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1066 lines
39 KiB
1066 lines
39 KiB
5 months ago
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"""Read and write graphs in GEXF format.
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.. warning::
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This parser uses the standard xml library present in Python, which is
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insecure - see :external+python:mod:`xml` for additional information.
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Only parse GEFX files you trust.
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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 http://gexf.net/schema.html for the
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specification and http://gexf.net/basic.html for examples.
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"""
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import itertools
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import time
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from xml.etree.ElementTree import (
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Element,
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ElementTree,
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SubElement,
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register_namespace,
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tostring,
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)
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import networkx as nx
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from networkx.utils import open_file
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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, 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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version: string (optional, default: '1.2draft')
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The version of GEXF to be used for nodes attributes checking
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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, http://gexf.net/
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.. [2] GEXF schema, http://gexf.net/schema.html
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"""
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writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint, 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 http://gexf.net/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))
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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, version=version)
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writer.add_graph(G)
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yield from str(writer).splitlines()
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@open_file(0, mode="rb")
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@nx._dispatchable(graphs=None, returns_graph=True)
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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 read.
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File names ending in .gz or .bz2 will be decompressed.
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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 http://gexf.net/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, http://gexf.net/
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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:
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versions = {
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"1.1draft": {
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"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(
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[
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"http://www.gexf.net/1.1draft",
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"http://www.gexf.net/1.1draft/gexf.xsd",
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]
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),
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"VERSION": "1.1",
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},
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"1.2draft": {
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"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(
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[
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"http://www.gexf.net/1.2draft",
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"http://www.gexf.net/1.2draft/gexf.xsd",
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]
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),
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"VERSION": "1.2",
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},
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}
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def construct_types(self):
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types = [
