Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/readwrite/graphml.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """ |
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2 ******* |
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3 GraphML |
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4 ******* |
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5 Read and write graphs in GraphML format. |
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6 |
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7 This implementation does not support mixed graphs (directed and unidirected |
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8 edges together), hyperedges, nested graphs, or ports. |
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9 |
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10 "GraphML is a comprehensive and easy-to-use file format for graphs. It |
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11 consists of a language core to describe the structural properties of a |
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12 graph and a flexible extension mechanism to add application-specific |
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13 data. Its main features include support of |
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14 |
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15 * directed, undirected, and mixed graphs, |
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16 * hypergraphs, |
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17 * hierarchical graphs, |
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18 * graphical representations, |
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19 * references to external data, |
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20 * application-specific attribute data, and |
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21 * light-weight parsers. |
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22 |
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23 Unlike many other file formats for graphs, GraphML does not use a |
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24 custom syntax. Instead, it is based on XML and hence ideally suited as |
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25 a common denominator for all kinds of services generating, archiving, |
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26 or processing graphs." |
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27 |
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28 http://graphml.graphdrawing.org/ |
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29 |
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30 Format |
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31 ------ |
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32 GraphML is an XML format. See |
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33 http://graphml.graphdrawing.org/specification.html for the specification and |
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34 http://graphml.graphdrawing.org/primer/graphml-primer.html |
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35 for examples. |
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36 """ |
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37 import warnings |
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38 from collections import defaultdict |
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39 |
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40 from xml.etree.ElementTree import Element, ElementTree, tostring, fromstring |
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41 |
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42 try: |
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43 import lxml.etree as lxmletree |
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44 except ImportError: |
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45 lxmletree = None |
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46 |
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47 import networkx as nx |
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48 from networkx.utils import open_file |
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49 |
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50 __all__ = [ |
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51 "write_graphml", |
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52 "read_graphml", |
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53 "generate_graphml", |
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54 "write_graphml_xml", |
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55 "write_graphml_lxml", |
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56 "parse_graphml", |
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57 "GraphMLWriter", |
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58 "GraphMLReader", |
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59 ] |
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60 |
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61 |
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62 @open_file(1, mode="wb") |
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63 def write_graphml_xml( |
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64 G, |
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65 path, |
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66 encoding="utf-8", |
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67 prettyprint=True, |
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68 infer_numeric_types=False, |
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69 named_key_ids=False, |
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70 ): |
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71 """Write G in GraphML XML format to path |
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72 |
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73 Parameters |
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74 ---------- |
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75 G : graph |
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76 A networkx graph |
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77 path : file or string |
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78 File or filename to write. |
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79 Filenames ending in .gz or .bz2 will be compressed. |
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80 encoding : string (optional) |
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81 Encoding for text data. |
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82 prettyprint : bool (optional) |
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83 If True use line breaks and indenting in output XML. |
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84 infer_numeric_types : boolean |
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85 Determine if numeric types should be generalized. |
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86 For example, if edges have both int and float 'weight' attributes, |
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87 we infer in GraphML that both are floats. |
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88 named_key_ids : bool (optional) |
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89 If True use attr.name as value for key elements' id attribute. |
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90 |
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91 Examples |
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92 -------- |
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93 >>> G = nx.path_graph(4) |
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94 >>> nx.write_graphml(G, "test.graphml") |
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95 |
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96 Notes |
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97 ----- |
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98 This implementation does not support mixed graphs (directed |
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99 and unidirected edges together) hyperedges, nested graphs, or ports. |
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100 """ |
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101 writer = GraphMLWriter( |
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102 encoding=encoding, |
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103 prettyprint=prettyprint, |
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104 infer_numeric_types=infer_numeric_types, |
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105 named_key_ids=named_key_ids, |
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106 ) |
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107 writer.add_graph_element(G) |
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108 writer.dump(path) |
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109 |
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110 |
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111 @open_file(1, mode="wb") |
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112 def write_graphml_lxml( |
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113 G, |
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114 path, |
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115 encoding="utf-8", |
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116 prettyprint=True, |
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117 infer_numeric_types=False, |
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118 named_key_ids=False, |
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119 ): |
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120 """Write G in GraphML XML format to path |
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121 |
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122 This function uses the LXML framework and should be faster than |
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123 the version using the xml library. |
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124 |
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125 Parameters |
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126 ---------- |
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127 G : graph |
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128 A networkx graph |
