Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/compare.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 # -*- coding: utf-8 -*-
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2 """
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3 A collection of utilities for canonicalizing and inspecting graphs.
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4
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5 Among other things, they solve of the problem of deterministic bnode
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6 comparisons.
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7
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8 Warning: the time to canonicalize bnodes may increase exponentially on
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9 degenerate larger graphs. Use with care!
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10
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11 Example of comparing two graphs::
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12
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13 >>> g1 = Graph().parse(format='n3', data='''
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14 ... @prefix : <http://example.org/ns#> .
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15 ... <http://example.org> :rel
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16 ... <http://example.org/same>,
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17 ... [ :label "Same" ],
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18 ... <http://example.org/a>,
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19 ... [ :label "A" ] .
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20 ... ''')
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21 >>> g2 = Graph().parse(format='n3', data='''
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22 ... @prefix : <http://example.org/ns#> .
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23 ... <http://example.org> :rel
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24 ... <http://example.org/same>,
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25 ... [ :label "Same" ],
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26 ... <http://example.org/b>,
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27 ... [ :label "B" ] .
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28 ... ''')
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29 >>>
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30 >>> iso1 = to_isomorphic(g1)
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31 >>> iso2 = to_isomorphic(g2)
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32
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33 These are not isomorphic::
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34
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35 >>> iso1 == iso2
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36 False
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37
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38 Diff the two graphs::
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39
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40 >>> in_both, in_first, in_second = graph_diff(iso1, iso2)
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41
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42 Present in both::
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43
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44 >>> def dump_nt_sorted(g):
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45 ... for l in sorted(g.serialize(format='nt').splitlines()):
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46 ... if l: print(l.decode('ascii'))
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47
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48 >>> dump_nt_sorted(in_both) #doctest: +SKIP
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49 <http://example.org>
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50 <http://example.org/ns#rel> <http://example.org/same> .
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51 <http://example.org>
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52 <http://example.org/ns#rel> _:cbcaabaaba17fecbc304a64f8edee4335e .
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53 _:cbcaabaaba17fecbc304a64f8edee4335e
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54 <http://example.org/ns#label> "Same" .
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55
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56 Only in first::
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57
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58 >>> dump_nt_sorted(in_first) #doctest: +SKIP
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59 <http://example.org>
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60 <http://example.org/ns#rel> <http://example.org/a> .
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61 <http://example.org>
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62 <http://example.org/ns#rel> _:cb124e4c6da0579f810c0ffe4eff485bd9 .
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63 _:cb124e4c6da0579f810c0ffe4eff485bd9
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64 <http://example.org/ns#label> "A" .
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65
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66 Only in second::
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67
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68 >>> dump_nt_sorted(in_second) #doctest: +SKIP
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69 <http://example.org>
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70 <http://example.org/ns#rel> <http://example.org/b> .
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71 <http://example.org>
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72 <http://example.org/ns#rel> _:cb558f30e21ddfc05ca53108348338ade8 .
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73 _:cb558f30e21ddfc05ca53108348338ade8
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74 <http://example.org/ns#label> "B" .
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75 """
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76
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77
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78 # TODO:
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79 # - Doesn't handle quads.
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80 # - Add warning and/or safety mechanism before working on large graphs?
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81 # - use this in existing Graph.isomorphic?
