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annotate planemo/lib/python3.7/site-packages/networkx/readwrite/graphml.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1 # Copyright (C) 2008-2019 by
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2 # Aric Hagberg <hagberg@lanl.gov>
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3 # Dan Schult <dschult@colgate.edu>
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4 # Pieter Swart <swart@lanl.gov>
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5 # All rights reserved.
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6 # BSD license.
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7 #
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8 # Authors: Salim Fadhley
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9 # Aric Hagberg (hagberg@lanl.gov)
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10 """
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11 *******
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12 GraphML
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13 *******
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14 Read and write graphs in GraphML format.
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15
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16 This implementation does not support mixed graphs (directed and unidirected
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17 edges together), hyperedges, nested graphs, or ports.
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18
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19 "GraphML is a comprehensive and easy-to-use file format for graphs. It
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20 consists of a language core to describe the structural properties of a
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21 graph and a flexible extension mechanism to add application-specific
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22 data. Its main features include support of
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23
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24 * directed, undirected, and mixed graphs,
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25 * hypergraphs,
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26 * hierarchical graphs,
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27 * graphical representations,
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28 * references to external data,
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29 * application-specific attribute data, and
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30 * light-weight parsers.
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31
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32 Unlike many other file formats for graphs, GraphML does not use a
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33 custom syntax. Instead, it is based on XML and hence ideally suited as
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34 a common denominator for all kinds of services generating, archiving,
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35 or processing graphs."
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36
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37 http://graphml.graphdrawing.org/
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38
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39 Format
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40 ------
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41 GraphML is an XML format. See
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42 http://graphml.graphdrawing.org/specification.html for the specification and
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43 http://graphml.graphdrawing.org/primer/graphml-primer.html
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44 for examples.
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45 """
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46 import warnings
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47 from collections import defaultdict
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48
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49 try:
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50 from xml.etree.cElementTree import Element, ElementTree
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51 from xml.etree.cElementTree import tostring, fromstring
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52 except ImportError:
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53 try:
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54 from xml.etree.ElementTree import Element, ElementTree
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55 from xml.etree.ElementTree import tostring, fromstring
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56 except ImportError:
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57 pass
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58
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59 try:
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60 import lxml.etree as lxmletree
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61 except ImportError:
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62 lxmletree = None
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63
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64 import networkx as nx
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65 from networkx.utils import open_file, make_str
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66
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67 __all__ = ['write_graphml', 'read_graphml', 'generate_graphml',
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68 'write_graphml_xml', 'write_graphml_lxml',
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69 'parse_graphml', 'GraphMLWriter', 'GraphMLReader']
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70
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71
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72 @open_file(1, mode='wb')
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73 def write_graphml_xml(G, path, encoding='utf-8', prettyprint=True,
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74 infer_numeric_types=False):
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75 """Write G in GraphML XML format to path
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76
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77 Parameters
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78 ----------
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79 G : graph
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80 A networkx graph
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81 path : file or string
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82 File or filename to write.
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83 Filenames ending in .gz or .bz2 will be compressed.
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84 encoding : string (optional)
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85 Encoding for text data.
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86 prettyprint : bool (optional)
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87 If True use line breaks and indenting in output XML.
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88 infer_numeric_types : boolean
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89 Determine if numeric types should be generalized.
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90 For example, if edges have both int and float 'weight' attributes,
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91 we infer in GraphML that both are floats.
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92
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93 Examples
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94 --------
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95 >>> G = nx.path_graph(4)
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96 >>> nx.write_graphml(G, "test.graphml")
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97
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98 Notes
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99 -----
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100 It may be a good idea in Python2 to convert strings to unicode
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101 before giving the graph to write_gml. At least the strings with
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102 either many characters to escape.
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103
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104 This implementation does not support mixed graphs (directed
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105 and unidirected edges together) hyperedges, nested graphs, or ports.
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106 """
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107 writer = GraphMLWriter(encoding=encoding, prettyprint=prettyprint,
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108 infer_numeric_types=infer_numeric_types)
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109 writer.add_graph_element(G)
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110 writer.dump(path)
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111
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112
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113 @open_file(1, mode='wb')
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114 def write_graphml_lxml(G, path, encoding='utf-8', prettyprint=True,
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115 infer_numeric_types=False):
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116 """Write G in GraphML XML format to path
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117
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118 This function uses the LXML framework and should be faster than
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119 the version using the xml library.
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120
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121 Parameters
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122 ----------
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123 G : graph
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124 A networkx graph
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125 path : file or string
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126 File or filename to write.
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127 Filenames ending in .gz or .bz2 will be compressed.
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128 encoding : string (optional)
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129 Encoding for text data.
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130 prettyprint : bool (optional)
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131 If True use line breaks and indenting in output XML.
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132 infer_numeric_types : boolean
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133 Determine if numeric types should be generalized.
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134 For example, if edges have both int and float 'weight' attributes,
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135 we infer in GraphML that both are floats.
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136
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137 Examples
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138 --------
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139 >>> G = nx.path_graph(4)
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140 >>> nx.write_graphml_lxml(G, "fourpath.graphml") # doctest: +SKIP
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141
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142 Notes
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143 -----
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144 This implementation does not support mixed graphs (directed
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145 and unidirected edges together) hyperedges, nested graphs, or ports.
