nwb-linkml/nwb_linkml/tests/test_maps/test_hdmf.py

import pdb

import pytest
import h5py
import time

from nwb_linkml.maps.hdmf import model_from_dynamictable, dynamictable_to_model
from ..fixtures import data_dir

NWBFILE = '/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb'

@pytest.mark.parametrize(
    'dataset',
    [
        'aibs.nwb'
    ]
)
def test_make_dynamictable(data_dir, dataset):
    nwbfile = data_dir / dataset
    h5f = h5py.File(nwbfile, 'r')
    group = h5f['units']

    start_time = time.time()
    model = model_from_dynamictable(group)
    data = dynamictable_to_model(group, model)

    ser = data.model_dump_json()
    end_time = time.time()
    total_time = end_time - start_time
Use dask instead of trying to make a dataframe compress arrays when serializing to json 2023-09-27 02:50:49 +00:00			`import pdb`

autogenerating models for dynamictable 2023-09-23 08:33:28 +00:00			`import pytest`
			`import h5py`
Use dask instead of trying to make a dataframe compress arrays when serializing to json 2023-09-27 02:50:49 +00:00			`import time`
autogenerating models for dynamictable 2023-09-23 08:33:28 +00:00
Use dask instead of trying to make a dataframe compress arrays when serializing to json 2023-09-27 02:50:49 +00:00			`from nwb_linkml.maps.hdmf import model_from_dynamictable, dynamictable_to_model`
re-enable janky hdmf mapping test just to have it on the board for morale Fix serializing datasets 2023-10-10 06:27:33 +00:00			`from ..fixtures import data_dir`
autogenerating models for dynamictable 2023-09-23 08:33:28 +00:00
			`NWBFILE = '/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb'`

re-enable janky hdmf mapping test just to have it on the board for morale Fix serializing datasets 2023-10-10 06:27:33 +00:00			`@pytest.mark.parametrize(`
			`'dataset',`
			`[`
			`'aibs.nwb'`
			`]`
			`)`
			`def test_make_dynamictable(data_dir, dataset):`
			`nwbfile = data_dir / dataset`
			`h5f = h5py.File(nwbfile, 'r')`
Use dask instead of trying to make a dataframe compress arrays when serializing to json 2023-09-27 02:50:49 +00:00			`group = h5f['units']`
autogenerating models for dynamictable 2023-09-23 08:33:28 +00:00
Use dask instead of trying to make a dataframe compress arrays when serializing to json 2023-09-27 02:50:49 +00:00			`start_time = time.time()`
autogenerating models for dynamictable 2023-09-23 08:33:28 +00:00			`model = model_from_dynamictable(group)`
Use dask instead of trying to make a dataframe compress arrays when serializing to json 2023-09-27 02:50:49 +00:00			`data = dynamictable_to_model(group, model)`
re-enable janky hdmf mapping test just to have it on the board for morale Fix serializing datasets 2023-10-10 06:27:33 +00:00
Use dask instead of trying to make a dataframe compress arrays when serializing to json 2023-09-27 02:50:49 +00:00			`ser = data.model_dump_json()`
			`end_time = time.time()`
			`total_time = end_time - start_time`
autogenerating models for dynamictable 2023-09-23 08:33:28 +00:00