def _list_outputs(self):
from bids.layout import BIDSLayout
base_dir = self.inputs.base_directory
os.makedirs(base_dir, exist_ok=True)
layout = BIDSLayout(base_dir, validate=False)
path_patterns = self.inputs.path_patterns
if not isdefined(path_patterns):
path_patterns = None
out_files = []
for entities, in_file in zip(self.inputs.entities,
self.inputs.in_file):
ents = {**self.inputs.fixed_entities}
ents.update(entities)
ents = {k: snake_to_camel(str(v)) for k, v in ents.items()}
out_fname = os.path.join(base_dir,
layout.build_path(ents, path_patterns))
makedirs(os.path.dirname(out_fname), exist_ok=True)
_copy_or_convert(in_file, out_fname)
out_files.append(out_fname)
return {'out_file': out_files}
def change_dir(request):
orig_dir = os.getcwd()
test_dir = os.path.join(orig_dir, "test_outputs_inner")
makedirs(test_dir, exist_ok=True)
os.chdir(test_dir)
def move2orig():
os.chdir(orig_dir)
request.addfinalizer(move2orig)
def _list_outputs(self):
base_dir = self.inputs.base_directory
layout = gb.BIDSLayout(base_dir)
if self.inputs.path_patterns:
layout.path_patterns[:0] = self.inputs.path_patterns
out_files = []
for entities, in_file in zip(self.inputs.entities,
self.inputs.in_file):
ents = {**self.inputs.fixed_entities}
ents.update(entities)
ents = {k: snake_to_camel(str(v)) for k, v in ents.items()}
out_fname = os.path.join(
base_dir, layout.build_path(ents))
makedirs(os.path.dirname(out_fname), exist_ok=True)
_copy_or_convert(in_file, out_fname)
out_files.append(out_fname)
return {'out_file': out_files}