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Source code for galaxy.workflow.run
import logging
import uuid
from typing import (
Any,
Dict,
List,
Optional,
Tuple,
TYPE_CHECKING,
Union,
)
from typing_extensions import Protocol
from galaxy import model
from galaxy.exceptions import MessageException
from galaxy.model import (
WorkflowInvocation,
WorkflowInvocationStep,
)
from galaxy.model.base import transaction
from galaxy.schema.invocation import (
CancelReason,
FailureReason,
InvocationCancellationHistoryDeleted,
InvocationFailureCollectionFailed,
InvocationFailureDatasetFailed,
InvocationFailureJobFailed,
InvocationFailureOutputNotFound,
InvocationUnexpectedFailure,
InvocationWarningWorkflowOutputNotFound,
WarningReason,
)
from galaxy.tools.parameters.basic import raw_to_galaxy
from galaxy.util import ExecutionTimer
from galaxy.workflow import modules
from galaxy.workflow.run_request import (
workflow_request_to_run_config,
workflow_run_config_to_request,
WorkflowRunConfig,
)
if TYPE_CHECKING:
from galaxy.model import (
Workflow,
WorkflowOutput,
WorkflowStep,
WorkflowStepConnection,
)
from galaxy.webapps.base.webapp import GalaxyWebTransaction
from galaxy.work.context import WorkRequestContext
log = logging.getLogger(__name__)
WorkflowOutputsType = Dict[int, Any]
# Entry point for core workflow scheduler.
def schedule(
trans: "WorkRequestContext",
workflow: "Workflow",
workflow_run_config: WorkflowRunConfig,
workflow_invocation: WorkflowInvocation,
) -> Tuple[WorkflowOutputsType, WorkflowInvocation]:
return __invoke(trans, workflow, workflow_run_config, workflow_invocation)
def __invoke(
trans: "WorkRequestContext",
workflow: "Workflow",
workflow_run_config: WorkflowRunConfig,
workflow_invocation: Optional[WorkflowInvocation] = None,
populate_state: bool = False,
) -> Tuple[WorkflowOutputsType, WorkflowInvocation]:
"""Run the supplied workflow in the supplied target_history."""
if populate_state:
modules.populate_module_and_state(
trans,
workflow,
workflow_run_config.param_map,
allow_tool_state_corrections=workflow_run_config.allow_tool_state_corrections,
)
invoker = WorkflowInvoker(
trans,
workflow,
workflow_run_config,
workflow_invocation=workflow_invocation,
)
workflow_invocation = invoker.workflow_invocation
outputs = {}
try:
outputs = invoker.invoke()
except modules.CancelWorkflowEvaluation as e:
if workflow_invocation.cancel():
workflow_invocation.add_message(e.why)
except modules.FailWorkflowEvaluation as e:
workflow_invocation.fail()
workflow_invocation.add_message(e.why)
except MessageException as e:
# Convention for safe message we can show to users
workflow_invocation.fail()
failure = InvocationUnexpectedFailure(reason=FailureReason.unexpected_failure, details=str(e))
workflow_invocation.add_message(failure)
except Exception:
# Could potentially be large and/or contain raw ids or other secrets, don't add details
log.exception("Failed to execute scheduled workflow.")
# Running workflow invocation in background, just mark
# persistent workflow invocation as failed.
failure = InvocationUnexpectedFailure(reason=FailureReason.unexpected_failure)
workflow_invocation.fail()
workflow_invocation.add_message(failure)
