Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/rdflib/compare.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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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 from __future__ import absolute_import
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77 from __future__ import division
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78 from __future__ import print_function
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79
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80
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81 # TODO:
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82 # - Doesn't handle quads.
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83 # - Add warning and/or safety mechanism before working on large graphs?
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84 # - use this in existing Graph.isomorphic?
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85
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86 __all__ = ['IsomorphicGraph', 'to_isomorphic', 'isomorphic',
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87 'to_canonical_graph', 'graph_diff', 'similar']
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88
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89 from rdflib.graph import Graph, ConjunctiveGraph, ReadOnlyGraphAggregate
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90 from rdflib.term import BNode, Node
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91 from hashlib import sha256
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92
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93 from datetime import datetime
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94 from collections import defaultdict
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95
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96 from six import text_type
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97
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98
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99 def _total_seconds(td):
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100 result = td.days * 24 * 60 * 60
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101 result += td.seconds
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102 result += td.microseconds / 1000000.0
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103 return result
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104
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105
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106 class _runtime(object):
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107 def __init__(self, label):
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108 self.label = label
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109
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110 def __call__(self, f):
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111 if self.label is None:
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112 self.label = f.__name__ + "_runtime"
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113
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114 def wrapped_f(*args, **kwargs):
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115 start = datetime.now()
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116 result = f(*args, **kwargs)
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117 if 'stats' in kwargs and kwargs['stats'] is not None:
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118 stats = kwargs['stats']
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119 stats[self.label] = _total_seconds(datetime.now() - start)
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120 return result
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121 return wrapped_f
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122
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123
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124 class _call_count(object):
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125 def __init__(self, label):
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126 self.label = label
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127
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128 def __call__(self, f):
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129 if self.label is None:
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130 self.label = f.__name__ + "_runtime"
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131
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132 def wrapped_f(*args, **kwargs):
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133 if 'stats' in kwargs and kwargs['stats'] is not None:
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134 stats = kwargs['stats']
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135 if self.label not in stats:
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136 stats[self.label] = 0
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137 stats[self.label] += 1
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138 return f(*args, **kwargs)
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139 return wrapped_f
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140
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141
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142 class IsomorphicGraph(ConjunctiveGraph):
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143 """An implementation of the RGDA1 graph digest algorithm.
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144
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145 An implementation of RGDA1 (publication below),
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146 a combination of Sayers & Karp's graph digest algorithm using
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147 sum and SHA-256 <http://www.hpl.hp.com/techreports/2003/HPL-2003-235R1.pdf>
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148 and traces <http://pallini.di.uniroma1.it>, an average case
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149 polynomial time algorithm for graph canonicalization.
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150
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151 McCusker, J. P. (2015). WebSig: A Digital Signature Framework for the Web.
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152 Rensselaer Polytechnic Institute, Troy, NY.
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153 http://gradworks.umi.com/3727015.pdf
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154 """
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155
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156 def __init__(self, **kwargs):
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157 super(IsomorphicGraph, self).__init__(**kwargs)
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158
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159 def __eq__(self, other):
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160 """Graph isomorphism testing."""
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161 if not isinstance(other, IsomorphicGraph):
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162 return False
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163 elif len(self) != len(other):
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164 return False
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165 return self.internal_hash() == other.internal_hash()
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166
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167 def __ne__(self, other):
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168 """Negative graph isomorphism testing."""
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169 return not self.__eq__(other)
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170
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171 def __hash__(self):
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172 return super(IsomorphicGraph, self).__hash__()
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173
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174 def graph_digest(self, stats=None):
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175 """Synonym for IsomorphicGraph.internal_hash."""
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176 return self.internal_hash(stats=stats)
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177
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178 def internal_hash(self, stats=None):
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179 """
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180 This is defined instead of __hash__ to avoid a circular recursion
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181 scenario with the Memory store for rdflib which requires a hash lookup
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182 in order to return a generator of triples.
