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🎨 Raise OrganismNotSet instead of AssertionError when organism is not set #144

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merged 3 commits into from
Nov 5, 2024
Merged

🎨 Raise OrganismNotSet instead of AssertionError when organism is not set #144

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a6aa9c9
:art: Use ValueError instead of AssertionError
Zethson Nov 5, 2024
ad3d2e8
:art: Use custom Error
Zethson Nov 5, 2024
d1fc8c7
:art: Move error
Zethson Nov 5, 2024
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8 changes: 7 additions & 1 deletion bionty/_bionty.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,12 @@
from types import ModuleType


class OrganismNotSet(SystemExit):
"""The `organism` parameter was not passed or is not globally set."""

pass


def create_or_get_organism_record(
organism: str | Record | None, registry: type[Record], field: str | None = None
) -> Record | None:
Expand Down Expand Up @@ -54,7 +60,7 @@ def create_or_get_organism_record(
"uid",
}:
return None
raise AssertionError(
raise OrganismNotSet(
f"{registry.__name__} requires to specify a organism name via `organism=` or `bionty.settings.organism=`!"
)

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2 changes: 1 addition & 1 deletion bionty/core/_add_ontology.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
from __future__ import annotations

from typing import TYPE_CHECKING, Iterable, List, Optional, Set, Tuple, Type, Union
from typing import TYPE_CHECKING, Iterable

from lamin_utils import logger

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