Use custom code for RDF (de)serialisation #635
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Since the normalised variant of SSSOM/RDF does not match the output produced (respectively expected) by the LinkML runtime's dumper (resp. loader), we implement our own serialisation/deserialisation routines for RDF. All the code for RDF import/export is contained within the sssom.rdf_internal module. The only class expected to be used outside of that module is the MappingSetRDFConverter class. The `from_sssom_rdf` and `to_rdf_graph` functions in the sssom.parsers and sssom.writers modules are rewritten to use that class.
The new RDF converter revealed several issues with our existing tests, which are fixed here. * test_convert.py (test_to_rdf_hydrated): That test used an incorrect "NOT" value for a predicate modifier slot (the correct value is "Not", and there is nothing in the spec to suggest it is case-insensitive); it also forgot to declare some prefixes; * test_writers.py (test_rdflib_endpoint): That test used "sssom:MappingCuration" as a column name in a MappingSetDataFrame, instead of the expected "mapping_justification"; it also forgot to declare some prefixes.
Add a couple of tests to check the behaviour of the new RDF parser. Also fix an issue (revealed by one of those tests) with the RECORD_ID slot, which must be compressed upon parsing since it is an EntityReference-typed slot.
Use the latest pre-release of the SSSOM schema, which includes the changes related to the latest draft of the SSSOM/RDF specification.
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This PR implements option ”A” mentioned in #628. That is, it replaces the LinkML-based code for serialising/deserialising to/from RDF by a completely custom code that implements the new SSSOM/RDF spec exactly as we want it.
All the new code is contained within the new
sssom.rdf_internalmodule, which as the name implies is not really supposed to be used outside of SSSOM-Py (though of course people can still do whatever they want!). The public interface to read from RDF is still thefrom_sssom_rdfmethod insssom.parsers, and the public interface to write to RDF is still theto_rdf_graphmethod insssom.writers. Both methods are rewritten to use the MappingSetRDFConverter class of thesssom.rdf_internalmodule, instead of methods from the LinkML runtime.closes #628