Mercurial > repos > shellac > guppy_basecaller

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

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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1 # Copyright (C) 2013-2019 by
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2 #
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3 # Authors: Aric Hagberg <hagberg@lanl.gov>
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4 # Dan Schult <dschult@colgate.edu>
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5 # Pieter Swart <swart@lanl.gov>
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6 # All rights reserved.
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7 # BSD license.
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8 # Based on GraphML NetworkX GraphML reader
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9 """Read and write graphs in GEXF format.
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10
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11 GEXF (Graph Exchange XML Format) is a language for describing complex
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12 network structures, their associated data and dynamics.
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13
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14 This implementation does not support mixed graphs (directed and
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15 undirected edges together).
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16
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17 Format
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18 ------
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19 GEXF is an XML format. See https://gephi.org/gexf/format/schema.html for the
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20 specification and https://gephi.org/gexf/format/basic.html for examples.
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21 """
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22 import itertools
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23 import time
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24
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25 import networkx as nx
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26 from networkx.utils import open_file, make_str
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27 try:
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28 from xml.etree.cElementTree import (Element, ElementTree, SubElement,
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29 tostring)
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30 except ImportError:
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31 try:
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32 from xml.etree.ElementTree import (Element, ElementTree, SubElement,
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33 tostring)
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34 except ImportError:
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35 pass
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36
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37 __all__ = ['write_gexf', 'read_gexf', 'relabel_gexf_graph', 'generate_gexf']
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38
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39
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40 @open_file(1, mode='wb')
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41 def write_gexf(G, path, encoding='utf-8', prettyprint=True,
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42 version='1.2draft'):
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43 """Write G in GEXF format to path.
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44
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45 "GEXF (Graph Exchange XML Format) is a language for describing
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46 complex networks structures, their associated data and dynamics" [1]_.
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47
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48 Node attributes are checked according to the version of the GEXF
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49 schemas used for parameters which are not user defined,
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50 e.g. visualization 'viz' [2]_. See example for usage.
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51
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52 Parameters
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53 ----------
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54 G : graph
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55 A NetworkX graph
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56 path : file or string
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57 File or file name to write.
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58 File names ending in .gz or .bz2 will be compressed.
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59 encoding : string (optional, default: 'utf-8')
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60 Encoding for text data.
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61 prettyprint : bool (optional, default: True)
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62 If True use line breaks and indenting in output XML.
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63
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64 Examples
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65 --------
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66 >>> G = nx.path_graph(4)
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67 >>> nx.write_gexf(G, "test.gexf")
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68
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69 # visualization data
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70 >>> G.nodes[0]['viz'] = {'size': 54}
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71 >>> G.nodes[0]['viz']['position'] = {'x' : 0, 'y' : 1}
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72 >>> G.nodes[0]['viz']['color'] = {'r' : 0, 'g' : 0, 'b' : 256}
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73
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74
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75 Notes
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76 -----
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77 This implementation does not support mixed graphs (directed and undirected
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78 edges together).
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79
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80 The node id attribute is set to be the string of the node label.
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81 If you want to specify an id use set it as node data, e.g.
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82 node['a']['id']=1 to set the id of node 'a' to 1.
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83
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84 References
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85 ----------
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86 .. [1] GEXF File Format, https://gephi.org/gexf/format/
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87 .. [2] GEXF viz schema 1.1, https://gephi.org/gexf/1.1draft/viz
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88 """
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89 writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint,
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90 version=version)
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91 writer.add_graph(G)
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92 writer.write(path)
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93
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94
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95 def generate_gexf(G, encoding='utf-8', prettyprint=True, version='1.2draft'):
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96 """Generate lines of GEXF format representation of G.
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97
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98 "GEXF (Graph Exchange XML Format) is a language for describing
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99 complex networks structures, their associated data and dynamics" [1]_.
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100
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101 Parameters
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102 ----------
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103 G : graph
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104 A NetworkX graph
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105 encoding : string (optional, default: 'utf-8')
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106 Encoding for text data.
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107 prettyprint : bool (optional, default: True)
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108 If True use line breaks and indenting in output XML.
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109 version : string (default: 1.2draft)
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110 Version of GEFX File Format (see https://gephi.org/gexf/format/schema.html)
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111 Supported values: "1.1draft", "1.2draft"
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112
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113
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114 Examples
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115 --------
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116 >>> G = nx.path_graph(4)
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117 >>> linefeed = chr(10) # linefeed=\n
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118 >>> s = linefeed.join(nx.generate_gexf(G)) # doctest: +SKIP
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119 >>> for line in nx.generate_gexf(G): # doctest: +SKIP
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120 ... print line
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121
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122 Notes
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123 -----
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124 This implementation does not support mixed graphs (directed and undirected
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125 edges together).
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126
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127 The node id attribute is set to be the string of the node label.
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128 If you want to specify an id use set it as node data, e.g.
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129 node['a']['id']=1 to set the id of node 'a' to 1.
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130
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131 References
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132 ----------
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133 .. [1] GEXF File Format, https://gephi.org/gexf/format/
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134 """
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135 writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint,
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136 version=version)
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137 writer.add_graph(G)
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138 for line in str(writer).splitlines():
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139 yield line
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140
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141
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142 @open_file(0, mode='rb')
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143 def read_gexf(path, node_type=None, relabel=False, version='1.2draft'):
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144 """Read graph in GEXF format from path.
