def _lib(old_name):
"""Deprecate a function moved to neutron_lib.api.converters/validators."""
new_func = getattr(lib_validators, old_name, None)
if not new_func:
# Try non-private name (without leading underscore)
new_func = getattr(lib_validators, old_name[1:], None)
if not new_func:
# If it isn't a validator, maybe it's a converter
new_func = getattr(lib_converters, old_name, None)
assert new_func
return moves.moved_function(new_func, old_name, __name__,
message='moved to neutron_lib',
version='mitaka', removal_version='ocata')
def _lib(old_name):
"""Deprecate a function moved to neutron_lib.api.converters/validators."""
new_func = getattr(lib_validators, old_name, None)
if not new_func:
# Try non-private name (without leading underscore)
new_func = getattr(lib_validators, old_name[1:], None)
if not new_func:
# If it isn't a validator, maybe it's a converter
new_func = getattr(lib_converters, old_name, None)
assert new_func
return moves.moved_function(new_func, old_name, __name__,
message='moved to neutron_lib',
version='mitaka', removal_version='ocata')
self.firewall.security_group_updated('sg_member', [],
updated_devices)
# If a device is both in new and updated devices
# avoid reprocessing it
updated_devices = ((updated_devices | devices_to_refilter) -
new_devices)
if updated_devices:
LOG.debug("Refreshing firewall for %d devices",
len(updated_devices))
self.refresh_firewall(updated_devices)
# TODO(armax): For bw compat with external dependencies; to be dropped in P.
# NOTE(dasm): Should be already removed, but didn't have DeprecationWarning.
SG_RPC_VERSION = moves.moved_function(
securitygroups_rpc.SecurityGroupAgentRpcApiMixin.SG_RPC_VERSION,
'SG_RPC_VERSION', __name__, version='Liberty', removal_version='Pike'
)
SecurityGroupServerRpcApi = moves.moved_class(
securitygroups_rpc.SecurityGroupServerRpcApi,
'SecurityGroupServerRpcApi', old_module_name=__name__, version='Liberty',
removal_version='Pike'
)
SecurityGroupAgentRpcApiMixin = moves.moved_class(
securitygroups_rpc.SecurityGroupAgentRpcApiMixin,
'SecurityGroupAgentRpcApiMixin', old_module_name=__name__,
version='Liberty', removal_version='Pike'
)
SecurityGroupAgentRpcCallbackMixin = moves.moved_class(
securitygroups_rpc.SecurityGroupAgentRpcCallbackMixin,
'SecurityGroupAgentRpcCallbackMixin', old_module_name=__name__,
version='Liberty', removal_version='Pike'
context_manager = enginefacade.transaction_context()
_FACADE = None
MAX_RETRIES = 10
def is_retriable(e):
if _is_nested_instance(e, (db_exc.DBDeadlock, exc.StaleDataError)):
return True
# looking savepoints mangled by deadlocks. see bug/1590298 for details.
return _is_nested_instance(e, db_exc.DBError) and '1305' in str(e)
is_deadlock = moves.moved_function(is_retriable, 'is_deadlock', __name__,
message='use "is_retriable" instead',
version='newton', removal_version='ocata')
retry_db_errors = oslo_db_api.wrap_db_retry(
max_retries=MAX_RETRIES,
retry_interval=0.1,
inc_retry_interval=True,
retry_on_request=True,
exception_checker=is_retriable
)
def _is_nested_instance(e, etypes):
"""Check if exception or its inner excepts are an instance of etypes."""
return (isinstance(e, etypes) or
isinstance(e, exceptions.MultipleExceptions) and
any(_is_nested_instance(i, etypes) for i in e.inner_exceptions))
from neutron.common import utils
from neutron.tests.functional import base
MARK_VALUE = '0x1'
MARK_MASK = '0xffffffff'
ICMP_MARK_RULE = ('-j MARK --set-xmark %(value)s/%(mask)s' % {
'value': MARK_VALUE,
'mask': MARK_MASK
})
MARKED_BLOCK_RULE = '-m mark --mark %s -j DROP' % MARK_VALUE
ICMP_BLOCK_RULE = '-p icmp -j DROP'
get_rand_name = moves.moved_function(
utils.get_rand_name,
'get_rand_name',
__name__,
message='use "neutron.common.utils.get_rand_name" instead',
version='Newton',
removal_version='Ocata')
# Regarding MRO, it goes BaseOVSLinuxTestCase, WithScenarios,
# BaseSudoTestCase, ..., UnitTest, object. setUp is not defined in
# WithScenarios, so it will correctly be found in BaseSudoTestCase.
class BaseOVSLinuxTestCase(testscenarios.WithScenarios, base.BaseSudoTestCase):
scenarios = [
('vsctl', dict(ovsdb_interface='vsctl')),
('native', dict(ovsdb_interface='native')),
]
def setUp(self):
def etcdir(*p):
return os.path.join(ETCDIR, *p)
def fake_use_fatal_exceptions(*args):
return True
for _name in ('get_related_rand_names', 'get_rand_name',
'get_rand_device_name', 'get_related_rand_device_names'):
setattr(
sys.modules[__name__], _name,
moves.moved_function(getattr(utils, _name),
_name,
__name__,
message='use "neutron.common.utils.%s" instead' %
_name,
version='Newton',
removal_version='Ocata'))
def bool_from_env(key, strict=False, default=False):
value = os.environ.get(key)
return strutils.bool_from_string(value, strict=strict, default=default)
def setup_test_logging(config_opts, log_dir, log_file_path_template):
# Have each test log into its own log file
config_opts.set_override('debug', True)
fileutils.ensure_tree(log_dir, mode=0o755)
log_file = sanitize_log_path(os.path.join(log_dir, log_file_path_template))
@removals.remove()
def red_comet():
return True
@removals.remove(category=PendingDeprecationWarning)
def blue_comet():
return True
def yellow_sun():
"""Yellow."""
return True
yellowish_sun = moves.moved_function(yellow_sun, 'yellowish_sun', __name__)
@removals.remove()
class EFSF(object):
pass
@removals.remove(category=PendingDeprecationWarning)
class EFSF_2(object):
pass
@removals.removed_class("StarLord")
class StarLord(object):
def __init__(self):
msg = ("N328: Use assertTrue(observed) instead of "
"assertEqual(True, observed)")
yield (0, msg)
if re.search(r"assertEqual\(\s*False,[^,]*(,[^,]*)?\)", logical_line):
msg = ("N328: Use assertFalse(observed) instead of "
"assertEqual(False, observed)")
yield (0, msg)
if re.search(r"assertEqual\([^,]*,\s*False(,[^,]*)?\)", logical_line):
msg = ("N328: Use assertFalse(observed) instead of "
"assertEqual(False, observed)")
yield (0, msg)
check_asserttrue = flake8ext(
moves.moved_function(
check_asserttruefalse, 'check_asserttrue', __name__,
version='Newton', removal_version='Ocata'))
check_assertfalse = flake8ext(
moves.moved_function(
check_asserttruefalse, 'check_assertfalse', __name__,
version='Newton', removal_version='Ocata'))
@flake8ext
def no_mutable_default_args(logical_line):
"""N329 - Don't use mutable default arguments."""
