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_uns_field.py
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_uns_field.py
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import logging
from typing import Optional
import rich
from anndata import AnnData
from scvi.data import _constants
from ._base_field import BaseAnnDataField
logger = logging.getLogger(__name__)
class BaseUnsField(BaseAnnDataField):
"""An abstract AnnDataField for .uns attributes in the AnnData data structure.
Parameters
----------
registry_key
Key to register field under in data registry.
uns_key
Key to access the field in the AnnData uns mapping. If None, defaults to `registry_key`.
required
If False, allows for `uns_key is None` and marks the field as `is_empty`.
"""
_attr_name = _constants._ADATA_ATTRS.UNS
def __init__(
self, registry_key: str, uns_key: Optional[str], required: bool = True
) -> None:
super().__init__()
if required and uns_key is None:
raise ValueError(
"`uns_key` cannot be `None` if `required=True`. Please provide an `uns_key`."
)
self._registry_key = registry_key
self._attr_key = uns_key
self._is_empty = uns_key is None
@property
def registry_key(self) -> str:
return self._registry_key
@property
def attr_name(self) -> str:
return self._attr_name
@property
def attr_key(self) -> str:
return self._attr_key
@property
def is_empty(self) -> bool:
return self._is_empty
class StringUnsField(BaseUnsField):
"""An AnnDataField for string .uns attributes in the AnnData data structure."""
def validate_field(self, adata: AnnData) -> None:
"""Validate the field."""
super().validate_field(adata)
if self.attr_key not in adata.uns:
raise KeyError(f"{self.attr_key} not found in adata.uns.")
def register_field(self, adata: AnnData) -> dict:
"""Register the field."""
return super().register_field(adata)
def transfer_field(
self,
state_registry: dict,
adata_target: AnnData,
**kwargs,
) -> dict:
"""Transfer the field."""
super().transfer_field(state_registry, adata_target, **kwargs)
return self.register_field(adata_target)
def get_summary_stats(self, _state_registry: dict) -> dict:
"""Get summary stats."""
return {}
def view_state_registry(self, _state_registry: dict) -> Optional[rich.table.Table]:
"""View the state registry."""
return None