Source code for networkx.readwrite.gexf

"""Read and write graphs in GEXF format.

GEXF (Graph Exchange XML Format) is a language for describing complex
network structures, their associated data and dynamics.

This implementation does not support mixed graphs (directed and
undirected edges together).

Format
------
GEXF is an XML format.  See https://gephi.org/gexf/format/schema.html for the
specification and https://gephi.org/gexf/format/basic.html for examples.
"""
import itertools
import time

import networkx as nx
from networkx.utils import open_file

from xml.etree.ElementTree import (
    Element,
    ElementTree,
    SubElement,
    tostring,
    register_namespace,
)

__all__ = ["write_gexf", "read_gexf", "relabel_gexf_graph", "generate_gexf"]


[docs]@open_file(1, mode="wb") def write_gexf(G, path, encoding="utf-8", prettyprint=True, version="1.2draft"): """Write G in GEXF format to path. "GEXF (Graph Exchange XML Format) is a language for describing complex networks structures, their associated data and dynamics" [1]_. Node attributes are checked according to the version of the GEXF schemas used for parameters which are not user defined, e.g. visualization 'viz' [2]_. See example for usage. Parameters ---------- G : graph A NetworkX graph path : file or string File or file name to write. File names ending in .gz or .bz2 will be compressed. encoding : string (optional, default: 'utf-8') Encoding for text data. prettyprint : bool (optional, default: True) If True use line breaks and indenting in output XML. version: string (optional, default: '1.2draft') The version of GEXF to be used for nodes attributes checking Examples -------- >>> G = nx.path_graph(4) >>> nx.write_gexf(G, "test.gexf") # visualization data >>> G.nodes[0]["viz"] = {"size": 54} >>> G.nodes[0]["viz"]["position"] = {"x": 0, "y": 1} >>> G.nodes[0]["viz"]["color"] = {"r": 0, "g": 0, "b": 256} Notes ----- This implementation does not support mixed graphs (directed and undirected edges together). The node id attribute is set to be the string of the node label. If you want to specify an id use set it as node data, e.g. node['a']['id']=1 to set the id of node 'a' to 1. References ---------- .. [1] GEXF File Format, https://gephi.org/gexf/format/ .. [2] GEXF schema, https://gephi.org/gexf/format/schema.html """ writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint, version=version) writer.add_graph(G) writer.write(path)
[docs]def generate_gexf(G, encoding="utf-8", prettyprint=True, version="1.2draft"): """Generate lines of GEXF format representation of G. "GEXF (Graph Exchange XML Format) is a language for describing complex networks structures, their associated data and dynamics" [1]_. Parameters ---------- G : graph A NetworkX graph encoding : string (optional, default: 'utf-8') Encoding for text data. prettyprint : bool (optional, default: True) If True use line breaks and indenting in output XML. version : string (default: 1.2draft) Version of GEFX File Format (see https://gephi.org/gexf/format/schema.html) Supported values: "1.1draft", "1.2draft" Examples -------- >>> G = nx.path_graph(4) >>> linefeed = chr(10) # linefeed=\n >>> s = linefeed.join(nx.generate_gexf(G)) >>> for line in nx.generate_gexf(G): # doctest: +SKIP ... print(line) Notes ----- This implementation does not support mixed graphs (directed and undirected edges together). The node id attribute is set to be the string of the node label. If you want to specify an id use set it as node data, e.g. node['a']['id']=1 to set the id of node 'a' to 1. References ---------- .. [1] GEXF File Format, https://gephi.org/gexf/format/ """ writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint, version=version) writer.add_graph(G) yield from str(writer).splitlines()
