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niworkflows.utils.bids.collect_data failing to retrieve BOLD images #293

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oesteban opened this issue Jan 28, 2019 · 5 comments
Closed

niworkflows.utils.bids.collect_data failing to retrieve BOLD images #293

oesteban opened this issue Jan 28, 2019 · 5 comments
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bug impact:high Estimated high impact task

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@oesteban
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It seems that the original bug causing nipreps/fmriprep#1481 is still there (https://neurostars.org/t/fmriprep-from-singularity-unboundlocalerror/3299/9?u=oesteban).

Not getting a 'bold' entry after the BIDSLayout query would explain the original UnboundLocalError symptom. @emdupre first noticed this during #285.

@effigies, any quick thoughts about what could've changed in pybids land that we did not account for in our end?
@oesteban oesteban added the bug label Jan 28, 2019
@effigies
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We're still depending on pybids 0.6.5... Nothing has changed in that. Unless there's some reason that 0.7.0 is getting pulled in?

@oesteban
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@emdupre could not replicate the original bug, and the error seems persistent only with singularity containers. Maybe a system-wide installation pybids installation is coming into play.

@effigies
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That's a thought I had, but the paths in their tracebacks are in the same directory as fmriprep.

@effigies
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Perhaps their singularity image is at fault. Do we have one we can verify works on our data, and give to them to see if they still reproduce the failure?

@effigies effigies added this to To do in pipelines Mar 6, 2019
@oesteban oesteban moved this from To do to Watching in pipelines Mar 6, 2019
@oesteban oesteban added the impact:high Estimated high impact task label Mar 12, 2019
@oesteban
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Seems like the original UnboundLocalError is not happening anymore. Please reopen in case of regression.

pipelines automation moved this from Awaiting for user input to Done Mar 14, 2019
@oesteban oesteban removed this from Done in pipelines Feb 26, 2020
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@effigies @oesteban