Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/plugins/sparql/sparql.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 import collections
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2 import itertools
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3 import datetime
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4
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5 from rdflib.namespace import NamespaceManager
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6 from rdflib import Variable, BNode, Graph, ConjunctiveGraph, URIRef, Literal
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7 from rdflib.term import Node
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8
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9 from .parserutils import CompValue
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10
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11 import rdflib.plugins.sparql
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12 from rdflib.plugins.sparql.compat import Mapping, MutableMapping
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13
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14
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15 class SPARQLError(Exception):
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16 def __init__(self, msg=None):
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17 Exception.__init__(self, msg)
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18
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19
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20 class NotBoundError(SPARQLError):
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21 def __init__(self, msg=None):
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22 SPARQLError.__init__(self, msg)
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23
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24
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25 class AlreadyBound(SPARQLError):
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26 """Raised when trying to bind a variable that is already bound!"""
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27 def __init__(self):
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28 SPARQLError.__init__(self)
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30
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31 class SPARQLTypeError(SPARQLError):
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32 def __init__(self, msg):
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33 SPARQLError.__init__(self, msg)
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34
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35
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36 class Bindings(MutableMapping):
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37
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38 """
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39
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40 A single level of a stack of variable-value bindings.
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41 Each dict keeps a reference to the dict below it,
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42 any failed lookup is propegated back
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43
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44 In python 3.3 this could be a collections.ChainMap
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45 """
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46
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47 def __init__(self, outer=None, d=[]):
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48 self._d = dict(d)
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49 self.outer = outer
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50
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51 def __getitem__(self, key):
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52 try:
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53 return self._d[key]
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54 except KeyError:
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55 if not self.outer:
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56 raise
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57 return self.outer[key]
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58
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59 def __contains__(self, key):
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60 try:
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61 self[key]
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62 return True
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63 except KeyError:
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64 return False
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65
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66 def __setitem__(self, key, value):
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67 self._d[key] = value
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68
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69 def __delitem__(self, key):
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70 raise Exception("DelItem is not implemented!")
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71
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72 def __len__(self):
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73 i = 0
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74 for x in self:
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75 i += 1
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76 return i
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77
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78 def __iter__(self):
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79 d = self
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80 while d is not None:
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81 for i in dict.__iter__(d._d):
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82 yield i
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83 d = d.outer
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84
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85 def __str__(self):
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86 return "Bindings({"+", ".join((k, self[k]) for k in self)+"})"
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87
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88 def __repr__(self):
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89 return str(self)
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90
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91
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92 class FrozenDict(Mapping):
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93 """
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94 An immutable hashable dict
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95
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96 Taken from http://stackoverflow.com/a/2704866/81121
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97
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98 """
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99 def __init__(self, *args, **kwargs):
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100 self._d = dict(*args, **kwargs)
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101 self._hash = None
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102
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103 def __iter__(self):
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104 return iter(self._d)
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105
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106 def __len__(self):
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107 return len(self._d)
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108
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109 def __getitem__(self, key):
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110 return self._d[key]
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111
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112 def __hash__(self):
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113 # It would have been simpler and maybe more obvious to
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114 # use hash(tuple(sorted(self._d.iteritems()))) from this discussion
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115 # so far, but this solution is O(n). I don't know what kind of
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116 # n we are going to run into, but sometimes it's hard to resist the
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117 # urge to optimize when it will gain improved algorithmic performance.
