Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/store.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 ============
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3 rdflib.store
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4 ============
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5
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6 Types of store
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7 --------------
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8
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9 ``Context-aware``: An RDF store capable of storing statements within contexts
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10 is considered context-aware. Essentially, such a store is able to partition
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11 the RDF model it represents into individual, named, and addressable
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12 sub-graphs.
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13
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14 Relevant Notation3 reference regarding formulae, quoted statements, and such:
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15 http://www.w3.org/DesignIssues/Notation3.html
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16
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17 ``Formula-aware``: An RDF store capable of distinguishing between statements
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18 that are asserted and statements that are quoted is considered formula-aware.
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19
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20 ``Transaction-capable``: capable of providing transactional integrity to the
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21 RDF operations performed on it.
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22
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23 ``Graph-aware``: capable of keeping track of empty graphs.
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24
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25 ------
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26 """
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27
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28 # Constants representing the state of a Store (returned by the open method)
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29 VALID_STORE = 1
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30 CORRUPTED_STORE = 0
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31 NO_STORE = -1
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32 UNKNOWN = None
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33
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34 from rdflib.events import Dispatcher, Event
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35
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36 __all__ = ['StoreCreatedEvent', 'TripleAddedEvent', 'TripleRemovedEvent',
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37 'NodePickler', 'Store']
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38
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39
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40 class StoreCreatedEvent(Event):
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41 """
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42 This event is fired when the Store is created, it has the following
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43 attribute:
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44
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45 - ``configuration``: string used to create the store
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46
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47 """
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48
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49
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50 class TripleAddedEvent(Event):
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51 """
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52 This event is fired when a triple is added, it has the following
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53 attributes:
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54
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55 - the ``triple`` added to the graph
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56 - the ``context`` of the triple, if any
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57 - the ``graph`` to which the triple was added
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58 """
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59
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60
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61 class TripleRemovedEvent(Event):
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62 """
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63 This event is fired when a triple is removed, it has the following
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64 attributes:
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65
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66 - the ``triple`` removed from the graph
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67 - the ``context`` of the triple, if any
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68 - the ``graph`` from which the triple was removed
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69 """
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70
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71 from pickle import Pickler, Unpickler, UnpicklingError
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72 try:
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73 from io import BytesIO
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74 assert BytesIO
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75 except ImportError:
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76 from io import StringIO as BytesIO
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77
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78
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79 class NodePickler(object):
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80 def __init__(self):
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81 self._objects = {}
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82 self._ids = {}
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83 self._get_object = self._objects.__getitem__
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84
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85 def _get_ids(self, key):
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86 try:
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87 return self._ids.get(key)
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88 except TypeError:
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89 return None
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90
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91 def register(self, object, id):
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92 self._objects[id] = object
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93 self._ids[object] = id
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94
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95 def loads(self, s):
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96 up = Unpickler(BytesIO(s))
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97 up.persistent_load = self._get_object
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98 try:
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99 return up.load()
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100 except KeyError as e:
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101 raise UnpicklingError("Could not find Node class for %s" % e)
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102
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103 def dumps(self, obj, protocol=None, bin=None):
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104 src = BytesIO()
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105 p = Pickler(src)
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106 p.persistent_id = self._get_ids
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107 p.dump(obj)
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108 return src.getvalue()
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109
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110 def __getstate__(self):
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111 state = self.__dict__.copy()
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112 del state['_get_object']
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113 state.update({
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114 '_ids': tuple(self._ids.items()),
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115 '_objects': tuple(self._objects.items())
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116 })
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117 return state
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118
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119 def __setstate__(self, state):
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120 self.__dict__.update(state)
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121 self._ids = dict(self._ids)
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122 self._objects = dict(self._objects)
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123 self._get_object = self._objects.__getitem__
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124
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125
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126 class Store(object):
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127 # Properties
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128 context_aware = False
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129 formula_aware = False
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130 transaction_aware = False
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131 graph_aware = False
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132
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133 def __init__(self, configuration=None, identifier=None):
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134 """
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135 identifier: URIRef of the Store. Defaults to CWD
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136 configuration: string containing infomation open can use to
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137 connect to datastore.
