How to use nottest method in Nose

Best Python code snippet using nose

test_basic.py

Source:test_basic.py

...22def nottest_unless(criteria):23    def _nottest_unless(f):24        if criteria:25            return f26        return nottest(f)27    return _nottest_unless28def nottest_if(criteria):29    def _nottest_if(f):30        if not criteria:31            return f32        return nottest(f)33    return _nottest_if34class EnumValuesMixin(object):35    @classmethod36    def setup_class(cls):37        cls.enum_values = set([v for v in Location])38        cls.app = QCoreApplication(sys.argv)39        cls.app.setApplicationName('Yksom')40        cls.app.setOrganizationName('uranusjr')41        configure(application_name='Yksom', organization_name='uranusjr')42    @classmethod43    def teardown_class(cls):44        # Make sure all locations are tested.45        eq_(cls.enum_values, set())46    def setUp(self):...

CordTestServer.py

Source:CordTestServer.py

1# Copyright 2017-present Open Networking Foundation2#3# Licensed under the Apache License, Version 2.0 (the "License");4# you may not use this file except in compliance with the License.5# You may obtain a copy of the License at6#7# http://www.apache.org/licenses/LICENSE-2.08#9# Unless required by applicable law or agreed to in writing, software10# distributed under the License is distributed on an "AS IS" BASIS,11# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.12# See the License for the specific language governing permissions and13# limitations under the License.14#15# Copyright 2016-present Ciena Corporation16#17# Licensed under the Apache License, Version 2.0 (the "License");18# you may not use this file except in compliance with the License.19# You may obtain a copy of the License at20#21# http://www.apache.org/licenses/LICENSE-2.022#23# Unless required by applicable law or agreed to in writing, software24# distributed under the License is distributed on an "AS IS" BASIS,25# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.26# See the License for the specific language governing permissions and27# limitations under the License.28#29from CordContainer import Container, Onos, OnosStopWrapper, OnosCord, OnosCordStopWrapper, Quagga, QuaggaStopWrapper, Radius, reinitContainerClients30from nose.tools import nottest31from SimpleXMLRPCServer import SimpleXMLRPCServer32from resource import getrlimit, RLIMIT_NOFILE33import daemon34import xmlrpclib35import os36import signal37import json38import time39import threading40##Server to handle container restart/stop requests from test container.41##Used now to restart ONOS from vrouter test container42CORD_TEST_HOST = '172.17.0.1'43CORD_TEST_PORT = 2500044class CordTestServer(object):45    onos_cord = None46    def __restart_onos(self, node = None, config = None, timeout = 10):47        if self.onos_cord:48            onos_config = '{}/network-cfg.json'.format(self.onos_cord.onos_config_dir)49        else:50            onos_config = '{}/network-cfg.json'.format(Onos.host_config_dir)51        if config is None:52            try:53                os.unlink(onos_config)54            except:55                pass56        print('Restarting ONOS')57        if self.onos_cord:58            self.onos_cord.start(restart = True, network_cfg = config)59        else:60            Onos.restart_node(node = node, network_cfg = config, timeout = timeout)61        return 'DONE'62    def restart_onos(self, kwargs):63        return self.__restart_onos(**kwargs)64    def __shutdown_onos(self, node = None):65        if node is None:66            node = Onos.NAME67        OnosStopWrapper(node)68        return 'DONE'69    def shutdown_onos(self, kwargs):70        return self.