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

import time

import h5py
import pytest

from nwb_linkml.maps.hdmf import dynamictable_to_model, model_from_dynamictable

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


@pytest.mark.xfail()
@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)

    _ = 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 time`
autogenerating models for dynamictable 2023-09-23 08:33:28 +00:00
ruff automatic fixes 2024-07-02 04:44:35 +00:00			`import h5py`
			`import pytest`

			`from nwb_linkml.maps.hdmf import dynamictable_to_model, model_from_dynamictable`
autogenerating models for dynamictable 2023-09-23 08:33:28 +00:00
black formatting 2024-07-02 04:23:31 +00:00			`NWBFILE = "/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb"`
autogenerating models for dynamictable 2023-09-23 08:33:28 +00:00
black formatting 2024-07-02 04:23:31 +00:00
continue removing NDArray type, since it's in numpydantic now. 2024-07-10 07:20:01 +00:00			`@pytest.mark.xfail()`
black formatting 2024-07-02 04:23:31 +00:00			`@pytest.mark.parametrize("dataset", ["aibs.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			`def test_make_dynamictable(data_dir, dataset):`
			`nwbfile = data_dir / dataset`
black formatting 2024-07-02 04:23:31 +00:00			`h5f = h5py.File(nwbfile, "r")`
			`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 _ for a variable which is not used 2024-04-17 19:55:52 +00:00			`_ = data.model_dump_json()`
Use dask instead of trying to make a dataframe compress arrays when serializing to json 2023-09-27 02:50:49 +00:00			`end_time = time.time()`
			`total_time = end_time - start_time`