Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/collection.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 from rdflib.namespace import RDF
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2 from rdflib.term import BNode
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3 from rdflib.term import Literal
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4 from rdflib.py3compat import format_doctest_out
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5
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6 __all__ = ['Collection']
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7
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8
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9 class Collection(object):
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10 __doc__ = format_doctest_out("""
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11 See "Emulating container types":
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12 https://docs.python.org/reference/datamodel.html#emulating-container-types
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13
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14 >>> from rdflib.graph import Graph
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15 >>> from pprint import pprint
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16 >>> listName = BNode()
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17 >>> g = Graph('IOMemory')
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18 >>> listItem1 = BNode()
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19 >>> listItem2 = BNode()
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20 >>> g.add((listName, RDF.first, Literal(1)))
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21 >>> g.add((listName, RDF.rest, listItem1))
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22 >>> g.add((listItem1, RDF.first, Literal(2)))
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23 >>> g.add((listItem1, RDF.rest, listItem2))
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24 >>> g.add((listItem2, RDF.rest, RDF.nil))
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25 >>> g.add((listItem2, RDF.first, Literal(3)))
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26 >>> c = Collection(g,listName)
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27 >>> pprint([term.n3() for term in c])
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28 [%(u)s'"1"^^<http://www.w3.org/2001/XMLSchema#integer>',
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29 %(u)s'"2"^^<http://www.w3.org/2001/XMLSchema#integer>',
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30 %(u)s'"3"^^<http://www.w3.org/2001/XMLSchema#integer>']
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31
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32 >>> Literal(1) in c
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33 True
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34 >>> len(c)
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35 3
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36 >>> c._get_container(1) == listItem1
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37 True
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38 >>> c.index(Literal(2)) == 1
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39 True
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40 """)
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41
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42 def __init__(self, graph, uri, seq=[]):
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43 self.graph = graph
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44 self.uri = uri or BNode()
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45 self += seq
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46
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47 def n3(self):
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48 """
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49 >>> from rdflib.graph import Graph
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50 >>> listName = BNode()
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51 >>> g = Graph('IOMemory')
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52 >>> listItem1 = BNode()
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53 >>> listItem2 = BNode()
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54 >>> g.add((listName, RDF.first, Literal(1)))
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55 >>> g.add((listName, RDF.rest, listItem1))
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56 >>> g.add((listItem1, RDF.first, Literal(2)))
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57 >>> g.add((listItem1, RDF.rest, listItem2))
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58 >>> g.add((listItem2, RDF.rest, RDF.nil))
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59 >>> g.add((listItem2, RDF.first, Literal(3)))
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60 >>> c = Collection(g, listName)
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61 >>> print(c.n3()) #doctest: +NORMALIZE_WHITESPACE
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62 ( "1"^^<http://www.w3.org/2001/XMLSchema#integer>
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63 "2"^^<http://www.w3.org/2001/XMLSchema#integer>
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64 "3"^^<http://www.w3.org/2001/XMLSchema#integer> )
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65 """
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66 return "( %s )" % (' '.join([i.n3() for i in self]))
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67
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68 def _get_container(self, index):
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69 """Gets the first, rest holding node at index."""
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70 assert isinstance(index, int)
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71 graph = self.graph
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72 container = self.uri
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73 i = 0
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74 while i < index:
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75 i += 1
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76 container = graph.value(container, RDF.rest)
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77 if container is None:
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78 break
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79 return container
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80
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81 def __len__(self):
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82 """length of items in collection."""
