Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/cwltool/tests/test_override.py @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author | shellac |
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date | Mon, 01 Jun 2020 08:59:25 -0400 |
parents | 79f47841a781 |
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--- a/env/lib/python3.7/site-packages/cwltool/tests/test_override.py Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,98 +0,0 @@ -import json - -from six import StringIO - -import pytest - -from cwltool.main import main -from cwltool import load_tool -from .util import get_data, needs_docker - -override_parameters = [ - ([get_data('tests/override/echo.cwl'), - get_data('tests/override/echo-job.yml')], - {"out": "zing hello1\n"} - ), - (["--overrides", - get_data('tests/override/ov.yml'), - get_data('tests/override/echo.cwl'), - get_data('tests/override/echo-job.yml')], - {"out": "zing hello2\n"} - ), - ([get_data('tests/override/echo.cwl'), - get_data('tests/override/echo-job-ov.yml')], - {"out": "zing hello3\n"} - ), - ([get_data('tests/override/echo-job-ov2.yml')], - {"out": "zing hello4\n"} - ), - (["--overrides", - get_data('tests/override/ov.yml'), - get_data('tests/override/echo-wf.cwl'), - get_data('tests/override/echo-job.yml')], - {"out": "zing hello2\n"} - ), - (["--overrides", - get_data('tests/override/ov2.yml'), - get_data('tests/override/echo-wf.cwl'), - get_data('tests/override/echo-job.yml')], - {"out": "zing hello5\n"} - ), - (["--overrides", - get_data('tests/override/ov3.yml'), - get_data('tests/override/echo-wf.cwl'), - get_data('tests/override/echo-job.yml')], - {"out": "zing hello6\n"} - ), - ([get_data('tests/override/env-tool_v1.1.cwl'), - get_data('tests/override/env-tool_cwl-requirement_override.yaml')], - {"value": "hello test env"} - ), - (["--enable-dev", - get_data('tests/override/env-tool_cwl-requirement_override_default.yaml')], - {"value": "hello test env"} - ), -] - -@needs_docker -@pytest.mark.parametrize('parameters,result', override_parameters) -def test_overrides(parameters, result): - sio = StringIO() - - assert main(parameters, stdout=sio) == 0 - assert json.loads(sio.getvalue()) == result - - -failing_override_parameters = [ - ([get_data('tests/override/env-tool.cwl'), - get_data('tests/override/env-tool_cwl-requirement_override.yaml')], - "`cwl:requirements` in the input object is not part of CWL v1.0. You can " - "adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to " - "v1.1" - ), - ([get_data('tests/override/env-tool_v1.1.0-dev1.cwl'), - get_data('tests/override/env-tool_cwl-requirement_override.yaml')], - "Version 'v1.1.0-dev1' is a development or deprecated version.\n" - " Update your document to a stable version (v1.0, v1.1) or use --enable-dev to " - "enable support for development and deprecated versions." - ), - ([get_data('tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml')], - "`cwl:requirements` in the input object is not part of CWL v1.0. You can " - "adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to " - "v1.1 or greater." - ), - ([get_data('tests/override/env-tool_cwl-requirement_override_default.yaml')], - "Version 'v1.1.0-dev1' is a development or deprecated version.\n" - " Update your document to a stable version (v1.0, v1.1) or use --enable-dev to " - "enable support for development and deprecated versions." - ), -] - -@needs_docker -@pytest.mark.parametrize('parameters,expected_error', failing_override_parameters) -def test_overrides_fails(parameters, expected_error): - sio = StringIO() - - assert main(parameters, stderr=sio) == 1 - stderr = sio.getvalue() - assert expected_error in stderr, stderr