msg = "N329: Method's default argument shouldn't be mutable!"
if checks.mutable_default_args.match(logical_line):
yield (0, msg)
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations
# under the License.
# TODO(dougwig) - remove this file at the beginning of N.
from debtcollector import moves
import neutron._i18n
message = "moved to neutron._i18n; please migrate to local oslo_i18n " \
"usage, as defined in the devref and at " \
"http://docs.openstack.org/developer/oslo.i18n/usage.html"
_ = moves.moved_function(neutron._i18n._, '_', __name__, message=message)
_LI = moves.moved_function(neutron._i18n._LI, '_LI', __name__, message=message)
_LW = moves.moved_function(neutron._i18n._LW, '_LW', __name__, message=message)
_LE = moves.moved_function(neutron._i18n._LE, '_LE', __name__, message=message)
_LC = moves.moved_function(neutron._i18n._LC, '_LC', __name__, message=message)
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations
# under the License.
# TODO(amotoki): Remove this file at the beginning of Nxx cycle.
from debtcollector import moves
from neutronclient import _i18n
message = ("moved to neutronclient._i18n; please migrate to local "
"oslo_i18n usage, as defined at "
"http://docs.openstack.org/developer/oslo.i18n/usage.html")
_ = moves.moved_function(_i18n._, '_', __name__, message=message)
def etcdir(*p):
return os.path.join(ETCDIR, *p)
def fake_use_fatal_exceptions(*args):
return True
for _name in ('get_related_rand_names',
'get_rand_name',
'get_rand_device_name',
'get_related_rand_device_names'):
setattr(sys.modules[__name__], _name, moves.moved_function(
getattr(utils, _name), _name, __name__,
message='use "neutron.common.utils.%s" instead' % _name,
version='Newton', removal_version='Ocata'))
def bool_from_env(key, strict=False, default=False):
value = os.environ.get(key)
return strutils.bool_from_string(value, strict=strict, default=default)
def setup_test_logging(config_opts, log_dir, log_file_path_template):
# Have each test log into its own log file
config_opts.set_override('debug', True)
utils.ensure_dir(log_dir)
log_file = sanitize_log_path(
os.path.join(log_dir, log_file_path_template))
config_opts.set_override('log_file', log_file)
class Psikit(object):
def __init__(self, threads=4, memory=4, debug=False):
import psi4
self.psi4 = psi4
self.psi4.set_memory("{} GB".format(memory))
#self.psi4.set_options({"save_jk": True}) # for JK calculation
self.psi4.set_num_threads(threads)
self.wfn = None
self.mol = None
self.debug = debug
self.tempdir = mkdtemp()
if self.debug:
self.psi4.core.set_output_file("psikit_out.dat", True)
else:
self.psi4.core.be_quiet()
def clean(self):
rmtree(self.tempdir)
def read_from_smiles(self, smiles_str, opt=True):
self.mol = Chem.MolFromSmiles(smiles_str)
if opt:
self.rdkit_optimize()
def read_from_molfile(self, molfile, opt=True, removeHs=False):
self.mol = Chem.MolFromMolFile(molfile, removeHs=removeHs)
if opt:
self.rdkit_optimize()
def rdkit_optimize(self, addHs=True):
if addHs:
self.mol = Chem.AddHs(self.mol)
AllChem.EmbedMolecule(self.mol, useExpTorsionAnglePrefs=True,useBasicKnowledge=True)
AllChem.UFFOptimizeMolecule(self.mol)
def geometry(self, multiplicity=1):
xyz = self.mol2xyz(multiplicity=multiplicity)
self.psi4.geometry(xyz)
def energy(self, basis_sets= "scf/6-31g**", return_wfn=True, multiplicity=1):
self.geometry(multiplicity=multiplicity)
scf_energy, wfn = self.psi4.energy(basis_sets, return_wfn=return_wfn)
self.psi4.core.clean()
self.wfn = wfn
self.mol = self.xyz2mol()
return scf_energy
def optimize(self, basis_sets= "scf/6-31g**", return_wfn=True, name=None, multiplicity=1, maxiter=50):
if not name:
name = uuid.uuid4().hex
self.psi4.core.IO.set_default_namespace(name)
self.geometry(multiplicity=multiplicity)
self.psi4.set_options({'GEOM_MAXITER':maxiter})
try:
scf_energy, wfn = self.psi4.optimize(basis_sets, return_wfn=return_wfn)
self.wfn = wfn
except self.psi4.OptimizationConvergenceError as cError:
print('Convergence error caught: {0}'.format(cError))
self.wfn = cError.wfn
scf_energy = self.wfn.energy()
self.psi4.core.clean()
self.mol = self.xyz2mol()
if not self.debug:
self.psi4.core.opt_clean() # Seg fault will occured when the function is called before optimize.
return scf_energy
def set_options(self, **kwargs):
"""
http://www.psicode.org/psi4manual/1.2/psiapi.html
IV. Analysis of Intermolecular Interactions
and
http://forum.psicode.org/t/how-can-i-change-max-iteration-in-energy-method/1238/2
"""
self.psi4.set_options(kwargs)
def mol2xyz(self, multiplicity=1):
return mol2xyz(self.mol)
def xyz2mol(self, confId=0):
natom = self.wfn.molecule().natom()
mol_array_bohr = self.wfn.molecule().geometry().to_array()
mol_array = mol_array_bohr * 0.52917721092
nmol = Chem.Mol(self.mol)
conf = nmol.GetConformer(confId)
for i in range(natom):
conf.SetAtomPosition(i, tuple(mol_array[i]))
return nmol
def clone_mol(self):
return Chem.Mol(self.mol)
def create_cube_files(self, gridspace=0.3):
if self.wfn == None:
print('wfn not found. run optimze()/energy()')
return None
else:
a = self.wfn.nalpha() # H**O
b = a + 1 # LUMO
self.psi4.set_options({"cubeprop_tasks": ['ESP', 'FRONTIER_ORBITALS', 'Density', 'DUAL_DESCRIPTOR'],
"cubic_grid_spacing": [gridspace, gridspace, gridspace],
"cubeprop_filepath": self.tempdir
})
Chem.MolToMolFile(self.mol, os.path.join(self.tempdir, 'target.mol'))
self.psi4.cubeprop(self.wfn)
getMOview = moves.moved_function(create_cube_files, 'getMOview', __name__)
def view_on_pymol(self, target='FRONTIER', maprange=0.05, gridspace=0.3):
self.create_cube_files(gridspace=gridspace)
run_pymol_server(self.tempdir, target=target, maprange=maprange)
def save_frontier(self, gridspace=0.3, isotype="isosurface"):
self.create_cube_files(gridspace=gridspace)
save_pyscript(self.tempdir, isotype=isotype)
def save_fchk(self, filename="output.fchk"):
fchk_writer = self.psi4.core.FCHKWriter(self.wfn)
fchk_writer.write(filename)
def save_cube(self):
self.psi4.cubeprop(self.wfn)
def calc_resp_charges(self):
if self.wfn.molecule() == None:
print('please run optimze() at first!')
