feat: add cat vrs pydantic models #4
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Note for myself. This is up-to-date with current submodules. Just want to test in MetaKB first. |
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@DanielPuthawala it would be nice once things are more stable to create a test suite of valid and invalid catvars. |
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@korikuzma , are you intending to include the maturity status (draft, trial-use, normalized, deprecated) in these models? |
| CopyChange(v.code.root) | ||
| except ValueError as e: | ||
| err_msg = f"copyChange, {v.code.root}, not one of {[cc.value for cc in CopyChange]}" | ||
| raise ValueError(err_msg) from e |
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@korikuzma Do you represent the EFO codes enum anywhere? I may be missing it, but I don't see it in here?
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@DanielPuthawala these are imported from VRS-Python : https://github.com/ga4gh/vrs-python/blob/main/src/ga4gh/vrs/models.py#L171-L181
| from pydantic import BaseModel, Field, field_validator | ||
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| class CatVrsType(str, Enum): |
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So this is less of a problem and more of a thin got keep in mind for later, there are an astronomically large number of possible CatVar types. What we represent in recipes is only a very small subset of that, and do not constitute limits on valid CatVars, they just serve to define common useful CatVar classes of particular interest to the implementors.
@DanielPuthawala Since VRS-Python does not currently, I was not going to. However, in my Pydantic --> JSON Schema / RST I did include this. Can we do this in a separate issue? |
close #2