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planemo workflow_edit currently not working? #1318

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jancrichter opened this issue Nov 10, 2022 · 1 comment
Closed

planemo workflow_edit currently not working? #1318

jancrichter opened this issue Nov 10, 2022 · 1 comment

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@jancrichter
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jancrichter commented Nov 10, 2022

When running planemo workflow_edit I am currently getting this error:

Traceback (most recent call last):
  File "/usr/local/bin/planemo", line 8, in <module>
    sys.exit(planemo())
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/click/decorators.py", line 84, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/planemo/cli.py", line 96, in handle_blended_options
    return f(*args, **kwds)
  File "/usr/local/lib/python3.8/dist-packages/planemo/commands/cmd_workflow_edit.py", line 21, in cli
    runnable = for_runnable_identifier(ctx, workflow_identifier, kwds.get("profile"))
  File "/usr/local/lib/python3.8/dist-packages/planemo/runnable_resolve.py", line 15, in for_runnable_identifier
    current_profile = kwds.get("profile")
AttributeError: 'NoneType' object has no attribute 'get'

I created the pull request #1300 to get me past this, however all I then get is a Galaxy instance just as I would using planemo serve. This Galaxy instance also does not contain my workflow, nor does it have any of the workflow's tools installed.

Planemo version 0.74.11 and 0.75.2
Galaxy versions 22.01 and 22.05

I seem to remember, that in the past the command directly opened only a workflow editor, with the workflow. Back then I wasn't able to use it directly, because I had not set up planemo to know my toolshed and therefore it couldn't get any tools from there.

@mvdbeek
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mvdbeek commented Feb 9, 2024

This is fixed in planemo 0.75.21 ... sorry for the long delay here.

@mvdbeek mvdbeek closed this as completed Feb 9, 2024
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