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mapping-commons / sssom-py

Python toolkit for SSSOM mapping format
https://mapping-commons.github.io/sssom-py/index.html#
MIT License
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SSSOM py should fail hard when a mapping is not parsed in strict mode #550

Open matentzn opened 3 weeks ago

matentzn commented 3 weeks ago

Context:

The original dataclass parser catches this:

WARNING:sssom.parsers:One mapping in the mapping set is not well-formed, and therfore not included in the mapping set ({'subject_id': 'NANDO:2200355', 'subject_label': 'Isolated ACTH deficiency', 'predicate_id': 'skos:exactMatch', 'object_id': 'MONDO:0008720|MONDO:0016042', 'mapping_justification': 'semapv:MappingCuration'}). Error: MONDO:0008720|MONDO:0016042 is not a valid URI or CURIE

_Originally posted by @matentzn in https://github.com/mapping-commons/sssom-py/pull/532#discussion_r1604435772_