Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Pull Location Uploading not working

Alex Skrenchuk alex.skrenchuk at stanford.edu
Wed Dec 7 10:37:39 PST 2016


Hi Vincent,

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.
 
-Alex

-----Original Message-----
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 
/srv/ncbo)


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,

Vincent

On 07/12/2016 03:36, John Graybeal wrote:
> Vincent,
>
> 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?
>>    https://github.com/nesquena/dante/blob/master/lib/dante/runner.rb#L91
> 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.
>
> John
>
>
>> On Dec 6, 2016, at 10:27 AM, Vincent Emonet <vincent.emonet at lirmm.fr> wrote:
>>
>> Hi,
>>
>> 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."
>>
>> https://github.com/sifrproject/ncbo_cron/blob/master/lib/ncbo_cron/ontology_submission_parser.rb#L168
>>
>> After adding some logs to understand where it really comes from, I found that it was hanging when copying the file:
>>
>> https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/ontology_submission.rb#L103:L109
>>
>> 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?
>>
>> Thanks!
>>
>> Vincent
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632
> skype: graybealski
>
>
>

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/bioontology-support



More information about the bioontology-support mailing list