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('GenericsAPI'): 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': 'GenericsAPI', 'method': 'please_never_use_it_in_production', 'method_params': [] }], 'authenticated': 1}) cls.wsURL = cls.cfg['workspace-url'] cls.wsClient = workspaceService(cls.wsURL) cls.serviceImpl = GenericsAPI(cls.cfg) cls.scratch = cls.cfg['scratch'] cls.callback_url = os.environ['SDK_CALLBACK_URL'] cls.dfu = DataFileUtil(cls.callback_url) cls.pca_util = PCAUtil(cls.cfg) suffix = int(time.time() * 1000) cls.wsName = "test_pca_util_" + str(suffix) ret = cls.wsClient.create_workspace({'workspace': cls.wsName}) cls.wsId = ret[0]
def setUpClass(cls): 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('GenericsAPI'): 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': 'GenericsAPI', 'method': 'please_never_use_it_in_production', 'method_params': [] }], 'authenticated': 1 }) cls.wsURL = cls.cfg['workspace-url'] cls.wsClient = workspaceService(cls.wsURL) cls.serviceImpl = GenericsAPI(cls.cfg) cls.scratch = cls.cfg['scratch'] cls.callback_url = os.environ['SDK_CALLBACK_URL'] cls.shockURL = cls.cfg['shock-url'] cls.dfu = DataFileUtil(cls.callback_url) cls.sample_uploader = sample_uploader(cls.callback_url, service_ver="dev") cls.sample_url = cls.cfg.get('kbase-endpoint') + '/sampleservice' cls.sample_ser = SampleService(cls.sample_url) cls.hs = HandleService(url=cls.cfg['handle-service-url'], token=cls.token) suffix = int(time.time() * 1000) cls.wsName = "test_GenericsAPI_" + str(suffix) ret = cls.wsClient.create_workspace({'workspace': cls.wsName}) cls.wsId = ret[0] small_file = os.path.join(cls.scratch, 'test.txt') with open(small_file, "w") as f: f.write("empty content") cls.test_shock = cls.dfu.file_to_shock({ 'file_path': small_file, 'make_handle': True }) cls.handles_to_delete = [] cls.nodes_to_delete = [] cls.handles_to_delete.append(cls.test_shock['handle']['hid']) cls.nodes_to_delete.append(cls.test_shock['shock_id']) cls.prepare_data()
def setUpClass(cls): cls.maxDiff = 70000 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('GenericsAPI'): 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': 'GenericsAPI', 'method': 'please_never_use_it_in_production', 'method_params': [] }], 'authenticated': 1}) cls.wsURL = cls.cfg['workspace-url'] cls.wsClient = workspaceService(cls.wsURL) cls.serviceImpl = GenericsAPI(cls.cfg) cls.serviceUtils = AttributesUtil(cls.cfg) cls.shockURL = cls.cfg['shock-url'] cls.scratch = cls.cfg['scratch'] cls.callback_url = os.environ['SDK_CALLBACK_URL'] cls.dfu = DataFileUtil(cls.callback_url) cls.hs = HandleService(url=cls.cfg['handle-service-url'], token=cls.token) suffix = int(time.time() * 1000) cls.wsName = "test_CompoundSetUtils_" + str(suffix) ret = cls.wsClient.create_workspace({'workspace': cls.wsName}) cls.wsId = ret[0] cls.attribute_mapping = json.load(open('data/AM1.json')) info = cls.dfu.save_objects({ "id": cls.wsId, "objects": [{ "type": "KBaseExperiments.AttributeMapping", "data": cls.attribute_mapping, "name": "test_cond_set" }] })[0] cls.attribute_mapping_ref = "%s/%s/%s" % (info[6], info[0], info[4]) cls.attribute_mapping_2 = json.load(open('data/AM2.json')) small_file = os.path.join(cls.scratch, 'test.txt') with open(small_file, "w") as f: f.write("empty content") cls.test_shock = cls.dfu.file_to_shock({'file_path': small_file, 'make_handle': True}) cls.handles_to_delete = [] cls.nodes_to_delete = [] cls.handles_to_delete.append(cls.test_shock['handle']['hid']) cls.nodes_to_delete.append(cls.test_shock['shock_id'])
def setUpClass(cls): cls.maxDiff = 70000 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('GenericsAPI'): 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': 'GenericsAPI', 'method': 'please_never_use_it_in_production', 'method_params': [] }], 'authenticated': 1}) cls.wsURL = cls.cfg['workspace-url'] cls.wsClient = workspaceService(cls.wsURL) cls.serviceImpl = GenericsAPI(cls.cfg) cls.serviceUtils = AttributesUtil(cls.cfg) cls.scratch = cls.cfg['scratch'] cls.callback_url = os.environ['SDK_CALLBACK_URL'] cls.dfu = DataFileUtil(cls.callback_url) suffix = int(time.time() * 1000) #cls.wsName = "test_CompoundSetUtils_" + str(suffix) cls.wsName = "man4ish_gupta:narrative_1568644342277" ret = cls.wsClient.create_workspace({'workspace': cls.wsName}) #exit(cls.wsId) #cls.wsId = ret[0] cls.wsid = 44071 cls.attribute_mapping = json.load(open('data/AM1.json')) info = cls.dfu.save_objects({ "id": cls.wsId, "objects": [{ "type": "KBaseExperiments.AttributeMapping", "data": cls.attribute_mapping, "name": "test_cond_set" }] })[0] cls.attribute_mapping_ref = "%s/%s/%s" % (info[6], info[0], info[4]) cls.attribute_mapping_2 = json.load(open('data/AM2.json'))
def __init__(self): submod = get_service_name() or 'GenericsAPI' 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_GenericsAPI.fetch_data, name='GenericsAPI.fetch_data', types=[dict]) self.method_authentication[ 'GenericsAPI.fetch_data'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.export_matrix, name='GenericsAPI.export_matrix', types=[dict]) self.method_authentication[ 'GenericsAPI.export_matrix'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.validate_data, name='GenericsAPI.validate_data', types=[dict]) self.method_authentication[ 'GenericsAPI.validate_data'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.import_matrix_from_excel, name='GenericsAPI.import_matrix_from_excel', types=[dict]) self.method_authentication[ 