def __init__(self): submod = get_service_name() or 'ExpressionUtils' 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_ExpressionUtils.upload_expression, name='ExpressionUtils.upload_expression', types=[dict]) self.method_authentication['ExpressionUtils.upload_expression'] = 'required' # noqa self.rpc_service.add(impl_ExpressionUtils.download_expression, name='ExpressionUtils.download_expression', types=[dict]) self.method_authentication['ExpressionUtils.download_expression'] = 'required' # noqa self.rpc_service.add(impl_ExpressionUtils.export_expression, name='ExpressionUtils.export_expression', types=[dict]) self.method_authentication['ExpressionUtils.export_expression'] = 'required' # noqa self.rpc_service.add(impl_ExpressionUtils.get_expressionMatrix, name='ExpressionUtils.get_expressionMatrix', types=[dict]) self.method_authentication['ExpressionUtils.get_expressionMatrix'] = 'required' # noqa self.rpc_service.add(impl_ExpressionUtils.status, name='ExpressionUtils.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) cls.callbackURL = environ.get('SDK_CALLBACK_URL') config_file = environ.get('KB_DEPLOYMENT_CONFIG', None) cls.cfg = {} config = ConfigParser() config.read(config_file) for nameval in config.items('ExpressionUtils'): 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(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': 'ExpressionUtils', 'method': 'please_never_use_it_in_production', 'method_params': [] }], 'authenticated': 1 }) cls.shockURL = cls.cfg['shock-url'] cls.wsURL = cls.cfg['workspace-url'] cls.service_wizard_url = cls.cfg['srv-wiz-url'] cls.wsClient = workspaceService(cls.wsURL) cls.ws = Workspace(cls.wsURL, token=cls.token) cls.hs = HandleService(url=cls.cfg['handle-service-url'], token=cls.token) # create workspace wssuffix = int(time.time() * 1000) wsname = "test_expression_" + str(wssuffix) cls.wsinfo = cls.wsClient.create_workspace({'workspace': wsname}) print('created workspace ' + cls.getWsName()) cls.serviceImpl = ExpressionUtils(cls.cfg) cls.readUtils = ReadsUtils(cls.callbackURL) cls.dfu = DataFileUtil(cls.callbackURL, service_ver='dev') cls.dfu.ws_name_to_id(wsname) cls.assemblyUtil = AssemblyUtil(cls.callbackURL) cls.gfu = GenomeFileUtil(cls.callbackURL) cls.gaAPI = GenomeAnnotationAPI(cls.service_wizard_url) cls.rau = ReadsAlignmentUtils(cls.callbackURL) cls.scratch = cls.cfg['scratch'] cls.staged = {} cls.nodes_to_delete = [] cls.handles_to_delete = [] cls.setupTestData()
def setUpClass(cls): cls.__LOGGER = logging.getLogger('ExpressionUtils_test') cls.__LOGGER.setLevel(logging.INFO) streamHandler = logging.StreamHandler(sys.stdout) formatter = logging.Formatter( "%(asctime)s - %(filename)s - %(lineno)d - %(levelname)s - %(message)s" ) formatter.converter = time.gmtime streamHandler.setFormatter(formatter) cls.__LOGGER.addHandler(streamHandler) cls.__LOGGER.info("Logger was set") 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('ExpressionUtils'): 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': 'ExpressionUtils', 'method': 'please_never_use_it_in_production', 'method_params': [] }], 'authenticated': 1 }) cls.wsURL = cls.cfg['workspace-url'] cls.callback_url = os.environ['SDK_CALLBACK_URL'] cls.cfg['SDK_CALLBACK_URL'] = cls.callback_url cls.wsClient = workspaceService(cls.wsURL) cls.serviceImpl = ExpressionUtils(cls.cfg) cls.scratch = cls.cfg['scratch']
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('ExpressionUtils'): cls.cfg[nameval[0]] = nameval[1] # Getting username from Auth profile for token authServiceUrl = cls.cfg['auth-service-url'] # authServiceUrlAllowInsecure = cls.cfg['auth_service_url_allow_insecure'] 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': 'ExpressionUtils', 'method': 'please_never_use_it_in_production', 'method_params': [] }], 'authenticated': 1 }) cls.wsURL = cls.cfg['workspace-url'] cls.wsClient = workspaceService(cls.wsURL) cls.serviceImpl = ExpressionUtils(cls.cfg) cls.scratch = cls.cfg['scratch'] cls.callback_url = os.environ['SDK_CALLBACK_URL'] cls.dfu = DataFileUtil(cls.callback_url) cls.gfu = GenomeFileUtil(cls.callback_url) suffix = int(time.time() * 1000) cls.wsName = "test_exprMatrixUtils_" + str(suffix) cls.wsClient.create_workspace({'workspace': cls.wsName}) cls.setupdata()