`toil.test.cwl.cwlTest`¶

Module Contents¶

Classes¶

`CWLWorkflowTest`	CWL tests included in Toil that don't involve the whole CWL conformance
`CWLv10Test`	Run the CWL 1.0 conformance tests in various environments.
`CWLv11Test`	Run the CWL 1.1 conformance tests in various environments.
`CWLv12Test`	Run the CWL 1.2 conformance tests in various environments.
`CWLOnARMTest`	Run the CWL 1.2 conformance tests on ARM specifically.

Functions¶

`run_conformance_tests`(workDir, yml[, runner, caching, ...])	Run the CWL conformance tests.
`test_workflow_echo_string_scatter_stderr_log_dir`(tmp_path)
`test_log_dir_echo_no_output`(tmp_path)
`test_log_dir_echo_stderr`(tmp_path)
`test_filename_conflict_resolution`(tmp_path)
`test_filename_conflict_detection`(tmp_path)	Make sure we don't just stage files over each other when using a container.
`test_filename_conflict_detection_at_root`(tmp_path)	Make sure we don't just stage files over each other.
`test_pick_value_with_one_null_value`(caplog)	Make sure toil-cwl-runner does not false log a warning when pickValue is
`test_usage_message`()	This is purely to ensure a (more) helpful error message is printed if a user does
`test_workflow_echo_string`()
`test_workflow_echo_string_scatter_capture_stdout`()
`test_visit_top_cwl_class`()
`test_visit_cwl_class_and_reduce`()
`test_download_structure`(tmp_path)	Make sure that download_structure makes the right calls to what it thinks is the file store.

Attributes¶

`pkg_root`
`log`
`CONFORMANCE_TEST_TIMEOUT`

toil.test.cwl.cwlTest.pkg_root¶

toil.test.cwl.cwlTest.log¶

toil.test.cwl.cwlTest.CONFORMANCE_TEST_TIMEOUT = 3600¶

toil.test.cwl.cwlTest.run_conformance_tests(workDir, yml, runner=None, caching=False, batchSystem=None, selected_tests=None, selected_tags=None, skipped_tests=None, extra_args=None, must_support_all_features=False, junit_file=None)¶

Run the CWL conformance tests.

Parameters

workDir (str) – Directory to run tests in.
yml (str) – CWL test list YML to run tests from.
runner (Optional[str]) – If set, use this cwl runner instead of the default toil-cwl-runner.
caching (bool) – If True, use Toil file store caching.
batchSystem (str) – If set, use this batch system instead of the default single_machine.
selected_tests (str) – If set, use this description of test numbers to run (comma-separated numbers or ranges)
selected_tags (str) – As an alternative to selected_tests, run tests with the given tags.
skipped_tests (str) – Comma-separated string labels of tests to skip.
extra_args (Optional[List[str]]) – Provide these extra arguments to runner for each test.
must_support_all_features (bool) – If set, fail if some CWL optional features are unsupported.
junit_file (Optional[str]) – JUnit XML file to write test info to.

class toil.test.cwl.cwlTest.CWLWorkflowTest(methodName='runTest')¶

Bases: toil.test.ToilTest

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CWL tests included in Toil that don’t involve the whole CWL conformance test suite. Tests Toil-specific functions like URL types supported for inputs.

setUp()¶: Runs anew before each test to create farm fresh temp dirs.

tearDown()¶: Clean up outputs.

revsort(cwl_filename, tester_fn)¶

revsort_no_checksum(cwl_filename, tester_fn)¶

download(inputs, tester_fn)¶

load_contents(inputs, tester_fn)¶

download_directory(inputs, tester_fn)¶

download_subdirectory(inputs, tester_fn)¶

test_mpi()¶

test_s3_as_secondary_file()¶

test_run_revsort()¶

test_run_revsort_nochecksum()¶

test_run_revsort2()¶

test_run_revsort_debug_worker()¶

test_run_colon_output()¶

test_download_s3()¶

test_download_http()¶

test_download_https()¶

test_download_file()¶

test_download_directory_s3()¶

test_download_directory_file()¶

test_download_subdirectory_s3()¶

test_download_subdirectory_file()¶

test_load_contents_s3()¶

test_load_contents_http()¶

test_load_contents_https()¶

test_load_contents_file()¶

test_bioconda()¶

test_biocontainers()¶

test_cuda()¶

test_restart()¶: Enable restarts with toil-cwl-runner – run failing test, re-run correct test. Only implemented for single machine.

test_streamable()¶: Test that a file with ‘streamable’=True is a named pipe. This is a CWL1.2 feature.

class toil.test.cwl.cwlTest.CWLv10Test(methodName='runTest')¶

Bases: toil.test.ToilTest

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Run the CWL 1.0 conformance tests in various environments.

setUp()¶: Runs anew before each test to create farm fresh temp dirs.

tearDown()¶: Clean up outputs.