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138 """
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139 self.__node_pickler = None
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140 self.dispatcher = Dispatcher()
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141 if configuration:
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142 self.open(configuration)
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143
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144 def __get_node_pickler(self):
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145 if self.__node_pickler is None:
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146 from rdflib.term import URIRef
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147 from rdflib.term import BNode
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148 from rdflib.term import Literal
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149 from rdflib.graph import Graph, QuotedGraph
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150 from rdflib.term import Variable
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151 from rdflib.term import Statement
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152 self.__node_pickler = np = NodePickler()
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153 np.register(self, "S")
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154 np.register(URIRef, "U")
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155 np.register(BNode, "B")
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156 np.register(Literal, "L")
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157 np.register(Graph, "G")
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158 np.register(QuotedGraph, "Q")
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159 np.register(Variable, "V")
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160 np.register(Statement, "s")
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161 return self.__node_pickler
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162 node_pickler = property(__get_node_pickler)
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163
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164 # Database management methods
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165 def create(self, configuration):
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166 self.dispatcher.dispatch(
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167 StoreCreatedEvent(configuration=configuration))
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168
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169 def open(self, configuration, create=False):
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170 """
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171 Opens the store specified by the configuration string. If
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172 create is True a store will be created if it does not already
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173 exist. If create is False and a store does not already exist
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174 an exception is raised. An exception is also raised if a store
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175 exists, but there is insufficient permissions to open the
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176 store. This should return one of:
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177 VALID_STORE, CORRUPTED_STORE, or NO_STORE
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178 """
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179 return UNKNOWN
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180
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181 def close(self, commit_pending_transaction=False):
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182 """
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183 This closes the database connection. The commit_pending_transaction
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184 parameter specifies whether to commit all pending transactions before
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185 closing (if the store is transactional).
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186 """
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187
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188 def destroy(self, configuration):
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189 """
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190 This destroys the instance of the store identified by the
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191 configuration string.
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192 """
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193
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194 def gc(self):
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195 """
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196 Allows the store to perform any needed garbage collection
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197 """
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198 pass
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199
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200 # RDF APIs
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201 def add(self, xxx_todo_changeme, context, quoted=False):
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202 """
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203 Adds the given statement to a specific context or to the model. The
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204 quoted argument is interpreted by formula-aware stores to indicate
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205 this statement is quoted/hypothetical It should be an error to not
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206 specify a context and have the quoted argument be True. It should also
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207 be an error for the quoted argument to be True when the store is not
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208 formula-aware.
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209 """
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210 (subject, predicate, object) = xxx_todo_changeme
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211 self.dispatcher.dispatch(
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212 TripleAddedEvent(
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213 triple=(subject, predicate, object), context=context))
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214
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215 def addN(self, quads):
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216 """
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217 Adds each item in the list of statements to a specific context. The
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218 quoted argument is interpreted by formula-aware stores to indicate this
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219 statement is quoted/hypothetical. Note that the default implementation
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220 is a redirect to add
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221 """
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222 for s, p, o, c in quads:
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223 assert c is not None, \
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224 "Context associated with %s %s %s is None!" % (s, p, o)
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225 self.add((s, p, o), c)
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226
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227 def remove(self, xxx_todo_changeme1, context=None):
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228 """ Remove the set of triples matching the pattern from the store """
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229 (subject, predicate, object) = xxx_todo_changeme1
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230 self.dispatcher.dispatch(
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231 TripleRemovedEvent(
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232 triple=(subject, predicate, object), context=context))
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233
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234 def triples_choices(self, xxx_todo_changeme2, context=None):
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235 """
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236 A variant of triples that can take a list of terms instead of a single
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237 term in any slot. Stores can implement this to optimize the response
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238 time from the default 'fallback' implementation, which will iterate
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239 over each term in the list and dispatch to triples
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240 """
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241 (subject, predicate, object_) = xxx_todo_changeme2
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242 if isinstance(object_, list):
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243 assert not isinstance(
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244 subject, list), "object_ / subject are both lists"
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245 assert not isinstance(
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246 predicate, list), "object_ / predicate are both lists"
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247 if object_:
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248 for obj in object_:
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249 for (s1, p1, o1), cg in self.triples(
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250 (subject, predicate, obj), context):
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251 yield (s1, p1, o1), cg
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252 else:
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253 for (s1, p1, o1), cg in self.triples(
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254 (subject, predicate, None), context):
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255 yield (s1, p1, o1), cg
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256
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257 elif isinstance(subject, list):
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258 assert not isinstance(
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259 predicate, list), "subject / predicate are both lists"
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260 if subject:
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261 for subj in subject:
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262 for (s1, p1, o1), cg in self.triples(
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263 (subj, predicate, object_), context):
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264 yield (s1, p1, o1), cg
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265 else:
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266 for (s1, p1, o1), cg in self.triples(
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267 (None, predicate, object_), context):
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268 yield (s1, p1, o1), cg
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269
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270 elif isinstance(predicate, list):
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271 assert not isinstance(
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272 subject, list), "predicate / subject are both lists"
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273 if predicate:
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274 for pred in predicate:
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275 for (s1, p1, o1), cg in self.triples(
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276 (subject, pred, object_), context):
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277 yield (s1, p1, o1), cg
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278 else:
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279 for (s1, p1, o1), cg in self.triples(
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280 (subject, None, object_), context):
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281 yield (s1, p1, o1), cg
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282
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283 def triples(self, triple_pattern, context=None):
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284 """
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285 A generator over all the triples matching the pattern. Pattern can
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286 include any objects for used for comparing against nodes in the store,
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287 for example, REGEXTerm, URIRef, Literal, BNode, Variable, Graph,
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288 QuotedGraph, Date? DateRange?
