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[bioontology-support] Help Deleting Troublesome Ontologies

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Jul 5 15:06:58 PDT 2018


Hi Sydney,

I’m glad it’s working for you now.

If you run into anything similar in the future, another issue could be a corrupt entry in the cache. You can clear the application caches via the “Admin" page in the user interface:


[cid:2F751492-B7CE-49BF-AACB-C1008A4CFCB7 at stanford.edu]
For Goo::Base::AttributeNotLoaded errors, you’d want to try flushing the Goo cache.

Another item of potential interest is turning on more extensive logging in order to debug issues like the one you saw. You would need to uncomment a couple of lines in your unicorn.rb file, i.e.:

https://github.com/ncbo/virtual_appliance/blob/master/appliance_config/ontologies_api/config/unicorn.rb#L11

… and restart your system.

Kind regards,
Jennifer



On Jul 5, 2018, at 1:48 PM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Hello!

I just wanted to send an update with a very simple fix. (So simple that it just went right over my head). Because my local instance did not recognize that Ontology XYZ existed, it did not object to me submitting a 'new' ontology with the same name and data. This solved the issue!

Thanks for taking the time to help me out.

Best,

Sydney

On Thu, Jul 5, 2018 at 2:15 PM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:
unfortunately that returns 'nil'

On Thu, Jul 5, 2018 at 2:08 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Are you able to access the ontology object from a console session using the following syntax:

ont = LinkedData::Models::Ontology.find(RDF::URI.new("http://data.bioontology.org/ontologies/IEV")).first

You would need to replace the URL passed to the new() method with your domain name and your problematic ontology acronym. If you get an object back, you should then be able to call delete on it.

Jennifer



On Jul 5, 2018, at 11:59 AM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Originally I was issuing a REST API call in order to delete the ontology. When that failed I have since tried both methods

On Thu, Jul 5, 2018 at 1:57 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Apologies - you already included that information and I missed it upon first reading.

Are you issuing a REST API call to delete the ontology? Or, are you doing it via a console session, as described here:

https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_delete_an_ontology.3F

Jennifer



On Jul 5, 2018, at 11:52 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Sydney,

Could you please clarify for us if you’re working on the main BioPortal, or a virtual appliance instance?

Jennifer



On Jul 5, 2018, at 11:48 AM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Hello,

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 ontology?)

Thank you for your help!
--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314
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--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314




--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314



--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314

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