Update MONDO local unique identifiers

[cthoyt]

Following #104 (comment), this PR implements the change that we won't make assumptions about how Identifiers.org might curate future OBO Foundry ontologies' local unique identifier patterns. Therefore, this PR removes the redundant prefixes in MONDO's local unique identifiers.

This PR could be merged directly or also combine into #104 if the diff would be a problem

[bgyori]

Okay. We should also look into validation functions and make sure they are consistent. The function check_valid_prefix_id is used in the following places:

tests/test_validity.py
23:from biomappings.utils import SKIP_BANANA, check_valid_prefix_id, get_canonical_tuple
124:        check_valid_prefix_id(
128:        check_valid_prefix_id(

src/biomappings/utils.py
147:def check_valid_prefix_id(prefix: str, identifier: str) -> None:

src/biomappings/wsgi.py
25:    check_valid_prefix_id,
216:            check_valid_prefix_id(source_prefix, source_id)
225:            check_valid_prefix_id(target_prefix, target_id)

However, its behavior doesn't make sense currently, and after some digging, I traced this back to a significant change in logic in Bioregistry's miriam_standardize_identifier function, which, when changed in biopragmatics/bioregistry#427 was not appropriately followed up by corresponding changes here. The issue is that this function used to return a useful value (i.e., an identifier) whether or not a resource had MIRIAM data, but now it just returns None. So the validity check in Biomappings returns incorrectly after a check for a MIRIAM-standardized identifier.

[cthoyt]

@bgyori in 0ab87e9 I took care of deduplicating two functions that both were doing validity checking (I favored the one that wasn't baked into the unittest since it was reused elsewhere in the package). Now it's more consistent how the logic is applied (no more need for the flags for NCIT and AGRO) and more clear that the potential None return in miriam_standardize_identifier() is not actually possible since there's a guard clause (i.e., check to make sure there's a miriam prefix available before even running miriam_standardize_identifier()).

The diff isn't so great but the function reads pretty nicely now:

biomappings/src/biomappings/utils.py

Lines 144 to 165 in 0ab87e9

	def check_valid_prefix_id(prefix: str, identifier: str) -> None:
	"""Check the prefix/identifier pair is valid."""
	resource = bioregistry.get_resource(prefix)
	if resource is None:
	raise InvalidPrefix(prefix)
	miriam_prefix = resource.get_miriam_prefix()
	if miriam_prefix is not None:
	norm_id = resource.miriam_standardize_identifier(identifier)
	if norm_id is None:
	raise ValueError(
	"should not be possible since we check for miriam prefix before running miriam_standardize_identifier"
	)
	if norm_id != identifier:
	raise InvalidNormIdentifier(prefix, identifier, norm_id)
	pattern = re.compile(resource.miriam["pattern"])
	else:
	norm_id = resource.standardize_identifier(identifier)
	if norm_id != identifier:
	raise InvalidNormIdentifier(prefix, identifier, norm_id)
	pattern = resource.get_pattern_re()
	if pattern is not None and not pattern.match(identifier):
	raise InvalidIdentifierPattern(prefix, identifier, pattern)

[bgyori]

Great, thanks!