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 get_config():
if not get_config_file():
return None
retconfig = {}
config = ConfigParser()
config.read(get_config_file())
for nameval in config.items(get_service_name() or 'ProkkaAnnotation'):
retconfig[nameval[0]] = nameval[1]
return retconfig
config = get_config()
from ProkkaAnnotation.ProkkaAnnotationImpl import ProkkaAnnotation # noqa @IgnorePep8
impl_ProkkaAnnotation = ProkkaAnnotation(config)
class JSONObjectEncoder(json.JSONEncoder):
def default(self, obj):
if isinstance(obj, set):
return list(obj)
if isinstance(obj, frozenset):
return list(obj)
if hasattr(obj, 'toJSONable'):
return obj.toJSONable()
return json.JSONEncoder.default(self, obj)
class JSONRPCServiceCustom(JSONRPCService):
def call(self, ctx, jsondata):