Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/readwrite/gml.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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 Read graphs in GML format. |
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3 |
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4 "GML, the Graph Modelling Language, is our proposal for a portable |
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5 file format for graphs. GML's key features are portability, simple |
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6 syntax, extensibility and flexibility. A GML file consists of a |
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7 hierarchical key-value lists. Graphs can be annotated with arbitrary |
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8 data structures. The idea for a common file format was born at the |
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9 GD'95; this proposal is the outcome of many discussions. GML is the |
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10 standard file format in the Graphlet graph editor system. It has been |
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11 overtaken and adapted by several other systems for drawing graphs." |
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12 |
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13 GML files are stored using a 7-bit ASCII encoding with any extended |
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14 ASCII characters (iso8859-1) appearing as HTML character entities. |
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15 You will need to give some thought into how the exported data should |
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16 interact with different languages and even different Python versions. |
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17 Re-importing from gml is also a concern. |
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18 |
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19 Without specifying a `stringizer`/`destringizer`, the code is capable of |
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20 handling `int`/`float`/`str`/`dict`/`list` data as required by the GML |
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21 specification. For other data types, you need to explicitly supply a |
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22 `stringizer`/`destringizer`. |
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23 |
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24 For additional documentation on the GML file format, please see the |
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25 `GML website <http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html>`_. |
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26 |
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27 Several example graphs in GML format may be found on Mark Newman's |
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28 `Network data page <http://www-personal.umich.edu/~mejn/netdata/>`_. |
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29 """ |
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30 from io import StringIO |
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31 from ast import literal_eval |
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32 from collections import defaultdict |
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33 from enum import Enum |
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34 from typing import Any, NamedTuple |
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35 import networkx as nx |
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36 from networkx.exception import NetworkXError |
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37 from networkx.utils import open_file |
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38 |
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39 import warnings |
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40 import re |
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41 import html.entities as htmlentitydefs |
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42 |
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43 __all__ = ["read_gml", "parse_gml", "generate_gml", "write_gml"] |
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44 |
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45 |
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46 def escape(text): |
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47 """Use XML character references to escape characters. |
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48 |
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49 Use XML character references for unprintable or non-ASCII |
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50 characters, double quotes and ampersands in a string |
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51 """ |
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52 |
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53 def fixup(m): |
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54 ch = m.group(0) |
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55 return "&#" + str(ord(ch)) + ";" |
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56 |
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57 text = re.sub('[^ -~]|[&"]', fixup, text) |
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58 return text if isinstance(text, str) else str(text) |
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59 |
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60 |
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61 def unescape(text): |
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62 """Replace XML character references with the referenced characters""" |
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63 |
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64 def fixup(m): |
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65 text = m.group(0) |
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66 if text[1] == "#": |
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67 # Character reference |
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68 if text[2] == "x": |
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69 code = int(text[3:-1], 16) |
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70 else: |
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71 code = int(text[2:-1]) |
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72 else: |
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73 # Named entity |
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74 try: |
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75 code = htmlentitydefs.name2codepoint[text[1:-1]] |
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76 except KeyError: |
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77 return text # leave unchanged |
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78 try: |
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79 return chr(code) |
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80 except (ValueError, OverflowError): |
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81 return text # leave unchanged |
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82 |
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83 return re.sub("&(?:[0-9A-Za-z]+|#(?:[0-9]+|x[0-9A-Fa-f]+));", fixup, text) |
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84 |
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85 |
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86 def literal_destringizer(rep): |
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87 """Convert a Python literal to the value it represents. |
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88 |
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89 Parameters |
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90 ---------- |
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91 rep : string |
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92 A Python literal. |
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93 |
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94 Returns |
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95 ------- |
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96 value : object |
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97 The value of the Python literal. |
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98 |
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99 Raises |
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100 ------ |
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101 ValueError |
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102 If `rep` is not a Python literal. |
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103 """ |
