find method on LinkedData::Client::Models::Class throws argument error

[jvendetti]

I couldn't find any functionality in the BioPortal RoR application that triggers a call to find on LinkedData::Client::Models::Class, nor do we have any unit tests that exercise that particular method.

If you attempt to call the method in a debugging environment, e.g.:

LinkedData::Client::Models::Class.find(
  'http://purl.bioontology.org/ontology/STY/T047', 
  'https://data.bioontology.org/ontologies/STY'
)

... the library throws an ArgumentError:

ArgumentError: wrong number of arguments (given 1, expected 0)

The method attempts to explore a non-existent type of hypermedia link on an ontology object (i.e., 'class' instead of 'single_class').

[syphax-bouazzouni]

Hi, Directly related, this PR: https://github.com/ncbo/ontologies_api_ruby_client/pull/15

I think that the current find in the api_client is not really well implemented, In the backend, it would be

LinkedData::Models::Class.find(RDF::URI.new(cls_id)).in(submission).first

But in our client, the .in(submission) (collection system) is not implemented (I think, I hope I'm not mistaken here)

I don't know what is your plan to fix this, but updating the api_client to handle collection, in general, would be great if you do it. So that we can have something like this

LinkedData::Client::Models::Class.find('http://purl.bioontology.org/ontology/STY/T047').in('https://data.bioontology.org/ontologies/STY') 
# will call https://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT047

Finally, I think also that the single_class endpoint is not really needed, doesn't follow the REST standard, and was only an ad-hoc solution no more needed when we have this https://github.com/ncbo/ontologies_api_ruby_client/pull/15

[jvendetti]

Hi Syphax. I hadn't planned on anything other than a simple fix. If you modify the code from what it is currently:

def self.find(id, ontology, params = {})
  ontology = HTTP.get(ontology, params)
  ontology.explore.class(URI.escape(id, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]")))
end

... to this:

def self.find(id, ontology, params = {})
  ontology = HTTP.get(ontology, params)
  ontology.explore.single_class(id)
end

... the method returns the requested class without errors.

With regard to the single_class endpoint, I'll post comments separately in PR #15.

[syphax-bouazzouni]

OK, in parallel I added this issue https://github.com/ontoportal-lirmm/ontologies_api_ruby_client/issues/8 so that we remember of a possible optimization here.