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Fixed database typo and removed unnecessary class identifier.

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Batuhan Berk Başoğlu 2020-10-14 10:10:37 -04:00
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"""
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
handling `int`/`float`/`str`/`dict`/`list` data as required by the GML
specification. For other data types, you need to explicitly supply a
`stringizer`/`destringizer`.
For additional documentation on the GML file format, please see the
`GML website <http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html>`_.
Several example graphs in GML format may be found on Mark Newman's
`Network data page <http://www-personal.umich.edu/~mejn/netdata/>`_.
"""
from io import StringIO
from ast import literal_eval
from collections import defaultdict
from enum import Enum
from typing import Any, NamedTuple
import networkx as nx
from networkx.exception import NetworkXError
from networkx.utils import open_file
import warnings
import re
import html.entities as htmlentitydefs
__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] == "#":
# 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)
except (ValueError, OverflowError):
return text # leave unchanged
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.
"""
msg = "literal_destringizer is deprecated and will be removed in 3.0."
warnings.warn(msg, DeprecationWarning)
if isinstance(rep, str):
orig_rep = rep
try:
return literal_eval(rep)
except SyntaxError as e:
raise ValueError(f"{orig_rep!r} is not a valid Python literal") from e
else:
raise ValueError(f"{rep!r} is not a string")
@open_file(0, mode="rb")
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
-----
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
handling `int`/`float`/`str`/`dict`/`list` data as required by the GML
specification. For other data types, you need to explicitly supply a
`stringizer`/`destringizer`.
For additional documentation on the GML file format, please see the
`GML url <http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html>`_.
See the module docstring :mod:`networkx.readwrite.gml` for more details.
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 as e:
raise NetworkXError("input is not ASCII-encoded") from e
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
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
handling `int`/`float`/`str`/`dict`/`list` data as required by the GML
specification. For other data types, you need to explicitly supply a
`stringizer`/`destringizer`.
For additional documentation on the GML file format, please see the
`GML url <http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html>`_.
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 e:
raise NetworkXError("input is not ASCII-encoded") from e
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", # keys
# reals
r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*)(?:[Ee][+-]?[0-9]+)?",
r"[+-]?[0-9]+", # ints
r'".*?"', # strings
r"\[", # dict start
r"\]", # dict end
r"#.*$|\s+", # comments and whitespaces
]
tokens = re.compile("|".join(f"({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 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: # 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 Token(Pattern(i), value, lineno + 1, pos + 1)
pos += len(group)
break
lineno += 1
yield Token(None, None, lineno + 1, 1) # EOF
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
curr_token = next(tokens)
elif category == Pattern.DICT_START:
curr_token, value = parse_dict(curr_token)
else:
# Allow for string convertible id and label values
if key in ("id", "label", "source", "target"):
try:
# String convert the token value
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"
+ " convertable ASCII value for node id or label"
)
unexpected(curr_token, msg)
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 e:
raise NetworkXError(f"{category} #{i} has no '{attr}' attribute") from e
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.
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
handling `int`/`float`/`str`/`dict`/`list` data as required by the GML
specification. For other data types, you need to explicitly supply a
`stringizer`/`destringizer`.
For additional documentation on the GML file format, please see the
`GML url <http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html>`_.
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 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 e:
raise NetworkXError(
f"{value!r} cannot be converted into a string"
) from e
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
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
handling `int`/`float`/`str`/`dict`/`list` data as required by the GML
specification. For other data types, 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 <http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html>`_.
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"))