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104 msg = "literal_destringizer is deprecated and will be removed in 3.0." |
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105 warnings.warn(msg, DeprecationWarning) |
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106 if isinstance(rep, str): |
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107 orig_rep = rep |
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108 try: |
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109 return literal_eval(rep) |
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110 except SyntaxError as e: |
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111 raise ValueError(f"{orig_rep!r} is not a valid Python literal") from e |
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112 else: |
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113 raise ValueError(f"{rep!r} is not a string") |
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114 |
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115 |
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116 @open_file(0, mode="rb") |
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117 def read_gml(path, label="label", destringizer=None): |
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118 """Read graph in GML format from `path`. |
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119 |
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120 Parameters |
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121 ---------- |
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122 path : filename or filehandle |
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123 The filename or filehandle to read from. |
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124 |
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125 label : string, optional |
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126 If not None, the parsed nodes will be renamed according to node |
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127 attributes indicated by `label`. Default value: 'label'. |
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128 |
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129 destringizer : callable, optional |
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130 A `destringizer` that recovers values stored as strings in GML. If it |
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131 cannot convert a string to a value, a `ValueError` is raised. Default |
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132 value : None. |
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133 |
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134 Returns |
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135 ------- |
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136 G : NetworkX graph |
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137 The parsed graph. |
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138 |
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139 Raises |
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140 ------ |
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141 NetworkXError |
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142 If the input cannot be parsed. |
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143 |
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144 See Also |
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145 -------- |
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146 write_gml, parse_gml |
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147 |
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148 Notes |
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149 ----- |
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150 GML files are stored using a 7-bit ASCII encoding with any extended |
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151 ASCII characters (iso8859-1) appearing as HTML character entities. |
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152 Without specifying a `stringizer`/`destringizer`, the code is capable of |
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153 handling `int`/`float`/`str`/`dict`/`list` data as required by the GML |
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154 specification. For other data types, you need to explicitly supply a |
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155 `stringizer`/`destringizer`. |
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156 |
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157 For additional documentation on the GML file format, please see the |
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158 `GML url <http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html>`_. |
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159 |
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160 See the module docstring :mod:`networkx.readwrite.gml` for more details. |
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161 |
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162 Examples |
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163 -------- |
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164 >>> G = nx.path_graph(4) |
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165 >>> nx.write_gml(G, "test.gml") |
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166 >>> H = nx.read_gml("test.gml") |
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167 """ |
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168 |
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169 def filter_lines(lines): |
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170 for line in lines: |
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171 try: |
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172 line = line.decode("ascii") |
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173 except UnicodeDecodeError as e: |
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174 raise NetworkXError("input is not ASCII-encoded") from e |
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175 if not isinstance(line, str): |
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176 lines = str(lines) |
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177 if line and line[-1] == "\n": |
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178 line = line[:-1] |
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179 yield line |
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180 |
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181 G = parse_gml_lines(filter_lines(path), label, destringizer) |
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182 return G |
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183 |
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184 |
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185 def parse_gml(lines, label="label", destringizer=None): |
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186 """Parse GML graph from a string or iterable. |
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187 |
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188 Parameters |
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189 ---------- |
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190 lines : string or iterable of strings |
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191 Data in GML format. |
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192 |
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193 label : string, optional |
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194 If not None, the parsed nodes will be renamed according to node |
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195 attributes indicated by `label`. Default value: 'label'. |
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196 |
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197 destringizer : callable, optional |
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198 A `destringizer` that recovers values stored as strings in GML. If it |
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199 cannot convert a string to a value, a `ValueError` is raised. Default |
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200 value : None. |
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201 |
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202 Returns |
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203 ------- |
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204 G : NetworkX graph |
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205 The parsed graph. |
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206 |
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207 Raises |
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208 ------ |
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209 NetworkXError |
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210 If the input cannot be parsed. |
