cwltool.workflow_job

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 directive.

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, ...[, ...])

Module Contents

class cwltool.workflow_job.WorkflowJobStep(step)

Generated for each step in Workflow.steps().

Parameters:

step (cwltool.workflow.WorkflowStep)

step
tool
id
submitted = False
iterable: cwltool.utils.JobsGeneratorType | None = None
completed = False
name
prov_obj
parent_wf
job(joborder, output_callback, runtimeContext)
Parameters:
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)

dest
processStatus = 'success'
total
output_callback
steps: list[cwltool.utils.JobsGeneratorType | None] = []
property completed: int

The number of completed internal jobs.

Return type:

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:
Return type:

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.nested_crossproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)
Parameters:
Return type:

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.crossproduct_size(joborder, scatter_keys)

Compute the size of a cross product.

Parameters:
Return type:

int

cwltool.workflow_job.flat_crossproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)
Parameters:
Return type:

cwltool.utils.JobsGeneratorType

cwltool.workflow_job.dotproduct_scatter(process, joborder, scatter_keys, output_callback, runtimeContext)
Parameters:
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
prov_obj: cwltool.cwlprov.provenance_profile.ProvenanceProfile | None = None
parent_wf: cwltool.cwlprov.provenance_profile.ProvenanceProfile | None = None
tool
steps
state: dict[str, cwltool.utils.WorkflowStateItem | None]
processStatus = ''
did_callback = False
made_progress: bool | None = None
outdir
name
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:
Return type:

cwltool.utils.JobsGeneratorType

run(runtimeContext, tmpdir_lock=None)

Log the start of each workflow.

Parameters:
Return type:

None

job(joborder, output_callback, runtimeContext)
Parameters:
Return type:

cwltool.utils.JobsGeneratorType

class cwltool.workflow_job.WorkflowJobLoopStep(step, container_engine)

Generated for each step in Workflow.steps() containing a loop directive.

Parameters:
step: WorkflowJobStep
container_engine: str
joborder: cwltool.utils.CWLObjectType | None = None
processStatus: str = 'success'
iteration: int = 0
output_buffer: collections.abc.MutableMapping[str, collections.abc.MutableSequence[cwltool.utils.CWLOutputType | None] | cwltool.utils.CWLOutputType | None]
job(joborder, output_callback, runtimeContext)

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

Parameters:
Return type:

cwltool.utils.JobsGeneratorType

loop_callback(runtimeContext, jobout, processStatus)

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

Parameters:
Return type:

None