toil.worker

Module Contents

Classes

StatsDict

Subclass of MagicExpando for type-checking purposes.

Functions

nextChainable(predecessor, jobStore, config)	Returns the next chainable job's JobDescription after the given predecessor
workerScript(jobStore, config, jobName, jobStoreID[, ...])	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])

Attributes

logger

toil.worker.logger

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

Bases: toil.lib.expando.MagicExpando

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Subclass of MagicExpando for type-checking purposes.

jobs: List[str]

toil.worker.nextChainable(predecessor, jobStore, 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

• jobStore (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(jobStore, config, jobName, jobStoreID, redirectOutputToLogFile=True)

Worker process script, runs a job.

Parameters:

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

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

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

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

• redirectOutputToLogFile (bool) –

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:

Iterator[None]

toil.worker.main(argv=None)

Parameters:

argv (Optional[List[str]]) –

Return type:

None