def unpack(cls, unpacker: Unpacker) -> "ClaimPredicate":
type = ClaimPredicateType.unpack(unpacker)
if type == ClaimPredicateType.CLAIM_PREDICATE_UNCONDITIONAL:
return cls(type)
if type == ClaimPredicateType.CLAIM_PREDICATE_AND:
length = unpacker.unpack_uint()
and_predicates = []
for _ in range(length):
and_predicates.append(ClaimPredicate.unpack(unpacker))
return cls(type, and_predicates=and_predicates)
if type == ClaimPredicateType.CLAIM_PREDICATE_OR:
length = unpacker.unpack_uint()
or_predicates = []
for _ in range(length):
or_predicates.append(ClaimPredicate.unpack(unpacker))
return cls(type, or_predicates=or_predicates)
if type == ClaimPredicateType.CLAIM_PREDICATE_NOT:
# not_predicate is optional.
not_predicate = ClaimPredicate.unpack(
unpacker) if unpacker.unpack_uint() else None
if not_predicate is None:
raise ValueError("not_predicate should not be None.")
return cls(type, not_predicate=not_predicate)
if type == ClaimPredicateType.CLAIM_PREDICATE_BEFORE_ABSOLUTE_TIME:
abs_before = Int64.unpack(unpacker)
if abs_before is None:
raise ValueError("abs_before should not be None.")
return cls(type, abs_before=abs_before)
if type == ClaimPredicateType.CLAIM_PREDICATE_BEFORE_RELATIVE_TIME:
rel_before = Int64.unpack(unpacker)
if rel_before is None:
raise ValueError("rel_before should not be None.")
return cls(type, rel_before=rel_before)
return cls(type)
def read_datagram(addr, data):
"""Yield all record (flow and counter records) from the sFlow v5
datagram given by up, which is expected to be an xdrlib.Unpacker
object."""
up = Unpacker(data)
version = up.unpack_int()
if not version == 5:
hexdump_bytes(data)
raise Exception()
af = up.unpack_int()
if af == 1: # IPv4
agent_address = ntohl(up.unpack_uint())
else:
raise Exception()
sf = Datagram(addr, agent_address)
sub_agent_id = up.unpack_uint()
sequence_number = up.unpack_uint()
uptime = up.unpack_uint()
nb_sample_records = up.unpack_uint()
# Iterating over sample records
for i in range(nb_sample_records):
try:
return read_sample_record(up, sf)
except EOFError:
stderr.write("read_sample_datagram: EOFError reading sample_record,", \
"Premature end of data stream, Skipping record\n")
up.set_position(len(up.get_buffer()))
break
def _parse_raw_sflow_datagram(self, unpacker: Unpacker):
self.sflow_version = unpacker.unpack_int()
if not self.sflow_version == 5:
logging.debug("Unimplemented sFlow version: {}".format(
self.sflow_version))
# TODO: read remainder if needed
return
self.agent_ip_version = unpacker.unpack_int()
if self.agent_ip_version == 1:
self.agent_ip_address = ntohl(unpacker.unpack_uint())
# TODO: implement other versions
else:
logging.debug("Unimplemented agent IP version: {}".format(
self.agent_ip_version))
return
self.sub_agent_id = unpacker.unpack_uint()
self.sequence_number = unpacker.unpack_uint()
self.switch_uptime = unpacker.unpack_uint()
samples_in_datagram = unpacker.unpack_uint()
for _ in range(samples_in_datagram):
try:
self.samples.append(SFlowSample(unpacker))
except Exception as e:
logging.warning("Bad sample")
raise e
def read_datagram(addr, data):
"""Yield all record (flow and counter records) from the sFlow v5
datagram given by up, which is expected to be an xdrlib.Unpacker
object."""
up = Unpacker(data)
version = up.unpack_int()
if not version == 5:
hexdump_bytes(data)
raise Exception()
af = up.unpack_int()
if af == 1: # IPv4
agent_address = ntohl(up.unpack_uint())
else:
raise Exception()
sf = Datagram(addr, agent_address)
sub_agent_id = up.unpack_uint()
sequence_number = up.unpack_uint()
uptime = up.unpack_uint()
nb_sample_records = up.unpack_uint()
# Iterating over sample records
for i in range(nb_sample_records):
try:
return read_sample_record(up, sf)
except EOFError:
stderr.write("read_sample_datagram: EOFError reading sample_record,", \
"Premature end of data stream, Skipping record\n")
up.set_position(len(up.get_buffer()))
break
def unpack(cls, unpacker: Unpacker) -> "AccountEntry":
account_id = AccountID.unpack(unpacker)
balance = Int64.unpack(unpacker)
seq_num = SequenceNumber.unpack(unpacker)
num_sub_entries = Uint32.unpack(unpacker)
inflation_dest = AccountID.unpack(unpacker) if unpacker.unpack_uint() else None
flags = Uint32.unpack(unpacker)
home_domain = String32.unpack(unpacker)
thresholds = Thresholds.unpack(unpacker)
length = unpacker.unpack_uint()
signers = []
for _ in range(length):
signers.append(Signer.unpack(unpacker))
ext = AccountEntryExt.unpack(unpacker)
return cls(
account_id=account_id,
balance=balance,
seq_num=seq_num,
num_sub_entries=num_sub_entries,
inflation_dest=inflation_dest,
flags=flags,
home_domain=home_domain,
thresholds=thresholds,
signers=signers,
ext=ext,
)
def _parse_raw_sflow_counter_sample(self, unpacker: Unpacker):
self.sequence_number = unpacker.unpack_uint()
