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[bioontology-support] VA ontology delete error

Paul R Alexander palexander at stanford.edu
Mon Jul 7 10:57:30 PDT 2014


Please try the following from the console:
ontology.bring(:submissions)
ontology.delete

Paul


On Jul 7, 2014, at 5:21 AM, Vitaly Zimukha <unknownnpc at gmail.com> wrote:

> Dear support team,
> 
> I can't delete ontology via using a console after server crash (problems
> with electricity). I want to note that other ontologies work fine except
> 'broken' one. 
> 
> What I trying to do in the ncbo cron console:
> pry(main)> ontology = LinkedData::Models::Ontology.find("MEDDRA").first
> => #<LinkedData::Models::Ontology:0x007fd984a19298
> @aggregates=nil,
> 
> @id=#<RDF::URI:0x3fecc250d5e0(http://data.bioontology.org/ontologies/MEDDRA)>,
> @loaded_attributes=#<Set: {}>,
> @modified_attributes=#<Set: {}>,
> @persistent=true,
> @previous_values=nil,
> @unmapped=nil>
> pry(main)> ontology.delete
> *Goo::Base::AttributeNotLoaded: Persistent object with `submissions` not
> loaded
> from
> /usr/local/rbenv/versions/2.0.0-p247/lib/ruby/gems/2.0.0/bundler/gems/goo-9e387b5224d7/lib/goo/base/settings/settings.rb:238:in
> `block in shape_attribute'*
> 
> In addition I can't see MEDDRA ontology on the web ui ontologies list
> (http://my.va/ontologies). Manual parse works fine.
> 
> Could you please help me to delete 'broken' ontology or free up the 'MEDDRA'
> acronym name. 
> 
> Best Regards,
> Vitaly 
> 
> 
> 
> 
> --
> View this message in context: http://ncbo-support.2288202.n4.nabble.com/VA-ontology-delete-error-tp4653139.html
> Sent from the NCBO Support mailing list archive at Nabble.com.
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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 




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