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 setup_class(cls):
TestBase.setup_class()
ctx = cls.local_stack.getAuthenticatedDataStoreCoordinator().getContext()
proj = ctx.insertProject('ABF import', 'ABF import', DateTime())
exp = proj.insertExperiment('ABF experiment', DateTime())
cls.device_info = {u'amplifier.mode': u'I-clamp',
u'amplifier.channels.0.gain': 2.5,
u'amplifier.channels.1.gain': 3.5}
# TODO when we move to beta3
#exp.setEquipmentSetupFromMap(to_map(cls.device_info))
cls.src = ctx.insertSource("recording source", "source-id")
abf_file = 'fixtures/example1.abf'
logging.info("Importing file...")
cls.epoch_group = import_file(abf_file,
exp,
"amplifier",
[cls.src])[0] #single block
reader = AxonIO(filename=abf_file)
cls.block = reader.read()[0] # single block