1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
|
# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
from pathlib import Path
import pytest
from mne.datasets.sleep_physionet import age, temazepam
from mne.datasets.sleep_physionet._utils import (
AGE_SLEEP_RECORDS,
TEMAZEPAM_SLEEP_RECORDS,
_update_sleep_age_records,
_update_sleep_temazepam_records,
)
from mne.utils import requires_good_network
@pytest.fixture(scope="session")
def physionet_tmpdir(tmp_path_factory):
"""Fixture exposing a temporary directory for testing."""
return str(tmp_path_factory.mktemp("physionet_files"))
def _keep_basename_only(paths):
return [Path(p).name for p in paths]
def _get_expected_url(name):
base = "https://physionet.org/physiobank/database/sleep-edfx/"
middle = "sleep-cassette/" if name.startswith("SC") else "sleep-telemetry/"
return base + middle + "/" + name
def _get_expected_path(base, name):
return Path(base, name)
def _check_mocked_function_calls(mocked_func, call_fname_hash_pairs, base_path):
# Check mocked_func has been called the right amount of times.
assert mocked_func.call_count == len(call_fname_hash_pairs)
# Check it has been called with the right parameters in the right
# order.
for idx, current in enumerate(call_fname_hash_pairs):
_, call_kwargs = mocked_func.call_args_list[idx]
hash_type, hash_ = call_kwargs["known_hash"].split(":")
assert call_kwargs["url"] == _get_expected_url(current["name"]), idx
assert Path(call_kwargs["path"], call_kwargs["fname"]) == _get_expected_path(
base_path, current["name"]
)
assert hash_ == current["hash"]
assert hash_type == "sha1"
@pytest.mark.timeout(60)
@pytest.mark.xfail(strict=False)
@requires_good_network
def test_run_update_age_records(tmp_path):
"""Test Sleep Physionet URL handling."""
pd = pytest.importorskip("pandas")
pytest.importorskip("xlrd", "0.9")
fname = tmp_path / "records.csv"
_update_sleep_age_records(fname)
data = pd.read_csv(fname)
pd.testing.assert_frame_equal(data, pd.read_csv(AGE_SLEEP_RECORDS))
@pytest.mark.parametrize("subject", [39, 68, 69, 78, 79, 83])
def test_sleep_physionet_age_missing_subjects(
physionet_tmpdir, subject, download_is_error
):
"""Test handling of missing subjects in Sleep Physionet age fetcher."""
with pytest.raises(ValueError, match="This dataset contains subjects 0 to 82"):
age.fetch_data(
subjects=[subject], recording=[1], on_missing="raise", path=physionet_tmpdir
)
with pytest.warns(RuntimeWarning, match="This dataset contains subjects 0 to 82"):
age.fetch_data(
subjects=[subject], recording=[1], on_missing="warn", path=physionet_tmpdir
)
paths = age.fetch_data(
subjects=[subject], recording=[1], on_missing="ignore", path=physionet_tmpdir
)
assert paths == []
@pytest.mark.parametrize("subject,recording", [(13, 2), (36, 1), (52, 1)])
def test_sleep_physionet_age_missing_recordings(
physionet_tmpdir, subject, recording, download_is_error
):
"""Test handling of missing recordings in Sleep Physionet age fetcher."""
with pytest.raises(
ValueError, match=f"Requested recording {recording} for subject"
):
age.fetch_data(
subjects=[subject],
recording=[recording],
on_missing="raise",
path=physionet_tmpdir,
)
with pytest.warns(
RuntimeWarning, match=f"Requested recording {recording} for subject"
):
age.fetch_data(
subjects=[subject],
recording=[recording],
on_missing="warn",
path=physionet_tmpdir,
)
paths = age.fetch_data(
subjects=[subject],
recording=[recording],
on_missing="ignore",
path=physionet_tmpdir,
)
assert paths == []
def test_sleep_physionet_age(physionet_tmpdir, fake_retrieve):
"""Test Sleep Physionet URL handling."""
paths = age.fetch_data(subjects=[0], recording=[1], path=physionet_tmpdir)
assert _keep_basename_only(paths[0]) == [
"SC4001E0-PSG.edf",
"SC4001EC-Hypnogram.edf",
]
paths = age.fetch_data(subjects=[0, 1], recording=[1], path=physionet_tmpdir)
assert _keep_basename_only(paths[0]) == [
"SC4001E0-PSG.edf",
"SC4001EC-Hypnogram.edf",
]
assert _keep_basename_only(paths[1]) == [
"SC4011E0-PSG.edf",
"SC4011EH-Hypnogram.edf",
]
paths = age.fetch_data(subjects=[0], recording=[1, 2], path=physionet_tmpdir)
assert _keep_basename_only(paths[0]) == [
"SC4001E0-PSG.edf",
"SC4001EC-Hypnogram.edf",
]
assert _keep_basename_only(paths[1]) == [
"SC4002E0-PSG.edf",
"SC4002EC-Hypnogram.edf",
]
EXPECTED_CALLS = (
{
"name": "SC4001E0-PSG.edf",
"hash": "adabd3b01fc7bb75c523a974f38ee3ae4e57b40f",
},
{
"name": "SC4001EC-Hypnogram.edf",
"hash": "21c998eadc8b1e3ea6727d3585186b8f76e7e70b",
},
{
"name": "SC4011E0-PSG.edf",
"hash": "4d17451f7847355bcab17584de05e7e1df58c660",
},
{
"name": "SC4011EH-Hypnogram.edf",
"hash": "d582a3cbe2db481a362af890bc5a2f5ca7c878dc",
},
{
"name": "SC4002E0-PSG.edf",
"hash": "c6b6d7a8605cc7e7602b6028ee77f6fbf5f7581d",
},
{
"name": "SC4002EC-Hypnogram.edf",
"hash": "386230188a3552b1fc90bba0fb7476ceaca174b6",
},
)
base_path = age.data_path(path=physionet_tmpdir)
_check_mocked_function_calls(fake_retrieve, EXPECTED_CALLS, base_path)
@pytest.mark.xfail(strict=False)
@requires_good_network
def test_run_update_temazepam_records(tmp_path):
"""Test Sleep Physionet URL handling."""
pd = pytest.importorskip("pandas")
pytest.importorskip("xlrd", "0.9")
fname = tmp_path / "records.csv"
_update_sleep_temazepam_records(fname)
data = pd.read_csv(fname)
pd.testing.assert_frame_equal(data, pd.read_csv(TEMAZEPAM_SLEEP_RECORDS))
def test_sleep_physionet_temazepam(physionet_tmpdir, fake_retrieve):
"""Test Sleep Physionet URL handling."""
paths = temazepam.fetch_data(subjects=[0], path=physionet_tmpdir)
assert _keep_basename_only(paths[0]) == [
"ST7011J0-PSG.edf",
"ST7011JP-Hypnogram.edf",
]
EXPECTED_CALLS = (
{
"name": "ST7011J0-PSG.edf",
"hash": "b9d11484126ebff1884034396d6a20c62c0ef48d",
},
{
"name": "ST7011JP-Hypnogram.edf",
"hash": "ff28e5e01296cefed49ae0c27cfb3ebc42e710bf",
},
)
base_path = temazepam.data_path(path=physionet_tmpdir)
_check_mocked_function_calls(fake_retrieve, EXPECTED_CALLS, base_path)
with pytest.raises(ValueError, match="This dataset contains subjects 0 to 21"):
paths = temazepam.fetch_data(subjects=[22], path=physionet_tmpdir)
|