[docs]@open_file(0, mode="rb") def read_gexf(path, node_type=None, relabel=False, version="1.2draft"): """Read graph in GEXF format from path. "GEXF (Graph Exchange XML Format) is a language for describing complex networks structures, their associated data and dynamics" [1]_. Parameters ---------- path : file or string File or file name to read. File names ending in .gz or .bz2 will be decompressed. node_type: Python type (default: None) Convert node ids to this type if not None. relabel : bool (default: False) If True relabel the nodes to use the GEXF node "label" attribute instead of the node "id" attribute as the NetworkX node label. version : string (default: 1.2draft) Version of GEFX File Format (see https://gephi.org/gexf/format/schema.html) Supported values: "1.1draft", "1.2draft" Returns ------- graph: NetworkX graph If no parallel edges are found a Graph or DiGraph is returned. Otherwise a MultiGraph or MultiDiGraph is returned. Notes ----- This implementation does not support mixed graphs (directed and undirected edges together). References ---------- .. [1] GEXF File Format, https://gephi.org/gexf/format/ """ reader = GEXFReader(node_type=node_type, version=version) if relabel: G = relabel_gexf_graph(reader(path)) else: G = reader(path) return G
class GEXF: versions = {} d = { "NS_GEXF": "http://www.gexf.net/1.1draft", "NS_VIZ": "http://www.gexf.net/1.1draft/viz", "NS_XSI": "http://www.w3.org/2001/XMLSchema-instance", "SCHEMALOCATION": " ".join( ["http://www.gexf.net/1.1draft", "http://www.gexf.net/1.1draft/gexf.xsd"] ), "VERSION": "1.1", } versions["1.1draft"] = d d = { "NS_GEXF": "http://www.gexf.net/1.2draft", "NS_VIZ": "http://www.gexf.net/1.2draft/viz", "NS_XSI": "http://www.w3.org/2001/XMLSchema-instance", "SCHEMALOCATION": " ".join( ["http://www.gexf.net/1.2draft", "http://www.gexf.net/1.2draft/gexf.xsd"] ), "VERSION": "1.2", } versions["1.2draft"] = d def construct_types(self): types = [ (int, "integer"), (float, "float"), (float, "double"), (bool, "boolean"), (list, "string"), (dict, "string"), (int, "long"), (str, "liststring"), (str, "anyURI"), (str, "string"), ] # These additions to types allow writing numpy types try: import numpy as np except ImportError: pass else: # prepend so that python types are created upon read (last entry wins) types = [ (np.float64, "float"), (np.float32, "float"), (np.float16, "float"), (np.float_, "float"), (np.int_, "int"), (np.int8, "int"), (np.int16, "int"), (np.int32, "int"), (np.int64, "int"), (np.uint8, "int"), (np.uint16, "int"), (np.uint32, "int"), (np.uint64, "int"), (np.int_, "int"), (np.intc, "int"), (np.intp, "int"), ] + types self.xml_type = dict(types) self.python_type = dict(reversed(a) for a in types) # http://www.w3.org/TR/xmlschema-2/#boolean convert_bool = { "true": True, "false": False, "True": True, "False": False, "0": False, 0: False, "1": True, 1: True, } def set_version(self, version): d = self.versions.get(version) if d is None: raise nx.NetworkXError(f"Unknown GEXF version {version}.") self.NS_GEXF = d["NS_GEXF"] self.NS_VIZ = d["NS_VIZ"] self.NS_XSI = d["NS_XSI"] self.SCHEMALOCATION = d["SCHEMALOCATION"] self.VERSION = d["VERSION"] self.version = version class GEXFWriter(GEXF): # class for writing GEXF format files # use write_gexf() function def __init__( self, graph=None, encoding="utf-8", prettyprint=True, version="1.2draft" ): self.construct_types() self.prettyprint = prettyprint self.encoding = encoding self.set_version(version) self.xml = Element( "gexf", { "xmlns": self.NS_GEXF, "xmlns:xsi": self.NS_XSI, "xsi:schemaLocation": self.SCHEMALOCATION, "version": self.VERSION, }, ) # Make meta element a non-graph element # Also add lastmodifieddate as attribute, not tag meta_element = Element("meta") subelement_text = f"NetworkX {nx.__version__}" SubElement(meta_element, "creator").text = subelement_text meta_element.set("lastmodifieddate", time.strftime("%Y-%m-%d")) self.xml.append(meta_element) register_namespace("viz", self.NS_VIZ) # counters for edge and attribute identifiers self.edge_id = itertools.count() self.attr_id = itertools.count() self.all_edge_ids = set() # default attributes are stored in dictionaries self.attr = {} self.attr["node"] = {} self.attr["edge"] = {} self.attr["node"]["dynamic"] = {} self.attr["node"]["static"] = {} self.attr["edge"]["dynamic"] = {} self.attr["edge"]["static"] = {} if graph is not None: self.add_graph(graph) def __str__(self): if self.prettyprint: self.indent(self.xml) s = tostring(self.xml).decode(self.encoding) return s def add_graph(self, G): # first pass through