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82
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83 __all__ = ['IsomorphicGraph', 'to_isomorphic', 'isomorphic',
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84 'to_canonical_graph', 'graph_diff', 'similar']
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85
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86 from rdflib.graph import Graph, ConjunctiveGraph, ReadOnlyGraphAggregate
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87 from rdflib.term import BNode, Node
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88 try:
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89 import hashlib
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90 sha256 = hashlib.sha256
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91 except ImportError:
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92 # for Python << 2.5
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93 import sha256
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94 sha256 = sha256.new
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95
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96 from datetime import datetime
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97 from collections import defaultdict
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98
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99
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100 def _total_seconds(td):
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101 result = td.days * 24 * 60 * 60
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102 result += td.seconds
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103 result += td.microseconds / 1000000.0
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104 return result
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105
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106
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107 class _runtime(object):
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108 def __init__(self, label):
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109 self.label = label
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110
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111 def __call__(self, f):
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112 if self.label is None:
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113 self.label = f.__name__ + "_runtime"
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114
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115 def wrapped_f(*args, **kwargs):
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116 start = datetime.now()
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117 result = f(*args, **kwargs)
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118 if 'stats' in kwargs and kwargs['stats'] is not None:
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119 stats = kwargs['stats']
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120 stats[self.label] = _total_seconds(datetime.now() - start)
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121 return result
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122 return wrapped_f
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123
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124
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125 class _call_count(object):
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126 def __init__(self, label):
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127 self.label = label
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128
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129 def __call__(self, f):
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130 if self.label is None:
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131 self.label = f.__name__ + "_runtime"
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132
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133 def wrapped_f(*args, **kwargs):
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134 if 'stats' in kwargs and kwargs['stats'] is not None:
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135 stats = kwargs['stats']
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136 if self.label not in stats:
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137 stats[self.label] = 0
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138 stats[self.label] += 1
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139 return f(*args, **kwargs)
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140 return wrapped_f
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141
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142
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143 class IsomorphicGraph(ConjunctiveGraph):
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144 """An implementation of the RGDA1 graph digest algorithm.
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145
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146 An implementation of RGDA1 (publication below),
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147 a combination of Sayers & Karp's graph digest algorithm using
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148 sum and SHA-256 <http://www.hpl.hp.com/techreports/2003/HPL-2003-235R1.pdf>
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149 and traces <http://pallini.di.uniroma1.it>, an average case
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150 polynomial time algorithm for graph canonicalization.
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151
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152 McCusker, J. P. (2015). WebSig: A Digital Signature Framework for the Web.
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153 Rensselaer Polytechnic Institute, Troy, NY.
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154 http://gradworks.umi.com/3727015.pdf
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155 """
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156
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157 def __init__(self, **kwargs):
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158 super(IsomorphicGraph, self).__init__(**kwargs)
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159
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160 def __eq__(self, other):
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161 """Graph isomorphism testing."""
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162 if not isinstance(other, IsomorphicGraph):
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163 return False
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164 elif len(self) != len(other):
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165 return False
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166 return self.internal_hash() == other.internal_hash()
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167
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168 def __ne__(self, other):
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169 """Negative graph isomorphism testing."""
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170 return not self.__eq__(other)
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171
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172 def graph_digest(self, stats=None):
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173 """Synonym for IsomorphicGraph.internal_hash."""
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174 return self.internal_hash(stats=stats)
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175
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176 def internal_hash(self, stats=None):
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177 """
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178 This is defined instead of __hash__ to avoid a circular recursion
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179 scenario with the Memory store for rdflib which requires a hash lookup
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180 in order to return a generator of triples.
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181 """
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182 return _TripleCanonicalizer(self).to_hash(stats=stats)
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183
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184
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185 class Color:
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186 def __init__(self, nodes, hashfunc, color=(), hash_cache=None):
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187 if hash_cache is None:
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188 hash_cache = {}
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189 self._hash_cache = hash_cache
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190 self.color = color
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191 self.nodes = nodes
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192 self.hashfunc = hashfunc
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193 self._hash_color = None
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194
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195 def key(self):
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196 return (len(self.nodes), self.hash_color())
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197
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198 def hash_color(self, color=None):
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199 if color is None:
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200 color = self.color
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201 if color in self._hash_cache:
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202 return self._hash_cache[color]
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203
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204 def stringify(x):
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205 if isinstance(x, Node):
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206 return x.n3()
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207 else:
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208 return str(x)
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209 if isinstance(color, Node):
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210 return stringify(color)
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211 value = 0
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212 for triple in color:
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213 value += self.hashfunc(' '.join([stringify(x) for x in triple]))
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214 val = "%x" % value
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215 self._hash_cache[color] = val
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216 return val
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217
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218 def distinguish(self, W, graph):
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219 colors = {}
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220 for n in self.nodes:
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221 new_color = list(self.color)
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222 for node in W.nodes:
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223 new_color += [
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224 (1, p, W.hash_color())
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225 for s, p, o in graph.triples((n, None, node))]
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226 new_color += [
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227 (W.hash_color(), p, 3)
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228 for s, p, o in graph.triples((node, None, n))]
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229 new_color = tuple(new_color)
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230 new_hash_color = self.hash_color(new_color)
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231
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232 if new_hash_color not in colors:
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233 c = Color(
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234 [], self.hashfunc, new_color,
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235 hash_cache=self._hash_cache)
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236 colors[new_hash_color] = c
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237 colors[new_hash_color].nodes.append(n)
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238 return list(colors.values())
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239
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240 def discrete(self):
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241 return len(self.nodes) == 1
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242
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243 def copy(self):
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244 return Color(
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245 self.nodes[:], self.hashfunc, self.color,
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246 hash_cache=self._hash_cache)
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247
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248
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249 class _TripleCanonicalizer(object):
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250
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251 def __init__(self, graph, hashfunc=sha256):
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252 self.graph = graph
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253
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254 def _hashfunc(s):
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255 h = hashfunc()
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256 h.update(str(s).encode("utf8"))
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257 return int(h.hexdigest(), 16)
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258 self._hash_cache = {}
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259 self.hashfunc = _hashfunc
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260
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261
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262 def _discrete(self, coloring):
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263 return len([c for c in coloring if not c.discrete()]) == 0
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264
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265
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266 def _initial_color(self):
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267 """Finds an initial color for the graph.