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145
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146 "GEXF (Graph Exchange XML Format) is a language for describing
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147 complex networks structures, their associated data and dynamics" [1]_.
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148
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149 Parameters
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150 ----------
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151 path : file or string
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152 File or file name to write.
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153 File names ending in .gz or .bz2 will be compressed.
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154 node_type: Python type (default: None)
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155 Convert node ids to this type if not None.
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156 relabel : bool (default: False)
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157 If True relabel the nodes to use the GEXF node "label" attribute
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158 instead of the node "id" attribute as the NetworkX node label.
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159 version : string (default: 1.2draft)
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160 Version of GEFX File Format (see https://gephi.org/gexf/format/schema.html)
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161 Supported values: "1.1draft", "1.2draft"
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162
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163 Returns
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164 -------
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165 graph: NetworkX graph
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166 If no parallel edges are found a Graph or DiGraph is returned.
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167 Otherwise a MultiGraph or MultiDiGraph is returned.
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168
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169 Notes
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170 -----
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171 This implementation does not support mixed graphs (directed and undirected
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172 edges together).
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173
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174 References
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175 ----------
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176 .. [1] GEXF File Format, https://gephi.org/gexf/format/
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177 """
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178 reader = GEXFReader(node_type=node_type, version=version)
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179 if relabel:
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180 G = relabel_gexf_graph(reader(path))
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181 else:
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182 G = reader(path)
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183 return G
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184
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185
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186 class GEXF(object):
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187 versions = {}
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188 d = {'NS_GEXF': "http://www.gexf.net/1.1draft",
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189 'NS_VIZ': "http://www.gexf.net/1.1draft/viz",
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190 'NS_XSI': "http://www.w3.org/2001/XMLSchema-instance",
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191 'SCHEMALOCATION': ' '.join(['http://www.gexf.net/1.1draft',
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192 'http://www.gexf.net/1.1draft/gexf.xsd']),
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193 'VERSION': '1.1'}
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194 versions['1.1draft'] = d
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195 d = {'NS_GEXF': "http://www.gexf.net/1.2draft",
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196 'NS_VIZ': "http://www.gexf.net/1.2draft/viz",
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197 'NS_XSI': "http://www.w3.org/2001/XMLSchema-instance",
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198 'SCHEMALOCATION': ' '.join(['http://www.gexf.net/1.2draft',
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199 'http://www.gexf.net/1.2draft/gexf.xsd']),
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200 'VERSION': '1.2'}
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201 versions['1.2draft'] = d
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202
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203 types = [(int, "integer"),
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204 (float, "float"),
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205 (float, "double"),
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206 (bool, "boolean"),
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207 (list, "string"),
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208 (dict, "string"),
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209 (int, "long"),
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210 (str, "liststring"),
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211 (str, "anyURI"),
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212 (str, "string")]
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213
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214 # These additions to types allow writing numpy types
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215 try:
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216 import numpy as np
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217 except ImportError:
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218 pass
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219 else:
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220 # prepend so that python types are created upon read (last entry wins)
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221 types = [(np.float64, "float"), (np.float32, "float"),
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222 (np.float16, "float"), (np.float_, "float"),
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223 (np.int, "int"), (np.int8, "int"),
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224 (np.int16, "int"), (np.int32, "int"),
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225 (np.int64, "int"), (np.uint8, "int"),
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226 (np.uint16, "int"), (np.uint32, "int"),
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227 (np.uint64, "int"), (np.int_, "int"),
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228 (np.intc, "int"), (np.intp, "int"),
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229 ] + types
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230
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231 xml_type = dict(types)
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232 python_type = dict(reversed(a) for a in types)
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233
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234 # http://www.w3.org/TR/xmlschema-2/#boolean
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235 convert_bool = {
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236 'true': True, 'false': False,
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237 'True': True, 'False': False,
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238 '0': False, 0: False,
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239 '1': True, 1: True
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240 }
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241
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242 def set_version(self, version):
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243 d = self.versions.get(version)
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244 if d is None:
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245 raise nx.NetworkXError('Unknown GEXF version %s.' % version)
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246 self.NS_GEXF = d['NS_GEXF']
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247 self.NS_VIZ = d['NS_VIZ']
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248 self.NS_XSI = d['NS_XSI']
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249 self.SCHEMALOCATION = d['SCHEMALOCATION']
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250 self.VERSION = d['VERSION']
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251 self.version = version
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252
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253
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254 class GEXFWriter(GEXF):
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255 # class for writing GEXF format files
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256 # use write_gexf() function
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257 def __init__(self, graph=None, encoding='utf-8', prettyprint=True,
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258 version='1.2draft'):
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259 try:
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260 import xml.etree.ElementTree as ET
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261 except ImportError:
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262 raise ImportError('GEXF writer requires '
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263 'xml.elementtree.ElementTree')
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264 self.prettyprint = prettyprint
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265 self.encoding = encoding
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266 self.set_version(version)
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267 self.xml = Element('gexf',
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268 {'xmlns': self.NS_GEXF,
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269 'xmlns:xsi': self.NS_XSI,
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270 'xsi:schemaLocation': self.SCHEMALOCATION,
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271 'version': self.VERSION})
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272
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273 # Make meta element a non-graph element
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274 # Also add lastmodifieddate as attribute, not tag
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275 meta_element = Element('meta')
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276 subelement_text = 'NetworkX {}'.format(nx.__version__)
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277 SubElement(meta_element, 'creator').text = subelement_text