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146 """
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147 writer = GraphMLWriterLxml(path, graph=G, encoding=encoding,
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148 prettyprint=prettyprint,
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149 infer_numeric_types=infer_numeric_types)
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150 writer.dump()
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151
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152
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153 def generate_graphml(G, encoding='utf-8', prettyprint=True):
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154 """Generate GraphML lines for G
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155
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156 Parameters
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157 ----------
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158 G : graph
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159 A networkx graph
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160 encoding : string (optional)
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161 Encoding for text data.
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162 prettyprint : bool (optional)
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163 If True use line breaks and indenting in output XML.
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164
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165 Examples
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166 --------
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167 >>> G = nx.path_graph(4)
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168 >>> linefeed = chr(10) # linefeed = \n
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169 >>> s = linefeed.join(nx.generate_graphml(G)) # doctest: +SKIP
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170 >>> for line in nx.generate_graphml(G): # doctest: +SKIP
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171 ... print(line)
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172
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173 Notes
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174 -----
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175 This implementation does not support mixed graphs (directed and unidirected
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176 edges together) hyperedges, nested graphs, or ports.
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177 """
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178 writer = GraphMLWriter(encoding=encoding, prettyprint=prettyprint)
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179 writer.add_graph_element(G)
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180 for line in str(writer).splitlines():
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181 yield line
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182
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183
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184 @open_file(0, mode='rb')
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185 def read_graphml(path, node_type=str, edge_key_type=int):
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186 """Read graph in GraphML format from path.
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187
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188 Parameters
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189 ----------
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190 path : file or string
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191 File or filename to write.
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192 Filenames ending in .gz or .bz2 will be compressed.
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193
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194 node_type: Python type (default: str)
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195 Convert node ids to this type
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196
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197 edge_key_type: Python type (default: int)
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198 Convert graphml edge ids to this type as key of multi-edges
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199
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200
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201 Returns
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202 -------
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203 graph: NetworkX graph
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204 If no parallel edges are found a Graph or DiGraph is returned.
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205 Otherwise a MultiGraph or MultiDiGraph is returned.
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206
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207 Notes
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208 -----
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209 Default node and edge attributes are not propagated to each node and edge.
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210 They can be obtained from `G.graph` and applied to node and edge attributes
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211 if desired using something like this:
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212
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213 >>> default_color = G.graph['node_default']['color'] # doctest: +SKIP
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214 >>> for node, data in G.nodes(data=True): # doctest: +SKIP
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215 ... if 'color' not in data:
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216 ... data['color']=default_color
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217 >>> default_color = G.graph['edge_default']['color'] # doctest: +SKIP
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218 >>> for u, v, data in G.edges(data=True): # doctest: +SKIP
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219 ... if 'color' not in data:
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220 ... data['color']=default_color
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221
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222 This implementation does not support mixed graphs (directed and unidirected
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223 edges together), hypergraphs, nested graphs, or ports.
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224
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225 For multigraphs the GraphML edge "id" will be used as the edge
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226 key. If not specified then they "key" attribute will be used. If
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227 there is no "key" attribute a default NetworkX multigraph edge key
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228 will be provided.
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229
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230 Files with the yEd "yfiles" extension will can be read but the graphics
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231 information is discarded.
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232
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233 yEd compressed files ("file.graphmlz" extension) can be read by renaming
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234 the file to "file.graphml.gz".
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235
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236 """
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237 reader = GraphMLReader(node_type=node_type, edge_key_type=edge_key_type)
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238 # need to check for multiple graphs
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239 glist = list(reader(path=path))
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240 if len(glist) == 0:
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241 # If no graph comes back, try looking for an incomplete header
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242 header = b'<graphml xmlns="http://graphml.graphdrawing.org/xmlns">'
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243 path.seek(0)
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244 old_bytes = path.read()
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245 new_bytes = old_bytes.replace(b'<graphml>', header)
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246 glist = list(reader(string=new_bytes))
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247 if len(glist) == 0:
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248 raise nx.NetworkXError('file not successfully read as graphml')
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249 return glist[0]
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250
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251
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252 def parse_graphml(graphml_string, node_type=str):
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253 """Read graph in GraphML format from string.
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254
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255 Parameters
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256 ----------
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257 graphml_string : string
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258 String containing graphml information
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259 (e.g., contents of a graphml file).
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260
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261 node_type: Python type (default: str)
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262 Convert node ids to this type
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263
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264 Returns
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265 -------
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266 graph: NetworkX graph
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267 If no parallel edges are found a Graph or DiGraph is returned.
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268 Otherwise a MultiGraph or MultiDiGraph is returned.
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269
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270 Examples
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271 --------
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272 >>> G = nx.path_graph(4)
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273 >>> linefeed = chr(10) # linefeed = \n
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274 >>> s = linefeed.join(nx.generate_graphml(G))
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275 >>> H = nx.parse_graphml(s)
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276
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277 Notes
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278 -----
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279 Default node and edge attributes are not propagated to each node and edge.