__shutdown_onos(**kwargs)71    def __restart_cluster(self, config = None, timeout = 10, setup = False):72        Onos.restart_cluster(network_cfg = config, timeout = timeout, setup = setup)73        return 'DONE'74    def restart_cluster(self, kwargs):75        return self.__restart_cluster(**kwargs)76    def __add_cluster_onos(self, count = 1, config = None):77        Onos.add_cluster(count = count, network_cfg = config)78        return 'DONE'79    def add_cluster_onos(self, kwargs):80        return self.__add_cluster_onos(**kwargs)81    def __restart_quagga(self, config = None, boot_delay = 30 ):82        config_file = Quagga.quagga_config_file83        if config is not None:84            quagga_config = '{}/testrib_gen.conf'.format(Quagga.host_quagga_config)85            config_file = '{}/testrib_gen.conf'.format(Quagga.guest_quagga_config)86            with open(quagga_config, 'w+') as fd:87                fd.write(str(config))88        print('Restarting QUAGGA with config file %s, delay %d' %(config_file, boot_delay))89        Quagga(prefix = Container.IMAGE_PREFIX, restart = True, config_file = config_file, boot_delay = boot_delay)90        return 'DONE'91    def restart_quagga(self, kwargs):92        return self.__restart_quagga(**kwargs)93    def stop_quagga(self):94        quaggaStop = QuaggaStopWrapper()95        time.sleep(5)96        try:97            quagga_config_gen = '{}/testrib_gen.conf'.format(Quagga.host_quagga_config)98            os.unlink(quagga_config_gen)99        except: pass100        return 'DONE'101    def __run_shell_quagga(self, cmd = None):102        ret = 0103        if cmd is not None:104            exec_cmd = 'docker exec {} {}'.format(Quagga.NAME, cmd)105            ret = os.system(exec_cmd)106        return ret107    def __run_shell(self, cmd = None):108        ret = 0109        if cmd is not None:110            ret = os.system(cmd)111        return ret112    def run_shell_quagga(self, kwargs):113        return self.__run_shell_quagga(**kwargs)114    def run_shell(self, kwargs):115        return self.__run_shell(**kwargs)116    def restart_radius(self):117        print('Restarting RADIUS Server')118        Radius(prefix = Container.IMAGE_PREFIX, restart = True)119        return 'DONE'120    def shutdown(self):121        print('Shutting down cord test server')122        os.kill(0, signal.SIGKILL)123        return 'DONE'124def find_files_by_path(*paths):125    wanted = []126    for p in paths:127        try:128            fd = os.open(p, os.O_RDONLY)129            wanted.append(os.fstat(fd)[1:3])130        finally:131            os.close(fd)132    def fd_wanted(fd):133        try:134            return os.fstat(fd)[1:3] in wanted135        except OSError:136            return False137    max_fd = getrlimit(RLIMIT_NOFILE)[1]138    return [ fd for fd in xrange(max_fd) if fd_wanted(fd) ]139@nottest140def cord_test_server_start(daemonize = True,141                           cord_test_host = CORD_TEST_HOST,142                           cord_test_port = CORD_TEST_PORT,143                           onos_cord = None,144                           foreground=False):145    server = SimpleXMLRPCServer( (cord_test_host, cord_test_port) )146    server.register_instance(CordTestServer())147    CordTestServer.onos_cord = onos_cord148    if daemonize is True:149        ##before daemonizing, preserve urandom needed by paramiko150        preserve_list = find_files_by_path('/dev/urandom')151        preserve_list.append(server)152        d = daemon.DaemonContext(files_preserve = preserve_list,153                                 detach_process = True)154        with d:155            reinitContainerClients()156            server.serve_forever()157    else:158        if foreground:159            try:160                server.serve_forever()161            except KeyboardInterrupt:162                