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129 path : file or string |
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130 File or filename to write. |
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131 Filenames ending in .gz or .bz2 will be compressed. |
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132 encoding : string (optional) |
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133 Encoding for text data. |
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134 prettyprint : bool (optional) |
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135 If True use line breaks and indenting in output XML. |
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136 infer_numeric_types : boolean |
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137 Determine if numeric types should be generalized. |
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138 For example, if edges have both int and float 'weight' attributes, |
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139 we infer in GraphML that both are floats. |
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140 named_key_ids : bool (optional) |
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141 If True use attr.name as value for key elements' id attribute. |
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142 |
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143 Examples |
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144 -------- |
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145 >>> G = nx.path_graph(4) |
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146 >>> nx.write_graphml_lxml(G, "fourpath.graphml") # doctest: +SKIP |
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147 |
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148 Notes |
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149 ----- |
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150 This implementation does not support mixed graphs (directed |
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151 and unidirected edges together) hyperedges, nested graphs, or ports. |
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152 """ |
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153 writer = GraphMLWriterLxml( |
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154 path, |
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155 graph=G, |
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156 encoding=encoding, |
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157 prettyprint=prettyprint, |
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158 infer_numeric_types=infer_numeric_types, |
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159 named_key_ids=named_key_ids, |
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160 ) |
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161 writer.dump() |
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162 |
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163 |
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164 def generate_graphml(G, encoding="utf-8", prettyprint=True, named_key_ids=False): |
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165 """Generate GraphML lines for G |
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166 |
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167 Parameters |
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168 ---------- |
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169 G : graph |
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170 A networkx graph |
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171 encoding : string (optional) |
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172 Encoding for text data. |
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173 prettyprint : bool (optional) |
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174 If True use line breaks and indenting in output XML. |
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175 named_key_ids : bool (optional) |
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176 If True use attr.name as value for key elements' id attribute. |
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177 |
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178 Examples |
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179 -------- |
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180 >>> G = nx.path_graph(4) |
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181 >>> linefeed = chr(10) # linefeed = \n |
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182 >>> s = linefeed.join(nx.generate_graphml(G)) # doctest: +SKIP |
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183 >>> for line in nx.generate_graphml(G): # doctest: +SKIP |
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184 ... print(line) |
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185 |
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186 Notes |
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187 ----- |
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188 This implementation does not support mixed graphs (directed and unidirected |
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189 edges together) hyperedges, nested graphs, or ports. |
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190 """ |
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191 writer = GraphMLWriter( |
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192 encoding=encoding, prettyprint=prettyprint, named_key_ids=named_key_ids |
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193 ) |
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194 writer.add_graph_element(G) |
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195 yield from str(writer).splitlines() |
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196 |
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197 |
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198 @open_file(0, mode="rb") |
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199 def read_graphml(path, node_type=str, edge_key_type=int, force_multigraph=False): |
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200 """Read graph in GraphML format from path. |
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201 |
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202 Parameters |
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203 ---------- |
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204 path : file or string |
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205 File or filename to write. |
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206 Filenames ending in .gz or .bz2 will be compressed. |
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207 |
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208 node_type: Python type (default: str) |
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209 Convert node ids to this type |
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210 |
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211 edge_key_type: Python type (default: int) |
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212 Convert graphml edge ids to this type. Multigraphs use id as edge key. |
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213 Non-multigraphs add to edge attribute dict with name "id". |
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214 |
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215 force_multigraph : bool (default: False) |
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216 If True, return a multigraph with edge keys. If False (the default) |
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217 return a multigraph when multiedges are in the graph. |
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218 |
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219 Returns |
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220 ------- |
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221 graph: NetworkX graph |
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222 If parallel edges are present or `force_multigraph=True` then |
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223 a MultiGraph or MultiDiGraph is returned. Otherwise a Graph/DiGraph. |
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224 The returned graph is directed if the file indicates it should be. |
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225 |
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226 Notes |
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227 ----- |
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228 Default node and edge attributes are not propagated to each node and edge. |
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229 They can be obtained from `G.graph` and applied to node and edge attributes |
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230 if desired using something like this: |
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231 |
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232 >>> default_color = G.graph["node_default"]["color"] # doctest: +SKIP |
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233 >>> for node, data in G.nodes(data=True): # doctest: +SKIP |
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234 ... if "color" not in data: |
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235 ... data["color"] = default_color |
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236 >>> default_color = G.graph["edge_default"]["color"] # doctest: +SKIP |
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237 >>> for u, v, data in G.edges(data=True): # doctest: +SKIP |
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238 ... if "color" not in data: |
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239 ... data["color"] = default_color |
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240 |
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241 This implementation does not support mixed graphs (directed and unidirected |
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242 edges together), hypergraphs, nested graphs, or ports. |
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243 |
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244 For multigraphs the GraphML edge "id" will be used as the edge |
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245 key. If not specified then they "key" attribute will be used. If |