return None
try:
import resp
except:
print('please install resp at first')
print('conda install -c psi4 resp')
return None
# https://www.cgl.ucsf.edu/chimerax/docs/user/radii.html
options = {'N_VDW_LAYERS' : 4,
'VDW_SCALE_FACTOR' : 1.4,
'VDW_INCREMENT' : 0.2,
'VDW_POINT_DENSITY' : 1.0,
'resp_a' : 0.0005,
'RESP_B' : 0.1,
'RADIUS' : {'Br':1.98, 'I':2.09, }
}
charges = resp.resp([self.wfn.molecule()], [options])
atoms = self.mol.GetAtoms()
for idx, atom in enumerate(atoms):
atom.SetDoubleProp("EP", charges[0][0][idx])
atom.SetDoubleProp("RESP", charges[0][1][idx])
return charges[0][1]
def calc_mulliken_charges(self):
'''
Compute Mulliken Charges
And return the results as numpy array.
'''
if self.wfn.molecule() == None:
print('please run optimze() at first!')
return None
self.psi4.oeprop(self.wfn, 'MULLIKEN_CHARGES')
mulliken_acp = self.wfn.atomic_point_charges()
atoms = self.mol.GetAtoms()
for idx, atom in enumerate(atoms):
atom.SetDoubleProp("MULLIKEN", mulliken_acp.np[idx])
return mulliken_acp.np
def calc_lowdin_charges(self):
'''
Compute Lowdin Charges
And return the results as numpy array.
'''
if self.wfn.molecule() == None:
print('please run optimze() at first!')
return None
self.psi4.oeprop(self.wfn, 'LOWDIN_CHARGES')
lowdin_acp = self.wfn.atomic_point_charges()
atoms = self.mol.GetAtoms()
for idx, atom in enumerate(atoms):
atom.SetDoubleProp("LOWDIN", lowdin_acp.np[idx])
return lowdin_acp.np
@property
def dipolemoment(self, basis_sets="scf/6-31g**", return_wfn=True):
# The three components of the SCF dipole [Debye]
x = self.psi4.get_variable('SCF DIPOLE X')
y = self.psi4.get_variable('SCF DIPOLE Y')
z = self.psi4.get_variable('SCF DIPOLE Z')
total = np.sqrt(x * x + y * y + z * z)
return (x, y, z, total)
@property
def H**O(self):
return self.wfn.epsilon_a_subset('AO', 'ALL').np[self.wfn.nalpha()-1]
@property
def LUMO(self):
return self.wfn.epsilon_a_subset('AO', 'ALL').np[self.wfn.nalpha()]
@property
def coulomb_matrix(self):
return self.wfn.jk().J[0].to_array()
@property
def exchange_matrix(self):
return self.wfn.jk().K[0].to_array()
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations
# under the License.
"""
NOTE: Do not use this module to add random utils.
We want to avoid having a generic utils.py dumping ground.
"""
from debtcollector import moves
from neutron_lib.api import attributes
populate_project_info = moves.moved_function(
attributes.populate_project_info, 'populate_project_info', __name__)
inc = n_bars - i
for col in cols:
df[f'{col}{i}'] = df[f'{col}{n_bars}'][inc:].append(
pd.Series([np.nan] * inc)).reset_index(drop=True)
# correct bar date (or datetime)
if datetime_col is not None:
df[datetime_col] = df[datetime_col][n_bars:].append(
pd.Series([np.nan] * n_bars)).reset_index(drop=True)
df = df.dropna()
return df
make_nbars = moves.moved_function(make_nbars_past, 'make_nbars', __name__)
def make_nbars_future(df: pd.DataFrame,
n_bars: int,
cols: List[str] = ['Close'],
datetime_col: Union[str, None] = 'Date') -> pd.DataFrame:
"""Make n bars dataframe seeing future n bars.
The row size of `df` must be greater than or equal to `n_bars`, or raise ValueError.
Args:
df (DataFrame): target data frame.
n_bars (int): number of bars.
cols (List[str], optional): column names. Defaults to ['Close'].
datetime_col (Union[str, None], optional): datetime column name. Defaults to 'Date'.
self.firewall.security_group_updated('sg_member', [],
updated_devices)
# If a device is both in new and updated devices
# avoid reprocessing it
updated_devices = ((updated_devices | devices_to_refilter) -
new_devices)
if updated_devices:
LOG.debug("Refreshing firewall for %d devices",
len(updated_devices))
self.refresh_firewall(updated_devices)
# TODO(armax): For bw compat with external dependencies; to be dropped in P.
# NOTE(dasm): Should be already removed, but didn't have DeprecationWarning.
SG_RPC_VERSION = moves.moved_function(
securitygroups_rpc.SecurityGroupAgentRpcApiMixin.SG_RPC_VERSION,
'SG_RPC_VERSION', __name__, version='Liberty', removal_version='Pike'
)
SecurityGroupServerRpcApi = moves.moved_class(
securitygroups_rpc.SecurityGroupServerRpcApi,
'SecurityGroupServerRpcApi', old_module_name=__name__, version='Liberty',
removal_version='Pike'
)
SecurityGroupAgentRpcApiMixin = moves.moved_class(
securitygroups_rpc.SecurityGroupAgentRpcApiMixin,
'SecurityGroupAgentRpcApiMixin', old_module_name=__name__,
version='Liberty', removal_version='Pike'
)
SecurityGroupAgentRpcCallbackMixin = moves.moved_class(
securitygroups_rpc.SecurityGroupAgentRpcCallbackMixin,
'SecurityGroupAgentRpcCallbackMixin', old_module_name=__name__,
version='Liberty', removal_version='Pike'
import testscenarios
from neutron.common import utils
from neutron.tests.functional import base
MARK_VALUE = '0x1'
MARK_MASK = '0xffffffff'
ICMP_MARK_RULE = ('-j MARK --set-xmark %(value)s/%(mask)s'
% {'value': MARK_VALUE, 'mask': MARK_MASK})
MARKED_BLOCK_RULE = '-m mark --mark %s -j DROP' % MARK_VALUE
ICMP_BLOCK_RULE = '-p icmp -j DROP'
get_rand_name = moves.moved_function(
utils.get_rand_name, 'get_rand_name', __name__,
message='use "neutron.common.utils.get_rand_name" instead',
version='Newton', removal_version='Ocata')
