Source code for toil.test.src.retainTempDirTest

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import os
import shutil

from toil.exceptions import FailedJobsException
from toil.job import Job
from toil.test import ToilTest


[docs] class CleanWorkDirTest(ToilTest): """ Tests testing :class:toil.fileStores.abstractFileStore.AbstractFileStore """
[docs] def setUp(self): super().setUp() self.testDir = self._createTempDir()
[docs] def tearDown(self): super().tearDown() shutil.rmtree(self.testDir)
[docs] def testNever(self): retainedTempData = self._runAndReturnWorkDir("never", job=tempFileTestJob) self.assertNotEqual( retainedTempData, [], "The worker's temporary workspace was deleted despite " "cleanWorkDir being set to 'never'", )
[docs] def testAlways(self): retainedTempData = self._runAndReturnWorkDir("always", job=tempFileTestJob) self.assertEqual( retainedTempData, [], "The worker's temporary workspace was not deleted despite " "cleanWorkDir being set to 'always'", )
[docs] def testOnErrorWithError(self): retainedTempData = self._runAndReturnWorkDir( "onError", job=tempFileTestErrorJob, expectError=True ) self.assertEqual( retainedTempData, [], "The worker's temporary workspace was not deleted despite " "an error occurring and cleanWorkDir being set to 'onError'", )
[docs] def testOnErrorWithNoError(self): retainedTempData = self._runAndReturnWorkDir("onError", job=tempFileTestJob) self.assertNotEqual( retainedTempData, [], "The worker's temporary workspace was deleted despite " "no error occurring and cleanWorkDir being set to 'onError'", )
[docs] def testOnSuccessWithError(self): retainedTempData = self._runAndReturnWorkDir( "onSuccess", job=tempFileTestErrorJob, expectError=True ) self.assertNotEqual( retainedTempData, [], "The worker's temporary workspace was deleted despite " "an error occurring and cleanWorkDir being set to 'onSuccesss'", )
[docs] def testOnSuccessWithSuccess(self): retainedTempData = self._runAndReturnWorkDir("onSuccess", job=tempFileTestJob) self.assertEqual( retainedTempData, [], "The worker's temporary workspace was not deleted despite " "a successful job execution and cleanWorkDir being set to 'onSuccesss'", )
def _runAndReturnWorkDir(self, cleanWorkDir, job, expectError=False): """ Runs toil with the specified job and cleanWorkDir setting. expectError determines whether the test's toil run is expected to succeed, and the test will fail if that expectation is not met. returns the contents of the workDir after completion of the run """ options = Job.Runner.getDefaultOptions(self._getTestJobStorePath()) options.workDir = self.testDir options.clean = "always" options.cleanWorkDir = cleanWorkDir A = Job.wrapJobFn(job) if expectError: self._launchError(A, options) else: self._launchRegular(A, options) return os.listdir(self.testDir) def _launchRegular(self, A, options): Job.Runner.startToil(A, options) def _launchError(self, A, options): try: Job.Runner.startToil(A, options) except FailedJobsException: pass # we expect a job to fail here else: self.fail("Toil run succeeded unexpectedly")
[docs] def tempFileTestJob(job): with open(job.fileStore.getLocalTempFile(), "w") as f: f.write("test file retention")
[docs] def tempFileTestErrorJob(job): with open(job.fileStore.getLocalTempFile(), "w") as f: f.write("test file retention") raise RuntimeError() # test failure