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278 meta_element.set('lastmodifieddate', time.strftime('%Y-%m-%d'))
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279 self.xml.append(meta_element)
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280
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281 ET.register_namespace('viz', self.NS_VIZ)
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282
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283 # counters for edge and attribute identifiers
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284 self.edge_id = itertools.count()
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285 self.attr_id = itertools.count()
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286 self.all_edge_ids = set()
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287 # default attributes are stored in dictionaries
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288 self.attr = {}
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289 self.attr['node'] = {}
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290 self.attr['edge'] = {}
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291 self.attr['node']['dynamic'] = {}
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292 self.attr['node']['static'] = {}
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293 self.attr['edge']['dynamic'] = {}
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294 self.attr['edge']['static'] = {}
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295
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296 if graph is not None:
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297 self.add_graph(graph)
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298
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299 def __str__(self):
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300 if self.prettyprint:
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301 self.indent(self.xml)
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302 s = tostring(self.xml).decode(self.encoding)
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303 return s
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304
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305 def add_graph(self, G):
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306 # first pass through G collecting edge ids
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307 for u, v, dd in G.edges(data=True):
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parents:
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308 eid = dd.get('id')
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parents:
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309 if eid is not None:
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parents:
diff changeset
310 self.all_edge_ids.add(make_str(eid))
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311 # set graph attributes
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parents:
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312 if G.graph.get('mode') == 'dynamic':
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parents:
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313 mode = 'dynamic'
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314 else:
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parents:
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315 mode = 'static'
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316 # Add a graph element to the XML
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317 if G.is_directed():
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318 default = 'directed'
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319 else:
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320 default = 'undirected'
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parents:
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321 name = G.graph.get('name', '')
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parents:
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322 graph_element = Element('graph', defaultedgetype=default, mode=mode,
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parents:
diff changeset
323 name=name)
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parents:
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324 self.graph_element = graph_element
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parents:
diff changeset
325 self.add_nodes(G, graph_element)
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parents:
diff changeset
326 self.add_edges(G, graph_element)
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parents:
diff changeset
327 self.xml.append(graph_element)
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parents:
diff changeset
328
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parents:
diff changeset
329 def add_nodes(self, G, graph_element):
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parents:
diff changeset
330 nodes_element = Element('nodes')
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parents:
diff changeset
331 for node, data in G.nodes(data=True):
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parents:
diff changeset
332 node_data = data.copy()
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parents:
diff changeset
333 node_id = make_str(node_data.pop('id', node))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
334 kw = {'id': node_id}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
335 label = make_str(node_data.pop('label', node))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
336 kw['label'] = label
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parents:
diff changeset
337 try:
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parents:
diff changeset
338 pid = node_data.pop('pid')
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parents:
diff changeset
339 kw['pid'] = make_str(pid)
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parents:
diff changeset
340 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
341 pass
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parents:
diff changeset
342 try:
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parents:
diff changeset
343 start = node_data.pop('start')
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shellac
parents:
diff changeset
344 kw['start'] = make_str(start)
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parents:
diff changeset
345 self.alter_graph_mode_timeformat(start)
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parents:
diff changeset
346 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
347 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
348 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
349 end = node_data.pop('end')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
350 kw['end'] = make_str(end)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
351 self.alter_graph_mode_timeformat(end)
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shellac
parents:
diff changeset
352 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
353 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
354 # add node element with attributes
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parents:
diff changeset
355 node_element = Element('node', **kw)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
356 # add node element and attr subelements
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
357 default = G.graph.get('node_default', {})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
358 node_data = self.add_parents(node_element, node_data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
359 if self.version == '1.1':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
360 node_data = self.add_slices(node_element, node_data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
361 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
362 node_data = self.add_spells(node_element, node_data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
363 node_data = self.add_viz(node_element, node_data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
364 node_data = self.add_attributes('node', node_element,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
365 node_data, default)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
366 nodes_element.append(node_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
367 graph_element.append(nodes_element)
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shellac
parents:
diff changeset
368
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
369 def add_edges(self, G, graph_element):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
370 def edge_key_data(G):
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parents:
diff changeset
371 # helper function to unify multigraph and graph edge iterator
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
372 if G.is_multigraph():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
373 for u, v, key, data in G.edges(data=True, keys=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
374 edge_data = data.copy()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
375 edge_data.update(key=key)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
376 edge_id = edge_data.pop('id', None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
377 if edge_id is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
378 edge_id = next(self.edge_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
379 while make_str(edge_id) in self.all_edge_ids:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
380 edge_id = next(self.edge_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
381 self.all_edge_ids.add(make_str(edge_id))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
382 yield u, v, edge_id, edge_data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
383 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
384 for u, v, data in G.edges(data=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
385 edge_data = data.copy()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
386 edge_id = edge_data.pop('id', None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
387 if edge_id is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
388 edge_id = next(self.edge_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
389 while make_str(edge_id) in self.all_edge_ids:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
390 edge_id = next(self.edge_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
391 self.all_edge_ids.add(make_str(edge_id))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
392 yield u, v, edge_id, edge_data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
393 edges_element = Element('edges')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
394 for u, v, key, edge_data in edge_key_data(G):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
395 kw = {'id': make_str(key)}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
396 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
397 edge_weight = edge_data.pop('weight')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
398 kw['weight'] = make_str(edge_weight)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
399 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
