1053 lines
40 KiB
Python
1053 lines
40 KiB
Python
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# Copyright (C) 2013-2019 by
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#
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# Authors: Aric Hagberg <hagberg@lanl.gov>
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# Dan Schult <dschult@colgate.edu>
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# Pieter Swart <swart@lanl.gov>
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# All rights reserved.
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# BSD license.
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# Based on GraphML NetworkX GraphML reader
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"""Read and write graphs in GEXF format.
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GEXF (Graph Exchange XML Format) is a language for describing complex
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network structures, their associated data and dynamics.
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This implementation does not support mixed graphs (directed and
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undirected edges together).
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Format
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------
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GEXF is an XML format. See https://gephi.org/gexf/format/schema.html for the
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specification and https://gephi.org/gexf/format/basic.html for examples.
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"""
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import itertools
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import time
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import networkx as nx
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from networkx.utils import open_file, make_str
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try:
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from xml.etree.cElementTree import (Element, ElementTree, SubElement,
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tostring)
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except ImportError:
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try:
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from xml.etree.ElementTree import (Element, ElementTree, SubElement,
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tostring)
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except ImportError:
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pass
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__all__ = ['write_gexf', 'read_gexf', 'relabel_gexf_graph', 'generate_gexf']
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@open_file(1, mode='wb')
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def write_gexf(G, path, encoding='utf-8', prettyprint=True,
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version='1.2draft'):
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"""Write G in GEXF format to path.
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"GEXF (Graph Exchange XML Format) is a language for describing
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complex networks structures, their associated data and dynamics" [1]_.
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Node attributes are checked according to the version of the GEXF
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schemas used for parameters which are not user defined,
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e.g. visualization 'viz' [2]_. See example for usage.
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Parameters
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----------
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G : graph
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A NetworkX graph
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path : file or string
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File or file name to write.
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File names ending in .gz or .bz2 will be compressed.
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encoding : string (optional, default: 'utf-8')
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Encoding for text data.
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prettyprint : bool (optional, default: True)
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If True use line breaks and indenting in output XML.
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Examples
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--------
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>>> G = nx.path_graph(4)
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>>> nx.write_gexf(G, "test.gexf")
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# visualization data
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>>> G.nodes[0]['viz'] = {'size': 54}
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>>> G.nodes[0]['viz']['position'] = {'x' : 0, 'y' : 1}
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>>> G.nodes[0]['viz']['color'] = {'r' : 0, 'g' : 0, 'b' : 256}
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Notes
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-----
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This implementation does not support mixed graphs (directed and undirected
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edges together).
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The node id attribute is set to be the string of the node label.
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If you want to specify an id use set it as node data, e.g.
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node['a']['id']=1 to set the id of node 'a' to 1.
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References
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----------
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.. [1] GEXF File Format, https://gephi.org/gexf/format/
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.. [2] GEXF viz schema 1.1, https://gephi.org/gexf/1.1draft/viz
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"""
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writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint,
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version=version)
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writer.add_graph(G)
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writer.write(path)
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def generate_gexf(G, encoding='utf-8', prettyprint=True, version='1.2draft'):
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"""Generate lines of GEXF format representation of G.
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"GEXF (Graph Exchange XML Format) is a language for describing
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complex networks structures, their associated data and dynamics" [1]_.
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Parameters
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----------
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G : graph
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A NetworkX graph
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encoding : string (optional, default: 'utf-8')
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Encoding for text data.
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prettyprint : bool (optional, default: True)
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If True use line breaks and indenting in output XML.
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version : string (default: 1.2draft)
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Version of GEFX File Format (see https://gephi.org/gexf/format/schema.html)
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Supported values: "1.1draft", "1.2draft"
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Examples
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--------
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>>> G = nx.path_graph(4)
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>>> linefeed = chr(10) # linefeed=\n
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>>> s = linefeed.join(nx.generate_gexf(G)) # doctest: +SKIP
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>>> for line in nx.generate_gexf(G): # doctest: +SKIP
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... print line
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Notes
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-----
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This implementation does not support mixed graphs (directed and undirected
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edges together).
