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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
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Pipestat warnings on dev are a bit verbose #331

Closed nsheff closed 12 months ago

nsheff commented 3 years ago

Right now I get this:

## [1 of 2] sample: sample1; pipeline: demo
Pipestat configuration incomplete for Sample 'sample1'; caught exception: AttributeError("'pipestat_config' attribute is missing")
Could not determine pipestat namespace. Caught exception: AttributeError("'pipestat_config' attribute is missing")

These will show up for any non-pipestat-compatible pipeline. These are confusing to a user. Are they necessary? Since pipestat-compatibility is optional, I would recommend no exception or Error messages printed. At most it could be maybe "This pipeline is not pipestat compatible. Add a 'pipestat_config' attribute to your PEP if you want to use pipestat" -- But even that is probably overkill... ?

Perhaps an error is warranted if the pipeline is pipestat-compatible, but there's something missing?

I think maybe a good way to approach this would be a check in the looper output, like

Checking for pipestat compatible: Pipeline is compatible with pipestat

Or something like that. I think we shouldn't show this for every sample, but rather just once per pipeline.

nsheff commented 2 years ago

@stolarczyk Do you have any comment on this?

donaldcampbelljr commented 1 year ago

Right now, this is logged to the terminal as: Pipestat compatible: False

And it appears to be showing up once per pipeline.

Therefore, I believe this issue has been solved.