self.source_id = unpacker.unpack_uint()
counters_in_sample = unpacker.unpack_uint()
for _ in range(counters_in_sample):
self.counters.append(SFlowCounterRecord(unpacker))
def _parse_raw_sflow_datagram(self, unpacker: Unpacker):
self.sflow_version = unpacker.unpack_int()
if not self.sflow_version == 5:
logging.debug("Unimplemented sFlow version: {}".format(self.sflow_version))
# TODO: read remainder if needed
return
self.agent_ip_version = unpacker.unpack_int()
if self.agent_ip_version == 1:
self.agent_ip_address = ntohl(unpacker.unpack_uint())
# TODO: implement other versions
else:
logging.debug("Unimplemented agent IP version: {}".format(self.agent_ip_version))
return
self.sub_agent_id = unpacker.unpack_uint()
self.sequence_number = unpacker.unpack_uint()
self.switch_uptime = unpacker.unpack_uint()
samples_in_datagram = unpacker.unpack_uint()
for _ in range(samples_in_datagram):
try:
self.samples.append(SFlowSample(unpacker))
except Exception as e:
logging.warning("Bad sample")
raise e
def is_tag_full(wrapped_message):
unpacker = Unpacker(wrapped_message)
try:
unpacker.unpack_uint()
unpacker.unpack_string()
except EOFError:
return False
return True
def unpack(cls, unpacker: Unpacker) -> "SetOptionsOp":
inflation_dest = AccountID.unpack(
unpacker) if unpacker.unpack_uint() else None
clear_flags = Uint32.unpack(
unpacker) if unpacker.unpack_uint() else None
set_flags = Uint32.unpack(unpacker) if unpacker.unpack_uint() else None
master_weight = Uint32.unpack(
unpacker) if unpacker.unpack_uint() else None
low_threshold = Uint32.unpack(
unpacker) if unpacker.unpack_uint() else None
med_threshold = Uint32.unpack(
unpacker) if unpacker.unpack_uint() else None
high_threshold = Uint32.unpack(
unpacker) if unpacker.unpack_uint() else None
home_domain = String32.unpack(
unpacker) if unpacker.unpack_uint() else None
signer = Signer.unpack(unpacker) if unpacker.unpack_uint() else None
return cls(
inflation_dest=inflation_dest,
clear_flags=clear_flags,
set_flags=set_flags,
master_weight=master_weight,
low_threshold=low_threshold,
med_threshold=med_threshold,
high_threshold=high_threshold,
home_domain=home_domain,
signer=signer,
)
def unpack(cls, unpacker: Unpacker) -> "SCPNomination":
quorum_set_hash = Hash.unpack(unpacker)
length = unpacker.unpack_uint()
votes = []
for _ in range(length):
votes.append(Value.unpack(unpacker))
length = unpacker.unpack_uint()
accepted = []
for _ in range(length):
accepted.append(Value.unpack(unpacker))
return cls(quorum_set_hash=quorum_set_hash, votes=votes, accepted=accepted,)
def unpack(cls, unpacker: Unpacker) -> "SCPQuorumSet":
threshold = Uint32.unpack(unpacker)
length = unpacker.unpack_uint()
validators = []
for _ in range(length):
validators.append(PublicKey.unpack(unpacker))
length = unpacker.unpack_uint()
inner_sets = []
for _ in range(length):
inner_sets.append(SCPQuorumSet.unpack(unpacker))
return cls(threshold=threshold, validators=validators, inner_sets=inner_sets,)
def unpack(self, u: xdrlib.Unpacker):
last = u.unpack_uint() + u.get_position()
ret = ReturnCode.unpack(u)
if ret == ReturnCode.OK:
last2 = u.unpack_uint() + u.get_position()
if u.get_position() < last2:
self.digest = u.unpack_fopaque(20)
if u.get_position() < last2:
self.salt = u.unpack_fopaque(8)
u.set_position(last2)
u.set_position(last)
def unpack(cls, unpacker: Unpacker) -> "LedgerSCPMessages":
ledger_seq = Uint32.unpack(unpacker)
length = unpacker.unpack_uint()
messages = []
for _ in range(length):
messages.append(SCPEnvelope.unpack(unpacker))
return cls(ledger_seq=ledger_seq, messages=messages,)
def __init__(self, unpacker: Unpacker):
self.counter_format = None
self.counter = None
self.counter_format = unpacker.unpack_uint()
counter_data = unpacker.unpack_opaque()
unpacker_counter_data = Unpacker(counter_data)
if self.counter_format == SFlowCounterRecord.COUNTER_DATA_GENERIC_INTERFACE:
self.counter = GenericInterfaceCounters(unpacker_counter_data)
elif self.counter_format == SFlowCounterRecord.COUNTER_DATA_ETHERNET_INTERFACE:
self.counter = EthernetInterfaceCounters(unpacker_counter_data)
elif self.counter_format == SFlowCounterRecord.COUNTER_DATA_TOKEN_RING:
pass
self.counter = TokenRingCounters(unpacker_counter_data)
elif self.counter_format == SFlowCounterRecord.COUNTER_DATA_VG_INTERFACE:
pass
self.counter = VgInterfaceCounters(unpacker_counter_data)
elif self.counter_format == SFlowCounterRecord.COUNTER_DATA_VLAN:
self.counter = VlanCounters(unpacker_counter_data)
elif self.counter_format == SFlowCounterRecord.COUNTER_DATA_PROCESSOR:
self.counter = ProcessorCounters(unpacker_counter_data)
else:
logging.debug('read_flow_record:Unimplemented data_format (%d)' %
self.flow_format)
def unpack(cls, unpacker: Unpacker) -> "PeerStatList":
length = unpacker.unpack_uint()
peer_stat_list = []
for _ in range(length):
