diff --git a/python/bids_import.py b/python/bids_import.py index aa7accd47..5f3e73a9f 100755 --- a/python/bids_import.py +++ b/python/bids_import.py @@ -56,8 +56,8 @@ def main(): '\t-i, --idsvalidation : to validate BIDS directory for a matching pscid/candid pair (optional)\n' '\t-b, --nobidsvalidation : to disable BIDS validation for BIDS compliance\n' '\t-a, --nocopy : to disable dataset copy in data assembly_bids\n' - '\t-t, --type : raw | derivatives. Specify the dataset type.' - 'If not set, the pipeline will look for both raw and derivatives files.\n' + '\t-t, --type : raw | derivative. Specify the dataset type.' + 'If not set, the pipeline will look for both raw and derivative files.\n' 'Required if no dataset_description.json is found.\n' '\t-v, --verbose : be verbose\n' ) @@ -100,8 +100,8 @@ def main(): print(usage) sys.exit(lib.exitcode.MISSING_ARG) - if type and type not in ('raw', 'derivatives'): - print("--type must be one of 'raw', 'derivatives'") + if type and type not in ('raw', 'derivative'): + print("--type must be one of 'raw', 'derivative'") print(usage) sys.exit(lib.exitcode.MISSING_ARG) @@ -201,7 +201,7 @@ def read_and_insert_bids( :type idsvalidation : bool :param nobidsvalidation : disable bids dataset validation :type nobidsvalidation : bool - :param type : raw | derivatives. Type of the dataset + :param type : raw | derivative. Type of the dataset :type type : string :param nocopy : disable bids dataset copy in assembly_bids :type nocopy : bool @@ -354,8 +354,8 @@ def read_and_insert_bids( default_visit_label = default_bids_vl, loris_bids_eeg_rel_dir = loris_bids_modality_rel_dir, loris_bids_root_dir = loris_bids_root_dir, - dataset_tag_dict = dataset_tag_dict - type = type + dataset_tag_dict = dataset_tag_dict, + dataset_type = type ) elif modality in ['anat', 'dwi', 'fmap', 'func']: diff --git a/python/lib/eeg.py b/python/lib/eeg.py index dc4ea156c..42caa19b1 100755 --- a/python/lib/eeg.py +++ b/python/lib/eeg.py @@ -105,7 +105,7 @@ def __init__(self, bids_reader, bids_sub_id, bids_ses_id, bids_modality, db, :type loris_bids_root_dir : str :param dataset_tag_dict : Dict of dataset-inherited HED tags :type dataset_tag_dict : dict - :param dataset_type : raw | derivatives. Type of the dataset + :param dataset_type : raw | derivative. Type of the dataset :type dataset_type : string """ @@ -169,7 +169,7 @@ def __init__(self, bids_reader, bids_sub_id, bids_ses_id, bids_modality, db, # register the data into LORIS if (dataset_type and dataset_type == 'raw'): self.register_data(detect=False) - elif (dataset_type and dataset_type == 'derivatives'): + elif (dataset_type and dataset_type == 'derivative'): self.register_data(derivatives=True, detect=False) else: self.register_data() @@ -966,7 +966,7 @@ def create_and_insert_event_archive(self, files_to_archive, archive_rel_name, ee return # create the archive file - utilities.create_archive(files_to_archive, archive_rel_name, self.data_dir) + utilities.create_archive(files_to_archive, archive_full_path) # insert the archive into the physiological_annotation_archive table blake2 = utilities.compute_blake2b_hash(archive_full_path)