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280 They can be obtained from `G.graph` and applied to node and edge attributes
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281 if desired using something like this:
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282
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283 >>> default_color = G.graph['node_default']['color'] # doctest: +SKIP
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284 >>> for node, data in G.nodes(data=True): # doctest: +SKIP
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285 ... if 'color' not in data:
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286 ... data['color']=default_color
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287 >>> default_color = G.graph['edge_default']['color'] # doctest: +SKIP
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288 >>> for u, v, data in G.edges(data=True): # doctest: +SKIP
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289 ... if 'color' not in data:
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290 ... data['color']=default_color
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291
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292 This implementation does not support mixed graphs (directed and unidirected
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293 edges together), hypergraphs, nested graphs, or ports.
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294
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295 For multigraphs the GraphML edge "id" will be used as the edge
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296 key. If not specified then they "key" attribute will be used. If
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297 there is no "key" attribute a default NetworkX multigraph edge key
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298 will be provided.
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299
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300 """
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301 reader = GraphMLReader(node_type=node_type)
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302 # need to check for multiple graphs
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303 glist = list(reader(string=graphml_string))
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304 if len(glist) == 0:
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305 # If no graph comes back, try looking for an incomplete header
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306 header = '<graphml xmlns="http://graphml.graphdrawing.org/xmlns">'
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307 new_string = graphml_string.replace('<graphml>', header)
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308 glist = list(reader(string=new_string))
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309 if len(glist) == 0:
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310 raise nx.NetworkXError('file not successfully read as graphml')
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311 return glist[0]
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312
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313
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314 class GraphML(object):
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315 NS_GRAPHML = "http://graphml.graphdrawing.org/xmlns"
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316 NS_XSI = "http://www.w3.org/2001/XMLSchema-instance"
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317 # xmlns:y="http://www.yworks.com/xml/graphml"
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318 NS_Y = "http://www.yworks.com/xml/graphml"
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319 SCHEMALOCATION = \
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320 ' '.join(['http://graphml.graphdrawing.org/xmlns',
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321 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd'])
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322
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323 try:
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324 chr(12345) # Fails on Py!=3.
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325 unicode = str # Py3k's str is our unicode type
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326 long = int # Py3K's int is our long type
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327 except ValueError:
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328 # Python 2.x
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329 pass
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330
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331 types = [(int, "integer"), # for Gephi GraphML bug
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332 (str, "yfiles"), (str, "string"), (unicode, "string"),
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333 (int, "int"), (long, "long"),
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334 (float, "float"), (float, "double"),
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335 (bool, "boolean")]
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336
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337 # These additions to types allow writing numpy types
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338 try:
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339 import numpy as np
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340 except:
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341 pass
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342 else:
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343 # prepend so that python types are created upon read (last entry wins)
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344 types = [(np.float64, "float"), (np.float32, "float"),
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345 (np.float16, "float"), (np.float_, "float"),
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346 (np.int, "int"), (np.int8, "int"),
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347 (np.int16, "int"), (np.int32, "int"),
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348 (np.int64, "int"), (np.uint8, "int"),
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349 (np.uint16, "int"), (np.uint32, "int"),
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350 (np.uint64, "int"), (np.int_, "int"),
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351 (np.intc, "int"), (np.intp, "int"),
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352 ] + types
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353
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354 xml_type = dict(types)
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355 python_type = dict(reversed(a) for a in types)
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356
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357 # This page says that data types in GraphML follow Java(TM).
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358 # http://graphml.graphdrawing.org/primer/graphml-primer.html#AttributesDefinition
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359 # true and false are the only boolean literals:
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360 # http://en.wikibooks.org/wiki/Java_Programming/Literals#Boolean_Literals
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361 convert_bool = {
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362 # We use data.lower() in actual use.
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363 'true': True, 'false': False,
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364 # Include integer strings for convenience.
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365 '0': False, 0: False,
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366 '1': True, 1: True
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367 }
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368
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369
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370 class GraphMLWriter(GraphML):
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371 def __init__(self, graph=None, encoding="utf-8", prettyprint=True,
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372 infer_numeric_types=False):
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373 try:
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374 import xml.etree.ElementTree
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375 except ImportError:
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376 msg = 'GraphML writer requires xml.elementtree.ElementTree'
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377 raise ImportError(msg)
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378 self.myElement = Element
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379
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380 self.infer_numeric_types = infer_numeric_types
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381 self.prettyprint = prettyprint
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382 self.encoding = encoding
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383 self.xml = self.myElement("graphml",
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384 {'xmlns': self.NS_GRAPHML,
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385 'xmlns:xsi': self.NS_XSI,
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parents:
diff changeset
386 'xsi:schemaLocation': self.SCHEMALOCATION})
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parents:
diff changeset
387 self.keys = {}
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diff changeset
388 self.attributes = defaultdict(list)
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diff changeset
389 self.attribute_types = defaultdict(set)
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diff changeset
390
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diff changeset
391 if graph is not None:
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diff changeset
392 self.add_graph_element(graph)
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diff changeset
393
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parents:
diff changeset
394 def __str__(self):
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parents:
diff changeset
395 if self.prettyprint:
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parents:
diff changeset
396 self.indent(self.xml)
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parents:
diff changeset
397 s = tostring(self.xml).decode(self.encoding)
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diff changeset
398 return s
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diff changeset
399
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parents:
diff changeset
400 def attr_type(self, name, scope, value):
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guerler
parents:
diff changeset
401 """Infer the attribute type of data named name. Currently this only
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guerler
parents:
diff changeset
402 supports inference of numeric types.