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The node id attribute is set to be the string of the node label.
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If you want to specify an id use set it as node data, e.g.
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node['a']['id']=1 to set the id of node 'a' to 1.
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References
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----------
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.. [1] GEXF File Format, https://gephi.org/gexf/format/
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"""
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writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint,
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version=version)
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writer.add_graph(G)
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for line in str(writer).splitlines():
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yield line
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@open_file(0, mode='rb')
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def read_gexf(path, node_type=None, relabel=False, version='1.2draft'):
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"""Read graph in GEXF format from path.
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"GEXF (Graph Exchange XML Format) is a language for describing
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complex networks structures, their associated data and dynamics" [1]_.
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Parameters
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----------
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path : file or string
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File or file name to write.
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File names ending in .gz or .bz2 will be compressed.
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node_type: Python type (default: None)
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Convert node ids to this type if not None.
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relabel : bool (default: False)
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If True relabel the nodes to use the GEXF node "label" attribute
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instead of the node "id" attribute as the NetworkX node label.
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version : string (default: 1.2draft)
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Version of GEFX File Format (see https://gephi.org/gexf/format/schema.html)
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Supported values: "1.1draft", "1.2draft"
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Returns
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-------
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graph: NetworkX graph
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If no parallel edges are found a Graph or DiGraph is returned.
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Otherwise a MultiGraph or MultiDiGraph is returned.
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Notes
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-----
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This implementation does not support mixed graphs (directed and undirected
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edges together).
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References
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----------
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.. [1] GEXF File Format, https://gephi.org/gexf/format/
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"""
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reader = GEXFReader(node_type=node_type, version=version)
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if relabel:
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G = relabel_gexf_graph(reader(path))
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else:
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G = reader(path)
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return G
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class GEXF(object):
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versions = {}
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d = {'NS_GEXF': "http://www.gexf.net/1.1draft",
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'NS_VIZ': "http://www.gexf.net/1.1draft/viz",
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'NS_XSI': "http://www.w3.org/2001/XMLSchema-instance",
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'SCHEMALOCATION': ' '.join(['http://www.gexf.net/1.1draft',
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'http://www.gexf.net/1.1draft/gexf.xsd']),
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'VERSION': '1.1'}
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versions['1.1draft'] = d
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d = {'NS_GEXF': "http://www.gexf.net/1.2draft",
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'NS_VIZ': "http://www.gexf.net/1.2draft/viz",
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'NS_XSI': "http://www.w3.org/2001/XMLSchema-instance",
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'SCHEMALOCATION': ' '.join(['http://www.gexf.net/1.2draft',
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'http://www.gexf.net/1.2draft/gexf.xsd']),
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'VERSION': '1.2'}
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versions['1.2draft'] = d
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types = [(int, "integer"),
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(float, "float"),
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(float, "double"),
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(bool, "boolean"),
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(list, "string"),
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(dict, "string"),
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(int, "long"),
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(str, "liststring"),
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(str, "anyURI"),
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(str, "string")]
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# These additions to types allow writing numpy types
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try:
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import numpy as np
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except ImportError:
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pass
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else:
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# prepend so that python types are created upon read (last entry wins)
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types = [(np.float64, "float"), (np.float32, "float"),
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(np.float16, "float"), (np.float_, "float"),
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(np.int, "int"), (np.int8, "int"),
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(np.int16, "int"), (np.int32, "int"),
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(np.int64, "int"), (np.uint8, "int"),
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(np.uint16, "int"), (np.uint32, "int"),
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(np.uint64, "int"), (np.int_, "int"),
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(np.intc, "int"), (np.intp, "int"),
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] + types
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xml_type = dict(types)
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python_type = dict(reversed(a) for a in types)
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# http://www.w3.org/TR/xmlschema-2/#boolean
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convert_bool = {
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'true': True, 'false': False,
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'True': True, 'False': False,
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'0': False, 0: False,
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'1': True, 1: True
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}
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def set_version(self, version):
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d = self.versions.get(version)
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if d is None:
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raise nx.NetworkXError('Unknown GEXF version %s.' % version)
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self.NS_GEXF = d['NS_GEXF']
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self.NS_VIZ = d['NS_VIZ']