# Regarding MRO, it goes BaseOVSLinuxTestCase, WithScenarios,
# BaseSudoTestCase, ..., UnitTest, object. setUp is not defined in
# WithScenarios, so it will correctly be found in BaseSudoTestCase.
class BaseOVSLinuxTestCase(testscenarios.WithScenarios, base.BaseSudoTestCase):
scenarios = [
('vsctl', dict(ovsdb_interface='vsctl')),
('native', dict(ovsdb_interface='native')),
]
def setUp(self):
super(BaseOVSLinuxTestCase, self).setUp()
self.config(group='OVS', ovsdb_interface=self.ovsdb_interface)
def is_bsd():
"""Return True on BSD-based systems."""
system = platform.system()
if system == 'Darwin':
return True
if 'bsd' in system.lower():
return True
return False
def reset_random_seed():
# reset random seed to make sure other processes extracting values from RNG
# don't get the same results (useful especially when you then use the
# random values to allocate system resources from global pool, like ports
# to listen). Use both current time and pid to make sure no tests started
# at the same time get the same values from RNG
seed = time.time() + os.getpid()
random.seed(seed)
def get_random_ipv6_mode():
return random.choice(constants.IPV6_MODES)
import_modules_recursively = moves.moved_function(
utils.import_modules_recursively, 'import_modules_recursively', __name__,
version='Newton', removal_version='Ocata')
class Psikit(object):
def __init__(self, threads=4, memory=4, debug=False):
import psi4
self.psi4 = psi4
self.psi4.set_memory("{} GB".format(memory))
#self.psi4.set_options({"save_jk": True}) # for JK calculation
self.psi4.set_num_threads(threads)
self.wfn = None
self.mol = None
self.debug = debug
if self.debug:
self.psi4.core.set_output_file("psikit_out.dat", True)
else:
self.psi4.core.be_quiet()
def read_from_smiles(self, smiles_str, opt=True):
self.mol = Chem.MolFromSmiles(smiles_str)
if opt:
self.rdkit_optimize()
def read_from_molfile(self, molfile, opt=True, removeHs=False):
self.mol = Chem.MolFromMolFile(molfile, removeHs=removeHs)
if opt:
self.rdkit_optimize()
def rdkit_optimize(self, addHs=True):
if addHs:
self.mol = Chem.AddHs(self.mol)
AllChem.EmbedMolecule(self.mol,
useExpTorsionAnglePrefs=True,
useBasicKnowledge=True)
AllChem.UFFOptimizeMolecule(self.mol)
def geometry(self, multiplicity=1):
xyz = self.mol2xyz(multiplicity=multiplicity)
self.psi4.geometry(xyz)
def energy(self,
basis_sets="scf/6-31g**",
return_wfn=True,
multiplicity=1):
self.geometry(multiplicity=multiplicity)
scf_energy, wfn = self.psi4.energy(basis_sets, return_wfn=return_wfn)
self.psi4.core.clean()
self.wfn = wfn
return scf_energy
def optimize(self,
basis_sets="scf/6-31g**",
return_wfn=True,
name=None,
multiplicity=1,
maxiter=50):
if not name:
name = uuid.uuid4().hex
self.psi4.core.IO.set_default_namespace(name)
self.geometry(multiplicity=multiplicity)
self.psi4.set_options({'GEOM_MAXITER': maxiter})
try:
scf_energy, wfn = self.psi4.optimize(basis_sets,
return_wfn=return_wfn)
self.wfn = wfn
except self.psi4.OptimizationConvergenceError as cError:
print('Convergence error caught: {0}'.format(cError))
self.wfn = cError.wfn
scf_energy = self.wfn.energy()
self.psi4.core.clean()
self.mol = self.xyz2mol()
if not self.debug:
self.psi4.core.opt_clean(
) # Seg fault will occured when the function is called before optimize.
return scf_energy
def set_options(self, **kwargs):
"""
http://www.psicode.org/psi4manual/1.2/psiapi.html
IV. Analysis of Intermolecular Interactions
and
http://forum.psicode.org/t/how-can-i-change-max-iteration-in-energy-method/1238/2
"""
self.psi4.set_options(kwargs)
def mol2xyz(self, multiplicity=1):
charge = Chem.GetFormalCharge(self.mol)
xyz_string = "\n{} {}\n".format(charge, multiplicity)
for atom in self.mol.GetAtoms():
pos = self.mol.GetConformer().GetAtomPosition(atom.GetIdx())
xyz_string += "{} {} {} {}\n".format(atom.GetSymbol(), pos.x,
pos.y, pos.z)
# the "no_com" stops Psi4 from moving your molecule to its center of mass,
# "no_reorient" stops it from spinning to align with axis of inertia
xyz_string += "no_reorient\n"
xyz_string += "no_com\n"
xyz_string += "units angstrom\n"
return xyz_string
def xyz2mol(self, confId=0):
natom = self.wfn.molecule().natom()
mol_array_bohr = self.wfn.molecule().geometry().to_array()
mol_array = mol_array_bohr * 0.52917721092
nmol = Chem.Mol(self.mol)
conf = nmol.GetConformer(confId)
for i in range(natom):
conf.SetAtomPosition(i, tuple(mol_array[i]))
return nmol
def clone_mol(self):
return Chem.Mol(self.mol)
def create_cube_files(self, gridspace=0.3):
if self.wfn == None:
print('please run optimze()/energy() at first!')
return None
else:
a = self.wfn.nalpha() # H**O
b = a + 1 # LUMO
self.psi4.set_options({
"cubeprop_tasks":
['ESP', 'FRONTIER_ORBITALS', 'Density', 'DUAL_DESCRIPTOR'],
"cubic_grid_spacing": [gridspace, gridspace, gridspace]
})
Chem.MolToMolFile(self.mol, 'target.mol')
self.psi4.cubeprop(self.wfn)
print('Done!')
getMOview = moves.moved_function(create_cube_files, 'getMOview', __name__)
def view_on_pymol(self, target='FRONTIER', maprange=0.05):
'''
To use the function, user need to install pymol and run the pymol for server mode
The command is pymol -R
target ['ESP', 'FRONTIER', 'DUAL']
'''
targetlist = ['ESP', 'FRONTIER', 'DUAL']
if target not in targetlist:
raise Exception(f'Please set target from ESP, FRONTIER, DENSITY!!')
