lamindb.curators.SpatialDataCurator

class lamindb.curators.SpatialDataCurator(dataset, schema, *, sample_metadata_key='sample')

Bases: SlotsCurator

Curator for SpatialData.

See also Curator and Schema.

Added in version 1.3.0.

Parameters:

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

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

Example:

import lamindb as ln
import bionty as bt

# define sample schema
sample_schema = ln.Schema(
    name="blobs_sample_level_metadata",
    features=[
        ln.Feature(name="assay", dtype=bt.ExperimentalFactor).save(),
        ln.Feature(name="disease", dtype=bt.Disease).save(),
        ln.Feature(name="development_stage", dtype=bt.DevelopmentalStage).save(),
    ],
    coerce_dtype=True
).save()

# define table obs schema
blobs_obs_schema = ln.Schema(
    name="blobs_obs_level_metadata",
    features=[
        ln.Feature(name="sample_region", dtype="str").save(),
    ],
    coerce_dtype=True
).save()

# define table var schema
blobs_var_schema = ln.Schema(
    name="blobs_var_schema",
    itype=bt.Gene.ensembl_gene_id,
    dtype=int
).save()

# define composite schema
spatialdata_schema = ln.Schema(
    name="blobs_spatialdata_schema",
    otype="SpatialData",
    components={
        "sample": sample_schema,
        "table:obs": blobs_obs_schema,
        "table:var": blobs_var_schema,
}).save()

# curate a SpatialData
spatialdata = ln.core.datasets.spatialdata_blobs()
curator = ln.curators.SpatialDataCurator(spatialdata, spatialdata_schema)
try:
    curator.validate()
except ln.errors.ValidationError as error:
    print(error)

# validate again (must pass now) and save artifact
artifact = curator.save_artifact(key="example_datasets/spatialdata1.zarr")
assert artifact.schema == spatialdata_schema

Attributes

property slots: dict[str, DataFrameCurator]

Curator objects by slot.

Added in version 1.1.1.

Methods

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.

validate()

Validate dataset against Schema.

Raises:

lamindb.errors.ValidationError – If validation fails.

Return type:

None