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(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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]
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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 = [
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(np.float64, "float"),
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(np.float32, "float"),
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(np.float16, "float"),
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(np.int_, "int"),
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(np.int8, "int"),
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(np.int16, "int"),
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(np.int32, "int"),
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(np.int64, "int"),
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(np.uint8, "int"),
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(np.uint16, "int"),
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(np.uint32, "int"),
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(np.uint64, "int"),
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(np.int_, "int"),
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(np.intc, "int"),
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(np.intp, "int"),
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] + types
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self.xml_type = dict(types)
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self.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,
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"false": False,
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"True": True,
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"False": False,
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"0": False,
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0: False,
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"1": True,
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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(f"Unknown GEXF version {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__(
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self, graph=None, encoding="utf-8", prettyprint=True, version="1.2draft"
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):
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self.construct_types()
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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(
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"gexf",
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{
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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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},
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)
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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 = f"NetworkX {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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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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||
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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(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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||
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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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||
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name = G.graph.get("name", "")
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||
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graph_element = Element("graph", defaultedgetype=default, mode=mode, name=name)
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||
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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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||
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self.xml.append(graph_element)
|
||
|
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|
||
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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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|
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node_id = str(node_data.pop("id", node))
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kw = {"id": node_id}
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label = str(node_data.pop("label", node))
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||
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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"] = str(pid)
|
||
|
|
except KeyError:
|
||
|
|
pass
|
||
|
|
try:
|
||
|
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start = node_data.pop("start")
|
||
|
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kw["start"] = str(start)
|
||
|
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self.alter_graph_mode_timeformat(start)
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||
|
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except KeyError:
|
||
|
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pass
|
||
|
|
try:
|
||
|
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end = node_data.pop("end")
|
||
|
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kw["end"] = str(end)
|
||
|
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self.alter_graph_mode_timeformat(end)
|
||
|
|
except KeyError:
|
||
|
|
pass
|
||
|
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# add node element with attributes
|
||
|
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node_element = Element("node", **kw)
|
||
|
|
# add node element and attr subelements
|
||
|
|
default = G.graph.get("node_default", {})
|
||
|
|
node_data = self.add_parents(node_element, node_data)
|
||
|
|
if self.VERSION == "1.1":
|
||
|
|
node_data = self.add_slices(node_element, node_data)
|
||
|
|
else:
|
||
|
|
node_data = self.add_spells(node_element, node_data)
|
||
|
|
node_data = self.add_viz(node_element, node_data)
|
||
|
|
node_data = self.add_attributes("node", node_element, node_data, default)
|
||
|
|
nodes_element.append(node_element)
|
||
|
|
graph_element.append(nodes_element)
|
||
|
|
|
||
|
|
def add_edges(self, G, graph_element):
|
||
|
|
def edge_key_data(G):
|
||
|
|
# helper function to unify multigraph and graph edge iterator
|
||
|
|
if G.is_multigraph():
|
||
|
|
for u, v, key, data in G.edges(data=True, keys=True):
|
||
|
|
edge_data = data.copy()
|
||
|
|
edge_data.update(key=key)
|
||
|
|
edge_id = edge_data.pop("id", None)
|
||
|
|
if edge_id is None:
|
||
|
|
edge_id = next(self.edge_id)
|
||
|
|
while str(edge_id) in self.all_edge_ids:
|
||
|
|
edge_id = next(self.edge_id)
|
||
|
|
self.all_edge_ids.add(str(edge_id))
|
||
|
|
yield u, v, edge_id, edge_data
|
||
|
|
else:
|
||
|
|
for u, v, data in G.edges(data=True):
|
||
|
|
edge_data = data.copy()
|
||
|
|
edge_id = edge_data.pop("id", None)
|
||
|
|
if edge_id is None:
|
||
|
|
edge_id = next(self.edge_id)
|
||
|
|
while str(edge_id) in self.all_edge_ids:
|
||
|
|
edge_id = next(self.edge_id)
|
||
|
|
self.all_edge_ids.add(str(edge_id))
|
||
|
|
yield u, v, edge_id, edge_data
|
||
|
|
|
||
|
|
edges_element = Element("edges")
|
||
|
|
for u, v, key, edge_data in edge_key_data(G):
|
||
|
|
kw = {"id": str(key)}
|
||
|
|
try:
|
||
|
|
edge_label = edge_data.pop("label")
|
||
|
|
kw["label"] = str(edge_label)
|
||
|
|
except KeyError:
|
||
|
|
pass
|
||
|
|
try:
|
||
|
|
edge_weight = edge_data.pop("weight")
|
||
|
|
kw["weight"] = str(edge_weight)
|
||
|
|
except KeyError:
|
||
|
|
pass
|
||
|
|
try:
|
||
|
|
edge_type = edge_data.pop("type")
|
||
|
|
kw["type"] = str(edge_type)
|
||
|
|
except KeyError:
|
||
|
|
pass
|
||
|
|
try:
|
||
|
|
start = edge_data.pop("start")
|
||
|
|
kw["start"] = str(start)
|
||
|
|
self.alter_graph_mode_timeformat(start)
|
||
|
|
except KeyError:
|
||
|
|
pass
|
||
|
|
try:
|
||
|
|
end = edge_data.pop("end")
|
||
|
|
kw["end"] = str(end)
|
||
|
|
self.alter_graph_mode_timeformat(end)
|
||
|
|
except KeyError:
|
||
|
|
pass
|
||
|
|
source_id = str(G.nodes[u].get("id", u))
|
||
|
|
target_id = str(G.nodes[v].get("id", v))
|
||
|
|
edge_element = Element("edge", source=source_id, target=target_id, **kw)
|
||
|
|
default = G.graph.get("edge_default", {})
|
||
|
|
if self.VERSION == "1.1":
|
||
|
|
edge_data = self.add_slices(edge_element, edge_data)
|
||
|
|
else:
|
||
|
|
edge_data = self.add_spells(edge_element, edge_data)
|
||
|
|
edge_data = self.add_viz(edge_element, edge_data)
|
||
|
|
edge_data = self.add_attributes("edge", edge_element, edge_data, default)
|
||
|
|
edges_element.append(edge_element)
|
||
|
|
graph_element.append(edges_element)
|
||
|
|
|
||
|
|
def add_attributes(self, node_or_edge, xml_obj, data, default):
|
||
|
|
# Add attrvalues to node or edge
|
||
|
|
attvalues = Element("attvalues")
|
||
|
|
if len(data) == 0:
|
||
|
|
return data
|
||
|
|
mode = "static"
|
||
|
|
for k, v in data.items():
|
||
|
|
# rename generic multigraph key to avoid any name conflict
|
||
|
|
if k == "key":
|
||
|
|
k = "networkx_key"
|
||
|
|
val_type = type(v)
|
||
|
|
if val_type not in self.xml_type:
|
||
|
|
raise TypeError(f"attribute value type is not allowed: {val_type}")
|
||
|
|
if isinstance(v, list):
|
||
|
|
# dynamic data
|
||
|
|
for val, start, end in v:
|
||
|
|
val_type = type(val)
|
||
|
|
if start is not None or end is not None:
|
||
|
|
mode = "dynamic"
|
||
|
|
self.alter_graph_mode_timeformat(start)
|
||
|
|
self.alter_graph_mode_timeformat(end)
|
||
|
|
break
|
||
|
|
attr_id = self.get_attr_id(
|
||
|
|
str(k), self.xml_type[val_type], node_or_edge, default, mode
|
||
|
|
)
|
||
|
|
for val, start, end in v:
|
||
|
|
e = Element("attvalue")
|
||
|
|
e.attrib["for"] = attr_id
|
||
|
|
e.attrib["value"] = str(val)
|
||
|
|
# Handle nan, inf, -inf differently
|
||
|
|
if val_type == float:
|
||
|
|
if e.attrib["value"] == "inf":
|
||
|
|
e.attrib["value"] = "INF"
|
||
|
|
elif e.attrib["value"] == "nan":
|
||
|
|
e.attrib["value"] = "NaN"
|
||
|
|
elif e.attrib["value"] == "-inf":
|
||
|
|
e.attrib["value"] = "-INF"
|
||
|
|
if start is not None:
|
||
|
|
e.attrib["start"] = str(start)
|
||
|
|
if end is not None:
|
||
|
|
