class JobGraphTest(ToilTest):
def setUp(self):
super(JobGraphTest, self).setUp()
self.jobStorePath = self._getTestJobStorePath()
parser = ArgumentParser()
Job.Runner.addToilOptions(parser)
options = parser.parse_args(args=[self.jobStorePath])
self.toil = Toil(options)
self.assertEquals( self.toil, self.toil.__enter__() )
def tearDown(self):
self.toil.__exit__(None, None, None)
self.toil._jobStore.destroy()
self.assertFalse(os.path.exists(self.jobStorePath))
super(JobGraphTest, self).tearDown()
def testJob(self):
"""
Tests functions of a job.
"""
command = "by your command"
memory = 2^32
disk = 2^32
cores = 1
preemptable = 1
jobStoreID = 100
remainingRetryCount = 5
predecessorNumber = 0
j = JobGraph(command=command, memory=memory, cores=cores, disk=disk, preemptable=preemptable,
jobStoreID=jobStoreID, remainingRetryCount=remainingRetryCount,
predecessorNumber=predecessorNumber, jobName='testJobGraph', unitName='noName')
#Check attributes
#
self.assertEquals(j.command, command)
self.assertEquals(j.memory, memory)
self.assertEquals(j.disk, disk)
self.assertEquals(j.cores, cores)
self.assertEquals(j.preemptable, preemptable)
self.assertEquals(j.jobStoreID, jobStoreID)
self.assertEquals(j.remainingRetryCount, remainingRetryCount)
self.assertEquals(j.predecessorNumber, predecessorNumber)
self.assertEquals(j.stack, [])
self.assertEquals(j.predecessorsFinished, set())
self.assertEquals(j.logJobStoreFileID, None)
#Check equals function
j2 = JobGraph(command=command, memory=memory, cores=cores, disk=disk,
preemptable=preemptable,
jobStoreID=jobStoreID, remainingRetryCount=remainingRetryCount,
predecessorNumber=predecessorNumber, jobName='testJobGraph', unitName='noName')
self.assertEquals(j, j2)
#Change an attribute and check not equal
j.predecessorsFinished = {"1", "2"}
self.assertNotEquals(j, j2)
class JobWrapperTest(ToilTest):
def setUp(self):
super(JobWrapperTest, self).setUp()
self.jobStorePath = self._getTestJobStorePath()
parser = ArgumentParser()
Job.Runner.addToilOptions(parser)
options = parser.parse_args(args=[self.jobStorePath])
self.toil = Toil(options)
self.assertEquals( self.toil, self.toil.__enter__() )
def tearDown(self):
self.toil.__exit__(None, None, None)
self.toil._jobStore.deleteJobStore()
self.assertFalse(os.path.exists(self.jobStorePath))
super(JobWrapperTest, self).tearDown()
def testJob(self):
"""
Tests functions of a job.
"""
command = "by your command"
memory = 2^32
disk = 2^32
cores = 1
preemptable = 1
jobStoreID = 100
remainingRetryCount = 5
predecessorNumber = 0
j = JobWrapper(command, memory, cores, disk, preemptable, jobStoreID,
remainingRetryCount, predecessorNumber)
#Check attributes
#
self.assertEquals(j.command, command)
self.assertEquals(j.memory, memory)
self.assertEquals(j.disk, disk)
self.assertEquals(j.cores, cores)
self.assertEquals(j.preemptable, preemptable)
self.assertEquals(j.jobStoreID, jobStoreID)
self.assertEquals(j.remainingRetryCount, remainingRetryCount)
self.assertEquals(j.predecessorNumber, predecessorNumber)
self.assertEquals(j.stack, [])
self.assertEquals(j.predecessorsFinished, set())
self.assertEquals(j.logJobStoreFileID, None)
#Check equals function
j2 = JobWrapper(command, memory, cores, disk, preemptable, jobStoreID,
remainingRetryCount, predecessorNumber)
self.assertEquals(j, j2)
#Change an attribute and check not equal
j.predecessorsFinished = {"1", "2"}
self.assertNotEquals(j, j2)
class JobDescriptionTest(ToilTest):
def setUp(self):
super().setUp()
self.jobStorePath = self._getTestJobStorePath()
parser = ArgumentParser()
Job.Runner.addToilOptions(parser)
options = parser.parse_args(args=[self.jobStorePath])
self.toil = Toil(options)
self.assertEqual( self.toil, self.toil.__enter__() )
def tearDown(self):
self.toil.__exit__(None, None, None)
self.toil._jobStore.destroy()
self.assertFalse(os.path.exists(self.jobStorePath))
super().tearDown()
@travis_test
def testJobDescription(self):
"""
Tests the public interface of a JobDescription.
"""
command = "by your command"
memory = 2^32
disk = 2^32
cores = "1"
preemptable = 1
j = JobDescription(command=command, requirements={"memory": memory, "cores": cores, "disk": disk, "preemptable": preemptable},
jobName='testJobGraph', unitName='noName')
#Check attributes
self.assertEqual(j.command, command)
self.assertEqual(j.memory, memory)
self.assertEqual(j.disk, disk)
self.assertEqual(j.cores, int(cores))
self.assertEqual(j.preemptable, bool(preemptable))
self.assertEqual(type(j.jobStoreID), TemporaryID)
self.assertEqual(list(j.successorsAndServiceHosts()), [])
self.assertEqual(list(j.allSuccessors()), [])
self.assertEqual(list(j.serviceHostIDsInBatches()), [])
self.assertEqual(list(j.services), [])
self.assertEqual(list(j.nextSuccessors()), [])
self.assertEqual(sum((len(level) for level in j.stack)), 0)
self.assertEqual(j.predecessorsFinished, set())
self.assertEqual(j.logJobStoreFileID, None)
#Check equals function (should be based on object identity and not contents)
j2 = JobDescription(command=command, requirements={"memory": memory, "cores": cores, "disk": disk, "preemptable": preemptable},
jobName='testJobGraph', unitName='noName')
self.assertNotEqual(j, j2)
###TODO test other functionality
@travis_test
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)
