|
""" |
|
Read graphs in GML format. |
|
|
|
"GML, the Graph 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." |
|
|
|
GML files are stored using a 7-bit ASCII encoding with any extended |
|
ASCII characters (iso8859-1) appearing as HTML character entities. |
|
You will need to give some thought into how the exported data should |
|
interact with different languages and even different Python versions. |
|
Re-importing from gml is also a concern. |
|
|
|
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 website <https://web.archive.org/web/20190207140002/http://www.fim.uni-passau.de/index.php?id=17297&L=1>`_. |
|
|
|
Several example graphs in GML format may be found on Mark Newman's |
|
`Network data page <http://www-personal.umich.edu/~mejn/netdata/>`_. |
|
""" |
|
import html.entities as htmlentitydefs |
|
import re |
|
import warnings |
|
from ast import literal_eval |
|
from collections import defaultdict |
|
from enum import Enum |
|
from io import StringIO |
|
from typing import Any, NamedTuple |
|
|
|
import networkx as nx |
|
from networkx.exception import NetworkXError |
|
from networkx.utils import open_file |
|
|
|
__all__ = ["read_gml", "parse_gml", "generate_gml", "write_gml"] |
|
|
|
|
|
def escape(text): |
|
"""Use XML character references to escape characters. |
|
|
|
Use XML character references for unprintable or non-ASCII |
|
characters, double quotes and ampersands in a string |
|
""" |
|
|
|
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 with the referenced characters""" |
|
|
|
def fixup(m): |
|
text = m.group(0) |
|
if text[1] == "#": |
|
|
|
if text[2] == "x": |
|
code = int(text[3:-1], 16) |
|
else: |
|
code = int(text[2:-1]) |
|
else: |
|
|
|
try: |
|
code = htmlentitydefs.name2codepoint[text[1:-1]] |
|
except KeyError: |
|
return text |
|
try: |
|
return chr(code) |
|
except (ValueError, OverflowError): |
|
return text |
|
|
|
return re.sub("&(?:[0-9A-Za-z]+|#(?:[0-9]+|x[0-9A-Fa-f]+));", fixup, text) |
|
|
|
|
|
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): |
|
orig_rep = rep |
|
try: |
|
return literal_eval(rep) |
|
except SyntaxError as err: |
|
raise ValueError(f"{orig_rep!r} is not a valid Python literal") from err |
|
else: |
|
raise ValueError(f"{rep!r} is not a string") |
|
|
|
|
|
@open_file(0, mode="rb") |
|
@nx._dispatchable(graphs=None, returns_graph=True) |
|
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 |
|
literal_destringizer |
|
|
|
Notes |
|
----- |
|
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.path_graph(4) |
|
>>> nx.write_gml(G, "test.gml") |
|
|
|
GML values are interpreted as strings by default: |
|
|
|
>>> H = nx.read_gml("test.gml") |
|
>>> H.nodes |
|
NodeView(('0', '1', '2', '3')) |
|
|
|
When a `destringizer` is provided, GML values are converted to the provided type. |
|
For example, integer nodes can be recovered as shown below: |
|
|
|
>>> J = nx.read_gml("test.gml", destringizer=int) |
|
>>> J.nodes |
|
NodeView((0, 1, 2, 3)) |
|
|
|
""" |
|
|
|
def filter_lines(lines): |
|
for line in lines: |
|
try: |
|
line = line.decode("ascii") |
|
except UnicodeDecodeError as err: |
|
raise NetworkXError("input is not ASCII-encoded") from err |
|
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 |
|
|
|
|
|
@nx._dispatchable(graphs=None, returns_graph=True) |
|
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. |
|
|
|
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. |
|
""" |
|
|
|
def decode_line(line): |
|
if isinstance(line, bytes): |
|
try: |
|
line.decode("ascii") |
|
except UnicodeDecodeError as err: |
|
raise NetworkXError("input is not ASCII-encoded") from err |
|
if not isinstance(line, str): |
|
line = str(line) |
|
return line |
|
|
|
def filter_lines(lines): |
|
if isinstance(lines, str): |
|
lines = decode_line(lines) |
|
lines = lines.splitlines() |
|
yield from lines |
|
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 |
|
|
|
|
|
class Pattern(Enum): |
|
"""encodes the index of each token-matching pattern in `tokenize`.""" |
|
|
|
KEYS = 0 |
|
REALS = 1 |
|
INTS = 2 |
|
STRINGS = 3 |
|
DICT_START = 4 |
|
DICT_END = 5 |
|
COMMENT_WHITESPACE = 6 |
|
|
|
|
|
class Token(NamedTuple): |
|
category: Pattern |
|
value: Any |
|
line: int |
|
position: int |
|
|
|
|
|
LIST_START_VALUE = "_networkx_list_start" |
|
|
|
|
|
def parse_gml_lines(lines, label, destringizer): |
|
"""Parse GML `lines` into a graph.""" |
|
|
|
def tokenize(): |
|
patterns = [ |
|
r"[A-Za-z][0-9A-Za-z_]*\b", |