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268
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269 Finds an initial color fo the graph by finding all blank nodes and
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270 non-blank nodes that are adjacent. Nodes that are not adjacent to blank
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271 nodes are not included, as they are a) already colored (by URI or literal)
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272 and b) do not factor into the color of any blank node.
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273 """
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274 bnodes = set()
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275 others = set()
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276 self._neighbors = defaultdict(set)
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277 for s, p, o in self.graph:
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278 nodes = set([s, o])
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279 b = set([x for x in nodes if isinstance(x, BNode)])
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280 if len(b) > 0:
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281 others |= nodes - b
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282 bnodes |= b
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283 if isinstance(s, BNode):
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284 self._neighbors[s].add(o)
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285 if isinstance(o, BNode):
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286 self._neighbors[o].add(s)
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287 if len(bnodes) > 0:
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288 return [
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289 Color(list(bnodes), self.hashfunc, hash_cache=self._hash_cache)
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290 ] + [
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291 Color([x], self.hashfunc, x, hash_cache=self._hash_cache)
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292 for x in others
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293 ]
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294 else:
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295 return []
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296
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297 def _individuate(self, color, individual):
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298 new_color = list(color.color)
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299 new_color.append((len(color.nodes),))
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300
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301 color.nodes.remove(individual)
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302 c = Color([individual], self.hashfunc, tuple(new_color),
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303 hash_cache=self._hash_cache)
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304 return c
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305
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306 def _get_candidates(self, coloring):
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307 candidates = [c for c in coloring if not c.discrete()]
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308 for c in [c for c in coloring if not c.discrete()]:
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309 for node in c.nodes:
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310 yield node, c
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311
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312 def _refine(self, coloring, sequence):
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313 sequence = sorted(sequence, key=lambda x: x.key(), reverse=True)
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314 coloring = coloring[:]
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315 while len(sequence) > 0 and not self._discrete(coloring):
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316 W = sequence.pop()
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317 for c in coloring[:]:
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318 if len(c.nodes) > 1:
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319 colors = sorted(c.distinguish(W, self.graph),
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320 key=lambda x: x.key(),
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321 reverse=True)
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322 coloring.remove(c)
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323 coloring.extend(colors)
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324 try:
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325 si = sequence.index(c)
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326 sequence = sequence[:si] + colors + sequence[si+1:]
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327 except ValueError:
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328 sequence = colors[1:] + sequence
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329
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330 return coloring
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331
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332 @_runtime("to_hash_runtime")
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parents:
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333 def to_hash(self, stats=None):
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334 result = 0
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parents:
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335 for triple in self.canonical_triples(stats=stats):
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parents:
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336 result += self.hashfunc(' '.join([x.n3() for x in triple]))
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337 if stats is not None:
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338 stats['graph_digest'] = "%x" % result
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339 return result
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340
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341 def _experimental_path(self, coloring):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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342 coloring = [c.copy() for c in coloring]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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343 while not self._discrete(coloring):
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344 color = [x for x in coloring if not x.discrete()][0]
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parents:
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345 node = color.nodes[0]
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parents:
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346 new_color = self._individuate(color, node)
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parents:
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347 coloring.append(new_color)
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parents:
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348 coloring = self._refine(coloring, [new_color])
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parents:
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349 return coloring
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350
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351 def _create_generator(self, colorings, groupings=None):
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parents:
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352 if not groupings:
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353 groupings = defaultdict(set)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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354 for group in zip(*colorings):
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parents:
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355 g = set([c.nodes[0] for c in group])
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parents:
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356 for n in group:
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diff changeset
357 g |= groupings[n]
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358 for n in g:
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parents:
diff changeset
359 groupings[n] = g
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
360 return groupings
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parents:
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361
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parents:
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362 @_call_count("individuations")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
363 def _traces(self, coloring, stats=None, depth=[0]):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
364 if stats is not None and 'prunings' not in stats:
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parents:
diff changeset
365 stats['prunings'] = 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
366 depth[0] += 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
367 candidates = self._get_candidates(coloring)
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parents:
diff changeset
368 best = []
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369 best_score = None
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parents:
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370 best_experimental = None
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parents:
diff changeset
371 best_experimental_score = None
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parents:
diff changeset
372 last_coloring = None
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parents:
diff changeset
373 generator = defaultdict(set)
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parents:
diff changeset
374 visited = set()
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parents:
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375 for candidate, color in candidates:
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parents:
diff changeset
376 if candidate in generator:
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parents:
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377 v = generator[candidate] & visited
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parents:
diff changeset
378 if len(v) > 0:
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parents:
diff changeset
379 visited.add(candidate)
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parents:
diff changeset
380 continue
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parents:
diff changeset
381 visited.add(candidate)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
382 coloring_copy = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
383 color_copy = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
384 for c in coloring:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
385 c_copy = c.copy()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
386 coloring_copy.append(c_copy)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
387 if c == color:
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parents:
diff changeset
388 color_copy = c_copy
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
389 new_color = self._individuate(color_copy, candidate)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
390 coloring_copy.append(new_color)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
391 refined_coloring = self._refine(coloring_copy, [new_color])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
392 color_score = tuple([c.key() for c in refined_coloring])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
393 experimental = self._experimental_path(coloring_copy)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
394 experimental_score = set([c.key() for c in experimental])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
395 if last_coloring:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
396 generator = self._create_generator(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
397 [last_coloring, experimental],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
398 generator)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
399 last_coloring = experimental
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
400 if best_score is None or best_score < color_score:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
401 best = [refined_coloring]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
402 best_score = color_score
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
403 best_experimental = experimental
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
404 best_experimental_score = experimental_score
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
405 elif best_score > color_score:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
406 # prune this branch.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
407 if stats is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
408 stats['prunings'] += 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
409 elif experimental_score != best_experimental_score:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
410 best.append(refined_coloring)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
411 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
412 # prune this branch.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
413 if stats is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
414 stats['prunings'] += 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
415 discrete = [x for x in best if self._discrete(x)]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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416 if len(discrete) == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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417 best_score = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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418 best_depth = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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419 for coloring in best:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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420 d = [depth[0]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
421 new_color = self._traces(coloring, stats=stats, depth=d)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
422 color_score = tuple([c.key() for c in refined_coloring])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
423 if best_score is None or color_score > best_score:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
424 discrete = [new_color]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
425 best_score = color_score
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
426 best_depth = d[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
427 depth[0] = best_depth
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
428 return discrete[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
429
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
430 def canonical_triples(self, stats=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
431 if stats is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
432 start_canonicalization = datetime.now()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
433 if stats is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
434 start_coloring = datetime.now()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
435 coloring = self._initial_color()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
436 if stats is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
437 stats['triple_count'] = len(self.graph)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
438 stats['adjacent_nodes'] = max(0, len(coloring) - 1)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
439 coloring = self._refine(coloring, coloring[:])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
440 if stats is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
441 stats['initial_coloring_runtime'] = _total_seconds(datetime.now() - start_coloring)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
442 stats['initial_color_count'] = len(coloring)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
443
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
444 if not self._discrete(coloring):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
445 depth = [0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
446 coloring = self._traces(coloring, stats=stats, depth=depth)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
447 if stats is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
448 stats['tree_depth'] = depth[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
449 elif stats is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
450 stats['individuations'] = 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
451 stats['tree_depth'] = 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
452 if stats is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
453 stats['color_count'] = len(coloring)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
454
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
455 bnode_labels = dict([(c.nodes[0], c.hash_color()) for c in coloring])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
456 if stats is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