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parents:
diff changeset
403
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parents:
diff changeset
404 If self.infer_numeric_types is false, type is used. Otherwise, pick the
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guerler
parents:
diff changeset
405 most general of types found across all values with name and scope. This
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guerler
parents:
diff changeset
406 means edges with data named 'weight' are treated separately from nodes
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guerler
parents:
diff changeset
407 with data named 'weight'.
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parents:
diff changeset
408 """
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parents:
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409 if self.infer_numeric_types:
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diff changeset
410 types = self.attribute_types[(name, scope)]
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diff changeset
411
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412 try:
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413 chr(12345) # Fails on Py<3.
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414 local_long = int # Py3's int is Py2's long type
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415 local_unicode = str # Py3's str is Py2's unicode type
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416 except ValueError:
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diff changeset
417 # Python 2.x
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418 local_long = long
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419 local_unicode = unicode
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420
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421 if len(types) > 1:
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422 if str in types:
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423 return str
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parents:
diff changeset
424 elif local_unicode in types:
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425 return local_unicode
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parents:
diff changeset
426 elif float in types:
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diff changeset
427 return float
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parents:
diff changeset
428 elif local_long in types:
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diff changeset
429 return local_long
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diff changeset
430 else:
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431 return int
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diff changeset
432 else:
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parents:
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433 return list(types)[0]
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diff changeset
434 else:
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parents:
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435 return type(value)
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diff changeset
436
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437 def get_key(self, name, attr_type, scope, default):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
438 keys_key = (name, attr_type, scope)
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diff changeset
439 try:
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diff changeset
440 return self.keys[keys_key]
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parents:
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441 except KeyError:
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parents:
diff changeset
442 new_id = "d%i" % len(list(self.keys))
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guerler
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443 self.keys[keys_key] = new_id
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444 key_kwargs = {"id": new_id,
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parents:
diff changeset
445 "for": scope,
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parents:
diff changeset
446 "attr.name": name,
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parents:
diff changeset
447 "attr.type": attr_type}
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parents:
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448 key_element = self.myElement("key", **key_kwargs)
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diff changeset
449 # add subelement for data default value if present
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diff changeset
450 if default is not None:
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parents:
diff changeset
451 default_element = self.myElement("default")
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parents:
diff changeset
452 default_element.text = make_str(default)
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parents:
diff changeset
453 key_element.append(default_element)
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parents:
diff changeset
454 self.xml.insert(0, key_element)
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diff changeset
455 return new_id
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diff changeset
456
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parents:
diff changeset
457 def add_data(self, name, element_type, value,
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parents:
diff changeset
458 scope="all",
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diff changeset
459 default=None):
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parents:
diff changeset
460 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
461 Make a data element for an edge or a node. Keep a log of the
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guerler
parents:
diff changeset
462 type in the keys table.
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parents:
diff changeset
463 """
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guerler
parents:
diff changeset
464 if element_type not in self.xml_type:
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465 msg = 'GraphML writer does not support %s as data values.'
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guerler
parents:
diff changeset
466 raise nx.NetworkXError(msg % element_type)
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guerler
parents:
diff changeset
467 keyid = self.get_key(name, self.xml_type[element_type], scope, default)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
468 data_element = self.myElement("data", key=keyid)
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guerler
parents:
diff changeset
469 data_element.text = make_str(value)
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guerler
parents:
diff changeset
470 return data_element
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guerler
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diff changeset
471
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guerler
parents:
diff changeset
472 def add_attributes(self, scope, xml_obj, data, default):
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guerler
parents:
diff changeset
473 """Appends attribute data to edges or nodes, and stores type information
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guerler
parents:
diff changeset
474 to be added later. See add_graph_element.
