toil.test.src.systemTest

Classes

ToilTest	A common base class for Toil tests.
SystemTest	Test various assumptions about the operating system's behavior.

Functions

mkdtemp([suffix, prefix, dir])	Make a temporary directory like tempfile.mkdtemp, but with relaxed permissions.
cpu_count()	Get the rounded-up integer number of whole CPUs available.

Module Contents

toil.test.src.systemTest.mkdtemp(suffix=None, prefix=None, dir=None)

Make a temporary directory like tempfile.mkdtemp, but with relaxed permissions.

The permissions on the directory will be 711 instead of 700, allowing the group and all other users to traverse the directory. This is necessary if the directory is on NFS and the Docker daemon would like to mount it or a file inside it into a container, because on NFS even the Docker daemon appears bound by the file permissions.

See <https://github.com/DataBiosphere/toil/issues/4644>, and <https://stackoverflow.com/a/67928880> which talks about a similar problem but in the context of user namespaces.

Parameters:

• suffix (Optional[str])

• prefix (Optional[str])

• dir (Optional[str])

Return type:

str

toil.test.src.systemTest.cpu_count()

Get the rounded-up integer number of whole CPUs available.

Counts hyperthreads as CPUs.

Uses the system’s actual CPU count, or the current v1 cgroup’s quota per period, if the quota is set.

Ignores the cgroup’s cpu shares value, because it’s extremely difficult to interpret. See https://github.com/kubernetes/kubernetes/issues/81021.

Caches result for efficiency.

Returns:

Integer count of available CPUs, minimum 1.

Return type:

int

class toil.test.src.systemTest.ToilTest(methodName='runTest')

Bases: unittest.TestCase

A common base class for Toil tests.

Please have every test case directly or indirectly inherit this one.

When running tests you may optionally set the TOIL_TEST_TEMP environment variable to the path of a directory where you want temporary test files be placed. The directory will be created if it doesn’t exist. The path may be relative in which case it will be assumed to be relative to the project root. If TOIL_TEST_TEMP is not defined, temporary files and directories will be created in the system’s default location for such files and any temporary files or directories left over from tests will be removed automatically removed during tear down. Otherwise, left-over files will not be removed.

setup_method(method)

Parameters:

method (Any)

Return type:

None

classmethod setUpClass()

Hook method for setting up class fixture before running tests in the class.

Return type:

None

classmethod tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

Return type:

None

setUp()

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

Return type:

None

tearDown()

Hook method for deconstructing the test fixture after testing it.

Return type:

None

classmethod awsRegion()

Pick an appropriate AWS region.

Use us-west-2 unless running on EC2, in which case use the region in which the instance is located

Return type:

str

class toil.test.src.systemTest.SystemTest(methodName='runTest')

Bases: toil.test.ToilTest

Test various assumptions about the operating system’s behavior.

testAtomicityOfNonEmptyDirectoryRenames()