peer_stat_list.append(PeerStats.unpack(unpacker))
return cls(peer_stat_list)
def gmetric_read(header_msg, data_msg):
header = Unpacker(header_msg)
data = Unpacker(data_msg)
values = dict()
header.unpack_int()
values['HOSTNAME'] = str(header.unpack_string().decode('ascii'))
values['NAME'] = str(header.unpack_string().decode('ascii'))
values['SPOOFENABLED'] = header.unpack_int()
values['TYPE'] = str(header.unpack_string().decode('ascii'))
values['NAME'] = str(header.unpack_string().decode('ascii'))
values['UNITS'] = str(header.unpack_string().decode('ascii'))
values['SLOPE'] = slope_int2str[header.unpack_int()]
values['TMAX'] = header.unpack_uint()
values['DMAX'] = header.unpack_uint()
if header.unpack_int() == 1:
header.unpack_string()
values['GROUP'] = str(header.unpack_string().decode('ascii'))
# Actual data in the second packet
data.unpack_int()
values['HOSTNAME'] = str(data.unpack_string().decode('ascii'))
values['NAME'] = str(data.unpack_string().decode('ascii'))
values['SPOOFENABLED'] = data.unpack_int()
data.unpack_string()
values['VAL'] = str(data.unpack_string().decode('ascii'))
header.done()
data.done()
return values
def unpack(self, u: xdrlib.Unpacker):
last = u.unpack_uint() + u.get_position()
if u.get_position() < last:
self.time_A = struct.unpack('>Q', u.unpack_fopaque(8))[0]
if u.get_position() < last:
self.time_B = struct.unpack('>Q', u.unpack_fopaque(8))[0]
u.set_position(last)
def unpack(cls, unpacker: Unpacker) -> "SCPHistoryEntryV0":
length = unpacker.unpack_uint()
quorum_sets = []
for _ in range(length):
quorum_sets.append(SCPQuorumSet.unpack(unpacker))
ledger_messages = LedgerSCPMessages.unpack(unpacker)
return cls(quorum_sets=quorum_sets, ledger_messages=ledger_messages,)
def unpack(cls, unpacker: Unpacker) -> "LedgerEntryChanges":
length = unpacker.unpack_uint()
ledger_entry_changes = []
for _ in range(length):
ledger_entry_changes.append(LedgerEntryChange.unpack(unpacker))
return cls(ledger_entry_changes)
def unpack(cls, unpacker: Unpacker) -> "Operation":
source_account = (MuxedAccount.unpack(unpacker)
if unpacker.unpack_uint() else None)
body = OperationBody.unpack(unpacker)
return cls(
source_account=source_account,
body=body,
)
def unpack(cls, unpacker: Unpacker) -> "TransactionResultSet":
length = unpacker.unpack_uint()
results = []
for _ in range(length):
results.append(TransactionResultPair.unpack(unpacker))
return cls(
results=results,
)
def get_tlv(wrapped_message):
unpacker = Unpacker(wrapped_message)
tag = unpacker.unpack_uint()
message = unpacker.unpack_string()
pos = unpacker.get_position()
buff = unpacker.get_buffer()
rest = buff[pos:]
return tag, message, rest
def unpack(cls, unpacker: Unpacker) -> "SCPStatementPrepare":
quorum_set_hash = Hash.unpack(unpacker)
ballot = SCPBallot.unpack(unpacker)
prepared = SCPBallot.unpack(
unpacker) if unpacker.unpack_uint() else None
prepared_prime = SCPBallot.unpack(
unpacker) if unpacker.unpack_uint() else None
n_c = Uint32.unpack(unpacker)
n_h = Uint32.unpack(unpacker)
return cls(
quorum_set_hash=quorum_set_hash,
ballot=ballot,
prepared=prepared,
prepared_prime=prepared_prime,
n_c=n_c,
n_h=n_h,
)
def unpack(cls, unpacker: Unpacker) -> "ManageDataOp":
data_name = String64.unpack(unpacker)
data_value = DataValue.unpack(
unpacker) if unpacker.unpack_uint() else None
return cls(
data_name=data_name,
data_value=data_value,
)
def parse(self, raw_data):
packet = SFlowPacket()
data = Unpacker(raw_data)
# sFlow version (2|4|5)
packet.version = data.unpack_uint()
if packet.version != 5:
logging.error("Only support version 5.")
raise RuntimeError("Only support version 5.")
logging.debug("Get version {0}".format(packet.version))
# IP version of the Agent/Switch (1=v4|2=v6)
packet.agent_ip_version = data.unpack_uint()
if packet.agent_ip_version != 1:
logging.error("Only support IPv4.")
raise RuntimeError("Only support IPv4.")
# Agent IP address (v4=4byte|v6=16byte)
packet.agent_ip_address = ntohl(data.unpack_uint())
# sub agent id
packet.sub_agent_id = data.unpack_uint()
# datagram sequence number
packet.datagram_sequence_num = data.unpack_uint()
# switch uptime in ms
packet.switch_uptime = data.unpack_uint()
# how many samples in datagram
packet.sample_amount = data.unpack_uint()
self._parse_samples(packet, data)
return packet
def parse(self, raw_data):
packet = SFlowPacket()
data = Unpacker(raw_data)
# sFlow version (2|4|5)
packet.version = data.unpack_uint()
if packet.version != 5:
logging.error("Only support version 5.")
raise RuntimeError("Only support version 5.")
logging.debug("Get version {0}".format(packet.version))
# IP version of the Agent/Switch (1=v4|2=v6)
packet.agent_ip_version = data.unpack_uint()
if packet.agent_ip_version != 1:
logging.error("Only support IPv4.")
raise RuntimeError("Only support IPv4.")
