Note

This documents the development version of NetworkX. Documentation for the current release can be found here.

Source code for networkx.readwrite.gml

"""
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)


[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. """ 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")
[docs]@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
[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. 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
[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 :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()
[docs]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 "]"
[docs]@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"))