def upload_files(connection, files, folder_name, folder_accession):
"""
:param genestack_client.Connection connection:
:param list[str] files:
:param str folder_name:
:param str folder_accession:
"""
importer = DataImporter(connection)
fu = FilesUtil(connection)
upload = fu.get_special_folder(SpecialFolders.UPLOADED)
if not folder_accession:
folder_name = folder_name or datetime.now().strftime(
'Upload %d.%m.%y %H:%M:%S')
folder_accession = fu.create_folder(
folder_name,
parent=upload,
description='Files uploaded by genestack-uploader')
else:
folder_name = fu.get_infos([folder_accession])[0]['name']
accession_file_map = {}
for f in files:
accession = importer.load_raw(f)
fu.link_file(accession, folder_accession)
fu.unlink_file(accession, upload)
accession_file_map[accession] = f
return folder_accession, folder_name, accession_file_map
help='Accession of the Genestack folder containing the files')
args = parser.parse_args()
csv_input = args.csv_file
local_key = args.local_key
print('Connecting to Genestack...')
# get connection and application handlers
connection = get_connection(args)
files_util = FilesUtil(connection)
print('Collecting files...')
files = files_util.get_file_children(args.folder)
print('Found %d files. Collecting metadata...' % len(files))
infos = files_util.get_infos(files)
identifier_map = {info['name']: info['accession'] for info in infos}
# parse the CSV file
with open(csv_input, 'r') as the_file:
reader = csv.DictReader(the_file, delimiter=",")
field_names = reader.fieldnames
if args.local_key not in field_names:
raise GenestackException(
"Error: the local key %s is not present in the supplied CSV file"
% args.local_key)
for file_data in reader:
# find the corresponding file
parser.add_argument('folder', help='Accession of the Genestack folder containing the files')
args = parser.parse_args()
csv_input = args.csv_file
local_key = args.local_key
print "Connecting to Genestack..."
# get connection and application handlers
connection = get_connection(args)
files_util = FilesUtil(connection)
print "Collecting files..."
files = files_util.get_file_children(args.folder)
print "Found %d files. Collecting metadata..." % len(files)
infos = files_util.get_infos(files)
identifier_map = {info['name']: info['accession'] for info in infos}
# parse the CSV file
with open(csv_input, 'r') as the_file:
reader = csv.DictReader(the_file, delimiter=",")
field_names = reader.fieldnames
if args.local_key not in field_names:
raise GenestackException("Error: the local key %s is not present in the supplied CSV file" % args.local_key)
for file_data in reader:
# find the corresponding file
local_identifier = file_data[local_key]
remote_file = identifier_map.get(local_identifier)
