def setUpClass(cls):
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('ProkkaAnnotation'):
cls.cfg[nameval[0]] = nameval[1]
# Token validation
token = environ.get('KB_AUTH_TOKEN', None)
authServiceUrl = cls.cfg.get('auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(token)
# WARNING: don't call any logging methods on the context object,
# it'll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({'token': token,
'user_id': user_id,
'provenance': [
{'service': 'ProkkaAnnotation',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL, token=token)
cls.serviceImpl = ProkkaAnnotation(cls.cfg)
def setUpClass(cls):
config_file = environ.get("KB_DEPLOYMENT_CONFIG", None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items("ProkkaAnnotation"):
cls.cfg[nameval[0]] = nameval[1]
# Token validation
token = environ.get("KB_AUTH_TOKEN", None)
authServiceUrl = cls.cfg.get("auth-service-url",
"https://kbase.us/services/authorization/Sessions/Login")
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(token)
# WARNING: don"t call any logging methods on the context object,
# it"ll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({"token": token,
"user_id": user_id,
"provenance": [
{"service": "ProkkaAnnotation",
"method": "please_never_use_it_in_production",
"method_params": []
}],
"authenticated": 1})
cls.wsURL = cls.cfg["workspace-url"]
cls.wsClient = workspaceService(cls.wsURL, token=token)
cls.serviceImpl = ProkkaAnnotation(cls.cfg)
def __init__(self):
submod = get_service_name() or 'ProkkaAnnotation'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_ProkkaAnnotation.annotate_contigs,
name='ProkkaAnnotation.annotate_contigs',
types=[dict])
self.method_authentication[
'ProkkaAnnotation.annotate_contigs'] = 'required' # noqa
self.rpc_service.add(impl_ProkkaAnnotation.status,
name='ProkkaAnnotation.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)