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[bioontology-support] Running ncbo_ontology_process

John Graybeal jgraybeal at
Tue Sep 20 07:48:02 PDT 2016

Hi Vincent,

The first thing I would check is whether all the target directories (including any temporary directories) are write-enabled. It is possible one of them got changed to read-only somehow.  (Alternatively, maybe the target directory for that ontology in particular is not what you'd expect and doesn't have write permissions, because the ontology itself is in an unusual place.)

Sorry that I can't give you a list of the directories to which BioPortal writes during this process, but an inspection of a previous log could reveal that fairly easily, with luck.  Would be nice if that got reported in the error log (you might look for it in the log above where the error is reported).


> On Sep 20, 2016, at 10:37 AM, Vincent Emonet <vincent.emonet at> wrote:
> Hi!
> I am trying to run the ncbo_ontology_process script to re-process some ontologies. I already used it in the past and it was working properly.
> But when in try to run it (as root) I get the following error:
>> Failed, exception: LinkedData::Security::WriteAccessDeniedError: Write access denied
>> /usr/local/rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/bundler/gems/ontologies_linked_data-84c8b6581581/lib/ontologies_linked_data/models/base.rb:182:in `write_permission_check'
>> /usr/local/rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/bundler/gems/ontologies_linked_data-84c8b6581581/lib/ontologies_linked_data/models/base.rb:12:in `save'
>> /usr/local/rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/bundler/gems/ontologies_linked_data-84c8b6581581/lib/ontologies_linked_data/models/ontology_submission.rb:1343:in `process_submission'
>> /srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:194:in `process_submission'
> It can't save the submission because of a "Write access denied". But I am running it from the command line as root user. Have you already faced this problem? Do you know where it could come from?
> Thanks,
> Vincent
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
skype: graybealski

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