silent
  @silent
end

#testing_file ⇒ Object

Returns the value of attribute testing_file.



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# File 'lib/nimbus/configuration.rb', line 14

def testing_file
  @testing_file
end

#training_file ⇒ Object

Returns the value of attribute training_file.



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# File 'lib/nimbus/configuration.rb', line 14

def training_file
  @training_file
end

#training_set ⇒ Object

Returns the value of attribute training_set.



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# File 'lib/nimbus/configuration.rb', line 14

def training_set
  @training_set
end

#tree_node_min_size ⇒ Object

Returns the value of attribute tree_node_min_size.



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# File 'lib/nimbus/configuration.rb', line 14

def tree_node_min_size
  @tree_node_min_size
end

#tree_SNP_sample_size ⇒ Object

Returns the value of attribute tree_SNP_sample_size.



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# File 'lib/nimbus/configuration.rb', line 14

def tree_SNP_sample_size
  @tree_SNP_sample_size
end

#tree_SNP_total_count ⇒ Object

Returns the value of attribute tree_SNP_total_count.



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# File 'lib/nimbus/configuration.rb', line 14

def tree_SNP_total_count
  @tree_SNP_total_count
end

Instance Method Details

#check_configuration ⇒ Object

Include tests to be passed by the info contained in the config file.

If some of the configuration data provided by the user is invalid, an error is raised and execution stops.

Raises:



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# File 'lib/nimbus/configuration.rb', line 206

def check_configuration
  raise Nimbus::ConfigurationError, "The mtry sample size must be smaller than the total SNPs count." if @tree_SNP_sample_size > @tree_SNP_total_count
end

#load(config_file = DEFAULTS[:config_file]) ⇒ Object

This is the first method to be called on Configuration when a config.yml file exists with user input options for the forest.

  • The method will read the config file and change the default value of the selected options.

  • Then based on the options and the existence of training, testing and forest files, it will mark:

    • if training is needed,

    • if testing is needed,

    • which forest will be used for the testing.

  • Finally it will run basic checks on the input data trying to prevent future program errors.



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# File 'lib/nimbus/configuration.rb', line 105

def load(config_file = DEFAULTS[:config_file])
  user_config_params = {}
  dirname = Dir.pwd
  if File.exist?(File.expand_path(config_file, Dir.pwd))
    begin
      config_file_path = File.expand_path config_file, Dir.pwd
      user_config_params = Psych.load(File.open(config_file_path))
      dirname = File.dirname config_file_path
    rescue ArgumentError => e
      raise Nimbus::WrongFormatFileError, "It was not posible to parse the config file (#{config_file}): \r\n#{e.message} "
    end
  end

  if user_config_params['input']
    @training_file = File.expand_path(user_config_params['input']['training'], dirname) if user_config_params['input']['training']
    @testing_file  = File.expand_path(user_config_params['input']['testing' ], dirname) if user_config_params['input']['testing']
    @forest_file   = File.expand_path(user_config_params['input']['forest'  ], dirname) if user_config_params['input']['forest']
    @classes       = user_config_params['input']['classes'] if user_config_params['input']['classes']
  else
    @training_file = File.expand_path(DEFAULTS[:training_file], Dir.pwd) if File.exist? File.expand_path(DEFAULTS[:training_file], Dir.pwd)
    @testing_file  = File.expand_path(DEFAULTS[:testing_file ], Dir.pwd) if File.exist? File.expand_path(DEFAULTS[:testing_file ], Dir.pwd)
    @forest_file   = File.expand_path(DEFAULTS[:forest_file  ], Dir.pwd) if File.exist? File.expand_path(DEFAULTS[:forest_file  ], Dir.pwd)
  end

  @do_training = true unless @training_file.nil?
  @do_testing  = true unless @testing_file.nil?
  @classes = @classes.map{|c| c.to_s.strip} if @classes

  if @do_testing && !@do_training && !@forest_file
    raise Nimbus::InputFileError, "There is not random forest data (training file not defined, and forest file not found)."
  end

  if user_config_params['forest']
    @forest_size          = user_config_params['forest']['forest_size'].to_i if user_config_params['forest']['forest_size']
    @tree_SNP_total_count = user_config_params['forest']['SNP_total_count'].to_i if user_config_params['forest']['SNP_total_count']
    @tree_SNP_sample_size = user_config_params['forest']['SNP_sample_size_mtry'].to_i  if user_config_params['forest']['SNP_sample_size_mtry']
    @tree_node_min_size   = user_config_params['forest']['node_min_size'].to_i if user_config_params['forest']['node_min_size']
    @do_importances       = user_config_params['forest']['var_importances'].to_s.strip.downcase
    @do_importances       = (@do_importances != 'no' && @do_importances != 'false')
  end

  check_configuration
  log_configuration
end

#load_forest ⇒ Object

Creates a Nimbus::Forest object from a user defined random forest data file.

The format of the input file should be the same as the forest output data of a Nimbus Application.



