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Galaxy should not try to chown() linked in files retry_job_output_collection times (or at all) #3990

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dpryan79 opened this issue Apr 27, 2017 · 0 comments

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commented Apr 27, 2017

I was just experiencing an NFS issue and then happened to then set retry_job_output_collection to a value > 0 when I noticed that this resulted in Galaxy repeatedly trying to chown() newly linked in files. The culprit in the code is https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/__init__.py#L1209

This ends up not being a fatal issue, just a warning, but it's mildly annoying nonetheless.

I'm not familiar with the whatever object that dataset is, but I imagine it has information about whether it's an external file, so one could toss an if not dataset.external: in there.

dpryan79 added a commit to dpryan79/galaxy that referenced this issue Jun 13, 2017

jmchilton added a commit that referenced this issue Jul 5, 2017

Merge pull request #4186 from dpryan79/fix3990
Fix #3990, don't chown non-galaxy files
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