lamindb.core.MuDataCurator¶

class lamindb.core.MuDataCurator(mdata, var_index, categoricals=None, using_key='default', verbosity='hint', organism=None, sources=None, exclude=None)¶

Bases: object

Curation flow for a MuData object.

See also Curator.

Note that if genes or other measurements are removed from the MuData object, the object should be recreated using from_mudata().

Parameters:

mdata (MuData) – The MuData object to curate.
var_index (dict[str, dict[str, DeferredAttribute]]) – The registry field for mapping the .var index for each modality. For example: {"modality_1": bt.Gene.ensembl_gene_id, "modality_2": ln.CellMarker.name}
categoricals (dict[str, DeferredAttribute] | None, default: None) – A dictionary mapping .obs.columns to a registry field. Use modality keys to specify categoricals for MuData slots such as "rna:cell_type": bt.CellType.name".
using_key (str, default: 'default') – A reference LaminDB instance.
verbosity (str, default: 'hint') – The verbosity level.
organism (str | None, default: None) – The organism name.
sources (dict[str, Record] | None, default: None) – A dictionary mapping .obs.columns to Source records.
exclude (dict | None, default: None) – A dictionary mapping column names to values to exclude.

Examples

>>> import bionty as bt
>>> curate = ln.Curator.from_mudata(
...     mdata,
...     var_index={
...         "rna": bt.Gene.ensembl_gene_id,
...         "adt": ln.CellMarker.name
...     },
...     categoricals={
...         "cell_type_ontology_id": bt.CellType.ontology_id,
...         "donor_id": ln.ULabel.name
...     },
...     organism="human",
... )

Attributes¶

property categoricals: dict¶: Return the obs fields to validate against.

property var_index: DeferredAttribute¶: Return the registry field to validate variables index against.

Methods¶

add_new_from(key, modality=None, organism=None, **kwargs)¶

Add validated & new categories.

Parameters:

key (str) – The key referencing the slot in the DataFrame.
modality (str | None, default: None) – The modality name.
organism (str | None, default: None) – The organism name.
**kwargs – Additional keyword arguments to pass to the registry model.

add_new_from_columns(modality, column_names=None, organism=None, **kwargs)¶

Update columns records.

Parameters:

modality (str) – The modality name.
column_names (list[str] | None, default: None) – The column names to save.
organism (str | None, default: None) – The organism name.
**kwargs – Additional keyword arguments to pass to the registry model.

add_new_from_var_index(modality, organism=None, **kwargs)¶

Update variable records.

Parameters:

modality (str) – The modality name.
organism (str | None, default: None) – The organism name.
**kwargs – Additional keyword arguments to pass to the registry model.

add_validated_from(key, modality=None, organism=None)¶

Add validated categories.

Parameters:

key (str) – The key referencing the slot in the DataFrame.
modality (str | None, default: None) – The modality name.
organism (str | None, default: None) – The organism name.

add_validated_from_var_index(modality, organism=None)¶

Add validated variable records.

Parameters:

modality (str) – The modality name.
organism (str | None, default: None) – The organism name.

lookup(using_key=None)¶

Lookup categories.

Parameters:: using_key (str | None, default: None) – The instance where the lookup is performed. if None (default), the lookup is performed on the instance specified in “using_key” parameter of the validator. if “public”, the lookup is performed on the public reference.
Return type:: CurateLookup

save_artifact(description=None, **kwargs)¶

Save the validated MuData and metadata.

Parameters:

description (str | None, default: None) – Description of the MuData object.
**kwargs – Object level metadata.

Return type:

Artifact

Returns:

A saved artifact record.

validate(organism=None)¶

Validate categories.

Return type:: bool