e.attrib["end"] = str(end)
|
||
|
|
attvalues.append(e)
|
||
|
|
else:
|
||
|
|
# static data
|
||
|
|
mode = "static"
|
||
|
|
attr_id = self.get_attr_id(
|
||
|
|
str(k), self.xml_type[val_type], node_or_edge, default, mode
|
||
|
|
)
|
||
|
|
e = Element("attvalue")
|
||
|
|
e.attrib["for"] = attr_id
|
||
|
|
if isinstance(v, bool):
|
||
|
|
e.attrib["value"] = str(v).lower()
|
||
|
|
else:
|
||
|
|
e.attrib["value"] = str(v)
|
||
|
|
# Handle float nan, inf, -inf differently
|
||
|
|
if val_type == float:
|
||
|
|
if e.attrib["value"] == "inf":
|
||
|
|
e.attrib["value"] = "INF"
|
||
|
|
elif e.attrib["value"] == "nan":
|
||
|
|
e.attrib["value"] = "NaN"
|
||
|
|
elif e.attrib["value"] == "-inf":
|
||
|
|
e.attrib["value"] = "-INF"
|
||
|
|
attvalues.append(e)
|
||
|
|
xml_obj.append(attvalues)
|
||
|
|
return data
|
||
|
|
|
||
|
|
def get_attr_id(self, title, attr_type, edge_or_node, default, mode):
|
||
|
|
# find the id of the attribute or generate a new id
|
||
|
|
try:
|
||
|
|
return self.attr[edge_or_node][mode][title]
|
||
|
|
except KeyError:
|
||
|
|
# generate new id
|
||
|
|
new_id = str(next(self.attr_id))
|
||
|
|
self.attr[edge_or_node][mode][title] = new_id
|
||
|
|
attr_kwargs = {"id": new_id, "title": title, "type": attr_type}
|
||
|
|
attribute = Element("attribute", **attr_kwargs)
|
||
|
|
# add subelement for data default value if present
|
||
|
|
default_title = default.get(title)
|
||
|
|
if default_title is not None:
|
||
|
|
default_element = Element("default")
|
||
|
|
default_element.text = str(default_title)
|
||
|
|
attribute.append(default_element)
|
||
|
|
# new insert it into the XML
|
||
|
|
attributes_element = None
|
||
|
|
for a in self.graph_element.findall("attributes"):
|
||
|
|
# find existing attributes element by class and mode
|
||
|
|
a_class = a.get("class")
|
||
|
|
a_mode = a.get("mode", "static")
|
||
|
|
if a_class == edge_or_node and a_mode == mode:
|
||
|
|
attributes_element = a
|
||
|
|
if attributes_element is None:
|
||
|
|
# create new attributes element
|
||
|
|
attr_kwargs = {"mode": mode, "class": edge_or_node}
|
||
|
|
attributes_element = Element("attributes", **attr_kwargs)
|
||
|
|
self.graph_element.insert(0, attributes_element)
|
||
|
|
attributes_element.append(attribute)
|
||
|
|
return new_id
|
||
|
|
|
||
|
|
def add_viz(self, element, node_data):
|
||
|
|
viz = node_data.pop("viz", False)
|
||
|
|
if viz:
|
||
|
|
color = viz.get("color")
|
||
|
|
if color is not None:
|
||
|
|
if self.VERSION == "1.1":
|
||
|
|
e = Element(
|
||
|
|
f"{{{self.NS_VIZ}}}color",
|
||
|
|
r=str(color.get("r")),
|
||
|
|
g=str(color.get("g")),
|
||
|
|
b=str(color.get("b")),
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
e = Element(
|
||
|
|
f"{{{self.NS_VIZ}}}color",
|
||
|
|
r=str(color.get("r")),
|
||
|
|
g=str(color.get("g")),
|
||
|
|
b=str(color.get("b")),
|
||
|
|
a=str(color.get("a", 1.0)),
|
||
|
|
)
|
||
|
|
element.append(e)
|
||
|
|
|
||
|
|
size = viz.get("size")
|
||
|
|
if size is not None:
|
||
|
|
e = Element(f"{{{self.NS_VIZ}}}size", value=str(size))
|
||
|
|
element.append(e)
|
||
|
|
|
||
|
|
thickness = viz.get("thickness")
|
||
|
|
if thickness is not None:
|
||
|
|
e = Element(f"{{{self.NS_VIZ}}}thickness", value=str(thickness))
|
||
|
|
element.append(e)
|
||
|
|
|
||
|
|
shape = viz.get("shape")
|
||
|
|
if shape is not None:
|
||
|
|
if shape.startswith("http"):
|
||
|
|
e = Element(
|
||
|
|
f"{{{self.NS_VIZ}}}shape", value="image", uri=str(shape)
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
e = Element(f"{{{self.NS_VIZ}}}shape", value=str(shape))
|
||
|
|
element.append(e)
|
||
|
|
|
||
|
|
position = viz.get("position")
|
||
|
|
if position is not None:
|
||
|
|
e = Element(
|
||
|
|
f"{{{self.NS_VIZ}}}position",
|
||
|
|
x=str(position.get("x")),
|
||
|
|
y=str(position.get("y")),
|
||
|
|
z=str(position.get("z")),
|
||
|
|
)
|
||
|
|
element.append(e)
|
||
|
|
return node_data
|
||
|
|
|
||
|
|
def add_parents(self, node_element, node_data):
|
||
|
|
parents = node_data.pop("parents", False)
|
||
|
|
if parents:
|
||
|
|
parents_element = Element("parents")
|
||
|
|
for p in parents:
|
||
|
|
e = Element("parent")
|
||
|
|
e.attrib["for"] = str(p)
|
||
|
|
parents_element.append(e)
|
||
|
|
node_element.append(parents_element)
|
||
|
|
return node_data
|
||
|
|
|
||
|
|
def add_slices(self, node_or_edge_element, node_or_edge_data):
|
||
|
|
slices = node_or_edge_data.pop("slices", False)
|
||
|
|
if slices:
|
||
|
|
slices_element = Element("slices")
|
||
|
|
for start, end in slices:
|
||
|
|
e = Element("slice", start=str(start), end=str(end))
|
||
|
|
slices_element.append(e)
|
||
|
|
node_or_edge_element.append(slices_element)
|
||
|
|
return node_or_edge_data
|
||
|
|
|
||
|
|
def add_spells(self, node_or_edge_element, node_or_edge_data):
|
||
|
|
spells = node_or_edge_data.pop("spells", False)
|
||
|
|
if spells:
|
||
|
|
spells_element = Element("spells")
|
||
|
|
for start, end in spells:
|
||
|
|
e = Element("spell")
|
||
|
|
if start is not None:
|
||
|
|
e.attrib["start"] = str(start)
|
||
|
|
self.alter_graph_mode_timeformat(start)
|
||
|
|
if end is not None:
|
||
|
|
e.attrib["end"] = str(end)
|
||
|