# Agent IP address (v4=4byte|v6=16byte)
packet.agent_ip_address = ntohl(data.unpack_uint())
# sub agent id
packet.sub_agent_id = data.unpack_uint()
# datagram sequence number
packet.datagram_sequence_num = data.unpack_uint()
# switch uptime in ms
packet.switch_uptime = data.unpack_uint()
# how many samples in datagram
packet.sample_amount = data.unpack_uint()
self._parse_samples(packet, data)
return packet
def unpack(cls, unpacker: Unpacker) -> "InflationResult":
code = InflationResultCode.unpack(unpacker)
if code == InflationResultCode.INFLATION_SUCCESS:
length = unpacker.unpack_uint()
payouts = []
for _ in range(length):
payouts.append(InflationPayout.unpack(unpacker))
return cls(code, payouts=payouts)
raise ValueError("Invalid code.")
def _parse_raw_sflow_flow_sample(self, unpacker: Unpacker):
self.sequence_number = unpacker.unpack_uint()
self.source_id = unpacker.unpack_uint()
self.sampling_rate = unpacker.unpack_uint()
self.sample_pool = unpacker.unpack_uint()
self.drops = unpacker.unpack_uint()
self.input_if = unpacker.unpack_uint()
self.output_if = unpacker.unpack_uint()
flows_in_sample = unpacker.unpack_uint()
for _ in range(flows_in_sample):
self.flows.append(SFlowFlowRecord(unpacker))
def unpack(cls, unpacker: Unpacker) -> "TransactionSet":
previous_ledger_hash = Hash.unpack(unpacker)
length = unpacker.unpack_uint()
txs = []
for _ in range(length):
txs.append(TransactionEnvelope.unpack(unpacker))
return cls(
previous_ledger_hash=previous_ledger_hash,
txs=txs,
)
def unpack(cls, unpacker: Unpacker) -> "ManageOfferSuccessResult":
length = unpacker.unpack_uint()
offers_claimed = []
for _ in range(length):
offers_claimed.append(ClaimOfferAtom.unpack(unpacker))
offer = ManageOfferSuccessResultOffer.unpack(unpacker)
return cls(
offers_claimed=offers_claimed,
offer=offer,
)
def unpack(cls, unpacker: Unpacker) -> "TransactionV1Envelope":
tx = Transaction.unpack(unpacker)
length = unpacker.unpack_uint()
signatures = []
for _ in range(length):
signatures.append(DecoratedSignature.unpack(unpacker))
return cls(
tx=tx,
signatures=signatures,
)
def unpack(cls, unpacker: Unpacker) -> "TransactionMetaV1":
tx_changes = LedgerEntryChanges.unpack(unpacker)
length = unpacker.unpack_uint()
operations = []
for _ in range(length):
operations.append(OperationMeta.unpack(unpacker))
return cls(
tx_changes=tx_changes,
operations=operations,
)
def unpack(self, u: xdrlib.Unpacker):
self.response_from_agent = u.unpack_bool()
self.agent_id = u.unpack_opaque()
n = u.unpack_uint()
self.controllers = []
for i in range(n):
c = AccessibleController()
c.trayId = u.unpack_uint()
c.slot = u.unpack_uint()
c.wwn = u.unpack_opaque()
c.token = u.unpack_fopaque(12)
c.controller_refs = []
m = u.unpack_uint()
for j in range(m):
c.controller_refs.append(u.unpack_fopaque(12))
self.controllers.append(c)
def unpack(cls, unpacker: Unpacker) -> "Transaction":
source_account = MuxedAccount.unpack(unpacker)
fee = Uint32.unpack(unpacker)
seq_num = SequenceNumber.unpack(unpacker)
time_bounds = TimeBounds.unpack(unpacker) if unpacker.unpack_uint() else None
memo = Memo.unpack(unpacker)
length = unpacker.unpack_uint()
operations = []
for _ in range(length):
operations.append(Operation.unpack(unpacker))
ext = TransactionExt.unpack(unpacker)
return cls(
source_account=source_account,
fee=fee,
seq_num=seq_num,
time_bounds=time_bounds,
memo=memo,
operations=operations,
ext=ext,
)
def unpack(self, u: xdrlib.Unpacker):
last = u.unpack_uint() + u.get_position()
if u.get_position() < last:
last2 = u.unpack_uint()
self.canditate_selection_type = CandidateSelectionType(
u.unpack_uint())
if self.canditate_selection_type == CandidateSelectionType.CANDIDATE_SEL_MANUAL:
last3 = u.unpack_uint() + u.get_position()
if u.get_position() < last3:
nb = u.unpack_uint()
self.drive_refs = []
for i in range(nb):
self.drive_refs.append(u.unpack_fopaque(20))
u.set_position(last3)
u.set_position(last2)
if u.get_position() < last:
self.raid_level = RaidLevel(u.unpack_int())
if u.get_position() < last:
self.phyiscal_drive_type = PhysicalDriveType(u.unpack_int())
def unpack(cls, unpacker: Unpacker) -> "StellarValue":
tx_set_hash = Hash.unpack(unpacker)
close_time = TimePoint.unpack(unpacker)
length = unpacker.unpack_uint()
upgrades = []
for _ in range(length):
upgrades.append(UpgradeType.unpack(unpacker))
ext = StellarValueExt.unpack(unpacker)
return cls(
tx_set_hash=tx_set_hash, close_time=close_time, upgrades=upgrades, ext=ext,
)
def unpack(cls,
unpacker: Unpacker) -> "PathPaymentStrictReceiveResultSuccess":
length = unpacker.unpack_uint()
offers = []
for _ in range(length):
offers.append(ClaimOfferAtom.unpack(unpacker))
last = SimplePaymentResult.unpack(unpacker)
return cls(
offers=offers,
last=last,
)
def gmetric_read(msg):
unpacker = Unpacker(msg)
values = dict()
unpacker.unpack_int()
values['TYPE'] = unpacker.unpack_string()
values['NAME'] = unpacker.unpack_string()
values['VAL'] = unpacker.unpack_string()
values['UNITS'] = unpacker.unpack_string()
values['SLOPE'] = slope_int2str[unpacker.unpack_int()]
values['TMAX'] = unpacker.unpack_uint()
values['DMAX'] = unpacker.unpack_uint()
unpacker.done()
return values
def gmetric_read(msg):
unpacker = Unpacker(msg)
values = dict()
unpacker.unpack_int()
values["TYPE"] = unpacker.unpack_string()
values["NAME"] = unpacker.unpack_string()
values["VAL"] = unpacker.unpack_string()
values["UNITS"] = unpacker.unpack_string()
values["SLOPE"] = slope_int2str[unpacker.unpack_int()]
values["TMAX"] = unpacker.unpack_uint()
values["DMAX"] = unpacker.unpack_uint()
unpacker.done()
return values
def _length_from_bytes(four_bytes):
"""
The RPC standard calls for the length of a message to be sent as the least
significant 31 bits of an XDR encoded unsigned integer. The most
significant bit encodes a True/False bit which indicates that this message
will be the last.