# Be sure to update state of workflow_invocation.
trans.sa_session.add(workflow_invocation)
with transaction(trans.sa_session):
trans.sa_session.commit()
return outputs, workflow_invocation
[docs]def queue_invoke(
trans: "GalaxyWebTransaction",
workflow: "Workflow",
workflow_run_config: WorkflowRunConfig,
request_params: Optional[Dict[str, Any]] = None,
populate_state: bool = True,
flush: bool = True,
) -> WorkflowInvocation:
request_params = request_params or {}
if populate_state:
modules.populate_module_and_state(
trans,
workflow,
workflow_run_config.param_map,
allow_tool_state_corrections=workflow_run_config.allow_tool_state_corrections,
)
workflow_invocation = workflow_run_config_to_request(trans, workflow_run_config, workflow)
workflow_invocation.workflow = workflow
return trans.app.workflow_scheduling_manager.queue(workflow_invocation, request_params, flush=flush)
class WorkflowInvoker:
def __init__(
self,
trans: "WorkRequestContext",
workflow: "Workflow",
workflow_run_config: WorkflowRunConfig,
workflow_invocation: Optional[WorkflowInvocation] = None,
progress: Optional["WorkflowProgress"] = None,
) -> None:
self.trans = trans
self.workflow = workflow
self.workflow_invocation: WorkflowInvocation
if progress is not None:
assert workflow_invocation is None
workflow_invocation = progress.workflow_invocation
if workflow_invocation is None:
invocation_uuid = uuid.uuid1()
workflow_invocation = WorkflowInvocation()
workflow_invocation.workflow = self.workflow
# In one way or another, following attributes will become persistent
# so they are available during delayed/revisited workflow scheduling.
workflow_invocation.uuid = invocation_uuid
workflow_invocation.history = workflow_run_config.target_history
self.workflow_invocation = workflow_invocation
module_injector = modules.WorkflowModuleInjector(trans)
if progress is None:
progress = WorkflowProgress(
self.workflow_invocation,
workflow_run_config.inputs,
module_injector,
param_map=workflow_run_config.param_map,
jobs_per_scheduling_iteration=getattr(
trans.app.config, "maximum_workflow_jobs_per_scheduling_iteration", -1
),
copy_inputs_to_history=workflow_run_config.copy_inputs_to_history,
use_cached_job=workflow_run_config.use_cached_job,
replacement_dict=workflow_run_config.replacement_dict,
)
self.progress = progress
def invoke(self) -> Dict[int, Any]:
workflow_invocation = self.workflow_invocation
config = self.trans.app.config
maximum_duration = getattr(config, "maximum_workflow_invocation_duration", -1)
if maximum_duration > 0 and workflow_invocation.seconds_since_created > maximum_duration:
log.debug(
f"Workflow invocation [{workflow_invocation.id}] exceeded maximum number of seconds allowed for scheduling [{maximum_duration}], failing."
)
workflow_invocation.set_state(model.WorkflowInvocation.states.FAILED)
# All jobs ran successfully, so we can save now
self.trans.sa_session.add(workflow_invocation)
# Not flushing in here, because web controller may create multiple
# invocations.
return self.progress.outputs
if workflow_invocation.history.deleted:
raise modules.CancelWorkflowEvaluation(
why=InvocationCancellationHistoryDeleted(
reason=CancelReason.history_deleted, history_id=workflow_invocation.history_id
)
)
remaining_steps = self.progress.remaining_steps()
delayed_steps = False
max_jobs_per_iteration_reached = False
for step, workflow_invocation_step in remaining_steps:
max_jobs_to_schedule = self.progress.maximum_jobs_to_schedule_or_none
if max_jobs_to_schedule is not None and max_jobs_to_schedule <= 0:
max_jobs_per_iteration_reached = True
break
step_delayed = False
step_timer = ExecutionTimer()
try:
self.__check_implicitly_dependent_steps(step)
if not workflow_invocation_step:
workflow_invocation_step = WorkflowInvocationStep()
assert workflow_invocation_step
workflow_invocation_step.workflow_invocation = workflow_invocation
workflow_invocation_step.workflow_step = step
workflow_invocation_step.state = "new"
workflow_invocation.steps.append(workflow_invocation_step)
assert workflow_invocation_step
incomplete_or_none = self._invoke_step(workflow_invocation_step)
if incomplete_or_none is False:
step_delayed = delayed_steps = True
workflow_invocation_step.state = "ready"
self.progress.mark_step_outputs_delayed(step, why="Not all jobs scheduled for state.")