|
self.alter_graph_mode_timeformat(end)
|
||
|
|
spells_element.append(e)
|
||
|
|
node_or_edge_element.append(spells_element)
|
||
|
|
return node_or_edge_data
|
||
|
|
|
||
|
|
def alter_graph_mode_timeformat(self, start_or_end):
|
||
|
|
# If 'start' or 'end' appears, alter Graph mode to dynamic and
|
||
|
|
# set timeformat
|
||
|
|
if self.graph_element.get("mode") == "static":
|
||
|
|
if start_or_end is not None:
|
||
|
|
if isinstance(start_or_end, str):
|
||
|
|
timeformat = "date"
|
||
|
|
elif isinstance(start_or_end, float):
|
||
|
|
timeformat = "double"
|
||
|
|
elif isinstance(start_or_end, int):
|
||
|
|
timeformat = "long"
|
||
|
|
else:
|
||
|
|
raise nx.NetworkXError(
|
||
|
|
"timeformat should be of the type int, float or str"
|
||
|
|
)
|
||
|
|
self.graph_element.set("timeformat", timeformat)
|
||
|
|
self.graph_element.set("mode", "dynamic")
|
||
|
|
|
||
|
|
def write(self, fh):
|
||
|
|
# Serialize graph G in GEXF to the open fh
|
||
|
|
if self.prettyprint:
|
||
|
|
self.indent(self.xml)
|
||
|
|
document = ElementTree(self.xml)
|
||
|
|
document.write(fh, encoding=self.encoding, xml_declaration=True)
|
||
|
|
|
||
|
|
def indent(self, elem, level=0):
|
||
|
|
# in-place prettyprint formatter
|
||
|
|
i = "\n" + " " * level
|
||
|
|
if len(elem):
|
||
|
|
if not elem.text or not elem.text.strip():
|
||
|
|
elem.text = i + " "
|
||
|
|
if not elem.tail or not elem.tail.strip():
|
||
|
|
elem.tail = i
|
||
|
|
for elem in elem:
|
||
|
|
self.indent(elem, level + 1)
|
||
|
|
if not elem.tail or not elem.tail.strip():
|
||
|
|
elem.tail = i
|
||
|
|
else:
|
||
|
|
if level and (not elem.tail or not elem.tail.strip()):
|
||
|
|
elem.tail = i
|
||
|
|
|
||
|
|
|
||
|
|
class GEXFReader(GEXF):
|
||
|
|
# Class to read GEXF format files
|
||
|
|
# use read_gexf() function
|
||
|
|
def __init__(self, node_type=None, version="1.2draft"):
|
||
|
|
self.construct_types()
|
||
|
|
self.node_type = node_type
|
||
|
|
# assume simple graph and test for multigraph on read
|
||
|
|
self.simple_graph = True
|
||
|
|
self.set_version(version)
|
||
|
|
|
||
|
|
def __call__(self, stream):
|
||
|
|
self.xml = ElementTree(file=stream)
|
||
|
|
g = self.xml.find(f"{{{self.NS_GEXF}}}graph")
|
||
|
|
if g is not None:
|
||
|
|
return self.make_graph(g)
|
||
|
|
# try all the versions
|
||
|
|
for version in self.versions:
|
||
|
|
self.set_version(version)
|
||
|
|
g = self.xml.find(f"{{{self.NS_GEXF}}}graph")
|
||
|
|
if g is not None:
|
||
|
|
return self.make_graph(g)
|
||
|
|
raise nx.NetworkXError("No <graph> element in GEXF file.")
|
||
|
|
|
||
|
|
def make_graph(self, graph_xml):
|
||
|
|
# start with empty DiGraph or MultiDiGraph
|
||
|
|
edgedefault = graph_xml.get("defaultedgetype", None)
|
||
|
|
if edgedefault == "directed":
|
||
|
|
G = nx.MultiDiGraph()
|
||
|
|
else:
|
||
|
|
G = nx.MultiGraph()
|
||
|
|
|
||
|
|
# graph attributes
|
||
|
|
graph_name = graph_xml.get("name", "")
|
||
|
|
if graph_name != "":
|
||
|
|
G.graph["name"] = graph_name
|
||
|
|
graph_start = graph_xml.get("start")
|
||
|
|
if graph_start is not None:
|
||
|
|
G.graph["start"] = graph_start
|
||
|
|
graph_end = graph_xml.get("end")
|
||
|
|
if graph_end is not None:
|
||
|
|
G.graph["end"] = graph_end
|
||
|
|
graph_mode = graph_xml.get("mode", "")
|
||
|
|
if graph_mode == "dynamic":
|
||
|
|
G.graph["mode"] = "dynamic"
|
||
|
|
else:
|
||
|
|
G.graph["mode"] = "static"
|
||
|
|
|
||
|
|
# timeformat
|
||
|
|
self.timeformat = graph_xml.get("timeformat")
|
||
|
|
if self.timeformat == "date":
|
||
|
|
self.timeformat = "string"
|
||
|
|
|
||
|
|
# node and edge attributes
|
||
|
|
attributes_elements = graph_xml.findall(f"{{{self.NS_GEXF}}}attributes")
|
||
|
|
# dictionaries to hold attributes and attribute defaults
|
||
|
|
node_attr = {}
|
||
|
|
node_default = {}
|
||
|
|
edge_attr = {}
|
||
|
|
edge_default = {}
|
||
|
|
for a in attributes_elements:
|
||
|
|
attr_class = a.get("class")
|
||
|
|
if attr_class == "node":
|
||
|
|
na, nd = self.find_gexf_attributes(a)
|
||
|
|
node_attr.update(na)
|
||
|
|
node_default.update(nd)
|
||
|
|
G.graph["node_default"] = node_default
|
||
|
|
elif attr_class == "edge":
|
||
|
|
ea, ed = self.find_gexf_attributes(a)
|
||
|
|
edge_attr.update(ea)
|
||
|
|
edge_default.update(ed)
|
||
|
|
G.graph["edge_default"] = edge_default
|
||
|
|
else:
|
||
|
|
raise # unknown attribute class
|
||
|
|
|
||
|
|
# Hack to handle Gephi0.7beta bug
|
||
|
|
# add weight attribute
|
||
|
|
ea = {"weight": {"type": "double", "mode": "static", "title": "weight"}}
|
||
|
|
ed = {}
|
||
|
|
edge_attr.update(ea)
|
||
|
|
edge_default.update(ed)
|
||
|
|
G.graph["edge_default"] = edge_default
|
||
|
|
|
||
|
|
# add nodes
|
||
|
|
nodes_element = graph_xml.find(f"{{{self.NS_GEXF}}}nodes")
|
||
|
|
if nodes_element is not None:
|
||
|
|
for node_xml in nodes_element.findall(f"{{{self.NS_GEXF}}}node"):
|
||
|
|
self.add_node(G, node_xml, node_attr)
|
||
|
|
|
||
|
|
# add edges
|
||
|
|
edges_element = graph_xml.find(f"{{{self.NS_GEXF}}}edges")
|
||
|
|
if edges_element is not None:
|
||
|
|
for edge_xml in edges_element.findall(f"{{{self.NS_GEXF}}}edge"):
|
||
|
|
self.add_edge(G, edge_xml, edge_attr)