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guerler
parents:
diff changeset
475 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
476 for k, v in data.items():
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guerler
parents:
diff changeset
477 self.attribute_types[(make_str(k), scope)].add(type(v))
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guerler
parents:
diff changeset
478 self.attributes[xml_obj].append([k, v, scope, default.get(k)])
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guerler
parents:
diff changeset
479
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guerler
parents:
diff changeset
480 def add_nodes(self, G, graph_element):
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guerler
parents:
diff changeset
481 default = G.graph.get('node_default', {})
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
482 for node, data in G.nodes(data=True):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
483 node_element = self.myElement("node", id=make_str(node))
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guerler
parents:
diff changeset
484 self.add_attributes("node", node_element, data, default)
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guerler
parents:
diff changeset
485 graph_element.append(node_element)
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guerler
parents:
diff changeset
486
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guerler
parents:
diff changeset
487 def add_edges(self, G, graph_element):
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guerler
parents:
diff changeset
488 if G.is_multigraph():
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guerler
parents:
diff changeset
489 for u, v, key, data in G.edges(data=True, keys=True):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
490 edge_element = self.myElement("edge", source=make_str(u),
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
491 target=make_str(v),
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
492 id=make_str(key))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
493 default = G.graph.get('edge_default', {})
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guerler
parents:
diff changeset
494 self.add_attributes("edge", edge_element, data, default)
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guerler
parents:
diff changeset
495 graph_element.append(edge_element)
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diff changeset
496 else:
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diff changeset
497 for u, v, data in G.edges(data=True):
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parents:
diff changeset
498 edge_element = self.myElement("edge", source=make_str(u),
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guerler
parents:
diff changeset
499 target=make_str(v))
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guerler
parents:
diff changeset
500 default = G.graph.get('edge_default', {})
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guerler
parents:
diff changeset
501 self.add_attributes("edge", edge_element, data, default)
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guerler
parents:
diff changeset
502 graph_element.append(edge_element)
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guerler
parents:
diff changeset
503
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parents:
diff changeset
504 def add_graph_element(self, G):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
505 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
506 Serialize graph G in GraphML to the stream.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
507 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
508 if G.is_directed():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
509 default_edge_type = 'directed'
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guerler
parents:
diff changeset
510 else:
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guerler
parents:
diff changeset
511 default_edge_type = 'undirected'
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guerler
parents:
diff changeset
512
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parents:
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513 graphid = G.graph.pop('id', None)
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514 if graphid is None:
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515 graph_element = self.myElement("graph",
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516 edgedefault=default_edge_type)
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517 else:
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518 graph_element = self.myElement("graph",
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519 edgedefault=default_edge_type,
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520 id=graphid)
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521 default = {}
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522 data = {k: v for (k, v) in G.graph.items()
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523 if k not in ['node_default', 'edge_default']}
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524 self.add_attributes("graph", graph_element, data, default)
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525 self.add_nodes(G, graph_element)
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526 self.add_edges(G, graph_element)
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527
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528 # self.attributes contains a mapping from XML Objects to a list of
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529 # data that needs to be added to them.
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530 # We postpone processing in order to do type inference/generalization.
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531 # See self.attr_type
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532 for (xml_obj, data) in self.attributes.items():
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533 for (k, v, scope, default) in data:
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534 xml_obj.append(self.add_data(make_str(k),
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535 self.attr_type(k, scope, v),
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536 make_str(v), scope, default))
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537 self.xml.append(graph_element)
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538
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539 def add_graphs(self, graph_list):
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540 """ Add many graphs to this GraphML document. """
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541 for G in graph_list:
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542 self.add_graph_element(G)
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543
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544 def dump(self, stream):
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545 if self.prettyprint:
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546 self.indent(self.xml)
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547 document = ElementTree(self.xml)
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548 document.write(stream, encoding=self.encoding, xml_declaration=True)
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549
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550 def indent(self, elem, level=0):
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551 # in-place prettyprint formatter
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552 i = "\n" + level * " "
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553 if len(elem):
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554 if not elem.text or not elem.text.strip():
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555 elem.text = i + " "
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556 if not elem.tail or not elem.tail.strip():
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557 elem.tail = i
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558 for elem in elem:
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559 self.indent(elem, level + 1)
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560 if not elem.tail or not elem.tail.strip():
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561 elem.tail = i
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562 else:
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563 if level and (not elem.tail or not elem.tail.strip()):
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564 elem.tail = i
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565
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566
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567 class IncrementalElement(object):
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568 """Wrapper for _IncrementalWriter providing an Element like interface.
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569
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570 This wrapper does not intend to be a complete implementation but rather to
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571 deal with those calls used in GraphMLWriter.
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572 """
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573
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574 def __init__(self, xml, prettyprint):
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575 self.xml = xml
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576 self.prettyprint = prettyprint
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577
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578 def append(self, element):
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579 self.xml.write(element, pretty_print=self.prettyprint)
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580
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581
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582 class GraphMLWriterLxml(GraphMLWriter):
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583 def __init__(self, path, graph=None, encoding='utf-8', prettyprint=True,
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584 infer_numeric_types=False):
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585 self.myElement = lxmletree.Element
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586
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587 self._encoding = encoding
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588 self._prettyprint = prettyprint
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589 self.infer_numeric_types = infer_numeric_types
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590
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591 self._xml_base = lxmletree.xmlfile(path, encoding=encoding)
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592 self._xml = self._xml_base.__enter__()
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593 self._xml.write_declaration()
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594
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595 # We need to have a xml variable that support insertion. This call is
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diff changeset
596 # used for adding the keys to the document.
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diff changeset
597 # We will store those keys in a plain list, and then after the graph
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diff changeset
598 # element is closed we will add them to the main graphml element.
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599 self.xml = []
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600 self._keys = self.xml
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601 self._graphml = self._xml.element(
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602 'graphml',
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603 {
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604 'xmlns': self.NS_GRAPHML,
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605 'xmlns:xsi': self.NS_XSI,
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diff changeset
606 'xsi:schemaLocation': self.SCHEMALOCATION
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607 })
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608 self._graphml.__enter__()
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609 self.keys = {}
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610 self.attribute_types = defaultdict(set)
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611
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612 if graph is not None:
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613 self.add_graph_element(graph)
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614
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615 def add_graph_element(self, G):
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616 """
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617 Serialize graph G in GraphML to the stream.
