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[bioontology-support] Help Deleting Troublesome Ontologies

Sydney Hoppe hoppesyd at
Thu Jul 5 11:48:38 PDT 2018


I have ran into a rather large issue: I attempted to delete an ontology but
at some point the delete failed, but was halfway complete. Let me give a
bit of further background.

Currently my submissions API page returns a 500 Internal Server Error.
Through further investigation I have determined that the error stems from
an uncaught exception produced in the
/srv/ncbo/ontologies_api/current/helpers/application_helper.rb file in the
retrieve_latest_submissions function on line 350. Within this function
there is a loop "submission.each do |sub|". After a few iterations of the
loop an error is thrown. The error is as follows :

class: Goo::Base::AttributeNotLoaded

message: Persistent object with `acronym` not loaded

For a while I was unable to determine which ontology this statement was
referring to because, as it states, there is no acronym loaded for that
particular ontology. But, I was able to print out the Description
associated with the ontology and I have determined which ontology I am
struggling with. (Which one it is does not necessarily matter, lets call it
Ontology XYZ). I Continued to search my local bioportal instance for
Ontology XYZ but it is nowhere to be found, not even in the API. I tried to
re-delete Ontology XYZ but, an ontology with that acronym can not be found.

To summarize, while attempting to delete Ontology XYZ the delete failed,
and I am now left with an ontology in my system that has no acronym
associated with it.

Now to my question, Is there any other way to delete an ontology without
using their acronym? (Perhaps with some other piece of data about the

Thank you for your help!
*Sydney Hoppe*
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at | 614.282.1314
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