|
||
|
|
|
||
|
|
# switch to Graph or DiGraph if no parallel edges were found.
|
||
|
|
if self.simple_graph:
|
||
|
|
if G.is_directed():
|
||
|
|
G = nx.DiGraph(G)
|
||
|
|
else:
|
||
|
|
G = nx.Graph(G)
|
||
|
|
return G
|
||
|
|
|
||
|
|
def add_node(self, G, node_xml, node_attr, node_pid=None):
|
||
|
|
# add a single node with attributes to the graph
|
||
|
|
|
||
|
|
# get attributes and subattributues for node
|
||
|
|
data = self.decode_attr_elements(node_attr, node_xml)
|
||
|
|
data = self.add_parents(data, node_xml) # add any parents
|
||
|
|
if self.VERSION == "1.1":
|
||
|
|
data = self.add_slices(data, node_xml) # add slices
|
||
|
|
else:
|
||
|
|
data = self.add_spells(data, node_xml) # add spells
|
||
|
|
data = self.add_viz(data, node_xml) # add viz
|
||
|
|
data = self.add_start_end(data, node_xml) # add start/end
|
||
|
|
|
||
|
|
# find the node id and cast it to the appropriate type
|
||
|
|
node_id = node_xml.get("id")
|
||
|
|
if self.node_type is not None:
|
||
|
|
node_id = self.node_type(node_id)
|
||
|
|
|
||
|
|
# every node should have a label
|
||
|
|
node_label = node_xml.get("label")
|
||
|
|
data["label"] = node_label
|
||
|
|
|
||
|
|
# parent node id
|
||
|
|
node_pid = node_xml.get("pid", node_pid)
|
||
|
|
if node_pid is not None:
|
||
|
|
data["pid"] = node_pid
|
||
|
|
|
||
|
|
# check for subnodes, recursive
|
||
|
|
subnodes = node_xml.find(f"{{{self.NS_GEXF}}}nodes")
|
||
|
|
if subnodes is not None:
|
||
|
|
for node_xml in subnodes.findall(f"{{{self.NS_GEXF}}}node"):
|
||
|
|
self.add_node(G, node_xml, node_attr, node_pid=node_id)
|
||
|
|
|
||
|
|
G.add_node(node_id, **data)
|
||
|
|
|
||
|
|
def add_start_end(self, data, xml):
|
||
|
|
# start and end times
|
||
|
|
ttype = self.timeformat
|
||
|
|
node_start = xml.get("start")
|
||
|
|
if node_start is not None:
|
||
|
|
data["start"] = self.python_type[ttype](node_start)
|
||
|
|
node_end = xml.get("end")
|
||
|
|
if node_end is not None:
|
||
|
|
data["end"] = self.python_type[ttype](node_end)
|
||
|
|
return data
|
||
|
|
|
||
|
|
def add_viz(self, data, node_xml):
|
||
|
|
# add viz element for node
|
||
|
|
viz = {}
|
||
|
|
color = node_xml.find(f"{{{self.NS_VIZ}}}color")
|
||
|
|
if color is not None:
|
||
|
|
if self.VERSION == "1.1":
|
||
|
|
viz["color"] = {
|
||
|
|
"r": int(color.get("r")),
|
||
|
|
"g": int(color.get("g")),
|
||
|
|
"b": int(color.get("b")),
|
||
|
|
}
|
||
|
|
else:
|
||
|
|
viz["color"] = {
|
||
|
|
"r": int(color.get("r")),
|
||
|
|
"g": int(color.get("g")),
|
||
|
|
"b": int(color.get("b")),
|
||
|
|
"a": float(color.get("a", 1)),
|
||
|
|
}
|
||
|
|
|
||
|
|
size = node_xml.find(f"{{{self.NS_VIZ}}}size")
|
||
|
|
if size is not None:
|
||
|
|
viz["size"] = float(size.get("value"))
|
||
|
|
|
||
|
|
thickness = node_xml.find(f"{{{self.NS_VIZ}}}thickness")
|
||
|
|
if thickness is not None:
|
||
|
|
viz["thickness"] = float(thickness.get("value"))
|
||
|
|
|
||
|
|
shape = node_xml.find(f"{{{self.NS_VIZ}}}shape")
|
||
|
|
if shape is not None:
|
||
|
|
viz["shape"] = shape.get("shape")
|
||
|
|
if viz["shape"] == "image":
|
||
|
|
viz["shape"] = shape.get("uri")
|
||
|
|
|
||
|
|
position = node_xml.find(f"{{{self.NS_VIZ}}}position")
|
||
|
|
if position is not None:
|
||
|
|
viz["position"] = {
|
||
|
|
"x": float(position.get("x", 0)),
|
||
|
|
"y": float(position.get("y", 0)),
|
||
|
|
"z": float(position.get("z", 0)),
|
||
|