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246 there is no "key" attribute a default NetworkX multigraph edge key |
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247 will be provided. |
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248 |
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249 Files with the yEd "yfiles" extension will can be read but the graphics |
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250 information is discarded. |
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251 |
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252 yEd compressed files ("file.graphmlz" extension) can be read by renaming |
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253 the file to "file.graphml.gz". |
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254 |
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255 """ |
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256 reader = GraphMLReader(node_type, edge_key_type, force_multigraph) |
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257 # need to check for multiple graphs |
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258 glist = list(reader(path=path)) |
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259 if len(glist) == 0: |
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260 # If no graph comes back, try looking for an incomplete header |
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261 header = b'<graphml xmlns="http://graphml.graphdrawing.org/xmlns">' |
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262 path.seek(0) |
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263 old_bytes = path.read() |
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264 new_bytes = old_bytes.replace(b"<graphml>", header) |
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265 glist = list(reader(string=new_bytes)) |
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266 if len(glist) == 0: |
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267 raise nx.NetworkXError("file not successfully read as graphml") |
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268 return glist[0] |
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269 |
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270 |
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271 def parse_graphml( |
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272 graphml_string, node_type=str, edge_key_type=int, force_multigraph=False |
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273 ): |
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274 """Read graph in GraphML format from string. |
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275 |
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276 Parameters |
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277 ---------- |
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278 graphml_string : string |
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279 String containing graphml information |
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280 (e.g., contents of a graphml file). |
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281 |
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282 node_type: Python type (default: str) |
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283 Convert node ids to this type |
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284 |
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285 edge_key_type: Python type (default: int) |
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286 Convert graphml edge ids to this type. Multigraphs use id as edge key. |
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287 Non-multigraphs add to edge attribute dict with name "id". |
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288 |
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289 force_multigraph : bool (default: False) |
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290 If True, return a multigraph with edge keys. If False (the default) |
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291 return a multigraph when multiedges are in the graph. |
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292 |
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293 |
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294 Returns |
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295 ------- |
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296 graph: NetworkX graph |
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297 If no parallel edges are found a Graph or DiGraph is returned. |
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298 Otherwise a MultiGraph or MultiDiGraph is returned. |
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299 |
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300 Examples |
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301 -------- |
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302 >>> G = nx.path_graph(4) |
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303 >>> linefeed = chr(10) # linefeed = \n |
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304 >>> s = linefeed.join(nx.generate_graphml(G)) |
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305 >>> H = nx.parse_graphml(s) |
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306 |
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307 Notes |
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308 ----- |
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309 Default node and edge attributes are not propagated to each node and edge. |
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310 They can be obtained from `G.graph` and applied to node and edge attributes |
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311 if desired using something like this: |
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312 |
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313 >>> default_color = G.graph["node_default"]["color"] # doctest: +SKIP |
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314 >>> for node, data in G.nodes(data=True): # doctest: +SKIP |
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315 ... if "color" not in data: |
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316 ... data["color"] = default_color |
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317 >>> default_color = G.graph["edge_default"]["color"] # doctest: +SKIP |
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318 >>> for u, v, data in G.edges(data=True): # doctest: +SKIP |
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319 ... if "color" not in data: |
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320 ... data["color"] = default_color |
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321 |
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322 This implementation does not support mixed graphs (directed and unidirected |
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323 edges together), hypergraphs, nested graphs, or ports. |
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324 |
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325 For multigraphs the GraphML edge "id" will be used as the edge |
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326 key. If not specified then they "key" attribute will be used. If |
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327 there is no "key" attribute a default NetworkX multigraph edge key |
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328 will be provided. |
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329 |
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330 """ |
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331 reader = GraphMLReader(node_type, edge_key_type, force_multigraph) |
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332 # need to check for multiple graphs |
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333 glist = list(reader(string=graphml_string)) |
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334 if len(glist) == 0: |
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335 # If no graph comes back, try looking for an incomplete header |
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336 header = '<graphml xmlns="http://graphml.graphdrawing.org/xmlns">' |
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337 new_string = graphml_string.replace("<graphml>", header) |
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338 glist = list(reader(string=new_string)) |
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339 if len(glist) == 0: |
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340 raise nx.NetworkXError("file not successfully read as graphml") |
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341 return glist[0] |
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342 |
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343 |
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344 class GraphML: |
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345 NS_GRAPHML = "http://graphml.graphdrawing.org/xmlns" |
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346 NS_XSI = "http://www.w3.org/2001/XMLSchema-instance" |
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347 # xmlns:y="http://www.yworks.com/xml/graphml" |
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348 NS_Y = "http://www.yworks.com/xml/graphml" |
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349 SCHEMALOCATION = " ".join( |
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350 [ |
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351 "http://graphml.graphdrawing.org/xmlns", |
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352 "http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd", |
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353 ] |
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354 ) |
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355 |
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356 types = [ |
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357 (int, "integer"), # for Gephi GraphML bug |
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358 (str, "yfiles"), |
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359 (str, "string"), |
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360 (int, "int"), |
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361 (float, "float"), |