G collecting edge ids for u, v, dd in G.edges(data=True): eid = dd.get("id") if eid is not None: self.all_edge_ids.add(str(eid)) # set graph attributes if G.graph.get("mode") == "dynamic": mode = "dynamic" else: mode = "static" # Add a graph element to the XML if G.is_directed(): default = "directed" else: default = "undirected" name = G.graph.get("name", "") graph_element = Element("graph", defaultedgetype=default, mode=mode, name=name) self.graph_element = graph_element self.add_nodes(G, graph_element) self.add_edges(G, graph_element) self.xml.append(graph_element) def add_nodes(self, G, graph_element): nodes_element = Element("nodes") for node, data in G.nodes(data=True): node_data = data.copy() node_id = str(node_data.pop("id", node)) kw = {"id": node_id} label = str(node_data.pop("label", node)) kw["label"] = label try: pid = node_data.pop("pid") kw["pid"] = str(pid) except KeyError: pass try: start = node_data.pop("start") kw["start"] = str(start) self.alter_graph_mode_timeformat(start) except KeyError: pass try: end = node_data.pop("end") kw["end"] = str(end) self.alter_graph_mode_timeformat(end) except KeyError: pass # add node element with attributes node_element = Element("node", **kw) # add node element and attr subelements default = G.graph.get("node_default", {}) node_data = self.add_parents(node_element, node_data) if self.VERSION == "1.1": node_data = self.add_slices(node_element, node_data) else: node_data = self.add_spells(node_element, node_data) node_data = self.add_viz(node_element, node_data) node_data = self.add_attributes("node", node_element, node_data, default) nodes_element.append(node_element) graph_element.append(nodes_element) def add_edges(self, G, graph_element): def edge_key_data(G): # helper function to unify multigraph and graph edge iterator if G.is_multigraph(): for u, v, key, data in G.edges(data=True, keys=True): edge_data = data.copy() edge_data.update(key=key) edge_id = edge_data.pop("id", None) if edge_id is None: edge_id = next(self.edge_id) while str(edge_id) in self.all_edge_ids: edge_id = next(self.edge_id) self.all_edge_ids.add(str(edge_id)) yield u, v, edge_id, edge_data else: for u, v, data in G.edges(data=True): edge_data = data.copy() edge_id = edge_data.pop("id", None) if edge_id is None: edge_id = next(self.edge_id) while str(edge_id) in self.all_edge_ids: edge_id = next(self.edge_id) self.all_edge_ids.add(str(edge_id)) yield u, v, edge_id, edge_data edges_element = Element("edges") for u, v, key, edge_data in edge_key_data(G): kw = {"id": str(key)} try: edge_label = edge_data.pop("label") kw["label"] = str(edge_label) except KeyError: pass try: edge_weight = edge_data.pop("weight") kw["weight"] = str(edge_weight) except KeyError: pass try: edge_type = edge_data.pop("type") kw["type"] = str(edge_type) except KeyError: pass try: start = edge_data.pop("start") kw["start"] = str(start) self.alter_graph_mode_timeformat(start) except KeyError: pass try: end = edge_data.pop("end") kw["end"] = str(end) self.alter_graph_mode_timeformat(end) except KeyError: pass source_id = str(G.nodes[u].get("id", u)) target_id = str(G.nodes[v].get("id", v)) edge_element = Element("edge", source=source_id, target=target_id, **kw) default = G.graph.get("edge_default", {}) if self.VERSION == "1.1": edge_data = self.add_slices(edge_element, edge_data) else: edge_data = self.add_spells(edge_element, edge_data) edge_data = self.add_viz(edge_element, edge_data) edge_data = self.add_attributes("edge", edge_element, edge_data, default) edges_element.append(edge_element) graph_element.append(edges_element) def add_attributes(self, node_or_edge, xml_obj, data, default): # Add attrvalues to node or edge attvalues = Element("attvalues") if len(data) == 0: return data mode = "static" for k, v in data.items(): # rename generic multigraph key to avoid any name conflict if k == "key": k = "networkx_key" val_type = type(v) if val_type not in self.xml_type: raise TypeError(f"attribute value type is not allowed: {val_type}") if isinstance(v, list): # dynamic data for val, start, end in v: val_type = type(val) if start is not None or end is not None: mode = "dynamic" self.alter_graph_mode_timeformat(start) self.alter_graph_mode_timeformat(end) break attr_id = self.get_attr_id( str(k), self.xml_type[val_type], node_or_edge, default, mode ) for val, start, end in v: e = Element("attvalue") e.attrib["for"] = attr_id e.attrib["value"] = str(val) # Handle nan, inf, -inf differently if val_type == float: if e.attrib["value"] == "inf": e.attrib["value"] = "INF" elif e.attrib["value"] == "nan": e.attrib["value"] = "NaN" elif e.attrib["value"] == "-inf": e.attrib["value"] = "-INF" if start is not None: e.attrib["start"] = str(start) if end is not None: e.attrib["end"] = str(end) attvalues.append(e) else: # static data mode = "static" attr_id = self.get_attr_id( str(k), self.xml_type[val_type], node_or_edge, default, mode ) e = Element("attvalue") e.attrib["for"] = attr_id if isinstance(v, bool): e.attrib["value"] = str(v).lower() else: e.attrib["value"] = str(v) # Handle float nan, inf, -inf differently if val_type == float: if e.attrib["value"] == "inf": e.attrib["value"] = "INF" elif e.attrib["value"] == "nan": e.attrib["value"] = "NaN" elif e.attrib["value"] == "-inf": e.attrib["value"] = "-INF" attvalues.append(e) xml_obj.append(attvalues) return data def get_attr_id(self, title, attr_type, edge_or_node, default, mode): # find the id of the attribute or generate a new id try: return self.attr[edge_or_node][mode][title] except KeyError: # generate new id new_id = str(next(self.attr_id)) self.attr[edge_or_node][mode][title] = new_id attr_kwargs = {"id": new_id, "title": title, "type": attr_type} attribute = Element("attribute", **attr_kwargs) # add subelement for data default value if present default_title = default.get(title) if default_title is not None: default_element = Element("default") default_element.text = str(default_title) attribute.append(default_element) # new insert it into the XML attributes_element = None for a in self.graph_element.findall("attributes"): # find existing attributes element by class and mode a_class = a.get("class") a_mode = a.get("mode", "static") if a_class == edge_or_node and a_mode == mode: attributes_element = a if attributes_element is None: # create new attributes element attr_kwargs = {"mode": mode, "class": edge_or_node} attributes_element = Element("attributes", **attr_kwargs) self.graph_element.insert(0, attributes_element) attributes_element.append(attribute) return new_id def add_viz(self, element, node_data): viz = node_data.pop("viz", False) if viz: color = viz.get("color") if color is not None: if self.VERSION == "1.1": e = Element( f"{{{self.NS_VIZ}}}color", r=str(color.get("r")), g=str(color.get("g")), b=str(color.get("b")), ) else: e = Element( f"{{{self.NS_VIZ}}}color", r=str(color.get("r")), g=str(color.get("g")), b=str(color.get("b")), a=str(color.get("a")), ) element.append(e) size = viz.get("size") if size is not None: e = Element(f"{{{self.NS_VIZ}}}size", value=str(size)) element.append(e) thickness = viz.get("thickness") if thickness is not None: e = Element(f"{{{self.NS_VIZ}}}thickness", value=str(thickness)) element.append(e) shape = viz.get("shape") if shape is not None: if shape.startswith("http"): e = Element( f"{{{self.NS_VIZ}}}shape", value="image", uri=str(shape) ) else: e = Element(f"{{{self.NS_VIZ}}}shape", value=str(shape)) element.append(e) position = viz.get("position") if position is not None: e = Element( f"{{{self.NS_VIZ}}}position", x=str(position.get("x")), y=str(position.get("y")), z=str(position.get("z")), ) element.append(e) return node_data def add_parents(self, node_element, node_data): parents = node_data.pop("parents", False) if parents: parents_element = Element("parents") for p in parents: e = Element("parent") e.attrib["for"] = str(p) parents_element.append(e) node_element.append(parents_element) return node_data def add_slices(self, node_or_edge_element, node_or_edge_data): slices = node_or_edge_data.pop("slices", False) if slices: slices_element = Element("slices") for start, end in slices: e = Element("slice", start=str(start), end=str(end)) slices_element.append(e) node_or_edge_element.append(slices_element) return node_or_edge_data def add_spells(self, node_or_edge_element, node_or_edge_data): spells = node_or_edge_data.pop("spells", False) if spells: spells_element = Element("spells") for start, end in spells: e = Element("spell") if start is not None: e.attrib["start"] = str(start) self.alter_graph_mode_timeformat(start) if end is not None: e.attrib["end"] = str(end) self.alter_graph_mode_timeformat(end) spells_element.append(e) node_or_edge_element.append(spells_element) return node_or_edge_data def alter_graph_mode_timeformat(self, start_or_end): # If 'start' or 'end' appears, alter Graph mode to dynamic and # set timeformat if self.graph_element.get("mode") == "static": if start_or_end is not None: if isinstance(start_or_end, str): timeformat = "date" elif isinstance(start_or_end, float): timeformat = "double" elif isinstance(start_or_end, int): timeformat = "long" else: raise nx.NetworkXError( "timeformat should be of the type int, float or str" ) self.graph_element.set("timeformat", timeformat) self.graph_element.set("mode", "dynamic") def write(self, fh): # Serialize graph G in GEXF to the open fh if self.prettyprint: self.indent(self.xml) document = ElementTree(self.xml) document.write(fh, encoding=self.encoding, xml_declaration=True) def indent(self, elem, level=0): # in-place prettyprint formatter i = "\n" + " " * level if len(elem): if not elem.text or not elem.text.strip(): elem.text = i + " " if not elem.tail or not elem.tail.strip(): elem.tail = i for elem in elem: self.indent(elem, level + 1) if not elem.tail or not elem.tail.strip(): elem.tail = i else: if level and (not elem.tail or not elem.tail.strip()): elem.tail = i class GEXFReader(GEXF): # Class to read GEXF format files # use read_gexf() function def __init__(self, node_type=None, version="1.2draft"): self.construct_types() self.node_type = node_type # assume simple graph and test for multigraph on read self.simple_graph = True self.set_version(version) def __call__(self, stream): self.xml = ElementTree(file=stream) g = self.xml.find(f"{{{self.NS_GEXF}}}graph") if g is not None: return self.make_graph(g) # try all the versions for version in self.versions: self.set_version(version) g = self.xml.find(f"{{{self.NS_GEXF}}}graph") if g is not None: return self.make_graph(g) raise nx.NetworkXError("No <graph> element in GEXF file.") def make_graph(self, graph_xml): # start with empty DiGraph or MultiDiGraph edgedefault = graph_xml.get("defaultedgetype", None) if edgedefault == "directed": G = nx.MultiDiGraph() else: G = nx.MultiGraph() # graph attributes graph_name = graph_xml.get("name", "") if graph_name != "": G.graph["name"] = graph_name graph_start = graph_xml.get("start") if graph_start is not None: G.graph["start"] = graph_start graph_end = graph_xml.get("end") if graph_end is not None: G.graph["end"] = graph_end graph_mode = graph_xml.get("mode", "") if graph_mode == "dynamic": G.graph["mode"] = "dynamic" else: G.graph["mode"] = "static" # timeformat self.timeformat = graph_xml.get("timeformat") if self.timeformat == "date": self.timeformat = "string" # node and edge attributes attributes_elements = graph_xml.findall(f"{{{self.NS_GEXF}}}attributes") # dictionaries to hold attributes and attribute defaults node_attr = {} node_default = {} edge_attr = {} edge_default = {} for a in attributes_elements: attr_class = a.get("class") if attr_class == "node": na, nd = self.find_gexf_attributes(a) node_attr.update(na) node_default.update(nd) G.graph["node_default"] = node_default elif attr_class == "edge": ea, ed = self.find_gexf_attributes(a) edge_attr.update(ea) edge_default.update(ed) G.graph["edge_default"] = edge_default else: raise # unknown attribute class # Hack to handle Gephi0.7beta bug # add weight attribute ea = {"weight": {"type": "double", "mode": "static", "title": "weight"}} ed = {} edge_attr.update(ea) edge_default.update(ed) G.graph["edge_default"] = edge_default # add nodes nodes_element = graph_xml.find(f"{{{self.NS_GEXF}}}nodes") if nodes_element is not None: for node_xml in nodes_element.findall(f"{{{self.NS_GEXF}}}node"): self.add_node(G, node_xml, node_attr) # add edges edges_element = graph_xml.find(f"{{{self.NS_GEXF}}}edges") if edges_element is not None: for edge_xml in