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211 |
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212 See Also |
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213 -------- |
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214 write_gml, read_gml |
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215 |
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216 Notes |
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217 ----- |
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218 This stores nested GML attributes as dictionaries in the NetworkX graph, |
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219 node, and edge attribute structures. |
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220 |
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221 GML files are stored using a 7-bit ASCII encoding with any extended |
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222 ASCII characters (iso8859-1) appearing as HTML character entities. |
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223 Without specifying a `stringizer`/`destringizer`, the code is capable of |
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224 handling `int`/`float`/`str`/`dict`/`list` data as required by the GML |
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225 specification. For other data types, you need to explicitly supply a |
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226 `stringizer`/`destringizer`. |
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227 |
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228 For additional documentation on the GML file format, please see the |
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229 `GML url <http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html>`_. |
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230 |
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231 See the module docstring :mod:`networkx.readwrite.gml` for more details. |
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232 """ |
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233 |
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234 def decode_line(line): |
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235 if isinstance(line, bytes): |
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236 try: |
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237 line.decode("ascii") |
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238 except UnicodeDecodeError as e: |
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239 raise NetworkXError("input is not ASCII-encoded") from e |
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240 if not isinstance(line, str): |
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241 line = str(line) |
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242 return line |
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243 |
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244 def filter_lines(lines): |
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245 if isinstance(lines, str): |
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246 lines = decode_line(lines) |
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247 lines = lines.splitlines() |
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248 yield from lines |
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249 else: |
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250 for line in lines: |
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251 line = decode_line(line) |
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252 if line and line[-1] == "\n": |
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253 line = line[:-1] |
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254 if line.find("\n") != -1: |
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255 raise NetworkXError("input line contains newline") |
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256 yield line |
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257 |
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258 G = parse_gml_lines(filter_lines(lines), label, destringizer) |
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259 return G |
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260 |
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261 |
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262 class Pattern(Enum): |
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263 """ encodes the index of each token-matching pattern in `tokenize`. """ |
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264 |
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265 KEYS = 0 |
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266 REALS = 1 |
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267 INTS = 2 |
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268 STRINGS = 3 |
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269 DICT_START = 4 |
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270 DICT_END = 5 |
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271 COMMENT_WHITESPACE = 6 |
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272 |
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273 |
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274 class Token(NamedTuple): |
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275 category: Pattern |
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276 value: Any |
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277 line: int |
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278 position: int |
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279 |
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280 |
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281 LIST_START_VALUE = "_networkx_list_start" |
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282 |
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283 |
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284 def parse_gml_lines(lines, label, destringizer): |
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285 """Parse GML `lines` into a graph. |
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286 """ |
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287 |
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288 def tokenize(): |
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289 patterns = [ |
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290 r"[A-Za-z][0-9A-Za-z_]*\b", # keys |
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291 # reals |
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292 r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*)(?:[Ee][+-]?[0-9]+)?", |
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293 r"[+-]?[0-9]+", # ints |
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294 r'".*?"', # strings |
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295 r"\[", # dict start |
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296 r"\]", # dict end |
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297 r"#.*$|\s+", # comments and whitespaces |
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298 ] |
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299 tokens = re.compile("|".join(f"({pattern})" for pattern in patterns)) |
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300 lineno = 0 |
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301 for line in lines: |
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302 length = len(line) |
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303 pos = 0 |
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304 while pos < length: |
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305 match = tokens.match(line, pos) |
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306 if match is None: |
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307 m = f"cannot tokenize {line[pos:]} at ({lineno + 1}, {pos + 1})" |
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308 raise NetworkXError(m) |
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309 for i in range(len(patterns)): |
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310 group = match.group(i + 1) |
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311 if group is not None: |
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312 if i == 0: # keys |
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313 value = group.rstrip() |
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314 elif i == 1: # reals |
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315 value = float(group) |
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316 elif i == 2: # ints |
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317 value = int(group) |
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318 else: |
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319 value = group |
