Error on deleting an ontology that has provisionalClasses

[syphax-bouazzouni]

At Agroportal, when we try to delete an ontology that has provisionalClasses, we get this exception :

NoMethodError: undefined method `select!' for #<LinkedData::Models::Ontology:0x0000000004896968>
from /srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-db2377e860d7/lib/ontologies_linked_data/models/ontology.rb:367:in `block in delete'

And i think that the cause of the problem is here : https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/ontology.rb#L366

[jonquet]

After discussing this with @syphax-bouazzouni we see a discrepancy between what is in the model and what is in the delete ontology script.
The first one assumes a provisional class has one and only one ontology (see https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/provisional_class.rb#L16)
The second one assumes a provisionnal class can be in several ontologies (thus the onts.select!)

We believe the model is right and the script is wrong.
@mdorf @jvendetti Do you confirm ?

In that case, the onts.select! will be removed and changed by a couple of lines of code that will delete all the provisional classes when the ontology containing them is itself deleted.

We can PR the change if confirmed by you.

[mdorf]

@jonquet, @syphax-bouazzouni, you are correct! This does appear to be a discrepancy. I think the code should be revised to:

self.bring(:provisionalClasses)
unless self.provisionalClasses.nil?
  self.provisionalClasses.each do |p|
    p.delete
  end
end

My concern is that our unit test suite did not catch this error. We should fix the corresponding unit test along with this change by adding a provisional class to one (or both) of the two ontologies created in the test:

https://github.com/ncbo/ontologies_linked_data/blob/master/test/models/test_ontology.rb#L298
https://github.com/ncbo/ontologies_linked_data/blob/master/test/models/test_ontology.rb#L299

Something like this on Line 303 should do the trick, I think (please verify):

pc = LinkedData::Models::ProvisionalClass.new({label: "Test Provisional Class", creator: u, ontology: o1})
pc.save

Good catch!

[jonquet]

@mdorf
We have fixed (@syphax-bouazzouni ) the script. Be sure to "update/control" the tests.