857 lines
29 KiB
Python
857 lines
29 KiB
Python
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"""
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Read graphs in GML format.
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"GML, the Graph Modelling Language, is our proposal for a portable
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file format for graphs. GML's key features are portability, simple
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syntax, extensibility and flexibility. A GML file consists of a
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hierarchical key-value lists. Graphs can be annotated with arbitrary
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data structures. The idea for a common file format was born at the
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GD'95; this proposal is the outcome of many discussions. GML is the
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standard file format in the Graphlet graph editor system. It has been
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overtaken and adapted by several other systems for drawing graphs."
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GML files are stored using a 7-bit ASCII encoding with any extended
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ASCII characters (iso8859-1) appearing as HTML character entities.
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You will need to give some thought into how the exported data should
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interact with different languages and even different Python versions.
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Re-importing from gml is also a concern.
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Without specifying a `stringizer`/`destringizer`, the code is capable of
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writing `int`/`float`/`str`/`dict`/`list` data as required by the GML
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specification. For writing other data types, and for reading data other
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than `str` you need to explicitly supply a `stringizer`/`destringizer`.
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For additional documentation on the GML file format, please see the
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`GML website <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_.
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Several example graphs in GML format may be found on Mark Newman's
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`Network data page <http://www-personal.umich.edu/~mejn/netdata/>`_.
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"""
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from io import StringIO
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from ast import literal_eval
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from collections import defaultdict
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from enum import Enum
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from typing import Any, NamedTuple
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import networkx as nx
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from networkx.exception import NetworkXError
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from networkx.utils import open_file
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import warnings
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import re
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import html.entities as htmlentitydefs
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__all__ = ["read_gml", "parse_gml", "generate_gml", "write_gml"]
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def escape(text):
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"""Use XML character references to escape characters.
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Use XML character references for unprintable or non-ASCII
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characters, double quotes and ampersands in a string
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"""
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def fixup(m):
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ch = m.group(0)
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return "&#" + str(ord(ch)) + ";"
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text = re.sub('[^ -~]|[&"]', fixup, text)
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return text if isinstance(text, str) else str(text)
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def unescape(text):
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"""Replace XML character references with the referenced characters"""
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def fixup(m):
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text = m.group(0)
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if text[1] == "#":
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# Character reference
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if text[2] == "x":
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code = int(text[3:-1], 16)
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else:
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code = int(text[2:-1])
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else:
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# Named entity
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try:
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code = htmlentitydefs.name2codepoint[text[1:-1]]
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except KeyError:
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return text # leave unchanged
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try:
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return chr(code)
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except (ValueError, OverflowError):
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return text # leave unchanged
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return re.sub("&(?:[0-9A-Za-z]+|#(?:[0-9]+|x[0-9A-Fa-f]+));", fixup, text)
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def literal_destringizer(rep):
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"""Convert a Python literal to the value it represents.
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Parameters
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----------
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rep : string
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A Python literal.
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Returns
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-------
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value : object
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The value of the Python literal.
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Raises
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------
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ValueError
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If `rep` is not a Python literal.
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"""
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msg = "literal_destringizer is deprecated and will be removed in 3.0."
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warnings.warn(msg, DeprecationWarning)
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if isinstance(rep, str):
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orig_rep = rep
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try:
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return literal_eval(rep)
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except SyntaxError as err:
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raise ValueError(f"{orig_rep!r} is not a valid Python literal") from err
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else:
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raise ValueError(f"{rep!r} is not a string")
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@open_file(0, mode="rb")
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def read_gml(path, label="label", destringizer=None):
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"""Read graph in GML format from `path`.
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Parameters
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----------
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path : filename or filehandle
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The filename or filehandle to read from.
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label : string, optional
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If not None, the parsed nodes will be renamed according to node
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attributes indicated by `label`. Default value: 'label'.
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destringizer : callable, optional
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A `destringizer` that recovers values stored as strings in GML. If it
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cannot convert a string to a value, a `ValueError` is raised. Default
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value : None.