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362 (float, "double"), |
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363 (bool, "boolean"), |
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364 ] |
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365 |
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366 # These additions to types allow writing numpy types |
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367 try: |
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368 import numpy as np |
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369 except: |
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370 pass |
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371 else: |
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372 # prepend so that python types are created upon read (last entry wins) |
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373 types = [ |
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374 (np.float64, "float"), |
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375 (np.float32, "float"), |
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376 (np.float16, "float"), |
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377 (np.float_, "float"), |
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378 (np.int_, "int"), |
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379 (np.int8, "int"), |
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380 (np.int16, "int"), |
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381 (np.int32, "int"), |
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382 (np.int64, "int"), |
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383 (np.uint8, "int"), |
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384 (np.uint16, "int"), |
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385 (np.uint32, "int"), |
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386 (np.uint64, "int"), |
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387 (np.int_, "int"), |
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388 (np.intc, "int"), |
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389 (np.intp, "int"), |
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390 ] + types |
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391 |
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392 xml_type = dict(types) |
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393 python_type = dict(reversed(a) for a in types) |
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394 |
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395 # This page says that data types in GraphML follow Java(TM). |
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396 # http://graphml.graphdrawing.org/primer/graphml-primer.html#AttributesDefinition |
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397 # true and false are the only boolean literals: |
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398 # http://en.wikibooks.org/wiki/Java_Programming/Literals#Boolean_Literals |
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399 convert_bool = { |
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400 # We use data.lower() in actual use. |
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401 "true": True, |
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402 "false": False, |
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403 # Include integer strings for convenience. |
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404 "0": False, |
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405 0: False, |
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406 "1": True, |
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407 1: True, |
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408 } |
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409 |
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410 |
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411 class GraphMLWriter(GraphML): |
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412 def __init__( |
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413 self, |
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414 graph=None, |
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415 encoding="utf-8", |
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416 prettyprint=True, |
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417 infer_numeric_types=False, |
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418 named_key_ids=False, |
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419 ): |
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420 self.myElement = Element |
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421 |
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422 self.infer_numeric_types = infer_numeric_types |
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423 self.prettyprint = prettyprint |
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424 self.named_key_ids = named_key_ids |
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425 self.encoding = encoding |
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426 self.xml = self.myElement( |
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427 "graphml", |
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428 { |
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429 "xmlns": self.NS_GRAPHML, |
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430 "xmlns:xsi": self.NS_XSI, |
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431 "xsi:schemaLocation": self.SCHEMALOCATION, |
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432 }, |
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433 ) |
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434 self.keys = {} |
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435 self.attributes = defaultdict(list) |
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436 self.attribute_types = defaultdict(set) |
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437 |
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438 if graph is not None: |
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439 self.add_graph_element(graph) |
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440 |
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441 def __str__(self): |
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442 if self.prettyprint: |
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443 self.indent(self.xml) |
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444 s = tostring(self.xml).decode(self.encoding) |
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445 return s |
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446 |
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447 def attr_type(self, name, scope, value): |
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448 """Infer the attribute type of data named name. Currently this only |
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449 supports inference of numeric types. |
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450 |
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451 If self.infer_numeric_types is false, type is used. Otherwise, pick the |
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452 most general of types found across all values with name and scope. This |
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453 means edges with data named 'weight' are treated separately from nodes |
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454 with data named 'weight'. |
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455 """ |
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456 if self.infer_numeric_types: |
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457 types = self.attribute_types[(name, scope)] |
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458 |
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459 if len(types) > 1: |
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460 types = {self.xml_type[t] for t in types} |
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461 if "string" in types: |
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462 return str |
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463 elif "float" in types or "double" in types: |
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464 return float |
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465 else: |
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466 return int |
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467 else: |
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468 return list(types)[0] |
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469 else: |
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470 return type(value) |
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471 |
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472 def get_key(self, name, attr_type, scope, default): |
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473 keys_key = (name, attr_type, scope) |
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474 try: |
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475 return self.keys[keys_key] |
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476 except KeyError: |
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477 if self.named_key_ids: |
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478 new_id = name |
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479 else: |
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480 new_id = f"d{len(list(self.keys))}" |
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481 |
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482 self.keys[keys_key] = new_id |
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483 key_kwargs = { |
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484 "id": new_id, |
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485 "for": scope, |
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486 "attr.name": name, |
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487 "attr.type": attr_type, |
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488 } |
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489 key_element = self.myElement("key", **key_kwargs) |
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490 # add subelement for data default value if present |
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491 if default is not None: |