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618 """
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619 if G.is_directed():
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620 default_edge_type = 'directed'
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621 else:
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622 default_edge_type = 'undirected'
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623
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624 graphid = G.graph.pop('id', None)
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625 if graphid is None:
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626 graph_element = self._xml.element('graph',
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627 edgedefault=default_edge_type)
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628 else:
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629 graph_element = self._xml.element('graph',
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630 edgedefault=default_edge_type,
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631 id=graphid)
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632
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633 # gather attributes types for the whole graph
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634 # to find the most general numeric format needed.
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635 # Then pass through attributes to create key_id for each.
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636 graphdata = {k: v for k, v in G.graph.items()
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637 if k not in ('node_default', 'edge_default')}
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638 node_default = G.graph.get('node_default', {})
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639 edge_default = G.graph.get('edge_default', {})
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640 # Graph attributes
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641 for k, v in graphdata.items():
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diff changeset
642 self.attribute_types[(make_str(k), "graph")].add(type(v))
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parents:
diff changeset
643 for k, v in graphdata.items():
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diff changeset
644 element_type = self.xml_type[self.attr_type(k, "graph", v)]
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diff changeset
645 self.get_key(make_str(k), element_type, "graph", None)
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parents:
diff changeset
646 # Nodes and data
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diff changeset
647 for node, d in G.nodes(data=True):
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diff changeset
648 for k, v in d.items():
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parents:
diff changeset
649 self.attribute_types[(make_str(k), "node")].add(type(v))
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diff changeset
650 for node, d in G.nodes(data=True):
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diff changeset
651 for k, v in d.items():
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diff changeset
652 T = self.xml_type[self.attr_type(k, "node", v)]
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diff changeset
653 self.get_key(make_str(k), T, "node", node_default.get(k))
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diff changeset
654 # Edges and data
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diff changeset
655 if G.is_multigraph():
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diff changeset
656 for u, v, ekey, d in G.edges(keys=True, data=True):
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diff changeset
657 for k, v in d.items():
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parents:
diff changeset
658 self.attribute_types[(make_str(k), "edge")].add(type(v))
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diff changeset
659 for u, v, ekey, d in G.edges(keys=True, data=True):
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parents:
diff changeset
660 for k, v in d.items():
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diff changeset
661 T = self.xml_type[self.attr_type(k, "edge", v)]
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diff changeset
662 self.get_key(make_str(k), T, "edge", edge_default.get(k))
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diff changeset
663 else:
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diff changeset
664 for u, v, d in G.edges(data=True):
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parents:
diff changeset
665 for k, v in d.items():
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diff changeset
666 self.attribute_types[(make_str(k), "edge")].add(type(v))
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diff changeset
667 for u, v, d in G.edges(data=True):
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parents:
diff changeset
668 for k, v in d.items():
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parents:
diff changeset
669 T = self.xml_type[self.attr_type(k, "edge", v)]
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diff changeset
670 self.get_key(make_str(k), T, "edge", edge_default.get(k))
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diff changeset
671
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diff changeset
672 # Now add attribute keys to the xml file
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diff changeset
673 for key in self.xml:
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diff changeset
674 self._xml.write(key, pretty_print=self._prettyprint)
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diff changeset
675
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parents:
diff changeset
676 # The incremental_writer writes each node/edge as it is created
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diff changeset
677 incremental_writer = IncrementalElement(self._xml, self._prettyprint)
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678 with graph_element:
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679 self.add_attributes('graph', incremental_writer, graphdata, {})
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diff changeset
680 self.add_nodes(G, incremental_writer) # adds attributes too
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diff changeset
681 self.add_edges(G, incremental_writer) # adds attributes too
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diff changeset
682
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diff changeset
683 def add_attributes(self, scope, xml_obj, data, default):
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diff changeset
684 """Appends attribute data."""
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diff changeset
685 for k, v in data.items():
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diff changeset
686 data_element = self.add_data(make_str(k),
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diff changeset
687 self.attr_type(make_str(k), scope, v),
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parents:
diff changeset
688 make_str(v), scope, default.get(k))
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diff changeset
689 xml_obj.append(data_element)
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diff changeset
690
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diff changeset
691 def __str__(self):
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diff changeset
692 return object.__str__(self)
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693
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diff changeset
694 def dump(self):
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diff changeset
695 self._graphml.__exit__(None, None, None)
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diff changeset
696 self._xml_base.__exit__(None, None, None)
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diff changeset
697
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diff changeset
698
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diff changeset
699 # Choose a writer function for default
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parents:
diff changeset
700 if lxmletree is None:
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parents:
diff changeset
701 write_graphml = write_graphml_xml
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diff changeset
702 else:
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diff changeset
703 write_graphml = write_graphml_lxml
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diff changeset
704
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diff changeset
705
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706 class GraphMLReader(GraphML):
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diff changeset
707 """Read a GraphML document. Produces NetworkX graph objects."""