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Returns
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-------
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G : NetworkX graph
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The parsed graph.
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Raises
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------
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NetworkXError
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If the input cannot be parsed.
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See Also
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--------
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write_gml, parse_gml
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literal_destringizer
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Notes
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-----
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GML files are stored using a 7-bit ASCII encoding with any extended
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ASCII characters (iso8859-1) appearing as HTML character entities.
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Without specifying a `stringizer`/`destringizer`, the code is capable of
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writing `int`/`float`/`str`/`dict`/`list` data as required by the GML
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specification. For writing other data types, and for reading data other
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than `str` you need to explicitly supply a `stringizer`/`destringizer`.
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For additional documentation on the GML file format, please see the
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`GML url <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_.
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See the module docstring :mod:`networkx.readwrite.gml` for more details.
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Examples
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--------
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>>> G = nx.path_graph(4)
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>>> nx.write_gml(G, "test.gml")
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GML values are interpreted as strings by default:
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>>> H = nx.read_gml("test.gml")
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>>> H.nodes
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NodeView(('0', '1', '2', '3'))
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When a `destringizer` is provided, GML values are converted to the provided type.
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For example, integer nodes can be recovered as shown below:
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>>> J = nx.read_gml("test.gml", destringizer=int)
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>>> J.nodes
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NodeView((0, 1, 2, 3))
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"""
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def filter_lines(lines):
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for line in lines:
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try:
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line = line.decode("ascii")
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except UnicodeDecodeError as err:
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raise NetworkXError("input is not ASCII-encoded") from err
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if not isinstance(line, str):
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lines = str(lines)
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if line and line[-1] == "\n":
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line = line[:-1]
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yield line
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G = parse_gml_lines(filter_lines(path), label, destringizer)
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return G
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def parse_gml(lines, label="label", destringizer=None):
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"""Parse GML graph from a string or iterable.
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Parameters
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----------
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lines : string or iterable of strings
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Data in GML format.
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label : string, optional
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If not None, the parsed nodes will be renamed according to node
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attributes indicated by `label`. Default value: 'label'.
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destringizer : callable, optional
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A `destringizer` that recovers values stored as strings in GML. If it
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cannot convert a string to a value, a `ValueError` is raised. Default
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value : None.
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Returns
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-------
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G : NetworkX graph
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The parsed graph.
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Raises
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------
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NetworkXError
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If the input cannot be parsed.
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See Also
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--------
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write_gml, read_gml
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Notes
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-----
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This stores nested GML attributes as dictionaries in the NetworkX graph,
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node, and edge attribute structures.
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GML files are stored using a 7-bit ASCII encoding with any extended
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ASCII characters (iso8859-1) appearing as HTML character entities.
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Without specifying a `stringizer`/`destringizer`, the code is capable of
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writing `int`/`float`/`str`/`dict`/`list` data as required by the GML
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specification. For writing other data types, and for reading data other
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than `str` you need to explicitly supply a `stringizer`/`destringizer`.
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For additional documentation on the GML file format, please see the
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`GML url <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_.
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See the module docstring :mod:`networkx.readwrite.gml` for more details.
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"""
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def decode_line(line):
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if isinstance(line, bytes):
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try:
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line.decode("ascii")
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except UnicodeDecodeError as err:
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raise NetworkXError("input is not ASCII-encoded") from err
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if not isinstance(line, str):
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line = str(line)
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return line
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def filter_lines(lines):
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if isinstance(lines, str):
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lines = decode_line(lines)
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lines = lines.splitlines()
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yield from lines
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else:
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for line in lines:
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line = decode_line(line)
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if line and line[-1] == "\n":
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line = line[:-1]
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if line.find("\n") != -1:
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raise NetworkXError("input line contains newline")
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yield line
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G = parse_gml_lines(filter_lines(lines), label, destringizer)
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return G
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class Pattern(Enum):
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"""encodes the index of each token-matching pattern in `tokenize`."""
