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

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/

"""
__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']

try:
    try:
        from cStringIO import StringIO
    except ImportError:
        from StringIO import StringIO
except ImportError:
    from io import StringIO
from ast import literal_eval
from collections import defaultdict
from lib2to3.pgen2.parse import ParseError
from lib2to3.pgen2.tokenize import TokenError
from lib2to3.refactor import RefactoringTool
import networkx as nx
from networkx.exception import NetworkXError
from networkx.utils import open_file

import re
try:
    import htmlentitydefs
except ImportError:
    # Python 3.x
    import html.entities as htmlentitydefs

try:
    long
except NameError:
    long = int
try:
    unicode
except NameError:
    unicode = str
try:
    unichr
except NameError:
    unichr = chr
try:
    literal_eval(r"u'\u4444'")
except SyntaxError:
    # Remove 'u' prefixes in unicode literals in Python 3
    rtp_fix_unicode = RefactoringTool(['lib2to3.fixes.fix_unicode'],
                                      {'print_function': True})
else:
    rtp_fix_unicode = None


def escape(text):
    """Escape unprintable or non-ASCII characters, double quotes and ampersands
    in a string using XML character references.
    """
    def fixup(m):
        ch = m.group(0)
        return '&#' + str(ord(ch)) + ';'

    text = re.sub('[^ -~]|[&"]', fixup, text)
    return text if isinstance(text, str) else str(text)


def unescape(text):
    """Replace XML character references in a string with the referenced
    characters.
    """
    def fixup(m):
        text = m.group(0)
        if text[1] == '#':
            # Character reference
            if text[2] == 'x':
                code = int(text[3:-1], 16)
            else:
                code = int(text[2:-1])
        else:
            # Named entity
            try:
                code = htmlentitydefs.name2codepoint[text[1:-1]]
            except KeyError:
                return text  # leave unchanged
        try:
            return chr(code) if code < 256 else unichr(code)
        except (ValueError, OverflowError):
            return text  # leave unchanged

    return re.sub("&(?:[0-9A-Za-z]+|#(?:[0-9]+|x[0-9A-Fa-f]+));", fixup, text)


