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Bug #22695 » update-cwltool.log

Brett Smith, 09/19/2025 01:47 PM

 
==================================== test session starts =====================================
platform linux -- Python 3.11.2, pytest-8.4.1, pluggy-1.6.0
rootdir: /home/brett/Curii/arvados/sdk/cwl
configfile: pytest.ini
plugins: cwltest-2.6.20250314152537
collected 50 items

tests/test_container.py ..FFFFFFF......................................... [100%]

========================================== FAILURES ==========================================
____________________________ TestContainer.test_gpu_requirement_0 ____________________________

a = (<tests.test_container.TestContainer testMethod=test_gpu_requirement_0>,), kw = {}

@wraps(func)
def standalone_func(*a, **kw):
> return func(*(a + p.args), **p.kwargs, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:620:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:93: in dummy_func
return orgfunc(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_container.py:1286: in test_gpu_requirement
arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:614: in load_tool
loadingContext, uri = resolve_and_validate_document(
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:507: in resolve_and_validate_document
document_loader.resolve_all(workflowobj, fileuri)
schema_salad/ref_resolver.py:988: in resolve_all
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

> ???
E schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
E checking item
E Field 'class' contains undefined reference to
E 'http://commonwl.org/cwltool#CUDARequirement'

schema_salad/ref_resolver.py:1194: ValidationException
____________________________ TestContainer.test_gpu_requirement_1 ____________________________

a = (<tests.test_container.TestContainer testMethod=test_gpu_requirement_1>,), kw = {}

@wraps(func)
def standalone_func(*a, **kw):
> return func(*(a + p.args), **p.kwargs, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:620:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:93: in dummy_func
return orgfunc(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_container.py:1286: in test_gpu_requirement
arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:614: in load_tool
loadingContext, uri = resolve_and_validate_document(
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:507: in resolve_and_validate_document
document_loader.resolve_all(workflowobj, fileuri)
schema_salad/ref_resolver.py:988: in resolve_all
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

> ???
E schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
E checking item
E Field 'class' contains undefined reference to
E 'http://commonwl.org/cwltool#CUDARequirement'

schema_salad/ref_resolver.py:1194: ValidationException
____________________________ TestContainer.test_gpu_requirement_2 ____________________________

a = (<tests.test_container.TestContainer testMethod=test_gpu_requirement_2>,), kw = {}

@wraps(func)
def standalone_func(*a, **kw):
> return func(*(a + p.args), **p.kwargs, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:620:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:93: in dummy_func
return orgfunc(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_container.py:1286: in test_gpu_requirement
arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:614: in load_tool
loadingContext, uri = resolve_and_validate_document(
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:507: in resolve_and_validate_document
document_loader.resolve_all(workflowobj, fileuri)
schema_salad/ref_resolver.py:988: in resolve_all
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

> ???
E schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
E checking item
E Field 'class' contains undefined reference to
E 'http://commonwl.org/cwltool#CUDARequirement'

schema_salad/ref_resolver.py:1194: ValidationException
____________________________ TestContainer.test_gpu_requirement_3 ____________________________

a = (<tests.test_container.TestContainer testMethod=test_gpu_requirement_3>,), kw = {}

@wraps(func)
def standalone_func(*a, **kw):
> return func(*(a + p.args), **p.kwargs, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:620:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:93: in dummy_func
return orgfunc(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_container.py:1286: in test_gpu_requirement
arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:614: in load_tool
loadingContext, uri = resolve_and_validate_document(
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:507: in resolve_and_validate_document
document_loader.resolve_all(workflowobj, fileuri)
schema_salad/ref_resolver.py:988: in resolve_all
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

> ???
E schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
E checking item
E Field 'class' contains undefined reference to
E 'http://commonwl.org/cwltool#CUDARequirement'

schema_salad/ref_resolver.py:1194: ValidationException
____________________________ TestContainer.test_gpu_requirement_4 ____________________________

a = (<tests.test_container.TestContainer testMethod=test_gpu_requirement_4>,), kw = {}

@wraps(func)
def standalone_func(*a, **kw):
> return func(*(a + p.args), **p.kwargs, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:620:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:93: in dummy_func
return orgfunc(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_container.py:1286: in test_gpu_requirement
arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:614: in load_tool
loadingContext, uri = resolve_and_validate_document(
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:507: in resolve_and_validate_document
document_loader.resolve_all(workflowobj, fileuri)
schema_salad/ref_resolver.py:988: in resolve_all
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

> ???
E schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
E checking item
E Field 'class' contains undefined reference to
E 'http://commonwl.org/cwltool#CUDARequirement'

schema_salad/ref_resolver.py:1194: ValidationException
____________________________ TestContainer.test_gpu_requirement_5 ____________________________

a = (<tests.test_container.TestContainer testMethod=test_gpu_requirement_5>,), kw = {}

@wraps(func)
def standalone_func(*a, **kw):
> return func(*(a + p.args), **p.kwargs, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:620:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:93: in dummy_func
return orgfunc(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_container.py:1286: in test_gpu_requirement
arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:614: in load_tool
loadingContext, uri = resolve_and_validate_document(
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:507: in resolve_and_validate_document
document_loader.resolve_all(workflowobj, fileuri)
schema_salad/ref_resolver.py:988: in resolve_all
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