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KEYS = 0
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REALS = 1
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INTS = 2
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STRINGS = 3
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DICT_START = 4
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DICT_END = 5
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COMMENT_WHITESPACE = 6
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class Token(NamedTuple):
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category: Pattern
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value: Any
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line: int
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position: int
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LIST_START_VALUE = "_networkx_list_start"
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def parse_gml_lines(lines, label, destringizer):
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"""Parse GML `lines` into a graph."""
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def tokenize():
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patterns = [
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r"[A-Za-z][0-9A-Za-z_]*\b", # keys
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# reals
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r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*|INF)(?:[Ee][+-]?[0-9]+)?",
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r"[+-]?[0-9]+", # ints
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r'".*?"', # strings
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r"\[", # dict start
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r"\]", # dict end
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r"#.*$|\s+", # comments and whitespaces
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]
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tokens = re.compile("|".join(f"({pattern})" for pattern in patterns))
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lineno = 0
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for line in lines:
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length = len(line)
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pos = 0
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while pos < length:
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match = tokens.match(line, pos)
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if match is None:
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m = f"cannot tokenize {line[pos:]} at ({lineno + 1}, {pos + 1})"
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raise NetworkXError(m)
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for i in range(len(patterns)):
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group = match.group(i + 1)
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if group is not None:
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if i == 0: # keys
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value = group.rstrip()
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elif i == 1: # reals
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value = float(group)
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elif i == 2: # ints
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value = int(group)
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else:
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value = group
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if i != 6: # comments and whitespaces
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yield Token(Pattern(i), value, lineno + 1, pos + 1)
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pos += len(group)
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break
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lineno += 1
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yield Token(None, None, lineno + 1, 1) # EOF
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def unexpected(curr_token, expected):
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category, value, lineno, pos = curr_token
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value = repr(value) if value is not None else "EOF"
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raise NetworkXError(f"expected {expected}, found {value} at ({lineno}, {pos})")
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def consume(curr_token, category, expected):
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if curr_token.category == category:
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return next(tokens)
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unexpected(curr_token, expected)
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def parse_kv(curr_token):
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dct = defaultdict(list)
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while curr_token.category == Pattern.KEYS:
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key = curr_token.value
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curr_token = next(tokens)
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category = curr_token.category
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if category == Pattern.REALS or category == Pattern.INTS:
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value = curr_token.value
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curr_token = next(tokens)
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elif category == Pattern.STRINGS:
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value = unescape(curr_token.value[1:-1])
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if destringizer:
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try:
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value = destringizer(value)
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except ValueError:
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pass
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curr_token = next(tokens)
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elif category == Pattern.DICT_START:
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curr_token, value = parse_dict(curr_token)
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else:
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# Allow for string convertible id and label values
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if key in ("id", "label", "source", "target"):
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try:
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# String convert the token value
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value = unescape(str(curr_token.value))
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if destringizer:
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try:
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value = destringizer(value)
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except ValueError:
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pass
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curr_token = next(tokens)
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except Exception:
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msg = (
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"an int, float, string, '[' or string"
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+ " convertable ASCII value for node id or label"
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)
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|
|
unexpected(curr_token, msg)
