Method: Constants#initialize

Defined in:
lib/protk/constants.rb

#initialize ⇒ Constants

Read the global constants file and initialize our class @env variable Initialize loggers



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# File 'lib/protk/constants.rb', line 140

def initialize() 

  @data_lib_dir="#{File.dirname(__FILE__)}/data"
  @protk_dir="#{Dir.home}/.protk"

  if ( ENV['PROTK_INSTALL_DIR']!=nil )
    p "Using protk install dir from shell"
    @protk_dir=ENV['PROTK_INSTALL_DIR']
  end

  # Load Protk Defaults
  #
  default_config_yml = YAML.load_file "#{File.dirname(__FILE__)}/data/default_config.yml"
  throw "Unable to read the config file at #{File.dirname(__FILE__)}/data/default_config.yml" unless default_config_yml!=nil

  # User-defined defaults override protk defaults
  #
  user_config_yml = nil
  user_config_yml = YAML.load_file "#{@protk_dir}/config.yml" if File.exist? "#{@protk_dir}/config.yml"
  if ( user_config_yml !=nil )
    @env = default_config_yml.merge user_config_yml
  else
    @env=default_config_yml
  end

  protk_tool_dirs=["tpp/bin","omssa","openms/bin","msgfplus","blast/bin","pwiz","tandem/bin"]

  # Construct the PATH variable by prepending our preferred paths
  #
  protk_paths=[]

  # Add PATHs if PROTK_XXX_ROOT is defined
  #
  protk_tool_dirs.each do |tooldir|  
    env_value = ENV["PROTK_#{tooldir.upcase}_ROOT"]
    if ( env_value!=nil)
      protk_paths<<env_value
    end
    protk_paths<<"#{@protk_dir}/tools/#{tooldir}"
  end

  original_path=ENV['PATH']
  protk_paths<<original_path


  ENV['PATH']=protk_paths.join(":")

  # puts "Path #{ENV['PATH']}"
  throw "No data found in config file" unless @env!=nil

  @info_level="fatal"
  @info_level=default_config_yml['message_level'] unless default_config_yml['message_level'].nil?

end