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[bioontology-support] Bug in VA 2.4 when adding private ontology

Emonet vincent.emonet at
Fri May 29 02:01:22 PDT 2015


We have met a problem by adding a private ontology to our BioPortal 
Virtual Appliance version 2.4

We have done this on the VA start (nothing was done before, so the VA 
was "clear", the only other ontology was STY the default ontology)
After adding the private ontology (which was a UMLS ontology generated 
by the umls2rdf python script) we could not access to the /ontologies 
browsing page when disconnected or connected with an account that 
doesn't have the view permission on the private ontology.

We got the classic " We're sorry but something has gone wrong. We have 
been notified of this error." on the UI.

     And here is the error raised in 

Started GET "/ontologies" for ***.***.***.** at 2015-05-29 01:37:21 -0700
Processing by OntologiesController#index as HTML
Completed 500 Internal Server Error in 33.6ms

ArgumentError (odd number of arguments for Hash):
   app/controllers/ontologies_controller.rb:51:in `[]'
   app/controllers/ontologies_controller.rb:51:in `index'

In the ontologies_controller.rb this line correspond to
     submissions_map = Hash[ {|sub| 
[sub.ontology.acronym, sub] }]

Other details:

  * We still can go to public ontology (in this case /ontologies/STY)
    directly using their UI URL (even when disconnected)
  * REST API show only public ontology (STY) if disconnect (so normal
  * The private ontology have been well uploaded (with metrics well
  * Same error if we use the
    (master branch) on production on the Virtual Machine
  * We don't get this error if we use the git version (master branch) in
    development environment on our machine

Do you have an idea what can cause this problem?


Vincent Emonet

SIFR Project, University of Montpellier

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