URI metadata fields can remain String after PATCH, causing indexing failure

[jvendetti]

When patching the KISAO ontology through the API, the request failed during save with:

ArgumentError: ID must be set to be able to index

goo/lib/goo/search/search.rb:29:in `index_update`
ontologies_linked_data/models/ontology.rb:476:in `index_latest_submission`
...
ontologies_api/controllers/ontologies_controller.rb:92

The latest submission was invalid before indexing:

sub.valid?
# => false

sub.errors
# => {
#   publication: { uri: "All values in attribute `publication` must be `RDF::URI`" },
#   uri: { uri: "Attribute `uri` with the value `http://www.biomodels.net/kisao/KISAO#` must be `RDF::URI`" }
# }

sub.publication
# => ["https://doi.org/10.1038/msb.2011.77"]

sub.uri
# => "http://www.biomodels.net/kisao/KISAO#"

These two ontology submission attributes (:publication and :uri) are URI-typed in OntologySubmission. The URI strings themselves appear valid when wrapped as RDF::URI; the problem is that they remain plain Ruby String values. Goo’s :uri validator requires actual RDF::URI instances, not just valid URI text.

Expected behavior:

• PATCH/update handling should coerce valid string values for URI-typed metadata fields into RDF::URI before save/indexing, or reject them with a clear validation response.
• The API shouldn't surface the later Solr/indexing error as the primary failure when the latest submission is invalid.

Candidate areas to inspect:

• Metadata assignment/coercion for OntologySubmission fields declared with type: :uri or type: %i[uri list].
• The ontology save callback Ontology#index_latest_submission, which may need to avoid indexing an invalid latest submission or raise/report validation errors more clearly.