|
||
|
|
# Special handling for nan and infinity. Since the gml language
|
||
|
|
# defines unquoted strings as keys, the numeric and string branches
|
||
|
|
# are skipped and we end up in this special branch, so we need to
|
||
|
|
# convert the current token value to a float for NAN and plain INF.
|
||
|
|
# +/-INF are handled in the pattern for 'reals' in tokenize(). This
|
||
|
|
# allows labels and values to be nan or infinity, but not keys.
|
||
|
|
elif curr_token.value in {"NAN", "INF"}:
|
||
|
|
value = float(curr_token.value)
|
||
|
|
curr_token = next(tokens)
|
||
|
|
else: # Otherwise error out
|
||
|
|
unexpected(curr_token, "an int, float, string or '['")
|
||
|
|
dct[key].append(value)
|
||
|
|
|
||
|
|
def clean_dict_value(value):
|
||
|
|
if not isinstance(value, list):
|
||
|
|
return value
|
||
|
|
if len(value) == 1:
|
||
|
|
return value[0]
|
||
|
|
if value[0] == LIST_START_VALUE:
|
||
|
|
return value[1:]
|
||
|
|
return value
|
||
|
|
|
||
|
|
dct = {key: clean_dict_value(value) for key, value in dct.items()}
|
||
|
|
return curr_token, dct
|
||
|
|
|
||
|
|
def parse_dict(curr_token):
|
||
|
|
# dict start
|
||
|
|
curr_token = consume(curr_token, Pattern.DICT_START, "'['")
|
||
|
|
# dict contents
|
||
|
|
curr_token, dct = parse_kv(curr_token)
|
||
|
|
# dict end
|
||
|
|
curr_token = consume(curr_token, Pattern.DICT_END, "']'")
|
||
|
|
return curr_token, dct
|
||
|
|
|
||
|
|
def parse_graph():
|
||
|
|
curr_token, dct = parse_kv(next(tokens))
|
||
|
|
if curr_token.category 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()
|
||
|
|
graph_attr = {k: v for k, v in graph.items() if k not in ("node", "edge")}
|
||
|
|
G.graph.update(graph_attr)
|
||
|
|
|
||
|
|
def pop_attr(dct, category, attr, i):
|
||
|
|
try:
|
||
|
|
return dct.pop(attr)
|
||
|
|
except KeyError as err:
|
||
|
|
raise NetworkXError(f"{category} #{i} has no {attr!r} attribute") from err
|
||
|
|
|
||
|
|
nodes = graph.get("node", [])
|
||
|
|
mapping = {}
|
||
|
|
node_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(f"node id {id!r} is duplicated")
|
||
|
|
if label is not None and label != "id":
|
||
|
|
node_label = pop_attr(node, "node", label, i)
|
||
|
|
if node_label in node_labels:
|
||
|
|
raise NetworkXError(f"node label {node_label!r} is duplicated")
|
||
|
|
node_labels.add(node_label)
|
||
|
|
mapping[id] = node_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(f"edge #{i} has undefined source {source!r}")
|
||
|
|
if target not in G:
|
||
|
|
raise NetworkXError(f"edge #{i} has undefined target {target!r}")
|
||
|
|
if not multigraph:
|
||
|
|
if not G.has_edge(source, target):
|
||
|
|
G.add_edge(source, target, **edge)
|
||
|
|
else:
|
||
|
|
arrow = "->" if directed else "--"
|
||
|
|
msg = f"edge #{i} ({source!r}{arrow}{target!r}) is duplicated"
|
||
|
|
raise nx.NetworkXError(msg)
|
||
|
|
else:
|
||
|
|
key = edge.pop("key", None)
|
||
|
|
if key is not None and G.has_edge(source, target, key):
|
||
|
|
arrow = "->" if directed else "--"
|
||
|
|
msg = f"edge #{i} ({source!r}{arrow}{target!r}, {key!r})"
|
||
|
|
msg2 = 'Hint: If multigraph add "multigraph 1" to file header.'
|
||
|
|
raise nx.NetworkXError(msg + " is duplicated\n" + msg2)
|
||
|
|
G.add_edge(source, target, key, **edge)
|
||
|
|
|
||
|
|
if label is not None and label != "id":
|
||
|
|
G = nx.relabel_nodes(G, mapping)
|
||
|
|
return G
|
||
|
|
|
||
|
|
|
||
|
|
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
|
||
|
|
:func:`networkx.readwrite.gml.literal_destringizer` function.
|
||
|
|
"""
|
||
|
|
msg = "literal_stringizer is deprecated and will be removed in 3.0."
|
||
|
|
warnings.warn(msg, DeprecationWarning)
|
||
|
|
|
||
|
|
def stringize(value):
|
||
|
|
if isinstance(value, (int, bool)) or value is None:
|
||
|
|
if value is True: # GML uses 1/0 for boolean values.