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320 if i != 6: # comments and whitespaces |
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321 yield Token(Pattern(i), value, lineno + 1, pos + 1) |
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322 pos += len(group) |
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323 break |
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324 lineno += 1 |
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325 yield Token(None, None, lineno + 1, 1) # EOF |
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326 |
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327 def unexpected(curr_token, expected): |
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328 category, value, lineno, pos = curr_token |
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329 value = repr(value) if value is not None else "EOF" |
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330 raise NetworkXError(f"expected {expected}, found {value} at ({lineno}, {pos})") |
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331 |
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332 def consume(curr_token, category, expected): |
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333 if curr_token.category == category: |
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334 return next(tokens) |
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335 unexpected(curr_token, expected) |
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336 |
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337 def parse_kv(curr_token): |
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338 dct = defaultdict(list) |
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339 while curr_token.category == Pattern.KEYS: |
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340 key = curr_token.value |
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341 curr_token = next(tokens) |
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342 category = curr_token.category |
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343 if category == Pattern.REALS or category == Pattern.INTS: |
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344 value = curr_token.value |
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345 curr_token = next(tokens) |
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346 elif category == Pattern.STRINGS: |
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347 value = unescape(curr_token.value[1:-1]) |
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348 if destringizer: |
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349 try: |
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350 value = destringizer(value) |
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351 except ValueError: |
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352 pass |
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353 curr_token = next(tokens) |
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354 elif category == Pattern.DICT_START: |
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355 curr_token, value = parse_dict(curr_token) |
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356 else: |
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357 # Allow for string convertible id and label values |
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358 if key in ("id", "label", "source", "target"): |
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359 try: |
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360 # String convert the token value |
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361 value = unescape(str(curr_token.value)) |
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362 if destringizer: |
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363 try: |
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364 value = destringizer(value) |
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365 except ValueError: |
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366 pass |
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367 curr_token = next(tokens) |
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368 except Exception: |
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369 msg = ( |
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370 "an int, float, string, '[' or string" |
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371 + " convertable ASCII value for node id or label" |
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372 ) |
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373 unexpected(curr_token, msg) |
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374 else: # Otherwise error out |
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375 unexpected(curr_token, "an int, float, string or '['") |
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376 dct[key].append(value) |
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377 |
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378 def clean_dict_value(value): |
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379 if not isinstance(value, list): |
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380 return value |
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381 if len(value) == 1: |
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382 return value[0] |
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383 if value[0] == LIST_START_VALUE: |
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384 return value[1:] |
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385 return value |
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386 |
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387 dct = {key: clean_dict_value(value) for key, value in dct.items()} |
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388 return curr_token, dct |
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389 |
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390 def parse_dict(curr_token): |
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391 # dict start |
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392 curr_token = consume(curr_token, Pattern.DICT_START, "'['") |
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393 # dict contents |
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394 curr_token, dct = parse_kv(curr_token) |
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395 # dict end |
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396 curr_token = consume(curr_token, Pattern.DICT_END, "']'") |
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397 return curr_token, dct |
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398 |
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399 def parse_graph(): |
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400 curr_token, dct = parse_kv(next(tokens)) |
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401 if curr_token.category is not None: # EOF |
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402 unexpected(curr_token, "EOF") |
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403 if "graph" not in dct: |
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404 raise NetworkXError("input contains no graph") |
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405 graph = dct["graph"] |
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406 if isinstance(graph, list): |
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407 raise NetworkXError("input contains more than one graph") |
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408 return graph |
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409 |
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410 tokens = tokenize() |
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411 graph = parse_graph() |
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shellac
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412 |
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413 directed = graph.pop("directed", False) |
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414 multigraph = graph.pop("multigraph", False) |
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415 if not multigraph: |
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416 G = nx.DiGraph() if directed else nx.Graph() |
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417 else: |
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418 G = nx.MultiDiGraph() if directed else nx.MultiGraph() |
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419 graph_attr = {k: v for k, v in graph.items() if k not in ("node", "edge")} |
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420 G.graph.update(graph_attr) |
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shellac
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421 |
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parents:
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422 def pop_attr(dct, category, attr, i): |
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423 try: |
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424 return dct.pop(attr) |
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425 except KeyError as e: |
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426 raise NetworkXError(f"{category} #{i} has no '{attr}' attribute") from e |
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427 |
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428 nodes = graph.get("node", []) |
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429 mapping = {} |
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430 node_labels = set() |
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431 for i, node in enumerate(nodes if isinstance(nodes, list) else [nodes]): |
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shellac
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432 id = pop_attr(node, "node", "id", i) |
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parents:
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433 if id in G: |
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shellac
parents:
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434 raise NetworkXError(f"node id {id!r} is duplicated") |
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shellac
parents:
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435 if label is not None and label != "id": |
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shellac
parents:
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436 node_label = pop_attr(node, "node", label, i) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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437 if node_label in node_labels: |
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shellac
parents:
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438 raise NetworkXError(f"node label {node_label!r} is duplicated") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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439 node_labels.add(node_label) |
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shellac
parents:
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440 mapping[id] = node_label |
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shellac
parents:
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441 G.add_node(id, **node) |
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shellac
parents:
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|
442 |
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shellac
parents:
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443 edges = graph.get("edge", []) |
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shellac
parents:
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444 for i, edge in enumerate(edges if isinstance(edges, list) else [edges]): |
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shellac
parents:
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445 source = pop_attr(edge, "edge", "source", i) |
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shellac
parents:
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446 target = pop_attr(edge, "edge", "target", i) |
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shellac
parents:
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447 if source not in G: |
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shellac
parents:
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448 raise NetworkXError(f"edge #{i} has undefined source {source!r}") |
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shellac
parents:
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changeset
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449 if target not in G: |
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shellac
parents:
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450 raise NetworkXError(f"edge #{i} has undefined target {target!r}") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
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451 if not multigraph: |
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shellac
parents:
diff
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452 if not G.has_edge(source, target): |
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shellac
parents:
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453 G.add_edge(source, target, **edge) |
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454 else: |
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455 arrow = "->" if directed else "--" |
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456 msg = f"edge #{i} ({source!r}{arrow}{target!r}) is duplicated" |
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457 raise nx.NetworkXError(msg) |
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458 else: |
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459 key = edge.pop("key", None) |
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460 if key is not None and G.has_edge(source, target, key): |
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461 arrow = "->" if directed else "--" |
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462 msg = f"edge #{i} ({source!r}{arrow}{target!r}, {key!r})" |
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463 msg2 = 'Hint: If multigraph add "multigraph 1" to file header.' |
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464 raise nx.NetworkXError(msg + " is duplicated\n" + msg2) |
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465 G.add_edge(source, target, key, **edge) |
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466 |
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467 if label is not None and label != "id": |
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468 G = nx.relabel_nodes(G, mapping) |
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469 return G |
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470 |
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471 |
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472 def literal_stringizer(value): |
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473 """Convert a `value` to a Python literal in GML representation. |
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474 |
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475 Parameters |
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476 ---------- |
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477 value : object |
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478 The `value` to be converted to GML representation. |
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479 |
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480 Returns |
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481 ------- |
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482 rep : string |
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483 A double-quoted Python literal representing value. Unprintable |
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484 characters are replaced by XML character references. |
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485 |
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486 Raises |
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487 ------ |
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488 ValueError |
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489 If `value` cannot be converted to GML. |
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490 |
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491 Notes |
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492 ----- |
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493 `literal_stringizer` is largely the same as `repr` in terms of |
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494 functionality but attempts prefix `unicode` and `bytes` literals with |
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495 `u` and `b` to provide better interoperability of data generated by |
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496 Python 2 and Python 3. |
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497 |
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498 The original value can be recovered using the |
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499 :func:`networkx.readwrite.gml.literal_destringizer` function. |
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500 """ |
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501 msg = "literal_stringizer is deprecated and will be removed in 3.0." |
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502 warnings.warn(msg, DeprecationWarning) |
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503 |
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504 def stringize(value): |