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diff changeset
708
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diff changeset
709 def __init__(self, node_type=str, edge_key_type=int):
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diff changeset
710 try:
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diff changeset
711 import xml.etree.ElementTree
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diff changeset
712 except ImportError:
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diff changeset
713 msg = 'GraphML reader requires xml.elementtree.ElementTree'
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diff changeset
714 raise ImportError(msg)
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parents:
diff changeset
715 self.node_type = node_type
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parents:
diff changeset
716 self.edge_key_type = edge_key_type
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diff changeset
717 self.multigraph = False # assume multigraph and test for multiedges
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diff changeset
718 self.edge_ids = {} # dict mapping (u,v) tuples to id edge attributes
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diff changeset
719
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diff changeset
720 def __call__(self, path=None, string=None):
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diff changeset
721 if path is not None:
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parents:
diff changeset
722 self.xml = ElementTree(file=path)
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parents:
diff changeset
723 elif string is not None:
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parents:
diff changeset
724 self.xml = fromstring(string)
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diff changeset
725 else:
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parents:
diff changeset
726 raise ValueError("Must specify either 'path' or 'string' as kwarg")
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diff changeset
727 (keys, defaults) = self.find_graphml_keys(self.xml)
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parents:
diff changeset
728 for g in self.xml.findall("{%s}graph" % self.NS_GRAPHML):
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parents:
diff changeset
729 yield self.make_graph(g, keys, defaults)
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parents:
diff changeset
730
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diff changeset
731 def make_graph(self, graph_xml, graphml_keys, defaults, G=None):
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parents:
diff changeset
732 # set default graph type
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diff changeset
733 edgedefault = graph_xml.get("edgedefault", None)
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parents:
diff changeset
734 if G is None:
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parents:
diff changeset
735 if edgedefault == 'directed':
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parents:
diff changeset
736 G = nx.MultiDiGraph()
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parents:
diff changeset
737 else:
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diff changeset
738 G = nx.MultiGraph()
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parents:
diff changeset
739 # set defaults for graph attributes
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diff changeset
740 G.graph['node_default'] = {}
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guerler
parents:
diff changeset
741 G.graph['edge_default'] = {}
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guerler
parents:
diff changeset
742 for key_id, value in defaults.items():
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guerler
parents:
diff changeset
743 key_for = graphml_keys[key_id]['for']
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guerler
parents:
diff changeset
744 name = graphml_keys[key_id]['name']
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guerler
parents:
diff changeset
745 python_type = graphml_keys[key_id]['type']
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guerler
parents:
diff changeset
746 if key_for == 'node':
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guerler
parents:
diff changeset
747 G.graph['node_default'].update({name: python_type(value)})
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guerler
parents:
diff changeset
748 if key_for == 'edge':
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parents:
diff changeset
749 G.graph['edge_default'].update({name: python_type(value)})
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guerler
parents:
diff changeset
750 # hyperedges are not supported
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parents:
diff changeset
751 hyperedge = graph_xml.find("{%s}hyperedge" % self.NS_GRAPHML)
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parents:
diff changeset
752 if hyperedge is not None:
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parents:
diff changeset
753 raise nx.NetworkXError("GraphML reader doesn't support hyperedges")
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guerler
parents:
diff changeset
754 # add nodes
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parents:
diff changeset
755 for node_xml in graph_xml.findall("{%s}node" % self.NS_GRAPHML):
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guerler
parents:
diff changeset
756 self.add_node(G, node_xml, graphml_keys, defaults)
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guerler
parents:
diff changeset
757 # add edges
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parents:
diff changeset
758 for edge_xml in graph_xml.findall("{%s}edge" % self.NS_GRAPHML):
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guerler
parents:
diff changeset
759 self.add_edge(G, edge_xml, graphml_keys)
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guerler
parents:
diff changeset
760 # add graph data
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diff changeset
761 data = self.decode_data_elements(graphml_keys, graph_xml)
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guerler
parents:
diff changeset
762 G.graph.update(data)
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guerler
parents:
diff changeset
763
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
764 # switch to Graph or DiGraph if no parallel edges were found.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
765 if not self.multigraph:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
766 if G.is_directed():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
767 G = nx.DiGraph(G)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
768 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
769 G = nx.Graph(G)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
770 nx.set_edge_attributes(G, values=self.edge_ids, name='id')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
771
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
772 return G
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
773
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
774 def add_node(self, G, node_xml, graphml_keys, defaults):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
775 """Add a node to the graph.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
776 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
777 # warn on finding unsupported ports tag
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
778 ports = node_xml.find("{%s}port" % self.NS_GRAPHML)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
779 if ports is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
780 warnings.warn("GraphML port tag not supported.")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
781 # find the node by id and cast it to the appropriate type
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
782 node_id = self.node_type(node_xml.get("id"))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
783 # get data/attributes for node
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
784 data = self.decode_data_elements(graphml_keys, node_xml)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
785 G.add_node(node_id, **data)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
786 # get child nodes
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
787 if node_xml.attrib.get('yfiles.foldertype') == 'group':
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
788 graph_xml = node_xml.find("{%s}graph" % self.NS_GRAPHML)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
789 self.make_graph(graph_xml, graphml_keys, defaults, G)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
790
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
791 def add_edge(self, G, edge_element, graphml_keys):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
792 """Add an edge to the graph.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
793 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
794 # warn on finding unsupported ports tag
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
795 ports = edge_element.find("{%s}port" % self.NS_GRAPHML)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
796 if ports is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
797 warnings.warn("GraphML port tag not supported.")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
798
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
799 # raise error if we find mixed directed and undirected edges
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
800 directed = edge_element.get("directed")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
801 if G.is_directed() and directed == 'false':
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
802 msg = "directed=false edge found in directed graph."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
803 raise nx.NetworkXError(msg)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
