lamindb.core.AnnDataCurator

class lamindb.core.AnnDataCurator(data, var_index, categoricals=None, obs_columns=FieldAttr(Feature.name), using_key=None, verbosity='hint', organism=None, sources=None, exclude=None)

Bases: DataFrameCurator

Curation flow for AnnData.

See also Curator.

Note that if genes are removed from the AnnData object, the object should be recreated using from_anndata().

See Curate AnnData based on the CELLxGENE schema for instructions on how to curate against a specific cellxgene schema version.

Parameters:

  • data (ad.AnnData | UPathStr) – The AnnData object or an AnnData-like path.

  • var_index (FieldAttr) – The registry field for mapping the .var index.

  • categoricals (dict[str, FieldAttr] | None, default: None) – A dictionary mapping .obs.columns to a registry field.

  • obs_columns (FieldAttr, default: FieldAttr(Feature.name)) – The registry field for mapping the .obs.columns.

  • using_key (str | None, default: None) – 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 from validation. When specific Source instances are pinned and may lack default values (e.g., “unknown” or “na”), using the exclude parameter ensures they are not validated.

Examples

>>> import bionty as bt
>>> curator = ln.Curator.from_anndata(
...     adata,
...     var_index=bt.Gene.ensembl_gene_id,
...     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 fields: dict

Return the columns fields to validate against.

property non_validated: dict[str, list[str]]

Return the non-validated features and labels.

property var_index: DeferredAttribute

Return the registry field to validate variables index against.

Methods

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

Add validated & new categories.

Parameters:

  • key (str) – The key referencing the slot in the DataFrame from which to draw terms.

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

  • **kwargs – Additional keyword arguments to pass to create new records

add_new_from_var_index(organism=None, **kwargs)

Update variable records.

Parameters:

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

  • **kwargs – Additional keyword arguments to pass to create new records.

clean_up_failed_runs()

Clean up previous failed runs that don’t save any outputs.

lookup(using_key=None, public=False)

Lookup categories.

Parameters:

using_key (str | None, default: None) – The instance where the lookup is performed. if “public”, the lookup is performed on the public reference.

Return type:

CurateLookup

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

Save the validated AnnData and metadata.

Parameters:

  • description (str | None, default: None) – A description of the AnnData object.

  • 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 revision 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.

Parameters:

key (str) –

The key referencing the slot in adata.obs from which to draw terms. Same as the key in categoricals.

  • If “var_index”, standardize the var.index.

  • If “all”, standardize all obs columns and var.index.

Inplace modification of the dataset.

validate(organism=None)

Validate categories.

This method also registers the validated records in the current instance.

Parameters:

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

Return type:

bool

Returns:

Whether the AnnData object is validated.