400 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
401 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
402 edge_type = edge_data.pop('type')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
403 kw['type'] = make_str(edge_type)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
404 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
405 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
406 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
407 start = edge_data.pop('start')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
408 kw['start'] = make_str(start)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
409 self.alter_graph_mode_timeformat(start)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
410 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
411 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
412 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
413 end = edge_data.pop('end')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
414 kw['end'] = make_str(end)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
415 self.alter_graph_mode_timeformat(end)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
416 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
417 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
418 source_id = make_str(G.nodes[u].get('id', u))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
419 target_id = make_str(G.nodes[v].get('id', v))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
420 edge_element = Element('edge',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
421 source=source_id, target=target_id, **kw)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
422 default = G.graph.get('edge_default', {})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
423 if self.version == '1.1':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
424 edge_data = self.add_slices(edge_element, edge_data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
425 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
426 edge_data = self.add_spells(edge_element, edge_data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
427 edge_data = self.add_viz(edge_element, edge_data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
428 edge_data = self.add_attributes('edge', edge_element,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
429 edge_data, default)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
430 edges_element.append(edge_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
431 graph_element.append(edges_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
432
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
433 def add_attributes(self, node_or_edge, xml_obj, data, default):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
434 # Add attrvalues to node or edge
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
435 attvalues = Element('attvalues')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
436 if len(data) == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
437 return data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
438 mode = 'static'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
439 for k, v in data.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
440 # rename generic multigraph key to avoid any name conflict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
441 if k == 'key':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
442 k = 'networkx_key'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
443 val_type = type(v)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
444 if val_type not in self.xml_type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
445 raise TypeError('attribute value type is not allowed: %s'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
446 % val_type)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
447 if isinstance(v, list):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
448 # dynamic data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
449 for val, start, end in v:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
450 val_type = type(val)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
451 if start is not None or end is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
452 mode = 'dynamic'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
453 self.alter_graph_mode_timeformat(start)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
454 self.alter_graph_mode_timeformat(end)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
455 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
456 attr_id = self.get_attr_id(make_str(k),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
457 self.xml_type[val_type],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
458 node_or_edge, default, mode)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
459 for val, start, end in v:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
460 e = Element('attvalue')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
461 e.attrib['for'] = attr_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
462 e.attrib['value'] = make_str(val)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
463 # Handle nan, inf, -inf differently
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
464 if val_type == float:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
465 if e.attrib['value'] == 'inf':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
466 e.attrib['value'] = 'INF'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
467 elif e.attrib['value'] == 'nan':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
468 e.attrib['value'] = 'NaN'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
469 elif e.attrib['value'] == '-inf':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
470 e.attrib['value'] = '-INF'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
471 if start is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
472 e.attrib['start'] = make_str(start)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
473 if end is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
474 e.attrib['end'] = make_str(end)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
475 attvalues.append(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
476 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
477 # static data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
478 mode = 'static'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
479 attr_id = self.get_attr_id(make_str(k),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
480 self.xml_type[val_type],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
481 node_or_edge, default, mode)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
482 e = Element('attvalue')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
483 e.attrib['for'] = attr_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
484 if isinstance(v, bool):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
485 e.attrib['value'] = make_str(v).lower()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
486 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
487 e.attrib['value'] = make_str(v)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
488 # Handle float nan, inf, -inf differently
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
489 if val_type == float:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
490 if e.attrib['value'] == 'inf':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
491 e.attrib['value'] = 'INF'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
492 elif e.attrib['value'] == 'nan':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
493 e.attrib['value'] = 'NaN'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
494 elif e.attrib['value'] == '-inf':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
495 e.attrib['value'] = '-INF'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
496 attvalues.append(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
497 xml_obj.append(attvalues)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
498 return data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
499
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
500 def get_attr_id(self, title, attr_type, edge_or_node, default, mode):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
501 # find the id of the attribute or generate a new id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
502 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
503 return self.attr[edge_or_node][mode][title]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
504 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
505 # generate new id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
506 new_id = str(next(self.attr_id))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
507 self.attr[edge_or_node][mode][title] = new_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
508 attr_kwargs = {'id': new_id, 'title': title, 'type': attr_type}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
509 attribute = Element('attribute', **attr_kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
510 # add subelement for data default value if present
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
511 default_title = default.get(title)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
512 if default_title is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
513 default_element = Element('default')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
514 default_element.text = make_str(default_title)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
515 attribute.append(default_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
516 # new insert it into the XML
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
517 attributes_element = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
518 for a in self.graph_element.findall('attributes'):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
519 # find existing attributes element by class and mode
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
520 a_class = a.get('class')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
521 a_mode = a.get('mode', 'static')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
522 if a_class == edge_or_node and a_mode == mode:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
523 attributes_element = a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
524 if attributes_element is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
525 # create new attributes element
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
526 attr_kwargs = {'mode': mode, 'class': edge_or_node}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
527 attributes_element = Element('attributes', **attr_kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
528 self.graph_element.insert(0, attributes_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
529 attributes_element.append(attribute)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
530 return new_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
531
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
532 def add_viz(self, element, node_data):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
533 viz = node_data.pop('viz', False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
534 if viz:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
