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def pack_load_local_registry(name, registryf=None):
value = {}
regpath = get_registry_path(name,
registryf=registryf,
registry_format='pack')
try:
if os.path.exists(regpath):
with open(regpath) as fic:
rvalue = fic.read()
value = __salt__['mc_utils.msgpack_load'](
rvalue)
except (msgpack.exceptions.UnpackValueError,
msgpack.exceptions.ExtraData):
log.error('decoding error, removing stale {0}'.format(regpath))
os.unlink(regpath)
value = {}
return value
def pack_load_local_registry(name, registryf=None):
value = {}
regpath = get_registry_path(name,
registryf=registryf,
registry_format='pack')
try:
if os.path.exists(regpath):
with open(regpath) as fic:
rvalue = fic.read()
value = __salt__['mc_utils.msgpack_load'](
rvalue)
except (msgpack.exceptions.UnpackValueError,
msgpack.exceptions.ExtraData):
log.error('decoding error, removing stale {0}'.format(regpath))
os.unlink(regpath)
value = {}
return value
session_id = session_id.decode("utf8")
except crypto.BadSignature:
return Session()
# Fetch the serialized data from redis
bdata = self.redis.get(self._redis_key(session_id))
# If the session didn't exist in redis, we'll give the user a new
# session.
if bdata is None:
return Session()
# De-serialize our session data
try:
data = msgpack.unpackb(bdata, encoding="utf8", use_list=True)
except (msgpack.exceptions.UnpackException, msgpack.exceptions.ExtraData):
# If the session data was invalid we'll give the user a new session
return Session()
# If we were able to load existing session data, load it into a
# Session class
session = Session(data, session_id, False)
return session
def unpackb(packed, **kwargs):
"""
Unpack an object from `packed`.
Raises `ExtraData` when `packed` contains extra bytes.
See :class:`Unpacker` for options.
"""
unpacker = Unpacker(None, **kwargs)
unpacker.feed(packed)
try:
ret = unpacker._fb_unpack()
except OutOfData:
raise UnpackValueError("Data is not enough.")
if unpacker._fb_got_extradata():
raise ExtraData(ret, unpacker._fb_get_extradata())
return ret
def unpackb(packed, **kwargs):
"""
Unpack an object from `packed`.
Raises `ExtraData` when `packed` contains extra bytes.
See :class:`Unpacker` for options.
"""
unpacker = Unpacker(None, **kwargs)
unpacker.feed(packed)
try:
ret = unpacker._unpack()
except OutOfData:
raise UnpackValueError("Data is not enough.")
if unpacker._got_extradata():
raise ExtraData(ret, unpacker._get_extradata())
return ret
def receive(self) -> bytes:
"""
Gets a message from the client.
Blocks until a message is received.
"""
message = self.socket.recv()
try:
response = msgpack.unpackb(message, raw=False)
except msgpack.exceptions.ExtraData:
response = message
return response
def unpack(stream, **kwargs):
"""
Unpack an object from `stream`.
Raises `ExtraData` when `packed` contains extra bytes.
See :class:`Unpacker` for options.
"""
unpacker = Unpacker(stream, **kwargs)
ret = unpacker._fb_unpack()
if unpacker._fb_got_extradata():
raise ExtraData(ret, unpacker._fb_get_extradata())
return ret
continue
# TODO: add try/except to download cif file as fallback like below?
if rez_cutoff and pdb.resolution:
if pdb.resolution > rez_cutoff:
log.debug('{}: structure does not meet experimental resolution cutoff'.format(pdb, pdb_file_type))
continue
# TODO: clean up these try/except things
try:
self.align_seqprop_to_structprop(seqprop=self.representative_sequence,
structprop=pdb,
outdir=seq_outdir,
engine=engine,
parse=True,
force_rerun=force_rerun)
except (PDBConstructionException, ExtraData) as e:
log.error('{}: unable to parse structure file as {}. Falling back to mmCIF format.'.format(pdb, pdb_file_type))
print(e)
# Fall back to using mmCIF file if structure cannot be parsed
try:
pdb.download_structure_file(outdir=struct_outdir, file_type='cif',
force_rerun=force_rerun)
# Download the mmCIF header file to get additional information
if 'cif' not in pdb_file_type:
pdb.download_cif_header_file(outdir=struct_outdir, force_rerun=force_rerun)
except (requests.exceptions.HTTPError, URLError):
log.error('{}: structure file could not be downloaded'.format(pdb))
continue
self.align_seqprop_to_structprop(seqprop=self.representative_sequence,
structprop=pdb,
outdir=seq_outdir,
engine=engine,