|
|
|
r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*|INF)(?:[Ee][+-]?[0-9]+)?", |
|
r"[+-]?[0-9]+", |
|
r'".*?"', |
|
r"\[", |
|
r"\]", |
|
r"#.*$|\s+", |
|
] |
|
tokens = re.compile("|".join(f"({pattern})" for pattern in patterns)) |
|
lineno = 0 |
|
multilines = [] |
|
for line in lines: |
|
pos = 0 |
|
|
|
|
|
|
|
|
|
if multilines: |
|
multilines.append(line.strip()) |
|
if line[-1] == '"': |
|
|
|
|
|
line = " ".join(multilines) |
|
multilines = [] |
|
else: |
|
lineno += 1 |
|
continue |
|
else: |
|
if line.count('"') == 1: |
|
if line.strip()[0] != '"' and line.strip()[-1] != '"': |
|
|
|
|
|
multilines = [line.rstrip()] |
|
lineno += 1 |
|
continue |
|
|
|
length = len(line) |
|
|
|
while pos < length: |
|
match = tokens.match(line, pos) |
|
if match is None: |
|
m = f"cannot tokenize {line[pos:]} at ({lineno + 1}, {pos + 1})" |
|
raise NetworkXError(m) |
|
for i in range(len(patterns)): |
|
group = match.group(i + 1) |
|
if group is not None: |
|
if i == 0: |
|
value = group.rstrip() |
|
elif i == 1: |
|
value = float(group) |
|
elif i == 2: |
|
value = int(group) |
|
else: |
|
value = group |
|
if i != 6: |
|
yield Token(Pattern(i), value, lineno + 1, pos + 1) |
|
pos += len(group) |
|
break |
|
lineno += 1 |
|
yield Token(None, None, lineno + 1, 1) |
|
|
|
def unexpected(curr_token, expected): |
|
category, value, lineno, pos = curr_token |
|
value = repr(value) if value is not None else "EOF" |
|
raise NetworkXError(f"expected {expected}, found {value} at ({lineno}, {pos})") |
|
|
|
def consume(curr_token, category, expected): |
|
if curr_token.category == category: |
|
return next(tokens) |
|
unexpected(curr_token, expected) |
|
|
|
def parse_kv(curr_token): |
|
dct = defaultdict(list) |
|
while curr_token.category == Pattern.KEYS: |
|
key = curr_token.value |
|
curr_token = next(tokens) |
|
category = curr_token.category |
|
if category == Pattern.REALS or category == Pattern.INTS: |
|
value = curr_token.value |
|
curr_token = next(tokens) |
|
elif category == Pattern.STRINGS: |
|
value = unescape(curr_token.value[1:-1]) |
|
if destringizer: |
|
try: |
|
value = destringizer(value) |
|
except ValueError: |
|
pass |
|
|
|
if value == "()": |
|
value = () |
|
if value == "[]": |
|
value = [] |
|
curr_token = next(tokens) |
|
elif category == Pattern.DICT_START: |
|
curr_token, value = parse_dict(curr_token) |
|
else: |
|
|
|
if key in ("id", "label", "source", "target"): |
|
try: |
|
|
|
value = unescape(str(curr_token.value)) |
|
if destringizer: |
|
try: |
|
value = destringizer(value) |
|
except ValueError: |
|
pass |
|
curr_token = next(tokens) |
|
except Exception: |
|
msg = ( |
|
"an int, float, string, '[' or string" |
|
+ " convertible ASCII value for node id or label" |
|
) |
|
unexpected(curr_token, msg) |
|
|
|
|
|
|
|
|
|
|
|
|
|
elif curr_token.value in {"NAN", "INF"}: |
|
value = float(curr_token.value) |
|
curr_token = next(tokens) |
|
else: |
|
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): |
|
|
|
curr_token = consume(curr_token, Pattern.DICT_START, "'['") |
|
|
|
curr_token, dct = parse_kv(curr_token) |
|
|
|
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: |
|
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 |
|
----- |
|
The original value can be recovered using the |
|
:func:`networkx.readwrite.gml.literal_destringizer` function. |
|
""" |
|
|
|
def stringize(value): |
|
if isinstance(value, int | bool) or value is None: |
|
if value is True: |
|
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 = f"{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.MultiGraph([("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: |
|
|
|
yield indent + key + " 1" |
|
elif value is False: |
|
yield indent + key + " 0" |
|
|
|
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() |
|
|
|
|
|
if text == repr(float("inf")).upper(): |
|
text = "+" + text |
|
else: |
|
|
|
|
|
|
|
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, tuple) and key == "label": |
|
yield indent + key + f" \"({','.join(repr(v) for v in value)})\"" |
|
elif isinstance(value, list | tuple) and key != "label" and not in_list: |
|
if len(value) == 0: |
|
yield indent + key + " " + f'"{value!r}"' |
|
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 [" |
|
|
|
|
|
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, " ") |
|
|
|
|
|
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 " ]" |
|
|
|
|
|
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")) |
|
|