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Closed
Created by Tiago Peixoto@count0Maintainer

Pickle Objects

Hi, during my work with graph-tool, I experienced a problem with the graph.save() method. My vertexes have a vertex property of type python::object. Those objects can not be pickled with the standard pickle protocol (protocol 0). The reason for that is, that the objects include the "dnspython" package which uses sockets. So I get the following error stack trace:

Traceback (most recent call last):
  File "Main.py", line 427, in <module>
    Main().control()
  File "Main.py", line 77, in control
    self.saveGraph()
  File "Main.py", line 409, in saveGraph
    self.graph.save(input)
  File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1362, in save
    self.__graph.WriteToFile(file_name, None, file_format, props)
  File "/usr/lib/python2.7/dist-packages/graph_tool/io.py", line 62, in pickler
    pickle.dump(obj, sstream)
  File "/usr/lib/python2.7/pickle.py", line 1370, in dump
    Pickler(file, protocol).dump(obj)
  File "/usr/lib/python2.7/pickle.py", line 224, in dump
    self.save(obj)
  File "/usr/lib/python2.7/pickle.py", line 331, in save
    self.save_reduce(obj=obj, *rv)
  File "/usr/lib/python2.7/pickle.py", line 419, in save_reduce
    save(state)
  File "/usr/lib/python2.7/pickle.py", line 286, in save
    f(self, obj) # Call unbound method with explicit self
  File "/usr/lib/python2.7/pickle.py", line 649, in save_dict
    self._batch_setitems(obj.iteritems())
  File "/usr/lib/python2.7/pickle.py", line 663, in _batch_setitems
    save(v)
  File "/usr/lib/python2.7/pickle.py", line 306, in save
    rv = reduce(self.proto)
  File "/usr/lib/python2.7/copy_reg.py", line 77, in _reduce_ex
    raise TypeError("a class that defines __slots__ without "
TypeError: a class that defines __slots__ without defining __getstate__ cannot be pickled

I fixed that issue by changing the method "pickler" in io.py from:

def pickler(stream, obj):
    sstream = StringIO()
    pickle.dump(obj, sstream)
    stream.write(base64.b64encode(sstream.getvalue()))

to:

def pickler(stream, obj):
    sstream = StringIO()
    pickle.dump(obj, sstream, -1)
    stream.write(base64.b64encode(sstream.getvalue()))

Doing so, pickle will use the highest protocol available. Since this fixed the problem, I was thinking if this change to the method would hurt anything and if it would make sense, to include this change in the next release of graph-tool. What do you think? I'm not sure, if I might be missing something.

Hope to hear from you soon,

Felix