Class: TavernaPlayer::Worker

Inherits:
Object
  • Object
show all
Includes:
Concerns::Callback, Concerns::Zip
Defined in:
lib/taverna_player/worker.rb

Constant Summary collapse

INTERACTION_REGEX =

How to get the interaction presentation frame out of the interaction page.

/document\.getElementById\(\'presentationFrame\'\)\.src = \"(.+)\";/

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Concerns::Zip

#read_file_from_zip

Methods included from Concerns::Callback

#callback

Constructor Details

#initialize(run, workflow_file = nil) ⇒ Worker

The workflow file to be run can be specified explicitly or it will be taken from the workflow model.



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# File 'lib/taverna_player/worker.rb', line 25

def initialize(run, workflow_file = nil)
  @run = run
  @workflow = workflow_file || TavernaPlayer.workflow_proxy.file(@run.workflow)
  @server = "Run not yet initialized"
end

Instance Attribute Details

#run ⇒ Object (readonly)

Returns the value of attribute run.



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# File 'lib/taverna_player/worker.rb', line 18

def run
  @run
end

Instance Method Details

#max_attempts ⇒ Object

This tells delayed_job to only try and complete each run once.



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# File 'lib/taverna_player/worker.rb', line 38

def max_attempts
  1
end

#perform ⇒ Object 



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# File 'lib/taverna_player/worker.rb', line 42

def perform
  return unless run_callback(TavernaPlayer.pre_run_callback, "pre-callback")

  status_message("connect")

  @server = URI.parse(ENV["TAVERNA_URI"] || TavernaPlayer.server_address)
  credentials = server_credentials
  conn_params = TavernaPlayer.server_connection

  begin
    server = T2Server::Server.new(@server, conn_params)
    workflow = File.read(@workflow)
    run = create_run(server, workflow, credentials)

    # If run is nil here then we could have failed or have been cancelled.
    return if run.nil?

    status_message("initialized")

    @run.run_id = run.id
    @run.state = run.status
    @run.create_time = run.create_time
    @run.save

    unless @run.inputs.size == 0
      status_message("inputs")
      @run.inputs.each do |input|
        unless input.file.blank?
          run.input_port(input.name).file = input.file.path
        else
          run.input_port(input.name).value = input.value
        end
      end
    end

    # Just add in all service credentials right now
    TavernaPlayer::ServiceCredential.all.each do |cred|
      run.add_password_credential(cred.uri, cred., cred.password)
    end

    status_message("start")
    run.name = @run.name

    # Try and start the run bearing in mind that the server might be at
    # the limit of runs that it can run at once.
    while !run.start
      status_message("busy")

      if cancelled?
        cancel(run)
        return
      end

      sleep(TavernaPlayer.server_retry_interval)
    end

    @run.state = run.status
    @run.start_time = run.start_time
    @run.save

    status_message("running")
    until run.finished?
      sleep(TavernaPlayer.server_poll_interval)
      waiting = false

      if cancelled?
        cancel(run)
        return
      end

      waiting = interactions(run, credentials)

      status_message(waiting ? "interact" : "running")
    end

    status_message("outputs")
    download_outputs(run)
    download_log(run)

    @run.outputs = process_outputs(run)
    @run.finish_time = run.finish_time
    @run.save

    run.delete
  rescue => exception
    failed(exception, run)
    return
  end

  return unless run_callback(TavernaPlayer.post_run_callback, "post-callback")

  @run.state = :finished
  status_message("finished")
end

#server ⇒ Object

Return the server address that this worker is using. Used mainly for testing.



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# File 'lib/taverna_player/worker.rb', line 33

def server
  @server.to_s
end