def test_named_tuple(self, file):
file.tags = {'attrA': Tag(None, 'apple'), 'attrB': Tag(None, 'banana')}
tup = file.as_named_tuple()
assert(tup.filename == file.path)
assert isinstance(tup, tuple)
assert not hasattr(tup, 'task')
assert tup.attrA == 'apple'
def test_build_path(self, writable_file):
writable_file.tags = {
'task': Tag(None, 'rest'),
'run': Tag(None, '2'),
'subject': Tag(None, '3')
}
# Single simple pattern
with pytest.raises(TypeError):
build_path(writable_file.entities)
pat = join(writable_file.dirname,
'{task}/sub-{subject}/run-{run}.nii.gz')
target = join(writable_file.dirname, 'rest/sub-3/run-2.nii.gz')
assert build_path(writable_file.entities, pat) == target
# Multiple simple patterns
pats = [
'{session}/{task}/r-{run}.nii.gz',
't-{task}/{subject}-{run}.nii.gz', '{subject}/{task}.nii.gz'
]
pats = [join(writable_file.dirname, p) for p in pats]
target = join(writable_file.dirname, 't-rest/3-2.nii.gz')
assert build_path(writable_file.entities, pats) == target
# Pattern with optional entity
pats = [
'[{session}/]{task}/r-{run}.nii.gz',
't-{task}/{subject}-{run}.nii.gz'
]
pats = [join(writable_file.dirname, p) for p in pats]
target = join(writable_file.dirname, 'rest/r-2.nii.gz')
assert build_path(writable_file.entities, pats) == target
# Pattern with conditional values
pats = [
'{task<func|acq>}/r-{run}.nii.gz',
't-{task}/{subject}-{run}.nii.gz'
]
pats = [join(writable_file.dirname, p) for p in pats]
target = join(writable_file.dirname, 't-rest/3-2.nii.gz')
assert build_path(writable_file.entities, pats) == target
# Pattern with valid conditional values
pats = [
'{task<func|rest>}/r-{run}.nii.gz',
't-{task}/{subject}-{run}.nii.gz'
]
pats = [join(writable_file.dirname, p) for p in pats]
target = join(writable_file.dirname, 'rest/r-2.nii.gz')
assert build_path(writable_file.entities, pats) == target
# Pattern with optional entity with conditional values
pats = [
'[{task<func|acq>}/]r-{run}.nii.gz',
't-{task}/{subject}-{run}.nii.gz'
]
pats = [join(writable_file.dirname, p) for p in pats]
target = join(writable_file.dirname, 'r-2.nii.gz')
assert build_path(writable_file.entities, pats) == target
def test_build_file(self, writable_file, tmpdir, caplog):
writable_file.tags = {
'task': Tag(None, 'rest'),
'run': Tag(None, '2'),
'subject': Tag(None, '3')
}
# Simple write out
new_dir = join(writable_file.dirname, 'rest')
pat = join(writable_file.dirname,
'{task}/sub-{subject}/run-{run}.nii.gz')
target = join(writable_file.dirname, 'rest/sub-3/run-2.nii.gz')
writable_file.copy(pat)
assert exists(target)
# Conflict handling
with pytest.raises(ValueError):
writable_file.copy(pat)
with pytest.raises(ValueError):
writable_file.copy(pat, conflicts='fail')
writable_file.copy(pat, conflicts='skip')
log_message = caplog.records[0].message
assert log_message == 'A file at path {} already exists, ' \
'skipping writing file.'.format(target)
writable_file.copy(pat, conflicts='append')
append_target = join(writable_file.dirname,
'rest/sub-3/run-2_1.nii.gz')
assert exists(append_target)
writable_file.copy(pat, conflicts='overwrite')
assert exists(target)
shutil.rmtree(new_dir)
# Symbolic linking
writable_file.copy(pat, symbolic_link=True)
assert islink(target)
shutil.rmtree(new_dir)
# Using different root
root = str(tmpdir.mkdir('tmp2'))
pat = join(root, '{task}/sub-{subject}/run-{run}.nii.gz')
target = join(root, 'rest/sub-3/run-2.nii.gz')
writable_file.copy(pat, root=root)
assert exists(target)
# Copy into directory functionality
pat = join(writable_file.dirname, '{task}/')
writable_file.copy(pat)
target = join(writable_file.dirname, 'rest', writable_file.filename)
assert exists(target)
shutil.rmtree(new_dir)
def test_matches(self, file):
assert file._matches()
assert file._matches(extensions='nii.gz')
assert not file._matches(extensions=['.txt', '.rtf'])
file.tags = {'task': Tag(None, 'rest'), 'run': Tag(None, '2')}
assert file._matches(entities={'task': 'rest', 'run': 2})
assert not file._matches(entities={'task': 'rest', 'run': 4})
assert not file._matches(entities={'task': 'st'})
assert file._matches(entities={'task': 'st'}, regex_search=True)
# With list of matches
assert not file._matches(entities={'task': ['A', 'B', 'C']})
assert file._matches(entities={'task': ['A', 'B', 'rest']})
assert file._matches(entities={'task': ['A', 'B', 'st']},
regex_search=True)
def test_named_tuple_with_reserved_name(self, file):
file = copy(file)
file.tags['class'] = Tag(None, 'invalid')
with pytest.warns(UserWarning) as w:
res = file.as_named_tuple()
assert w[0].message.args[0].startswith('Entity names cannot')
assert hasattr(res, 'class_')
assert not hasattr(res, 'class')