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505 if isinstance(value, (int, bool)) or value is None: |
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506 if value is True: # GML uses 1/0 for boolean values. |
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507 buf.write(str(1)) |
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508 elif value is False: |
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509 buf.write(str(0)) |
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510 else: |
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511 buf.write(str(value)) |
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512 elif isinstance(value, str): |
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513 text = repr(value) |
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514 if text[0] != "u": |
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515 try: |
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516 value.encode("latin1") |
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517 except UnicodeEncodeError: |
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518 text = "u" + text |
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519 buf.write(text) |
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520 elif isinstance(value, (float, complex, str, bytes)): |
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521 buf.write(repr(value)) |
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522 elif isinstance(value, list): |
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523 buf.write("[") |
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524 first = True |
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525 for item in value: |
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526 if not first: |
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527 buf.write(",") |
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528 else: |
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529 first = False |
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530 stringize(item) |
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531 buf.write("]") |
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532 elif isinstance(value, tuple): |
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533 if len(value) > 1: |
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534 buf.write("(") |
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535 first = True |
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536 for item in value: |
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537 if not first: |
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538 buf.write(",") |
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539 else: |
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540 first = False |
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541 stringize(item) |
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542 buf.write(")") |
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543 elif value: |
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544 buf.write("(") |
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545 stringize(value[0]) |
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546 buf.write(",)") |
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547 else: |
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548 buf.write("()") |
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549 elif isinstance(value, dict): |
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550 buf.write("{") |
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551 first = True |
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552 for key, value in value.items(): |
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553 if not first: |
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554 buf.write(",") |
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555 else: |
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556 first = False |
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557 stringize(key) |
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558 buf.write(":") |
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559 stringize(value) |
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560 buf.write("}") |
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561 elif isinstance(value, set): |
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562 buf.write("{") |
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563 first = True |
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564 for item in value: |
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565 if not first: |
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566 buf.write(",") |
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567 else: |
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568 first = False |
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569 stringize(item) |
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570 buf.write("}") |
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571 else: |
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572 msg = "{value!r} cannot be converted into a Python literal" |
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573 raise ValueError(msg) |
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574 |
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575 buf = StringIO() |
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576 stringize(value) |
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577 return buf.getvalue() |
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578 |
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579 |
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580 def generate_gml(G, stringizer=None): |
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581 r"""Generate a single entry of the graph `G` in GML format. |
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582 |
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583 Parameters |
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584 ---------- |
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585 G : NetworkX graph |
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586 The graph to be converted to GML. |
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587 |
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588 stringizer : callable, optional |
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589 A `stringizer` which converts non-int/non-float/non-dict values into |
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590 strings. If it cannot convert a value into a string, it should raise a |
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591 `ValueError` to indicate that. Default value: None. |
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592 |
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593 Returns |
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594 ------- |
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595 lines: generator of strings |
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596 Lines of GML data. Newlines are not appended. |
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597 |
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598 Raises |
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599 ------ |
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600 NetworkXError |
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601 If `stringizer` cannot convert a value into a string, or the value to |
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602 convert is not a string while `stringizer` is None. |
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603 |
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604 Notes |
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605 ----- |
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606 Graph attributes named 'directed', 'multigraph', 'node' or |
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607 'edge', node attributes named 'id' or 'label', edge attributes |
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608 named 'source' or 'target' (or 'key' if `G` is a multigraph) |
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609 are ignored because these attribute names are used to encode the graph |
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610 structure. |
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611 |
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612 GML files are stored using a 7-bit ASCII encoding with any extended |
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613 ASCII characters (iso8859-1) appearing as HTML character entities. |
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614 Without specifying a `stringizer`/`destringizer`, the code is capable of |
