toil.test.utils.utilsTest

Module Contents

Classes

UtilsTest	Tests the utilities that toil ships with, e.g. stats and status, in conjunction with restart
RunTwoJobsPerWorker	Runs child job with same resources as self in an attempt to chain the jobs on the same worker

Functions

printUnicodeCharacter()

Attributes

pkg_root
logger

toil.test.utils.utilsTest.pkg_root

toil.test.utils.utilsTest.logger

class toil.test.utils.utilsTest.UtilsTest(methodName='runTest')

Bases: toil.test.ToilTest

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Tests the utilities that toil ships with, e.g. stats and status, in conjunction with restart functionality.

property toilMain

property cleanCommand

property statsCommand

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

statusCommand(failIfNotComplete=False)

test_config_functionality()

Ensure that creating and reading back the config file works

testAWSProvisionerUtils()

Runs a number of the cluster utilities in sequence.

Launches a cluster with custom tags. Verifies the tags exist. ssh’s into the cluster. Does some weird string comparisons. Makes certain that TOIL_WORKDIR is set as expected in the ssh’ed cluster. Rsyncs a file and verifies it exists on the leader. Destroys the cluster.

Returns:

testUtilsSort()

Tests the status and stats commands of the toil command line utility using the sort example with the –restart flag.

testUtilsStatsSort()

Tests the stats commands on a complete run of the stats test.

testUnicodeSupport()

testMultipleJobsPerWorkerStats()

Tests case where multiple jobs are run on 1 worker to ensure that all jobs report back their data

check_status(status, status_fn, seconds=20)

testGetPIDStatus()

Test that ToilStatus.getPIDStatus() behaves as expected.

testGetStatusFailedToilWF()

Test that ToilStatus.getStatus() behaves as expected with a failing Toil workflow. While this workflow could be called by importing and evoking its main function, doing so would remove the opportunity to test the ‘RUNNING’ functionality of getStatus().

testGetStatusFailedCWLWF()

Test that ToilStatus.getStatus() behaves as expected with a failing CWL workflow.

testGetStatusSuccessfulCWLWF()

Test that ToilStatus.getStatus() behaves as expected with a successful CWL workflow.

testPrintJobLog(mock_print)

Test that ToilStatus.printJobLog() reads the log from a failed command without error.

testRestartAttribute()

Test that the job store is only destroyed when we observe a succcessful workflow run. The following simulates a failing workflow that attempts to resume without restart(). In this case, the job store should not be destroyed until restart() is called.

toil.test.utils.utilsTest.printUnicodeCharacter()

class toil.test.utils.utilsTest.RunTwoJobsPerWorker

Bases: toil.job.Job

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Runs child job with same resources as self in an attempt to chain the jobs on the same worker

run(fileStore)

Override this function to perform work and dynamically create successor jobs.

Parameters:

fileStore – Used to create local and globally sharable temporary files and to send log messages to the leader process.

Returns:

The return value of the function can be passed to other jobs by means of toil.job.Job.rv().