import sys
import xmlrpc.client as xmlrpc
filepath = os.getcwd()
nalpha = self.wfn.nalpha()
srv = xmlrpc.ServerProxy('http://localhost:9123')
srv.do('delete *')
srv.do('load ' + os.path.join(filepath, 'target.mol'))
srv.do('as sticks, target')
if target == 'FRONTIER':
homof = glob.glob(f'Psi_a_{nalpha}*_HOMO.cube')[0]
lumof = glob.glob(f'Psi_a_{nalpha+1}*_LUMO.cube')[0]
srv.do('load ' + os.path.join(filepath, homof) + ',H**O')
srv.do('load ' + os.path.join(filepath, lumof) + ',LUMO')
srv.do(f'isosurface HOMO_A, H**O, -0.02')
srv.do(f'isosurface HOMO_B, H**O, 0.02')
srv.do(f'isosurface LUMO_A, LUMO, -0.02')
srv.do(f'isosurface LUMO_B, LUMO, 0.02')
srv.do('color blue, HOMO_A')
srv.do('color red, HOMO_B')
srv.do('color green, LUMO_A')
srv.do('color yellow, LUMO_B')
srv.do('set transparency, 0.2')
srv.do('disable HOMO_A')
srv.do('disable HOMO_B')
abb = 'frontier_'
elif target == 'ESP':
srv.do('load ' + 'ESP.cube' + ', ESP')
srv.do('show surface, target')
srv.do(f'ramp_new cmap, ESP, [-{maprange}, {maprange}]')
srv.do('color cmap, target')
srv.do('set transparency, 0.2')
abb = 'esp_'
elif target == 'DUAL':
dualf = glob.glob('DUAL*.cube')[0]
srv.do('load ' + dualf + ', DUAL_DESC')
srv.do('show surface, target')
srv.do(f'ramp_new cmap, DUAL_DESC, [-{maprange}, {maprange}]')
srv.do('color cmap, target')
srv.do('set transparency, 0.2')
abb = 'dual_'
outputpath = os.path.join(filepath, abb + 'mo.pse')
srv.do(f'save {outputpath}')
print('finished !')
def save_frontier(self, gridspace=0.15):
if self.wfn == None:
print('please run optimze()/energy() at first!')
else:
a = self.wfn.nalpha() # H**O
b = a + 1 # LUMO
self.psi4.set_options({
"cubeprop_tasks": ['orbitals'],
"cubeprop_orbitals": [a, b, -a, -b],
"cubic_grid_spacing": [gridspace, gridspace, gridspace]
})
Chem.MolToMolFile(self.mol, 'target.mol')
self.psi4.cubeprop(self.wfn)
homo_a = "Psi_a_{0}_{0}-A".format(a)
homo_b = "Psi_b_{0}_{0}-A".format(a)
lumo_a = "Psi_a_{0}_{0}-A".format(b)
lumo_b = "Psi_b_{0}_{0}-A".format(b)
with open("frontier.py", "w") as f:
f.write('from pymol import *\n')
f.write('cmd.load("{0}.cube")\n'.format(homo_a))
f.write('cmd.load("{0}.cube")\n'.format(homo_b))
f.write('cmd.load("{0}.cube")\n'.format(lumo_a))
f.write('cmd.load("{0}.cube")\n'.format(lumo_b))
f.write('cmd.load("target.mol")\n')
f.write('cmd.isomesh("HOMO_A", "{0}", -0.02)\n'.format(homo_a))
f.write('cmd.isomesh("HOMO_B", "{0}", 0.02)\n'.format(homo_b))
f.write('cmd.isomesh("LUMO_A", "{0}", 0.02)\n'.format(lumo_a))
f.write('cmd.isomesh("LUMO_B", "{0}", -0.02)\n'.format(lumo_b))
f.write('cmd.color("blue", "HOMO_A")\n')
f.write('cmd.color("red", "HOMO_B")\n')
f.write('cmd.color("blue", "LUMO_A")\n')
f.write('cmd.color("red", "LUMO_B")\n')
f.write('cmd.disable("LUMO_A")\n')
f.write('cmd.disable("LUMO_B")\n')
def save_fchk(self, filename="output.fchk"):
fchk_writer = self.psi4.core.FCHKWriter(self.wfn)
fchk_writer.write(filename)
def save_cube(self):
self.psi4.cubeprop(self.wfn)
def calc_resp_charges(self):
if self.wfn.molecule() == None:
print('please run optimze() at first!')
return None
try:
import resp
except:
print('please install resp at first')
print('conda install -c psi4 resp')
return None
# https://www.cgl.ucsf.edu/chimerax/docs/user/radii.html
options = {
'N_VDW_LAYERS': 4,
'VDW_SCALE_FACTOR': 1.4,
'VDW_INCREMENT': 0.2,
'VDW_POINT_DENSITY': 1.0,
'resp_a': 0.0005,
'RESP_B': 0.1,
'RADIUS': {
'Br': 1.98,
'I': 2.09,
}
}
charges = resp.resp([self.wfn.molecule()], [options])
atoms = self.mol.GetAtoms()
for idx, atom in enumerate(atoms):
atom.SetDoubleProp("EP", charges[0][0][idx])
atom.SetDoubleProp("RESP", charges[0][1][idx])
return charges[0][1]
def calc_mulliken_charges(self):
'''
Compute Mulliken Charges
And return the results as numpy array.
'''
if self.wfn.molecule() == None:
print('please run optimze() at first!')
return None
self.psi4.oeprop(self.wfn, 'MULLIKEN_CHARGES')
mulliken_acp = self.wfn.atomic_point_charges()
atoms = self.mol.GetAtoms()
for idx, atom in enumerate(atoms):
atom.SetDoubleProp("MULLIKEN", mulliken_acp.np[idx])
return mulliken_acp.np
def calc_lowdin_charges(self):
'''
Compute Lowdin Charges
And return the results as numpy array.