"""
from xdrlib import Unpacker
unpacker = Unpacker(four_bytes)
val = unpacker.unpack_uint()
unpacker.done()
if val < 2**31:
return (val, False)
return (val-2**31, True)
def datagramReceived(self, datagram, address):
values = dict()
unpacker = Unpacker(datagram)
packet_type = unpacker.unpack_uint()
if packet_type == 128:
self.unpack_meta(unpacker)
return
elif packet_type == 136:
#unpack_metareq function works, but serves no purpose right now
#commented out unless anyone comes up with a good reason to respond
#to metadata requests.
#self.unpack_metareq(unpacker)
return
elif 128 < packet_type < 136:
self.unpack_data(unpacker, packet_type, address)
return
else:
return
def __init__(self, unpacker: Unpacker):
self.flow_format = None
self.flow = None
self.flow_format = unpacker.unpack_uint()
flow_data = unpacker.unpack_opaque()
unpacker_flow_data = Unpacker(flow_data)
if self.flow_format == SFlowFlowRecord.FLOW_DATA_RAW_HEADER:
self.flow = FlowDataRawHeader(unpacker_flow_data)
elif self.flow_format == SFlowFlowRecord.FLOW_DATA_ETHERNET_HEADER:
self.flow = FlowDataEthernetHeader(unpacker_flow_data)
elif self.flow_format == SFlowFlowRecord.FLOW_DATA_IPV4_HEADER:
self.flow = FlowDataIPv4Header(unpacker_flow_data)
elif self.flow_format == SFlowFlowRecord.FLOW_DATA_EXT_SWITCH:
self.flow = FlowDataExtSwitch(unpacker_flow_data)
else:
logging.debug('read_flow_record:Unimplemented data_format (%d)' % self.flow_format)
def __init__(self, unpacker: Unpacker):
self.type = None
self.sample = None
self.type = unpacker.unpack_uint()
if self.type == SFlowSample.SAMPLE_DATA_FLOW_SAMPLE:
self.sample = SFlowFlowSample(unpacker)
elif self.type == SFlowSample.SAMPLE_DATA_COUNTER_SAMPLE:
self.sample = SFlowCounterSample(unpacker)
elif self.type == SFlowSample.SAMPLE_DATA_EXPANDED_FLOW_SAMPLE:
self.sample = SFlowExpandedFlowSample(unpacker)
elif self.type == SFlowSample.SAMPLE_DATA_EXPANDED_COUNTER_SAMPLE:
self.sample = SFlowExpandedCounterSample(unpacker)
else:
logging.debug("Unknown data format: {}".format(type))
logging.debug(unpacker.unpack_opaque())
def __init__(self, unpacker: Unpacker):
self.counter_format = None
self.counter = None
self.counter_format = unpacker.unpack_uint()
counter_data = unpacker.unpack_opaque()
unpacker_counter_data = Unpacker(counter_data)
if self.counter_format == SFlowCounterRecord.COUNTER_DATA_GENERIC_INTERFACE:
self.counter = GenericInterfaceCounters(unpacker_counter_data)
elif self.counter_format == SFlowCounterRecord.COUNTER_DATA_ETHERNET_INTERFACE:
self.counter = EthernetInterfaceCounters(unpacker_counter_data)
elif self.counter_format == SFlowCounterRecord.COUNTER_DATA_TOKEN_RING:
pass
self.counter = TokenRingCounters(unpacker_counter_data)
elif self.counter_format == SFlowCounterRecord.COUNTER_DATA_VG_INTERFACE:
pass
self.counter = VgInterfaceCounters(unpacker_counter_data)
elif self.counter_format == SFlowCounterRecord.COUNTER_DATA_VLAN:
self.counter = VlanCounters(unpacker_counter_data)
elif self.counter_format == SFlowCounterRecord.COUNTER_DATA_PROCESSOR:
self.counter = ProcessorCounters(unpacker_counter_data)
else:
logging.debug('read_flow_record:Unimplemented data_format (%d)' % self.flow_format)
def _parse_raw_generic_interface_counters(self, unpacker: Unpacker):
# Unpack Generic Interface Counters
# unsigned int ifIndex;
# unsigned int ifType;
# unsigned hyper ifSpeed;
# unsigned int ifDirection; derived from MAU MIB (RFC 2668)
# 0 = unkown, 1=full-duplex, 2=half-duplex,
# 3 = in, 4=out
# unsigned int ifStatus; bit field with the following bits assigned
# bit 0 = ifAdminStatus (0 = down, 1 = up)
# bit 1 = ifOperStatus (0 = down, 1 = up)
# unsigned hyper ifInOctets;
# unsigned int ifInUcastPkts;
# unsigned int ifInMulticastPkts;
# unsigned int ifInBroadcastPkts;
# unsigned int ifInDiscards;
# unsigned int ifInErrors;
# unsigned int ifInUnknownProtos;
# unsigned hyper ifOutOctets;
# unsigned int ifOutUcastPkts;
# unsigned int ifOutMulticastPkts;
# unsigned int ifOutBroadcastPkts;
# unsigned int ifOutDiscards;
# unsigned int ifOutErrors;
# unsigned int ifPromiscuousMode;
self.if_index = unpacker.unpack_uint()