[docs]def literal_destringizer(rep): """Convert a Python literal to the value it represents. Parameters ---------- rep : string A Python literal. Returns ------- value : object The value of the Python literal. Raises ------ ValueError If ``rep`` is not a Python literal. """ if isinstance(rep, (str, unicode)): orig_rep = rep try: # Python 3.2 does not recognize 'u' prefixes before string literals if rtp_fix_unicode: rep = str(rtp_fix_unicode.refactor_string( rep + '\n', '<string>'))[:-1] return literal_eval(rep) except (ParseError, SyntaxError, TokenError): raise ValueError('%r is not a valid Python literal' % (orig_rep,)) else: raise ValueError('%r is not a string' % (rep,))
@open_file(0, mode='rb')
[docs]def read_gml(path, label='label', destringizer=None): """Read graph in GML format from path. Parameters ---------- path : filename or filehandle The filename or filehandle to read from. label : string, optional If not None, the parsed nodes will be renamed according to node attributes indicated by ``label``. Default value: ``'label'``. destringizer : callable, optional A destringizer that recovers values stored as strings in GML. If it cannot convert a string to a value, a ``ValueError`` is raised. Default value : ``None``. Returns ------- G : NetworkX graph The parsed graph. Raises ------ NetworkXError If the input cannot be parsed. See Also -------- write_gml, parse_gml Notes ----- 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') """ def filter_lines(lines): for line in lines: try: line = line.decode('ascii') except UnicodeDecodeError: raise NetworkXError('input is not ASCII-encoded') if not isinstance(line, str): lines = str(lines) if line and line[-1] == '\n': line = line[:-1] yield line G = parse_gml_lines(filter_lines(path), label, destringizer) return G
[docs]def parse_gml(lines, label='label', destringizer=None): """Parse GML graph from a string or iterable. Parameters ---------- lines : string or iterable of strings Data in GML format. label : string, optional If not None, the parsed nodes will be renamed according to node attributes indicated by ``label``. Default value: ``'label'``. destringizer : callable, optional A destringizer that recovers values stored as strings in GML. If it cannot convert a string to a value, a ``ValueError`` is raised. Default value : ``None``. Returns ------- G : NetworkX graph The parsed graph. Raises ------ NetworkXError If the input cannot be parsed. See Also -------- write_gml, read_gml Notes ----- This stores nested GML attributes as dictionaries in the NetworkX graph, node, and edge attribute structures. References ---------- GML specification: http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html """ def decode_line(line): if isinstance(line, bytes): try: line.decode('ascii') except UnicodeDecodeError: raise NetworkXError('input is not ASCII-encoded') if not isinstance(line, str): line = str(line) return line def filter_lines(lines): if isinstance(lines, (str, unicode)): lines = decode_line(lines) lines = lines.splitlines() for line in lines: yield line else: for line in lines: line = decode_line(line) if line and line[-1] == '\n': line = line[:-1] if line.find('\n') != -1: raise NetworkXError('input line contains newline') yield line G = parse_gml_lines(filter_lines(lines), label, destringizer) return G
def parse_gml_lines(lines, label, destringizer): """Parse GML into a graph. """ def tokenize(): patterns = [ r'[A-Za-z][0-9A-Za-z]*\s+', # keys r'[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*)(?:[Ee][+-]?[0-9]+)?', # reals r'[+-]?[0-9]+', # ints r'".*?"', # strings r'\[', # dict start r'\]', # dict end r'#.*$|\s+' # comments and whitespaces ] tokens = re.compile( '|'.join('(' + pattern + ')' for pattern in patterns)) lineno = 0 for line in lines: length = len(line) pos = 0 while pos < length: match = tokens.match(line, pos) if match is not None: for i in range(len(patterns)): group = match.group(i + 1) if group is not None: if i == 0: # keys value = group.rstrip() elif i == 1: # reals value = float(group) elif i == 2: # ints value = int(group) else: value = group if i != 6: # comments and whitespaces yield (i, value, lineno + 1, pos + 1) pos += len(group) break else: raise NetworkXError('cannot tokenize %r at (%d, %d)' % (line[pos:], lineno + 1, pos + 1)) lineno += 1 yield (None, None, lineno + 1, 1) # EOF def unexpected(curr_token, expected): type, value, lineno, pos = curr_token raise NetworkXError( 'expected %s, found %s at (%d, %d)' % (expected, repr(value) if value is not None else 'EOF', lineno, pos)) def consume(curr_token, type, expected): if curr_token[0] == type: return next(tokens) unexpected(curr_token, expected) def parse_kv(curr_token): dct = defaultdict(list) while curr_token[0] == 0: # keys key = curr_token[1] curr_token = next(tokens) type = curr_token[0] if type == 1 or type == 2: # reals or ints value = curr_token[1] curr_token = next(tokens) elif type == 3: # strings value = unescape(curr_token[1][1:-1]) if destringizer: try: value = destringizer(value) except ValueError: pass curr_token = next(tokens) elif type == 4: # dict start curr_token, value = parse_dict(curr_token) else: unexpected(curr_token, "an int, float, string or '['") dct[key].append(value) dct = {key: (value if not isinstance(value, list) or len(value) != 1 else value[0]) for key, value in dct.items()} return curr_token, dct def parse_dict(curr_token): curr_token = consume(curr_token, 4, "'['") # dict start curr_token, dct = parse_kv(curr_token) curr_token = consume(curr_token, 5, "']'") # dict end return curr_token, dct def parse_graph(): curr_token, dct = parse_kv(next(tokens)) if curr_token[0] is not None: # EOF unexpected(curr_token, 'EOF') if 'graph' not in dct: raise NetworkXError('input contains no graph') graph = dct['graph'] if isinstance(graph, list): raise NetworkXError('input contains more than one graph') return graph tokens = tokenize() graph = parse_graph() directed = graph.pop('directed', False) multigraph = graph.pop('multigraph', False) if not multigraph: G = nx.DiGraph() if directed else nx.Graph() else: G = nx.MultiDiGraph() if directed else nx.MultiGraph() G.graph.update((key, value) for key, value in graph.items() if key != 'node' and key != 'edge') def pop_attr(dct, type, attr, i): try: return dct.pop(attr) except KeyError: raise NetworkXError( "%s #%d has no '%s' attribute" % (type, i, attr)) nodes = graph.get('node', []) mapping = {} labels = set() for i, node in enumerate(nodes if isinstance(nodes, list) else [nodes]): id = pop_attr(node, 'node', 'id', i) if id in G: raise NetworkXError('node id %r is duplicated' % (id,)) if label != 'id': label = pop_attr(node, 'node', 'label', i) if label in labels: raise NetworkXError('node label %r is duplicated' % (label,)) labels.add(label) mapping[id] = label G.add_node(id, node) edges = graph.get('edge', []) for i, edge in enumerate(edges if isinstance(edges, list) else [edges]): source = pop_attr(edge, 'edge', 'source', i) target = pop_attr(edge, 'edge', 'target', i) if source not in G: raise NetworkXError( 'edge #%d has an undefined source %r' % (i, source)) if target not in G: raise NetworkXError( 'edge #%d has an undefined target %r' % (i, target)) if not multigraph: if not G.has_edge(source, target): G.add_edge(source, target, edge) else: raise nx.NetworkXError( 'edge #%d (%r%s%r) is duplicated' % (i, source, '->' if directed else '--', target)) else: key = edge.pop('key', None) if key is not None and G.has_edge(source, target, key): raise nx.NetworkXError( 'edge #%d (%r%s%r, %r) is duplicated' % (i, source, '->' if directed else '--', target, key)) G.add_edge(source, target, key, edge) if label != 'id': G = nx.relabel_nodes(G, mapping) if 'name' in graph: G.graph['name'] = graph['name'] else: del G.graph['name'] return G
[docs]def literal_stringizer(value): """Convert a value to a Python literal in GML representation. Parameters ---------- value : object The value to be converted to GML representation. Returns ------- rep : string A double-quoted Python literal representing value. Unprintable characters are replaced by XML character references. Raises ------ ValueError If ``value`` cannot be converted to GML. Notes ----- ``literal_stringizer`` is largely the same as ``repr`` in terms of functionality but attempts prefix ``unicode`` and ``bytes`` literals with ``u`` and ``b`` to provide better interoperability of data generated by Python 2 and Python 3. The original value can be recovered using the ``networkx.readwrite.gml.literal_destringizer`` function. """ def stringize(value): if isinstance(value, (int, long, bool)) or value is None: buf.write(str(value)) elif isinstance(value, unicode): text = repr(value) if text[0] != 'u': try: value.encode('latin1') except UnicodeEncodeError: text = 'u' + text buf.write(text) elif isinstance(value, (float, complex, str, bytes)): buf.write(repr(value)) elif isinstance(value, list): buf.write('[') first = True for item in value: if not first: buf.write(',') else: first = False stringize(item) buf.write(']') elif isinstance(value, tuple): if len(value) > 1: buf.write('(') first = True for item in value: if not first: buf.write(',') else: first = False stringize(item) buf.write(')') elif value: buf.write('(') stringize(value[0]) buf.write(',)') else: buf.write('()') elif isinstance(value, dict): buf.write('{') first = True for key, value in value.items(): if not first: buf.write(',') else: first = False stringize(key) buf.write(':') stringize(value) buf.write('}') elif isinstance(value, set): buf.write('{') first = True for item in value: if not first: buf.write(',') else: first = False stringize(item) buf.write('}') else: raise ValueError( '%r cannot be converted into a Python literal' % (value,)) buf = StringIO() stringize(value) return buf.getvalue()