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615 handling `int`/`float`/`str`/`dict`/`list` data as required by the GML |
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616 specification. For other data types, you need to explicitly supply a |
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617 `stringizer`/`destringizer`. |
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618 |
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619 For additional documentation on the GML file format, please see the |
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620 `GML url <http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html>`_. |
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621 |
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622 See the module docstring :mod:`networkx.readwrite.gml` for more details. |
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623 |
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624 Examples |
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625 -------- |
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626 >>> G = nx.Graph() |
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627 >>> G.add_node("1") |
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628 >>> print("\n".join(nx.generate_gml(G))) |
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629 graph [ |
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630 node [ |
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631 id 0 |
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632 label "1" |
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633 ] |
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634 ] |
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635 >>> G = nx.OrderedMultiGraph([("a", "b"), ("a", "b")]) |
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636 >>> print("\n".join(nx.generate_gml(G))) |
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637 graph [ |
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638 multigraph 1 |
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639 node [ |
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640 id 0 |
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641 label "a" |
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642 ] |
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643 node [ |
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644 id 1 |
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645 label "b" |
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646 ] |
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647 edge [ |
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648 source 0 |
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649 target 1 |
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650 key 0 |
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651 ] |
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652 edge [ |
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653 source 0 |
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654 target 1 |
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655 key 1 |
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656 ] |
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657 ] |
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658 """ |
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659 valid_keys = re.compile("^[A-Za-z][0-9A-Za-z_]*$") |
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660 |
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661 def stringize(key, value, ignored_keys, indent, in_list=False): |
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662 if not isinstance(key, str): |
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663 raise NetworkXError(f"{key!r} is not a string") |
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664 if not valid_keys.match(key): |
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665 raise NetworkXError(f"{key!r} is not a valid key") |
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666 if not isinstance(key, str): |
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667 key = str(key) |
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668 if key not in ignored_keys: |
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669 if isinstance(value, (int, bool)): |
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670 if key == "label": |
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671 yield indent + key + ' "' + str(value) + '"' |
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672 elif value is True: |
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673 # python bool is an instance of int |
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674 yield indent + key + " 1" |
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675 elif value is False: |
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676 yield indent + key + " 0" |
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677 # GML only supports signed 32-bit integers |
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678 elif value < -(2 ** 31) or value >= 2 ** 31: |
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679 yield indent + key + ' "' + str(value) + '"' |
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680 else: |
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681 yield indent + key + " " + str(value) |
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682 elif isinstance(value, float): |
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683 text = repr(value).upper() |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
684 # GML requires that a real literal contain a decimal point, but |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
685 # repr may not output a decimal point when the mantissa is |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
686 # integral and hence needs fixing. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
687 epos = text.rfind("E") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
688 if epos != -1 and text.find(".", 0, epos) == -1: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
689 text = text[:epos] + "." + text[epos:] |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
690 if key == "label": |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
691 yield indent + key + ' "' + text + '"' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
692 else: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
693 yield indent + key + " " + text |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
694 elif isinstance(value, dict): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
695 yield indent + key + " [" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
696 next_indent = indent + " " |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
697 for key, value in value.items(): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
698 yield from stringize(key, value, (), next_indent) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
699 yield indent + "]" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
700 elif ( |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
701 isinstance(value, (list, tuple)) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
702 and key != "label" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
703 and value |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
704 and not in_list |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
705 ): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
706 if len(value) == 1: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
707 yield indent + key + " " + f'"{LIST_START_VALUE}"' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
708 for val in value: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
709 yield from stringize(key, val, (), indent, True) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
710 else: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
711 if stringizer: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
712 try: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
713 value = stringizer(value) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
714 except ValueError as e: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
715 raise NetworkXError( |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
716 f"{value!r} cannot be converted into a string" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
717 ) from e |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
718 if not isinstance(value, str): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
719 raise NetworkXError(f"{value!r} is not a string") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
720 yield indent + key + ' "' + escape(value) + '"' |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
721 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
