lamindb.curators.TiledbsomaCatManager

class lamindb.curators.TiledbsomaCatManager(experiment_uri, var_index, categoricals=None, obs_columns=FieldAttr(Feature.name), sources=None)

Bases: CatManager

Categorical manager for tiledbsoma.Experiment.

Attributes

property categoricals: dict[str, DeferredAttribute]

Return the obs fields to validate against.

property non_validated: dict[str, list]

Return the non-validated features and labels.

property var_index: dict[str, DeferredAttribute]

Return the registry fields with flattened keys to validate variables indices against.

Class methods

classmethod from_anndata(data, var_index, categoricals=None, obs_columns=FieldAttr(Feature.name), organism=None, sources=None)

Return type:

AnnDataCatManager

classmethod from_df(df, categoricals=None, columns=FieldAttr(Feature.name), organism=None)

Return type:

DataFrameCatManager

classmethod from_mudata(mdata, var_index, categoricals=None, organism=None)

Return type:

MuDataCatManager

classmethod from_spatialdata(sdata, var_index, categoricals=None, organism=None, sources=None, *, sample_metadata_key='sample')

classmethod from_tiledbsoma(experiment_uri, var_index, categoricals=None, obs_columns=FieldAttr(Feature.name), organism=None, sources=None)

Return type:

TiledbsomaCatManager

Methods

add_new_from(key, **kwargs)

Add validated & new categories.

Parameters:

key (str) – The key referencing the slot in the tiledbsoma store. It should be '{measurement name}__{column name in .var}' for columns in .var or a column name in .obs.

Return type:

None

lookup(public=False)

Lookup categories.

Parameters:

public (bool, default: False) – If “public”, the lookup is performed on the public reference.

Return type:

CatLookup

save_artifact(*, key=None, description=None, revises=None, run=None)

Save the validated tiledbsoma store and metadata.

Parameters:

• description (str | None, default: None) – A description of the tiledbsoma store.

• key (str | None, default: None) – A path-like key to reference artifact in default storage, e.g., "myfolder/mystore.tiledbsoma". Artifacts with the same key form a version family.

• revises (Artifact | None, default: None) – Previous version of the artifact. Triggers a revision.

• run (Run | None, default: None) – The run that creates the artifact.

Return type:

Artifact

Returns:

A saved artifact record.

standardize(key)

Replace synonyms with standardized values.

Modifies the dataset inplace.

Parameters:

key (str) – The key referencing the slot in the tiledbsoma store. It should be '{measurement name}__{column name in .var}' for columns in .var or a column name in .obs.

validate()

Validate categories.