Source code for allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.mouse_id

from allensdk.core import (
    DataObject,
    JsonReadableInterface,
    LimsReadableInterface,
    NwbReadableInterface,
)
from allensdk.internal.api import PostgresQueryMixin
from pynwb import NWBFile


class MouseId(
    DataObject,
    LimsReadableInterface,
    JsonReadableInterface,
    NwbReadableInterface,
):
    """the LabTracks ID"""

    def __init__(self, mouse_id: str):
        super().__init__(name="mouse_id", value=mouse_id)

    @classmethod
    def from_json(cls, dict_repr: dict) -> "MouseId":
        mouse_id = dict_repr["external_specimen_name"]
        # Check to make sure the dictionary value is string type and if not
        # make it so.
        if not isinstance(mouse_id, str):
            mouse_id = str(mouse_id)
        return cls(mouse_id=mouse_id)

    @classmethod
    def from_lims(
        cls, behavior_session_id: int, lims_db: PostgresQueryMixin
    ) -> "MouseId":
        # TODO: Should this even be included?
        # Found sometimes there were entries with NONE which is
        # why they are filtered out; also many entries in the table
        # match the donor_id, which is why used DISTINCT
        query = f"""
            SELECT DISTINCT(sp.external_specimen_name)
            FROM behavior_sessions bs
            JOIN donors d ON bs.donor_id=d.id
            JOIN specimens sp ON sp.donor_id=d.id
            WHERE bs.id={behavior_session_id}
            AND sp.external_specimen_name IS NOT NULL;
            """
        mouse_id = lims_db.fetchone(query, strict=True)
        return cls(mouse_id=mouse_id)

    @classmethod
    def from_nwb(cls, nwbfile: NWBFile) -> "MouseId":
        return cls(mouse_id=nwbfile.subject.subject_id)