json_utils

lacuna.core.json_utils

Shared JSON serialization helpers.

NumpyJSONEncoder

Bases: JSONEncoder

JSON encoder that serializes numpy scalars and arrays.

numpy types are not JSON-serializable by json out of the box, and analysis results and provenance routinely contain them (e.g. np.float32 summary stats, np.int64 counts). Pass cls=NumpyJSONEncoder to json.dump/json.dumps to handle them.

Source code in src/lacuna/core/json_utils.py

class NumpyJSONEncoder(json.JSONEncoder):
    """JSON encoder that serializes numpy scalars and arrays.

    numpy types are not JSON-serializable by ``json`` out of the box, and
    analysis results and provenance routinely contain them (e.g. ``np.float32``
    summary stats, ``np.int64`` counts). Pass ``cls=NumpyJSONEncoder`` to
    ``json.dump``/``json.dumps`` to handle them.
    """

    def default(self, obj):
        if isinstance(obj, np.integer):
            return int(obj)
        if isinstance(obj, np.floating):
            return float(obj)
        if isinstance(obj, np.ndarray):
            return obj.tolist()
        return super().default(obj)