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WIP fix #1330 #1566

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WIP fix #1330 #1566

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fbed7db
WIP fix #1330
manabuishii Nov 11, 2021
2414df9
Revert cwltool/process.py
manabuishii Mar 29, 2022
1862895
Update to fix #1330
manabuishii Mar 29, 2022
40a22d8
Merge branch 'main' into fix_issue_1330
manabuishii Mar 30, 2022
59c97cf
Fix lint problem
manabuishii Mar 30, 2022
a7a66cf
Fix for mypy
manabu Mar 30, 2022
8031b3d
Fix podman v1.0 error
manabuishii Mar 31, 2022
a6caace
Remove items for evalResources
manabuishii Apr 1, 2022
8c08318
Add expressiontool conformance test case
manabuishii Apr 5, 2022
14a2ded
Improve ExpressionTool inputs
manabuishii Jun 30, 2022
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4 changes: 4 additions & 0 deletions cwltool/process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -775,6 +775,10 @@ def _init_job(
)

job = copy.deepcopy(joborder)
if len(job.keys()) > 0:
for jo in joborder:
field = shortname(jo)
job[field] = joborder[jo]

make_fs_access = getdefault(runtime_context.make_fs_access, StdFsAccess)
fs_access = make_fs_access(runtime_context.basedir)
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9 changes: 5 additions & 4 deletions cwltool/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -440,10 +440,11 @@ def job(
)

step_input = {}
for inp in self.tool["inputs"]:
field = shortname(inp["id"])
if not inp.get("not_connected"):
step_input[field] = job_order[inp["id"]]
for inp in job_order:
field = shortname(inp)
step_input[field] = job_order[inp]
# if not inp.get("not_connected"):
# step_input[field] = job_order[field]

try:
yield from self.embedded_tool.job(
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2 changes: 2 additions & 0 deletions cwltool/workflow_job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -386,6 +386,8 @@ def object_from_state(
incomplete: bool = False,
) -> Optional[CWLObjectType]:
inputobj = {} # type: CWLObjectType
for s in state.keys():
inputobj[s] = state[s].value
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I think we can avoid accessing keys & values separately. Something like:

for k, v in state.items():
  inputobj[k] = v

Or start inputobj by deep-cloning state.

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@manabuishii manabuishii Mar 30, 2022 •
edited
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Current commited version is
https://github.com/common-workflow-language/cwltool/pull/1566/files#diff-ed87d61e2237460638e7f3ddb21bafc9969d8c142c804d79f94801142342f3d6R389-R391

My local version is following .
It handles 1330 well and pass py39-unit
But I can not pass py39-mypy

    for s in state.keys():
        if hasattr(state[s], "value"):
            inputobj[s] = state[s].value

Now I try to replace it to your code, because it looks good.
But I can not pass py39-mypy

    for k,v  in state.items():
        if type(v) is WorkflowStateItem:
            if hasattr(v, "value"):
                inputobj[k] = v.value

currently

for inp in parms:
iid = original_id = cast(str, inp["id"])
if frag_only:
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