def __init__(self,
args: Union["Namespace", None] = None,
conf_file: str = "config.ini"):
self.path = conf_file
super().__init__()
self.read(self.path)
self.logfile_path = self["general"]["logfile"]
self.dump_intermediate = self["general"].getboolean(
"dump_intermediate")
self.input = self.parse_input(args)
self.output = self.parse_output(args)
if args.single:
self.dump_intermediate = False
if args.lab:
LAB_INST.configure(**self.lab_options(args.lab))
elif not (args.lab or args.single):
LAB_INST.configure(**self.pedia_lab_options)
# configure api components
ERRORFIXER_INST.configure(**self.errorfixer_options)
JANNOVAR_INST.configure(**self.jannovar_options)
OMIM_INST.configure(**self.omim_options)
PHENOMIZER_INST.configure(**self.phenomizer_options)
def __init__(self,
args: Union["Namespace", None] = None,
conf_file: str = "config.ini"):
self.path = args.config
super().__init__()
self.read(self.path)
self.dump_intermediate = self["general"].getboolean(
"dump_intermediate")
self.data_path = self["general"]["data_path"] if self["general"][
"data_path"] else "data"
self.train_pickle = args.train_pickle_path
if self["classifier"]["train_pickle_path"]:
self.train_pickle = self["classifier"]["train_pickle_path"]
self.param_c = args.param_c
if self["classifier"]["param_c"]:
self.param_c = self["classifier"]["param_c"]
self.input = self.parse_input(args)
self.output = self.parse_output(args)
if args.output and args.single:
filename = os.path.basename(args.single)
case_id = filename.split('.json')[0]
log_dir = os.path.join(args.output, 'logs/{}/'.format(case_id))
if not os.path.exists(log_dir):
os.makedirs(log_dir, exist_ok=True)
self.logfile_path = os.path.join(log_dir, 'preprocess.log')
else:
self.logfile_path = self["general"]["logfile"]
if args.single:
self.dump_intermediate = False
if args.lab:
LAB_INST.configure(**self.lab_options(args.lab))
elif not (args.lab or args.single):
LAB_INST.configure(**self.pedia_lab_options)
# check phenomizer
if self["phenomizer"]["user"] and self["phenomizer"]["password"]:
self.use_phenomizer = True
else:
self.use_phenomizer = False
# configure api components
ERRORFIXER_INST.configure(**self.errorfixer_options)
JANNOVAR_INST.configure(**self.jannovar_options)
OMIM_INST.configure(**self.omim_options)
PHENOMIZER_INST.configure(**self.phenomizer_options)