diff env/lib/python3.7/site-packages/networkx/readwrite/gexf.py @ 2:6af9afd405e9 draft

"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/networkx/readwrite/gexf.py	Thu May 14 14:56:58 2020 -0400
@@ -0,0 +1,1052 @@
+# Copyright (C) 2013-2019 by
+#
+# Authors: Aric Hagberg <hagberg@lanl.gov>
+#          Dan Schult <dschult@colgate.edu>
+#          Pieter Swart <swart@lanl.gov>
+# All rights reserved.
+# BSD license.
+# Based on GraphML NetworkX GraphML reader
+"""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, make_str
+try:
+    from xml.etree.cElementTree import (Element, ElementTree, SubElement,
+                                        tostring)
+except ImportError:
+    try:
+        from xml.etree.ElementTree import (Element, ElementTree, SubElement,
+                                           tostring)
+    except ImportError:
+        pass
+
+__all__ = ['write_gexf', 'read_gexf', 'relabel_gexf_graph', 'generate_gexf']
+
+
+@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.
+
+    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 viz schema 1.1, https://gephi.org/gexf/1.1draft/viz
+    """
+    writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint,
+                        version=version)
+    writer.add_graph(G)
+    writer.write(path)
+
+
+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))  # doctest: +SKIP
+    >>> 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)
+    for line in str(writer).splitlines():
+        yield line
+
+
+@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 write.
+       File names ending in .gz or .bz2 will be compressed.
+    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(object):
+    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
+
+    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
+
+    xml_type = dict(types)
+    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('Unknown GEXF version %s.' % 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'):
+        try:
+            import xml.etree.ElementTree as ET
+        except ImportError:
+            raise ImportError('GEXF writer requires '
+                              'xml.elementtree.ElementTree')
+        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 = 'NetworkX {}'.format(nx.__version__)
+        SubElement(meta_element, 'creator').text = subelement_text
+        meta_element.set('lastmodifieddate', time.strftime('%Y-%m-%d'))
+        self.xml.append(meta_element)
+
+        ET.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(make_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 = make_str(node_data.pop('id', node))
+            kw = {'id': node_id}
+            label = make_str(node_data.pop('label', node))
+            kw['label'] = label
+            try:
+                pid = node_data.pop('pid')
+                kw['pid'] = make_str(pid)
+            except KeyError:
+                pass
+            try:
+                start = node_data.pop('start')
+                kw['start'] = make_str(start)
+                self.alter_graph_mode_timeformat(start)
+            except KeyError:
+                pass
+            try:
+                end = node_data.pop('end')
+                kw['end'] = make_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 make_str(edge_id) in self.all_edge_ids:
+                            edge_id = next(self.edge_id)
+                        self.all_edge_ids.add(make_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 make_str(edge_id) in self.all_edge_ids:
+                            edge_id = next(self.edge_id)
+                        self.all_edge_ids.add(make_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': make_str(key)}
+            try:
+                edge_weight = edge_data.pop('weight')
+                kw['weight'] = make_str(edge_weight)
+            except KeyError:
+                pass
+            try:
+                edge_type = edge_data.pop('type')
+                kw['type'] = make_str(edge_type)
+            except KeyError:
+                pass
+            try:
+                start = edge_data.pop('start')
+                kw['start'] = make_str(start)
+                self.alter_graph_mode_timeformat(start)
+            except KeyError:
+                pass
+            try:
+                end = edge_data.pop('end')
+                kw['end'] = make_str(end)
+                self.alter_graph_mode_timeformat(end)
+            except KeyError:
+                pass
+            source_id = make_str(G.nodes[u].get('id', u))
+            target_id = make_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('attribute value type is not allowed: %s'
+                                % 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(make_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'] = make_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'] = make_str(start)
+                    if end is not None:
+                        e.attrib['end'] = make_str(end)
+                    attvalues.append(e)
+            else:
+                # static data
+                mode = 'static'
+                attr_id = self.get_attr_id(make_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'] = make_str(v).lower()
+                else:
+                    e.attrib['value'] = make_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 = make_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('{%s}color' % self.NS_VIZ,
+                                r=str(color.get('r')),
+                                g=str(color.get('g')),
+                                b=str(color.get('b')))
+                else:
+                    e = Element('{%s}color' % self.NS_VIZ,
+                                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('{%s}size' % self.NS_VIZ, value=str(size))
+                element.append(e)
+
+            thickness = viz.get('thickness')
+            if thickness is not None:
+                e = Element('{%s}thickness' % self.NS_VIZ,
+                            value=str(thickness))
+                element.append(e)
+
+            shape = viz.get('shape')
+            if shape is not None:
+                if shape.startswith('http'):
+                    e = Element('{%s}shape' % self.NS_VIZ,
+                                value='image', uri=str(shape))
+                else:
+                    e = Element('{%s}shape' % self.NS_VIZ, value=str(shape))
+                element.append(e)
+
+            position = viz.get('position')
+            if position is not None:
+                e = Element('{%s}position' % self.NS_VIZ,
+                            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'] = make_str(start)
+                    self.alter_graph_mode_timeformat(start)
+                if end is not None:
+                    e.attrib['end'] = make_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'):
+        try:
+            import xml.etree.ElementTree
+        except ImportError:
+            raise ImportError('GEXF reader requires '
+                              'xml.elementtree.ElementTree.')
