SemanticallyStandardizable

class SemanticallyStandardizable

Bases: ABC

An object that can be standardized.

In the following example, a simple object is constructed:

from typing_extensions import Self
from curies import Converter, Reference, SemanticallyStandardizable


class ReferenceHolder(SemanticallyStandardizable):
    def __init__(self, reference):
        self.reference = reference

    def standardize(self, converter: Converter) -> Self:
        return ReferenceHolder(converter.standardize_reference(self.reference, strict=True))

It’s good form to make these operations return new objects, but there’s no reason you couldn’t update the object in place like in :

from typing_extensions import Self
from curies import Converter, Reference, SemanticallyStandardizable


class ReferenceHolder(SemanticallyStandardizable):
    def __init__(self, reference):
        self.reference = reference

    def standardize(self, converter: Converter) -> Self:
        self.reference = converter.standardize_reference(self.reference, strict=True)
        return self

In the following example, the pydantic.BaseModel.model_copy() is used to automatically reuse all other fields that aren’t updated, which creates a new object.

import datetime
from typing_extensions import Self
from curies import Converter, Reference, SemanticallyStandardizable
from pydantic import BaseModel


class Triple(BaseModel, SemanticallyStandardizable):
    subject: Reference
    predicate: Reference
    object: Reference
    date_asserted: datetime.date

    def standardize(self, converter: Converter) -> Self:
        return self.model_copy(
            update={
                "subject": converter.standardize_reference(self.subject, strict=True),
                "predicate": converter.standardize_reference(self.predicate, strict=True),
                "object": converter.standardize_reference(self.object, strict=True),
            }
        )

curies provides a high-level interface for standardizing classes in curies.standardize().

from curies import Converter

converter = Converter()
converter.add_prefix("CHEBI", "http://purl.obolibrary.org/obo/CHEBI_")
converter.add_synonym("CHEBI", "chebi")

r1 = ReferenceHolder(Reference.from_curie("chebi:1"))
r2 = ReferenceHolder(Reference.from_curie("chebi:2"))

# can be used directly on an object
assert ReferenceHolder(Reference.from_curie("CHEBI:1")) == curies.standardize(r1, converter)

# can also be used on an iterable/collection
assert [
    ReferenceHolder(Reference.from_curie("CHEBI:1")),
    ReferenceHolder(Reference.from_curie("CHEBI:2")),
] == curies.standardize((r1, r2), converter)

Methods Summary

standardize(converter)

Standardize all references in the object.

Methods Documentation

abstractmethod standardize(converter: Converter) → Self

Standardize all references in the object.