def setUpClass(cls):
token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('MetagenomeUtils'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
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': 'MetagenomeUtils',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = MetagenomeUtils(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
def setUpClass(cls):
token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('MetagenomeUtils'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
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': 'MetagenomeUtils',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = MetagenomeUtils(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
suffix = int(time.time() * 1000)
wsName = "test_kb_maxbin_" + str(suffix)
cls.ws_info = cls.wsClient.create_workspace({'workspace': wsName})
cls.dfu = DataFileUtil(os.environ['SDK_CALLBACK_URL'], token=token)
cls.au = AssemblyUtil(os.environ['SDK_CALLBACK_URL'], token=token)
cls.metagenome_ref = None
cls.handleURL = cls.cfg['handle-service-url']
cls.hs = HandleService(cls.handleURL)
cls.object_ref = 'KBaseTestData/test_metagenome/1'
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 'MetagenomeUtils'):
retconfig[nameval[0]] = nameval[1]
return retconfig
config = get_config()
from MetagenomeUtils.MetagenomeUtilsImpl import MetagenomeUtils # noqa @IgnorePep8
impl_MetagenomeUtils = MetagenomeUtils(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):