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492 default_element = self.myElement("default") |
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493 default_element.text = str(default) |
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494 key_element.append(default_element) |
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495 self.xml.insert(0, key_element) |
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496 return new_id |
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497 |
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498 def add_data(self, name, element_type, value, scope="all", default=None): |
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499 """ |
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500 Make a data element for an edge or a node. Keep a log of the |
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501 type in the keys table. |
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502 """ |
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503 if element_type not in self.xml_type: |
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504 msg = f"GraphML writer does not support {element_type} as data values." |
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505 raise nx.NetworkXError(msg) |
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506 keyid = self.get_key(name, self.xml_type[element_type], scope, default) |
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507 data_element = self.myElement("data", key=keyid) |
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508 data_element.text = str(value) |
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509 return data_element |
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510 |
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511 def add_attributes(self, scope, xml_obj, data, default): |
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512 """Appends attribute data to edges or nodes, and stores type information |
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513 to be added later. See add_graph_element. |
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514 """ |
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515 for k, v in data.items(): |
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516 self.attribute_types[(str(k), scope)].add(type(v)) |
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517 self.attributes[xml_obj].append([k, v, scope, default.get(k)]) |
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518 |
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519 def add_nodes(self, G, graph_element): |
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520 default = G.graph.get("node_default", {}) |
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521 for node, data in G.nodes(data=True): |
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522 node_element = self.myElement("node", id=str(node)) |
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523 self.add_attributes("node", node_element, data, default) |
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524 graph_element.append(node_element) |
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525 |
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526 def add_edges(self, G, graph_element): |
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527 if G.is_multigraph(): |
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528 for u, v, key, data in G.edges(data=True, keys=True): |
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529 edge_element = self.myElement( |
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530 "edge", source=str(u), target=str(v), id=str(key) |
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531 ) |
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532 default = G.graph.get("edge_default", {}) |
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533 self.add_attributes("edge", edge_element, data, default) |
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534 graph_element.append(edge_element) |
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535 else: |
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536 for u, v, data in G.edges(data=True): |
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537 edge_element = self.myElement("edge", source=str(u), target=str(v)) |
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538 default = G.graph.get("edge_default", {}) |
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539 self.add_attributes("edge", edge_element, data, default) |
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540 graph_element.append(edge_element) |
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541 |
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542 def add_graph_element(self, G): |
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543 """ |
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544 Serialize graph G in GraphML to the stream. |
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545 """ |
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546 if G.is_directed(): |
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547 default_edge_type = "directed" |
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548 else: |
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549 default_edge_type = "undirected" |
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550 |
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551 graphid = G.graph.pop("id", None) |
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552 if graphid is None: |
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553 graph_element = self.myElement("graph", edgedefault=default_edge_type) |
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554 else: |
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555 graph_element = self.myElement( |
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556 "graph", edgedefault=default_edge_type, id=graphid |
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557 ) |
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558 default = {} |
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559 data = { |
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560 k: v |
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561 for (k, v) in G.graph.items() |
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562 if k not in ["node_default", "edge_default"] |
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563 } |
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564 self.add_attributes("graph", graph_element, data, default) |
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565 self.add_nodes(G, graph_element) |
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566 self.add_edges(G, graph_element) |
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567 |
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568 # self.attributes contains a mapping from XML Objects to a list of |
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569 # data that needs to be added to them. |
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570 # We postpone processing in order to do type inference/generalization. |
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571 # See self.attr_type |
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572 for (xml_obj, data) in self.attributes.items(): |
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573 for (k, v, scope, default) in data: |
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574 xml_obj.append( |
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575 self.add_data( |
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576 str(k), self.attr_type(k, scope, v), str(v), scope, default |
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577 ) |
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578 ) |
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579 self.xml.append(graph_element) |
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580 |
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581 def add_graphs(self, graph_list): |
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582 """ Add many graphs to this GraphML document. """ |
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583 for G in graph_list: |
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584 self.add_graph_element(G) |
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585 |
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586 def dump(self, stream): |
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587 if self.prettyprint: |
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588 self.indent(self.xml) |
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589 document = ElementTree(self.xml) |
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590 document.write(stream, encoding=self.encoding, xml_declaration=True) |
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591 |
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592 def indent(self, elem, level=0): |
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593 # in-place prettyprint formatter |
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594 i = "\n" + level * " " |
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595 if len(elem): |
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596 if not elem.text or not elem.text.strip(): |
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597 elem.text = i + " " |
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598 if not elem.tail or not elem.tail.strip(): |
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599 elem.tail = i |
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600 for elem in elem: |
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601 self.indent(elem, level + 1) |
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602 if not elem.tail or not elem.tail.strip(): |
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603 elem.tail = i |
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604 else: |
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605 if level and (not elem.tail or not elem.tail.strip()): |
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606 elem.tail = i |
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607 |
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608 |
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609 class IncrementalElement: |
