Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/plugins/memory.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 from rdflib.term import BNode
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2 from rdflib.store import Store, NO_STORE, VALID_STORE
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3
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4 __all__ = ['Memory', 'IOMemory']
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5
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6 ANY = Any = None
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7
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8
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9 class Memory(Store):
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10 """\
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11 An in memory implementation of a triple store.
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12
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13 This triple store uses nested dictionaries to store triples. Each
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14 triple is stored in two such indices as follows spo[s][p][o] = 1 and
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15 pos[p][o][s] = 1.
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16
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17 Authors: Michel Pelletier, Daniel Krech, Stefan Niederhauser
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18 """
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19 def __init__(self, configuration=None, identifier=None):
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20 super(Memory, self).__init__(configuration)
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21 self.identifier = identifier
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22
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23 # indexed by [subject][predicate][object]
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24 self.__spo = {}
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25
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26 # indexed by [predicate][object][subject]
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27 self.__pos = {}
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28
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29 # indexed by [predicate][object][subject]
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30 self.__osp = {}
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31
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32 self.__namespace = {}
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33 self.__prefix = {}
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34
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35 def add(self, xxx_todo_changeme, context, quoted=False):
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36 """\
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37 Add a triple to the store of triples.
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38 """
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39 (subject, predicate, object) = xxx_todo_changeme
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40 spo = self.__spo
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41 try:
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42 po = spo[subject]
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43 except:
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44 po = spo[subject] = {}
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45 try:
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46 o = po[predicate]
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47 except:
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48 o = po[predicate] = {}
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49 o[object] = 1
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50
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51 pos = self.__pos
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52 try:
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53 os = pos[predicate]
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54 except:
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55 os = pos[predicate] = {}
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56 try:
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57 s = os[object]
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58 except:
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59 s = os[object] = {}
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60 s[subject] = 1
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61
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62 osp = self.__osp
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63 try:
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64 sp = osp[object]
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65 except:
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66 sp = osp[object] = {}
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67 try:
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68 p = sp[subject]
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69 except:
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70 p = sp[subject] = {}
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71 p[predicate] = 1
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72
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73 def remove(self, xxx_todo_changeme1, context=None):
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74 (subject, predicate, object) = xxx_todo_changeme1
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75 for (subject, predicate, object), c in self.triples(
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76 (subject, predicate, object)):
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77 del self.__spo[subject][predicate][object]
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78 del self.__pos[predicate][object][subject]
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79 del self.__osp[object][subject][predicate]
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80
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81 def triples(self, xxx_todo_changeme2, context=None):
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82 """A generator over all the triples matching """
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83 (subject, predicate, object) = xxx_todo_changeme2
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84 if subject != ANY: # subject is given
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85 spo = self.__spo
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86 if subject in spo:
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87 subjectDictionary = spo[subject]
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88 if predicate != ANY: # subject+predicate is given
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89 if predicate in subjectDictionary:
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90 if object != ANY: # subject+predicate+object is given
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91 if object in subjectDictionary[predicate]:
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92 yield (subject, predicate, object), \
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93 self.__contexts()
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94 else: # given object not found
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95 pass
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96 else: # subject+predicate is given, object unbound
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97 for o in list(subjectDictionary[predicate].keys()):
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98 yield (subject, predicate, o), \
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99 self.__contexts()
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100 else: # given predicate not found
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101 pass
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102 else: # subject given, predicate unbound
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103 for p in list(subjectDictionary.keys()):
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104 if object != ANY: # object is given
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105 if object in subjectDictionary[p]:
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106 yield (subject, p, object), self.__contexts()
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107 else: # given object not found
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108 pass
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109 else: # object unbound
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110 for o in list(subjectDictionary[p].keys()):
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111 yield (subject, p, o), self.__contexts()
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112 else: # given subject not found
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113 pass
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114 elif predicate != ANY: # predicate is given, subject unbound
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115 pos = self.__pos
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116 if predicate in pos:
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117 predicateDictionary = pos[predicate]
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118 if object != ANY: # predicate+object is given, subject unbound
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119 if object in predicateDictionary:
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120 for s in list(predicateDictionary[object].keys()):
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121 yield (s, predicate, object), self.__contexts()
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122 else: # given object not found
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123 pass
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124 else: # predicate is given, object+subject unbound
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125 for o in list(predicateDictionary.keys()):
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126 for s in list(predicateDictionary[o].keys()):
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127 yield (s, predicate, o), self.__contexts()
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128 elif object != ANY: # object is given, subject+predicate unbound
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129 osp = self.__osp
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130 if object in osp:
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131 objectDictionary = osp[object]
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132 for s in list(objectDictionary.keys()):
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133 for p in list(objectDictionary[s].keys()):
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134 yield (s, p, object), self.__contexts()
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135 else: # subject+predicate+object unbound
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136 spo = self.__spo
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137 for s in list(spo.keys()):
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138 subjectDictionary = spo[s]
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139 for p in list(subjectDictionary.keys()):
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140 for o in list(subjectDictionary[p].keys()):
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141 yield (s, p, o), self.__contexts()
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142
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143 def __len__(self, context=None):
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144 #@@ optimize
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145 i = 0
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146 for triple in self.triples((None, None, None)):
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147 i += 1
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148 return i
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149
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150 def bind(self, prefix, namespace):
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151 self.__prefix[namespace] = prefix
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152 self.__namespace[prefix] = namespace
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153
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154 def namespace(self, prefix):
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155 return self.__namespace.get(prefix, None)
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156
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157 def prefix(self, namespace):
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158 return self.__prefix.get(namespace, None)
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159
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160 def namespaces(self):
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161 for prefix, namespace in self.__namespace.items():
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162 yield prefix, namespace
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163
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164 def __contexts(self):
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165 return (c for c in []) # TODO: best way to return empty generator
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166
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167
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168 class IOMemory(Store):
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169 """\
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170 An integer-key-optimized context-aware in-memory store.