|
}
|
||
|
|
|
||
|
|
if len(viz) > 0:
|
||
|
|
data["viz"] = viz
|
||
|
|
return data
|
||
|
|
|
||
|
|
def add_parents(self, data, node_xml):
|
||
|
|
parents_element = node_xml.find(f"{{{self.NS_GEXF}}}parents")
|
||
|
|
if parents_element is not None:
|
||
|
|
data["parents"] = []
|
||
|
|
for p in parents_element.findall(f"{{{self.NS_GEXF}}}parent"):
|
||
|
|
parent = p.get("for")
|
||
|
|
data["parents"].append(parent)
|
||
|
|
return data
|
||
|
|
|
||
|
|
def add_slices(self, data, node_or_edge_xml):
|
||
|
|
slices_element = node_or_edge_xml.find(f"{{{self.NS_GEXF}}}slices")
|
||
|
|
if slices_element is not None:
|
||
|
|
data["slices"] = []
|
||
|
|
for s in slices_element.findall(f"{{{self.NS_GEXF}}}slice"):
|
||
|
|
start = s.get("start")
|
||
|
|
end = s.get("end")
|
||
|
|
data["slices"].append((start, end))
|
||
|
|
return data
|
||
|
|
|
||
|
|
def add_spells(self, data, node_or_edge_xml):
|
||
|
|
spells_element = node_or_edge_xml.find(f"{{{self.NS_GEXF}}}spells")
|
||
|
|
if spells_element is not None:
|
||
|
|
data["spells"] = []
|
||
|
|
ttype = self.timeformat
|
||
|
|
for s in spells_element.findall(f"{{{self.NS_GEXF}}}spell"):
|
||
|
|
start = self.python_type[ttype](s.get("start"))
|
||
|
|
end = self.python_type[ttype](s.get("end"))
|
||
|
|
data["spells"].append((start, end))
|
||
|
|
return data
|
||
|
|
|
||
|
|
def add_edge(self, G, edge_element, edge_attr):
|
||
|
|
# add an edge to the graph
|
||
|
|
|
||
|
|
# raise error if we find mixed directed and undirected edges
|
||
|
|
edge_direction = edge_element.get("type")
|
||
|
|
if G.is_directed() and edge_direction == "undirected":
|
||
|
|
raise nx.NetworkXError("Undirected edge found in directed graph.")
|
||
|
|
if (not G.is_directed()) and edge_direction == "directed":
|
||
|
|
raise nx.NetworkXError("Directed edge found in undirected graph.")
|
||
|
|
|
||
|
|
# Get source and target and recast type if required
|
||
|
|
source = edge_element.get("source")
|
||
|
|
target = edge_element.get("target")
|
||
|
|
if self.node_type is not None:
|
||
|
|
source = self.node_type(source)
|
||
|
|
target = self.node_type(target)
|
||
|
|
|
||
|
|
data = self.decode_attr_elements(edge_attr, edge_element)
|
||
|
|
data = self.add_start_end(data, edge_element)
|
||
|
|
|
||
|
|
if self.VERSION == "1.1":
|
||
|
|
data = self.add_slices(data, edge_element) # add slices
|
||
|
|
else:
|
||
|
|
data = self.add_spells(data, edge_element) # add spells
|
||
|
|
|
||
|
|
# GEXF stores edge ids as an attribute
|
||
|
|
# NetworkX uses them as keys in multigraphs
|
||
|
|
# if networkx_key is not specified as an attribute
|
||
|
|
edge_id = edge_element.get("id")
|
||
|
|
if edge_id is not None:
|
||
|
|
data["id"] = edge_id
|
||
|
|
|
||
|
|
# check if there is a 'multigraph_key' and use that as edge_id
|
||
|
|
multigraph_key = data.pop("networkx_key", None)
|
||
|
|
if multigraph_key is not None:
|
||
|
|
edge_id = multigraph_key
|
||
|
|
|
||
|
|
weight = edge_element.get("weight")
|
||
|
|
if weight is not None:
|
||
|
|
data["weight"] = float(weight)
|
||
|
|
|
||
|
|
edge_label = edge_element.get("label")
|
||
|
|
if edge_label is not None:
|
||
|
|
data["label"] = edge_label
|
||
|
|
|
||
|
|
if G.has_edge(source, target):
|
||
|
|
# seen this edge before - this is a multigraph
|
||
|
|
self.simple_graph = False
|
||
|
|
G.add_edge(source, target, key=edge_id, **data)
|
||
|
|