return server163        else:164            task = threading.Thread(target = server.serve_forever)165            ##terminate when main thread exits166            task.daemon = True167            task.start()168    return server169@nottest170def cord_test_server_stop(server):171    server.shutdown()172    server.server_close()173@nottest174def get_cord_test_loc():175    host = os.getenv('CORD_TEST_HOST', CORD_TEST_HOST)176    port = int(os.getenv('CORD_TEST_PORT', CORD_TEST_PORT))177    return host, port178def rpc_server_instance():179    '''Stateless'''180    host, port = get_cord_test_loc()181    rpc_server = 'http://{}:{}'.format(host, port)182    return xmlrpclib.Server(rpc_server, allow_none = True)183@nottest184def __cord_test_onos_restart(**kwargs):185    return rpc_server_instance().restart_onos(kwargs)186@nottest187def cord_test_onos_restart(node = None, config = None, timeout = 10):188    '''Send ONOS restart to server'''189    for i in range(3):190        try:191            data = __cord_test_onos_restart(node = node, config = config, timeout = timeout)192            if data == 'DONE':193                return True194        except:195            time.sleep(2)196    return False197@nottest198def __cord_test_onos_shutdown(**kwargs):199    return rpc_server_instance().shutdown_onos(kwargs)200@nottest201def cord_test_onos_shutdown(node = None):202    data = __cord_test_onos_shutdown(node = node)203    if data == 'DONE':204        return True205    return False206@nottest207def __cord_test_restart_cluster(**kwargs):208    return rpc_server_instance().restart_cluster(kwargs)209@nottest210def cord_test_restart_cluster(config = None, timeout = 10, setup = False):211    for i in range(3):212        try:213            data = __cord_test_restart_cluster(config = config, timeout = timeout, setup = setup)214            if data == 'DONE':215                return True216        except:217            time.sleep(2)218    return False219@nottest220def __cord_test_onos_add_cluster(**kwargs):221    return rpc_server_instance().add_cluster_onos(kwargs)222@nottest223def cord_test_onos_add_cluster(count = 1, config = None):224    data = __cord_test_onos_add_cluster(count = count, config = config)225    if data == 'DONE':226        return True227    return False228@nottest229def __cord_test_quagga_restart(**kwargs):230    return rpc_server_instance().restart_quagga(kwargs)231@nottest232def cord_test_quagga_restart(config = None, boot_delay = 30):233    '''Send QUAGGA restart to server'''234    data = __cord_test_quagga_restart(config = config, boot_delay = boot_delay)235    if data == 'DONE':236        return True237    return False238@nottest239def __cord_test_quagga_shell(**kwargs):240    return rpc_server_instance().run_shell_quagga(kwargs)241@nottest242def cord_test_quagga_shell(cmd = None):243    '''Send QUAGGA shell cmd to server'''244    return __cord_test_quagga_shell(cmd = cmd)245@nottest246def __cord_test_shell(**kwargs):247    return rpc_server_instance().run_shell(kwargs)248@nottest249def cord_test_shell(cmd = None):250    '''Send shell cmd to run remotely'''251    return __cord_test_shell(cmd = cmd)252@nottest253def cord_test_quagga_stop():254    data = rpc_server_instance().stop_quagga()255    if data == 'DONE':256        return True257    return False258@nottest259def cord_test_radius_restart():260    '''Send Radius server restart to server'''261    data = rpc_server_instance().restart_radius()262    if data == 'DONE':263        return True264    return False265@nottest266def cord_test_server_shutdown(host, port):267    '''Shutdown the cord test server'''268    rpc_server = 'http://{}:{}'.format(host, port)269    try:270        xmlrpclib.Server(rpc_server, allow_none = True).shutdown()271    except: pass...

