Class: WadrcBcpScripts::BasicTask

Inherits:
Object
  • Object
show all
Defined in:
lib/wadrc-bcp-scripts/basic_task.rb

Overview

Enviornment and configuration checks common between processing streams.

Direct Known Subclasses

Dtitask, FreesurferRoiTask

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#config ⇒ Object

Task Configuration Options Hash



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# File 'lib/wadrc-bcp-scripts/basic_task.rb', line 9

def config
  @config
end

Instance Method Details

#check_setup(input_directory = @input_directory, output_directory = @output_directory) ⇒ Object

Basic IO Directory Checks

Raises:

  • (IOError) 


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# File 'lib/wadrc-bcp-scripts/basic_task.rb', line 64

def check_setup(input_directory = @input_directory, output_directory = @output_directory)
  # Check Input Directory
  raise(IOError, "#{input_directory}: not found.") unless File.directory?(input_directory)

  # Check Gradient Tensor Files
  ensure_file_exists @config[:bvectors_file], @config[:bvalues_file] 
  
  unless @config[:dry_run]
    # Check Working Input Directory
    if @config[:force_sandbox]
      path = Pathname.new(input_directory)
      # @working_input_directory = path.sandbox(input_directory)
      @working_input_directory = path.prep_mise(input_directory + '/', Dir.mktmpdir + '/')
      @working_input_directory = File.join(@working_input_directory, File.basename(input_directory))
    else
      @working_input_directory = input_directory
    end
  
    # Check Output Directory and force cleanup if necessary.
    colliding_files = Dir.glob(File.join(output_directory, @file_prefix) + '*')
    puts colliding_files
    if File.directory?(output_directory) && colliding_files.empty? == false
      if @config[:force_overwrite] then colliding_files.each {|file| puts "Removing #{file}..."; File.delete(file) }
      else raise(IOError, "#{output_directory} already exists. Set force_overwite in your spec file to overwrite the directory.") 
      end
    end
    FileUtils.mkdir_p(output_directory)
  else
    # Use the real input directory if the working directory was not assigned 
    # (ie during dry run)
    @working_input_directory = input_directory
  end
  
  # Setup Logging
  logfile = File.join(output_directory, "#{File.basename(input_directory)}_#{today}.log")
  if File.writable?(output_directory) && ! @config[:dry_run]
    $LOG = Logger.new(logfile)
  else
    $LOG = Logger.new(STDOUT)
  end
  
  # Switch CWD (default output location for rotbvecs script)
  @cwd = Dir.pwd
  Dir.chdir(output_directory) unless @config[:dry_run]
end

#config_requires(*args) ⇒ Object

Check for required keys in the @config hash.



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# File 'lib/wadrc-bcp-scripts/basic_task.rb', line 41

def config_requires(*args)
  missing_keys = []
  args.each do |required_key|
    unless @config.has_key?(required_key)
      missing_keys << required_key
    end
  end
  
  unless missing_keys.size == 0
    error = "
    Warning: Misconfiguration detected.
    You are missing the following keys from your spec file:
    - #{missing_keys.join(', ')}


    Please install the missing programs, run this script from a properly configured workstation,
    or use the dry_run option to output your script to the terminal.\n "
    puts error
    raise(ScriptError, "Missing Keys: #{missing_keys.join(", ")}")
  end
end

#ensure_file_exists(*args) ⇒ Object 



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# File 'lib/wadrc-bcp-scripts/basic_task.rb', line 110

def ensure_file_exists(*args)
  args.each do |file|
    raise(IOError, "#{file} not found.") unless File.exists?(file)
  end
  
end

#environment_requires(*args) ⇒ Object

Check for some required helper applications that must be installed on the system prior to use. It returns true if there are no missing processing program binaries, otherwise it puts them to the screen and raises a ScriptError.



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# File 'lib/wadrc-bcp-scripts/basic_task.rb', line 15

def environment_requires(*args)
  missing_binaries = []
  args.each do |required_binary|
    if system("which #{required_binary.to_s} > /dev/null") == false
      missing_binaries << required_binary
    end
  end
  
  begin
    unless missing_binaries.size == 0
      error = "
      Warning: The following processing tools weren't found on your system.
      - #{missing_binaries.join(', ')}
  
  
      Please install the missing programs, run this script from a properly configured workstation,
      or use the dry_run option to output your script to the terminal.\n "
      puts error
      raise(ScriptError, "Missing #{missing_binaries.join(", ")}")
    end
  end
  
  return
end