Convert IRI -> CURIE using bioregistry while parse-ing a KGCL command.
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src/kgcl_schema/grammar/parser.py
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| pref, i = parse_iri(uri[0].replace("<", "").replace(">","")) | ||
| pref = get_preferred_prefix(pref) | ||
| curie = curie_to_str(pref, i) | ||
| input = input.replace(uri[0], curie) |
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Beter use https://github.com/cthoyt/curies
| pref = get_preferred_prefix(pref) | ||
| curie = curie_to_str(pref, i) | ||
| input = input.replace(uri[0], curie) | ||
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It seems very hacky to replace URIs with CURIEs just so the KGCL parser works. Why is that necessary?
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When adding synonyms, apparently only CURIEs are expected and ehnce the conversion from URI => CURIE. Just a judgement call, there could be a better way of handling this. Ideas?
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I dont know how that parser works, but if CURIES are expected, wouldn't it be better to make sure the input is "valid kgcl" using a validator and not trying to hack anything? The user can be forced to provide CURIEs if that is what the spec wants..
In any case, I would for sure factor out the method def replace_uris_with_curies_in_kgcl_command(input) into its how, document it etc. Not convinced this is great but if its necessary to be parseable than so be it.
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curie_from_iri<>around URIs : fixes Do not require <>s in URIs kgcl-rdflib#58