def setUpClass(cls): token = os.environ.get('KB_AUTH_TOKEN', None) config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None) cls.cfg = {} config = ConfigParser() config.read(config_file) for nameval in config.items('OntologyAPI'): 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': 'OntologyAPI', 'method': 'please_never_use_it_in_production', 'method_params': [] }], 'authenticated': 1 }) cls.wsURL = cls.cfg['workspace-url'] cls.wsClient = Workspace(cls.wsURL) cls.serviceImpl = OntologyAPI(cls.cfg) cls.scratch = cls.cfg['scratch'] #cls.callback_url = os.environ['SDK_CALLBACK_URL'] suffix = int(time.time() * 1000) cls.wsName = "test_OntologyAPI_" + str(suffix) ret = cls.wsClient.create_workspace({'workspace': cls.wsName}) # noqa
def __init__(self): submod = get_service_name() or 'OntologyAPI' 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_OntologyAPI.get_descendants, name='OntologyAPI.get_descendants', types=[dict]) self.method_authentication[ 'OntologyAPI.get_descendants'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_ancestors, name='OntologyAPI.get_ancestors', types=[dict]) self.method_authentication[ 'OntologyAPI.get_ancestors'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_children, name='OntologyAPI.get_children', types=[dict]) self.method_authentication[ 'OntologyAPI.get_children'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_parents, name='OntologyAPI.get_parents', types=[dict]) self.method_authentication[ 'OntologyAPI.get_parents'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_related, name='OntologyAPI.get_related', types=[dict]) self.method_authentication[ 'OntologyAPI.get_related'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_siblings, name='OntologyAPI.get_siblings', types=[dict]) self.method_authentication[ 'OntologyAPI.get_siblings'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_terms, name='OntologyAPI.get_terms', types=[dict]) self.method_authentication[ 'OntologyAPI.get_terms'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_hierarchical_ancestors, name='OntologyAPI.get_hierarchical_ancestors', types=[dict]) self.method_authentication[ 'OntologyAPI.get_hierarchical_ancestors'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_hierarchical_children, name='OntologyAPI.get_hierarchical_children', types=[dict]) self.method_authentication[ 'OntologyAPI.get_hierarchical_children'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_hierarchical_descendants, name='OntologyAPI.get_hierarchical_descendants', types=[dict]) self.method_authentication[ 'OntologyAPI.get_hierarchical_descendants'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_hierarchical_parents, name='OntologyAPI.get_hierarchical_parents', types=[dict]) self.method_authentication[ 'OntologyAPI.get_hierarchical_parents'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_associated_ws_genomes, name='OntologyAPI.get_associated_ws_genomes', types=[dict]) self.method_authentication[ 'OntologyAPI.get_associated_ws_genomes'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_associated_ws_features, name='OntologyAPI.get_associated_ws_features', types=[dict]) self.method_authentication[ 'OntologyAPI.get_associated_ws_features'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_terms_from_ws_feature, name='OntologyAPI.get_terms_from_ws_feature', types=[dict]) self.method_authentication[ 'OntologyAPI.get_terms_from_ws_feature'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_terms_from_ws_object, name='OntologyAPI.get_terms_from_ws_object', types=[dict]) self.method_authentication[ 'OntologyAPI.get_terms_from_ws_object'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.get_associated_samples, name='OntologyAPI.get_associated_samples', types=[dict]) self.method_authentication[ 'OntologyAPI.get_associated_samples'] = 'optional' # noqa self.rpc_service.add(impl_OntologyAPI.status, name='OntologyAPI.status', types=[dict]) authurl = config.get(AUTH) if config else None self.auth_client = _KBaseAuth(authurl)