Hi Michael,
I checked the situation in cwltool git and got:
=================================== FAILURES ===================================
_____________________ test_load_graph_fragment_from_packed _____________________
[gw2] linux -- Python 3.7.7 /usr/bin/python3.7
def test_load_graph_fragment_from_packed():
"""Loading a fragment from packed with update."""
loadingContext = LoadingContext()
uri = Path(get_data("tests/wf/packed-with-loadlisting.cwl")).as_uri() +
"#main"
try:
with open(get_data("cwltool/extensions.yml"), "r") as res:
use_custom_schema("v1.0", "http://commonwl.org/cwltool";,
res.read())
# The updater transforms LoadListingRequirement from an
# extension (in v1.0) to a core feature (in v1.1) but there
# was a bug when loading a packed workflow and loading a
# specific fragment it would get the un-updated document.
# This recreates that case and asserts that we are using the
# updated document like we should.
> tool = load_tool(uri, loadingContext)
cwltool/tests/test_load_tool.py:105:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cwltool/load_tool.py:436: in load_tool
return make_tool(uri, loadingContext)
cwltool/load_tool.py:414: in make_tool
tool = loadingContext.construct_tool_object(processobj, loadingContext)
cwltool/workflow.py:61: in default_make_tool
return Workflow(toolpath_object, loadingContext)
cwltool/workflow.py:716: in __init__
step, index, loadingContext, loadingContext.prov_obj
cwltool/workflow.py:762: in make_workflow_step
return WorkflowStep(toolpath_object, pos, loadingContext,
parentworkflowProv)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <cwltool.workflow.WorkflowStep object at 0x7fa566554590>
toolpath_object = ordereddict([('in', [ordereddict([('source',
'file:///build/cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loa...step.cwl'),
('id',
'file:///build/cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl#main/step1')])
pos = 0
loadingContext = <cwltool.context.LoadingContext object at 0x7fa5665a8e10>
parentworkflowProv = None
def __init__(
self,
toolpath_object, # type: Dict[str, Any]
pos, # type: int
loadingContext, # type: LoadingContext
parentworkflowProv=None, # type: Optional[ProvenanceProfile]
): # type: (...) -> None
"""Initialize this WorkflowStep."""
if "id" in toolpath_object:
self.id = toolpath_object["id"]
else:
self.id = "#step" + str(pos)
loadingContext = loadingContext.copy()
loadingContext.requirements = copy.deepcopy(
getdefault(loadingContext.requirements, [])
)
assert loadingContext.requirements is not None # nosec
loadingContext.requirements.extend(toolpath_object.get("requirements",
[]))
loadingContext.requirements.extend(
get_overrides(getdefault(loadingContext.overrides_list, []),
self.id).get(
"requirements", []
)
)
hints = copy.deepcopy(getdefault(loadingContext.hints, []))
hints.extend(toolpath_object.get("hints", []))
loadingContext.hints = hints
try:
if isinstance(toolpath_object["run"], MutableMapping):
self.embedded_tool = loadingContext.construct_tool_object(
toolpath_object["run"], loadingContext
) # type: Process
else:
loadingContext.metadata = {}
self.embedded_tool = load_tool(toolpath_object["run"],
loadingContext)
except validate.ValidationException as vexc:
if loadingContext.debug:
_logger.exception("Validation exception")
raise WorkflowException(
"Tool definition %s failed validation:\n%s"
% (toolpath_object["run"], indent(str(vexc)))
> ) from vexc
E cwltool.errors.WorkflowException: Tool definition
file:///build/cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl#16169-step.cwl
failed validation:
E
../../../../cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl:3:9:
checking object
E
`../../../../cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl#main`
E
../../../../cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl:5:11:
checking field
E
`requirements`
E
../../../../cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl:6:13:
checking item
E
../../../../cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl:8:15:
Field `class`
E
contains undefined
E
reference to
E
`http://commonwl.org/cwltool#LoadListingRequirement`
cwltool/workflow.py:850: WorkflowException
=============================== warnings summary ===============================
/usr/lib/python3/dist-packages/rdflib/plugins/sparql/compat.py:8
/usr/lib/python3/dist-packages/rdflib/plugins/sparql/compat.py:8
/usr/lib/python3/dist-packages/rdflib/plugins/sparql/compat.py:8:
DeprecationWarning: Using or importing the ABCs from 'collections' instead of
from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop
working
from collections import Mapping, MutableMapping # was added in 2.6
-- Docs: https://docs.pytest.org/en/latest/warnings.html
======== 1 failed, 224 passed, 100 skipped, 2 warnings in 90.13 seconds ========
E: pybuild pybuild:352: test: plugin custom failed with: exit code=1: cd
/build/cwltool-3.0.20200324120055+dfsg; export
PATH=/build/cwltool-3.0.20200324120055+dfsg/debian/python3-cwltool/usr/bin:/usr/sbin:/usr/b
can you have a look?
Kind regards
Andreas.
----- Forwarded message from Debian testing autoremoval watch
<nore...@release.debian.org> -----
Date: Mon, 30 Mar 2020 04:39:17 +0000
From: Debian testing autoremoval watch <nore...@release.debian.org>
To: cwlt...@packages.debian.org
Subject: cwltool is marked for autoremoval from testing
cwltool 2.0.20200224214940+dfsg-1 is marked for autoremoval from testing on
2020-05-05
It is affected by these RC bugs:
954496: cwltool: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i
python{version} -p "3.7 3.8" returned exit code 13
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