def __init__(self):
submod = get_service_name() or 'kb_quast'
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_kb_quast.run_QUAST_app,
name='kb_quast.run_QUAST_app',
types=[dict])
self.method_authentication['kb_quast.run_QUAST_app'] = 'required' # noqa
self.rpc_service.add(impl_kb_quast.run_QUAST,
name='kb_quast.run_QUAST',
types=[dict])
self.method_authentication['kb_quast.run_QUAST'] = 'required' # noqa
self.rpc_service.add(impl_kb_quast.status,
name='kb_quast.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def setUpClass(cls):
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('kb_quast'):
cls.cfg[nameval[0]] = nameval[1]
authServiceUrl = cls.cfg.get(
'auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(cls.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':
cls.token,
'user_id':
user_id,
'provenance': [{
'service': 'kb_quast',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.shockURL = cls.cfg['shock-url']
cls.ws = Workspace(cls.cfg['workspace-url'], token=cls.token)
cls.hs = HandleService(url=cls.cfg['handle-service-url'],
token=cls.token)
cls.au = AssemblyUtil(os.environ['SDK_CALLBACK_URL'])
cls.impl = kb_quast(cls.cfg)
cls.scratch = cls.cfg['scratch']
shutil.rmtree(cls.scratch)
os.mkdir(cls.scratch)
suffix = int(time.time() * 1000)
wsName = "test_ReadsUtils_" + str(suffix)
cls.ws_info = cls.ws.create_workspace({'workspace': wsName})
cls.dfu = DataFileUtil(os.environ['SDK_CALLBACK_URL'])
cls.staged = {}
cls.nodes_to_delete = []
cls.handles_to_delete = []
# cls.setupTestData()
print('\n\n=============== Starting tests ==================')