def test_append_list_as_row(tmpdir):
file_name = tmpdir.join('test_row.tsv')
list_of_elem = ["01", "32", 'some_info', "132.98", 'M']
utils.append_list_as_row(file_name, list_of_elem)
with open(file_name, mode='r') as tsv:
tsv_read = reader(tsv, delimiter="\t")
for row in tsv_read:
assert row == list_of_elem
def participants_file(outdir, yml, sub):
"""
Create participants.tsv file if it does not exist.
If it exists and the subject is missing, then add it.
Otherwise, do nothing.
Parameters
----------
outdir: path
Full path to the output directory.
yml: path
Full path to the yaml file.
sub: str
Subject ID.
"""
LGR.info('Updating participants.tsv ...')
file_path = os.path.join(outdir, 'participants.tsv')
if not os.path.exists(file_path):
LGR.warning('phys2bids could not find participants.tsv')
# Read yaml info if file exists
if '.yml' in yml and os.path.exists(yml):
LGR.info('Using yaml data to populate participants.tsv')
with open(yml) as f:
yaml_data = yaml.load(f, Loader=yaml.FullLoader)
p_id = f'sub-{sub}'
p_age = yaml_data['participant']['age']
p_sex = yaml_data['participant']['sex']
p_handedness = yaml_data['participant']['handedness']
else:
LGR.info('No yaml file was provided. Using phys2bids data to '
'populate participants.tsv')
# Fill in with data from phys2bids
p_id = f'sub-{sub}'
p_age = 'n/a'
p_sex = 'n/a'
p_handedness = 'n/a'
# Write to participants.tsv file
header = ['participant_id', 'age', 'sex', 'handedness']
utils.append_list_as_row(file_path, header)
participants_data = [p_id, p_age, p_sex, p_handedness]
utils.append_list_as_row(file_path, participants_data)
else: # If participants.tsv exists only update when subject is not there
LGR.info('phys2bids found participants.tsv. Updating if needed...')
# Find participant_id column in header
pf = open(file_path, 'r')
header = pf.readline().split("\t")
header_length = len(header)
pf.close()
p_id_idx = header.index('participant_id')
# Check if subject is already in the file
sub_exists = False
with open(file_path) as pf:
tsvreader = reader(pf, delimiter="\t")
for line in tsvreader:
if sub in line[p_id_idx]:
sub_exists = True
break
# Only append to file if subject is not in the file
if not sub_exists:
LGR.info(f'Appending subjet sub-{sub} to participants.tsv ...')
participants_data = ['n/a'] * header_length
participants_data[p_id_idx] = f'sub-{sub}'
utils.append_list_as_row(file_path, participants_data)