else:
workflow_invocation_step.state = "scheduled"
except modules.DelayedWorkflowEvaluation as de:
step_delayed = delayed_steps = True
self.progress.mark_step_outputs_delayed(step, why=de.why)
except Exception as e:
log.exception(
"Failed to schedule %s, problem occurred on %s.",
self.workflow_invocation.workflow.log_str(),
step.log_str(),
)
if isinstance(e, MessageException):
# This is the highest level at which we can inject the step id
# to provide some more context to the exception.
raise modules.FailWorkflowEvaluation(
why=InvocationUnexpectedFailure(
reason=FailureReason.unexpected_failure, details=str(e), workflow_step_id=step.id
)
)
raise
if not step_delayed:
log.debug(f"Workflow step {step.id} of invocation {workflow_invocation.id} invoked {step_timer}")
if delayed_steps or max_jobs_per_iteration_reached:
state = model.WorkflowInvocation.states.READY
else:
state = model.WorkflowInvocation.states.SCHEDULED
workflow_invocation.set_state(state)
# All jobs ran successfully, so we can save now
self.trans.sa_session.add(workflow_invocation)
# Not flushing in here, because web controller may create multiple
# invocations.
return self.progress.outputs
def __check_implicitly_dependent_steps(self, step):
"""Method will delay the workflow evaluation if implicitly dependent
steps (steps dependent but not through an input->output way) are not
yet complete.
"""
for input_connection in step.input_connections:
if input_connection.non_data_connection:
output_id = input_connection.output_step.id
self.__check_implicitly_dependent_step(output_id, step.id)
def __check_implicitly_dependent_step(self, output_id: int, step_id: int):
step_invocation = self.workflow_invocation.step_invocation_for_step_id(output_id)
# No steps created yet - have to delay evaluation.
if not step_invocation:
delayed_why = f"depends on step [{output_id}] but that step has not been invoked yet"
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
if step_invocation.state != "scheduled":
delayed_why = f"depends on step [{output_id}] job has not finished scheduling yet"
raise modules.DelayedWorkflowEvaluation(delayed_why)
# TODO: Handle implicit dependency on stuff like pause steps.
for job in step_invocation.jobs:
# At least one job in incomplete.
if not job.finished:
delayed_why = (
f"depends on step [{output_id}] but one or more jobs created from that step have not finished yet"
)
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
if job.state != job.states.OK:
raise modules.FailWorkflowEvaluation(
why=InvocationFailureJobFailed(
reason=FailureReason.job_failed,
job_id=job.id,
workflow_step_id=step_id,
dependent_workflow_step_id=output_id,
)
)
def _invoke_step(self, invocation_step: WorkflowInvocationStep) -> Optional[bool]:
incomplete_or_none = invocation_step.workflow_step.module.execute(
self.trans,
self.progress,
invocation_step,
use_cached_job=self.progress.use_cached_job,
)
return incomplete_or_none
STEP_OUTPUT_DELAYED = object()
class ModuleInjector(Protocol):
trans: "WorkRequestContext"
def inject(self, step, step_args=None, steps=None, **kwargs):
pass
def inject_all(self, workflow: "Workflow", param_map=None, ignore_tool_missing_exception=True, **kwargs):
pass
def compute_runtime_state(self, step, step_args=None):
pass
class WorkflowProgress:
def __init__(
self,
workflow_invocation: WorkflowInvocation,
inputs_by_step_id: Any,
module_injector: ModuleInjector,
param_map: Dict[int, Dict[str, Any]],
jobs_per_scheduling_iteration: int = -1,
copy_inputs_to_history: bool = False,
use_cached_job: bool = False,
replacement_dict: Optional[Dict[str, str]] = None,
subworkflow_collection_info=None,
when_values=None,
) -> None:
self.outputs: Dict[int, Any] = {}
self.module_injector = module_injector
self.workflow_invocation = workflow_invocation
self.inputs_by_step_id = inputs_by_step_id
self.param_map = param_map
self.jobs_per_scheduling_iteration = jobs_per_scheduling_iteration
self.jobs_scheduled_this_iteration = 0
self.copy_inputs_to_history = copy_inputs_to_history
self.use_cached_job = use_cached_job
self.replacement_dict = replacement_dict or {}
self.runtime_replacements: Dict[str, str] = {}
self.subworkflow_collection_info = subworkflow_collection_info
self.subworkflow_structure = subworkflow_collection_info.structure if subworkflow_collection_info else None
self.when_values = when_values
@property
def maximum_jobs_to_schedule_or_none(self) -> Optional[int]:
if self.jobs_per_scheduling_iteration > 0:
return self.jobs_per_scheduling_iteration - self.jobs_scheduled_this_iteration
else:
return None
def record_executed_job_count(self, job_count: int) -> None:
self.jobs_scheduled_this_iteration += job_count
def remaining_steps(
self,
) -> List[Tuple["WorkflowStep", Optional[WorkflowInvocationStep]]]:
