Warning
This documents an unmaintained version of NetworkX. Please upgrade to a maintained version and see the current NetworkX documentation.
Source code for networkx.readwrite.gml
# encoding: utf-8
"""
Read graphs in GML format.
"GML, the G>raph Modelling Language, is our proposal for a portable
file format for graphs. GML's key features are portability, simple
syntax, extensibility and flexibility. A GML file consists of a
hierarchical key-value lists. Graphs can be annotated with arbitrary
data structures. The idea for a common file format was born at the
GD'95; this proposal is the outcome of many discussions. GML is the
standard file format in the Graphlet graph editor system. It has been
overtaken and adapted by several other systems for drawing graphs."
See http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html
Requires pyparsing: http://pyparsing.wikispaces.com/
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/
"""
from __future__ import unicode_literals
__author__ = """Aric Hagberg (hagberg@lanl.gov)"""
# Copyright (C) 2008-2010 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', 'generate_gml', 'write_gml']
from cgi import escape
import networkx as nx
from networkx.exception import NetworkXError
from networkx.utils import is_string_like, open_file
##
# Removes HTML or XML character references and entities from a text string.
#
# @param text The HTML (or XML) source text (as a unicode object)
# @return The plain text, as a Unicode string, if necessary.
#
# Source: http://effbot.org/zone/re-sub.htm#unescape-html
#
import re
try:
import htmlentitydefs
except ImportError:
# Python 3.x
import html.entities as htmlentitydefs
def unescape(text):
def fixup(m):
text = m.group(0)
if text[:2] == "&#":
# character reference
try:
if text[:3] == "&#x":
return unichr(int(text[3:-1], 16))
else:
return unichr(int(text[2:-1]))
except ValueError:
pass
else:
# named entity
try:
text = unichr(htmlentitydefs.name2codepoint[text[1:-1]])
except KeyError:
pass
return text # leave as is
return re.sub("&#?\w+;", fixup, text)
@open_file(0, mode='rb')
[docs]def read_gml(path, relabel=False):
"""Read graph in GML format from path.
Parameters
----------
path : filename or filehandle
The filename or filehandle to read from.
relabel : bool, optional
If True use the GML node label attribute for node names otherwise use
the node id.
Returns
-------
G : MultiGraph or MultiDiGraph
Raises
------
ImportError
If the pyparsing module is not available.
See Also
--------
write_gml, parse_gml
Notes
-----
Requires pyparsing: http://pyparsing.wikispaces.com/
The GML specification says that files should be ASCII encoded, with any
extended ASCII characters (iso8859-1) appearing as HTML character entities.
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')
"""
lines = (unescape(line.decode('ascii')) for line in path)
G = parse_gml(lines, relabel=relabel)
return G
[docs]def parse_gml(lines, relabel=True):
"""Parse GML graph from a string or iterable.
Parameters
----------
lines : string or iterable
Data in GML format.
relabel : bool, optional
If True use the GML node label attribute for node names otherwise use
the node id.
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 dictionaries in the
NetworkX graph, node, and edge attribute structures.
Requires pyparsing: http://pyparsing.wikispaces.com/
References
----------
GML specification:
http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html
"""
try:
from pyparsing import ParseException
except ImportError:
try:
from matplotlib.pyparsing import ParseException
except:
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 as 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[str(k)] = wrap(v)
else:
result[str(k)] = v
return result
# Set flag
multigraph = False
# but assume multigraphs to start
if tokens.directed == 1:
G=nx.MultiDiGraph()
else:
G=nx.MultiGraph()
for k,v in tokens.asList():
if k=="node":
vdict=wrap(v)
node=vdict['id']
G.add_node(node,attr_dict=vdict)
elif k=="edge":
vdict=wrap(v)
source=vdict.pop('source')
target=vdict.pop('target')
if G.has_edge(source,target):
multigraph=True
G.add_edge(source,target,attr_dict=vdict)
else:
G.graph[k]=v
# switch to Graph or DiGraph if no parallel edges were found.
if not multigraph:
if G.is_directed():
G=nx.DiGraph(G)
else:
G=nx.Graph(G)
if relabel:
# relabel, but check for duplicate labels first
mapping=[(n,d['label']) for n,d in G.node.items()]
x,y=zip(*mapping)
if len(set(y))!=len(G):
raise NetworkXError('Failed to relabel nodes: '
'duplicate node labels found. '
'Use relabel=False.')
