def _mockJobDescription(self, jobStoreID=None, command=None, **kwargs):
"""
Create a mock-up JobDescription with the given ID, command, and other parameters.
"""
# TODO: Use a real unittest.Mock? For now we make a real instance and just hack it up.
desc = JobDescription(**kwargs)
# Normally we can't pass in a command or ID, and the job
# serialization logic takes care of filling them in. We set them
# here.
if command is not None:
desc.command = command
if jobStoreID is not None:
desc.jobStoreID = jobStoreID
return desc
def testJobDescriptionSequencing(self):
j = JobDescription(command='command', requirements={}, jobName='unimportant')
j.addChild('child')
j.addFollowOn('followOn')
# With a command, nothing should be ready to run
self.assertEqual(list(j.nextSuccessors()), [])
# With command cleared, child should be ready to run
j.command = None
self.assertEqual(list(j.nextSuccessors()), ['child'])
# Without the child, the follow-on should be ready to run
j.filterSuccessors(lambda jID: jID != 'child')
self.assertEqual(list(j.nextSuccessors()), ['followOn'])
# Without the follow-on, we should return None, to be distinct from an
# empty list. Nothing left to do!
j.filterSuccessors(lambda jID: jID != 'followOn')
self.assertEqual(j.nextSuccessors(), None)
def _buildToilState(self, jobDesc: JobDescription) -> None:
"""
Traverses tree of jobs down from the subtree root JobDescription
(jobDesc), building the ToilState class.
:param jobDesc: The description for the root job of the workflow being run.
"""
# If the job description has a command, is a checkpoint, has services
# or is ready to be deleted it is ready to be processed (i.e. it is updated)
if (jobDesc.command is not None
or (isinstance(jobDesc, CheckpointJobDescription)
and jobDesc.checkpoint is not None)
or len(jobDesc.services) > 0
or jobDesc.nextSuccessors() is None):
logger.debug(
"Found job to run: %s, with command: %s, with checkpoint: %s, with "
"services: %s, with no next successors: %s",
jobDesc.jobStoreID,
jobDesc.command is not None,
isinstance(jobDesc, CheckpointJobDescription)
and jobDesc.checkpoint is not None,
len(jobDesc.services) > 0,
jobDesc.nextSuccessors() is None,
)
# Set the job updated because we should be able to make progress on it.
self.bus.put(JobUpdatedMessage(str(jobDesc.jobStoreID), 0))
if isinstance(jobDesc, CheckpointJobDescription
) and jobDesc.checkpoint is not None:
jobDesc.command = jobDesc.checkpoint
else: # There exist successors
logger.debug(
"Adding job: %s to the state with %s successors",
jobDesc.jobStoreID,
len(jobDesc.nextSuccessors()),
)
# Record the number of successors
self.successorCounts[str(jobDesc.jobStoreID)] = len(
jobDesc.nextSuccessors())
def processSuccessorWithMultiplePredecessors(
successor: JobDescription) -> None:
# If jobDesc is not reported as complete by the successor
if jobDesc.jobStoreID not in successor.predecessorsFinished:
# Update the successor's status to mark the predecessor complete
successor.predecessorsFinished.add(jobDesc.jobStoreID)
# If the successor has no predecessors to finish
assert len(successor.predecessorsFinished
) <= successor.predecessorNumber
if len(successor.predecessorsFinished
) == successor.predecessorNumber:
# It is ready to be run, so remove it from the set of waiting jobs
self.jobsToBeScheduledWithMultiplePredecessors.remove(
successorJobStoreID)
# Recursively consider the successor
self._buildToilState(successor)
# For each successor
for successorJobStoreID in jobDesc.nextSuccessors():
# If the successor does not yet point back at a
# predecessor we have not yet considered it
if successorJobStoreID not in self.successor_to_predecessors:
# Add the job as a predecessor
self.successor_to_predecessors[successorJobStoreID] = {
str(jobDesc.jobStoreID)
}
# We load the successor job
successor = self.get_job(successorJobStoreID)
# If predecessor number > 1 then the successor has multiple predecessors
if successor.predecessorNumber > 1:
# We put the successor job in the set of waiting successor
# jobs with multiple predecessors
assert successorJobStoreID not in self.jobsToBeScheduledWithMultiplePredecessors
self.jobsToBeScheduledWithMultiplePredecessors.add(
successorJobStoreID)
# Process successor
processSuccessorWithMultiplePredecessors(successor)
else:
# The successor has only this job as a predecessor so
# recursively consider the successor
self._buildToilState(successor)
else:
# We've already seen the successor
# Add the job as a predecessor
assert (jobDesc.jobStoreID not in self.
successor_to_predecessors[successorJobStoreID])
self.successor_to_predecessors[successorJobStoreID].add(
str(jobDesc.jobStoreID))
# If the successor has multiple predecessors
if successorJobStoreID in self.jobsToBeScheduledWithMultiplePredecessors:
# Get the successor from cache
successor = self.get_job(successorJobStoreID)
# Process successor
processSuccessorWithMultiplePredecessors(successor)