toil.test.wdl.wdltoil_test¶
Attributes¶
Classes¶
Base test class for WDL tests. |
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WDL conformance tests for Toil. |
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Tests for Toil's MiniWDL-based implementation. |
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Tests for Toil's MiniWDL-based implementation that don't run workflows. |
Module Contents¶
- toil.test.wdl.wdltoil_test.logger¶
- class toil.test.wdl.wdltoil_test.BaseWDLTest(methodName='runTest')¶
Bases:
toil.test.ToilTest
Base test class for WDL tests.
- setUp()¶
Runs anew before each test to create farm fresh temp dirs.
- Return type:
None
- tearDown()¶
Hook method for deconstructing the test fixture after testing it.
- Return type:
None
- toil.test.wdl.wdltoil_test.WDL_CONFORMANCE_TEST_REPO = 'https://github.com/DataBiosphere/wdl-conformance-tests.git'¶
- toil.test.wdl.wdltoil_test.WDL_CONFORMANCE_TEST_COMMIT = 'baf44bcc7e6f6927540adf77d91b26a5558ae4b7'¶
- toil.test.wdl.wdltoil_test.WDL_CONFORMANCE_TESTS_UNSUPPORTED_BY_TOIL = [16, 21, 64, 77]¶
- toil.test.wdl.wdltoil_test.WDL_UNIT_TESTS_UNSUPPORTED_BY_TOIL = [14, 19, 52, 58, 59, 66, 67, 68, 69, 87, 97, 105, 107, 108, 109, 110, 120, 131, 134, 144]¶
- class toil.test.wdl.wdltoil_test.WDLConformanceTests(methodName='runTest')¶
Bases:
BaseWDLTest
WDL conformance tests for Toil.
- wdl_dir = 'wdl-conformance-tests'¶
- classmethod setUpClass()¶
Hook method for setting up class fixture before running tests in the class.
- Return type:
None
- check(p)¶
Make sure a call completed or explain why it failed.
- Parameters:
- Return type:
None
- test_unit_tests_v11()¶
- test_conformance_tests_v10()¶
- test_conformance_tests_v11()¶
- test_conformance_tests_integration()¶
- classmethod tearDownClass()¶
Hook method for deconstructing the class fixture after running all tests in the class.
- Return type:
None
- class toil.test.wdl.wdltoil_test.WDLTests(methodName='runTest')¶
Bases:
BaseWDLTest
Tests for Toil’s MiniWDL-based implementation.
- classmethod setUpClass()¶
Runs once for all tests.
- Return type:
None
- test_MD5sum()¶
Test if Toil produces the same outputs as known good outputs for WDL’s GATK tutorial #1.
- test_url_to_file()¶
Test if web URL strings can be coerced to usable Files.
- test_wait()¶
Test if Bash “wait” works in WDL scripts.
- test_all_call_outputs()¶
Test if Toil can collect all call outputs from a workflow that doesn’t expose them.
- test_croo_detection()¶
Test if Toil can detect and do something sensible with Cromwell Output Organizer workflows.
- test_caching()¶
Test if Toil can cache task runs.
- test_url_to_optional_file()¶
Test if missing and error-producing URLs are handled correctly for optional File? values.
- test_missing_output_directory()¶
Test if Toil can run a WDL workflow into a new directory.
- test_miniwdl_self_test(extra_args=None)¶
Test if the MiniWDL self test runs and produces the expected output.
- test_miniwdl_self_test_by_reference()¶
Test if the MiniWDL self test works when passing input files by URL reference.
- Return type:
None
- test_giraffe_deepvariant()¶
Test if Giraffe and GPU DeepVariant run. This could take 25 minutes.
- test_giraffe()¶
Test if Giraffe runs. This could take 12 minutes. Also we scale it down but it still demands lots of memory.
- test_gs_uri()¶
Test if Toil can access Google Storage URIs.
- class toil.test.wdl.wdltoil_test.WDLToilBenchTests(methodName='runTest')¶
Bases:
toil.test.ToilTest
Tests for Toil’s MiniWDL-based implementation that don’t run workflows.
- test_coalesce()¶
Test if WDLSectionJob can coalesce WDL decls.
White box test; will need to be changed or removed if the WDL interpreter changes.
- make_string_expr(to_parse)¶
Parse pseudo-WDL for testing whitespace removal.
- Parameters:
to_parse (str)
- Return type:
WDL.Expr.String
- test_remove_common_leading_whitespace()¶
Make sure leading whitespace removal works properly.
- test_choose_human_readable_directory()¶
Test to make sure that we pick sensible but non-colliding directories to put files in.
- test_uri_packing()¶
Test to make sure Toil URI packing brings through the required information.
- test_disk_parse()¶
Test to make sure the disk parsing is correct