Module: Workflow::Data

Defined in:
lib/rbbt/workflow/util/data.rb

Defined Under Namespace

Classes: DataNotFound

Instance Method Summary collapse

Instance Method Details

#data(name, options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/workflow/util/data.rb', line 99

def data(name, options = {}, &block)
  dep do |jobname, job_options, dependencies|
    if block_given?
      block.call jobname, job_options.merge(options), dependencies
    else
      begin
        path = get_file jobname, name, options[:extension]
        job = Step.new path
        job.task_name = name
        job.result_type = options[:result_type] || options[:type] || options[:extension]
        job
      rescue DataNotFound
        {:task => name, :options => options, :jobname => jobname}
      end
    end
  end
end

#data_dir(directory) ⇒ Object 



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# File 'lib/rbbt/workflow/util/data.rb', line 8

def data_dir(directory)
  @@data_directory = directory
end

#data_task(name, workflow, oname, *rest, &block) ⇒ Object 



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# File 'lib/rbbt/workflow/util/data.rb', line 43

def data_task(name, workflow, oname, *rest, &block)
  dep_task(name, workflow, oname, *rest) do |jobname, options,dependencies|
    begin
      task_info = workflow.nil? ? nil : workflow.task_info(oname) 
      options[:extension] ||= task_info[:extension]
      path = get_file jobname, name, options[:extension]
      job = Step.new path
      job.task_name = name
      job.result_type = options[:result_type] || options[:type] || options[:extension]
      job
    rescue DataNotFound
    end

    next job if job

    data_options = {}
    data_options = data_options.merge(Workflow.load_inputs(File.join(@@data_directory,"options"), task_info[:inputs], task_info[:input_types]))

    begin
      data_options = data_options.merge(Workflow.load_inputs(get_file(jobname, :options), task_info[:inputs], task_info[:input_types]))
    rescue DataNotFound
    end

    begin
      data_options = data_options.merge(Workflow.load_inputs(get_datadir(jobname).options, task_info[:inputs], task_info[:input_types]))
    rescue DataNotFound
    end

    begin
      task_info = workflow.nil? ? nil : workflow.task_info(oname) 
      data_options = block.call get_datadir(jobname), data_options, task_info
    rescue
      Log.exception $!
    end if block_given?

    case data_options
    when Step
      next data_options
    when Hash
      if data_options.include?(:inputs)
        data_options = data_options.merge(options)
        workflow = data_options[:workflow] if data_options[:workflow]
        oname = data_options[:task] if data_options[:task]
        inputs = options.merge(data_options[:inputs])
      else
        inputs = options.merge(data_options)
      end

      {:workflow => workflow, :task => oname, :jobname => jobname, :inputs => inputs}
    else
      raise "Cannot understand data_options: #{data_options}"
    end

  end
end

#get_datadir(clean_name) ⇒ Object

Raises:



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# File 'lib/rbbt/workflow/util/data.rb', line 12

def get_datadir(clean_name)
  data_dir = File.join(@@data_directory, clean_name)
  raise DataNotFound, "Data dir not found for #{clean_name} in #{@@data_directory}" unless File.directory?(data_dir)
  if Path === @@data_directory
    @@data_directory.annotate data_dir
  else
    Path.setup(data_dir)
  end
end

#get_file(clean_name, type = nil, extension = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/util/data.rb', line 22

def get_file(clean_name, type = nil, extension = nil)
  begin
    extension = nil if String === extension && extension.empty?
    file1 = File.join(@@data_directory, type.to_s, (extension.nil? ? clean_name.to_s : clean_name.to_s + ".#{extension}"))
    file2 = File.join(@@data_directory, clean_name.to_s, (extension.nil? ? type.to_s : type.to_s + ".#{extension}"))
    if Open.exists?(file1)
      data_file = file1
    elsif Open.exists?(file2)
      data_file = file2
    else
      raise DataNotFound, "Data type #{type} not found for #{clean_name} in #{@@data_directory}"
    end
  end

  if Path === @@data_directory
    @@data_directory.annotate data_file
  else
    Path.setup(data_file)
  end
end