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183 """
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184 return _TripleCanonicalizer(self).to_hash(stats=stats)
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185
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186
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187 class Color:
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188 def __init__(self, nodes, hashfunc, color=(), hash_cache=None):
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189 if hash_cache is None:
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190 hash_cache = {}
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191 self._hash_cache = hash_cache
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192 self.color = color
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193 self.nodes = nodes
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194 self.hashfunc = hashfunc
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195 self._hash_color = None
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196
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197 def __str__(self):
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198 nodes, color = self.key()
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199 return "Color %s (%s nodes)" % (color, nodes)
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200
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201 def key(self):
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202 return (len(self.nodes), self.hash_color())
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203
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204 def hash_color(self, color=None):
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205 if color is None:
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206 color = self.color
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207 if color in self._hash_cache:
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208 return self._hash_cache[color]
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209
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210 def stringify(x):
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211 if isinstance(x, Node):
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212 return x.n3()
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213 else:
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214 return text_type(x)
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215 if isinstance(color, Node):
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216 return stringify(color)
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217 value = 0
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218 for triple in color:
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219 value += self.hashfunc(' '.join([stringify(x) for x in triple]))
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220 val = u"%x" % value
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221 self._hash_cache[color] = val
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222 return val
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223
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224 def distinguish(self, W, graph):
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225 colors = {}
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226 for n in self.nodes:
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227 new_color = list(self.color)
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228 for node in W.nodes:
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229 new_color += [
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230 (1, p, W.hash_color())
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231 for s, p, o in graph.triples((n, None, node))]
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232 new_color += [
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233 (W.hash_color(), p, 3)
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234 for s, p, o in graph.triples((node, None, n))]
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235 new_color = tuple(new_color)
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236 new_hash_color = self.hash_color(new_color)
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237
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238 if new_hash_color not in colors:
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239 c = Color(
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240 [], self.hashfunc, new_color,
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241 hash_cache=self._hash_cache)
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242 colors[new_hash_color] = c
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243 colors[new_hash_color].nodes.append(n)
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244 return colors.values()
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245
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246 def discrete(self):
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247 return len(self.nodes) == 1
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248
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249 def copy(self):
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250 return Color(
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251 self.nodes[:], self.hashfunc, self.color,
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252 hash_cache=self._hash_cache)
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253
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254
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255 class _TripleCanonicalizer(object):
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256
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257 def __init__(self, graph, hashfunc=sha256):
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258 self.graph = graph
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259
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260 def _hashfunc(s):
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261 h = hashfunc()
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parents:
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262 h.update(text_type(s).encode("utf8"))
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parents:
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263 return int(h.hexdigest(), 16)
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parents:
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264 self._hash_cache = {}
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parents:
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265 self.hashfunc = _hashfunc
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266
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267 def _discrete(self, coloring):
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268 return len([c for c in coloring if not c.discrete()]) == 0
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269
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270 def _initial_color(self):
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271 """Finds an initial color for the graph.
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272
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273 Finds an initial color fo the graph by finding all blank nodes and
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274 non-blank nodes that are adjacent. Nodes that are not adjacent to blank
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275 nodes are not included, as they are a) already colored (by URI or literal)
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276 and b) do not factor into the color of any blank node.
