Rethink sssom strict mode as default for lexmatch

[cmungall]

I frequently run lexmatch on a new set, wait, then see a message

ValueError: [''] are used in the SSSOM mapping set but it does not exist in the prefix map

I then remember to set --no-ensure-strict-prefixes

Either:

• --no-ensure-strict-prefixes should be default
• an automatic repair with warnings should be default
• an initial scan should be performed and failure should happen before my CPU has wasted a lot of cycles doing an alignment

[matentzn]

Can we generate a random prefix and curify in this case, adding logger warning?

[cmungall]

you mean a random prefix expansion? I think having some kind of example.org/unknown/ type default expansion + warning would be ok. This would be trivial to fix in the header during post-processing / editing

[hrshdhgd]

I remember fixing the code such that "" is not flagged as a missing prefix. Which version of sssom-py is this?

[hrshdhgd]

I fixed it 4 months ago

[cmungall]

ontology-access-kit/pyproject.toml

Lines 17 to 18 in e98824e

	sssom-schema = ">=0.11.0"
	sssom = ">=0.3.26"

[hrshdhgd]

Yeah then this should not be happening. Can you show me an example for this?