535 color = viz.get('color')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
536 if color is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
537 if self.VERSION == '1.1':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
538 e = Element('{%s}color' % self.NS_VIZ,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
539 r=str(color.get('r')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
540 g=str(color.get('g')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
541 b=str(color.get('b')))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
542 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
543 e = Element('{%s}color' % self.NS_VIZ,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
544 r=str(color.get('r')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
545 g=str(color.get('g')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
546 b=str(color.get('b')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
547 a=str(color.get('a')))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
548 element.append(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
549
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
550 size = viz.get('size')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
551 if size is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
552 e = Element('{%s}size' % self.NS_VIZ, value=str(size))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
553 element.append(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
554
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
555 thickness = viz.get('thickness')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
556 if thickness is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
557 e = Element('{%s}thickness' % self.NS_VIZ,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
558 value=str(thickness))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
559 element.append(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
560
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
561 shape = viz.get('shape')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
562 if shape is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
563 if shape.startswith('http'):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
564 e = Element('{%s}shape' % self.NS_VIZ,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
565 value='image', uri=str(shape))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
566 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
567 e = Element('{%s}shape' % self.NS_VIZ, value=str(shape))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
568 element.append(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
569
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
570 position = viz.get('position')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
571 if position is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
572 e = Element('{%s}position' % self.NS_VIZ,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
573 x=str(position.get('x')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
574 y=str(position.get('y')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
575 z=str(position.get('z')))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
576 element.append(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
577 return node_data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
578
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
579 def add_parents(self, node_element, node_data):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
580 parents = node_data.pop('parents', False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
581 if parents:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
582 parents_element = Element('parents')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
583 for p in parents:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
584 e = Element('parent')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
585 e.attrib['for'] = str(p)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
586 parents_element.append(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
587 node_element.append(parents_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
588 return node_data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
589
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
590 def add_slices(self, node_or_edge_element, node_or_edge_data):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
591 slices = node_or_edge_data.pop('slices', False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
592 if slices:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
593 slices_element = Element('slices')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
594 for start, end in slices:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
595 e = Element('slice', start=str(start), end=str(end))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
596 slices_element.append(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
597 node_or_edge_element.append(slices_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
598 return node_or_edge_data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
599
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
600 def add_spells(self, node_or_edge_element, node_or_edge_data):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
601 spells = node_or_edge_data.pop('spells', False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
602 if spells:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
603 spells_element = Element('spells')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
604 for start, end in spells:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
605 e = Element('spell')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
606 if start is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
607 e.attrib['start'] = make_str(start)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
608 self.alter_graph_mode_timeformat(start)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
609 if end is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
610 e.attrib['end'] = make_str(end)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
611 self.alter_graph_mode_timeformat(end)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
612 spells_element.append(e)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
613 node_or_edge_element.append(spells_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
614 return node_or_edge_data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
615
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
616 def alter_graph_mode_timeformat(self, start_or_end):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
617 # If 'start' or 'end' appears, alter Graph mode to dynamic and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
618 # set timeformat
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
619 if self.graph_element.get('mode') == 'static':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
620 if start_or_end is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
621 if isinstance(start_or_end, str):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
622 timeformat = 'date'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
623 elif isinstance(start_or_end, float):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
624 timeformat = 'double'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
625 elif isinstance(start_or_end, int):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
626 timeformat = 'long'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
627 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
628 raise nx.NetworkXError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
629 'timeformat should be of the type int, float or str')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
630 self.graph_element.set('timeformat', timeformat)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
631 self.graph_element.set('mode', 'dynamic')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
632
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
633 def write(self, fh):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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634 # Serialize graph G in GEXF to the open fh
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parents:
diff changeset
635 if self.prettyprint:
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parents:
diff changeset
636 self.indent(self.xml)
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parents:
diff changeset
637 document = ElementTree(self.xml)
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parents:
diff changeset
638 document.write(fh, encoding=self.encoding, xml_declaration=True)
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parents:
diff changeset
639
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parents:
diff changeset
640 def indent(self, elem, level=0):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
641 # in-place prettyprint formatter
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parents:
diff changeset
642 i = "\n" + " " * level
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
643 if len(elem):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
644 if not elem.text or not elem.text.strip():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
645 elem.text = i + " "
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parents:
diff changeset
646 if not elem.tail or not elem.tail.strip():
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parents:
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647 elem.tail = i
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
648 for elem in elem:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
649 self.indent(elem, level + 1)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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650 if not elem.tail or not elem.tail.strip():
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parents:
diff changeset
651 elem.tail = i
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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652 else:
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parents:
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653 if level and (not elem.tail or not elem.tail.strip()):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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654 elem.tail = i
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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655
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656
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parents:
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657 class GEXFReader(GEXF):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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658 # Class to read GEXF format files
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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659 # use read_gexf() function
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660 def __init__(self, node_type=None, version='1.2draft'):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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661 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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662 import xml.etree.ElementTree