|
||
|
|
buf.write(str(1))
|
||
|
|
elif value is False:
|
||
|
|
buf.write(str(0))
|
||
|
|
else:
|
||
|
|
buf.write(str(value))
|
||
|
|
elif isinstance(value, str):
|
||
|
|
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:
|
||
|
|
msg = "{value!r} cannot be converted into a Python literal"
|
||
|
|
raise ValueError(msg)
|
||
|
|
|
||
|
|
buf = StringIO()
|
||
|
|
stringize(value)
|
||
|
|
return buf.getvalue()
|
||
|
|
|
||
|
|
|
||
|
|
def generate_gml(G, stringizer=None):
|
||
|
|
r"""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/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.
|
||
|
|
|
||
|
|
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.
|
||
|
|
|
||
|
|
See Also
|
||
|
|
--------
|
||
|
|
literal_stringizer
|
||
|
|
|
||
|
|
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.
|
||
|
|
|
||
|
|
GML files are stored using a 7-bit ASCII encoding with any extended
|
||
|
|
ASCII characters (iso8859-1) appearing as HTML character entities.
|
||
|
|
Without specifying a `stringizer`/`destringizer`, the code is capable of
|
||
|
|
writing `int`/`float`/`str`/`dict`/`list` data as required by the GML
|
||
|
|
specification. For writing other data types, and for reading data other
|
||
|
|
than `str` you need to explicitly supply a `stringizer`/`destringizer`.
|
||
|
|
|
||
|
|
For additional documentation on the GML file format, please see the
|
||
|
|
`GML url <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_.
|
||
|
|
|
||
|
|
See the module docstring :mod:`networkx.readwrite.gml` for more details.
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> G = nx.Graph()
|
||
|
|
>>> G.add_node("1")
|
||
|
|
>>> print("\n".join(nx.generate_gml(G)))
|
||
|
|
graph [
|
||
|
|
node [
|
||
|
|
id 0
|
||
|
|
label "1"
|
||
|
|
]
|
||
|
|
]
|
||
|
|
>>> G = nx.OrderedMultiGraph([("a", "b"), ("a", "b")])
|
||
|
|
>>> print("\n".join(nx.generate_gml(G)))
|
||
|
|
graph [
|
||
|
|
multigraph 1
|
||
|
|
node [
|
||
|
|
id 0
|
||
|
|
label "a"
|
||
|
|
]
|
||
|
|
node [
|
||
|
|
id 1
|
||
|
|
label "b"
|
||
|
|
]
|
||
|
|
edge [
|
||
|
|
source 0
|
||
|
|
target 1
|
||
|
|
key 0
|
||
|
|
]
|
||
|
|
edge [
|
||
|
|
source 0
|
||
|
|
target 1
|
||
|
|
key 1
|
||
|
|
]
|
||
|
|
]
|
||
|
|
"""
|
||
|
|
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):
|
||
|
|
raise NetworkXError(f"{key!r} is not a string")
|
||
|
|
if not valid_keys.match(key):
|
||
|
|
raise NetworkXError(f"{key!r} is not a valid key")
|
||
|
|
if not isinstance(key, str):
|
||
|
|
key = str(key)
|
||
|
|
if key not in ignored_keys:
|
||
|
|
if isinstance(value, (int, bool)):
|
||
|
|
if key == "label":
|
||
|
|
yield indent + key + ' "' + str(value) + '"'
|
||
|
|
elif value is True:
|
||
|
|
# python bool is an instance of int
|
||
|
|
yield indent + key + " 1"
|
||
|
|
elif value is False:
|
||
|
|
yield indent + key + " 0"
|
||
|
|
# GML only supports signed 32-bit integers
|
||
|
|
elif value < -(2 ** 31) or value >= 2 ** 31:
|
||
|
|
yield indent + key + ' "' + str(value) + '"'
|
||
|
|
else:
|
||
|
|
yield indent + key + " " + str(value)
|
||
|
|
elif isinstance(value, float):
|
||
|
|
text = repr(value).upper()