self.if_type = unpacker.unpack_uint()
self.if_speed = unpacker.unpack_uhyper()
self.if_direction = unpacker.unpack_uint()
self.if_status = unpacker.unpack_uint()
self.if_in_octets = unpacker.unpack_uhyper()
self.if_in_ucasts = unpacker.unpack_uint()
self.if_in_mcasts = unpacker.unpack_uint()
self.if_in_bcasts = unpacker.unpack_uint()
self.if_in_discards = unpacker.unpack_uint()
self.if_in_errors = unpacker.unpack_uint()
self.if_in_unknown_protos = unpacker.unpack_uint()
self.if_out_octets = unpacker.unpack_uhyper()
self.if_out_ucasts = unpacker.unpack_uint()
self.if_out_mcasts = unpacker.unpack_uint()
self.if_out_bcasts = unpacker.unpack_uint()
self.if_out_discards = unpacker.unpack_uint()
self.if_out_errors = unpacker.unpack_uint()
self.if_promiscuous_mode = unpacker.unpack_uint()
def _parse_raw_expanded_sflow_flow_sample(self, unpacker: Unpacker):
self.sequence_number = unpacker.unpack_uint()
self.source_id['type'] = unpacker.unpack_uint()
self.source_id['index'] = unpacker.unpack_uint()
self.sampling_rate = unpacker.unpack_uint()
self.sample_pool = unpacker.unpack_uint()
self.drops = unpacker.unpack_uint()
self.input_if['format'] = unpacker.unpack_uint()
self.input_if['value'] = unpacker.unpack_uint()
self.output_if['format'] = unpacker.unpack_uint()
self.output_if['value'] = unpacker.unpack_uint()
flows_in_sample = unpacker.unpack_uint()
for _ in range(flows_in_sample):
self.flows.append(SFlowFlowRecord(unpacker))
def _parse_raw_ethernet_interface_counters(self, unpacker: Unpacker):
# Unpack ethernet_counters structure
# unsigned int dot3_stats_alignment_errors;
# unsigned int dot3_stats_fcs_errors;
# unsigned int dot3_stats_single_collision_frames;
# unsigned int dot3_stats_multiple_collision_frames;
# unsigned int dot3_stats_sqe_test_errors;
# unsigned int dot3_stats_deferred_transmissions;
# unsigned int dot3_stats_late_collisions;
# unsigned int dot3_stats_excessive_collisions;
# unsigned int dot3_stats_internal_mac_transmit_errors;
# unsigned int dot3_stats_carrier_sense_errors;
# unsigned int dot3_stats_frame_too_longs;
# unsigned int dot3_stats_internal_mac_receive_errors;
# unsigned int dot3_stats_symbol_errors;
self.dot3_stats_alignment_errors = unpacker.unpack_uint()
self.dot3_stats_fcs_errors = unpacker.unpack_uint()
self.dot3_stats_single_collision_frames = unpacker.unpack_uint()
self.dot3_stats_multiple_collision_frames = unpacker.unpack_uint()
self.dot3_stats_sqe_test_errors = unpacker.unpack_uint()
self.dot3_stats_deferred_transmissions = unpacker.unpack_uint()
self.dot3_stats_late_collisions = unpacker.unpack_uint()
self.dot3_stats_excessive_collisions = unpacker.unpack_uint()
self.dot3_stats_internal_mac_transmit_errors = unpacker.unpack_uint()
self.dot3_stats_carrier_sense_errors = unpacker.unpack_uint()
self.dot3_stats_frame_too_longs = unpacker.unpack_uint()
self.dot3_stats_internal_mac_receive_errors = unpacker.unpack_uint()
self.dot3_stats_symbol_errors = unpacker.unpack_uint()
class TprTopology:
funcNames = [
"bonds", "g96bonds", "morse", "cubicbonds", "connbonds",
"harmonic", "fenebonds", "tabbonds", "tabbondsnc",
"angles", "g96angles", "cross_bond_bond",
"cross_bond_angle", "urey_bradley", "qangles",
"tabangles", "pdihs", "rbdihs", "fourdihs", "idihs",
"pidihs", "tabdihs", "lj14", "coul14", "ljc14_q",
"ljc_nb", "lj_sr", "bham", "lj_lr", "bham_lr",
"dispcorr", "coul_sr", "coul_lr", "rf_excl",
"coul_recip", "dpd", "polarization", "waterpol",
"thole", "posres", "disres", "drviol", "orires",
"ordev", "angres", "angresz", "dihres", "dihviol",
"constr", "constrnc", "settle", "vsite2", "vsite3",
"vsite3fd", "vsite3fad", "vsite3out", "vsite4fd",
"vsite4fdn", "vsiten", "com_pull", "eqm", "epot",
"ekin", "etot", "econs", "temp", "pres", "dv/dl",
"dk/dl", "dg/dl_con"
]
def __init__(self, topology):
from OpenSave import osOpen
topFile = osOpen(topology, 'rb')
import os
self.topFileSize = os.stat(topology).st_size
from xdrlib import Unpacker
self.fileString = FileString(topFile, 0, self.topFileSize)
self.xdr = Unpacker(self.fileString)
version = self._readHeader()
self._readTopology(version)
def _do_block(self, version):