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171
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172 Uses three dict indices (for subjects, objects and predicates) holding
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173 sets of triples. Context information is tracked in a separate dict, with
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174 the triple as key and a dict of {context: quoted} items as value. The
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175 context information is used to filter triple query results.
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176
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177 Memory usage is low due to several optimizations. RDF nodes are not
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178 stored directly in the indices; instead, the indices hold integer keys
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179 and the actual nodes are only stored once in int-to-object and
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180 object-to-int mapping dictionaries. A default context is determined
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181 based on the first triple that is added to the store, and no context
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182 information is actually stored for subsequent other triples with the
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183 same context information.
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184
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185 Most operations should be quite fast, but a triples() query with two
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186 bound parts requires a set intersection operation, which may be slow in
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187 some cases. When multiple contexts are used in the same store, filtering
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188 based on context has to be done after each query, which may also be
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189 slow.
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190
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191 """
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192 context_aware = True
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193 formula_aware = True
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194 graph_aware = True
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195
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196 # The following variable name conventions are used in this class:
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197 #
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198 # subject, predicate, object unencoded triple parts
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199 # triple = (subject, predicate, object) unencoded triple
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200 # context: unencoded context
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201 #
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202 # sid, pid, oid integer-encoded triple parts
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203 # enctriple = (sid, pid, oid) integer-encoded triple
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204 # cid integer-encoded context
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205
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206 def __init__(self, configuration=None, identifier=None):
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207 super(IOMemory, self).__init__()
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208 self.__namespace = {}
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209 self.__prefix = {}
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210
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211 # Mappings for encoding RDF nodes using integer keys, to save memory
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212 # in the indexes Note that None is always mapped to itself, to make
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213 # it easy to test for it in either encoded or unencoded form.
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214 self.__int2obj = {None: None} # maps integer keys to objects
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215 self.__obj2int = {None: None} # maps objects to integer keys
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216
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217 # Indexes for each triple part, and a list of contexts for each triple
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218 self.__subjectIndex = {} # key: sid val: set(enctriples)
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219 self.__predicateIndex = {} # key: pid val: set(enctriples)
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220 self.__objectIndex = {} # key: oid val: set(enctriples)
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221 self.__tripleContexts = {
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222 } # key: enctriple val: {cid1: quoted, cid2: quoted ...}
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223 self.__contextTriples = {None: set()} # key: cid val: set(enctriples)
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224
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225 # all contexts used in store (unencoded)
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226 self.__all_contexts = set()
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227 # default context information for triples
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228 self.__defaultContexts = None
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229
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230 def bind(self, prefix, namespace):
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231 self.__prefix[namespace] = prefix
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232 self.__namespace[prefix] = namespace
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233
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234 def namespace(self, prefix):
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235 return self.__namespace.get(prefix, None)
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236
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237 def prefix(self, namespace):
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238 return self.__prefix.get(namespace, None)
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239
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240 def namespaces(self):
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241 for prefix, namespace in self.__namespace.items():
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242 yield prefix, namespace
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243
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244 def add(self, triple, context, quoted=False):
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245 Store.add(self, triple, context, quoted)
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246
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247 if context is not None:
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248 self.__all_contexts.add(context)
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249
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250 enctriple = self.__encodeTriple(triple)
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251 sid, pid, oid = enctriple
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252
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253 self.__addTripleContext(enctriple, context, quoted)
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254
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255 if sid in self.__subjectIndex:
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256 self.__subjectIndex[sid].add(enctriple)
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257 else:
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258 self.__subjectIndex[sid] = set([enctriple])
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259
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260 if pid in self.__predicateIndex:
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261 self.__predicateIndex[pid].add(enctriple)
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262 else:
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263 self.__predicateIndex[pid] = set([enctriple])
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264
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265 if oid in self.__objectIndex:
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266 self.__objectIndex[oid].add(enctriple)
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267 else:
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268 self.__objectIndex[oid] = set([enctriple])
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269
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270 def remove(self, triplepat, context=None):
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271 req_cid = self.__obj2id(context)
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272 for triple, contexts in self.triples(triplepat, context):
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273 enctriple = self.__encodeTriple(triple)
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274 for cid in self.__getTripleContexts(enctriple):
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275 if context is not None and req_cid != cid:
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276 continue
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277 self.__removeTripleContext(enctriple, cid)
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278 ctxs = self.__getTripleContexts(enctriple, skipQuoted=True)
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279 if None in ctxs and (context is None or len(ctxs) == 1):