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83 return len(list(self.graph.items(self.uri)))
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84
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85 def index(self, item):
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86 """
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87 Returns the 0-based numerical index of the item in the list
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88 """
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89 listName = self.uri
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90 index = 0
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91 while True:
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92 if (listName, RDF.first, item) in self.graph:
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93 return index
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94 else:
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95 newLink = list(self.graph.objects(listName, RDF.rest))
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96 index += 1
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97 if newLink == [RDF.nil]:
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98 raise ValueError("%s is not in %s" % (item, self.uri))
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99 elif not newLink:
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100 raise Exception("Malformed RDF Collection: %s" % self.uri)
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101 else:
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102 assert len(newLink) == 1, \
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103 "Malformed RDF Collection: %s" % self.uri
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104 listName = newLink[0]
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105
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106 def __getitem__(self, key):
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107 """TODO"""
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108 c = self._get_container(key)
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109 if c:
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110 v = self.graph.value(c, RDF.first)
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111 if v:
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112 return v
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113 else:
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114 raise KeyError(key)
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115 else:
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116 raise IndexError(key)
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117
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118 def __setitem__(self, key, value):
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119 """TODO"""
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120 c = self._get_container(key)
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121 if c:
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122 self.graph.set((c, RDF.first, value))
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123 else:
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124 raise IndexError(key)
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125
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126 def __delitem__(self, key):
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127 """
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128 >>> from rdflib.namespace import RDF, RDFS
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129 >>> from rdflib import Graph
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130 >>> from pprint import pformat
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131 >>> g = Graph()
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132 >>> a = BNode('foo')
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133 >>> b = BNode('bar')
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134 >>> c = BNode('baz')
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135 >>> g.add((a, RDF.first, RDF.type))
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136 >>> g.add((a, RDF.rest, b))
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137 >>> g.add((b, RDF.first, RDFS.label))
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138 >>> g.add((b, RDF.rest, c))
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139 >>> g.add((c, RDF.first, RDFS.comment))
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140 >>> g.add((c, RDF.rest, RDF.nil))
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141 >>> len(g)
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142 6
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143 >>> def listAncestry(node, graph):
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144 ... for i in graph.subjects(RDF.rest, node):
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145 ... yield i
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146 >>> [str(node.n3())
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147 ... for node in g.transitiveClosure(listAncestry, RDF.nil)]
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148 ['_:baz', '_:bar', '_:foo']
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149 >>> lst = Collection(g, a)
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150 >>> len(lst)
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151 3
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152 >>> b == lst._get_container(1)
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153 True
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154 >>> c == lst._get_container(2)
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155 True
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156 >>> del lst[1]
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157 >>> len(lst)
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158 2
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159 >>> len(g)
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160 4
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161
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162 """
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163 self[key] # to raise any potential key exceptions
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164 graph = self.graph
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165 current = self._get_container(key)
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166 assert current
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167 if len(self) == 1 and key > 0:
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168 pass
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169 elif key == len(self) - 1:
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170 # the tail
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171 priorLink = self._get_container(key - 1)
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172 self.graph.set((priorLink, RDF.rest, RDF.nil))
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173 graph.remove((current, None, None))
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174 else:
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175 next = self._get_container(key + 1)
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176 prior = self._get_container(key - 1)
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177 assert next and prior
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178 graph.remove((current, None, None))
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179 graph.set((prior, RDF.rest, next))
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180
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181 def __iter__(self):
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182 """Iterator over items in Collections"""
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183 return self.graph.items(self.uri)
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184
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185 def _end(self):
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186 # find end of list
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187 container = self.uri
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188 while True:
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189 rest = self.graph.value(container, RDF.rest)
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190 if rest == None or rest == RDF.nil:
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191 return container
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192 else:
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193 container = rest
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194
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195 def append(self, item):
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196 """
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197 >>> from rdflib.graph import Graph
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198 >>> listName = BNode()
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199 >>> g = Graph()
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200 >>> c = Collection(g,listName,[Literal(1),Literal(2)])
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201 >>> links = [
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202 ... list(g.subjects(object=i, predicate=RDF.first))[0] for i in c]
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203 >>> len([i for i in links if (i, RDF.rest, RDF.nil) in g])
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204 1
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205
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206 """
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207
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208 end = self._end()
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209 if (end, RDF.first, None) in self.graph:
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210 # append new node to the end of the linked list
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211 node = BNode()
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212 self.graph.set((end, RDF.rest, node))
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213 end = node
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214
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215 self.graph.add((end, RDF.first, item))
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216 self.graph.add((end, RDF.rest, RDF.nil))
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217
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218 def __iadd__(self, other):
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219
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220 end = self._end()
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221 self.graph.remove((end, RDF.rest, None))
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222
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223 for item in other:
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224 if (end, RDF.first, None) in self.graph:
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225 nxt = BNode()
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226 self.graph.add((end, RDF.rest, nxt))
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227 end = nxt
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228
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229 self.graph.add((end, RDF.first, item))
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230
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231
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232 self.graph.add((end, RDF.rest, RDF.nil))
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233
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234 def clear(self):
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235 container = self.uri
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236 graph = self.graph
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237 while container:
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238 rest = graph.value(container, RDF.rest)
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239 graph.remove((container, RDF.first, None))
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240 graph.remove((container, RDF.rest, None))
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241 container = rest
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242
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243
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244 def test():
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245 import doctest
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246 doctest.testmod()
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247
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248 if __name__ == "__main__":
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249 test()
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250
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251 from rdflib import Graph
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252 g = Graph()
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253
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254 c = Collection(g, BNode())
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255
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256 assert len(c) == 0
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257
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258 c = Collection(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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259 g, BNode(), [Literal("1"), Literal("2"), Literal("3"), Literal("4")])
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260
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261 assert len(c) == 4
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262
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263 assert c[1] == Literal("2"), c[1]
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264
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265 del c[1]
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266
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267 assert list(c) == [Literal("1"), Literal("3"), Literal("4")], list(c)
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268
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269 try:
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270 del c[500]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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271 except IndexError as i:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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272 pass
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273
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274 c.append(Literal("5"))
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275
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276 print((list(c)))
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277
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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278 for i in c:
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279 print(i)
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280
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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281 del c[3]
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282
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283 c.clear()
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284
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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285 assert len(c) == 0