804 if (not G.is_directed()) and directed == 'true':
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
805 msg = "directed=true edge found in undirected graph."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
806 raise nx.NetworkXError(msg)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
807
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
808 source = self.node_type(edge_element.get("source"))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
809 target = self.node_type(edge_element.get("target"))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
810 data = self.decode_data_elements(graphml_keys, edge_element)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
811 # GraphML stores edge ids as an attribute
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
812 # NetworkX uses them as keys in multigraphs too if no key
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
813 # attribute is specified
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
814 edge_id = edge_element.get("id")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
815 if edge_id:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
816 # self.edge_ids is used by `make_graph` method for non-multigraphs
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
817 self.edge_ids[source, target] = edge_id
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
818 try:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
819 edge_id = self.edge_key_type(edge_id)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
820 except ValueError: # Could not convert.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
821 pass
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
822 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
823 edge_id = data.get('key')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
824
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
825 if G.has_edge(source, target):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
826 # mark this as a multigraph
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
827 self.multigraph = True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
828
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
829 # Use add_edges_from to avoid error with add_edge when `'key' in data`
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
830 G.add_edges_from([(source, target, edge_id, data)])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
831
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
832 def decode_data_elements(self, graphml_keys, obj_xml):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
833 """Use the key information to decode the data XML if present."""
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
834 data = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
835 for data_element in obj_xml.findall("{%s}data" % self.NS_GRAPHML):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
836 key = data_element.get("key")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
837 try:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
838 data_name = graphml_keys[key]['name']
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
839 data_type = graphml_keys[key]['type']
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
840 except KeyError:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
841 raise nx.NetworkXError("Bad GraphML data: no key %s" % key)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
842 text = data_element.text
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
843 # assume anything with subelements is a yfiles extension
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
844 if text is not None and len(list(data_element)) == 0:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
845 if data_type == bool:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
846 # Ignore cases.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
847 # http://docs.oracle.com/javase/6/docs/api/java/lang/
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
848 # Boolean.html#parseBoolean%28java.lang.String%29
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
849 data[data_name] = self.convert_bool[text.lower()]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
850 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
851 data[data_name] = data_type(text)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
852 elif len(list(data_element)) > 0:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
853 # Assume yfiles as subelements, try to extract node_label
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
854 node_label = None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
855 for node_type in ['ShapeNode', 'SVGNode', 'ImageNode']:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
856 pref = "{%s}%s/{%s}" % (self.NS_Y, node_type, self.NS_Y)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
857 geometry = data_element.find("%sGeometry" % pref)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
858 if geometry is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
859 data['x'] = geometry.get('x')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
860 data['y'] = geometry.get('y')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
861 if node_label is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
862 node_label = data_element.find("%sNodeLabel" % pref)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
863 if node_label is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
864 data['label'] = node_label.text
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
865
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
866 # check all the different types of edges avaivable in yEd.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
867 for e in ['PolyLineEdge', 'SplineEdge', 'QuadCurveEdge',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
868 'BezierEdge', 'ArcEdge']:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
869 pref = "{%s}%s/{%s}" % (self.NS_Y, e, self.NS_Y)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
870 edge_label = data_element.find("%sEdgeLabel" % pref)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
871 if edge_label is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
872 break
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
873
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
874 if edge_label is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
875 data['label'] = edge_label.text
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
876 return data
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
877
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
878 def find_graphml_keys(self, graph_element):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
879 """Extracts all the keys and key defaults from the xml.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
880 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
881 graphml_keys = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
882 graphml_key_defaults = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
883 for k in graph_element.findall("{%s}key" % self.NS_GRAPHML):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
884 attr_id = k.get("id")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
885 attr_type = k.get('attr.type')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
886 attr_name = k.get("attr.name")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
887 yfiles_type = k.get("yfiles.type")
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888 if yfiles_type is not None:
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889 attr_name = yfiles_type
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890 attr_type = 'yfiles'
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891 if attr_type is None:
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892 attr_type = "string"
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893 warnings.warn("No key type for id %s. Using string" % attr_id)
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894 if attr_name is None:
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895 raise nx.NetworkXError("Unknown key for id %s." % attr_id)
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896 graphml_keys[attr_id] = {"name": attr_name,
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897 "type": self.python_type[attr_type],
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898 "for": k.get("for")}
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899 # check for "default" subelement of key element
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900 default = k.find("{%s}default" % self.NS_GRAPHML)
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901 if default is not None:
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902 graphml_key_defaults[attr_id] = default.text
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903 return graphml_keys, graphml_key_defaults
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904
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905
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906 # fixture for pytest
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907 def setup_module(module):
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908 import pytest
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909 xml.etree.ElementTree = pytest.importorskip('xml.etree.ElementTree')
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910
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911
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912 # fixture for pytest
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913 def teardown_module(module):
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914 import os
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915 try:
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916 os.unlink('test.graphml')
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917 except:
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918 pass