G=nx.relabel_nodes(G,dict(mapping))
return G
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
"""
try:
from pyparsing import \
Literal, CaselessLiteral, Word, Forward,\
ZeroOrMore, Group, Dict, Optional, Combine,\
ParseException, restOfLine, White, alphas, alphanums, nums,\
OneOrMore,quotedString,removeQuotes,dblQuotedString, Regex
except ImportError:
try:
from matplotlib.pyparsing import \
Literal, CaselessLiteral, Word, Forward,\
ZeroOrMore, Group, Dict, Optional, Combine,\
ParseException, restOfLine, White, alphas, alphanums, nums,\
OneOrMore,quotedString,removeQuotes,dblQuotedString, Regex
except:
raise ImportError('pyparsing not found',
'http://pyparsing.wikispaces.com/')
lbrack = Literal("[").suppress()
rbrack = Literal("]").suppress()
pound = ("#")
comment = pound + Optional( restOfLine )
integer = Word(nums+'-').setParseAction(lambda s,l,t:[ int(t[0])])
real = Regex(r"[+-]?\d+\.\d*([eE][+-]?\d+)?").setParseAction(
lambda s,l,t:[ float(t[0]) ])
dblQuotedString.setParseAction( removeQuotes )
key = Word(alphas,alphanums+'_')
value_atom = (real | integer | Word(alphanums) | dblQuotedString)
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 = Dict (Optional(creator)+Optional(version)+\
graphkey + lbrack + ZeroOrMore( (node|edge|keyvalue) ) + rbrack )
graph.ignore(comment)
return graph
[docs]def generate_gml(G):
"""Generate a single entry of the graph G in GML format.
Parameters
----------
G : NetworkX graph
Returns
-------
lines: string
Lines in GML format.
Notes
-----
This implementation does not support all Python data types as GML
data. Nodes, node attributes, edge attributes, and graph
attributes must be either dictionaries or single stings or
numbers. If they are not an attempt is made to represent them as
strings. For example, a list as edge data
G[1][2]['somedata']=[1,2,3], will be represented in the GML file
as::
edge [
source 1
target 2
somedata "[1, 2, 3]"
]
"""
# recursively make dicts into gml brackets
def listify(d,indent,indentlevel):
result='[ \n'
for k,v in d.items():
result += (indentlevel+1)*indent + \
string_item(k,v,indentlevel*indent)+'\n'
return result+indentlevel*indent+"]"
def string_item(k,v,indent):
# try to make a string of the data
if type(v) == dict:
v = listify(v, indent, 2)
elif is_string_like(v):
v = '"{0}"'.format(escape(v, quote=True))
#v = '"{0}"'.format(v, quote=True)
elif type(v) == bool:
v = int(v)
return "{0} {1}".format(k,v)
# 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(len(G)))
node_id = {}
yield "graph ["
if G.is_directed():
yield indent + "directed 1"
# write graph attributes
for k,v in G.graph.items():
if k == 'directed':
continue
yield indent + string_item(k,v,indent)
# write nodes
for n in G:
yield indent + "node ["
# get id or assign number
nid = G.node[n].get('id',next(count))
node_id[n] = nid
yield 2 * indent + "id {0}".format(nid)
# Uses customized __str__, if implemented.
label = str(G.node[n].get('label',n))
# Need to escape & and " with HTML entities
label = escape(label, quote=True)
yield 2 * indent + 'label "{0}"'.format(label)
if n in G:
for k,v in G.node[n].items():
if k == 'id' or k == 'label': continue
yield 2 * indent + string_item(k,v,indent)
yield indent + "]"
# write edges
for u,v,edgedata in G.edges_iter(data=True):
yield indent + "edge ["
yield 2 * indent + "source {0}".format(node_id[u])
yield 2 * indent + "target {0}".format(node_id[v])
for k, v in edgedata.items():
if k == 'source': continue
if k == 'target': continue
yield 2 * indent + string_item(k, v, indent)
yield indent + "]"
yield "]"
@open_file(1, mode='wb')
[docs]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
-----
GML specifications indicate that the file should only use
7bit ASCII text encoding.iso8859-1 (latin-1).
This implementation does not support all Python data types as GML
data. Nodes, node attributes, edge attributes, and graph
attributes must be either dictionaries or single stings or
numbers. If they are not an attempt is made to represent them as
strings. For example, a list as edge data
G[1][2]['somedata']=[1,2,3], will be represented in the GML file
as::
edge [
source 1
target 2
somedata "[1, 2, 3]"
]
Examples
---------
>>> G=nx.path_graph(4)
>>> nx.write_gml(G,"test.gml")
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_gml(G,"test.gml.gz")
"""
for line in generate_gml(G):
line += '\n'
path.write(line.encode('ascii', 'xmlcharrefreplace'))
# fixture for nose tests
def setup_module(module):
from nose import SkipTest
try:
import pyparsing
except:
try:
import matplotlib.pyparsing
except:
raise SkipTest("pyparsing not available")
# fixture for nose tests
def teardown_module(module):
import os
os.unlink('test.gml')
os.unlink('test.gml.gz')