'GenericsAPI.import_matrix_from_excel'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.import_matrix_from_biom, name='GenericsAPI.import_matrix_from_biom', types=[dict]) self.method_authentication[ 'GenericsAPI.import_matrix_from_biom'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.save_object, name='GenericsAPI.save_object', types=[dict]) self.method_authentication[ 'GenericsAPI.save_object'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.search_matrix, name='GenericsAPI.search_matrix', types=[dict]) self.method_authentication[ 'GenericsAPI.search_matrix'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.filter_matrix, name='GenericsAPI.filter_matrix', types=[dict]) self.method_authentication[ 'GenericsAPI.filter_matrix'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.standardize_matrix, name='GenericsAPI.standardize_matrix', types=[dict]) self.method_authentication[ 'GenericsAPI.standardize_matrix'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.file_to_attribute_mapping, name='GenericsAPI.file_to_attribute_mapping', types=[dict]) self.method_authentication[ 'GenericsAPI.file_to_attribute_mapping'] = 'required' # noqa self.rpc_service.add( impl_GenericsAPI.update_matrix_attribute_mapping, name='GenericsAPI.update_matrix_attribute_mapping', types=[dict]) self.method_authentication[ 'GenericsAPI.update_matrix_attribute_mapping'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.attribute_mapping_to_tsv_file, name='GenericsAPI.attribute_mapping_to_tsv_file', types=[dict]) self.method_authentication[ 'GenericsAPI.attribute_mapping_to_tsv_file'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.export_attribute_mapping_tsv, name='GenericsAPI.export_attribute_mapping_tsv', types=[dict]) self.method_authentication[ 'GenericsAPI.export_attribute_mapping_tsv'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.export_attribute_mapping_excel, name='GenericsAPI.export_attribute_mapping_excel', types=[dict]) self.method_authentication[ 'GenericsAPI.export_attribute_mapping_excel'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.export_cluster_set_excel, name='GenericsAPI.export_cluster_set_excel', types=[dict]) self.method_authentication[ 'GenericsAPI.export_cluster_set_excel'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.export_corr_matrix_excel, name='GenericsAPI.export_corr_matrix_excel', types=[dict]) self.method_authentication[ 'GenericsAPI.export_corr_matrix_excel'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.export_pca_matrix_excel, name='GenericsAPI.export_pca_matrix_excel', types=[dict]) self.method_authentication[ 'GenericsAPI.export_pca_matrix_excel'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.export_amplicon_set_tsv, name='GenericsAPI.export_amplicon_set_tsv', types=[dict]) self.method_authentication[ 'GenericsAPI.export_amplicon_set_tsv'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.compute_correlation_matrix, name='GenericsAPI.compute_correlation_matrix', types=[dict]) self.method_authentication[ 'GenericsAPI.compute_correlation_matrix'] = 'required' # noqa self.rpc_service.add( impl_GenericsAPI.compute_correlation_across_matrices, name='GenericsAPI.compute_correlation_across_matrices', types=[dict]) self.method_authentication[ 'GenericsAPI.compute_correlation_across_matrices'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.build_network, name='GenericsAPI.build_network', types=[dict]) self.method_authentication[ 'GenericsAPI.build_network'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.run_pca, name='GenericsAPI.run_pca', types=[dict]) self.method_authentication['GenericsAPI.run_pca'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.view_matrix, name='GenericsAPI.view_matrix', types=[dict]) self.method_authentication[ 'GenericsAPI.view_matrix'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.status, name='GenericsAPI.status', types=[dict]) authurl = config.get(AUTH) if config else None self.auth_client = _KBaseAuth(authurl)
def __init__(self): submod = get_service_name() or 'GenericsAPI' 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_GenericsAPI.fetch_data, name='GenericsAPI.fetch_data', types=[dict]) self.method_authentication[ 'GenericsAPI.fetch_data'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.generate_matrix_html, name='GenericsAPI.generate_matrix_html', types=[dict]) self.method_authentication[ 'GenericsAPI.generate_matrix_html'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.export_matrix, name='GenericsAPI.export_matrix', types=[dict]) self.method_authentication[ 'GenericsAPI.export_matrix'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.validate_data, name='GenericsAPI.validate_data', types=[dict]) self.method_authentication[ 'GenericsAPI.validate_data'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.import_matrix_from_excel, name='GenericsAPI.import_matrix_from_excel', types=[dict]) self.method_authentication[ 'GenericsAPI.import_matrix_from_excel'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.save_object, name='GenericsAPI.save_object', types=[dict]) self.method_authentication[ 'GenericsAPI.save_object'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.search_matrix, name='GenericsAPI.search_matrix', types=[dict]) self.method_authentication[ 'GenericsAPI.search_matrix'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.filter_matrix, name='GenericsAPI.filter_matrix', types=[dict]) self.method_authentication[ 'GenericsAPI.filter_matrix'] = 'required' # noqa self.rpc_service.add(impl_GenericsAPI.status, name='GenericsAPI.status', types=[dict]) authurl = config.get(AUTH) if config else None self.auth_client = _KBaseAuth(authurl)