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Fix #3990, don't chown non-galaxy files #4186

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merged 1 commit into from Jul 5, 2017

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commented Jun 13, 2017

This should fix #3990, which is due to Galaxy trying to chown files that it may not own. The easy fix is to just ignore linked in files, which I presume will always have external_filename is not None.

@galaxybot galaxybot added the triage label Jun 13, 2017

@galaxybot galaxybot added this to the 17.09 milestone Jun 13, 2017

@bgruening bgruening added area/jobs and removed triage labels Jun 13, 2017

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commented Jun 14, 2017

Looks good to me! @natefoo what do you think?

@jmchilton jmchilton merged commit 3529897 into galaxyproject:dev Jul 5, 2017

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commented Jul 5, 2017

Great - thanks @dpryan79 - it looks good to me. @natefoo if this should be undone - let me know!

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commented Sep 28, 2017

Alternatively, we could turn that os.chown() into an os.lchown(). But if the file is external and it's a tool output and it's a symlink, this can only mean that it's a library upload where the user has selected not to copy the dataset into Galaxy and thus the NFS attributes should not have changed since before the job even began, right?

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commented Sep 28, 2017

External files aren't actually symlinked.

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commented Sep 28, 2017

Right, duh. All good then.

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commented Sep 28, 2017

No worries, it's confusing nomenclature :)

@dpryan79 dpryan79 deleted the dpryan79:fix3990 branch Sep 28, 2017

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commented Sep 29, 2017

Right, but I think I implemented that feature. 😆

@martenson martenson added the kind/bug label Oct 9, 2017

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