def test_entity_matches(tmpdir):
filename = "aardvark-4-reporting-for-duty.txt"
tmpdir.mkdir("tmp").join(filename).write("###")
f = BIDSFile(os.path.join(str(tmpdir), filename))
e = Entity('avaricious', r'aardvark-(\d+)')
result = e.match_file(f)
assert result == '4'
def writable_file(tmpdir):
engine = create_engine('sqlite://')
Base.metadata.create_all(engine)
Session = sessionmaker(bind=engine)
session = Session()
testfile = 'sub-03_ses-2_task-rest_acq-fullbrain_run-2_bold.nii.gz'
fn = tmpdir.mkdir("tmp").join(testfile)
fn.write('###')
bf = BIDSFile(os.path.join(str(fn)))
tag_dict = {'task': 'rest', 'run': 2, 'subject': '3'}
ents = {name: Entity(name) for name in tag_dict.keys()}
tags = [Tag(bf, ents[k], value=v) for k, v in tag_dict.items()]
session.add_all(list(ents.values()) + tags + [bf])
session.commit()
return bf
def test_file_associations():
session = create_session()
img = BIDSFile('sub-03/func/sub-03_task-rest_run-2_bold.nii.gz')
md1 = BIDSFile('sub-03/func/sub-03_task-rest_run-2_bold.json')
md2 = BIDSFile('task-rest_run-2_bold.json')
assocs = [
FileAssociation(src=md1.path, dst=img.path, kind="MetadataFor"),
FileAssociation(src=img.path, dst=md1.path, kind="MetadataIn"),
FileAssociation(src=md1.path, dst=md2.path, kind="Child"),
FileAssociation(src=md2.path, dst=md1.path, kind="Parent"),
FileAssociation(src=md2.path, dst=img.path, kind="Informs")
]
session.add_all([img, md1, md2] + assocs)
session.commit()
assert img._associations == [md1, md2] == img.get_associations()
assert md2._associations == [md1]
assert img.get_associations(kind='MetadataFor') == []
assert img.get_associations(kind='MetadataIn') == [md1]
results = img.get_associations(kind='MetadataIn', include_parents=True)
assert set(results) == {md1, md2}
def sample_bidsfile(tmpdir):
testfile = 'sub-03_ses-2_task-rest_acq-fullbrain_run-2_bold.nii.gz'
fn = tmpdir.mkdir("tmp").join(testfile)
fn.write('###')
return BIDSFile(os.path.join(str(fn)))
def to_fileobj(obj: BIDSFile, basemetadata: dict) -> File | None:
entitydict: dict = obj.get_entities()
datatype: str | None = entitydict.get("datatype")
suffix: str | None = entitydict.get("suffix")
extension: str | None = entitydict.get("extension")
if datatype is None:
return None # exclude README and dataset_description.json etc
if extension is not None:
if not extension.startswith("."):
extension = f".{extension}"
if not isinstance(obj.path, str):
return None # need path
path: str = obj.path
metadata: dict = dict(**basemetadata)
metadata.update(obj.get_metadata())
tags: dict = dict()
for k, v in entitydict.items():
entity = entity_shortnames[k] if k in entity_shortnames else k
if entity in entities:
tags[entity] = str(v)
filedict: dict[str, Any] = dict(
datatype=datatype,
suffix=suffix,
extension=extension,
path=path,
tags=tags,
metadata=metadata,
)
try:
fileobj = file_schema.load(filedict, unknown=EXCLUDE)
if isinstance(fileobj, File):
return fileobj
except marshmallow.exceptions.ValidationError as e:
log_method = logger.warning
if extension == ".json":
log_method = logger.debug # silence
elif datatype == "dwi":
log_method = logger.debug # silence
elif datatype == "anat":
log_method = logger.info # T2w and FLAIR
elif basename(path).startswith("."): # is hidden
log_method = logger.debug # silence
log_method(
f'Skipping unsupported file "{path}" because %s',
e,
exc_info=False,
stack_info=False,
)
return None
