Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/tools/graphisomorphism.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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0
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1 """
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2 A commandline tool for testing if RDF graphs are isomorpic, i.e. equal
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3 if BNode labels are ignored.
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4 """
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5
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6 from rdflib.graph import Graph
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7 from rdflib import BNode
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8 try:
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9 from itertools import combinations
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10 assert combinations
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11 except ImportError: # Python == 2.5
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12 # Copied from
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13 # http://docs.python.org/2/library/itertools.html#itertools.combinations
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14 def combinations(iterable, r):
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15 # combinations('ABCD', 2) --> AB AC AD BC BD CD
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16 # combinations(range(4), 3) --> 012 013 023 123
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17 pool = tuple(iterable)
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18 n = len(pool)
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19 if r > n:
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20 return
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21 indices = list(range(r))
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22 yield tuple(pool[i] for i in indices)
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23 while True:
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24 for i in reversed(list(range(r))):
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25 if indices[i] != i + n - r:
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26 break
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27 else:
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28 return
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29 indices[i] += 1
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30 for j in range(i + 1, r):
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31 indices[j] = indices[j - 1] + 1
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32 yield tuple(pool[i] for i in indices)
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33
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34
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35 class IsomorphicTestableGraph(Graph):
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36 """
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37 Ported from:
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38 http://www.w3.org/2001/sw/DataAccess/proto-tests/tools/rdfdiff.py
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39 (Sean B Palmer's RDF Graph Isomorphism Tester)
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40 """
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41 def __init__(self, **kargs):
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42 super(IsomorphicTestableGraph, self).__init__(**kargs)
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43 self.hash = None
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44
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45 def internal_hash(self):
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46 """
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47 This is defined instead of __hash__ to avoid a circular recursion
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48 scenario with the Memory store for rdflib which requires a hash
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49 lookup in order to return a generator of triples
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50 """
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51 return hash(tuple(sorted(self.hashtriples())))
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52
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53 def hashtriples(self):
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54 for triple in self:
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55 g = ((isinstance(t, BNode) and self.vhash(t)) or t for t in triple)
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56 yield hash(tuple(g))
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57
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58 def vhash(self, term, done=False):
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59 return tuple(sorted(self.vhashtriples(term, done)))
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60
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61 def vhashtriples(self, term, done):
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62 for t in self:
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63 if term in t:
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64 yield tuple(self.vhashtriple(t, term, done))
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65
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66 def vhashtriple(self, triple, term, done):
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67 for p in range(3):
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68 if not isinstance(triple[p], BNode):
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69 yield triple[p]
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70 elif done or (triple[p] == term):
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71 yield p
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72 else:
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73 yield self.vhash(triple[p], done=True)
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74
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75 def __eq__(self, G):
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76 """Graph isomorphism testing."""
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77 if not isinstance(G, IsomorphicTestableGraph):
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78 return False
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79 elif len(self) != len(G):
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80 return False
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81 elif list.__eq__(list(self), list(G)):
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82 return True # @@
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83 return self.internal_hash() == G.internal_hash()
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84
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85 def __ne__(self, G):
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86 """Negative graph isomorphism testing."""
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87 return not self.__eq__(G)
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88
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89
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90 def main():
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91 import sys
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92 from optparse import OptionParser
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93 usage = '''usage: %prog [options] file1 file2 ... fileN'''
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94 op = OptionParser(usage=usage)
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95 op.add_option('-s', '--stdin', action='store_true', default=False,
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96 help='Load from STDIN as well')
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97 op.add_option('--format',
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98 default='xml',
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99 dest='inputFormat',
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100 metavar='RDF_FORMAT',
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101 choices=['xml', 'trix', 'n3', 'nt', 'rdfa'],
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102 help="The format of the RDF document(s) to compare" +
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103 "One of 'xml','n3','trix', 'nt', " +
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104 "or 'rdfa'. The default is %default")
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105
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106 (options, args) = op.parse_args()
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107
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108 graphs = []
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109 graph2FName = {}
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110 if options.stdin:
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111 graph = IsomorphicTestableGraph().parse(
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112 sys.stdin, format=options.inputFormat)
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113 graphs.append(graph)
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114 graph2FName[graph] = '(STDIN)'
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115 for fn in args:
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116 graph = IsomorphicTestableGraph().parse(
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117 fn, format=options.inputFormat)
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118 graphs.append(graph)
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119 graph2FName[graph] = fn
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120 checked = set()
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121 for graph1, graph2 in combinations(graphs, 2):
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122 if (graph1, graph2) not in checked and (graph2, graph1) not in checked:
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123 assert graph1 == graph2, "%s != %s" % (
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124 graph2FName[graph1], graph2FName[graph2])
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125
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126 if __name__ == '__main__':
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127 main()