def test_parse_file_entities_from_layout(layout_synthetic):
layout = layout_synthetic
filename = '/sub-03_ses-07_run-4_desc-bleargh_sekret.nii.gz'
# Test with entities taken from bids config
target = {
'subject': '03',
'session': '07',
'run': 4,
'suffix': 'sekret',
'extension': 'nii.gz'
}
assert target == layout.parse_file_entities(filename, config='bids')
config = Config.load('bids')
assert target == layout.parse_file_entities(filename, config=[config])
assert target == layout.parse_file_entities(filename, scope='raw')
# Test with default scope--i.e., everything
target = {
'subject': '03',
'session': '07',
'run': 4,
'suffix': 'sekret',
'desc': 'bleargh',
'extension': 'nii.gz'
}
assert target == layout.parse_file_entities(filename)
# Test with only the fmriprep pipeline (which includes both configs)
assert target == layout.parse_file_entities(filename, scope='fmriprep')
assert target == layout.parse_file_entities(filename, scope='derivatives')
# Test with only the derivative config
target = {'desc': 'bleargh'}
assert target == layout.parse_file_entities(filename, config='derivatives')
def test_load_existing_config():
session = create_session()
first = Config('dummy')
session.add(first)
session.commit()
second = Config.load({"name": "dummy"}, session=session)
assert first == second
session.add(second)
session.commit()
from sqlalchemy.orm.exc import FlushError
with pytest.raises(FlushError):
second = Config.load({"name": "dummy"})
session.add(second)
session.commit()
def test_parse_file_entities():
filename = '/sub-03_ses-07_run-4_desc-bleargh_sekret.nii.gz'
# Test with entities taken from bids config
target = {'subject': '03', 'session': '07', 'run': 4, 'suffix': 'sekret',
'extension': 'nii.gz'}
assert target == parse_file_entities(filename, config='bids')
config = Config.load('bids')
assert target == parse_file_entities(filename, config=[config])
# Test with entities taken from bids and derivatives config
target = {'subject': '03', 'session': '07', 'run': 4, 'suffix': 'sekret',
'desc': 'bleargh', 'extension': 'nii.gz'}
assert target == parse_file_entities(filename)
assert target == parse_file_entities(filename, config=['bids', 'derivatives'])
# Test with list of Entities
entities = [
Entity('subject', "[/\\\\]sub-([a-zA-Z0-9]+)"),
Entity('run', "[_/\\\\]run-0*(\\d+)", dtype=int),
Entity('suffix', "[._]*([a-zA-Z0-9]*?)\\.[^/\\\\]+$"),
Entity('desc', "desc-([a-zA-Z0-9]+)"),
]
# Leave out session to distinguish from previous test target
target = {'subject': '03', 'run': 4, 'suffix': 'sekret', 'desc': 'bleargh'}
assert target == parse_file_entities(filename, entities=entities)
def test_add_config_paths():
bids_dir = dirname(bids.__file__)
bids_json = os.path.join(bids_dir, 'layout', 'config', 'bids.json')
with pytest.raises(ValueError) as exc:
add_config_paths(test_config1='nonexistentpath.json')
assert str(exc.value).startswith('Configuration file')
with pytest.raises(ValueError) as exc:
add_config_paths(bids=bids_json)
assert str(exc.value).startswith("Configuration 'bids' already")
add_config_paths(dummy=bids_json)
config = Config.load('dummy')
assert 'subject' in config.entities
def test_config_init_with_args():
session = create_session()
ents = [{
"name": "task",
"pattern": "[_/\\\\]task-([a-zA-Z0-9]+)"
}, {
"name": "acquisition",
"pattern": "[_/\\\\]acq-([a-zA-Z0-9]+)"
}]
patterns = ['this_will_never_match_anything', 'and_neither_will_this']
config = Config('custom', entities=ents, default_path_patterns=patterns)
assert config.name == 'custom'
target = {'task', 'acquisition'}
assert set(ent.name for ent in config.entities.values()) == target
assert config.default_path_patterns == patterns
def loadBidsEntities() -> dict:
"""
Loads all accepted BIDS entities from PyBids into a dictionary.
Returns:
A dictionary mapping the entity names to the PyBids Entity object
containing information about that entity.
"""
# PyBids uses its own, internal bids.json to configure what entities it
# accepts and what form they take. A custom config could be specified with a
# full path name, but using just 'bids' will direct the PyBids Config class
# to get the bids.json from its own internal package.
BIDS_DEFAULT_CONFIG_NAME = 'bids'
BIDS_DERIVATIES_CONFIG_NAME = 'derivatives'
entities = {}
for configName in [BIDS_DEFAULT_CONFIG_NAME, BIDS_DERIVATIES_CONFIG_NAME]:
entities.update(BidsConfig.load(configName).entities)
return entities
def test_parse_file_entities_from_layout_cached_db_replay(
layout_synthetic_cached_db_replay):
"""
We need to ensure that after caching the database requesting cached values
provides all the original values.
:param layout_synthetic_cached_db_replay:
"""
layout = layout_synthetic_cached_db_replay
filename = '/sub-03_ses-07_run-4_desc-bleargh_sekret.nii.gz'
# Test with entities taken from bids config
target = {
'subject': '03',
'session': '07',
'run': 4,
'suffix': 'sekret',
'extension': 'nii.gz'
}
assert target == layout.parse_file_entities(filename, config='bids')
config = Config.load('bids')
assert target == layout.parse_file_entities(filename, config=[config])
assert target == layout.parse_file_entities(filename, scope='raw')
# Test with default scope--i.e., everything
target = {
'subject': '03',
'session': '07',
'run': 4,
'suffix': 'sekret',
'desc': 'bleargh',
'extension': 'nii.gz'
}
assert target == layout.parse_file_entities(filename)
# Test with only the fmriprep pipeline (which includes both configs)
assert target == layout.parse_file_entities(filename, scope='fmriprep')
assert target == layout.parse_file_entities(filename, scope='derivatives')
# Test with only the derivative config
target = {'desc': 'bleargh'}
assert target == layout.parse_file_entities(filename, config='derivatives')