lamindb.curators.SpatialDataCurator¶

class lamindb.curators.SpatialDataCurator(dataset, schema)¶

Bases: SlotsCurator

Curator for SpatialData.

Parameters:

dataset (SpatialData | Artifact) – The SpatialData-like object to validate & annotate.
schema (Schema) – A Schema object that defines the validation constraints.

Example

curate_spatialdata.py¶

import lamindb as ln

spatialdata = ln.core.datasets.spatialdata_blobs()
sdata_schema = ln.Schema.get(name="spatialdata_blobs_schema")
curator = ln.curators.SpatialDataCurator(spatialdata, sdata_schema)
try:
    curator.validate()
except ln.errors.ValidationError:
    pass

spatialdata.tables["table"].var.drop(index="ENSG00000999999", inplace=True)

# validate again (must pass now) and save artifact
artifact = ln.Artifact.from_spatialdata(
    spatialdata, key="examples/spatialdata1.zarr", schema=sdata_schema
).save()
artifact.describe()

Attributes¶

property slots: dict[str, DataFrameCurator]¶: 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.