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# File 'lib/nimbus/configuration.rb', line 187

def load_forest
  trees = []
  if File.exist?(@forest_file)
    begin
      trees = Psych.load(File.open @forest_file)
    rescue ArgumentError => e
      raise Nimbus::WrongFormatFileError, "It was not posible to parse the random forest file (#{@forest_file}): \r\n#{e.message} "
    end
  else
    raise Nimbus::InputFileError, "Forest file not found (#{@forest_file})"
  end
  forest = Nimbus::Forest.new self
  forest.trees = trees
  forest
end

#load_training_data ⇒ Object

The method reads the training file, and if the data is valid, creates a Nimbus::TrainingSet containing every individual to be used as training sample for a random forest.



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# File 'lib/nimbus/configuration.rb', line 152

def load_training_data
  File.open(@training_file) {|file|
    @training_set = Nimbus::TrainingSet.new({}, {})
    file.each do |line|
      next if line.strip == ''
      data_feno, data_id, *snp_list = line.strip.split
      raise Nimbus::InputFileError, "Individual ##{data_id} from training set has no value for all #{@tree_SNP_total_count} SNPs" unless snp_list.size == @tree_SNP_total_count
      raise Nimbus::InputFileError, "There are individuals with no ID, please check data in training file." unless (!data_id.nil? && data_id.strip != '')
      raise Nimbus::InputFileError, "Individual ##{data_id} has no fenotype value, please check data in training file." unless (!data_feno.nil? && data_feno.strip != '')
      raise Nimbus::InputFileError, "Individual ##{data_id} has invalid class (not in [#{classes*', '}]), please check data in training file." unless (@classes.nil? || @classes.include?(data_feno))

      data_feno = (@classes ? data_feno.to_s : data_feno.to_f)
      @training_set.individuals[data_id.to_i] = Nimbus::Individual.new(data_id.to_i, data_feno, snp_list.map{|snp| snp.to_i})
      @training_set.ids_fenotypes[data_id.to_i] = data_feno
    end
  }
end

#log_configuration ⇒ Object

Prints the information stored in the Nimbus::Configuration object

It could include errors on the configuration input data, training related info and/or testing related info.



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# File 'lib/nimbus/configuration.rb', line 213

def log_configuration
  return if @silent
  if !@do_training && !@do_testing
    Nimbus.message "*" * 50
    Nimbus.message "* Nimbus could not find any input file: "
    Nimbus.message "*   No training file (default: training.data)"
    Nimbus.message "*   No testing file (default: testing.data)"
    Nimbus.message "*   Not defined in config file (default: config.yml)"
    Nimbus.message "* Nothing to do."
    Nimbus.message "*" * 50
    Nimbus.stop "Error: No input data. Nimbus finished."
  end

  Nimbus.message "*" * 50
  Nimbus.message "* Nimbus version #{::Nimbus::VERSION}"
  Nimbus.message "* configured with the following parameters: "
  Nimbus.message "*   Forest size: #{@forest_size} trees"
  Nimbus.message "*   Total SNP count: #{@tree_SNP_total_count}"
  Nimbus.message "*   SNPs sample size (mtry): #{@tree_SNP_sample_size}"
  Nimbus.message "*   Minimun node size in tree: #{@tree_node_min_size}"

  if @classes
    Nimbus.message "*   Mode: CLASSIFICATION"
    Nimbus.message "*     Classes: [#{@classes*', '}]"
  else
    Nimbus.message "*   Mode: REGRESSION"
  end
  Nimbus.message "*" * 50

  if @do_training
    Nimbus.message "* Training data:"
    Nimbus.message "*   Training file: #{@training_file}"
    Nimbus.message "*" * 50
  end

  if @do_testing
    Nimbus.message "* Data to be tested:"
    Nimbus.message "*   Testing file: #{@testing_file}"
    if @forest_file
      Nimbus.message "* using the structure of the random forest stored in:"
      Nimbus.message "*   Random forest file: #{@forest_file}"
    end
    Nimbus.message "*" * 50
  end
end

#read_testing_data ⇒ Object

Reads the testing file, and if the data is valid, yields one Nimbus::Individual at a time.



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# File 'lib/nimbus/configuration.rb', line 171

def read_testing_data
  File.open(@testing_file) {|file|
    file.each do |line|
      next if line.strip == ''
      data_id, *snp_list = line.strip.split
      raise Nimbus::InputFileError, "There are individuals with no ID, please check data in Testing file." unless (!data_id.nil? && data_id.strip != '')
      raise Nimbus::InputFileError, "Individual ##{data_id} from testing set has no value for all #{@tree_SNP_total_count} SNPs." unless snp_list.size == @tree_SNP_total_count
      individual_test = Nimbus::Individual.new(data_id.to_i, nil, snp_list.map{|snp| snp.to_i})
      yield individual_test
    end
  }
end

#tree ⇒ Object

Accessor method for the tree-related subset of options.



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# File 'lib/nimbus/configuration.rb', line 86

def tree
  {
    snp_sample_size: @tree_SNP_sample_size,
    snp_total_count: @tree_SNP_total_count,
    tree_node_min_size: @tree_node_min_size,
    classes: @classes
  }
end