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277 """
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278 bnodes = set()
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279 others = set()
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280 self._neighbors = defaultdict(set)
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281 for s, p, o in self.graph:
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282 nodes = set([s, p, o])
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283 b = set([x for x in nodes if isinstance(x, BNode)])
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284 if len(b) > 0:
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parents:
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285 others |= nodes - b
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286 bnodes |= b
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parents:
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287 if isinstance(s, BNode):
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288 self._neighbors[s].add(o)
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289 if isinstance(o, BNode):
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290 self._neighbors[o].add(s)
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291 if isinstance(p, BNode):
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292 self._neighbors[p].add(s)
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293 self._neighbors[p].add(p)
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294 if len(bnodes) > 0:
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parents:
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295 return [
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parents:
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296 Color(list(bnodes), self.hashfunc, hash_cache=self._hash_cache)
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297 ] + [
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298 Color([x], self.hashfunc, x, hash_cache=self._hash_cache)
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parents:
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299 for x in others
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300 ]
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301 else:
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302 return []
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303
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304 def _individuate(self, color, individual):
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305 new_color = list(color.color)
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306 new_color.append((len(color.nodes),))
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307
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308 color.nodes.remove(individual)
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309 c = Color([individual], self.hashfunc, tuple(new_color),
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310 hash_cache=self._hash_cache)
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311 return c
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312
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313 def _get_candidates(self, coloring):
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314 candidates = [c for c in coloring if not c.discrete()]
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315 for c in [c for c in coloring if not c.discrete()]:
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parents:
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316 for node in c.nodes:
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parents:
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317 yield node, c
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318
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319 def _refine(self, coloring, sequence):
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320 sequence = sorted(sequence, key=lambda x: x.key(), reverse=True)
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321 coloring = coloring[:]
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322 while len(sequence) > 0 and not self._discrete(coloring):
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323 W = sequence.pop()
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parents:
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324 for c in coloring[:]:
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parents:
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325 if len(c.nodes) > 1 or isinstance(c.nodes[0], BNode):
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326 colors = sorted(c.distinguish(W, self.graph),
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327 key=lambda x: x.key(),
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parents:
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328 reverse=True)
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parents:
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329 coloring.remove(c)
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parents:
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330 coloring.extend(colors)
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parents:
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331 try:
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parents:
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332 si = sequence.index(c)
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parents:
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333 sequence = sequence[:si] + colors + sequence[si+1:]
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parents:
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334 except ValueError:
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parents:
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335 sequence = colors[1:] + sequence
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parents:
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336 combined_colors = []
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parents:
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337 combined_color_map = dict()
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parents:
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338 for color in coloring:
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parents:
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339 color_hash = color.hash_color()
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parents:
diff changeset
340 # This is a hash collision, and be combined into a single color for individuation.
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parents:
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341 if color_hash in combined_color_map:
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parents:
diff changeset
342 combined_color_map[color_hash].nodes.extend(color.nodes)
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parents:
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343 else:
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parents:
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344 combined_colors.append(color)
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parents:
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345 combined_color_map[color_hash] = color
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parents:
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346 return combined_colors
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parents:
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347
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348 @_runtime("to_hash_runtime")
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parents:
diff changeset
349 def to_hash(self, stats=None):
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parents:
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350 result = 0
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parents:
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351 for triple in self.canonical_triples(stats=stats):
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parents:
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352 result += self.hashfunc(' '.join([x.n3() for x in triple]))
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parents:
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353 if stats is not None:
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parents:
diff changeset
354 stats['graph_digest'] = "%x" % result
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parents:
diff changeset
355 return result
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parents:
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356
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parents:
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357 def _experimental_path(self, coloring):
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parents:
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358 coloring = [c.copy() for c in coloring]
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parents:
diff changeset
359 while not self._discrete(coloring):
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parents:
diff changeset
360 color = [x for x in coloring if not x.discrete()][0]
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parents:
diff changeset
361 node = color.nodes[0]
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parents:
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362 new_color = self._individuate(color, node)
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parents:
diff changeset
363 coloring.append(new_color)
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parents:
diff changeset
364 coloring = self._refine(coloring, [new_color])
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parents:
diff changeset
365 return coloring
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parents:
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366
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parents:
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367 def _create_generator(self, colorings, groupings=None):
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parents:
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368 if not groupings:
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parents:
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369 groupings = defaultdict(set)
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parents:
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370 for group in zip(*colorings):
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parents:
diff changeset
371 g = set([c.nodes[0] for c in group])
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parents:
diff changeset
372 for n in group:
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parents:
diff changeset
373 g |= groupings[n]
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parents:
diff changeset
374 for n in g:
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parents:
diff changeset
375 groupings[n] = g
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parents:
diff changeset
376 return groupings
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parents:
diff changeset
377
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parents:
diff changeset
378 @_call_count("individuations")
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parents:
diff changeset
379 def _traces(self, coloring, stats=None, depth=[0]):
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parents:
diff changeset
380 if stats is not None and 'prunings' not in stats:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
381 stats['prunings'] = 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
382 depth[0] += 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
383 candidates = self._get_candidates(coloring)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
384 best = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
385 best_score = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
386 best_experimental = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
387 best_experimental_score = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
388 last_coloring = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
389 generator = defaultdict(set)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
390 visited = set()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
391 for candidate, color in candidates:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
392 if candidate in generator:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
393 v = generator[candidate] & visited
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
394 if len(v) > 0:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
395 visited.add(candidate)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
396 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
397 visited.add(candidate)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
398 coloring_copy = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
399 color_copy = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
400 for c in coloring:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
401 c_copy = c.copy()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
402 coloring_copy.append(c_copy)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
403 if c == color:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
404 color_copy = c_copy
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
405 new_color = self._individuate(color_copy, candidate)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
406 coloring_copy.append(new_color)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
407 refined_coloring = self._refine(coloring_copy, [new_color])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
408 color_score = tuple([c.key() for c in refined_coloring])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
409 experimental = self._experimental_path(coloring_copy)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
410 experimental_score = set([c.key() for c in experimental])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
411 if last_coloring:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
412 generator = self._create_generator(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
413 [last_coloring, experimental],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
414 generator)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
415 last_coloring = experimental
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
416 if best_score is None or best_score < color_score:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
417 best = [refined_coloring]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
418 best_score = color_score
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
419 best_experimental = experimental
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
420 best_experimental_score = experimental_score
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
421 elif best_score > color_score:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
422 # prune this branch.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
423 if stats is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
424 stats['prunings'] += 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
425 elif experimental_score != best_experimental_score:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
426 best.append(refined_coloring)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
427 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
428 # prune this branch.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
429 if stats is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
430 stats['prunings'] += 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
431 discrete = [x for x in best if self._discrete(x)]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
432 if len(discrete) == 0:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
433 best_score = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
434 best_depth = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
435 for coloring in best:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
436 d = [depth[0]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
437 new_color = self._traces(coloring, stats=stats, depth=d)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
438 color_score = tuple([c.key() for c in refined_coloring])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
439 if best_score is None or color_score > best_score:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
440 discrete = [new_color]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
441 best_score = color_score
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
442 best_depth = d[0]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
443 depth[0] = best_depth
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
444 return discrete[0]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
445
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
446 def canonical_triples(self, stats=None):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
447 if stats is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
448 start_canonicalization = datetime.now()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
449 if stats is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
450 start_coloring = datetime.now()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
451 coloring = self._initial_color()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
452 if stats is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
453 stats['triple_count'] = len(self.graph)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
454 stats['adjacent_nodes'] = max(0, len(coloring) - 1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
455 coloring = self._refine(coloring, coloring[:])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
456 if stats is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
457 stats['initial_coloring_runtime'] = _total_seconds(datetime.now() - start_coloring)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
458 stats['initial_color_count'] = len(coloring)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
459
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
460 if not self._discrete(coloring):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
461 depth = [0]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
462 coloring = self._traces(coloring, stats=stats, depth=depth)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
463 if stats is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
464 stats['tree_depth'] = depth[0]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
465 elif stats is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
466 stats['individuations'] = 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
467 stats['tree_depth'] = 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
468 if stats is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
469 stats['color_count'] = len(coloring)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
470
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
471 bnode_labels = dict([(c.nodes[0], c.hash_color()) for c in coloring])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
472 if stats is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
473 stats["canonicalize_triples_runtime"] = _total_seconds(datetime.now() - start_coloring)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
474 for triple in self.graph:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
475 result = tuple(self._canonicalize_bnodes(triple, bnode_labels))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
476 yield result
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
477
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
478 def _canonicalize_bnodes(self, triple, labels):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
479 for term in triple:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
480 if isinstance(term, BNode):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
481 yield BNode(value="cb%s" % labels[term])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
482 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
483 yield term
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
484
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
485
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
486 def to_isomorphic(graph):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
487 if isinstance(graph, IsomorphicGraph):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
488 return graph
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
489 result = IsomorphicGraph()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
490 if hasattr(graph, "identifier"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
491 result = IsomorphicGraph(identifier=graph.identifier)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
492 result += graph
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
493 return result
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
494
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
495
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
496 def isomorphic(graph1, graph2):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
497 """Compare graph for equality.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
498
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
499 Uses an algorithm to compute unique hashes which takes bnodes into account.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
500
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
501 Examples::
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
502
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
503 >>> g1 = Graph().parse(format='n3', data='''
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
504 ... @prefix : <http://example.org/ns#> .