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610 """Wrapper for _IncrementalWriter providing an Element like interface. |
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611 |
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612 This wrapper does not intend to be a complete implementation but rather to |
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613 deal with those calls used in GraphMLWriter. |
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614 """ |
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615 |
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616 def __init__(self, xml, prettyprint): |
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617 self.xml = xml |
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618 self.prettyprint = prettyprint |
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619 |
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620 def append(self, element): |
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621 self.xml.write(element, pretty_print=self.prettyprint) |
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622 |
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623 |
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624 class GraphMLWriterLxml(GraphMLWriter): |
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625 def __init__( |
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626 self, |
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627 path, |
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628 graph=None, |
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629 encoding="utf-8", |
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630 prettyprint=True, |
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631 infer_numeric_types=False, |
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632 named_key_ids=False, |
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633 ): |
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634 self.myElement = lxmletree.Element |
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635 |
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636 self._encoding = encoding |
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637 self._prettyprint = prettyprint |
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638 self.named_key_ids = named_key_ids |
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639 self.infer_numeric_types = infer_numeric_types |
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640 |
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641 self._xml_base = lxmletree.xmlfile(path, encoding=encoding) |
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642 self._xml = self._xml_base.__enter__() |
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643 self._xml.write_declaration() |
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644 |
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645 # We need to have a xml variable that support insertion. This call is |
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646 # used for adding the keys to the document. |
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647 # We will store those keys in a plain list, and then after the graph |
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648 # element is closed we will add them to the main graphml element. |
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649 self.xml = [] |
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650 self._keys = self.xml |
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651 self._graphml = self._xml.element( |
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652 "graphml", |
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653 { |
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654 "xmlns": self.NS_GRAPHML, |
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655 "xmlns:xsi": self.NS_XSI, |
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656 "xsi:schemaLocation": self.SCHEMALOCATION, |
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657 }, |
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658 ) |
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659 self._graphml.__enter__() |
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660 self.keys = {} |
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661 self.attribute_types = defaultdict(set) |
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662 |
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663 if graph is not None: |
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664 self.add_graph_element(graph) |
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665 |
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666 def add_graph_element(self, G): |
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667 """ |
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668 Serialize graph G in GraphML to the stream. |
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669 """ |
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670 if G.is_directed(): |
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671 default_edge_type = "directed" |
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672 else: |
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673 default_edge_type = "undirected" |
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674 |
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675 graphid = G.graph.pop("id", None) |
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676 if graphid is None: |
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677 graph_element = self._xml.element("graph", edgedefault=default_edge_type) |
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678 else: |
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679 graph_element = self._xml.element( |
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680 "graph", edgedefault=default_edge_type, id=graphid |
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681 ) |
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682 |
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683 # gather attributes types for the whole graph |
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684 # to find the most general numeric format needed. |
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685 # Then pass through attributes to create key_id for each. |
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686 graphdata = { |
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687 k: v |
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688 for k, v in G.graph.items() |
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689 if k not in ("node_default", "edge_default") |
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690 } |
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691 node_default = G.graph.get("node_default", {}) |
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692 edge_default = G.graph.get("edge_default", {}) |
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693 # Graph attributes |
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694 for k, v in graphdata.items(): |
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695 self.attribute_types[(str(k), "graph")].add(type(v)) |
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696 for k, v in graphdata.items(): |
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697 element_type = self.xml_type[self.attr_type(k, "graph", v)] |
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698 self.get_key(str(k), element_type, "graph", None) |
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699 # Nodes and data |
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700 for node, d in G.nodes(data=True): |
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701 for k, v in d.items(): |
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702 self.attribute_types[(str(k), "node")].add(type(v)) |
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703 for node, d in G.nodes(data=True): |
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704 for k, v in d.items(): |
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705 T = self.xml_type[self.attr_type(k, "node", v)] |
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706 self.get_key(str(k), T, "node", node_default.get(k)) |
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707 # Edges and data |
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708 if G.is_multigraph(): |
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709 for u, v, ekey, d in G.edges(keys=True, data=True): |
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710 for k, v in d.items(): |
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711 self.attribute_types[(str(k), "edge")].add(type(v)) |
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712 for u, v, ekey, d in G.edges(keys=True, data=True): |
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713 for k, v in d.items(): |
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714 T = self.xml_type[self.attr_type(k, "edge", v)] |
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715 self.get_key(str(k), T, "edge", edge_default.get(k)) |
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716 else: |
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717 for u, v, d in G.edges(data=True): |
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718 for k, v in d.items(): |
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719 self.attribute_types[(str(k), "edge")].add(type(v)) |
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720 for u, v, d in G.edges(data=True): |
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721 for k, v in d.items(): |
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722 T = self.xml_type[self.attr_type(k, "edge", v)] |
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723 self.get_key(str(k), T, "edge", edge_default.get(k)) |
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724 |
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725 # Now add attribute keys to the xml file |
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726 for key in self.xml: |
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727 self._xml.write(key, pretty_print=self._prettyprint) |
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728 |
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729 # The incremental_writer writes each node/edge as it is created |