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280 self.__removeTripleContext(enctriple, None)
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281 if len(self.__getTripleContexts(enctriple)) == 0:
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282 # triple has been removed from all contexts
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283 sid, pid, oid = enctriple
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284 self.__subjectIndex[sid].remove(enctriple)
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285 self.__predicateIndex[pid].remove(enctriple)
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286 self.__objectIndex[oid].remove(enctriple)
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287
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288 del self.__tripleContexts[enctriple]
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289
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290 if not req_cid is None and \
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291 req_cid in self.__contextTriples and \
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292 len(self.__contextTriples[req_cid]) == 0:
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293 # all triples are removed out of this context
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294 # and it's not the default context so delete it
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295 del self.__contextTriples[req_cid]
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296
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297 if triplepat == (None, None, None) and \
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298 context in self.__all_contexts and \
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299 not self.graph_aware:
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300 # remove the whole context
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301 self.__all_contexts.remove(context)
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302
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303 def triples(self, triplein, context=None):
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304 if context is not None:
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305 if context == self: # hmm...does this really ever happen?
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306 context = None
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307
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308 cid = self.__obj2id(context)
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309 enctriple = self.__encodeTriple(triplein)
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310 sid, pid, oid = enctriple
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311
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312 # all triples case (no triple parts given as pattern)
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313 if sid is None and pid is None and oid is None:
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314 return self.__all_triples(cid)
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315
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316 # optimize "triple in graph" case (all parts given)
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317 if sid is not None and pid is not None and oid is not None:
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318 if sid in self.__subjectIndex and \
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319 enctriple in self.__subjectIndex[sid] and \
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320 self.__tripleHasContext(enctriple, cid):
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321 return ((triplein, self.__contexts(enctriple)) for i in [0])
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322 else:
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323 return self.__emptygen()
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324
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325 # remaining cases: one or two out of three given
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326 sets = []
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327 if sid is not None:
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328 if sid in self.__subjectIndex:
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329 sets.append(self.__subjectIndex[sid])
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330 else:
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331 return self.__emptygen()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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332 if pid is not None:
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333 if pid in self.__predicateIndex:
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334 sets.append(self.__predicateIndex[pid])
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335 else:
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336 return self.__emptygen()
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337 if oid is not None:
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338 if oid in self.__objectIndex:
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339 sets.append(self.__objectIndex[oid])
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340 else:
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341 return self.__emptygen()
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342
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343 # to get the result, do an intersection of the sets (if necessary)
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344 if len(sets) > 1:
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345 enctriples = sets[0].intersection(*sets[1:])
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346 else:
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347 enctriples = sets[0].copy()
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348
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349 return ((self.__decodeTriple(enctriple), self.__contexts(enctriple))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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350 for enctriple in enctriples
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diff changeset
351 if self.__tripleHasContext(enctriple, cid))
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352
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353 def contexts(self, triple=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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354 if triple is None or triple is (None,None,None):
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355 return (context for context in self.__all_contexts)
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356
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357 enctriple = self.__encodeTriple(triple)
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358 sid, pid, oid = enctriple
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
359 if sid in self.__subjectIndex and enctriple in self.__subjectIndex[sid]:
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360 return self.__contexts(enctriple)
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361 else:
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362 return self.__emptygen()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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363
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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364 def __len__(self, context=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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365 cid = self.__obj2id(context)
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diff changeset
366 if cid not in self.__contextTriples:
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diff changeset
367 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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368 return len(self.__contextTriples[cid])
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369
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370 def add_graph(self, graph):
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371 if not self.graph_aware:
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372 Store.add_graph(self, graph)
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373 else:
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374 self.__all_contexts.add(graph)
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375
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376 def remove_graph(self, graph):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
377 if not self.graph_aware:
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378 Store.remove_graph(self, graph)
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379 else:
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380 self.remove((None,None,None), graph)
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diff changeset
381 try:
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diff changeset
382 self.__all_contexts.remove(graph)
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parents:
diff changeset
383 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
384 pass # we didn't know this graph, no problem
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385
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386
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387
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388 # internal utility methods below
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389
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390 def __addTripleContext(self, enctriple, context, quoted):
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391 """add the given context to the set of contexts for the triple"""
