"""
Read graphs in GML format.
See http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html
for format specification.
Example graphs in GML format:
http://www-personal.umich.edu/~mejn/netdata/
Requires pyparsing: http://pyparsing.wikispaces.com/
"""
__author__ = """Aric Hagberg (hagberg@lanl.gov)"""
# Copyright (C) 2008-2009 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
__all__ = ['read_gml', 'parse_gml', 'write_gml']
import networkx as nx
from networkx.exception import NetworkXException,NetworkXError
from networkx.utils import _get_fh,is_string_like
def read_gml(path):
"""Read graph in GML format from path.
Parameters
----------
path : filename or filehandle
The filename or filehandle to read from.
Returns
-------
G : MultiGraph or MultiDiGraph
Raises
------
ImportError
If the pyparsing module is not available.
See Also
--------
write_gml, parse_gml
Notes
-----
This doesn't implement the complete GML specification for
nested attributes for graphs, edges, and nodes.
Requires pyparsing: http://pyparsing.wikispaces.com/
References
----------
GML specification:
http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_gml(G,'test.gml')
>>> H=nx.read_gml('test.gml')
"""
fh=_get_fh(path,mode='r')
G=parse_gml(fh)
return G
def parse_gml(lines):
"""Parse GML graph from a string or iterable.
Parameters
----------
lines : string or iterable
Data in GML format.
Returns
-------
G : MultiGraph or MultiDiGraph
Raises
------
ImportError
If the pyparsing module is not available.
See Also
--------
write_gml, read_gml
Notes
-----
This stores nested GML attributes as dicts in the
NetworkX Graph attribute structures.
Requires pyparsing: http://pyparsing.wikispaces.com/
References
----------
GML specification:
http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_gml(G,'test.gml')
>>> fh=open('test.gml')
>>> H=nx.read_gml(fh)
"""
try:
from pyparsing import ParseException
except ImportError:
raise ImportError, \
"Import Error: not able to import pyparsing: http://pyparsing.wikispaces.com/"
try:
data = "".join(lines)
gml = pyparse_gml()
tokens =gml.parseString(data)
except ParseException, err:
print err.line
print " "*(err.column-1) + "^"
print err
raise
# function to recursively make dicts of key/value pairs
def wrap(tok):
listtype=type(tok)
result={}
for k,v in tok:
if type(v)==listtype:
result[k]=wrap(v)
else:
result[k]=v
return result
# storage areas
node_labels={}
graphs=[]
nodes=[]
edges=[]
directed=False
# process parsed info
tokenlist=tokens.asList()
for k,v in tokenlist:
if k=="node":
vdict=wrap(v)
id=vdict['id']
label=vdict['label']
node_labels[id]=label
nodes.append((label,vdict))
elif k=="edge":
vdict=wrap(v)
edges.append((vdict.pop('source'), vdict.pop('target'), vdict))
else:
if type(v)==type(tokenlist):
graphs.append((k,wrap(v)))
else:
graphs.append((k,v))
if k=="directed" and v==1:
directed=True
# Now create the Graph
if directed:
G=nx.MultiDiGraph()
else:
G=nx.MultiGraph()
G.graph.update(graphs)
G.add_nodes_from(nodes)
G.add_edges_from( (node_labels[s],node_labels[t],d) for s,t,d in edges)
return G
graph = None
def pyparse_gml():
"""A pyparsing tokenizer for GML graph format.
This is not intended to be called directly.
See Also
--------
write_gml, read_gml, parse_gml
Notes
-----
This doesn't implement the complete GML specification for
nested attributes for graphs, edges, and nodes.
"""
global graph
try:
from pyparsing import \
Literal, CaselessLiteral, Word, Forward,\
ZeroOrMore, Group, Dict, Optional, Combine,\
ParseException, restOfLine, White, alphas, alphanums, nums,\
OneOrMore,quotedString,removeQuotes,dblQuotedString
except ImportError:
raise ImportError, \
"Import Error: not able to import pyparsing: http://pyparsing.wikispaces.com/"
if not graph:
lbrack = Literal("[").suppress()
rbrack = Literal("]").suppress()
pound = ("#")
comment = pound + Optional( restOfLine )
white = White(" \t\n")
point = Literal(".")
