Class: Nimbus::Application

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

Overview

Nimbus main application object.

When invoking nimbus from the command line, a Nimbus::Application object is created and run.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(c = nil) ⇒ Application

Initialize a Nimbus::Application object. Check and load the configuration options.



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

def initialize(c = nil)
  @config = c unless c.nil?
  nimbus_exception_handling do
    config.load
    @forest = nil
  end
end

Instance Attribute Details

#config ⇒ Object

Creates an instance of Nimbus::Configuration if it does not exist. This config object contains every option to be used for the random forest including the user input set through the config.yml file.



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# File 'lib/nimbus/application.rb', line 52

def config
  @config
end

Instance Method Details

#display_error_message(ex) ⇒ Object

Display an error message that caused a exception.



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# File 'lib/nimbus/application.rb', line 72

def display_error_message(ex)
  Nimbus.error_message "* Nimbus encountered an error! The random forest was not generated *"
  Nimbus.error_message "#{ex.class}: #{ex.message}"
  # if config.trace
  #   Nimbus.error_message ex.backtrace.join("\n")
  # else
  #   Nimbus.error_message "(See full error trace by running Nimbus with --trace)"
  # end
end

#nimbus_exception_handling ⇒ Object

Provides the default exception handling for the given block.



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# File 'lib/nimbus/application.rb', line 57

def nimbus_exception_handling
  begin
    yield
  rescue SystemExit => ex
    raise
  rescue Nimbus::Error => ex
    display_error_message(ex)
    Nimbus.stop
  rescue Exception => ex
    display_error_message(ex)
    Nimbus.stop
  end
end

#run ⇒ Object

Run the Nimbus application. The run method performs the following three steps:

  • Create a Nimbus::Forest object.

  • Decide action to take: training a random forest and/or use the forest to predict values for a testing set

  • Write results to output files.



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# File 'lib/nimbus/application.rb', line 28

def run
  nimbus_exception_handling do

    if @config.do_training && @config.load_training_data
      @forest = ::Nimbus::Forest.new @config
      @forest.grow
      output_random_forest_file(@forest)
      output_tree_errors_file(@forest)
      output_training_file_predictions(@forest)
      output_snp_importances_file(@forest) if @config.do_importances
    end

    if @config.do_testing
      @forest = @config.load_forest if @config.forest_file
      @forest.traverse
      output_testing_set_predictions(@forest)
    end

  end
end