|
||
|
|
# GML matches INF to keys, so prepend + to INF. Use repr(float(*))
|
||
|
|
# instead of string literal to future proof against changes to repr.
|
||
|
|
if text == repr(float("inf")).upper():
|
||
|
|
text = "+" + text
|
||
|
|
else:
|
||
|
|
# 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:]
|
||
|
|
if key == "label":
|
||
|
|
yield indent + key + ' "' + text + '"'
|
||
|
|
else:
|
||
|
|
yield indent + key + " " + text
|
||
|
|
elif isinstance(value, dict):
|
||
|
|
yield indent + key + " ["
|
||
|
|
next_indent = indent + " "
|
||
|
|
for key, value in value.items():
|
||
|
|
yield from stringize(key, value, (), next_indent)
|
||
|
|
yield indent + "]"
|
||
|
|
elif (
|
||
|
|
isinstance(value, (list, tuple))
|
||
|
|
and key != "label"
|
||
|
|
and value
|
||
|
|
and not in_list
|
||
|
|
):
|
||
|
|
if len(value) == 1:
|
||
|
|
yield indent + key + " " + f'"{LIST_START_VALUE}"'
|
||
|
|
for val in value:
|
||
|
|
yield from stringize(key, val, (), indent, True)
|
||
|
|
else:
|
||
|
|
if stringizer:
|
||
|
|
try:
|
||
|
|
value = stringizer(value)
|
||
|
|
except ValueError as err:
|
||
|
|
raise NetworkXError(
|
||
|
|
f"{value!r} cannot be converted into a string"
|
||
|
|
) from err
|
||
|
|
if not isinstance(value, str):
|
||
|
|
raise NetworkXError(f"{value!r} is not a string")
|
||
|
|
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():
|
||
|
|
yield from stringize(attr, value, ignored_keys, " ")
|
||
|
|
|
||
|
|
# Output node data
|
||
|
|
node_id = dict(zip(G, range(len(G))))
|
||
|
|
ignored_keys = {"id", "label"}
|
||
|
|
for node, attrs in G.nodes.items():
|
||
|
|
yield " node ["
|
||
|
|
yield " id " + str(node_id[node])
|
||
|
|
yield from stringize("label", node, (), " ")
|
||
|
|
for attr, value in attrs.items():
|
||
|
|
yield from stringize(attr, value, ignored_keys, " ")
|
||
|
|
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(**kwargs):
|
||
|
|
yield " edge ["
|
||
|
|
yield " source " + str(node_id[e[0]])
|
||
|
|
yield " target " + str(node_id[e[1]])
|
||
|
|
if multigraph:
|
||
|
|
yield from stringize("key", e[2], (), " ")
|
||
|
|
for attr, value in e[-1].items():
|
||
|
|
yield from stringize(attr, value, ignored_keys, " ")
|
||
|
|
yield " ]"
|
||
|
|
yield "]"
|
||
|
|
|
||
|
|
|
||
|
|
@open_file(1, mode="wb")
|
||
|
|
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
|
||
|
|
literal_stringizer
|
||
|
|
|
||
|
|
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.
|
||
|
|
|
||
|
|
GML files are stored using a 7-bit ASCII encoding with any extended
|
||
|
|
ASCII characters (iso8859-1) appearing as HTML character entities.
|
||
|
|
Without specifying a `stringizer`/`destringizer`, the code is capable of
|
||
|
|
writing `int`/`float`/`str`/`dict`/`list` data as required by the GML
|
||
|
|
specification. For writing other data types, and for reading data other
|
||
|
|
than `str` you need to explicitly supply a `stringizer`/`destringizer`.
|
||
|
|
|
||
|
|
Note that while we allow non-standard GML to be read from a file, we make
|
||
|
|
sure to write GML format. In particular, underscores are not allowed in
|
||
|
|
attribute names.
|
||
|
|
For additional documentation on the GML file format, please see the
|
||
|
|
`GML url <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_.
|
||
|
|
|
||
|
|
See the module docstring :mod:`networkx.readwrite.gml` for more details.
|
||
|
|
|
||
|
|
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"))
|