def test_bidstree_to_bidstree():
# Test writing one BIDSTree object to a new empty BIDSTree location.
with tempfile.TemporaryDirectory() as tmp:
dest_bf = BIDSTree(tmp, False)
src_bt = BIDSTree(TESTPATH2)
dest_bf.add(src_bt)
assert len(dest_bf.projects) == 1
assert dest_bf.project('test1').subject('1').subject_data['age'] == 2.0
def _transfer(self):
"""Transfer all the files in each of the sources to the destination."""
copy_func = BIDSCopy(overwrite=self.force_override.get(),
verify=self.verify.get(),
file_name_tracker=self.curr_file,
file_num_tracker=self.transferred_count,
file_prog_tracker=self.curr_file_progress)
self.curr_file.set('Mapping destination BIDS structure...')
dst_folder = BIDSTree(self.dst)
for src in self.srcs:
dst_folder.add(src, copier=copy_func.copy_files)
if self.set_copied:
self._rename_complete(src)
self.transferred_count.set(self.file_count)
self.curr_file.set('Complete!')
def test_add_new_project_recursively():
# Add a scan existing in a project that doesn't exist in the dst folder
# This will recursively add the project, subject and session.
with tempfile.TemporaryDirectory() as tmp:
# copy the dst to a temp folder
shutil.copytree(TESTPATH2, op.join(tmp, 'BIDSTEST2'))
src_bt = BIDSTree(TESTPATH1)
dst_bt = BIDSTree(op.join(tmp, 'BIDSTEST2'))
scan = src_bt.project('test2').subject('3').session('1').scan(
task='resting', run='1')
assert scan.emptyroom is not None
dst_bt.add(scan)
# make sure the project was added
assert len(dst_bt.projects) == 2
assert op.exists(dst_bt.project('test2').readme)
assert op.exists(dst_bt.project('test2').description)
# make sure the subject was added and the empty room data was too
assert len(dst_bt.project('test2').subjects) == 2
# make sure the scan was added
scans_tsv = dst_bt.project('test2').subject('3').session('1').scans_tsv
assert op.exists(scans_tsv)
dst_bt.project('test2').subject('emptyroom')
def test_merge_bidstrees():
# Test completely merging one BIDS folder into another.
with tempfile.TemporaryDirectory() as tmp:
# copy the dst to a temp folder
shutil.copytree(TESTPATH2, op.join(tmp, 'BIDSTEST2'))
src_bt = BIDSTree(TESTPATH1)
dst_bt = BIDSTree(op.join(tmp, 'BIDSTEST2'))
with pytest.warns(UserWarning):
dst_bt.add(src_bt)
assert len(dst_bt.projects) == 2
# proj:test1, subj:2, sess: 1 will not have been merged
assert (src_bt.project('test1').subject(2).session(2)
not in dst_bt.project('test1').subject(2))
# To rectify this, rename the folder-less session then re-add
dst_bt.project('test1').subject(2).session('none').rename('1')
dst_bt.project('test1').subject(2).add(
src_bt.project('test1').subject(2).session(2))
assert len(dst_bt.project('test1').subject(2).sessions) == 2
# check that extra files are brought along
sess = dst_bt.project('test2').subject(3).session(1)
assert 'code' in sess.extra_data
assert 'extradata' in sess.extra_data
assert op.exists(op.join(sess.path, 'code', 'analysis.py'))
assert op.exists(op.join(sess.path, 'extradata', 'extra.txt'))