'''
if self.wfn.molecule() == None:
print('please run optimze() at first!')
return None
self.psi4.oeprop(self.wfn, 'LOWDIN_CHARGES')
lowdin_acp = self.wfn.atomic_point_charges()
atoms = self.mol.GetAtoms()
for idx, atom in enumerate(atoms):
atom.SetDoubleProp("LOWDIN", lowdin_acp.np[idx])
return lowdin_acp.np
@property
def dipolemoment(self, basis_sets="scf/6-31g**", return_wfn=True):
# The three components of the SCF dipole [Debye]
x = self.psi4.get_variable('SCF DIPOLE X')
y = self.psi4.get_variable('SCF DIPOLE Y')
z = self.psi4.get_variable('SCF DIPOLE Z')
total = np.sqrt(x * x + y * y + z * z)
return (x, y, z, total)
@property
def H**O(self):
return self.wfn.epsilon_a_subset('AO', 'ALL').np[self.wfn.nalpha() - 1]
@property
def LUMO(self):
return self.wfn.epsilon_a_subset('AO', 'ALL').np[self.wfn.nalpha()]
@property
def coulomb_matrix(self):
return self.wfn.jk().J[0].to_array()
@property
def exchange_matrix(self):
return self.wfn.jk().K[0].to_array()
LOG = logging.getLogger(__name__)
def is_retriable(e):
if _is_nested_instance(
e,
(db_exc.DBDeadlock, exc.StaleDataError, db_exc.DBConnectionError,
db_exc.DBDuplicateEntry, db_exc.RetryRequest)):
return True
# looking savepoints mangled by deadlocks. see bug/1590298 for details.
return _is_nested_instance(e, db_exc.DBError) and '1305' in str(e)
is_deadlock = moves.moved_function(is_retriable,
'is_deadlock',
__name__,
message='use "is_retriable" instead',
version='newton',
removal_version='ocata')
_retry_db_errors = oslo_db_api.wrap_db_retry(max_retries=MAX_RETRIES,
retry_interval=0.1,
inc_retry_interval=True,
exception_checker=is_retriable)
def retry_db_errors(f):
"""Log retriable exceptions before retry to help debugging."""
@_retry_db_errors
@six.wraps(f)
def wrapped(*args, **kwargs):
try:
return f(*args, **kwargs)
from neutron._i18n import _LE
from neutron.db.models import securitygroup as sg_models
from neutron.db import models_v2
from neutron.db import segments_db
from neutron.extensions import portbindings
from neutron import manager
from neutron.plugins.ml2 import models
LOG = log.getLogger(__name__)
# limit the number of port OR LIKE statements in one query
MAX_PORTS_PER_QUERY = 500
# The API methods from segments_db
add_network_segment = moves.moved_function(
segments_db.add_network_segment, 'add_network_segment', __name__,
version='Newton', removal_version='Ocata')
get_network_segments = moves.moved_function(
segments_db.get_network_segments, 'get_network_segments', __name__,
version='Newton', removal_version='Ocata')
get_networks_segments = moves.moved_function(
segments_db.get_networks_segments, 'get_networks_segments', __name__,
version='Newton', removal_version='Ocata')
get_segment_by_id = moves.moved_function(
segments_db.get_segment_by_id, 'get_segment_by_id', __name__,
version='Newton', removal_version='Ocata')
get_dynamic_segment = moves.moved_function(
@removals.remove()
def red_comet():
return True
@removals.remove(category=PendingDeprecationWarning)
def blue_comet():
return True
def yellow_sun():
"""Yellow."""
return True
yellowish_sun = moves.moved_function(yellow_sun, 'yellowish_sun', __name__)
@removals.remove()
class EFSF(object):
pass
@removals.remove(category=PendingDeprecationWarning)
class EFSF_2(object):
pass
class ThingB(object):
@removals.remove()
def black_tristars(self):
if os.path.exists(disabled_ipv6_path):
with open(disabled_ipv6_path, 'r') as f:
disabled = f.read().strip()
_IS_IPV6_ENABLED = disabled == "0"
else:
_IS_IPV6_ENABLED = False
if not _IS_IPV6_ENABLED:
LOG.info(_LI("IPv6 not present or configured not to bind to new "
"interfaces on this system. Please ensure IPv6 is "
"enabled and /proc/sys/net/ipv6/conf/default/"
"disable_ipv6 is set to 1 to enable IPv6."))
return _IS_IPV6_ENABLED
is_enabled = moves.moved_function(is_enabled_and_bind_by_default,
'is_enabled', __name__, version='Ocata',
removal_version='Pike')
def is_auto_address_subnet(subnet):
"""Check if subnet is an auto address subnet."""
modes = [const.IPV6_SLAAC, const.DHCPV6_STATELESS]
return (subnet['ipv6_address_mode'] in modes
or subnet['ipv6_ra_mode'] in modes)
def is_eui64_address(ip_address):
"""Check if ip address is EUI64."""
ip = netaddr.IPAddress(ip_address)
# '0xfffe' addition is used to build EUI-64 from MAC (RFC4291)
# Look for it in the middle of the EUI-64 part of address
# Copyright (c) 2015 Red Hat, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations
# under the License.
import functools
from debtcollector import moves
from ovsdbapp.schema.open_vswitch import helpers
from neutron.agent.common import utils
_connection_to_manager_uri = moves.moved_function(
helpers._connection_to_manager_uri, '_connection_to_manager_uri', __name__)
enable_connection_uri = functools.partial(helpers.enable_connection_uri,
execute=utils.execute,
run_as_root=True,
log_fail_as_error=False,
check_exit_code=False)
"""Return True on BSD-based systems."""
system = platform.system()
if system == 'Darwin':
return True
if 'bsd' in system.lower():
return True
return False
def reset_random_seed():
# reset random seed to make sure other processes extracting values from RNG
# don't get the same results (useful especially when you then use the
# random values to allocate system resources from global pool, like ports
# to listen). Use both current time and pid to make sure no tests started
# at the same time get the same values from RNG
seed = time.time() + os.getpid()
random.seed(seed)
def get_random_ipv6_mode():
return random.choice(constants.IPV6_MODES)
import_modules_recursively = moves.moved_function(
utils.import_modules_recursively,
'import_modules_recursively',
__name__,
version='Newton',
removal_version='Ocata')
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations
# under the License.
"""
NOTE: Do not use this module to add random utils.
We want to avoid having a generic utils.py dumping ground.
"""
from debtcollector import moves
from neutron_lib.api import attributes
populate_project_info = moves.moved_function(
attributes.populate_project_info, 'populate_project_info', __name__)
from neutron.db.models import securitygroup as sg_models
from neutron.db import models_v2
from neutron.db import segments_db
from neutron.extensions import portbindings
from neutron import manager
from neutron.plugins.ml2 import models
LOG = log.getLogger(__name__)
# limit the number of port OR LIKE statements in one query
MAX_PORTS_PER_QUERY = 500
# The API methods from segments_db
add_network_segment = moves.moved_function(segments_db.add_network_segment,
'add_network_segment',
__name__,
version='Newton',
removal_version='Ocata')
get_network_segments = moves.moved_function(segments_db.get_network_segments,
'get_network_segments',
__name__,
version='Newton',
removal_version='Ocata')
get_networks_segments = moves.moved_function(segments_db.get_networks_segments,
'get_networks_segments',
__name__,
version='Newton',
removal_version='Ocata')
class VolumesClient(base_client.BaseClient):
"""Client class to send CRUD Volume V2 API requests"""
api_version = "v2"
create_volume_transfer = moves.moved_function(
transfers_client.TransfersClient.create_volume_transfer,
'VolumesClient.create_volume_transfer', __name__,
message='Use create_volume_transfer from new location.',
version='Pike', removal_version='Queens')
show_volume_transfer = moves.moved_function(
transfers_client.TransfersClient.show_volume_transfer,
'VolumesClient.show_volume_transfer', __name__,
message='Use show_volume_transfer from new location.',
version='Pike', removal_version='Queens')
list_volume_transfers = moves.moved_function(
transfers_client.TransfersClient.list_volume_transfers,
'VolumesClient.list_volume_transfers', __name__,
message='Use list_volume_transfer from new location.',
version='Pike', removal_version='Queens')
delete_volume_transfer = moves.moved_function(
transfers_client.TransfersClient.delete_volume_transfer,
'VolumesClient.delete_volume_transfer', __name__,
message='Use delete_volume_transfer from new location.',
version='Pike', removal_version='Queens')
accept_volume_transfer = moves.moved_function(
transfers_client.TransfersClient.accept_volume_transfer,
'VolumesClient.accept_volume_transfer', __name__,
message='Use accept_volume_transfer from new location.',
version='Pike', removal_version='Queens')
def _prepare_params(self, params):
"""Prepares params for use in get or _ext_get methods.
