torchcell.datasets.scerevisiae.yoshida2012.OrganicAcidYoshida2012Dataset

class OrganicAcidYoshida2012Dataset(root: str = 'data/torchcell/organic_acid_yoshida2012', io_workers: int = 0, transform: Callable[[...], Any] | None = None, pre_transform: Callable[[...], Any] | None = None, **kwargs: Any)

Bases: ExperimentDataset

HPLC organic-acid titers of 17 yeast deletion mutants (Yoshida 2012, Table 3).

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 sha256-pinned mirror PDF the Table 3 literal was transcribed from.

download() → None

Stage the mirror paper.pdf into raw_dir and verify its sha256.

The dataset values are the embedded TABLE_3 literal, but the canonical source artifact (the paper PDF) is staged + hash-verified here so every built LMDB traces to an exact, hash-pinned raw file.

process() → None

Build per-strain Metabolite experiments from the Table 3 literal, write LMDB.

Every record is built and every refusal raised BEFORE data.csv or the store is written, so a refused table leaves nothing for a retry to serve. The one refusal (0 of the 17 strains of the released Table 3) is a NaN mean or SD; every name is stored as released, so no name can fail (#1045).

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

Preprocessing is handled inside process() for this dataset.

create_experiment(row: dict[str, Any]) → tuple[MetaboliteExperiment, MetaboliteExperimentReference, Publication]

Build the Metabolite experiment/reference/publication for one deletion strain.