def main(args=sys.argv, dsc=None):
def parser_callback(parser):
csv_group = parser.add_argument_group("CSV")
csv_group.add_argument('--header-rows',
help='number of csv header rows. Default = 2',
default=CSV_HEADER_ROW)
csv_group.add_argument(
'--date-column',
help='column number of measurement date (0-indexed). Default = {}'.
format(DATE_COLUMN_NUMBER),
default=DATE_COLUMN_NUMBER)
csv_group.add_argument(
'--measurement-column',
help='column number of first measurement. Default = {}'.format(
FIRST_MEASUREMENT_COLUMN_NUMBER),
default=FIRST_MEASUREMENT_COLUMN_NUMBER)
return parser
def import_wrapper(ctx,
container=None,
protocol=None,
files=None,
timezone=None,
header_rows=None,
date_column=None,
measurement_column=None,
**args):
return import_csv(ctx,
container_uri=container,
protocol_uri=protocol,
files=files,
timezone=timezone,
csv_header_row=header_rows,
date_column=date_column,
first_measurement_column=measurement_column)
return import_main(argv=args,
name='field_data',
description=DESCRIPTION,
file_ext='csv',
parser_callback=parser_callback,
import_fn=import_wrapper,
dsc=dsc)
def main(argv=sys.argv, dsc=None):
def import_wrapper(data_context,
container=None,
protocol=None,
files=None,
sources=None,
equipment_setup_root=None,
**args):
container = data_context.getObjectWithURI(container)
protocol_entity = data_context.getObjectWithURI(protocol)
if protocol_entity:
protocol = asclass("Protocol", protocol_entity)
else:
protocol = None
sources = [data_context.getObjectWithURI(source) for source in sources]
for file in files:
import_file(file,
container,
equipment_setup_root,
sources,
protocol=protocol)
return 0
def parser_wrapper(parser):
# Add equipment setup root
equipment_group = parser.add_argument_group('hardware')
equipment_group.add_argument('--equipment-setup-root',
help='Physiology hardware root in Equipment setup')
return parser
return import_main(argv=argv,
name='neo_import',
description=DESCRIPTION,
file_ext='plx|abf',
import_fn=import_wrapper,
parser_callback=parser_wrapper,
dsc=dsc)
def main(args=sys.argv, dsc=None):
def parser_callback(parser):
csv_group = parser.add_argument_group("CSV")
csv_group.add_argument('--header-rows',
help='number of csv header rows. Default = 2',
default=CSV_HEADER_ROW)
csv_group.add_argument('--date-column',
help='column number of measurement date (0-indexed). Default = {}'.format(DATE_COLUMN_NUMBER),
default=DATE_COLUMN_NUMBER)
csv_group.add_argument('--measurement-column',
help='column number of first measurement. Default = {}'.format(FIRST_MEASUREMENT_COLUMN_NUMBER),
default=FIRST_MEASUREMENT_COLUMN_NUMBER)
return parser
def import_wrapper(ctx,
container=None,
protocol=None,
files=None,
timezone=None,
header_rows=None,
date_column=None,
measurement_column=None,
**args):
return import_csv(ctx,
container_uri=container,
protocol_uri=protocol,
files=files,
timezone=timezone,
csv_header_row=header_rows,
date_column=date_column,
first_measurement_column=measurement_column)
return import_main(argv=args,
name='field_data',
description=DESCRIPTION,
file_ext='csv',
parser_callback=parser_callback,
import_fn=import_wrapper,
dsc=dsc)
def main(argv=sys.argv, dsc=None):
def import_wrapper(data_context,
container=None,
protocol=None,
files=None,
sources=None,
epoch_group_label=None,
event_file=None,
protocol_parameters=None,
epoch_start_event_id=None,
epoch_end_event_id=None,
include_interepoch=False,
timezone=None,
**args):
container = data_context.getObjectWithURI(container)
protocol_entity = data_context.getObjectWithURI(protocol)
if protocol_entity:
protocol = asclass("Protocol", protocol_entity)
else:
protocol = None
if protocol_parameters is None:
protocol_parameters = {}
else:
protocol_parameters = dict(protocol_parameters)
if not sources is None:
sources = [asclass('Source', data_context.getObjectWithURI(source)) for source in sources]
importer = NeuralynxImporter(
protocol=protocol,
protocol_parameters=protocol_parameters,
timezone=timezone)
data_context.beginTransaction()
logging.info("Starting import...")
try:
importer.import_ncs(container,
sources,
epoch_group_label,
ncs_files=files,
event_file=event_file,
start_id=epoch_start_event_id,
end_id=epoch_end_event_id,
include_interepoch=include_interepoch)
except Exception as e:
logging.error("Import failed, aborting.")
logging.error("Error: %s" % e)
traceback.print_exc(file=sys.stdout)
data_context.abortTransaction()
else:
logging.info("Import complete.")
data_context.commitTransaction()
time.sleep(2) # wait for file service to recognize pending uploads
logging.info("Waiting for file uploads...")
file_service = data_context.getFileService()
while file_service.hasPendingUploads():
logging.info(' .')
time.sleep(2)
logging.info("Done.")
return 0
def parse_wrapper(parser):
parser.add_argument("-l", "--label", dest="epoch_group_label",
help="Epoch group label", default="Neuralynx")
parser.add_argument("-e", "--event-file", dest="event_file",
help="Neuralynx event (.nev) file", metavar="FILE")
parser.add_argument("--protocol-parameter", dest="protocol_parameters",
nargs=2, action="append")
event_group = parser.add_argument_group("epoch boundaries",
description="Epoch boundaries may be defined by events. If either start or end boundary events are defined, an event file (.nev) must be provided")
event_group.add_argument("--epoch-start", dest="epoch_start_event_id",
help="Epoch start event I.D.", type=int)
event_group.add_argument("--epoch-end", dest="epoch_end_event_id",
help="Epoch end event I.D.", type=int)
event_group.add_argument("--include-interepoch",
action="store_true",
dest="include_interepoch",
help="Import inter-epoch data")
return parser
return import_main(argv=argv,
name='neuralynx_import',
description=DESCRIPTION,
file_ext='ncs',
import_fn=import_wrapper,
parser_callback=parse_wrapper,
dsc=dsc)