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289
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290 :param context: A conjunctive query can be indicated by either
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291 providing a value of None, or a specific context can be
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292 queries by passing a Graph instance (if store is context aware).
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293 """
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294 subject, predicate, object = triple_pattern
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295
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296 # variants of triples will be done if / when optimization is needed
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297
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298 def __len__(self, context=None):
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299 """
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300 Number of statements in the store. This should only account for non-
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301 quoted (asserted) statements if the context is not specified,
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302 otherwise it should return the number of statements in the formula or
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303 context given.
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304
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305 :param context: a graph instance to query or None
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306 """
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307
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308 def contexts(self, triple=None):
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309 """
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310 Generator over all contexts in the graph. If triple is specified,
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311 a generator over all contexts the triple is in.
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312
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313 if store is graph_aware, may also return empty contexts
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314
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315 :returns: a generator over Nodes
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316 """
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317
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318 def query(self, query, initNs, initBindings, queryGraph, **kwargs):
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319 """
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320 If stores provide their own SPARQL implementation, override this.
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321
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322 queryGraph is None, a URIRef or '__UNION__'
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323 If None the graph is specified in the query-string/object
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324 If URIRef it specifies the graph to query,
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325 If '__UNION__' the union of all named graphs should be queried
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326 (This is used by ConjunctiveGraphs
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327 Values other than None obviously only makes sense for
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328 context-aware stores.)
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329
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330 """
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331
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332 raise NotImplementedError
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333
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334 def update(self, update, initNs, initBindings, queryGraph, **kwargs):
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335 """
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336 If stores provide their own (SPARQL) Update implementation,
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337 override this.
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338
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339 queryGraph is None, a URIRef or '__UNION__'
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340 If None the graph is specified in the query-string/object
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341 If URIRef it specifies the graph to query,
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342 If '__UNION__' the union of all named graphs should be queried
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343 (This is used by ConjunctiveGraphs
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344 Values other than None obviously only makes sense for
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345 context-aware stores.)
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346
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347 """
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348
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349 raise NotImplementedError
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350
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351 # Optional Namespace methods
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352
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353 def bind(self, prefix, namespace):
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354 """ """
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355
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356 def prefix(self, namespace):
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357 """ """
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358
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359 def namespace(self, prefix):
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360 """ """
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361
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362 def namespaces(self):
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363 """ """
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364 if False:
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365 yield None
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366
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367 # Optional Transactional methods
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368
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369 def commit(self):
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370 """ """
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371
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372 def rollback(self):
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373 """ """
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374
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375 # Optional graph methods
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376
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377 def add_graph(self, graph):
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378 """
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379 Add a graph to the store, no effect if the graph already
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380 exists.
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381 :param graph: a Graph instance
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382 """
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383 raise Exception("Graph method called on non-graph_aware store")
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384
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385 def remove_graph(self, graph):
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386 """
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387 Remove a graph from the store, this shoud also remove all
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388 triples in the graph
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389
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390 :param graphid: a Graph instance
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391 """
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392 raise Exception("Graph method called on non-graph_aware store")