toil.worker

Attributes

logger

Classes

StatsDict

Subclass of MagicExpando for type-checking purposes.

Functions

nextChainable(predecessor, job_store, config)	Returns the next chainable job's JobDescription after the given predecessor
workerScript(job_store, config, job_name, job_store_id)	Worker process script, runs a job.
parse_args(args)	Parse command-line arguments to the worker.
in_contexts(contexts)	Unpickle and enter all the pickled, base64-encoded context managers in the
main([argv])

Module Contents

toil.worker.logger

class toil.worker.StatsDict(*args, **kwargs)

Bases: toil.lib.expando.MagicExpando

Subclass of MagicExpando for type-checking purposes.

jobs: list[toil.lib.expando.MagicExpando]

toil.worker.nextChainable(predecessor, job_store, config)

Returns the next chainable job’s JobDescription after the given predecessor JobDescription, if one exists, or None if the chain must terminate.

Parameters:

• predecessor (toil.job.JobDescription) – The job to chain from

• job_store (toil.jobStores.abstractJobStore.AbstractJobStore) – The JobStore to fetch JobDescriptions from.

• config (toil.common.Config) – The configuration for the current run.

Return type:

Optional[toil.job.JobDescription]

toil.worker.workerScript(job_store, config, job_name, job_store_id, redirect_output_to_log_file=True, local_worker_temp_dir=None, debug_flags=None)

Worker process script, runs a job.

Parameters:

• job_store (toil.jobStores.abstractJobStore.AbstractJobStore) – The JobStore to fetch JobDescriptions from.

• config (toil.common.Config) – The configuration for the current run.

• job_name (str) – The “job name” (a user friendly name) of the job to be run

• job_store_id (str) – The job store ID of the job to be run

• redirect_output_to_log_file (bool) – If False, log directly to the console instead of capturing job output.

• local_worker_temp_dir (Optional[str]) – The directory for the worker to work in. May be recursively removed after the job runs.

• debug_flags (Optional[set[str]]) – Flags to set on each job before running it.

Return int:

1 if a job failed, or 0 if all jobs succeeded

Return type:

int

toil.worker.parse_args(args)

Parse command-line arguments to the worker.

Parameters:

args (list[str])

Return type:

Any

toil.worker.in_contexts(contexts)

Unpickle and enter all the pickled, base64-encoded context managers in the given list. Then do the body, then leave them all.

Parameters:

contexts (list[str])

Return type:

collections.abc.Iterator[None]

toil.worker.main(argv=None)

Parameters:

argv (Optional[list[str]])

Return type:

None