> ???
E schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
E checking item
E Field 'class' contains undefined reference to
E 'http://commonwl.org/cwltool#CUDARequirement'

schema_salad/ref_resolver.py:1194: ValidationException
____________________________ TestContainer.test_gpu_requirement_6 ____________________________

a = (<tests.test_container.TestContainer testMethod=test_gpu_requirement_6>,), kw = {}

@wraps(func)
def standalone_func(*a, **kw):
> return func(*(a + p.args), **p.kwargs, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:620:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/parameterized/parameterized.py:93: in dummy_func
return orgfunc(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3.11/unittest/mock.py:1369: in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_container.py:1286: in test_gpu_requirement
arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:614: in load_tool
loadingContext, uri = resolve_and_validate_document(
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/cwltool/load_tool.py:543: in resolve_and_validate_document
validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

> ???
E schema_salad.exceptions.ValidationException: test:1:1: Object '_:2b4990b2-b392-4ec9-b04a-0275f0c59c7f' is not valid because
E tried 'CommandLineTool' but
E the 'requirements' field is not valid because
E tried array of <InlineJavascriptRequirement or SchemaDefRequirement or
E LoadListingRequirement or DockerRequirement or SoftwareRequirement or
E InitialWorkDirRequirement or EnvVarRequirement or ShellCommandRequirement or
E ResourceRequirement or WorkReuse or NetworkAccess or InplaceUpdateRequirement or
E ToolTimeLimit or SubworkflowFeatureRequirement or ScatterFeatureRequirement or
E MultipleInputFeatureRequirement or StepInputExpressionRequirement> but
E item is invalid because
E - tried InlineJavascriptRequirement but
E Expected class 'org.w3id.cwl.cwl.InlineJavascriptRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried SchemaDefRequirement but
E Expected class 'org.w3id.cwl.cwl.SchemaDefRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried LoadListingRequirement but
E Expected class 'org.w3id.cwl.cwl.LoadListingRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried DockerRequirement but
E Expected class 'org.w3id.cwl.cwl.DockerRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried SoftwareRequirement but
E Expected class 'org.w3id.cwl.cwl.SoftwareRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried InitialWorkDirRequirement but
E Expected class 'org.w3id.cwl.cwl.InitialWorkDirRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried EnvVarRequirement but
E Expected class 'org.w3id.cwl.cwl.EnvVarRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried ShellCommandRequirement but
E Expected class 'org.w3id.cwl.cwl.ShellCommandRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried ResourceRequirement but
E Expected class 'org.w3id.cwl.cwl.ResourceRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried WorkReuse but
E Expected class 'org.w3id.cwl.cwl.WorkReuse' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried NetworkAccess but
E Expected class 'org.w3id.cwl.cwl.NetworkAccess' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried InplaceUpdateRequirement but
E Expected class 'org.w3id.cwl.cwl.InplaceUpdateRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried ToolTimeLimit but
E Expected class 'org.w3id.cwl.cwl.ToolTimeLimit' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried SubworkflowFeatureRequirement but
E Expected class 'org.w3id.cwl.cwl.SubworkflowFeatureRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried ScatterFeatureRequirement but
E Expected class 'org.w3id.cwl.cwl.ScatterFeatureRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried MultipleInputFeatureRequirement but
E Expected class 'org.w3id.cwl.cwl.MultipleInputFeatureRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'
E - tried StepInputExpressionRequirement but
E Expected class 'org.w3id.cwl.cwl.StepInputExpressionRequirement' but this is
E 'http://arvados.org/cwl#ROCmRequirement'

schema_salad/schema.py:405: ValidationException
====================================== warnings summary ======================================
tests/test_container.py::TestContainer::test_done
tests/test_container.py::TestContainer::test_done
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/crunchstat_summary/dygraphs.py:42: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
importlib.resources.read_text('crunchstat_summary', jsa, encoding='utf-8')

tests/test_container.py: 107 warnings
/usr/lib/python3.11/importlib/resources/_legacy.py:80: DeprecationWarning: open_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
with open_text(package, resource, encoding, errors) as fp:

tests/test_container.py: 105 warnings
/home/brett/.cache/arvados-test/VENV3DIR/lib/python3.11/site-packages/arvados_cwl/__init__.py:299: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
customschema = importlib.resources.read_text(__name__, f'arv-cwl-schema-{s}.yml', encoding='utf-8')

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================================== short test summary info ===================================
FAILED tests/test_container.py::TestContainer::test_gpu_requirement_0 - schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
FAILED tests/test_container.py::TestContainer::test_gpu_requirement_1 - schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
FAILED tests/test_container.py::TestContainer::test_gpu_requirement_2 - schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
FAILED tests/test_container.py::TestContainer::test_gpu_requirement_3 - schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
FAILED tests/test_container.py::TestContainer::test_gpu_requirement_4 - schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
FAILED tests/test_container.py::TestContainer::test_gpu_requirement_5 - schema_salad.exceptions.ValidationException: test:1:1: checking field 'requirements'
FAILED tests/test_container.py::TestContainer::test_gpu_requirement_6 - schema_salad.exceptions.ValidationException: test:1:1: Object '_:2b4990b2-b392-4ec9-b04a-...
========================= 7 failed, 43 passed, 214 warnings in 3.49s =========================
======= sdk/cwl tests -- FAILED
======= test sdk/cwl -- 4s
(2-2/2)