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from dateutil import tz
from datetime import datetime
from uuid import uuid4
import os
from hdmf.term_set import TermSetWrapper
from pynwb import NWBFile, get_loaded_type_config, load_type_config, unload_type_config
from pynwb.file import Subject
from pynwb.testing import TestCase
try:
from linkml_runtime.utils.schemaview import SchemaView # noqa: F401
REQUIREMENTS_INSTALLED = True
except ImportError:
REQUIREMENTS_INSTALLED = False
class TestPyNWBTypeConfig(TestCase):
def setUp(self):
if not REQUIREMENTS_INSTALLED:
self.skipTest("optional LinkML module is not installed")
CUR_DIR = os.path.dirname(os.path.realpath(__file__))
path_to_config = os.path.join(CUR_DIR, 'test_config/test_nwb_config.yaml')
load_type_config(config_path=path_to_config)
def tearDown(self):
unload_type_config()
def test_get_loaded_type_config(self):
config = get_loaded_type_config()
self.assertEqual(config,
{'namespaces': {'core': {'version': '2.7.0-alpha',
'data_types': {'Subject': {'species': {'termset': 'nwb_subject_termset.yaml'}}}}}})
def test_default_config(self):
session_start_time = datetime(2018, 4, 25, 2, 30, 3, tzinfo=tz.gettz("US/Pacific"))
nwbfile = NWBFile(
session_description="Mouse exploring an open field", # required
identifier=str(uuid4()), # required
session_start_time=session_start_time, # required
session_id="session_1234", # optional
experimenter=[
"Ryan Ly",
], # optional
lab="Bag End Laboratory", # optional
institution="University of My Institution", # optional
experiment_description="I went on an adventure to reclaim vast treasures.", # optional
related_publications="DOI:10.1016/j.neuron.2016.12.011", # optional
)
subject = Subject(
subject_id="01",
age="One shouldn't ask",
description="A human.",
species="Homo sapiens",
sex="M",
)
nwbfile.subject = subject
self.assertIsInstance(nwbfile.subject.species, TermSetWrapper)
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