def __init__(self):
submod = get_service_name() or 'kb_stringtie'
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_stringtie.run_stringtie_app,
name='kb_stringtie.run_stringtie_app',
types=[dict])
self.method_authentication[
'kb_stringtie.run_stringtie_app'] = 'required' # noqa
self.rpc_service.add(impl_kb_stringtie.status,
name='kb_stringtie.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
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('kb_stringtie'):
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': 'kb_stringtie',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.ws = Workspace(cls.wsURL, token=token)
cls.serviceImpl = kb_stringtie(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.gfu = GenomeFileUtil(cls.callback_url)
cls.dfu = DataFileUtil(cls.callback_url)
cls.ru = ReadsUtils(cls.callback_url)
cls.rau = ReadsAlignmentUtils(cls.callback_url)
cls.au = AssemblyUtil(cls.callback_url)
cls.stringtie_runner = StringTieUtil(cls.cfg)
suffix = int(time.time() * 1000)
cls.wsName = "test_kb_stringtie_" + str(suffix)
# cls.wsName = "jjeffryes:narrative_1516993063374"
cls.wsClient.create_workspace({'workspace': cls.wsName})
cls.prepare_data()