if version < 44:
for i in range(256):
self.xdr.unpack_uint()
blockNR = self.xdr.unpack_uint()
if version < 51:
blockNRA = self.xdr.unpack_uint()
for i in range(blockNR + 1):
self.xdr.unpack_uint()
if version < 51:
for i in range(blockNRA):
self.xdr.unpack_uint()
def _do_blocka(self, version):
if version < 44:
for i in range(256):
self.xdr.unpack_uint()
blockNR = self.xdr.unpack_uint()
blockNRA = self.xdr.unpack_uint()
for i in range(blockNR + blockNRA + 1):
self.xdr.unpack_uint()
def _do_ffparams(self, version):
self.funcNumber = {}
for i, fn in enumerate(self.funcNames):
self.funcNumber[fn] = i
self.funcNumberUpdate = [
(20, "cubicbonds"), (20, "connbonds"), (20, "harmonic"),
(34, "fenebonds"), (43, "tabbonds"),
(43, "tabbondsnc"), (30, "cross_bond_bond"),
(30, "cross_bond_angle"), (30, "urey_bradley"),
(34, "qangles"), (43, "tabangles"),
(26, "fourdihs"), (26, "pdihs"), (43, "tabdihs"),
(41, "ljc14_q"), (41, "ljc_nb"),
(32, "bham_lr"), (32, "rf_excl"), (32, "coul_recip"),
(46, "dpd"), (30, "polarization"), (36, "thole"),
(22, "drviol"), (22, "orires"), (22, "ordev"),
(26, "dihres"), (26, "dihviol"),
(49, "vsite4fdn"), (50, "vsiten"), (46, "com_pull"),
(20, "eqm"), (46, "econs"), (54, "dg/dl_con")
]
self.xdr.unpack_uint()
if version < 57:
self.xdr.unpack_uint()
ntypes = self.xdr.unpack_uint()
functions = []
for i in range(ntypes):
fnum = self.xdr.unpack_uint()
for vn, funcName in self.funcNumberUpdate:
if version < vn \
and fnum >= self.funcNumber[funcName]:
fnum += 1
funcName = self.funcNames[fnum]
functions.append(funcName)
if version >= 57:
self.unpackFloatFunc()
for i, funcName in enumerate(functions):
if funcName in ["angles", "g96angles", "bonds",
"g96bonds", "harmonic", "idihs",
"cross_bond_angle", "urey_bradley",
"thole", "lj14", "ljc_nb"]:
floatInts = "rrrr"
elif funcName in ["fenebonds", "lj_sr", "constr",
"constrnc", "settle", "vsite3",
"vsite3fd", "vsite3fad"]:
floatInts = "rr"
elif funcName in ["cross_bond_bond", "bham", "morse",
"cubic_bonds", "vsite3out", "vsite4fd",
"vsite4fdn"]:
floatInts = "rrr"
elif funcName in ["qangles", "waterpol"]:
floatInts = "rrrrrr"
elif funcName in ["connbonds"]:
floatInts = ""
elif funcName in ["polarization", "vsite2"]:
floatInts = "r"
elif funcName in ["pdihs", "pidihs"]:
floatInts = "rrrri"
elif funcName in ["disres"]:
floatInts = "iirrrr"
elif funcName in ["orires"]:
floatInts = "iiirrr"
elif funcName in ["dihres"]:
floatInts = "iirrr"
elif funcName in ["posres"]:
if version < 27:
floatInts = "rrrrrr"
else:
floatInts = "rrrrrrrrrrrr"
elif funcName in ["rbdihs"]:
if version >= 25:
floatInts = "rrrrrrrrrrrr"
else:
floatInts = "rrrrrr"
elif funcName in ["fourdihs"]:
floatInts = "rrrrrrrrrrrr"
elif funcName in ["tabbonds", "tabbondsnc", "tabangles",
"tabdihs"]:
floatInts = "rir"
elif funcName in ["ljc14_q"]:
floatInts = "rrrrr"
elif funcName in ["angres", "angresz"]:
if version < 42:
floatInts = "rrrr"
else:
floatInts = "rrrri"
elif funcName in ["vsiten"]:
floatInts = "ir"
else:
raise ValueError("Don't know correct"
" parameters for '%s' function"
% funcName)
for fi in floatInts:
if fi == 'r':
t = self.unpackFloatFunc()
else:
t = self.xdr.unpack_uint()
def _do_ilists(self, version):
# bonds is first func, at least
seen = set()
self.bonds = []
checklist = set()
def addBond(a1, a2):
if (a1, a2) in checklist:
return
self.bonds.append((a1, a2))
checklist.add((a1, a2))
checklist.add((a2, a1))
seen.add(a1)
seen.add(a2)
for fname in self.funcNames:
for uv, uname in self.funcNumberUpdate:
if version < uv and fname == uname:
skip = True
break
else:
skip = False
if skip:
continue
if version < 44:
for i in range(256):
self.xdr.unpack_uint()
nr = self.xdr.unpack_uint()
if fname == "bonds":
for i in range(nr/3):
self.xdr.unpack_uint()
a1index = self.xdr.unpack_uint()
a2index = self.xdr.unpack_uint()
addBond(a1index, a2index)
elif fname in ["angles", "g96angles"]:
for i in range(nr/4):
self.xdr.unpack_uint()
a1index = self.xdr.unpack_uint()
a2index = self.xdr.unpack_uint()
a3index = self.xdr.unpack_uint()
addBond(a1index, a2index)
addBond(a2index, a3index)
else:
for i in range(nr):
self.xdr.unpack_uint()