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118 if self._hash is None:
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119 self._hash = 0
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120 for key, value in self.items():
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121 self._hash ^= hash(key)
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122 self._hash ^= hash(value)
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123 return self._hash
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124
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125 def project(self, vars):
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126 return FrozenDict(
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127 (x for x in self.items() if x[0] in vars))
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128
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129 def disjointDomain(self, other):
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130 return not bool(set(self).intersection(other))
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131
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132 def compatible(self, other):
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133 for k in self:
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134 try:
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135 if self[k] != other[k]:
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136 return False
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137 except KeyError:
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138 pass
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139
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140 return True
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141
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142 def merge(self, other):
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143 res = FrozenDict(
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144 itertools.chain(iter(self.items()), iter(other.items())))
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145
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146 return res
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147
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148 def __str__(self):
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149 return str(self._d)
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150
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151 def __repr__(self):
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152 return repr(self._d)
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153
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154
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155 class FrozenBindings(FrozenDict):
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156
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157 def __init__(self, ctx, *args, **kwargs):
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158 FrozenDict.__init__(self, *args, **kwargs)
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159 self.ctx = ctx
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160
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161 def __getitem__(self, key):
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162
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163 if not isinstance(key, Node):
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164 key = Variable(key)
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165
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166 if not type(key) in (BNode, Variable):
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167 return key
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168
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169 return self._d[key]
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170
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171 def project(self, vars):
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172 return FrozenBindings(
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173 self.ctx, (x for x in self.items() if x[0] in vars))
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174
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175 def merge(self, other):
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176 res = FrozenBindings(
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177 self.ctx, itertools.chain(iter(self.items()), iter(other.items())))
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178
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179 return res
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180
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181 def _now(self):
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182 return self.ctx.now
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183
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184 def _bnodes(self):
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185 return self.ctx.bnodes
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186
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187 def _prologue(self):
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188 return self.ctx.prologue
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189
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190 prologue = property(_prologue)
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191 bnodes = property(_bnodes)
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192 now = property(_now)
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193
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194 def forget(self, before, _except=None):
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195 """
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196 return a frozen dict only of bindings made in self
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197 since before
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198 """
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199 if not _except : _except = []
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200 # bindings from initBindings are newer forgotten
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201 return FrozenBindings(self.ctx, (x for x in self.items() if x[0] in _except or x[0] in self.ctx.initBindings or before[x[0]] is None))
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202
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203 def remember(self, these):
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204 """
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205 return a frozen dict only of bindings in these
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206 """
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207 return FrozenBindings(self.ctx, (x for x in self.items() if x[0] in these))
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208
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209
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210 class QueryContext(object):
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211
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212 """
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213 Query context - passed along when evaluating the query
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214 """
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215
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216 def __init__(self, graph=None, bindings=None, initBindings=None):
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217 self.initBindings = initBindings
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218 self.bindings = Bindings(d=bindings or [])
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219 if initBindings: self.bindings.update(initBindings)
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220
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221 if isinstance(graph, ConjunctiveGraph):
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222 self._dataset = graph
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223 if rdflib.plugins.sparql.SPARQL_DEFAULT_GRAPH_UNION:
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224 self.graph = self.dataset
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225 else:
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226 self.graph = self.dataset.default_context
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227 else:
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228 self._dataset = None
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229 self.graph = graph
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230
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231 self.prologue = None
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232 self.now = datetime.datetime.now()
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233
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234 self.bnodes = collections.defaultdict(BNode)
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235
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236 def clone(self, bindings=None):
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237 r = QueryContext(
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238 self._dataset if self._dataset is not None else self.graph, bindings or self.bindings, initBindings=self.initBindings)
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239 r.prologue = self.prologue
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240 r.graph = self.graph
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241 r.bnodes = self.bnodes
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242 return r
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243
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244 def _get_dataset(self):
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245 if self._dataset is None:
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246 raise Exception(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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247 'You performed a query operation requiring ' +
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248 'a dataset (i.e. ConjunctiveGraph), but ' +
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249 'operating currently on a single graph.')
