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[bioontology-support] Pull Location Uploading not working

John Graybeal jgraybeal at stanford.edu
Tue Dec 6 18:36:47 PST 2016


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





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