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self.NS_XSI = d['NS_XSI']
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self.SCHEMALOCATION = d['SCHEMALOCATION']
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self.VERSION = d['VERSION']
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self.version = version
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class GEXFWriter(GEXF):
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# class for writing GEXF format files
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# use write_gexf() function
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def __init__(self, graph=None, encoding='utf-8', prettyprint=True,
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version='1.2draft'):
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try:
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import xml.etree.ElementTree as ET
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except ImportError:
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raise ImportError('GEXF writer requires '
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'xml.elementtree.ElementTree')
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self.prettyprint = prettyprint
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self.encoding = encoding
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self.set_version(version)
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self.xml = Element('gexf',
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{'xmlns': self.NS_GEXF,
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'xmlns:xsi': self.NS_XSI,
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'xsi:schemaLocation': self.SCHEMALOCATION,
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'version': self.VERSION})
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# Make meta element a non-graph element
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# Also add lastmodifieddate as attribute, not tag
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meta_element = Element('meta')
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subelement_text = 'NetworkX {}'.format(nx.__version__)
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SubElement(meta_element, 'creator').text = subelement_text
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meta_element.set('lastmodifieddate', time.strftime('%Y-%m-%d'))
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self.xml.append(meta_element)
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ET.register_namespace('viz', self.NS_VIZ)
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# counters for edge and attribute identifiers
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self.edge_id = itertools.count()
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self.attr_id = itertools.count()
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self.all_edge_ids = set()
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# default attributes are stored in dictionaries
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self.attr = {}
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self.attr['node'] = {}
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self.attr['edge'] = {}
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self.attr['node']['dynamic'] = {}
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self.attr['node']['static'] = {}
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self.attr['edge']['dynamic'] = {}
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self.attr['edge']['static'] = {}
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if graph is not None:
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self.add_graph(graph)
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def __str__(self):
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if self.prettyprint:
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self.indent(self.xml)
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s = tostring(self.xml).decode(self.encoding)
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return s
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def add_graph(self, G):
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# first pass through G collecting edge ids
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for u, v, dd in G.edges(data=True):
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eid = dd.get('id')
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if eid is not None:
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self.all_edge_ids.add(make_str(eid))
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# set graph attributes
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if G.graph.get('mode') == 'dynamic':
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mode = 'dynamic'
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else:
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mode = 'static'
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# Add a graph element to the XML
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if G.is_directed():
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default = 'directed'
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else:
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default = 'undirected'
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name = G.graph.get('name', '')
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graph_element = Element('graph', defaultedgetype=default, mode=mode,
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name=name)
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self.graph_element = graph_element
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self.add_nodes(G, graph_element)
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self.add_edges(G, graph_element)
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self.xml.append(graph_element)
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def add_nodes(self, G, graph_element):
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nodes_element = Element('nodes')
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for node, data in G.nodes(data=True):
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node_data = data.copy()
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node_id = make_str(node_data.pop('id', node))
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kw = {'id': node_id}
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label = make_str(node_data.pop('label', node))
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kw['label'] = label
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try:
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pid = node_data.pop('pid')
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kw['pid'] = make_str(pid)
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except KeyError:
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pass
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try:
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start = node_data.pop('start')
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kw['start'] = make_str(start)
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self.alter_graph_mode_timeformat(start)
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except KeyError:
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pass
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try:
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end = node_data.pop('end')
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kw['end'] = make_str(end)
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self.alter_graph_mode_timeformat(end)
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except KeyError:
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pass
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# add node element with attributes
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node_element = Element('node', **kw)
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# add node element and attr subelements
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default = G.graph.get('node_default', {})
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node_data = self.add_parents(node_element, node_data)
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if self.version == '1.1':
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node_data = self.add_slices(node_element, node_data)
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else:
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node_data = self.add_spells(node_element, node_data)
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node_data = self.add_viz(node_element, node_data)
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|
|
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
|