test_run_conformance_with_caching()¶

test_run_conformance(batchSystem=None, caching=False, selected_tests=None)¶

test_lsf_cwl_conformance(**kwargs)¶

test_slurm_cwl_conformance(**kwargs)¶

test_torque_cwl_conformance(**kwargs)¶

test_gridengine_cwl_conformance(**kwargs)¶

test_mesos_cwl_conformance(**kwargs)¶

test_parasol_cwl_conformance(**kwargs)¶

test_kubernetes_cwl_conformance(**kwargs)¶

test_lsf_cwl_conformance_with_caching()¶

test_slurm_cwl_conformance_with_caching()¶

test_torque_cwl_conformance_with_caching()¶

test_gridengine_cwl_conformance_with_caching()¶

test_mesos_cwl_conformance_with_caching()¶

test_parasol_cwl_conformance_with_caching()¶

test_kubernetes_cwl_conformance_with_caching()¶

class toil.test.cwl.cwlTest.CWLv11Test(methodName='runTest')¶

Bases: toil.test.ToilTest

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Run the CWL 1.1 conformance tests in various environments.

classmethod setUpClass()¶: Runs anew before each test.

tearDown()¶: Clean up outputs.

test_run_conformance(**kwargs)¶

test_run_conformance_with_caching()¶

test_kubernetes_cwl_conformance(**kwargs)¶

test_kubernetes_cwl_conformance_with_caching()¶

class toil.test.cwl.cwlTest.CWLv12Test(methodName='runTest')¶

Bases: toil.test.ToilTest

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Run the CWL 1.2 conformance tests in various environments.

classmethod setUpClass()¶: Runs anew before each test.

tearDown()¶: Clean up outputs.

test_run_conformance(**kwargs)¶

test_run_conformance_with_caching()¶

test_run_conformance_with_in_place_update()¶: Make sure that with –bypass-file-store we properly support in place update on a single node, and that this doesn’t break any other features.

test_kubernetes_cwl_conformance(**kwargs)¶

test_kubernetes_cwl_conformance_with_caching()¶

test_wes_server_cwl_conformance()¶

Run the CWL conformance tests via WES. TOIL_WES_ENDPOINT must be specified. If the WES server requires authentication, set TOIL_WES_USER and TOIL_WES_PASSWORD.

To run manually:

TOIL_WES_ENDPOINT=http://localhost:8080 TOIL_WES_USER=test TOIL_WES_PASSWORD=password python -m pytest src/toil/test/cwl/cwlTest.py::CWLv12Test::test_wes_server_cwl_conformance -vv –log-level INFO –log-cli-level INFO

class toil.test.cwl.cwlTest.CWLOnARMTest(methodName)¶

Bases: toil.test.provisioners.clusterTest.AbstractClusterTest

digraph inheritance1d0c418345 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "AbstractClusterTest" [URL="../../provisioners/clusterTest/index.html#toil.test.provisioners.clusterTest.AbstractClusterTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "ToilTest" -> "AbstractClusterTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "CWLOnARMTest" [URL="#toil.test.cwl.cwlTest.CWLOnARMTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Run the CWL 1.2 conformance tests on ARM specifically."]; "AbstractClusterTest" -> "CWLOnARMTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Run the CWL 1.2 conformance tests on ARM specifically.

setUp()¶: Set up for the test. Must be overridden to call this method and set self.jobStore.

test_cwl_on_arm()¶

toil.test.cwl.cwlTest.test_workflow_echo_string_scatter_stderr_log_dir(tmp_path)¶

Parameters: tmp_path (pathlib.Path) –

toil.test.cwl.cwlTest.test_log_dir_echo_no_output(tmp_path)¶

Parameters: tmp_path (pathlib.Path) –
Return type: None

toil.test.cwl.cwlTest.test_log_dir_echo_stderr(tmp_path)¶

Parameters: tmp_path (pathlib.Path) –
Return type: None

toil.test.cwl.cwlTest.test_filename_conflict_resolution(tmp_path)¶

Parameters: tmp_path (pathlib.Path) –

toil.test.cwl.cwlTest.test_filename_conflict_detection(tmp_path)¶

Make sure we don’t just stage files over each other when using a container.

Parameters: tmp_path (pathlib.Path) –

toil.test.cwl.cwlTest.test_filename_conflict_detection_at_root(tmp_path)¶

Make sure we don’t just stage files over each other.

Specifically, when using a container and the files are at the root of the work dir.

Parameters: tmp_path (pathlib.Path) –

toil.test.cwl.cwlTest.test_pick_value_with_one_null_value(caplog)¶: Make sure toil-cwl-runner does not false log a warning when pickValue is used but outputSource only contains one null value. See: #3991.

toil.test.cwl.cwlTest.test_usage_message()¶: This is purely to ensure a (more) helpful error message is printed if a user does not order their positional args correctly [cwl, cwl-job (json/yml/yaml), jobstore].

toil.test.cwl.cwlTest.test_workflow_echo_string()¶

toil.test.cwl.cwlTest.test_workflow_echo_string_scatter_capture_stdout()¶

toil.test.cwl.cwlTest.test_visit_top_cwl_class()¶

toil.test.cwl.cwlTest.test_visit_cwl_class_and_reduce()¶

toil.test.cwl.cwlTest.test_download_structure(tmp_path)¶

Make sure that download_structure makes the right calls to what it thinks is the file store.

Return type: None

`toil.test.cwl.cwlTest`¶

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Functions¶

Attributes¶

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toil.test.cwl.cwlTest¶

Module Contents¶

Classes¶

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Attributes¶

`toil.test.cwl.cwlTest`¶