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392 cid = self.__obj2id(context)
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393
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394 sid, pid, oid = enctriple
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395 if sid in self.__subjectIndex and enctriple in self.__subjectIndex[sid]:
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396 # we know the triple exists somewhere in the store
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397 if enctriple not in self.__tripleContexts:
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398 # triple exists with default ctx info
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399 # start with a copy of the default ctx info
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400 self.__tripleContexts[
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401 enctriple] = self.__defaultContexts.copy()
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402
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403 self.__tripleContexts[enctriple][cid] = quoted
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404 if not quoted:
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405 self.__tripleContexts[enctriple][None] = quoted
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406 else:
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407 # the triple didn't exist before in the store
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408 if quoted: # this context only
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409 self.__tripleContexts[enctriple] = {cid: quoted}
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410 else: # default context as well
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411 self.__tripleContexts[enctriple] = {cid: quoted, None: quoted}
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412
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413 # if the triple is not quoted add it to the default context
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414 if not quoted:
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415 self.__contextTriples[None].add(enctriple)
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416
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417 # always add the triple to given context, making sure it's initialized
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418 if cid not in self.__contextTriples:
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419 self.__contextTriples[cid] = set()
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420 self.__contextTriples[cid].add(enctriple)
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421
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422 # if this is the first ever triple in the store, set default ctx info
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423 if self.__defaultContexts is None:
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424 self.__defaultContexts = self.__tripleContexts[enctriple]
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425
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426 # if the context info is the same as default, no need to store it
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427 if self.__tripleContexts[enctriple] == self.__defaultContexts:
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428 del self.__tripleContexts[enctriple]
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429
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430 def __getTripleContexts(self, enctriple, skipQuoted=False):
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431 """return a list of (encoded) contexts for the triple, skipping
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432 quoted contexts if skipQuoted==True"""
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433
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434 ctxs = self.__tripleContexts.get(enctriple, self.__defaultContexts)
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435
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436 if not skipQuoted:
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437 return list(ctxs.keys())
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438
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439 return [cid for cid, quoted in ctxs.items() if not quoted]
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440
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441 def __tripleHasContext(self, enctriple, cid):
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442 """return True iff the triple exists in the given context"""
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443 ctxs = self.__tripleContexts.get(enctriple, self.__defaultContexts)
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444 return (cid in ctxs)
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445
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446 def __removeTripleContext(self, enctriple, cid):
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447 """remove the context from the triple"""
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448 ctxs = self.__tripleContexts.get(
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449 enctriple, self.__defaultContexts).copy()
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450 del ctxs[cid]
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451 if ctxs == self.__defaultContexts:
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452 del self.__tripleContexts[enctriple]
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453 else:
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454 self.__tripleContexts[enctriple] = ctxs
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455 self.__contextTriples[cid].remove(enctriple)
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456
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457 def __obj2id(self, obj):
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458 """encode object, storing it in the encoding map if necessary,
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459 and return the integer key"""
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460 if obj not in self.__obj2int:
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461 id = randid()
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462 while id in self.__int2obj:
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463 id = randid()
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464 self.__obj2int[obj] = id
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465 self.__int2obj[id] = obj
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466 return id
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467 return self.__obj2int[obj]
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468
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469 def __encodeTriple(self, triple):
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470 """encode a whole triple, returning the encoded triple"""
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471 return tuple(map(self.__obj2id, triple))
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472
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473 def __decodeTriple(self, enctriple):
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474 """decode a whole encoded triple, returning the original
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475 triple"""
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476 return tuple(map(self.__int2obj.get, enctriple))
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477
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478 def __all_triples(self, cid):
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479 """return a generator which yields all the triples (unencoded)
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480 of the given context"""
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481 if cid not in self.__contextTriples:
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482 return
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483 for enctriple in self.__contextTriples[cid].copy():
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484 yield self.__decodeTriple(enctriple), self.__contexts(enctriple)
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485
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486 def __contexts(self, enctriple):
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487 """return a generator for all the non-quoted contexts
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488 (unencoded) the encoded triple appears in"""
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489 return (self.__int2obj.get(cid) for cid in self.__getTripleContexts(enctriple, skipQuoted=True) if cid is not None)
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490
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491 def __emptygen(self):
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492 """return an empty generator"""
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493 if False:
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494 yield
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495
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496
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497 import random
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498
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499
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500 def randid(randint=random.randint, choice=random.choice, signs=(-1, 1)):
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501 return choice(signs) * randint(1, 2000000000)
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502
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503 del random