edges_element.findall(f"{{{self.NS_GEXF}}}edge"): self.add_edge(G, edge_xml, edge_attr) # switch to Graph or DiGraph if no parallel edges were found. if self.simple_graph: if G.is_directed(): G = nx.DiGraph(G) else: G = nx.Graph(G) return G def add_node(self, G, node_xml, node_attr, node_pid=None): # add a single node with attributes to the graph # get attributes and subattributues for node data = self.decode_attr_elements(node_attr, node_xml) data = self.add_parents(data, node_xml) # add any parents if self.VERSION == "1.1": data = self.add_slices(data, node_xml) # add slices else: data = self.add_spells(data, node_xml) # add spells data = self.add_viz(data, node_xml) # add viz data = self.add_start_end(data, node_xml) # add start/end # find the node id and cast it to the appropriate type node_id = node_xml.get("id") if self.node_type is not None: node_id = self.node_type(node_id) # every node should have a label node_label = node_xml.get("label") data["label"] = node_label # parent node id node_pid = node_xml.get("pid", node_pid) if node_pid is not None: data["pid"] = node_pid # check for subnodes, recursive subnodes = node_xml.find(f"{{{self.NS_GEXF}}}nodes") if subnodes is not None: for node_xml in subnodes.findall(f"{{{self.NS_GEXF}}}node"): self.add_node(G, node_xml, node_attr, node_pid=node_id) G.add_node(node_id, **data) def add_start_end(self, data, xml): # start and end times ttype = self.timeformat node_start = xml.get("start") if node_start is not None: data["start"] = self.python_type[ttype](node_start) node_end = xml.get("end") if node_end is not None: data["end"] = self.python_type[ttype](node_end) return data def add_viz(self, data, node_xml): # add viz element for node viz = {} color = node_xml.find(f"{{{self.NS_VIZ}}}color") if color is not None: if self.VERSION == "1.1": viz["color"] = { "r": int(color.get("r")), "g": int(color.get("g")), "b": int(color.get("b")), } else: viz["color"] = { "r": int(color.get("r")), "g": int(color.get("g")), "b": int(color.get("b")), "a": float(color.get("a", 1)), } size = node_xml.find(f"{{{self.NS_VIZ}}}size") if size is not None: viz["size"] = float(size.get("value")) thickness = node_xml.find(f"{{{self.NS_VIZ}}}thickness") if thickness is not None: viz["thickness"] = float(thickness.get("value")) shape = node_xml.find(f"{{{self.NS_VIZ}}}shape") if shape is not None: viz["shape"] = shape.get("shape") if viz["shape"] == "image": viz["shape"] = shape.get("uri") position = node_xml.find(f"{{{self.NS_VIZ}}}position") if position is not None: viz["position"] = { "x": float(position.get("x", 0)), "y": float(position.get("y", 0)), "z": float(position.get("z", 0)), } if len(viz) > 0: data["viz"] = viz return data def add_parents(self, data, node_xml): parents_element = node_xml.find(f"{{{self.NS_GEXF}}}parents") if parents_element is not None: data["parents"] = [] for p in parents_element.findall(f"{{{self.NS_GEXF}}}parent"): parent = p.get("for") data["parents"].append(parent) return data def add_slices(self, data, node_or_edge_xml): slices_element = node_or_edge_xml.find(f"{{{self.NS_GEXF}}}slices") if slices_element is not None: data["slices"] = [] for s in slices_element.findall(f"{{{self.NS_GEXF}}}slice"): start = s.get("start") end = s.get("end") data["slices"].append((start, end)) return data def add_spells(self, data, node_or_edge_xml): spells_element = node_or_edge_xml.find(f"{{{self.NS_GEXF}}}spells") if spells_element is not None: data["spells"] = [] ttype = self.timeformat for s in spells_element.findall(f"{{{self.NS_GEXF}}}spell"): start = self.python_type[ttype](s.get("start")) end = self.python_type[ttype](s.get("end")) data["spells"].append((start, end)) return data def add_edge(self, G, edge_element, edge_attr): # add an edge to the graph # raise error if we find mixed directed and undirected edges edge_direction = edge_element.get("type") if G.is_directed() and edge_direction == "undirected": raise nx.NetworkXError("Undirected edge found in directed graph.") if (not G.is_directed()) and edge_direction == "directed": raise nx.NetworkXError("Directed edge found in undirected graph.") # Get source and target and recast type if required source = edge_element.get("source") target = edge_element.get("target") if self.node_type is not None: source = self.node_type(source) target = self.node_type(target) data = self.decode_attr_elements(edge_attr, edge_element) data = self.add_start_end(data, edge_element) if self.VERSION == "1.1": data = self.add_slices(data, edge_element) # add slices else: data = self.add_spells(data, edge_element) # add spells # GEXF stores edge ids as an attribute # NetworkX uses them as keys in multigraphs # if networkx_key is not specified as an attribute edge_id = edge_element.get("id") if edge_id is not None: data["id"] = edge_id # check if there is a 'multigraph_key' and use that as edge_id multigraph_key = data.pop("networkx_key", None) if multigraph_key is not None: edge_id = multigraph_key weight = edge_element.get("weight") if weight is not None: data["weight"] = float(weight) edge_label = edge_element.get("label") if edge_label is not None: data["label"] = edge_label if G.has_edge(source, target): # seen this edge before - this is a multigraph self.simple_graph = False G.add_edge(source, target, key=edge_id, **data) if edge_direction == "mutual": G.add_edge(target, source, key=edge_id, **data) def decode_attr_elements(self, gexf_keys, obj_xml): # Use the key information to decode the attr XML attr = {} # look for outer '<attvalues>' element attr_element = obj_xml.find(f"{{{self.NS_GEXF}}}attvalues") if attr_element is not None: # loop over <attvalue> elements for a in attr_element.findall(f"{{{self.NS_GEXF}}}attvalue"): key = a.get("for") # for is required try: # should be in our gexf_keys dictionary title = gexf_keys[key]["title"] except KeyError as e: raise nx.NetworkXError(f"No attribute defined for={key}.") from e atype = gexf_keys[key]["type"] value = a.get("value") if atype == "boolean": value = self.convert_bool[value] else: value = self.python_type[atype](value) if gexf_keys[key]["mode"] == "dynamic": # for dynamic graphs use list of three-tuples # [(value1,start1,end1), (value2,start2,end2), etc] ttype = self.timeformat start = self.python_type[ttype](a.get("start")) end = self.python_type[ttype](a.get("end")) if title in attr: attr[title].append((value, start, end)) else: attr[title] = [(value, start, end)] else: # for static graphs just assign the value attr[title] = value return attr def find_gexf_attributes(self, attributes_element): # Extract all the attributes and defaults attrs = {} defaults = {} mode = attributes_element.get("mode") for k in attributes_element.findall(f"{{{self.NS_GEXF}}}attribute"): attr_id = k.get("id") title = k.get("title") atype = k.get("type") attrs[attr_id] = {"title": title, "type": atype, "mode": mode} # check for the 'default' subelement of key element and add default = k.find(f"{{{self.NS_GEXF}}}default") if default is not None: if atype == "boolean": value = self.convert_bool[default.text] else: value = self.python_type[atype](default.text) defaults[title] = value return attrs, defaults
[docs]def relabel_gexf_graph(G): """Relabel graph using "label" node keyword for node label. Parameters ---------- G : graph A NetworkX graph read from GEXF data Returns ------- H : graph A NetworkX graph with relabeled nodes Raises ------ NetworkXError If node labels are missing or not unique while relabel=True. Notes ----- This function relabels the nodes in a NetworkX graph with the "label" attribute. It also handles relabeling the specific GEXF node attributes "parents", and "pid". """ # build mapping of node labels, do some error checking try: mapping = [(u, G.nodes[u]["label"]) for u in G] except KeyError as e: raise nx.NetworkXError( "Failed to relabel nodes: missing node labels found. Use relabel=False." ) from e x, y = zip(*mapping) if len(set(y)) != len(G): raise nx.NetworkXError( "Failed to relabel nodes: " "duplicate node labels found. " "Use relabel=False." ) mapping = dict(mapping) H = nx.relabel_nodes(G, mapping) # relabel attributes for n in G: m = mapping[n] H.nodes[m]["id"] = n H.nodes[m].pop("label") if "pid" in H.nodes[m]: H.nodes[m]["pid"] = mapping[G.nodes[n]["pid"]] if "parents" in H.nodes[m]: H.nodes[m]["parents"] = [mapping[p] for p in G.nodes[n]["parents"]] return H