test_standard_stats.py

Source:test_standard_stats.py

1"""2Currently just running and making sure there's no uncaught exceptions.3TODO: check that the correct output is generated too4In future we should put this in a web-accessible place5Usage:  pytest test_standard_stats.py6"""7import tempfile8import pytest9import toml10from pathlib import Path11from lama.tests import (wt_registration_dir, mut_registration_dir, target_dir,12                        stats_output_dir)13from lama.stats.standard_stats import lama_stats_new14root_config = dict(15    stats_types=[16        'organ_volumes',17         'intensity',18        'jacobians'19    ],20    normalise_organ_vol_to_mask=True,21    use_log_jacobians = True,22    reg_folder='similarity',23    jac_folder='similarity',24    mask='mask_tight.nrrd',25    label_info='label_info.csv',26    label_map='labels.nrrd',27    blur_fwhm=100,28    voxel_size=14.0,29    invert_stats=True,30    normalise='mask',31    use_staging=True,32    memmap=True33)34@pytest.fixture()35def get_config() -> Path:36    """37    Fixture to get stats config and to write it to temporary file38    Returns39    -------40    location of stats config temporary file41    """42    def make_config(config_updates={}):43        # Create a nested function to allow the fixture to take arguments44        c = root_config.copy()45        c.update(config_updates)46        with tempfile.NamedTemporaryFile(mode='w+', delete=False, suffix='.toml') as fh:47            fh.write(toml.dumps(c))48        return c, fh.name49    return make_config50def test_all(get_config):51    """52    Run the stats module. The data required for this to work must be initially made53    by running the test:  tests/test_data_generation.py54    """55    config, config_file = get_config()56    lama_stats_new.run(config_file, wt_registration_dir, mut_registration_dir, stats_output_dir, target_dir)57@pytest.mark.skip58def test_no_mask(get_config):59    config, config_file = get_config({'mask': None})60    # Should get value errors if mask not specified61    # with pytest.raises(ValueError):62    #     lama_stats_new.run(config_file, wt_registration_dir, mut_registration_dir, stats_output_dir, target_dir)63# # @nottest64# # def test_no_use():65# #     """66# #     For the organ volume test, if the meta data dataframe has a column of 'no_analysis', do not include the label in the67# #     analysis68# #     """69# #     pass70#71# @nottest72# def test_mutant_id_subset():73#     """74#     Thest whether specifying mutant id subset works75#     """76#77#     config = stats_config_dir / 'new_stats_config_test_mutant_id_subset.toml'78#     lama_stats_new.run(config, wt_registration_dir, mut_registration_dir, stats_output_dir, target_dir)79#80# @nottest81# def test_specifiy_line():82#     """83#     Run the stats module. The data requirted for this to work must be initially made84#     by running the test:  tests/test_lama.py:test_lama_job_runner()85#     """86#     line = 'mutant_1'  # Only run this line87#88#     # Remove any previous output89#     if stats_output_dir.is_dir():90#         shutil.rmtree(stats_output_dir)91#92#     config = stats_config_dir / 'new_stats_config.toml'93#     lama_stats_new.run(config, wt_registration_dir, mut_registration_dir, stats_output_dir, target_dir, lines_to_process=[line])94#95#     output_lines = [x.name for x in stats_output_dir.iterdir() if x.is_dir()]96#     assert_equal([line],  output_lines)97#98#99# @nottest100# def test_erroneuos_configs():101#     error_config_dir = stats_config_dir / 'erroneous_configs'102#103#     for config in error_config_dir.iterdir():104#         lama_stats_new.run(config, wt_registration_dir, mut_registration_dir, stats_output_dir, target_dir)105#106# # @nottest107# # def test_organ_vols():108# #     config = join(CONFIG_DIR, 'organ_vols.yaml')109# #     run_lama_stats.run(config)110# #111# # @nottest112# # def test_glcm():113# #     config = join(CONFIG_DIR, 'test_glcm.yaml')114# #     run_lama_stats.run(config)115# #116# # @nottest117# # def test_from_arbitrary_directory():118# #     config = join(CONFIG_DIR, 'all_specimens.yaml')119# #     os.chdir(os.path.expanduser('~'))120# #     run_lama_stats.run(config)121# #122# # @nottest123# # def test_missing_config():124# #     config = join(CONFIG_DIR, 'all_specimens.flaml')125# #     assert_raises(Exception, run_lama_stats.run, config)126# #127# # @nottest128# # def test_misc():129# #     config = join(CONFIG_DIR, 'misc_test.yaml')130# #     run_lama_stats.run(config)131# #132# #133# # @nottest134# # def test_incorrect_staging_file():135# #     pass136#...