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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663 except ImportError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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664 raise ImportError('GEXF reader requires '
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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665 'xml.elementtree.ElementTree.')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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666 self.node_type = node_type
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parents:
diff changeset
667 # assume simple graph and test for multigraph on read
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668 self.simple_graph = True
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669 self.set_version(version)
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670
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671 def __call__(self, stream):
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672 self.xml = ElementTree(file=stream)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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673 g = self.xml.find('{%s}graph' % self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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674 if g is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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675 return self.make_graph(g)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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676 # try all the versions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
677 for version in self.versions:
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parents:
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678 self.set_version(version)
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diff changeset
679 g = self.xml.find('{%s}graph' % self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
680 if g is not None:
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diff changeset
681 return self.make_graph(g)
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parents:
diff changeset
682 raise nx.NetworkXError('No <graph> element in GEXF file.')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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683
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684 def make_graph(self, graph_xml):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
685 # start with empty DiGraph or MultiDiGraph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
686 edgedefault = graph_xml.get('defaultedgetype', None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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687 if edgedefault == 'directed':
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688 G = nx.MultiDiGraph()
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689 else:
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690 G = nx.MultiGraph()
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691
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diff changeset
692 # graph attributes
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diff changeset
693 graph_name = graph_xml.get('name', '')
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parents:
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694 if graph_name != '':
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diff changeset
695 G.graph['name'] = graph_name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
696 graph_start = graph_xml.get('start')
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697 if graph_start is not None:
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diff changeset
698 G.graph['start'] = graph_start
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
699 graph_end = graph_xml.get('end')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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700 if graph_end is not None:
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parents:
diff changeset
701 G.graph['end'] = graph_end
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
702 graph_mode = graph_xml.get('mode', '')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
703 if graph_mode == 'dynamic':
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parents:
diff changeset
704 G.graph['mode'] = 'dynamic'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
705 else:
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diff changeset
706 G.graph['mode'] = 'static'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
707
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parents:
diff changeset
708 # timeformat
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parents:
diff changeset
709 self.timeformat = graph_xml.get('timeformat')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
710 if self.timeformat == 'date':
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parents:
diff changeset
711 self.timeformat = 'string'
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parents:
diff changeset
712
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parents:
diff changeset
713 # node and edge attributes
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parents:
diff changeset
714 attributes_elements = graph_xml.findall('{%s}attributes' %
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
715 self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
716 # dictionaries to hold attributes and attribute defaults
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parents:
diff changeset
717 node_attr = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
718 node_default = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
719 edge_attr = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
720 edge_default = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
721 for a in attributes_elements:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
722 attr_class = a.get('class')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
723 if attr_class == 'node':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
724 na, nd = self.find_gexf_attributes(a)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
725 node_attr.update(na)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
726 node_default.update(nd)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
727 G.graph['node_default'] = node_default
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
728 elif attr_class == 'edge':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
729 ea, ed = self.find_gexf_attributes(a)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
730 edge_attr.update(ea)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
731 edge_default.update(ed)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
732 G.graph['edge_default'] = edge_default
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
733 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
734 raise # unknown attribute class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
735
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
736 # Hack to handle Gephi0.7beta bug
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
737 # add weight attribute
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
738 ea = {'weight': {'type': 'double', 'mode': 'static',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
739 'title': 'weight'}}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
740 ed = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
741 edge_attr.update(ea)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
742 edge_default.update(ed)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
743 G.graph['edge_default'] = edge_default
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
744
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
745 # add nodes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
746 nodes_element = graph_xml.find('{%s}nodes' % self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
747 if nodes_element is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
748 for node_xml in nodes_element.findall('{%s}node' % self.NS_GEXF):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
749 self.add_node(G, node_xml, node_attr)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
750
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
751 # add edges
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
752 edges_element = graph_xml.find('{%s}edges' % self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
753 if edges_element is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
754 for edge_xml in edges_element.findall('{%s}edge' % self.NS_GEXF):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
755 self.add_edge(G, edge_xml, edge_attr)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
756
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
757 # switch to Graph or DiGraph if no parallel edges were found.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
758 if self.simple_graph:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
759 if G.is_directed():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
760 G = nx.DiGraph(G)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
761 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
762 G = nx.Graph(G)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
763 return G
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
764
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
765 def add_node(self, G, node_xml, node_attr, node_pid=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
766 # add a single node with attributes to the graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
767
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
768 # get attributes and subattributues for node
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
769 data = self.decode_attr_elements(node_attr, node_xml)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
770 data = self.add_parents(data, node_xml) # add any parents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
771 if self.version == '1.1':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
772 data = self.add_slices(data, node_xml) # add slices
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
773 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
774 data = self.add_spells(data, node_xml) # add spells
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
775 data = self.add_viz(data, node_xml) # add viz
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
776 data = self.add_start_end(data, node_xml) # add start/end
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
777
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
778 # find the node id and cast it to the appropriate type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
779 node_id = node_xml.get('id')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
780 if self.node_type is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
781 node_id = self.node_type(node_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
782
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
783 # every node should have a label
