Search Mailing List Archives
[bioontology-support] Pull Location Uploading not working
alex.skrenchuk at stanford.edu
Wed Dec 7 10:37:39 PST 2016
Appliance has proper file ownership out the box but file permissions/ownership can get messed up if for example ncbo_cron was run manually as a root user instead of the ncbobp user. It's a very easy mistake to make and perhaps we could provide a script for resetting permissions with the appliance.
My earlier comments in 2014 about umask/wrong permissions relate to an existing issue with our codebase where sometimes new files in /srv/ncbo/repository directory are created writable by all users which is less than idea but has no impact on the application.
From: bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Vincent Emonet
Sent: Wednesday, December 07, 2016 8:40 AM
To: John Graybeal <jgraybeal at stanford.edu>
Cc: NCBO User Support <support at bioontology.org>
Subject: Re: [bioontology-support] Pull Location Uploading not working
Thanks for the help. I resolved that
I was also thinking about permissions problems (it's always permissions problems!). But was looking at the wrong place.
It was due to the fact that some files in ontologies_api/ncbo_cron was
under root owner instead of ncbobp owner.
I resolved it by changing all owner of ontologies_api, ncbo_cron,
repository to ncbobp (making sure ncbobp is the owner, of everything in
How are you doing on your side? Is it root or ncbobp that is the owner
of the code projects (ncbo_cron, ontologies_api...). When your pulling
from git and "bundle install" are you doing it from root or ncbobp?
Have a good day,
On 07/12/2016 03:36, John Graybeal wrote:
> Just throwing an idea out there before the end of our day, since we have a long turnaround time across the big water.
> This feels like a permissions problem. If it's running OK manually, maybe you have a permission that the automated process doesn't.
> And now that I've looked at the github code, it seems even more likely.
> And the jira issue reinforces this: "Newly upload files have wrong permissions". It appears files in the repository directory are created with the wrong permissions, but we've never figured out why.
> Alex fixed it as a one-off back in 2014: "I manually reset file permissions for repository directory; however, it is unclear why those files are created with wrong permissions". The debug code was put in to try to determine when/why the permissions are failing; initial indications are the file has the wrong permission, maybe 0 instead of something readable. But not sure how it gets that way.
> Ah, the last comment is in 2015, Alex writes:
>> is it happening because dante sets umask 0000 when forking?
> So, short term, try resetting the permissions of files in the source directory to allow them to be read, and make sure the destination directory is writeable.
> As far as the root cause of this problem, maybe we've learned something since 2015, I'll let the experts weigh in on that possibility.
>> On Dec 6, 2016, at 10:27 AM, Vincent Emonet <vincent.emonet at lirmm.fr> wrote:
>> On our local VA when we "add a submission" using a pull location the parsing of the ontology is hanging on:
>> "DEBUG -- : Pull location found, but no file in the upload file path. Retrying download."
>> After adding some logs to understand where it really comes from, I found that it was hanging when copying the file:
>> Notice that the 2 logger.debug of copy_file_repository don't produce anything when run automatically
>> The mysterious thing, is that if I run the processing manually "/srv/ncbo/ncbo_cron/bin/ncbo_ontology_process -o MY_ONT".
>> It's working without any problem.
>> I never touched this part of the code, and I experience this problem on the production and staging machines (and it was working before)
>> In the code I can see you already had some problems with it and added some logs to debug it (and did not remove them).
>> Do you have an idea where it could come from?
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> skype: graybealski
bioontology-support mailing list
bioontology-support at lists.stanford.edu
More information about the bioontology-support