def test_prepare_for_datalad(tmpdir):
pytest.importorskip("datalad", minversion=MIN_VERSION)
studydir = tmpdir.join("PI").join("study")
studydir_ = str(studydir)
os.makedirs(studydir_)
populate_bids_templates(studydir_)
add_to_datalad(str(tmpdir), studydir_, None, False)
from datalad.api import Dataset
superds = Dataset(str(tmpdir))
assert superds.is_installed()
assert not superds.repo.dirty
subdss = superds.subdatasets(recursive=True, result_xfm='relpaths')
for ds_path in sorted(subdss):
ds = Dataset(opj(superds.path, ds_path))
assert ds.is_installed()
assert not ds.repo.dirty
# the last one should have been the study
target_files = {
'.gitattributes',
'.datalad/config', '.datalad/.gitattributes',
'dataset_description.json',
'CHANGES', 'README'}
assert set(ds.repo.get_indexed_files()) == target_files
# and all are under git
for f in target_files:
assert not ds.repo.is_under_annex(f)
assert not ds.repo.is_under_annex('.gitattributes')
# Above call to add_to_datalad does not create .heudiconv subds since
# directory does not exist (yet).
# Let's first check that it is safe to call it again
add_to_datalad(str(tmpdir), studydir_, None, False)
assert not ds.repo.dirty
old_hexsha = ds.repo.get_hexsha()
# Now let's check that if we had previously converted data so that
# .heudiconv was not a submodule, we still would not fail
dsh_path = os.path.join(ds.path, '.heudiconv')
dummy_path = os.path.join(dsh_path, 'dummy.nii.gz')
create_file_if_missing(dummy_path, '')
ds.add(dummy_path, message="added a dummy file")
# next call must not fail, should just issue a warning
add_to_datalad(str(tmpdir), studydir_, None, False)
ds.repo.is_under_annex(dummy_path)
assert not ds.repo.dirty
assert '.heudiconv/dummy.nii.gz' in ds.repo.get_files()
# Let's now roll back and make it a proper submodule
ds.repo._git_custom_command([], ['git', 'reset', '--hard', old_hexsha])
# now we do not add dummy to git
create_file_if_missing(dummy_path, '')
add_to_datalad(str(tmpdir), studydir_, None, False)
assert '.heudiconv' in ds.subdatasets(result_xfm='relpaths')
assert not ds.repo.dirty
assert '.heudiconv/dummy.nii.gz' not in ds.repo.get_files()
def test_populate_bids_templates(tmpdir):
populate_bids_templates(str(tmpdir),
defaults={'Acknowledgements': 'something'})
for f in "README", "dataset_description.json", "CHANGES":
# Just test that we have created them and they all have stuff TODO
assert "TODO" in tmpdir.join(f).read()
description_file = tmpdir.join('dataset_description.json')
assert "something" in description_file.read()
# it should also be available as a command
os.unlink(str(description_file))
# it must fail if no heuristic was provided
with pytest.raises(ValueError) as cme:
runner(['--command', 'populate-templates', '--files', str(tmpdir)])
assert str(cme.value).startswith("Specify heuristic using -f. Known are:")
assert "convertall," in str(cme.value)
assert not description_file.exists()
runner([
'--command', 'populate-templates', '-f', 'convertall', '--files',
str(tmpdir)
])
assert "something" not in description_file.read()
assert "TODO" in description_file.read()
assert load_json(tmpdir / "scans.json") == SCANS_FILE_FIELDS
def test_populate_bids_templates(tmpdir):
populate_bids_templates(
str(tmpdir),
defaults={'Acknowledgements': 'something'})
for f in "README", "dataset_description.json", "CHANGES":
# Just test that we have created them and they all have stuff TODO
assert "TODO" in tmpdir.join(f).read()
assert "something" in tmpdir.join('dataset_description.json').read()
def test_populate_bids_templates(tmpdir):
populate_bids_templates(str(tmpdir),
defaults={'Acknowledgements': 'something'})
for f in "README", "dataset_description.json", "CHANGES":
# Just test that we have created them and they all have stuff TODO
assert "TODO" in tmpdir.join(f).read()
description_file = tmpdir.join('dataset_description.json')
assert "something" in description_file.read()
# it should also be available as a command
os.unlink(str(description_file))
runner([
'--command', 'populate-templates', '-f', 'convertall', '--files',
str(tmpdir)
])
assert "something" not in description_file.read()
assert "TODO" in description_file.read()
