""" 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 # Dan Schult # Pieter Swart # 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("]")