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250 return self._dataset
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251
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252 dataset = property(_get_dataset, doc="current dataset")
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253
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254 def load(self, source, default=False, **kwargs):
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255
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256 def _load(graph, source):
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257 try:
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258 return graph.load(source, **kwargs)
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259 except:
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260 pass
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261 try:
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262 return graph.load(source, format='n3', **kwargs)
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263 except:
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264 pass
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265 try:
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266 return graph.load(source, format='nt', **kwargs)
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267 except:
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268 raise Exception(
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269 "Could not load %s as either RDF/XML, N3 or NTriples" % (
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270 source))
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271
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272 if not rdflib.plugins.sparql.SPARQL_LOAD_GRAPHS:
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273 # we are not loading - if we already know the graph
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274 # being "loaded", just add it to the default-graph
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275 if default:
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276 self.graph += self.dataset.get_context(source)
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277 else:
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278
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279 if default:
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280 _load(self.graph, source)
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281 else:
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282 _load(self.dataset, source)
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283
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284 def __getitem__(self, key):
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285 # in SPARQL BNodes are just labels
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286 if not type(key) in (BNode, Variable):
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287 return key
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288 try:
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289 return self.bindings[key]
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290 except KeyError:
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291 return None
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292
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293 def get(self, key, default=None):
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294 try:
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295 return self[key]
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296 except KeyError:
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297 return default
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298
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299 def solution(self, vars=None):
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300 """
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301 Return a static copy of the current variable bindings as dict
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302 """
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303 if vars:
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304 return FrozenBindings(
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305 self, ((k, v)
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306 for k, v in self.bindings.items()
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307 if k in vars))
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308 else:
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309 return FrozenBindings(self, iter(self.bindings.items()))
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310
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311 def __setitem__(self, key, value):
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312 if key in self.bindings and self.bindings[key] != value:
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313 raise AlreadyBound()
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314
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315 self.bindings[key] = value
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316
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317 def pushGraph(self, graph):
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318 r = self.clone()
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319 r.graph = graph
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320 return r
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321
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322 def push(self):
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323 r = self.clone(Bindings(self.bindings))
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324 return r
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325
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326 def clean(self):
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327 return self.clone([])
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328
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329 # def pop(self):
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330 # self.bindings = self.bindings.outer
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331 # if self.bindings is None:
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332 # raise Exception("We've bottomed out of the bindings stack!")
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333
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334 def thaw(self, frozenbindings):
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335 """
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336 Create a new read/write query context from the given solution
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337 """
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338 c = self.clone(frozenbindings)
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339
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340 return c
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341
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342
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343 class Prologue(object):
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344
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345 """
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346 A class for holding prefixing bindings and base URI information
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347 """
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348
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349 def __init__(self):
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350 self.base = None
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351 self.namespace_manager = NamespaceManager(
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352 Graph()) # ns man needs a store
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353
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354 def resolvePName(self, prefix, localname):
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355 ns = self.namespace_manager.store.namespace(prefix or "")
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parents:
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356 if ns is None:
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357 raise Exception('Unknown namespace prefix : %s' % prefix)
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parents:
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358 return URIRef(ns + (localname or ""))
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359
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360 def bind(self, prefix, uri):
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parents:
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361 self.namespace_manager.bind(prefix, uri, replace=True)
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362
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parents:
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363 def absolutize(self, iri):
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364
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365 """
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parents:
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366 Apply BASE / PREFIXes to URIs
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parents:
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367 (and to datatypes in Literals)
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368
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369 TODO: Move resolving URIs to pre-processing
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parents:
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370 """
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371
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parents:
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372 if isinstance(iri, CompValue):
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parents:
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373 if iri.name == 'pname':
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parents:
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374 return self.resolvePName(iri.prefix, iri.localname)
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parents:
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375 if iri.name == 'literal':
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parents:
diff changeset
376 return Literal(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
377 iri.string, lang=iri.lang,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
378 datatype=self.absolutize(iri.datatype))
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parents:
diff changeset
379 elif isinstance(iri, URIRef) and not ':' in iri:
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parents:
diff changeset
380 return URIRef(iri, base=self.base)
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parents:
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381
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parents:
diff changeset
382 return iri
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383
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384
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385 class Query(object):
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386 """
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diff changeset
387 A parsed and translated query
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388 """
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389
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diff changeset
390 def __init__(self, prologue, algebra):
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diff changeset
391 self.prologue = prologue
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parents:
diff changeset
392 self.algebra = algebra