test_lama_stats.py

Source:test_lama_stats.py

1"""2Currently just running and making sure there's no uncaught exceptions.3TODO: check that the correct output is generated too4To run these tests, the test data needs to be fechted from bit/dev/lama_stats_test_data5In future we should put this in a web-accessible place6Usage:  pytest -v -m "not notest"7"""8import shutil9import tempfile10from nose.tools import nottest, assert_equal11import toml12# import paths from the __init__13from . import (stats_config_dir, wt_registration_dir, mut_registration_dir, target_dir,14               stats_output_dir)15from lama.stats.standard_stats import lama_stats_new16root_config = dict(17    stats_types=[18        'organ_volumes'19        # 'intensity',20        # 'jacobians'21    ],22    reg_folder='similarity',23    jac_folder='similarity',24    mask='mask_tight.nrrd',25    label_info='label_info.csv',26    label_map='labels.nrrd',27    blur_fwhm=100,28    voxel_size=14.0,29    invert_stats=True,30    normalise='mask',31    use_staging=False,32)33# @nottest34def test_all():35    """36    Run the stats module. The data requirted for this to work must be initially made37    by running the test:  tests/test_lama.py:test_lama_job_runner()38    """39    with tempfile.NamedTemporaryFile(mode='w+', delete=False) as fh:40        # print(fh.name)41        fh.write(toml.dumps(root_config))42    lama_stats_new.run(fh.name, wt_registration_dir, mut_registration_dir, stats_output_dir, target_dir)43# @nottest44# def test_no_use():45#     """46#     For the organ volume test, if the meta data dataframe has a column of 'no_analysis', do not include the label in the47#     analysis48#     """49#     pass50@nottest51def test_mutant_id_subset():52    """53    Thest whether specifying mutant id subset works54    """55    config = stats_config_dir / 'new_stats_config_test_mutant_id_subset.toml'56    lama_stats_new.run(config, wt_registration_dir, mut_registration_dir, stats_output_dir, target_dir)57@nottest58def test_specifiy_line():59    """60    Run the stats module. The data requirted for this to work must be initially made61    by running the test:  tests/test_lama.py:test_lama_job_runner()62    """63    line = 'mutant_1'  # Only run this line64    # Remove any previous output65    if stats_output_dir.is_dir():66        shutil.rmtree(stats_output_dir)67    config = stats_config_dir / 'new_stats_config.toml'68    lama_stats_new.run(config, wt_registration_dir, mut_registration_dir, stats_output_dir, target_dir, lines_to_process=[line])69    output_lines = [x.name for x in stats_output_dir.iterdir() if x.is_dir()]70    assert_equal([line],  output_lines)71@nottest72def test_erroneuos_configs():73    error_config_dir = stats_config_dir / 'erroneous_configs'74    for config in error_config_dir.iterdir():75        lama_stats_new.run(config, wt_registration_dir, mut_registration_dir, stats_output_dir, target_dir)76# @nottest77# def test_organ_vols():78#     config = join(CONFIG_DIR, 'organ_vols.yaml')79#     run_lama_stats.run(config)80#81# @nottest82# def test_glcm():83#     config = join(CONFIG_DIR, 'test_glcm.yaml')84#     run_lama_stats.run(config)85#86# @nottest87# def test_from_arbitrary_directory():88#     config = join(CONFIG_DIR, 'all_specimens.yaml')89#     os.chdir(os.path.expanduser('~'))90#     run_lama_stats.run(config)91#92# @nottest93# def test_missing_config():94#     config = join(CONFIG_DIR, 'all_specimens.flaml')95#     assert_raises(Exception, run_lama_stats.run, config)96#97# @nottest98# def test_misc():99#     config = join(CONFIG_DIR, 'misc_test.yaml')100#     run_lama_stats.run(config)101#102#103# @nottest104# def test_incorrect_staging_file():105#     pass106if __name__ == '__main__':...

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