def test_cleanup(self): ''' Cleanup objects created by tests. ''' # Delete all of the objects in the test workspace. wsClient = Workspace(self._config["workspace_url"], token=self._token) listObjectsParams = dict() listObjectsParams['workspaces'] = [ self._config['test_ws'] ] objectList = wsClient.list_objects(listObjectsParams) deleteList = list() for object in objectList: deleteList.append( { 'wsid': object[6], 'objid': object[0], 'ver': object[4] }) wsClient.delete_objects(deleteList) objectList = wsClient.list_objects(listObjectsParams) for object in objectList: print 'After delete Object %s %s' %(object[1], object[4])
def test_cleanup(self): ''' Cleanup objects created by tests. ''' # Delete all of the objects in the test workspace. wsClient = Workspace(self._config["workspace_url"], token=self._token) listObjectsParams = dict() listObjectsParams['workspaces'] = [self._config['test_ws']] objectList = wsClient.list_objects(listObjectsParams) deleteList = list() for object in objectList: deleteList.append({ 'wsid': object[6], 'objid': object[0], 'ver': object[4] }) wsClient.delete_objects(deleteList) objectList = wsClient.list_objects(listObjectsParams) for object in objectList: print 'After delete Object %s %s' % (object[1], object[4])
def setUp(cls): token = environ.get('KB_AUTH_TOKEN', None) if token is None: sys.stderr.write( "Error: Unable to run tests without authentication token!\n") sys.exit(1) token_file = open('ltest/script_test/token.txt', 'w') token_file.write(token) config_file = environ.get('KB_DEPLOYMENT_CONFIG', None) cls.cfg = {} config = ConfigParser() config.read(config_file) for nameval in config.items('CoExpression'): cls.cfg[nameval[0]] = nameval[1] auth_service_url = cls.cfg.get( 'auth-service-url', "https://kbase.us/services/authorization/Sessions/Login") ws_url = cls.cfg['ws_url'] auth_service_url_allow_insecure = cls.cfg[ 'auth-service-url-allow-insecure'] auth_client = _KBaseAuth(auth_service_url) user_id = auth_client.get_user(token) ws = Workspace( url=ws_url, token=token, auth_svc=auth_service_url, trust_all_ssl_certificates=auth_service_url_allow_insecure) # update input data in reverse order of references ordered_file_list = [ INPUT_META_DATA_DIR + '/test_diff_p_distribution_input_ref2.json', INPUT_META_DATA_DIR + '/test_diff_p_distribution_input_ref1.json', INPUT_META_DATA_DIR + '/test_diff_p_distribution_input.json', INPUT_META_DATA_DIR + '/test_view_heatmap_input_ref1.json', INPUT_META_DATA_DIR + '/test_view_heatmap_input.json', INPUT_META_DATA_DIR + '/test_coex_clust_input.json', INPUT_META_DATA_DIR + '/test_filter_genes_input.json' ] for filename in ordered_file_list: with open(filename, 'r') as infile: input_meta_data = json.load(infile) # create workspace that is local to the user if it does not exist workspace_name_t = Template( str(input_meta_data['params'][0]['workspace_name'])) workspace_name = workspace_name_t.substitute(user_id=user_id) print('workspace_name: ' + workspace_name) try: ws_info = ws.get_workspace_info({'workspace': workspace_name}) print("workspace already exists: " + str(ws_info)) except: ws_info = ws.create_workspace({ 'workspace': workspace_name, 'description': 'Workspace for ' + str(input_meta_data['method']) }) print("Created new workspace: " + str(ws_info)) print('reading input file: ' + filename) object_name = str(input_meta_data['params'][0]['object_name']) print('object_name: ' + object_name) input_data_filename = INPUT_DATA_DIR + '/' + object_name + '.json' print('input data filename: ' + input_data_filename) with open(input_data_filename, 'r') as infile: input_data = json.load(infile) # update workspace name in input data input_data_str = json.dumps(input_data) input_data_t = Template(input_data_str) input_data_str = input_data_t.substitute( workspace_name=workspace_name) input_data = json.loads(input_data_str) print('type: ' + input_data[0]['info'][2]) #upload data (no effect if data already exists in workspace) print('uploading input data to workspace') ws.save_objects({ 'workspace': workspace_name, 'objects': [{ 'type': input_data[0]['info'][2], 'data': input_data[0]['data'], 'name': object_name }] }) print('ws objects: ' + str(ws.list_objects({'workspaces': [workspace_name]})))
def setUp(cls): token = environ.get('KB_AUTH_TOKEN', None) if token is None: sys.stderr.write("Error: Unable to run tests without authentication token!\n") sys.exit(1) token_file = open('ltest/script_test/token.txt', 'w') token_file.write(token) config_file = environ.get('KB_DEPLOYMENT_CONFIG', None) cls.cfg = {} config = ConfigParser() config.read(config_file) for nameval in config.items('CoExpression'): cls.cfg[nameval[0]] = nameval[1] auth_service_url = cls.cfg.get('auth-service-url', "https://kbase.us/services/authorization/Sessions/Login") ws_url = cls.cfg['ws_url'] auth_service_url_allow_insecure = cls.cfg['auth-service-url-allow-insecure'] auth_client = _KBaseAuth(auth_service_url) user_id = auth_client.get_user(token) ws = Workspace(url=ws_url, token=token, auth_svc=auth_service_url, trust_all_ssl_certificates=auth_service_url_allow_insecure) # update input data in reverse order of references ordered_file_list = [INPUT_META_DATA_DIR+'/test_diff_p_distribution_input_ref2.json', INPUT_META_DATA_DIR+'/test_diff_p_distribution_input_ref1.json', INPUT_META_DATA_DIR+'/test_diff_p_distribution_input.json', INPUT_META_DATA_DIR+'/test_view_heatmap_input_ref1.json', INPUT_META_DATA_DIR+'/test_view_heatmap_input.json', INPUT_META_DATA_DIR+'/test_coex_clust_input.json', INPUT_META_DATA_DIR+'/test_filter_genes_input.json'] for filename in ordered_file_list: with open(filename, 'r') as infile: input_meta_data = json.load(infile) # create workspace that is local to the user if it does not exist workspace_name_t = Template(str(input_meta_data['params'][0]['workspace_name'])) workspace_name = workspace_name_t.substitute(user_id=user_id) print('workspace_name: ' + workspace_name) try: ws_info = ws.get_workspace_info({'workspace': workspace_name}) print("workspace already exists: " + str(ws_info)) except: ws_info = ws.create_workspace( {'workspace': workspace_name, 'description': 'Workspace for ' + str(input_meta_data['method'])}) print("Created new workspace: " + str(ws_info)) print('reading input file: '+filename) object_name = str(input_meta_data['params'][0]['object_name']) print('object_name: '+object_name) input_data_filename = INPUT_DATA_DIR + '/' + object_name + '.json' print('input data filename: ' + input_data_filename) with open(input_data_filename, 'r') as infile: input_data = json.load(infile) # update workspace name in input data input_data_str = json.dumps(input_data) input_data_t = Template(input_data_str) input_data_str = input_data_t.substitute(workspace_name=workspace_name) input_data = json.loads(input_data_str) print('type: '+input_data[0]['info'][2]) #upload data (no effect if data already exists in workspace) print('uploading input data to workspace') ws.save_objects( {'workspace': workspace_name, 'objects': [{'type': input_data[0]['info'][2], 'data': input_data[0]['data'], 'name': object_name}]}) print('ws objects: ' + str(ws.list_objects({'workspaces': [workspace_name]})))