from typing import ClassVar, List
from czbenchmarks.datasets.single_cell import SingleCellDataset
from czbenchmarks.datasets.single_cell_labeled import SingleCellLabeledDataset
from ...datasets import Organism
from .dataset_validator import DatasetValidator
[docs]
class SingleCellLabeledValidator(DatasetValidator):
"""Base validator for single-cell labeled datasets.
Provides validation logic for single-cell labeled datasets, including:
- Checking if the dataset organism is supported
- Validating presence of required observation and variable keys in AnnData
"""
dataset_type: ClassVar[type] = SingleCellLabeledDataset
available_organisms: ClassVar[List[Organism]]
required_obs_keys: ClassVar[List[str]]
required_var_keys: ClassVar[List[str]]
[docs]
def __init_subclass__(cls) -> None:
"""Ensure required class variables are defined in subclasses.
Subclasses must define:
- available_organisms
- required_obs_keys
- required_var_keys
Raises:
TypeError: If any required class variable is missing in the subclass
"""
super().__init_subclass__()
if not hasattr(cls, "available_organisms"):
raise TypeError(
f"Can't instantiate {cls.__name__} "
"without available_organisms class variable"
)
if not hasattr(cls, "required_obs_keys"):
raise TypeError(
f"Can't instantiate {cls.__name__} "
"without required_obs_keys class variable"
)
if not hasattr(cls, "required_var_keys"):
raise TypeError(
f"Can't instantiate {cls.__name__} "
"without required_var_keys class variable"
)
def _validate_dataset(self, dataset: SingleCellDataset):
"""Validate a single-cell dataset.
Checks:
1. Dataset organism is in available_organisms
2. All required observation keys are present in dataset.adata.obs.columns
3. All required variable keys are present in dataset.adata.var.columns
Args:
dataset: SingleCellDataset to validate
Raises:
ValueError: If any validation check fails
"""
if dataset.organism not in self.available_organisms:
raise ValueError(
f"Dataset organism {dataset.organism} "
"is not supported for {self.__class__.__name__}"
)
# Check for missing required observation keys in AnnData obs
missing_keys = [
key
for key in self.required_obs_keys
if key not in dataset.adata.obs.columns
]
if missing_keys:
raise ValueError(f"Missing required obs keys: {missing_keys}")
# Check for missing required variable keys in AnnData var
missing_keys = [
key
for key in self.required_var_keys
if key not in dataset.adata.var.columns
]
if missing_keys:
raise ValueError(f"Missing required var keys: {missing_keys}")