# Copyright (C) 2015-2021 Regents of the University of California
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import os
from configargparse import ArgumentParser
from toil.common import Toil
from toil.job import Job, JobDescription, TemporaryID
from toil.resource import ModuleDescriptor
from toil.test import ToilTest
[docs]
class JobDescriptionTest(ToilTest):
[docs]
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__() )
[docs]
def tearDown(self):
self.toil.__exit__(None, None, None)
self.toil._jobStore.destroy()
self.assertFalse(os.path.exists(self.jobStorePath))
super().tearDown()
[docs]
def testJobDescription(self):
"""
Tests the public interface of a JobDescription.
"""
memory = 2^32
disk = 2^32
cores = "1"
preemptible = 1
j = JobDescription(requirements={"memory": memory, "cores": cores, "disk": disk, "preemptible": preemptible},
jobName='testJobGraph', unitName='noName')
# Without a body, and with nothing to run, nextSuccessors will be None
self.assertEqual(j.has_body(), False)
self.assertEqual(j.nextSuccessors(), None)
# Attach a body so the job has something to do itself.
j.attach_body("fake", ModuleDescriptor.forModule("toil"))
self.assertEqual(j.has_body(), True)
#Check attributes
self.assertEqual(j.memory, memory)
self.assertEqual(j.disk, disk)
self.assertEqual(j.cores, int(cores))
self.assertEqual(j.preemptible, bool(preemptible))
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(j.predecessorsFinished, set())
self.assertEqual(j.logJobStoreFileID, None)
#Check equals function (should be based on object identity and not contents)
j2 = JobDescription(requirements={"memory": memory, "cores": cores, "disk": disk, "preemptible": preemptible},
jobName='testJobGraph', unitName='noName')
j2.attach_body("fake", ModuleDescriptor.forModule("toil"))
self.assertNotEqual(j, j2)
###TODO test other functionality
[docs]
def testJobDescriptionSequencing(self):
j = JobDescription(requirements={}, jobName='unimportant')
j.addChild('child')
j.addFollowOn('followOn')
# With a body, nothing should be ready to run
j.attach_body("fake", ModuleDescriptor.forModule("toil"))
self.assertEqual(list(j.nextSuccessors()), [])
# With body cleared, child should be ready to run
j.detach_body()
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)