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
505 ... <http://example.org> :rel <http://example.org/a> .
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
506 ... <http://example.org> :rel <http://example.org/b> .
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
507 ... <http://example.org> :rel [ :label "A bnode." ] .
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508 ... ''')
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509 >>> g2 = Graph().parse(format='n3', data='''
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510 ... @prefix ns: <http://example.org/ns#> .
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511 ... <http://example.org> ns:rel [ ns:label "A bnode." ] .
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512 ... <http://example.org> ns:rel <http://example.org/b>,
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513 ... <http://example.org/a> .
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514 ... ''')
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515 >>> isomorphic(g1, g2)
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516 True
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517
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518 >>> g3 = Graph().parse(format='n3', data='''
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519 ... @prefix : <http://example.org/ns#> .
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520 ... <http://example.org> :rel <http://example.org/a> .
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521 ... <http://example.org> :rel <http://example.org/b> .
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522 ... <http://example.org> :rel <http://example.org/c> .
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523 ... ''')
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524 >>> isomorphic(g1, g3)
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525 False
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526 """
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527 gd1 = _TripleCanonicalizer(graph1).to_hash()
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528 gd2 = _TripleCanonicalizer(graph2).to_hash()
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529 return gd1 == gd2
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530
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531
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532 def to_canonical_graph(g1, stats=None):
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533 """Creates a canonical, read-only graph.
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534
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535 Creates a canonical, read-only graph where all bnode id:s are based on
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536 deterministical SHA-256 checksums, correlated with the graph contents.
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537 """
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538 graph = Graph()
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539 graph += _TripleCanonicalizer(g1).canonical_triples(stats=stats)
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540 return ReadOnlyGraphAggregate([graph])
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541
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542
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543 def graph_diff(g1, g2):
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544 """Returns three sets of triples: "in both", "in first" and "in second"."""
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545 # bnodes have deterministic values in canonical graphs:
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546 cg1 = to_canonical_graph(g1)
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547 cg2 = to_canonical_graph(g2)
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548 in_both = cg1 * cg2
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549 in_first = cg1 - cg2
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550 in_second = cg2 - cg1
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551 return (in_both, in_first, in_second)
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552
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553
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554 _MOCK_BNODE = BNode()
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555
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556
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557 def similar(g1, g2):
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558 """Checks if the two graphs are "similar".
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559
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560 Checks if the two graphs are "similar", by comparing sorted triples where
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561 all bnodes have been replaced by a singular mock bnode (the
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562 ``_MOCK_BNODE``).
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563
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564 This is a much cheaper, but less reliable, alternative to the comparison
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565 algorithm in ``isomorphic``.
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566 """
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567 return all(t1 == t2 for (t1, t2) in _squashed_graphs_triples(g1, g2))
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568
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569
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570 def _squashed_graphs_triples(g1, g2):
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571 for (t1, t2) in zip(sorted(_squash_graph(g1)), sorted(_squash_graph(g2))):
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572 yield t1, t2
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573
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574
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575 def _squash_graph(graph):
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576 return (_squash_bnodes(triple) for triple in graph)
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577
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578
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579 def _squash_bnodes(triple):
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580 return tuple((isinstance(t, BNode) and _MOCK_BNODE) or t for t in triple)