Patch for issues 348

[RichardBruskiewich]

• Update requirements.txt of KGX to be more permissive of its linkml version (this eliminates the designated_type error, but still has some other unit test failures). Resolves ValueError: Unknown argument: designates_type = True error in 'make tests' #348

[RichardBruskiewich]

Hi @deepakunni3 ,

Unit tests are failing on the RDF and OWL code. The strange thing is that they fail both before and after the flipping of a relational operator which seems a bit odd as it relates to the edge cache of the rdf_source.py (see https://github.com/biolink/kgx/blob/master/kgx/source/rdf_source.py#L276). Can you take a closer look?

I also wonder about the dereify (https://github.com/biolink/kgx/blob/master/kgx/source/rdf_source.py#L332) method which ignores OBAN node properties like http://purl.org/oban/association_has_subject, http://purl.org/oban/association_has_predicate and http://purl.org/oban/association_has_object, which are used in the OBAN NT file (how universal are those properties in RDF inputs?) @balhoff maybe you have an opinion about this?

I need to spend time on some other KGX issues, so I can put this issue on the back burner pending your inputs?

[RichardBruskiewich]

Splitting out the RDF/OWL concerns to PR #351

[deepakunni3]

Not sure what is going on here. I'll take a look at the linked tickets and PR.

[deepakunni3]

@RichardBruskiewich Incrementing linkml fixed the tests?

[RichardBruskiewich]

@RichardBruskiewich Incrementing linkml fixed the tests?

Hi @deepakunni3, only the original "designates_type" error was fixed. The other RDF and OWL test failures continued. See PR #351