+        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('{%s}graph' % self.NS_GEXF)
+        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('{%s}graph' % self.NS_GEXF)
+            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('{%s}attributes' %
+                                                self.NS_GEXF)
+        # 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('{%s}nodes' % self.NS_GEXF)
+        if nodes_element is not None:
+            for node_xml in nodes_element.findall('{%s}node' % self.NS_GEXF):
+                self.add_node(G, node_xml, node_attr)
+
+        # add edges
+        edges_element = graph_xml.find('{%s}edges' % self.NS_GEXF)
+        if edges_element is not None:
+            for edge_xml in edges_element.findall('{%s}edge' % self.NS_GEXF):
+                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('{%s}nodes' % self.NS_GEXF)
+        if subnodes is not None:
+            for node_xml in subnodes.findall('{%s}node' % self.NS_GEXF):
+                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('{%s}color' % self.NS_VIZ)
+        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('{%s}size' % self.NS_VIZ)
+        if size is not None:
+            viz['size'] = float(size.get('value'))
+
+        thickness = node_xml.find('{%s}thickness' % self.NS_VIZ)
+        if thickness is not None:
+            viz['thickness'] = float(thickness.get('value'))
+
+        shape = node_xml.find('{%s}shape' % self.NS_VIZ)
+        if shape is not None:
+            viz['shape'] = shape.get('shape')
+            if viz['shape'] == 'image':
+                viz['shape'] = shape.get('uri')
+
+        position = node_xml.find('{%s}position' % self.NS_VIZ)
+        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('{%s}parents' % self.NS_GEXF)
+        if parents_element is not None:
+            data['parents'] = []
+            for p in parents_element.findall('{%s}parent' % self.NS_GEXF):
+                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('{%s}slices' % self.NS_GEXF)
+        if slices_element is not None:
+            data['slices'] = []
+            for s in slices_element.findall('{%s}slice' % self.NS_GEXF):
+                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('{%s}spells' % self.NS_GEXF)
+        if spells_element is not None:
+            data['spells'] = []
+            ttype = self.timeformat
+            for s in spells_element.findall('{%s}spell' % self.NS_GEXF):
+                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('{%s}attvalues' % self.NS_GEXF)
+        if attr_element is not None:
+            # loop over <attvalue> elements
+            for a in attr_element.findall('{%s}attvalue' % self.NS_GEXF):
+                key = a.get('for')  # for is required
+                try:  # should be in our gexf_keys dictionary
+                    title = gexf_keys[key]['title']
+                except KeyError:
+                    raise nx.NetworkXError('No attribute defined for=%s.'
+                                           % key)
+                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('{%s}attribute' % self.NS_GEXF):
+            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('{%s}default' % self.NS_GEXF)
+            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
+
+
+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 relabed 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:
+        raise nx.NetworkXError('Failed to relabel nodes: '
+                               'missing node labels found. '
+                               'Use relabel=False.')
+    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
+
+
+# fixture for pytest
+def setup_module(module):
+    import pytest
+    xml.etree.cElementTree = pytest.importorskip('xml.etree.cElementTree')
+
+
+# fixture for pytest
+def teardown_module(module):
+    import os
+    try:
+        os.unlink('test.gexf')
+    except Exception as e:
+        pass