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
784 node_label = node_xml.get('label')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
785 data['label'] = node_label
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
786
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
787 # parent node id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
788 node_pid = node_xml.get('pid', node_pid)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
789 if node_pid is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
790 data['pid'] = node_pid
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
791
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
792 # check for subnodes, recursive
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
793 subnodes = node_xml.find('{%s}nodes' % self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
794 if subnodes is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
795 for node_xml in subnodes.findall('{%s}node' % self.NS_GEXF):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
796 self.add_node(G, node_xml, node_attr, node_pid=node_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
797
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
798 G.add_node(node_id, **data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
799
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
800 def add_start_end(self, data, xml):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
801 # start and end times
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
802 ttype = self.timeformat
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
803 node_start = xml.get('start')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
804 if node_start is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
805 data['start'] = self.python_type[ttype](node_start)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
806 node_end = xml.get('end')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
807 if node_end is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
808 data['end'] = self.python_type[ttype](node_end)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
809 return data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
810
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
811 def add_viz(self, data, node_xml):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
812 # add viz element for node
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
813 viz = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
814 color = node_xml.find('{%s}color' % self.NS_VIZ)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
815 if color is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
816 if self.VERSION == '1.1':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
817 viz['color'] = {'r': int(color.get('r')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
818 'g': int(color.get('g')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
819 'b': int(color.get('b'))}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
820 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
821 viz['color'] = {'r': int(color.get('r')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
822 'g': int(color.get('g')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
823 'b': int(color.get('b')),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
824 'a': float(color.get('a', 1))}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
825
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
826 size = node_xml.find('{%s}size' % self.NS_VIZ)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
827 if size is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
828 viz['size'] = float(size.get('value'))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
829
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
830 thickness = node_xml.find('{%s}thickness' % self.NS_VIZ)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
831 if thickness is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
832 viz['thickness'] = float(thickness.get('value'))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
833
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
834 shape = node_xml.find('{%s}shape' % self.NS_VIZ)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
835 if shape is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
836 viz['shape'] = shape.get('shape')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
837 if viz['shape'] == 'image':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
838 viz['shape'] = shape.get('uri')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
839
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
840 position = node_xml.find('{%s}position' % self.NS_VIZ)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
841 if position is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
842 viz['position'] = {'x': float(position.get('x', 0)),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
843 'y': float(position.get('y', 0)),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
844 'z': float(position.get('z', 0))}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
845
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
846 if len(viz) > 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
847 data['viz'] = viz
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
848 return data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
849
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
850 def add_parents(self, data, node_xml):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
851 parents_element = node_xml.find('{%s}parents' % self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
852 if parents_element is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
853 data['parents'] = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
854 for p in parents_element.findall('{%s}parent' % self.NS_GEXF):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
855 parent = p.get('for')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
856 data['parents'].append(parent)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
857 return data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
858
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
859 def add_slices(self, data, node_or_edge_xml):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
860 slices_element = node_or_edge_xml.find('{%s}slices' % self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
861 if slices_element is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
862 data['slices'] = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
863 for s in slices_element.findall('{%s}slice' % self.NS_GEXF):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
864 start = s.get('start')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
865 end = s.get('end')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
866 data['slices'].append((start, end))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
867 return data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
868
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
869 def add_spells(self, data, node_or_edge_xml):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
870 spells_element = node_or_edge_xml.find('{%s}spells' % self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
871 if spells_element is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
872 data['spells'] = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
873 ttype = self.timeformat
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
874 for s in spells_element.findall('{%s}spell' % self.NS_GEXF):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
875 start = self.python_type[ttype](s.get('start'))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
876 end = self.python_type[ttype](s.get('end'))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
877 data['spells'].append((start, end))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
878 return data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
879
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
880 def add_edge(self, G, edge_element, edge_attr):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
881 # add an edge to the graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
882
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
883 # raise error if we find mixed directed and undirected edges
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
884 edge_direction = edge_element.get('type')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
885 if G.is_directed() and edge_direction == 'undirected':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
886 raise nx.NetworkXError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
887 'Undirected edge found in directed graph.')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
888 if (not G.is_directed()) and edge_direction == 'directed':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
889 raise nx.NetworkXError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
890 'Directed edge found in undirected graph.')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
891
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
892 # Get source and target and recast type if required
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
893 source = edge_element.get('source')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
894 target = edge_element.get('target')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
895 if self.node_type is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
896 source = self.node_type(source)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
897 target = self.node_type(target)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
898
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
899 data = self.decode_attr_elements(edge_attr, edge_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
900 data = self.add_start_end(data, edge_element)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
901
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
902 if self.version == '1.1':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
903 data = self.add_slices(data, edge_element) # add slices
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
904 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
905 data = self.add_spells(data, edge_element) # add spells
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
906
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
907 # GEXF stores edge ids as an attribute
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
908 # NetworkX uses them as keys in multigraphs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
909 # if networkx_key is not specified as an attribute
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
910 edge_id = edge_element.get('id')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
911 if edge_id is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
912 data['id'] = edge_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
913
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
914 # check if there is a 'multigraph_key' and use that as edge_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
915 multigraph_key = data.pop('networkx_key', None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
