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()
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_stringtie'): retconfig[nameval[0]] = nameval[1] return retconfig config = get_config() from kb_stringtie.kb_stringtieImpl import kb_stringtie # noqa @IgnorePep8 impl_kb_stringtie = kb_stringtie(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):