# Previously computed and persisted step states.
step_states = self.workflow_invocation.step_states_by_step_id()
steps = self.workflow_invocation.workflow.steps
# TODO: Wouldn't a generator be much better here so we don't have to reason about
# steps we are no where near ready to schedule?
remaining_steps = []
step_invocations_by_id = self.workflow_invocation.step_invocations_by_step_id()
self.module_injector.inject_all(self.workflow_invocation.workflow, param_map=self.param_map)
for step in steps:
step_id = step.id
step_args = self.param_map.get(step_id, {})
self.module_injector.compute_runtime_state(step, step_args=step_args)
if step_id not in step_states:
# Can this ever happen?
public_message = f"Workflow invocation has no step state for step {step.order_index + 1}"
log.error(f"{public_message}. State is known for these step ids: {list(step_states.keys())}.")
raise MessageException(public_message)
runtime_state = step_states[step_id].value
assert step.module
step.state = step.module.decode_runtime_state(step, runtime_state)
invocation_step = step_invocations_by_id.get(step_id, None)
if invocation_step and invocation_step.state == "scheduled":
self._recover_mapping(invocation_step)
else:
remaining_steps.append((step, invocation_step))
return remaining_steps
def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[str, Any]) -> Any:
replacement: Union[
modules.NoReplacement,
model.DatasetCollectionInstance,
List[model.DatasetCollectionInstance],
] = modules.NO_REPLACEMENT
prefixed_name = input_dict["name"]
multiple = input_dict["multiple"]
is_data = input_dict["input_type"] in ["dataset", "dataset_collection"]
if prefixed_name in step.input_connections_by_name:
connection = step.input_connections_by_name[prefixed_name]
if input_dict["input_type"] == "dataset" and multiple:
temp = [self.replacement_for_connection(c) for c in connection]
# If replacement is just one dataset collection, replace tool
# input_dict with dataset collection - tool framework will extract
# datasets properly.
if len(temp) == 1:
if isinstance(temp[0], model.HistoryDatasetCollectionAssociation):
replacement = temp[0]
else:
replacement = temp
else:
replacement = temp
else:
replacement = self.replacement_for_connection(connection[0], is_data=is_data)
else:
for step_input in step.inputs:
if step_input.name == prefixed_name and step_input.default_value_set:
if is_data:
replacement = raw_to_galaxy(trans, step_input.default_value)
return replacement
def replacement_for_connection(self, connection: "WorkflowStepConnection", is_data: bool = True) -> Any:
output_step_id = connection.output_step.id
output_name = connection.output_name
if output_step_id not in self.outputs:
raise modules.FailWorkflowEvaluation(
why=InvocationFailureOutputNotFound(
reason=FailureReason.output_not_found,
workflow_step_id=connection.input_step_id,
output_name=output_name,
dependent_workflow_step_id=output_step_id,
)
)
step_outputs = self.outputs[output_step_id]
if step_outputs is STEP_OUTPUT_DELAYED:
delayed_why = f"dependent step [{output_step_id}] delayed, so this step must be delayed"
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
try:
replacement = step_outputs[output_name]
except KeyError:
raise modules.FailWorkflowEvaluation(
why=InvocationFailureOutputNotFound(
reason=FailureReason.output_not_found,
workflow_step_id=connection.input_step_id,
output_name=output_name,
dependent_workflow_step_id=output_step_id,
)
)
if isinstance(replacement, model.HistoryDatasetCollectionAssociation):
if not replacement.collection.populated:
if not replacement.waiting_for_elements:
