torchcell.datasets.scerevisiae.wildenhain2015.EnvChemgenWildenhain2015Dataset

class EnvChemgenWildenhain2015Dataset(root: str = 'data/torchcell/env_chemgen_wildenhain2015', io_workers: int = 0, transform: Callable[[...], Any] | None = None, pre_transform: Callable[[...], Any] | None = None, **kwargs: Any)

Bases: ExperimentDataset

Wildenhain 2015 chemical-genetic matrix: env x geno -> growth-inhibition z-score.

organism: ClassVar[Organism] = 'scerevisiae'

each loader declares its own, the build’s organism switch reads it off the class (dataset_organism), and a loader that forgot it is refused by name instead of inheriting an organism it may not have.

Type:

The host organism every record describes. Annotated here WITHOUT a value

property experiment_class: type[Experiment]

Experiment schema class produced by this dataset.

property reference_class: type[ExperimentReference]

Experiment-reference schema class produced by this dataset.

property raw_file_names: list[str]

The datapoint export and the AID description the protocol is sourced from.

download() → None

Link the mirror files into raw/ after verifying each against its pin.

DATA_SHA256 and AID_SHA256 are the pins; the manifest is the retrieval record and must carry the same digests, else ManifestPinMismatchError names both. The mirror is canonical. The FTP container is 151 MB and its sha256 is recorded with the member’s, so deposit_raw_mirror’s retrieval re-runs the download and detects a re-packed archive; a build never depends on that URL being alive.

process() → None

Collapse the datapoint export into the CGM matrix; write LMDB.

preprocess_raw(df: Any, preprocess: dict[str, Any] | None = None) → Any

Preprocessing is handled inside process() for this dataset.

create_experiment() → None

Experiment construction is handled inline in process() for this dataset.