lamindb.curators.AnnDataCurator

class lamindb.curators.AnnDataCurator(dataset, schema)

Bases: SlotsCurator

Curator for AnnData.

Uses slots to specify which component contains which schema. Slots are keys that identify where features are stored within composite data structures.

Parameters:

  • dataset (AnnData | Artifact) – The AnnData-like object to validate & annotate.

  • schema (Schema) – A Schema object that defines the validation constraints.

Examples

Curate Ensembl gene IDs and valid features in obs:

curate_anndata_flexible.py
import lamindb as ln

ln.examples.datasets.mini_immuno.define_features_labels()
adata = ln.examples.datasets.mini_immuno.get_dataset1(otype="AnnData")
artifact = ln.Artifact.from_anndata(
    adata,
    key="examples/mini_immuno.h5ad",
    schema="ensembl_gene_ids_and_valid_features_in_obs",
).save()
artifact.describe()

Curate uns dictionary:

curate_anndata_uns.py
import lamindb as ln

ln.examples.datasets.mini_immuno.define_features_labels()
adata = ln.examples.datasets.mini_immuno.get_dataset1(otype="AnnData")
schema = ln.Schema.get(name="Study metadata schema")
artifact = ln.Artifact.from_anndata(
    adata, schema=schema, key="examples/mini_immuno_uns.h5ad"
)
artifact.describe()

See also

from_anndata().

Attributes

property slots: dict[str, ComponentCurator]

Access sub curators by slot.

Methods

validate()

Validate dataset against Schema.

Raises:

lamindb.errors.ValidationError – If validation fails.

Return type:

None

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

Save an annotated artifact.

Parameters:

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

  • description (str | None, default: None) – A description.

  • revises (Artifact | None, default: None) – Previous version of the artifact. Is an alternative way to passing key to trigger a new version.

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

Return type:

Artifact

Returns:

A saved artifact record.