def setUpClass(cls): token = environ.get('KB_AUTH_TOKEN', None) cls.ctx = {'token': token} config_file = environ.get('KB_DEPLOYMENT_CONFIG', None) cls.cfg = {} config = ConfigParser() config.read(config_file) for nameval in config.items('kb_cummerbund'): cls.cfg[nameval[0]] = nameval[1] cls.wsURL = cls.cfg['ws_url'] cls.wsClient = workspaceService(cls.wsURL, token=token) cls.serviceImpl = kb_cummerbund(cls.cfg)
def setUpClass(cls): token = environ.get('KB_AUTH_TOKEN', None) cls.callback_url = os.environ['SDK_CALLBACK_URL'] cls.ctx = {'token': token} config_file = environ.get('KB_DEPLOYMENT_CONFIG', None) cls.cfg = {} config = ConfigParser() config.read(config_file) for nameval in config.items('kb_cummerbund'): cls.cfg[nameval[0]] = nameval[1] cls.scratch = cls.cfg['scratch'] cls.wsURL = cls.cfg['ws_url'] cls.gfu = GenomeFileUtil(cls.callback_url) cls.ru = ReadsUtils(cls.callback_url) cls.rau = ReadsAlignmentUtils(cls.callback_url, service_ver='dev') cls.eu = ExpressionUtils(cls.callback_url, service_ver='dev') cls.wsClient = workspaceService(cls.wsURL, token=token) cls.dfu = DataFileUtil(cls.callback_url, token=token) cls.serviceImpl = kb_cummerbund(cls.cfg) cls.prepare_data()
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_cummerbund'): retconfig[nameval[0]] = nameval[1] return retconfig config = get_config() from kb_cummerbund.kb_cummerbundImpl import kb_cummerbund # @IgnorePep8 impl_kb_cummerbund = kb_cummerbund(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 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_cummerbund'): retconfig[nameval[0]] = nameval[1] return retconfig config = get_config() from kb_cummerbund.kb_cummerbundImpl import kb_cummerbund # noqa @IgnorePep8 impl_kb_cummerbund = kb_cummerbund(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):