e = CaselessLiteral("E")
integer = Word(nums).setParseAction(lambda s,l,t:[ int(t[0])])
real = Combine( Word("+-"+nums, nums )+
Optional(point+Optional(Word(nums)))+
Optional(e+Word("+-"+nums, nums))).setParseAction(
lambda s,l,t:[ float(t[0]) ])
key = Word(alphas,alphanums+'_')
value_atom = integer^real^Word(alphanums)^quotedString.setParseAction(removeQuotes)
value = Forward() # to be defined later with << operator
keyvalue = Group(key+value)
value << (value_atom | Group( lbrack + ZeroOrMore(keyvalue) + rbrack ))
node = Group(Literal("node") + lbrack + Group(OneOrMore(keyvalue)) + rbrack)
edge = Group(Literal("edge") + lbrack + Group(OneOrMore(keyvalue)) + rbrack)
creator = Group(Literal("Creator")+ Optional( restOfLine ))
version = Group(Literal("Version")+ Optional( restOfLine ))
graphkey = Literal("graph").suppress()
graph = Optional(creator)+Optional(version)+\
graphkey + lbrack + ZeroOrMore( (node|edge|keyvalue) ) + rbrack
graph.ignore(comment)
return graph
def write_gml(G, path):
"""
Write the graph G in GML format to the file or file handle path.
Parameters
----------
path : filename or filehandle
The filename or filehandle to write. Filenames ending in
.gz or .gz2 will be compressed.
See Also
--------
read_gml, parse_gml
Notes
-----
The output file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> G=nx.path_graph(4)
>>> import codecs
>>> fh=codecs.open('test.gml','w',encoding='iso8859-1')# use iso8859-1
>>> nx.write_gml(G,fh)
GML specifications indicate that the file should only use
7bit ASCII text encoding.iso8859-1 (latin-1).
For nested attributes for graphs, nodes, and edges you should
use dicts for the value of the attribute.
Examples
---------
>>> G=nx.path_graph(4)
>>> nx.write_gml(G,"test.gml")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.gml",'w')
>>> nx.write_gml(G,fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_gml(G,"test.gml.gz")
"""
fh=_get_fh(path,mode='w')
# check for attributes or assign empty dict
if hasattr(G,'graph_attr'):
graph_attr=G.graph_attr
else:
graph_attr={}
if hasattr(G,'node_attr'):
node_attr=G.node_attr
else:
node_attr={}
indent=2*' '
count=iter(range(G.number_of_nodes()))
node_id={}
dicttype=type({})
# recursively make dicts into gml brackets
def listify(d,indent,indentlevel):
result='[ \n'
dicttype=type({})
for k,v in d.iteritems():
if type(v)==dicttype:
v=listify(v,indent,indentlevel+1)
result += indentlevel*indent+"%s %s\n"%(k,v)
return result+indentlevel*indent+"]"
fh.write("graph [\n")
if G.is_directed():
fh.write(indent+"directed 1\n")
# write graph attributes
for k,v in G.graph.items():
if is_string_like(v):
v='"'+v+'"'
elif type(v)==dicttype:
v=listify(v,indent,1)
fh.write(indent+"%s %s\n"%(k,v))
# write nodes
for n in G:
fh.write(indent+"node [\n")
# get id or assign number
nid=G.node[n].get('id',count.next())
node_id[n]=nid
fh.write(2*indent+"id %s\n"%nid)
fh.write(2*indent+"label \"%s\"\n"%n)
if n in G:
for k,v in G.node[n].items():
if is_string_like(v): v='"'+v+'"'
if type(v)==dicttype: v=listify(v,indent,2)
if k=='id': continue
fh.write(2*indent+"%s %s\n"%(k,v))
fh.write(indent+"]\n")
# write edges
for u,v,edgedata in G.edges_iter(data=True):
# try to guess what is on the edge and do something reasonable
fh.write(indent+"edge [\n")
fh.write(2*indent+"source %s\n"%node_id[u])
fh.write(2*indent+"target %s\n"%node_id[v])
for k,v in edgedata.items():
if k=='source': continue
if k=='target': continue
if is_string_like(v): v='"'+v+'"'
if type(v)==dicttype: v=listify(v,indent,2)
fh.write(2*indent+"%s %s\n"%(k,v))
fh.write(indent+"]\n")
fh.write("]")
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