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"""Test BIDSValidator functionality.
git-annex and datalad are used to download a test data structure without the
actual file contents.
"""
import os
import pytest
import datalad.api
from bids_validator import BIDSValidator
HOME = os.path.expanduser('~')
TEST_DATA_DICT = {
'eeg_matchingpennies': (
'https://gin.g-node.org/sappelhoff/eeg_matchingpennies'
),
}
EXCLUDE_KEYWORDS = ['git', 'datalad', 'sourcedata', 'bidsignore']
def _download_test_data(test_data_dict, dsname):
"""Download test data using datalad."""
url = test_data_dict[dsname]
dspath = os.path.join(HOME, dsname)
datalad.api.clone(source=url, path=dspath)
return dspath
def _gather_test_files(dspath, exclude_keywords):
"""Get test files from dataset path, relative to dataset."""
files = []
for r, _, f in os.walk(dspath):
for file in f:
fname = os.path.join(r, file)
fname = fname.replace(dspath, '')
if not any(keyword in fname for keyword in exclude_keywords):
files.append(fname)
return files
dspath = _download_test_data(TEST_DATA_DICT, 'eeg_matchingpennies')
files = _gather_test_files(dspath, EXCLUDE_KEYWORDS)
@pytest.fixture(scope='module')
def validator():
"""Return a BIDSValidator instance."""
validator = BIDSValidator()
return validator
@pytest.mark.parametrize('fname', files)
def test_datasets(validator, fname):
"""Test that is_bids returns true for each file in a valid BIDS dataset."""
assert validator.is_bids(fname)
@pytest.mark.parametrize('fname, matches', [
('/T1w.json', True),
('/dataset_description.json', True),
('/README', True),
('/CHANGES', True),
('/participants.tsv', True),
('/sub-01/anat/sub-01_T1w.nii.gz', False),
])
def test_top_level(validator, fname, matches):
"""Test that is_top_level returns true for top-level files."""
assert validator.is_top_level(fname) is matches
@pytest.mark.parametrize('fname, matches', [
('/sourcedata/unstructured_data.nii.gz', True),
('/sourcedata/dicom_dir/xyz.dcm', True),
('/code/my_analysis/analysis.py', True),
('/derivatives/preproc/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz', True),
('/stimuli/pic.jpg', True),
('/sub-01/anat/sub-01_T1w.nii.gz', False),
])
def test_associated_data(validator, fname, matches):
"""Test that is_associated_data returns true for associated data."""
assert validator.is_associated_data(fname) is matches
@pytest.mark.parametrize('fname, matches', [
('/sub-01/ses-1/sub-01_ses-1_scans.tsv', True),
('/sub-01/ses-1/sub-01_ses-1_scans.json', True),
('/sub-01/sub-01_scans.tsv', True),
('/sub-01/sub-01_scans.json', True),
('/sub-01/ses-1/sub-01_ses-1_task-rest_bold.json', True),
('/sub-01/sub-01_task-rest_bold.json', True),
('/sub-01/ses-1/sub-01_ses-1_asl.json', True),
('/sub-01/sub-01_asl.json', True),
('/sub-01/ses-1/sub-01_ses-1_pet.json', True),
('/sub-01/sub-01_pet.json', True),
('/sub-01/ses-1/sub-01_ses-1_proc-test_channels.tsv', True),
('/sub-01/ses-1/sub-01_ses-1_channels.json', True),
('/sub-01/sub-01_proc-test_channels.tsv', True),
('/sub-01/sub-01_channels.json', True),
('/sub-01/ses-1/sub-01_ses-1_space-CapTrak_electrodes.tsv', True),
('/sub-01/ses-1/sub-01_ses-1_coordsystem.json', True),
('/sub-01/sub-01_space-CapTrak_electrodes.tsv', True),
('/sub-01/sub-01_coordsystem.json', True),
('/sub-01/ses-1/sub-01_ses-1_motion.json', True),
('/sub-01/sub-01_motion.json', True),
('/sub-01/ses-1/sub-01_ses-1_TEM.json', True),
('/sub-01/sub-01_TEM.json', True),
('/sub-01/ses-1/sub-01_ses-1_nirs.json', True),
('/sub-01/sub-01_nirs.json', True),
# Mismatch sessions
('/sub-01/sub-01_ses-1_scans.tsv', False),
('/sub-01/sub-01_ses-1_scans.json', False),
('/sub-01/ses-1/sub-01_ses-2_scans.tsv', False),
# File-level
('/sub-01/ses-1/func/sub-01_ses-1_task-rest_bold.nii.gz', False),
('/sub-01/anat/sub-01_T1w.nii.gz', False),
])
def test_session_level(validator, fname, matches):
"""Test that is_session_level returns true for session level files."""
assert validator.is_session_level(fname) is matches
@pytest.mark.parametrize('fname, matches', [
('/sub-01/sub-01_sessions.tsv', True),
('/sub-01/sub-01_sessions.json', True),
('/sub-01/anat/sub-01_T1w.nii.gz', False),
])
def test_subject_level(validator, fname, matches):
"""Test that is_subject_level returns true for subject level files."""
assert validator.is_subject_level(fname) is matches
@pytest.mark.parametrize('fname, matches', [
('/phenotype/measure.tsv', True),
('/phenotype/measure.json', True),
('/sub-01/anat/sub-01_T1w.nii.gz', False),
])
def test_phenotpic(validator, fname, matches):
"""Test that is_phenotypic returns true for phenotypic files."""
assert validator.is_phenotypic(fname) is matches
@pytest.mark.parametrize('fname, matches', [
('/sub-01/ses-1/func/sub-01_ses-1_task-rest_bold.nii.gz', True),
('/sub-01/anat/sub-01_T1w.nii.gz', True),
])
def test_file_level(validator, fname, matches):
"""Test that is_file returns true for file level files."""
assert validator.is_file(fname) is matches
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