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730 incremental_writer = IncrementalElement(self._xml, self._prettyprint) |
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731 with graph_element: |
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732 self.add_attributes("graph", incremental_writer, graphdata, {}) |
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733 self.add_nodes(G, incremental_writer) # adds attributes too |
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734 self.add_edges(G, incremental_writer) # adds attributes too |
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735 |
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736 def add_attributes(self, scope, xml_obj, data, default): |
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737 """Appends attribute data.""" |
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738 for k, v in data.items(): |
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739 data_element = self.add_data( |
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740 str(k), self.attr_type(str(k), scope, v), str(v), scope, default.get(k) |
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741 ) |
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742 xml_obj.append(data_element) |
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743 |
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744 def __str__(self): |
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745 return object.__str__(self) |
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746 |
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747 def dump(self): |
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748 self._graphml.__exit__(None, None, None) |
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749 self._xml_base.__exit__(None, None, None) |
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750 |
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751 |
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752 # Choose a writer function for default |
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753 if lxmletree is None: |
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754 write_graphml = write_graphml_xml |
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755 else: |
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756 write_graphml = write_graphml_lxml |
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757 |
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758 |
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759 class GraphMLReader(GraphML): |
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760 """Read a GraphML document. Produces NetworkX graph objects.""" |
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761 |
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762 def __init__(self, node_type=str, edge_key_type=int, force_multigraph=False): |
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763 self.node_type = node_type |
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764 self.edge_key_type = edge_key_type |
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765 self.multigraph = force_multigraph # If False, test for multiedges |
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766 self.edge_ids = {} # dict mapping (u,v) tuples to edge id attributes |
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767 |
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768 def __call__(self, path=None, string=None): |
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769 if path is not None: |
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770 self.xml = ElementTree(file=path) |
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771 elif string is not None: |
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772 self.xml = fromstring(string) |
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773 else: |
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774 raise ValueError("Must specify either 'path' or 'string' as kwarg") |
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775 (keys, defaults) = self.find_graphml_keys(self.xml) |
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776 for g in self.xml.findall(f"{{{self.NS_GRAPHML}}}graph"): |
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777 yield self.make_graph(g, keys, defaults) |
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778 |
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779 def make_graph(self, graph_xml, graphml_keys, defaults, G=None): |
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780 # set default graph type |
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781 edgedefault = graph_xml.get("edgedefault", None) |
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782 if G is None: |
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783 if edgedefault == "directed": |
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784 G = nx.MultiDiGraph() |
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785 else: |
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786 G = nx.MultiGraph() |
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787 # set defaults for graph attributes |
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788 G.graph["node_default"] = {} |
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789 G.graph["edge_default"] = {} |
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790 for key_id, value in defaults.items(): |
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791 key_for = graphml_keys[key_id]["for"] |
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792 name = graphml_keys[key_id]["name"] |
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793 python_type = graphml_keys[key_id]["type"] |
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794 if key_for == "node": |
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795 G.graph["node_default"].update({name: python_type(value)}) |
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796 if key_for == "edge": |
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797 G.graph["edge_default"].update({name: python_type(value)}) |
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798 # hyperedges are not supported |
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799 hyperedge = graph_xml.find(f"{{{self.NS_GRAPHML}}}hyperedge") |
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800 if hyperedge is not None: |
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801 raise nx.NetworkXError("GraphML reader doesn't support hyperedges") |
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802 # add nodes |
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803 for node_xml in graph_xml.findall(f"{{{self.NS_GRAPHML}}}node"): |
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804 self.add_node(G, node_xml, graphml_keys, defaults) |
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805 # add edges |
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806 for edge_xml in graph_xml.findall(f"{{{self.NS_GRAPHML}}}edge"): |
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807 self.add_edge(G, edge_xml, graphml_keys) |
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808 # add graph data |
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809 data = self.decode_data_elements(graphml_keys, graph_xml) |
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810 G.graph.update(data) |
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811 |
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812 # switch to Graph or DiGraph if no parallel edges were found |
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813 if self.multigraph: |
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814 return G |
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815 |
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816 G = nx.DiGraph(G) if G.is_directed() else nx.Graph(G) |
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817 # add explicit edge "id" from file as attribute in NX graph. |
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818 nx.set_edge_attributes(G, values=self.edge_ids, name="id") |
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819 return G |
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820 |
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821 def add_node(self, G, node_xml, graphml_keys, defaults): |
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822 """Add a node to the graph. |
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823 """ |
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824 # warn on finding unsupported ports tag |
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825 ports = node_xml.find(f"{{{self.NS_GRAPHML}}}port") |
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826 if ports is not None: |
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827 warnings.warn("GraphML port tag not supported.") |
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828 # find the node by id and cast it to the appropriate type |
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829 node_id = self.node_type(node_xml.get("id")) |
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830 # get data/attributes for node |
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831 data = self.decode_data_elements(graphml_keys, node_xml) |
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832 G.add_node(node_id, **data) |
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833 # get child nodes |
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834 if node_xml.attrib.get("yfiles.foldertype") == "group": |
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835 graph_xml = node_xml.find(f"{{{self.NS_GRAPHML}}}graph") |
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836 self.make_graph(graph_xml, graphml_keys, defaults, G) |
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837 |
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838 def add_edge(self, G, edge_element, graphml_keys): |
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839 """Add an edge to the graph. |
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840 """ |
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841 # warn on finding unsupported ports tag |
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842 ports = edge_element.find(f"{{{self.NS_GRAPHML}}}port") |
