def replacement_for_connection(self, connection, is_data=True):
output_step_id = connection.output_step.id
if output_step_id not in self.outputs:
template = "No outputs found for step id %s, outputs are %s"
message = template % (output_step_id, self.outputs)
raise Exception(message)
step_outputs = self.outputs[output_step_id]
if step_outputs is STEP_OUTPUT_DELAYED:
delayed_why = "dependent step [%s] delayed, so this step must be delayed" % output_step_id
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
output_name = connection.output_name
try:
replacement = step_outputs[output_name]
except KeyError:
replacement = self.inputs_by_step_id.get(output_step_id)
if connection.output_step.type == 'parameter_input' and output_step_id is not None:
# FIXME: parameter_input step outputs should be properly recorded as step outputs, but for now we can
# short-circuit and just pick the input value
pass
else:
# Must resolve.
template = "Workflow evaluation problem - failed to find output_name %s in step_outputs %s"
message = template % (output_name, step_outputs)
raise Exception(message)
if isinstance(replacement, model.HistoryDatasetCollectionAssociation):
if not replacement.collection.populated:
if not replacement.collection.waiting_for_elements:
# If we are not waiting for elements, there was some
# problem creating the collection. Collection will never
# be populated.
# TODO: consider distinguish between cancelled and failed?
raise modules.CancelWorkflowEvaluation()
delayed_why = "dependent collection [%s] not yet populated with datasets" % replacement.id
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
data_inputs = (model.HistoryDatasetAssociation,
model.HistoryDatasetCollectionAssociation,
model.DatasetCollection)
if not is_data and isinstance(replacement, data_inputs):
if isinstance(replacement, model.HistoryDatasetAssociation):
if replacement.is_pending:
raise modules.DelayedWorkflowEvaluation()
if not replacement.is_ok:
raise modules.CancelWorkflowEvaluation()
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.CancelWorkflowEvaluation()
if pending:
raise modules.DelayedWorkflowEvaluation()
return replacement
def replacement_for_connection(self, connection, is_data=True):
output_step_id = connection.output_step.id
if output_step_id not in self.outputs:
message = f"No outputs found for step id {output_step_id}, outputs are {self.outputs}"
raise Exception(message)
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)
output_name = connection.output_name
try:
replacement = step_outputs[output_name]
except KeyError:
# Must resolve.
template = "Workflow evaluation problem - failed to find output_name %s in step_outputs %s"
message = template % (output_name, step_outputs)
raise Exception(message)
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.
# TODO: consider distinguish between cancelled and failed?
raise modules.CancelWorkflowEvaluation()
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.CancelWorkflowEvaluation()
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.CancelWorkflowEvaluation()
if pending:
raise modules.DelayedWorkflowEvaluation()
return replacement
def __check_implicitly_dependent_step(self, output_id):
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 = "depends on step [%s] but that step has not been invoked yet" % output_id
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
if step_invocation.state != 'scheduled':
delayed_why = "depends on step [%s] job has not finished scheduling yet" % output_id
raise modules.DelayedWorkflowEvaluation(delayed_why)
for job_assoc in step_invocation.jobs:
job = job_assoc.job
if job:
# At least one job in incomplete.
if not job.finished:
delayed_why = "depends on step [%s] but one or more jobs created from that step have not finished yet" % output_id
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
if job.state != job.states.OK:
raise modules.CancelWorkflowEvaluation()
else:
# TODO: Handle implicit dependency on stuff like
# pause steps.
pass
def replacement_for_connection(self, connection, is_data=True):
output_step_id = connection.output_step.id
if output_step_id not in self.outputs:
template = "No outputs found for step id %s, outputs are %s"
message = template % (output_step_id, self.outputs)
raise Exception(message)
step_outputs = self.outputs[output_step_id]
if step_outputs is STEP_OUTPUT_DELAYED:
delayed_why = "dependent step [%s] delayed, so this step must be delayed" % output_step_id
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
output_name = connection.output_name
try:
replacement = step_outputs[output_name]
except KeyError:
if is_data:
# Must resolve.
template = "Workflow evaluation problem - failed to find output_name %s in step_outputs %s"
message = template % (output_name, step_outputs)
raise Exception(message)
else:
replacement = modules.NO_REPLACEMENT
if isinstance(replacement, model.HistoryDatasetCollectionAssociation):
if not replacement.collection.populated:
if not replacement.collection.waiting_for_elements:
# If we are not waiting for elements, there was some
# problem creating the collection. Collection will never
# be populated.
# TODO: consider distinguish between cancelled and failed?
raise modules.CancelWorkflowEvaluation()
delayed_why = "dependent collection [%s] not yet populated with datasets" % replacement.id
raise modules.DelayedWorkflowEvaluation(why=delayed_why)
return replacement
def replacement_for_connection(self, connection):
step_outputs = self.outputs[connection.output_step.id]
if step_outputs is STEP_OUTPUT_DELAYED:
raise modules.DelayedWorkflowEvaluation()
replacement = step_outputs[connection.output_name]
if isinstance(replacement, model.HistoryDatasetCollectionAssociation):
if not replacement.collection.populated:
if not replacement.collection.waiting_for_elements:
# If we are not waiting for elements, there was some
# problem creating the collection. Collection will never
# be populated.
# TODO: consider distinguish between cancelled and failed?
raise modules.CancelWorkflowEvaluation()
raise modules.DelayedWorkflowEvaluation()
return replacement
def replacement_for_connection(self, connection, is_data=True):
output_step_id = connection.output_step.id
if output_step_id not in self.outputs:
template = "No outputs found for step id %s, outputs are %s"
message = template % (output_step_id, self.outputs)
raise Exception(message)
step_outputs = self.outputs[output_step_id]
if step_outputs is STEP_OUTPUT_DELAYED:
raise modules.DelayedWorkflowEvaluation()
output_name = connection.output_name
for key in step_outputs:
print "Output name: " + str(output_name)
#print "Output name, output1, result of object at ouput name: " + str(step_outputs["output1"])
#print "Result of object at output name: " + str(step_outputs[output_name])
#print "Object stuff: " + str(dir(step_outputs[key]))
print "Type of object: " + str(type(step_outputs))
try:
replacement = step_outputs[output_name]
except KeyError:
if is_data:
# Must resolve.
print "From run.py: " + str(step_outputs.viewvalues)
for key in step_outputs:
print "Key: " + key + " Value: " + str(step_outputs[key])
print "Object stuff: " + str(dir(step_outputs[key]))
template = "Workflow evaluation problem - failed to find output_name %s in step_outputs %s"
message = template % (output_name, step_outputs)
raise Exception(message)
else:
replacement = modules.NO_REPLACEMENT
if isinstance(replacement, model.HistoryDatasetCollectionAssociation):
if not replacement.collection.populated:
if not replacement.collection.waiting_for_elements:
# If we are not waiting for elements, there was some
# problem creating the collection. Collection will never
# be populated.
# TODO: consider distinguish between cancelled and failed?
raise modules.CancelWorkflowEvaluation()
raise modules.DelayedWorkflowEvaluation()
return replacement
def __check_implicitly_dependent_step( self, output_id ):
step_invocations = self.workflow_invocation.step_invocations_for_step_id( output_id )
# No steps created yet - have to delay evaluation.
if not step_invocations:
raise modules.DelayedWorkflowEvaluation()
for step_invocation in step_invocations:
job = step_invocation.job
if job:
# At least one job in incomplete.
if not job.finished:
raise modules.DelayedWorkflowEvaluation()
if job.state != job.states.OK:
raise modules.CancelWorkflowEvaluation()
else:
# TODO: Handle implicit dependency on stuff like
# pause steps.
pass
def replacement_for_connection( self, connection ):
step_outputs = self.outputs[ connection.output_step.id ]
if step_outputs is STEP_OUTPUT_DELAYED:
raise modules.DelayedWorkflowEvaluation()
output_name = connection.output_name
try:
replacement = step_outputs[ output_name ]
except KeyError:
template = "Workflow evaluation problem - failed to find output_name %s in step_outputs %s"
message = template % ( output_name, step_outputs )
raise Exception( message )
if isinstance( replacement, model.HistoryDatasetCollectionAssociation ):
if not replacement.collection.populated:
if not replacement.collection.waiting_for_elements:
# If we are not waiting for elements, there was some
# problem creating the collection. Collection will never
# be populated.
# TODO: consider distinguish between cancelled and failed?
raise modules.CancelWorkflowEvaluation()
raise modules.DelayedWorkflowEvaluation()
return replacement
def invoke(self):
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(
"Workflow invocation [%s] exceeded maximum number of seconds allowed for scheduling [%s], failing."
% (workflow_invocation.id, maximum_duration))
workflow_invocation.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:
log.info("Cancelled workflow evaluation due to deleted history")
raise modules.CancelWorkflowEvaluation()
remaining_steps = self.progress.remaining_steps()
delayed_steps = False
for (step, workflow_invocation_step) in remaining_steps:
step_delayed = False
step_timer = ExecutionTimer()
try:
self.__check_implicitly_dependent_steps(step)
if not workflow_invocation_step:
workflow_invocation_step = model.WorkflowInvocationStep()
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)
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:
log.exception(
"Failed to schedule %s, problem occurred on %s.",
self.workflow_invocation.workflow.log_str(),
step.log_str(),
)
raise
if not step_delayed:
log.debug("Workflow step %s of invocation %s invoked %s" %
(step.id, workflow_invocation.id, step_timer))
if delayed_steps:
state = model.WorkflowInvocation.states.READY
else:
state = model.WorkflowInvocation.states.SCHEDULED
workflow_invocation.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 invoke(self):
workflow_invocation = self.workflow_invocation
maximum_duration = getattr(self.trans.app.config,
"maximum_workflow_invocation_duration", -1)
if maximum_duration > 0 and workflow_invocation.seconds_since_created > maximum_duration:
log.debug(
"Workflow invocation [%s] exceeded maximum number of seconds allowed for scheduling [%s], failing."
% (workflow_invocation.id, maximum_duration))
workflow_invocation.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:
log.info("Cancelled workflow evaluation due to deleted history")
raise modules.CancelWorkflowEvaluation()
remaining_steps = self.progress.remaining_steps()
delayed_steps = False
for step in remaining_steps:
step_delayed = False
step_timer = ExecutionTimer()
jobs = None
try:
self.__check_implicitly_dependent_steps(step)
# TODO: step may fail to invoke, do something about that.
jobs = self._invoke_step(step)
for job in (util.listify(jobs) or [None]):
# Record invocation
workflow_invocation_step = model.WorkflowInvocationStep()
workflow_invocation_step.workflow_invocation = workflow_invocation
workflow_invocation_step.workflow_step = step
# Job may not be generated in this thread if bursting is enabled
# https://github.com/galaxyproject/galaxy/issues/2259
if job:
workflow_invocation_step.job_id = job.id
except modules.DelayedWorkflowEvaluation as de:
step_delayed = delayed_steps = True
self.progress.mark_step_outputs_delayed(step, why=de.why)
except Exception:
log.exception(
"Failed to schedule %s, problem occurred on %s.",
self.workflow_invocation.workflow.log_str(),
step.log_str(),
)
raise
if not step_delayed:
log.debug("Workflow step %s of invocation %s invoked %s" %
(step.id, workflow_invocation.id, step_timer))
if delayed_steps:
state = model.WorkflowInvocation.states.READY
else:
state = model.WorkflowInvocation.states.SCHEDULED
workflow_invocation.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