722 multigraph = G.is_multigraph() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
723 yield "graph [" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
724 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
725 # Output graph attributes |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
726 if G.is_directed(): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
727 yield " directed 1" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
728 if multigraph: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
729 yield " multigraph 1" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
730 ignored_keys = {"directed", "multigraph", "node", "edge"} |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
731 for attr, value in G.graph.items(): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
732 yield from stringize(attr, value, ignored_keys, " ") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
733 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
734 # Output node data |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
735 node_id = dict(zip(G, range(len(G)))) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
736 ignored_keys = {"id", "label"} |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
737 for node, attrs in G.nodes.items(): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
738 yield " node [" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
739 yield " id " + str(node_id[node]) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
740 yield from stringize("label", node, (), " ") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
741 for attr, value in attrs.items(): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
742 yield from stringize(attr, value, ignored_keys, " ") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
743 yield " ]" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
744 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
745 # Output edge data |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
746 ignored_keys = {"source", "target"} |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
747 kwargs = {"data": True} |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
748 if multigraph: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
749 ignored_keys.add("key") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
750 kwargs["keys"] = True |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
751 for e in G.edges(**kwargs): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
752 yield " edge [" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
753 yield " source " + str(node_id[e[0]]) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
754 yield " target " + str(node_id[e[1]]) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
755 if multigraph: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
756 yield from stringize("key", e[2], (), " ") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
757 for attr, value in e[-1].items(): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
758 yield from stringize(attr, value, ignored_keys, " ") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
759 yield " ]" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
760 yield "]" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
761 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
762 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
763 @open_file(1, mode="wb") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
764 def write_gml(G, path, stringizer=None): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
765 """Write a graph `G` in GML format to the file or file handle `path`. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
766 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
767 Parameters |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
768 ---------- |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
769 G : NetworkX graph |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
770 The graph to be converted to GML. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
771 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
772 path : filename or filehandle |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
773 The filename or filehandle to write. Files whose names end with .gz or |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
774 .bz2 will be compressed. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
775 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
776 stringizer : callable, optional |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
777 A `stringizer` which converts non-int/non-float/non-dict values into |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
778 strings. If it cannot convert a value into a string, it should raise a |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
779 `ValueError` to indicate that. Default value: None. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
780 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
781 Raises |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
782 ------ |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
783 NetworkXError |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
784 If `stringizer` cannot convert a value into a string, or the value to |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
785 convert is not a string while `stringizer` is None. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
786 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
787 See Also |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
788 -------- |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
789 read_gml, generate_gml |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
790 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
791 Notes |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
792 ----- |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
793 Graph attributes named 'directed', 'multigraph', 'node' or |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
794 'edge', node attributes named 'id' or 'label', edge attributes |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
795 named 'source' or 'target' (or 'key' if `G` is a multigraph) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
796 are ignored because these attribute names are used to encode the graph |
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797 structure. |
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798 |
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799 GML files are stored using a 7-bit ASCII encoding with any extended |
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800 ASCII characters (iso8859-1) appearing as HTML character entities. |
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801 Without specifying a `stringizer`/`destringizer`, the code is capable of |
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802 handling `int`/`float`/`str`/`dict`/`list` data as required by the GML |
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803 specification. For other data types, you need to explicitly supply a |
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804 `stringizer`/`destringizer`. |
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805 |
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806 Note that while we allow non-standard GML to be read from a file, we make |
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807 sure to write GML format. In particular, underscores are not allowed in |
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808 attribute names. |
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809 For additional documentation on the GML file format, please see the |
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810 `GML url <http://www.infosun.fim.uni-passau.de/Graphlet/GML/gml-tr.html>`_. |
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811 |
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812 See the module docstring :mod:`networkx.readwrite.gml` for more details. |
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813 |
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814 Examples |
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815 -------- |
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816 >>> G = nx.path_graph(4) |
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817 >>> nx.write_gml(G, "test.gml") |
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818 |
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819 Filenames ending in .gz or .bz2 will be compressed. |
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820 |
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821 >>> nx.write_gml(G, "test.gml.gz") |
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822 """ |
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823 for line in generate_gml(G, stringizer): |
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824 path.write((line + "\n").encode("ascii")) |