# If we are not waiting for elements, there was some
# problem creating the collection. Collection will never
# be populated.
raise modules.FailWorkflowEvaluation(
why=InvocationFailureCollectionFailed(
reason=FailureReason.collection_failed,
hdca_id=replacement.id,
workflow_step_id=connection.input_step_id,
dependent_workflow_step_id=output_step_id,
)
)
delayed_why = f"dependent collection [{replacement.id}] not yet populated with datasets"
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
if isinstance(replacement, model.DatasetCollection):
raise NotImplementedError
if not is_data and isinstance(
replacement, (model.HistoryDatasetAssociation, model.HistoryDatasetCollectionAssociation)
):
if isinstance(replacement, model.HistoryDatasetAssociation):
if replacement.is_pending:
raise modules.DelayedWorkflowEvaluation()
if not replacement.is_ok:
raise modules.FailWorkflowEvaluation(
why=InvocationFailureDatasetFailed(
reason=FailureReason.dataset_failed,
hda_id=replacement.id,
workflow_step_id=connection.input_step_id,
dependent_workflow_step_id=output_step_id,
)
)
else:
if not replacement.collection.populated:
raise modules.DelayedWorkflowEvaluation()
pending = False
for dataset_instance in replacement.dataset_instances:
if dataset_instance.is_pending:
pending = True
elif not dataset_instance.is_ok:
raise modules.FailWorkflowEvaluation(
why=InvocationFailureDatasetFailed(
reason=FailureReason.dataset_failed,
hda_id=replacement.id,
workflow_step_id=connection.input_step_id,
dependent_workflow_step_id=output_step_id,
)
)
if pending:
raise modules.DelayedWorkflowEvaluation()
return replacement
def get_replacement_workflow_output(self, workflow_output: "WorkflowOutput") -> Any:
step = workflow_output.workflow_step
output_name = workflow_output.output_name
step_outputs = self.outputs[step.id]
if step_outputs is STEP_OUTPUT_DELAYED:
delayed_why = f"depends on workflow output [{output_name}] but that output has not been created yet"
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
else:
return step_outputs[output_name]
def set_outputs_for_input(
self, invocation_step: WorkflowInvocationStep, outputs: Any = None, already_persisted: bool = False
) -> None:
step = invocation_step.workflow_step
if outputs is None:
outputs = {}
if self.inputs_by_step_id:
step_id = step.id
if step_id not in self.inputs_by_step_id and "output" not in outputs:
default_value = step.input_default_value
if default_value or step.input_optional:
outputs["output"] = default_value
else:
log.error(f"{step.log_str()} not found in inputs_step_id {self.inputs_by_step_id}")
raise modules.FailWorkflowEvaluation(
why=InvocationFailureOutputNotFound(
reason=FailureReason.output_not_found,
workflow_step_id=invocation_step.workflow_step_id,
output_name="output",
dependent_workflow_step_id=invocation_step.workflow_step_id,
)
)
elif step_id in self.inputs_by_step_id:
outputs["output"] = self.inputs_by_step_id[step_id]
if step.label and step.type == "parameter_input" and "output" in outputs:
self.runtime_replacements[step.label] = str(outputs["output"])
self.set_step_outputs(invocation_step, outputs, already_persisted=already_persisted)
def effective_replacement_dict(self):
replacement_dict = {}
for key, value in self.replacement_dict.items():
replacement_dict[key] = value
for key, value in self.runtime_replacements.items():
if key not in replacement_dict:
replacement_dict[key] = value
return replacement_dict
def set_step_outputs(
self, invocation_step: WorkflowInvocationStep, outputs: Dict[str, Any], already_persisted: bool = False
) -> None:
step = invocation_step.workflow_step
if invocation_step.output_value:
outputs[invocation_step.output_value.workflow_output.output_name] = invocation_step.output_value.value
self.outputs[step.id] = outputs
if not already_persisted:
workflow_outputs_by_name = {wo.output_name: wo for wo in step.workflow_outputs}
for output_name, output_object in outputs.items():
if hasattr(output_object, "history_content_type"):
invocation_step.add_output(output_name, output_object)
else:
# Add this non-data, non workflow-output output to the workflow outputs.
# This is required for recovering the output in the next scheduling iteration,
# and should be replaced with a WorkflowInvocationStepOutputValue ASAP.
if not workflow_outputs_by_name.get(output_name) and not output_object == modules.NO_REPLACEMENT:
workflow_output = model.WorkflowOutput(step, output_name=output_name)
step.workflow_outputs.append(workflow_output)
for workflow_output in step.workflow_outputs:
output_name = workflow_output.output_name
if output_name not in outputs:
invocation_step.workflow_invocation.add_message(
InvocationWarningWorkflowOutputNotFound(
reason=WarningReason.workflow_output_not_found,
workflow_step_id=step.id,
output_name=output_name,
)
)
message = f"Failed to find expected workflow output [{output_name}] in step outputs [{outputs}]"
log.debug(message)
continue
output = outputs[output_name]
self._record_workflow_output(
step,
workflow_output,
output=output,
)
def _record_workflow_output(self, step: "WorkflowStep", workflow_output: "WorkflowOutput", output: Any) -> None:
self.workflow_invocation.add_output(workflow_output, step, output)
def mark_step_outputs_delayed(self, step: "WorkflowStep", why: Optional[str] = None) -> None:
if why:
message = f"Marking step {step.id} outputs of invocation {self.workflow_invocation.id} delayed ({why})"
log.debug(message)
self.outputs[step.id] = STEP_OUTPUT_DELAYED
def _subworkflow_invocation(self, step: "WorkflowStep") -> WorkflowInvocation:
workflow_invocation = self.workflow_invocation
subworkflow_invocation = workflow_invocation.get_subworkflow_invocation_for_step(step)
if subworkflow_invocation is None:
raise MessageException(f"Failed to find persisted subworkflow invocation for step [{step.order_index + 1}]")
return subworkflow_invocation
def subworkflow_invoker(
self,
trans: "WorkRequestContext",
step: "WorkflowStep",
use_cached_job: bool = False,
subworkflow_collection_info=None,
when_values=None,
) -> WorkflowInvoker:
subworkflow_invocation = self._subworkflow_invocation(step)
subworkflow_invocation.handler = self.workflow_invocation.handler
subworkflow_invocation.scheduler = self.workflow_invocation.scheduler
workflow_run_config = workflow_request_to_run_config(subworkflow_invocation, use_cached_job)
subworkflow_progress = self.subworkflow_progress(
subworkflow_invocation,
step,
workflow_run_config.param_map,
subworkflow_collection_info=subworkflow_collection_info,
when_values=when_values,
)
subworkflow_invocation = subworkflow_progress.workflow_invocation
return WorkflowInvoker(
trans,
workflow=subworkflow_invocation.workflow,
workflow_run_config=workflow_run_config,
progress=subworkflow_progress,
)
def subworkflow_progress(
self,
subworkflow_invocation: WorkflowInvocation,
step: "WorkflowStep",
param_map: Dict,
subworkflow_collection_info=None,
when_values=None,
) -> "WorkflowProgress":
subworkflow = subworkflow_invocation.workflow
subworkflow_inputs = {}
for input_subworkflow_step in subworkflow.input_steps:
connection_found = False
subworkflow_step_id = input_subworkflow_step.id
for input_connection in step.input_connections:
if input_connection.input_subworkflow_step_id == subworkflow_step_id:
is_data = input_connection.output_step.type != "parameter_input"
replacement = self.replacement_for_connection(
input_connection,
is_data=is_data,
)
subworkflow_inputs[subworkflow_step_id] = replacement
connection_found = True
break
if not connection_found and not input_subworkflow_step.input_optional:
raise modules.FailWorkflowEvaluation(
InvocationFailureOutputNotFound(
reason=FailureReason.output_not_found,
workflow_step_id=step.id,
output_name=input_connection.output_name,
dependent_workflow_step_id=input_connection.output_step.id,
)
)
return WorkflowProgress(
subworkflow_invocation,
subworkflow_inputs,
self.module_injector,
param_map=param_map,
use_cached_job=self.use_cached_job,
replacement_dict=self.replacement_dict,
subworkflow_collection_info=subworkflow_collection_info,
when_values=when_values,
)
def raw_to_galaxy(self, value: dict):
return raw_to_galaxy(self.module_injector.trans, value)
def _recover_mapping(self, step_invocation: WorkflowInvocationStep) -> None:
try:
step_invocation.workflow_step.module.recover_mapping(step_invocation, self)
except modules.DelayedWorkflowEvaluation as de:
self.mark_step_outputs_delayed(step_invocation.workflow_step, de.why)
__all__ = ("queue_invoke", "WorkflowRunConfig")