[docs]def generate_gml(G, stringizer=None): """Generate a single entry of the graph G in GML format. Parameters ---------- G : NetworkX graph The graph to be converted to GML. stringizer : callable, optional A stringizer which converts non-int/float/dict values into strings. If it cannot convert a value into a string, it should raise a ``ValueError`` raised to indicate that. Default value: ``None``. Returns ------- lines: generator of strings Lines of GML data. Newlines are not appended. Raises ------ NetworkXError If ``stringizer`` cannot convert a value into a string, or the value to convert is not a string while ``stringizer`` is ``None``. Notes ----- Graph attributes named ``'directed'``, ``'multigraph'``, ``'node'`` or ``'edge'``,node attributes named ``'id'`` or ``'label'``, edge attributes named ``'source'`` or ``'target'`` (or ``'key'`` if ``G`` is a multigraph) are ignored because these attribute names are used to encode the graph structure. """ valid_keys = re.compile('^[A-Za-z][0-9A-Za-z]*$') def stringize(key, value, ignored_keys, indent, in_list=False): if not isinstance(key, (str, unicode)): raise NetworkXError('%r is not a string' % (key,)) if not valid_keys.match(key): raise NetworkXError('%r is not a valid key' % (key,)) if not isinstance(key, str): key = str(key) if key not in ignored_keys: if isinstance(value, (int, long)): yield indent + key + ' ' + str(value) elif isinstance(value, float): text = repr(value).upper() # GML requires that a real literal contain a decimal point, but # repr may not output a decimal point when the mantissa is # integral and hence needs fixing. epos = text.rfind('E') if epos != -1 and text.find('.', 0, epos) == -1: text = text[:epos] + '.' + text[epos:] yield indent + key + ' ' + text elif isinstance(value, dict): yield indent + key + ' [' next_indent = indent + ' ' for key, value in value.items(): for line in stringize(key, value, (), next_indent): yield line yield indent + ']' elif isinstance(value, list) and value and not in_list: next_indent = indent + ' ' for value in value: for line in stringize(key, value, (), next_indent, True): yield line else: if stringizer: try: value = stringizer(value) except ValueError: raise NetworkXError( '%r cannot be converted into a string' % (value,)) if not isinstance(value, (str, unicode)): raise NetworkXError('%r is not a string' % (value,)) yield indent + key + ' "' + escape(value) + '"' multigraph = G.is_multigraph() yield 'graph [' # Output graph attributes if G.is_directed(): yield ' directed 1' if multigraph: yield ' multigraph 1' ignored_keys = {'directed', 'multigraph', 'node', 'edge'} for attr, value in G.graph.items(): for line in stringize(attr, value, ignored_keys, ' '): yield line # Output node data node_id = dict(zip(G, range(len(G)))) ignored_keys = {'id', 'label'} for node, attrs in G.node.items(): yield ' node [' yield ' id ' + str(node_id[node]) for line in stringize('label', node, (), ' '): yield line for attr, value in attrs.items(): for line in stringize(attr, value, ignored_keys, ' '): yield line yield ' ]' # Output edge data ignored_keys = {'source', 'target'} kwargs = {'data': True} if multigraph: ignored_keys.add('key') kwargs['keys'] = True for e in G.edges_iter(**kwargs): yield ' edge [' yield ' source ' + str(node_id[e[0]]) yield ' target ' + str(node_id[e[1]]) if multigraph: for line in stringize('key', e[2], (), ' '): yield line for attr, value in e[-1].items(): for line in stringize(attr, value, ignored_keys, ' '): yield line yield ' ]' yield ']'
@open_file(1, mode='wb')
[docs]def write_gml(G, path, stringizer=None): """Write a graph ``G`` in GML format to the file or file handle ``path``. Parameters ---------- G : NetworkX graph The graph to be converted to GML. path : filename or filehandle The filename or filehandle to write. Files whose names end with .gz or .bz2 will be compressed. stringizer : callable, optional A stringizer which converts non-int/non-float/non-dict values into strings. If it cannot convert a value into a string, it should raise a ``ValueError`` to indicate that. Default value: ``None``. Raises ------ NetworkXError If ``stringizer`` cannot convert a value into a string, or the value to convert is not a string while ``stringizer`` is ``None``. See Also -------- read_gml, generate_gml Notes ----- Graph attributes named ``'directed'``, ``'multigraph'``, ``'node'`` or ``'edge'``,node attributes named ``'id'`` or ``'label'``, edge attributes named ``'source'`` or ``'target'`` (or ``'key'`` if ``G`` is a multigraph) are ignored because these attribute names are used to encode the graph structure. 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, stringizer): path.write((line + '\n').encode('ascii')) # fixture for nose
def teardown_module(module): import os for fname in ['test.gml', 'test.gml.gz']: if os.path.isfile(fname): os.unlink(fname)