If params is a string it will be left as it is, but if it's not it will
be urlencoded.
"""
if isinstance(params, six.string_types):
return params
return urllib.urlencode(params)
def list_volumes(self, detail=False, params=None):
"""List all the volumes created.
Params can be a string (must be urlencoded) or a dictionary.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#list-volumes-with-details
http://developer.openstack.org/api-ref/block-storage/v2/#list-volumes
"""
url = 'volumes'
if detail:
url += '/detail'
if params:
url += '?%s' % self._prepare_params(params)
resp, body = self.get(url)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def show_volume(self, volume_id):
"""Returns the details of a single volume."""
url = "volumes/%s" % volume_id
resp, body = self.get(url)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def create_volume(self, **kwargs):
"""Creates a new Volume.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#create-volume
"""
post_body = json.dumps({'volume': kwargs})
resp, body = self.post('volumes', post_body)
body = json.loads(body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def update_volume(self, volume_id, **kwargs):
"""Updates the Specified Volume.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#update-volume
"""
put_body = json.dumps({'volume': kwargs})
resp, body = self.put('volumes/%s' % volume_id, put_body)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def delete_volume(self, volume_id, **params):
"""Deletes the Specified Volume.
For a full list of available parameters, please refer to the official
API reference:
https://developer.openstack.org/api-ref/block-storage/v2/#delete-volume
"""
url = 'volumes/%s' % volume_id
if params:
url += '?%s' % urllib.urlencode(params)
resp, body = self.delete(url)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def upload_volume(self, volume_id, **kwargs):
"""Uploads a volume in Glance."""
post_body = json.dumps({'os-volume_upload_image': kwargs})
url = 'volumes/%s/action' % (volume_id)
resp, body = self.post(url, post_body)
body = json.loads(body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def attach_volume(self, volume_id, **kwargs):
"""Attaches a volume to a given instance on a given mountpoint.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#attach-volume-to-server
"""
post_body = json.dumps({'os-attach': kwargs})
url = 'volumes/%s/action' % (volume_id)
resp, body = self.post(url, post_body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def set_bootable_volume(self, volume_id, **kwargs):
"""Set a bootable flag for a volume - true or false.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#update-volume-bootable-status
"""
post_body = json.dumps({'os-set_bootable': kwargs})
url = 'volumes/%s/action' % (volume_id)
resp, body = self.post(url, post_body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def detach_volume(self, volume_id):
"""Detaches a volume from an instance."""
post_body = json.dumps({'os-detach': {}})
url = 'volumes/%s/action' % (volume_id)
resp, body = self.post(url, post_body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def reserve_volume(self, volume_id):
"""Reserves a volume."""
post_body = json.dumps({'os-reserve': {}})
url = 'volumes/%s/action' % (volume_id)
resp, body = self.post(url, post_body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def unreserve_volume(self, volume_id):
"""Restore a reserved volume ."""
post_body = json.dumps({'os-unreserve': {}})
url = 'volumes/%s/action' % (volume_id)
resp, body = self.post(url, post_body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def is_resource_deleted(self, id):
try:
self.show_volume(id)
except lib_exc.NotFound:
return True
return False
@property
def resource_type(self):
"""Returns the primary type of resource this client works with."""
return 'volume'
def extend_volume(self, volume_id, **kwargs):
"""Extend a volume.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#extend-volume-size
"""
post_body = json.dumps({'os-extend': kwargs})
url = 'volumes/%s/action' % (volume_id)
resp, body = self.post(url, post_body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def reset_volume_status(self, volume_id, **kwargs):
"""Reset the Specified Volume's Status.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#reset-volume-statuses
"""
post_body = json.dumps({'os-reset_status': kwargs})
resp, body = self.post('volumes/%s/action' % volume_id, post_body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def update_volume_readonly(self, volume_id, **kwargs):
"""Update the Specified Volume readonly."""
post_body = json.dumps({'os-update_readonly_flag': kwargs})
url = 'volumes/%s/action' % (volume_id)
resp, body = self.post(url, post_body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def force_delete_volume(self, volume_id):
"""Force Delete Volume."""
post_body = json.dumps({'os-force_delete': {}})
resp, body = self.post('volumes/%s/action' % volume_id, post_body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def create_volume_metadata(self, volume_id, metadata):
"""Create metadata for the volume.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#create-volume-metadata
"""
put_body = json.dumps({'metadata': metadata})
url = "volumes/%s/metadata" % volume_id
resp, body = self.post(url, put_body)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def show_volume_metadata(self, volume_id):
"""Get metadata of the volume."""
url = "volumes/%s/metadata" % volume_id
resp, body = self.get(url)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def update_volume_metadata(self, volume_id, metadata):
"""Update metadata for the volume.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#update-volume-metadata
"""
put_body = json.dumps({'metadata': metadata})
url = "volumes/%s/metadata" % volume_id
resp, body = self.put(url, put_body)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def show_volume_metadata_item(self, volume_id, id):
"""Show metadata item for the volume."""
url = "volumes/%s/metadata/%s" % (volume_id, id)
resp, body = self.get(url)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def update_volume_metadata_item(self, volume_id, id, meta_item):
"""Update metadata item for the volume."""
put_body = json.dumps({'meta': meta_item})
url = "volumes/%s/metadata/%s" % (volume_id, id)
resp, body = self.put(url, put_body)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def delete_volume_metadata_item(self, volume_id, id):
"""Delete metadata item for the volume."""
url = "volumes/%s/metadata/%s" % (volume_id, id)
resp, body = self.delete(url)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def retype_volume(self, volume_id, **kwargs):
"""Updates volume with new volume type.