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843 if ports is not None: |
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844 warnings.warn("GraphML port tag not supported.") |
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845 |
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846 # raise error if we find mixed directed and undirected edges |
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847 directed = edge_element.get("directed") |
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848 if G.is_directed() and directed == "false": |
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849 msg = "directed=false edge found in directed graph." |
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850 raise nx.NetworkXError(msg) |
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851 if (not G.is_directed()) and directed == "true": |
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852 msg = "directed=true edge found in undirected graph." |
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853 raise nx.NetworkXError(msg) |
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854 |
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855 source = self.node_type(edge_element.get("source")) |
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856 target = self.node_type(edge_element.get("target")) |
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857 data = self.decode_data_elements(graphml_keys, edge_element) |
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858 # GraphML stores edge ids as an attribute |
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859 # NetworkX uses them as keys in multigraphs too if no key |
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860 # attribute is specified |
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861 edge_id = edge_element.get("id") |
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862 if edge_id: |
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863 # self.edge_ids is used by `make_graph` method for non-multigraphs |
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864 self.edge_ids[source, target] = edge_id |
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865 try: |
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866 edge_id = self.edge_key_type(edge_id) |
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867 except ValueError: # Could not convert. |
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868 pass |
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869 else: |
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870 edge_id = data.get("key") |
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871 |
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872 if G.has_edge(source, target): |
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873 # mark this as a multigraph |
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874 self.multigraph = True |
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875 |
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876 # Use add_edges_from to avoid error with add_edge when `'key' in data` |
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877 # Note there is only one edge here... |
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878 G.add_edges_from([(source, target, edge_id, data)]) |
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879 |
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880 def decode_data_elements(self, graphml_keys, obj_xml): |
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881 """Use the key information to decode the data XML if present.""" |
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882 data = {} |
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883 for data_element in obj_xml.findall(f"{{{self.NS_GRAPHML}}}data"): |
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884 key = data_element.get("key") |
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885 try: |
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886 data_name = graphml_keys[key]["name"] |
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887 data_type = graphml_keys[key]["type"] |
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888 except KeyError as e: |
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889 raise nx.NetworkXError(f"Bad GraphML data: no key {key}") from e |
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890 text = data_element.text |
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891 # assume anything with subelements is a yfiles extension |
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892 if text is not None and len(list(data_element)) == 0: |
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893 if data_type == bool: |
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894 # Ignore cases. |
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895 # http://docs.oracle.com/javase/6/docs/api/java/lang/ |
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896 # Boolean.html#parseBoolean%28java.lang.String%29 |
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897 data[data_name] = self.convert_bool[text.lower()] |
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898 else: |
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899 data[data_name] = data_type(text) |
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900 elif len(list(data_element)) > 0: |
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901 # Assume yfiles as subelements, try to extract node_label |
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902 node_label = None |
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903 for node_type in ["ShapeNode", "SVGNode", "ImageNode"]: |
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904 pref = f"{{{self.NS_Y}}}{node_type}/{{{self.NS_Y}}}" |
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905 geometry = data_element.find(f"{pref}Geometry") |
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906 if geometry is not None: |
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907 data["x"] = geometry.get("x") |
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908 data["y"] = geometry.get("y") |
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909 if node_label is None: |
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910 node_label = data_element.find(f"{pref}NodeLabel") |
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911 if node_label is not None: |
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912 data["label"] = node_label.text |
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913 |
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914 # check all the different types of edges avaivable in yEd. |
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915 for e in [ |
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916 "PolyLineEdge", |
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917 "SplineEdge", |
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918 "QuadCurveEdge", |
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919 "BezierEdge", |
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920 "ArcEdge", |
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921 ]: |
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922 pref = f"{{{self.NS_Y}}}{e}/{{{self.NS_Y}}}" |
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923 edge_label = data_element.find(f"{pref}EdgeLabel") |
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924 if edge_label is not None: |
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925 break |
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926 |
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927 if edge_label is not None: |
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928 data["label"] = edge_label.text |
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929 return data |
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930 |
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931 def find_graphml_keys(self, graph_element): |
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932 """Extracts all the keys and key defaults from the xml. |
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933 """ |
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934 graphml_keys = {} |
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935 graphml_key_defaults = {} |
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936 for k in graph_element.findall(f"{{{self.NS_GRAPHML}}}key"): |
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937 attr_id = k.get("id") |
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938 attr_type = k.get("attr.type") |
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939 attr_name = k.get("attr.name") |
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940 yfiles_type = k.get("yfiles.type") |
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941 if yfiles_type is not None: |
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942 attr_name = yfiles_type |
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943 attr_type = "yfiles" |
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944 if attr_type is None: |
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945 attr_type = "string" |
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946 warnings.warn(f"No key type for id {attr_id}. Using string") |
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947 if attr_name is None: |
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948 raise nx.NetworkXError(f"Unknown key for id {attr_id}.") |
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949 graphml_keys[attr_id] = { |
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950 "name": attr_name, |
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951 "type": self.python_type[attr_type], |
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952 "for": k.get("for"), |
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953 } |
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954 # check for "default" subelement of key element |
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955 default = k.find(f"{{{self.NS_GRAPHML}}}default") |
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956 if default is not None: |
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957 graphml_key_defaults[attr_id] = default.text |
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958 return graphml_keys, graphml_key_defaults |