# Copyright (c) 2014, SRI International
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# the following conditions:
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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This module handles basic operations for receiving and sending messages via a
network socket to Pathway Tools.
No major class is defined in this file, but only toplevel functions and
some simple classes for errors handling.
import socket as so
Receive the entire message sent by Pathway Tools on socket s.
The message starts with a single character type, which is either 'A'
or 'L'. The 'A' time is used without providing a length but can take
longer to receive because it uses a timeout technique to read the entire
message. The 'L' type assumes that the length of the message, in characters,
is given on the next 10 characters as an integer. The message length is the
number of characters after these 10 characters.
s, an open network socket.
the message received on socket s as a string.
print 'recvAll ...'
# Get the type of message which is one character long.
type = s.recv(1)
# print "type ", type
if type == 'A':
# The length of the message is not given, use time out approach.
elif type == 'L':
# The next 10 characters give the length.
lengthMsg = int(recvFixedLength(s, 10))
print "lengthMsg ", lengthMsg
return recvFixedLength(s, lengthMsg)
# Something is broken on the server side, so
# use recv with a long timeout to try flushing
# the sent message.
return recvTimeOut(s, timeOut=5)
[docs]def sendAll(s, query):
sent_len = 0
query_len = len(query)
while sent_len < query_len:
nb_chars = s.send(query[sent_len:])
if nb_chars == 0:
raise PythonCycError("Connection to Pathway Tools broke while sending query %s." % query)
sent_len = sent_len + nb_chars
[docs]def recvFixedLength(s, lengthMsg):
Receive a fixed length message on socket s.
lengthMsg, an integer, which is the length in characters of the
message to receive.
the message received as a string.
pieces = 
nbBytesRecv = 0
while nbBytesRecv < lengthMsg:
piece = s.recv(min(lengthMsg - nbBytesRecv, 4096))
if piece == '':
# Give up now because nothing was received.
nbBytesRecv = nbBytesRecv + len(piece)
# print 'Fixed receive: ', ''.join(pieces)
[docs]def recvTimeOut(socket, timeOut=2):
Receive a message of unknown length on socket. While receiving a message, if no
more characters are sent on socket after timeOut seconds, it is
assumed that the message has ended. Therefore, it will always, whatever the lenght
of the message, take at least timeOut seconds to execute this method. If no character
is received after 60 seconds, this method returns with an empty message.
socket, an open network socket.
timeOut, number of seconds before timing out between fragments of the received
The received message, as a string, on socket.
# Keep each received packet in an array.
pieces = 
# Keep track of time between recvs.
begin = time.time()
# If we started to get data and the timeOut occurs,
# we assume that Pathway Tools sent everything.
if pieces and time.time() - begin > timeOut:
elif time.time() - begin > 60:
# Try to receive some text.
data = socket.recv(4096)
# Reset beginning time for next recv.
begin = time.time()
# Slow down in case timeOut is small.
# Join all the pieces together.
if pieces == :
# Call a PTools function synchronously for any PGDB.
"""Error generated by one of the module of PythonCyc due to an incorrect
use of its methods or functions.