toil.test.wdl.wdltoil_test¶
Attributes¶
Classes¶
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. |
Functions¶
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Module Contents¶
- toil.test.wdl.wdltoil_test.logger¶
- 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]¶
- toil.test.wdl.wdltoil_test.wdl_conformance_test_repo(tmp_path)¶
- Parameters:
tmp_path (pathlib.Path)
- Return type:
- class toil.test.wdl.wdltoil_test.TestWDLConformance¶
WDL conformance tests for Toil.
- check(p)¶
Make sure a call completed or explain why it failed.
- Parameters:
- Return type:
None
- test_unit_tests_v11(wdl_conformance_test_repo)¶
- Parameters:
wdl_conformance_test_repo (pathlib.Path)
- Return type:
None
- test_conformance_tests_v10(wdl_conformance_test_repo)¶
- Parameters:
wdl_conformance_test_repo (pathlib.Path)
- Return type:
None
- test_conformance_tests_v11(wdl_conformance_test_repo)¶
- Parameters:
wdl_conformance_test_repo (pathlib.Path)
- Return type:
None
- test_conformance_tests_integration(wdl_conformance_test_repo)¶
- Parameters:
wdl_conformance_test_repo (pathlib.Path)
- Return type:
None
- class toil.test.wdl.wdltoil_test.TestWDL¶
Tests for Toil’s MiniWDL-based implementation.
- base_command¶
- test_MD5sum(tmp_path)¶
Test if Toil produces the same outputs as known good outputs for WDL’s GATK tutorial #1.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_url_to_file(tmp_path)¶
Test if web URL strings can be coerced to usable Files.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_string_file_coercion(tmp_path)¶
Test if input Files can be coerced to string and back.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_wait(tmp_path)¶
Test if Bash “wait” works in WDL scripts.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_restart(tmp_path)¶
Test if a WDL workflow can be restarted and finish successfully.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_workflow_file_deletion(tmp_path)¶
Test if Toil can delete non-output outputs at the end of a workflow.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_all_call_outputs(tmp_path)¶
Test if Toil can collect all call outputs from a workflow that doesn’t expose them.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_croo_detection(tmp_path)¶
Test if Toil can detect and do something sensible with Cromwell Output Organizer workflows.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_caching(tmp_path)¶
Test if Toil can cache task runs.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_url_to_optional_file(tmp_path)¶
Test if missing and error-producing URLs are handled correctly for optional File? values.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_missing_output_directory(tmp_path)¶
Test if Toil can run a WDL workflow into a new directory.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_miniwdl_self_test(tmp_path, extra_args=None)¶
Test if the MiniWDL self test runs and produces the expected output.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_miniwdl_self_test_by_reference(tmp_path)¶
Test if the MiniWDL self test works when passing input files by URL reference.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_dockstore_trs(tmp_path, extra_args=None)¶
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_dockstore_metrics_publication(tmp_path, extra_args=None)¶
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_giraffe_deepvariant(tmp_path)¶
Test if Giraffe and GPU DeepVariant run. This could take 25 minutes.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_giraffe(tmp_path)¶
Test if Giraffe runs. This could take 12 minutes. Also we scale it down but it still demands lots of memory.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_gs_uri(tmp_path)¶
Test if Toil can access Google Storage URIs.
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- test_check(tmp_path)¶
Test that Toil’s lint check works
- Parameters:
tmp_path (pathlib.Path)
- Return type:
None
- class toil.test.wdl.wdltoil_test.TestWDLToilBench(methodName='runTest')¶
Bases:
unittest.TestCase
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.
- Return type:
None
- 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.
- Return type:
None
- test_choose_human_readable_directory()¶
Test to make sure that we pick sensible but non-colliding directories to put files in.
- Return type:
None
- test_uri_packing()¶
Test to make sure Toil URI packing brings through the required information.
- Return type:
None
- test_disk_parse()¶
Test to make sure the disk parsing is correct
- Return type:
None