916 if multigraph_key is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
917 edge_id = multigraph_key
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
918
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
919 weight = edge_element.get('weight')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
920 if weight is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
921 data['weight'] = float(weight)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
922
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
923 edge_label = edge_element.get('label')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
924 if edge_label is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
925 data['label'] = edge_label
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
926
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
927 if G.has_edge(source, target):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
928 # seen this edge before - this is a multigraph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
929 self.simple_graph = False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
930 G.add_edge(source, target, key=edge_id, **data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
931 if edge_direction == 'mutual':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
932 G.add_edge(target, source, key=edge_id, **data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
933
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
934 def decode_attr_elements(self, gexf_keys, obj_xml):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
935 # Use the key information to decode the attr XML
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
936 attr = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
937 # look for outer '<attvalues>' element
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
938 attr_element = obj_xml.find('{%s}attvalues' % self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
939 if attr_element is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
940 # loop over <attvalue> elements
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
941 for a in attr_element.findall('{%s}attvalue' % self.NS_GEXF):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
942 key = a.get('for') # for is required
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
943 try: # should be in our gexf_keys dictionary
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
944 title = gexf_keys[key]['title']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
945 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
946 raise nx.NetworkXError('No attribute defined for=%s.'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
947 % key)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
948 atype = gexf_keys[key]['type']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
949 value = a.get('value')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
950 if atype == 'boolean':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
951 value = self.convert_bool[value]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
952 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
953 value = self.python_type[atype](value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
954 if gexf_keys[key]['mode'] == 'dynamic':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
955 # for dynamic graphs use list of three-tuples
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
956 # [(value1,start1,end1), (value2,start2,end2), etc]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
957 ttype = self.timeformat
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
958 start = self.python_type[ttype](a.get('start'))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
959 end = self.python_type[ttype](a.get('end'))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
960 if title in attr:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
961 attr[title].append((value, start, end))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
962 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
963 attr[title] = [(value, start, end)]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
964 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
965 # for static graphs just assign the value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
966 attr[title] = value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
967 return attr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
968
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
969 def find_gexf_attributes(self, attributes_element):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
970 # Extract all the attributes and defaults
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
971 attrs = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
972 defaults = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
973 mode = attributes_element.get('mode')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
974 for k in attributes_element.findall('{%s}attribute' % self.NS_GEXF):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
975 attr_id = k.get('id')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
976 title = k.get('title')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
977 atype = k.get('type')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
978 attrs[attr_id] = {'title': title, 'type': atype, 'mode': mode}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
979 # check for the 'default' subelement of key element and add
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
980 default = k.find('{%s}default' % self.NS_GEXF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
981 if default is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
982 if atype == 'boolean':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
983 value = self.convert_bool[default.text]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
984 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
985 value = self.python_type[atype](default.text)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
986 defaults[title] = value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
987 return attrs, defaults
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
988
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
989
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
990 def relabel_gexf_graph(G):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
991 """Relabel graph using "label" node keyword for node label.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
992
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
993 Parameters
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
994 ----------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
995 G : graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
996 A NetworkX graph read from GEXF data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
997
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
998 Returns
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
999 -------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1000 H : graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1001 A NetworkX graph with relabed nodes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1002
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1003 Raises
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1004 ------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1005 NetworkXError
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1006 If node labels are missing or not unique while relabel=True.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1007
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1008 Notes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1009 -----
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1010 This function relabels the nodes in a NetworkX graph with the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1011 "label" attribute. It also handles relabeling the specific GEXF
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1012 node attributes "parents", and "pid".
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1013 """
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1014 # build mapping of node labels, do some error checking
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1015 try:
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1016 mapping = [(u, G.nodes[u]['label']) for u in G]
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1017 except KeyError:
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1018 raise nx.NetworkXError('Failed to relabel nodes: '
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1019 'missing node labels found. '
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1020 'Use relabel=False.')
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1021 x, y = zip(*mapping)
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1022 if len(set(y)) != len(G):
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1023 raise nx.NetworkXError('Failed to relabel nodes: '
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1024 'duplicate node labels found. '
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1025 'Use relabel=False.')
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1026 mapping = dict(mapping)
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1027 H = nx.relabel_nodes(G, mapping)
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1028 # relabel attributes
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1029 for n in G:
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1030 m = mapping[n]
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1031 H.nodes[m]['id'] = n
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1032 H.nodes[m].pop('label')
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1033 if 'pid' in H.nodes[m]:
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1034 H.nodes[m]['pid'] = mapping[G.nodes[n]['pid']]
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1035 if 'parents' in H.nodes[m]:
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1036 H.nodes[m]['parents'] = [mapping[p] for p in G.nodes[n]['parents']]
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1037 return H
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1038
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1039
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1040 # fixture for pytest
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1041 def setup_module(module):
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1042 import pytest
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1043 xml.etree.cElementTree = pytest.importorskip('xml.etree.cElementTree')
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1044
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1045
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1046 # fixture for pytest
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1047 def teardown_module(module):
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1048 import os
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1049 try:
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1050 os.unlink('test.gexf')
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1051 except Exception as e:
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1052 pass