For a full list of available parameters, please refer to the official
API reference:
https://developer.openstack.org/api-ref/block-storage/v2/#retype-volume
"""
post_body = json.dumps({'os-retype': kwargs})
resp, body = self.post('volumes/%s/action' % volume_id, post_body)
self.expected_success(202, resp.status)
def force_detach_volume(self, volume_id, **kwargs):
"""Force detach a volume.
For a full list of available parameters, please refer to the official
API reference:
https://developer.openstack.org/api-ref/block-storage/v2/#force-detach-volume
"""
post_body = json.dumps({'os-force_detach': kwargs})
url = 'volumes/%s/action' % volume_id
resp, body = self.post(url, post_body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
def update_volume_image_metadata(self, volume_id, **kwargs):
"""Update image metadata for the volume.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#set-image-metadata-for-volume
"""
post_body = json.dumps({'os-set_image_metadata': {'metadata': kwargs}})
url = "volumes/%s/action" % (volume_id)
resp, body = self.post(url, post_body)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def delete_volume_image_metadata(self, volume_id, key_name):
"""Delete image metadata item for the volume."""
post_body = json.dumps({'os-unset_image_metadata': {'key': key_name}})
url = "volumes/%s/action" % (volume_id)
resp, body = self.post(url, post_body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
@removals.remove(message="use list_pools from tempest.lib.services."
"volume.v2.scheduler_stats_client")
def show_pools(self, detail=False):
# List all the volumes pools (hosts)
url = 'scheduler-stats/get_pools'
if detail:
url += '?detail=True'
resp, body = self.get(url)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
@removals.remove(message="use show_backend_capabilities from tempest.lib."
"services.volume.v2.capabilities_client")
def show_backend_capabilities(self, host):
"""Shows capabilities for a storage back end.
For a full list of available parameters, please refer to the official
API reference:
http://developer.openstack.org/api-ref/block-storage/v2/#show-back-end-capabilities
"""
url = 'capabilities/%s' % host
resp, body = self.get(url)
body = json.loads(body)
self.expected_success(200, resp.status)
return rest_client.ResponseBody(resp, body)
def unmanage_volume(self, volume_id):
"""Unmanage volume.
For a full list of available parameters, please refer to the official
API reference:
https://developer.openstack.org/api-ref/block-storage/v2/#unmanage-volume
"""
post_body = json.dumps({'os-unmanage': {}})
resp, body = self.post('volumes/%s/action' % volume_id, post_body)
self.expected_success(202, resp.status)
return rest_client.ResponseBody(resp, body)
disabled = f.read().strip()
_IS_IPV6_ENABLED = disabled == "0"
else:
_IS_IPV6_ENABLED = False
if not _IS_IPV6_ENABLED:
LOG.info(
_LI("IPv6 not present or configured not to bind to new "
"interfaces on this system. Please ensure IPv6 is "
"enabled and /proc/sys/net/ipv6/conf/default/"
"disable_ipv6 is set to 1 to enable IPv6."))
return _IS_IPV6_ENABLED
is_enabled = moves.moved_function(is_enabled_and_bind_by_default,
'is_enabled',
__name__,
version='Ocata',
removal_version='Pike')
def is_auto_address_subnet(subnet):
"""Check if subnet is an auto address subnet."""
modes = [const.IPV6_SLAAC, const.DHCPV6_STATELESS]
return (subnet['ipv6_address_mode'] in modes
or subnet['ipv6_ra_mode'] in modes)
def is_eui64_address(ip_address):
"""Check if ip address is EUI64."""
ip = netaddr.IPAddress(ip_address)
# '0xfffe' addition is used to build EUI-64 from MAC (RFC4291)
def etcdir(*p):
return os.path.join(ETCDIR, *p)
def fake_use_fatal_exceptions(*args):
return True
for _name in ("get_related_rand_names", "get_rand_name", "get_rand_device_name", "get_related_rand_device_names"):
setattr(
sys.modules[__name__],
_name,
moves.moved_function(
getattr(utils, _name),
_name,
__name__,
message='use "neutron.common.utils.%s" instead' % _name,
version="Newton",
removal_version="Ocata",
),
)
def bool_from_env(key, strict=False, default=False):
value = os.environ.get(key)
return strutils.bool_from_string(value, strict=strict, default=default)
def setup_test_logging(config_opts, log_dir, log_file_path_template):
# Have each test log into its own log file
config_opts.set_override("debug", True)
fileutils.ensure_tree(log_dir, mode=0o755)
# Copyright (c) 2015 Red Hat, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations
# under the License.
import functools
from debtcollector import moves
from ovsdbapp.schema.open_vswitch import helpers
from neutron.agent.common import utils
_connection_to_manager_uri = moves.moved_function(
helpers._connection_to_manager_uri,
'_connection_to_manager_uri', __name__)
enable_connection_uri = functools.partial(
helpers.enable_connection_uri, execute=utils.execute, run_as_root=True,
log_fail_as_error=False, check_exit_code=False)
"assertEqual(True, observed)")
yield (0, msg)
if re.search(r"assertEqual\(\s*False,[^,]*(,[^,]*)?", logical_line):
msg = ("N328: Use assertFalse(observed) instead of "
"assertEqual(False, observed)")
yield (0, msg)
if re.search(r"assertEqual\([^,]*,\s*False(,[^,]*)?", logical_line):
msg = ("N328: Use assertFalse(observed) instead of "
"assertEqual(False, observed)")
yield (0, msg)
check_asserttrue = flake8ext(
moves.moved_function(check_asserttruefalse,
'check_asserttrue',
__name__,
version='Newton',
removal_version='Ocata'))
check_assertfalse = flake8ext(
moves.moved_function(check_asserttruefalse,
'check_assertfalse',
__name__,
version='Newton',
removal_version='Ocata'))
@flake8ext
def no_mutable_default_args(logical_line):
"""N329 - Don't use mutable default arguments."""
msg = "N329: Method's default argument shouldn't be mutable!"
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations
# under the License.
# TODO(amotoki): Remove this file at the beginning of Nxx cycle.
from debtcollector import moves
from neutronclient import _i18n
message = (
"moved to neutronclient._i18n; please migrate to local "
"oslo_i18n usage, as defined at "
"http://docs.openstack.org/developer/oslo.i18n/usage.html"
)
_ = moves.moved_function(_i18n._, "_", __name__, message=message)
_LC = moves.moved_function(_i18n._LC, "_LC", __name__, message=message)
_LE = moves.moved_function(_i18n._LE, "_LE", __name__, message=message)
_LW = moves.moved_function(_i18n._LW, "_LW", __name__, message=message)
_LI = moves.moved_function(_i18n._LI, "_LI", __name__, message=message)