Updating to Pydantic v2

[glass-ships]

Closes #260

Summary

• Updates Pydantic to v2.5, along with some other packages to allow this
• Updates fixtures, scripts, and migrate related code
• Updates tests
  • curie expansion fails: on omim, ensembl, uberon, and wormbase (potentially unrelated?)

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[glass-ships]

curie expansion fails on: omim, ensembl, uberon, and wormbase (returns None)
@cthoyt do you by chance have an idea why this would be the case?
related code: https://github.com/monarch-initiative/monarch-app/blob/pydantic-v2/backend/src/monarch_py/service/curie_service.py

[cthoyt]

I can suggest you update the tests to use strict=True in the expand call then debug how prefix maps is constructing the EPM. This seems like a data and not a code issue

[glass-ships]

interesting, yeah...

        prefix, identifier = self.parse_curie(curie)
        rv = self.expand_pair(prefix, identifier)
        if rv:
            return rv
        if strict:
>           raise ExpansionError(curie)
E           curies.api.ExpansionError: WormBase:WBGene00000001

not sure where to start digging to sus this out

[cthoyt]

@glass-ships I wrote a minimal test that shows that there is no WormBase prefix available through the "merged" context in prefixmaps https://gist.github.com/cthoyt/ef44b41c11da966cfde322a9fac26859.

Here's the situation:

1. The source file for the v0.2.0 release, merged.csv, has several different related records that differ in http vs. https, but this shouldn't cause the issue

2. On a first pass, I thought this was related to an issue with the merging algorithm (which is definitely apparent from this screenshot), but I don't think this is the case. Some context about that thought process:

   I think there is an assumption that this situation does not happen - there should only be one "canonical" record with a given namespace. Therefore, this seems like an issue with the construction of the merged context.

   • I previously observed a similar issue for Wikidata and reported it in Duplicate entries for Wikidata linkml/prefixmaps#49
   • This could be a bug in the algorithm that makes the merged context, which I reported in Potential bug in the merge algorithm linkml/prefixmaps#50

   Discussion on Add tests for integrity of merged contexts linkml/prefixmaps#26 is also relevant - there, I suggested to apply some data integrity testing to the merged contexts

3. On a second thought, this seems like an even weirder error since WormBase isn't getting loaded at all in the converter (see the notebook). I still think this is a data issue and is not coming from curies

[glass-ships]

maybe a silly question but, when you say data error, what data in particular do you refer to?

[cthoyt]

The issue is happening because the wrong data is inside the curies.Converter object, not because there is a bug in the curies code. This means we need to look in the prefixmaps code or data to figure out why the right stuff doesn't make it inside the object that you're actually interacting with