Creating and registering a Transformer

Transformers are often short Python functions that convert one file format or data type to another file format or data type. These functions are never directly called by users or developers, so by convention they don’t get informative function names (as the annotations of the input and output provide complete detail on what they do).

Here’s are two example transformer that are defined and registered in q2-types:

import skbio

from ..plugin_setup import plugin
from .
import LSMatFormat


@plugin.register_transformer
def _1(data: skbio.DistanceMatrix) -> LSMatFormat:
    ff = LSMatFormat()
    with ff.open() as fh:
        data.write(fh, format='lsmat')
    return ff


@plugin.register_transformer
def _2(ff: LSMatFormat) -> skbio.DistanceMatrix:
    return skbio.DistanceMatrix.read(str(ff), format='lsmat', verify=False)

These transformers define how an skbio.DistanceMatrix object is transformed into an LSMatFormat object (the underlying format of the data in a DistanceMatrix artifact class, defined here in q2-types, and registered to the DistanceMatrix semantic type here). The transformers are registered using the @plugin.register_transformer decorator.