auto_process_ngs.cli.transfer_data

class auto_process_ngs.cli.transfer_data.TransferData(runner, working_dir, poll_interval)

Class for handling workflow for data transfer

Wraps the “SimpleScheduler” class and provides the following methods:

  • run_job: runs a “Command” instance

  • wait: blocks until specified jobs (or all jobs) have completed

  • finish: checks the exit status of all jobs

Parameters:

  • runner (JobRunner) – the default job runner to use when executing jobs

  • working_dir (str) – path to the working directory

  • poll_interval (int) – polling interval for scheduler

finish()

Wait for all jobs then check and return status

Returns:

status code (0 for success, 1 if any

of the jobs failed).

Return type:

Integer

run_job(name, cmd, runner=None, wait_for=None)

Submits the specified command to the scheduler

Parameters:

  • name (str) – name for the command

  • cmd (Command) – the command to run

  • runner (JobRunner) – optional, job runner to use

  • wait_for (list) – optional, list of jobs to wait for before scheduling this command

Returns:

a SchedulerJob instance for the submitted

job.

Return type:

SchedulerJob

wait(*jobs)

Block until specified jobs have completed.

If one or more jobs are supplied then wait for those jobs to complete before returning; otherwise wait for all jobs currently scheduled to complete.

Parameters:

jobs (list) – optional list of SchedulerJobs to wait for (otherwise wait for all jobs)

class auto_process_ngs.cli.transfer_data.TransferDataSchedulerReporter

Custom reporter for scheduler

auto_process_ngs.cli.transfer_data.get_templates_dir()

Return location of ‘templates’ directory

Returns the path to the ‘templates’ directory, or None if it doesn’t exist.

auto_process_ngs.cli.transfer_data.main(argv=None)

Run the ‘transfer_data’ utility

Parameters:

argv (list) – optional, command line arguments to process (otherwise take arguments from ‘sys.argv’)

Returns:

0 on success, 1 on failure.

Return type:

Integer