Permissions inside container result in root owned files externally

[hexylena]

The notebook process runs as root internally, so whenever it generates checkpoints, those retain those permissions in the shared directory, and as a result cannot be cleaned up by galaxy.

hxr@emi:~/work/galaxy-central/database/tmp$ rm -rf *
rm: cannot remove ‘tmpfUhBgD/.ipynb_checkpoints/ipython_galaxy_notebook-checkpoint.ipynb’: Permission denied
rm: cannot remove ‘tmp_jH6Kz/.ipynb_checkpoints/ipython_galaxy_notebook-checkpoint.ipynb’: Permission denied
rm: cannot remove ‘tmpMmq8FU/.ipynb_checkpoints/ipython_galaxy_notebook-checkpoint.ipynb’: Permission denied

[bgruening]

I will try to get a workaround for it, but it seems hard at the moment. moby/moby#3124

[hexylena]

Hmmm, yeah that is tough. If there's a way we can pass the container our uid/gid and just chown the files, that might be an option.

[bgruening]

We could save them in /import/ and before we kill ipython (in the monitor_traffic script) we could chmod the entire /import/ directory.... uh dirty ...

[hexylena]

That's actually a decent suggestion:

• The only time they need to be owned by galaxy, is whenever the temp folder is being cleaned up.
• The temp files should not be cleaned while in use.
• Once we're done with them, the system should be free to clean them.

Therefore, chowning them once we're done is perfectly acceptable. Thoughts?

[bgruening]

Thinking about that a little bit more, is there any reason why we can't delete all from within docker?

[hexylena]

No reason we couldn't do that, especially if we're doing persistence via creation of a new galaxy history element. Let's clean up properly after ourselves.

On July 26, 2014 1:35:59 PM CDT, "Björn Grüning" notifications@github.com wrote:

Thinking about that a little bit more, is there any reason why we can't
delete all from within docker?

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Sent from my Android device with K-9 Mail. Please excuse my brevity.

[bgruening]

Let's see if that fixes the problem: 43c8ac8

[hexylena]

Works correctly except if the container was intentionally killed before shutdown. This is completely acceptable.