cwltool.workflow_job

Module Contents

Classes

WorkflowJobStep	Generated for each step in Workflow.steps().
ReceiveScatterOutput	Produced by the scatter generators.
WorkflowJob	Generates steps from the Workflow.
WorkflowJobLoopStep	Generated for each step in Workflow.steps() containing a Loop requirement.

Functions

parallel_steps(steps, rc, runtimeContext)
nested_crossproduct_scatter(process, joborder, ...)
crossproduct_size(joborder, scatter_keys)	Compute the size of a cross product.
flat_crossproduct_scatter(process, joborder, ...)
dotproduct_scatter(process, joborder, scatter_keys, ...)
match_types(sinktype, src, iid, inputobj, linkMerge, ...)
object_from_state(state, params, frag_only, ...[, ...])

class cwltool.workflow_job.WorkflowJobStep(step)

Generated for each step in Workflow.steps().

Parameters:

step (cwltool.workflow.WorkflowStep)

job(joborder, output_callback, runtimeContext)

Parameters:

• joborder (cwltool.utils.CWLObjectType)

• output_callback (Optional[cwltool.utils.OutputCallbackType])

• runtimeContext (cwltool.context.RuntimeContext)

Return type:

cwltool.utils.JobsGeneratorType

class cwltool.workflow_job.ReceiveScatterOutput(output_callback, dest, total)

Produced by the scatter generators.

Parameters:

• output_callback (cwltool.utils.ScatterOutputCallbackType)

• dest (cwltool.utils.ScatterDestinationsType)

• total (int)

receive_scatter_output(index, jobout, processStatus)

Record the results of a scatter operation.

Parameters:

• index (int)

• jobout (cwltool.utils.CWLObjectType)

• processStatus (str)

Return type:

None

setTotal(total, steps)

Set the total number of expected outputs along with the steps.

This is necessary to finish the setup.

Parameters:

• total (int)

• steps (List[Optional[cwltool.utils.JobsGeneratorType]])

Return type:

None

cwltool.workflow_job.parallel_steps(steps, rc, runtimeContext)

Parameters:

• steps (List[Optional[cwltool.utils.JobsGeneratorType]])

• rc (ReceiveScatterOutput)

• runtimeContext (cwltool.context.RuntimeContext)

Return type:

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.nested_crossproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)

Parameters:

• process (WorkflowJobStep)

• joborder (cwltool.utils.CWLObjectType)

• scatter_keys (MutableSequence[str])

• output_callback (cwltool.utils.ScatterOutputCallbackType)

• runtimeContext (cwltool.context.RuntimeContext)

Return type:

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.crossproduct_size(joborder, scatter_keys)

Compute the size of a cross product.

Parameters:

• joborder (cwltool.utils.CWLObjectType)

• scatter_keys (MutableSequence[str])

Return type:

int

cwltool.workflow_job.flat_crossproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)

Parameters:

• process (WorkflowJobStep)

• joborder (cwltool.utils.CWLObjectType)

• scatter_keys (MutableSequence[str])

• output_callback (cwltool.utils.ScatterOutputCallbackType)

• runtimeContext (cwltool.context.RuntimeContext)

Return type:

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.dotproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)

Parameters:

• process (WorkflowJobStep)

• joborder (cwltool.utils.CWLObjectType)

• scatter_keys (MutableSequence[str])

• output_callback (cwltool.utils.ScatterOutputCallbackType)

• runtimeContext (cwltool.context.RuntimeContext)

Return type:

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.match_types(sinktype, src, iid, inputobj, linkMerge, valueFrom)

Parameters:

• sinktype (Optional[cwltool.utils.SinkType])

• src (cwltool.utils.WorkflowStateItem)

• iid (str)

• inputobj (cwltool.utils.CWLObjectType)

• linkMerge (Optional[str])

• valueFrom (Optional[str])

Return type:

bool

cwltool.workflow_job.object_from_state(state, params, frag_only, supportsMultipleInput, sourceField, incomplete=False)

Parameters:

• state (Dict[str, Optional[cwltool.utils.WorkflowStateItem]])

• params (cwltool.utils.ParametersType)

• frag_only (bool)

• supportsMultipleInput (bool)

• sourceField (str)

• incomplete (bool)

Return type:

Optional[cwltool.utils.CWLObjectType]

class cwltool.workflow_job.WorkflowJob(workflow, runtimeContext)

Generates steps from the Workflow.

Parameters:

• workflow (cwltool.workflow.Workflow)

• runtimeContext (cwltool.context.RuntimeContext)

do_output_callback(final_output_callback)

Parameters:

final_output_callback (cwltool.utils.OutputCallbackType)

Return type:

None

receive_output(step, outputparms, final_output_callback, jobout, processStatus)

Parameters:

• step (WorkflowJobStep)

• outputparms (List[cwltool.utils.CWLObjectType])

• final_output_callback (cwltool.utils.OutputCallbackType)

• jobout (cwltool.utils.CWLObjectType)

• processStatus (str)

Return type:

None

try_make_job(step, final_output_callback, runtimeContext)

Parameters:

• step (WorkflowJobStep)

• final_output_callback (Optional[cwltool.utils.OutputCallbackType])

• runtimeContext (cwltool.context.RuntimeContext)

Return type:

cwltool.utils.JobsGeneratorType

run(runtimeContext, tmpdir_lock=None)

Log the start of each workflow.

Parameters:

• runtimeContext (cwltool.context.RuntimeContext)

• tmpdir_lock (Optional[threading.Lock])

Return type:

None

job(joborder, output_callback, runtimeContext)

Parameters:

• joborder (cwltool.utils.CWLObjectType)

• output_callback (Optional[cwltool.utils.OutputCallbackType])

• runtimeContext (cwltool.context.RuntimeContext)

Return type:

cwltool.utils.JobsGeneratorType

class cwltool.workflow_job.WorkflowJobLoopStep(step, container_engine)

Generated for each step in Workflow.steps() containing a Loop requirement.

Parameters:

• step (WorkflowJobStep)

• container_engine (str)

job(joborder, output_callback, runtimeContext)

Generate a WorkflowJobStep job until the loopWhen condition evaluates to False.

Parameters:

• joborder (cwltool.utils.CWLObjectType)

• output_callback (cwltool.utils.OutputCallbackType)

• runtimeContext (cwltool.context.RuntimeContext)

Return type:

cwltool.utils.JobsGeneratorType

loop_callback(runtimeContext, jobout, processStatus)

Update the joborder object with output values from the last iteration.

Parameters:

• runtimeContext (cwltool.context.RuntimeContext)

• jobout (cwltool.utils.CWLObjectType)

• processStatus (str)

Return type:

None