if edge_direction == "mutual":
|
||
|
|
G.add_edge(target, source, key=edge_id, **data)
|
||
|
|
|
||
|
|
def decode_attr_elements(self, gexf_keys, obj_xml):
|
||
|
|
# Use the key information to decode the attr XML
|
||
|
|
attr = {}
|
||
|
|
# look for outer '<attvalues>' element
|
||
|
|
attr_element = obj_xml.find(f"{{{self.NS_GEXF}}}attvalues")
|
||
|
|
if attr_element is not None:
|
||
|
|
# loop over <attvalue> elements
|
||
|
|
for a in attr_element.findall(f"{{{self.NS_GEXF}}}attvalue"):
|
||
|
|
key = a.get("for") # for is required
|
||
|
|
try: # should be in our gexf_keys dictionary
|
||
|
|
title = gexf_keys[key]["title"]
|
||
|
|
except KeyError as err:
|
||
|
|
raise nx.NetworkXError(f"No attribute defined for={key}.") from err
|
||
|
|
atype = gexf_keys[key]["type"]
|
||
|
|
value = a.get("value")
|
||
|
|
if atype == "boolean":
|
||
|
|
value = self.convert_bool[value]
|
||
|
|
else:
|
||
|
|
value = self.python_type[atype](value)
|
||
|
|
if gexf_keys[key]["mode"] == "dynamic":
|
||
|
|
# for dynamic graphs use list of three-tuples
|
||
|
|
# [(value1,start1,end1), (value2,start2,end2), etc]
|
||
|
|
ttype = self.timeformat
|
||
|
|
start = self.python_type[ttype](a.get("start"))
|
||
|
|
end = self.python_type[ttype](a.get("end"))
|
||
|
|
if title in attr:
|
||
|
|
attr[title].append((value, start, end))
|
||
|
|
else:
|
||
|
|
attr[title] = [(value, start, end)]
|
||
|
|
else:
|
||
|
|
# for static graphs just assign the value
|
||
|
|
attr[title] = value
|
||
|
|
return attr
|
||
|
|
|
||
|
|
def find_gexf_attributes(self, attributes_element):
|
||
|
|
# Extract all the attributes and defaults
|
||
|
|
attrs = {}
|
||
|
|
defaults = {}
|
||
|
|
mode = attributes_element.get("mode")
|
||
|
|
for k in attributes_element.findall(f"{{{self.NS_GEXF}}}attribute"):
|
||
|
|
attr_id = k.get("id")
|
||
|
|
title = k.get("title")
|
||
|
|
atype = k.get("type")
|
||
|
|
attrs[attr_id] = {"title": title, "type": atype, "mode": mode}
|
||
|
|
# check for the 'default' subelement of key element and add
|
||
|
|
default = k.find(f"{{{self.NS_GEXF}}}default")
|
||
|
|
if default is not None:
|
||
|
|
if atype == "boolean":
|
||
|
|
value = self.convert_bool[default.text]
|
||
|
|
else:
|
||
|
|
value = self.python_type[atype](default.text)
|
||
|
|
defaults[title] = value
|
||
|
|
return attrs, defaults
|
||
|
|
|
||
|
|
|
||
|
|
def relabel_gexf_graph(G):
|
||
|
|
"""Relabel graph using "label" node keyword for node label.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
G : graph
|
||
|
|
A NetworkX graph read from GEXF data
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
H : graph
|
||
|
|
A NetworkX graph with relabeled nodes
|
||
|
|
|
||
|
|
Raises
|
||
|
|
------
|
||
|
|
NetworkXError
|
||
|
|
If node labels are missing or not unique while relabel=True.
|
||
|
|
|
||
|
|
Notes
|
||
|
|
-----
|
||
|
|
This function relabels the nodes in a NetworkX graph with the
|
||
|
|
"label" attribute. It also handles relabeling the specific GEXF
|
||
|
|
node attributes "parents", and "pid".
|
||
|
|
"""
|
||
|
|
# build mapping of node labels, do some error checking
|
||
|
|
try:
|
||
|
|
mapping = [(u, G.nodes[u]["label"]) for u in G]
|
||
|
|
except KeyError as err:
|
||
|
|
raise nx.NetworkXError(
|
||
|
|
"Failed to relabel nodes: missing node labels found. Use relabel=False."
|
||
|
|
) from err
|
||
|
|
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
|