# okay, the above doesn't hook up water (and maybe methane?)...
hyds = {}
heavys = {}
for i, element in enumerate(self.elements):
if i in seen:
continue
key = self.resNums[i]
if element.number == 1:
hyds.setdefault(key, []).append(i)
else:
heavys.setdefault(key, []).append(i)
for i, heavysList in heavys.items():
if len(heavysList) != 1 or i not in hyds:
# beats me what to do
continue
heavy = heavysList[0]
for hyd in hyds[i]:
self.bonds.append((heavy, hyd))
self.molInfo.append((self.atomNames, self.resNames,
self.resIndices, self.bonds, self.elements))
def _readHeader(self):
# version string
replyobj.info("%s\n" % self._readString())
realSize = self.xdr.unpack_uint()
if realSize == 4:
self.unpackFloatFunc = self.xdr.unpack_float
replyobj.info("using floats\n")
elif realSize == 8:
self.unpackFloatFunc = self.xdr.unpack_double
replyobj.info("using doubles\n")
else:
raise ValueError("Floating-point values in .tpr file"
" are not the same as either single-precision"
" or double-precision floating point on this"
" machine")
version = self.xdr.unpack_uint()
if version >= 26:
generation = self.xdr.unpack_uint()
else:
generation = 0
replyobj.info("version %d, generation %d\n"
% (version, generation))
natoms = self.xdr.unpack_uint()
replyobj.info("%d atoms\n" % natoms)
if version >= 28:
tempCouplingGroups = self.xdr.unpack_uint()
curStep = self.xdr.unpack_uint()
curTime = self.unpackFloatFunc()
curLambda = self.unpackFloatFunc()
hasInputRec = self.xdr.unpack_uint()
hasTopology = self.xdr.unpack_uint()
if not hasTopology:
raise ValueError(
".tpr file does not have topology section")
hasCoord = self.xdr.unpack_uint()
hasVelocities = self.xdr.unpack_uint()
hasForces = self.xdr.unpack_uint()
hasBbox = self.xdr.unpack_uint()
if hasBbox:
for i in range(9):
self.unpackFloatFunc()
if version >= 51:
for i in range(9):
self.unpackFloatFunc()
if version >= 28:
for i in range(9):
self.unpackFloatFunc()
if version < 56:
for i in range(9):
self.unpackFloatFunc()
if version >= 28 and tempCouplingGroups > 0:
for i in range(tempCouplingGroups):
self.unpackFloatFunc()
self.unpackFloatFunc()
if version < 26 and hasInputRec:
raise ValueError("Cannot read version 26 or earlier"
" .tpr files")
return version
def _readString(self):
strlen = self.xdr.unpack_uint()
self.xdr.unpack_uint()
return self.xdr.unpack_fstring(strlen-1)
def _readTopology(self, version):
self.molInfo = []
numStrings = self.xdr.unpack_uint()
symbols = []
for i in range(numStrings):
symbols.append(self._readString())
name = symbols[self.xdr.unpack_uint()]
replyobj.info("%s\n" % name)
if version >= 57:
self._do_ffparams(version)
numMolTypes = self.xdr.unpack_uint()
else:
numMolTypes = 1
from Trajectory import determineElementFromMass
for i in range(numMolTypes):
if version >= 57:
molName = symbols[self.xdr.unpack_uint()]
replyobj.info("mol name: %s\n" % molName)
numAtoms = self.xdr.unpack_uint()
replyobj.info("%d atoms\n" % numAtoms)
numResidues = self.xdr.unpack_uint()
replyobj.info("%d residues\n" % numResidues)
if version < 57:
numGroupNames = self.xdr.unpack_uint()
if version < 23:
numGroups = 8
elif version < 39:
numGroups = 9
else:
numGroups = 10
self.elements = []
self.resNums = []
for i in range(numAtoms):
mass = self.unpackFloatFunc()
self.elements.append(
determineElementFromMass(mass))
charge = self.unpackFloatFunc()
self.unpackFloatFunc()
self.unpackFloatFunc()
for j in range(3):
self.xdr.unpack_uint()
resNum = self.xdr.unpack_uint()
self.resNums.append(resNum)
if version >= 52:
self.xdr.unpack_uint()
if version < 57:
for j in range(numGroups):
self.xdr.unpack_uint()
self.atomNames = [symbols[self.xdr.unpack_uint()]
for i in range(numAtoms)]
for i in range(numAtoms*2):
self.xdr.unpack_uint()
self.resNames = [symbols[self.xdr.unpack_uint()]
for i in range(numResidues)]
self.resIndices = []
curResNum = None
for i, rn in enumerate(self.resNums):
if curResNum != rn:
self.resIndices.append(i+1)
curResNum = rn
if version < 57:
# group names
for i in range(numGroupNames):
gn = symbols[self.xdr.unpack_uint()]
# group contents
for i in range(numGroups):
grpN = self.xdr.unpack_uint()
for j in range(grpN):
self.xdr.unpack_uint()
if version >= 57:
self._do_ilists(version)
self._do_block(version)
self._do_blocka(version)
if version >= 57:
self.atomNames = []
self.resNames = []
self.resIndices = []
self.bonds = []
self.elements = []
numMolBlocks = self.xdr.unpack_uint()
for i in range(numMolBlocks):
self.xdr.unpack_uint()
repeat = self.xdr.unpack_uint()
self.xdr.unpack_uint()
# position restraints
for j in range(2):
npr = self.xdr.unpack_uint()
for k in range(npr):
self.unpackFloatFunc()
self.unpackFloatFunc()
self.unpackFloatFunc()
atomNames, resNames, resIndices, bonds, \
elements = self.molInfo[i]
for j in range(repeat):
aBase = len(self.atomNames)
self.atomNames.extend(atomNames)
self.resNames.extend(resNames)
for ri in resIndices:
self.resIndices.append(
aBase + ri)
for a1, a2 in bonds:
self.bonds.append((aBase + a1,
aBase + a2))
self.elements.extend(elements)
self.xdr.unpack_uint()
# atom types
if version > 25:
nr = self.xdr.unpack_uint()
# radii
for i in range(nr):
self.unpackFloatFunc()
# volume
for i in range(nr):
self.unpackFloatFunc()
# surface tension
for i in range(nr):
self.unpackFloatFunc()
if version >= 40:
# atom number
for i in range(nr):
self.xdr.unpack_uint()
if version < 57:
self._do_ffparams(version)
if version >= 54:
self.unpackFloatFunc()
self._do_ilists(version)