457 stats["canonicalize_triples_runtime"] = _total_seconds(datetime.now() - start_coloring)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
458 for triple in self.graph:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
459 result = tuple(self._canonicalize_bnodes(triple, bnode_labels))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
460 yield result
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
461
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
462 def _canonicalize_bnodes(self, triple, labels):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
463 for term in triple:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
464 if isinstance(term, BNode):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
465 yield BNode(value="cb%s" % labels[term])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
466 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
467 yield term
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
468
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
469
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
470 def to_isomorphic(graph):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
471 if isinstance(graph, IsomorphicGraph):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
472 return graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
473 return IsomorphicGraph(store=graph.store)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
474
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
475
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
476 def isomorphic(graph1, graph2):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
477 """Compare graph for equality.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
478
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
479 Uses an algorithm to compute unique hashes which takes bnodes into account.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
480
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
481 Examples::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
482
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
483 >>> g1 = Graph().parse(format='n3', data='''
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
484 ... @prefix : <http://example.org/ns#> .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
485 ... <http://example.org> :rel <http://example.org/a> .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
486 ... <http://example.org> :rel <http://example.org/b> .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
487 ... <http://example.org> :rel [ :label "A bnode." ] .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
488 ... ''')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
489 >>> g2 = Graph().parse(format='n3', data='''
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
490 ... @prefix ns: <http://example.org/ns#> .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
491 ... <http://example.org> ns:rel [ ns:label "A bnode." ] .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
492 ... <http://example.org> ns:rel <http://example.org/b>,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
493 ... <http://example.org/a> .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
494 ... ''')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
495 >>> isomorphic(g1, g2)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
496 True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
497
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
498 >>> g3 = Graph().parse(format='n3', data='''
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
499 ... @prefix : <http://example.org/ns#> .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
500 ... <http://example.org> :rel <http://example.org/a> .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
501 ... <http://example.org> :rel <http://example.org/b> .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
502 ... <http://example.org> :rel <http://example.org/c> .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
503 ... ''')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
504 >>> isomorphic(g1, g3)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
505 False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
506 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
507 gd1 = _TripleCanonicalizer(graph1).to_hash()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
508 gd2 = _TripleCanonicalizer(graph2).to_hash()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
509 return gd1 == gd2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
510
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
511
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
512
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
513 def to_canonical_graph(g1):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
514 """Creates a canonical, read-only graph.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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515
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516 Creates a canonical, read-only graph where all bnode id:s are based on
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517 deterministical SHA-256 checksums, correlated with the graph contents.
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518 """
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519 graph = Graph()
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520 graph += _TripleCanonicalizer(g1).canonical_triples()
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521 return ReadOnlyGraphAggregate([graph])
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522
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523
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524 def graph_diff(g1, g2):
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525 """Returns three sets of triples: "in both", "in first" and "in second"."""
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526 # bnodes have deterministic values in canonical graphs:
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527 cg1 = to_canonical_graph(g1)
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528 cg2 = to_canonical_graph(g2)
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529 in_both = cg1 * cg2
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530 in_first = cg1 - cg2
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531 in_second = cg2 - cg1
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532 return (in_both, in_first, in_second)
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533
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534
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535
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536 _MOCK_BNODE = BNode()
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537
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538
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539 def similar(g1, g2):
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540 """Checks if the two graphs are "similar".
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541
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542 Checks if the two graphs are "similar", by comparing sorted triples where
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543 all bnodes have been replaced by a singular mock bnode (the
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544 ``_MOCK_BNODE``).
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545
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546 This is a much cheaper, but less reliable, alternative to the comparison
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547 algorithm in ``isomorphic``.
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548 """
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549 return all(t1 == t2 for (t1, t2) in _squashed_graphs_triples(g1, g2))
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550
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551
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552 def _squashed_graphs_triples(g1, g2):
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553 for (t1, t2) in zip(sorted(_squash_graph(g1)), sorted(_squash_graph(g2))):
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554 yield t1, t2
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555
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556
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557 def _squash_graph(graph):
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558 return (_squash_bnodes(triple) for triple in graph)
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559
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560
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561 def _squash_bnodes(triple):
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562 return tuple((isinstance(t, BNode) and _MOCK_BNODE) or t for t in triple)