def setUpClass(cls):
cls.token = environ.get('KB_AUTH_TOKEN')
cls.callbackURL = environ.get('SDK_CALLBACK_URL')
print('CB URL: ' + cls.callbackURL)
# 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':
cls.token,
'provenance': [{
'service': 'kb_SPAdes',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('kb_SPAdes'):
cls.cfg[nameval[0]] = nameval[1]
cls.wsURL = cls.cfg['workspace-url']
cls.shockURL = cls.cfg['shock-url']
cls.hs = HandleService(url=cls.cfg['handle-service-url'],
token=cls.token)
cls.wsClient = workspaceService(cls.wsURL, token=cls.token)
wssuffix = int(time.time() * 1000)
wsName = "test_kb_SPAdes_" + str(wssuffix)
cls.wsinfo = cls.wsClient.create_workspace({'workspace': wsName})
print('created workspace ' + cls.getWsName())
cls.serviceImpl = kb_SPAdes(cls.cfg)
cls.readUtilsImpl = ReadsUtils(cls.callbackURL, token=cls.token)
cls.staged = {}
cls.nodes_to_delete = []
cls.handles_to_delete = []
cls.setupTestData()
print('\n\n=============== Starting tests ==================')
def setUpClass(cls):
cls.token = environ.get('KB_AUTH_TOKEN')
cls.callbackURL = environ.get('SDK_CALLBACK_URL')
# 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': cls.token,
'provenance': [
{'service': 'kb_SPAdes',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('kb_SPAdes'):
cls.cfg[nameval[0]] = nameval[1]
cls.cfg["SDK_CALLBACK_URL"] = cls.callbackURL
cls.cfg["KB_AUTH_TOKEN"] = cls.token
cls.serviceImpl = kb_SPAdes(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 'kb_SPAdes'):
retconfig[nameval[0]] = nameval[1]
return retconfig
config = get_config()
from kb_SPAdes.kb_SPAdesImpl import kb_SPAdes # noqa @IgnorePep8
impl_kb_SPAdes = kb_SPAdes(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):