Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/plugins/serializers/turtle.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 """
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2 Turtle RDF graph serializer for RDFLib.
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3 See <http://www.w3.org/TeamSubmission/turtle/> for syntax specification.
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4 """
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5
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6 from collections import defaultdict
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7
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8 from rdflib.compat import cmp_to_key
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9 from rdflib.term import BNode, Literal, URIRef
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10 from rdflib.exceptions import Error
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11 from rdflib.serializer import Serializer
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12 from rdflib.namespace import RDF, RDFS
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13
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14 __all__ = ['RecursiveSerializer', 'TurtleSerializer']
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15
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16 def _object_comparator(a,b):
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17 """
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18 for nice clean output we sort the objects of triples,
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19 some of them are literals,
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20 these are sorted according to the sort order of the underlying python objects
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21 in py3 not all things are comparable.
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22 This falls back on comparing string representations when not.
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23 """
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24
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25 try:
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26 if a>b: return 1
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27 if a<b: return -1
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28 return 0
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29
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30 except TypeError:
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31 a = str(a)
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32 b = str(b)
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33 return (a > b) - (a < b)
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34
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35
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36 class RecursiveSerializer(Serializer):
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37
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38 topClasses = [RDFS.Class]
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39 predicateOrder = [RDF.type, RDFS.label]
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40 maxDepth = 10
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41 indentString = " "
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42
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43 def __init__(self, store):
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44
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45 super(RecursiveSerializer, self).__init__(store)
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46 self.stream = None
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47 self.reset()
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48
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49 def addNamespace(self, prefix, uri):
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50 if prefix in self.namespaces and self.namespaces[prefix]!=uri:
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51 raise Exception("Trying to override namespace prefix %s => %s, but it's already bound to %s"%(prefix, uri, self.namespaces[prefix]))
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52 self.namespaces[prefix] = uri
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53
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54 def checkSubject(self, subject):
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55 """Check to see if the subject should be serialized yet"""
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56 if ((self.isDone(subject))
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57 or (subject not in self._subjects)
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58 or ((subject in self._topLevels) and (self.depth > 1))
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59 or (isinstance(subject, URIRef)
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60 and (self.depth >= self.maxDepth))):
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61 return False
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62 return True
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63
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64 def isDone(self, subject):
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65 """Return true if subject is serialized"""
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66 return subject in self._serialized
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67
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68 def orderSubjects(self):
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69 seen = {}
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70 subjects = []
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71
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72 for classURI in self.topClasses:
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73 members = list(self.store.subjects(RDF.type, classURI))
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74 members.sort()
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75
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76 for member in members:
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77 subjects.append(member)
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78 self._topLevels[member] = True
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79 seen[member] = True
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80
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81 recursable = [
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82 (isinstance(subject, BNode),
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83 self._references[subject], subject)
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84 for subject in self._subjects if subject not in seen]
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85
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86 recursable.sort()
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87 subjects.extend([subject for (isbnode, refs, subject) in recursable])
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88
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89 return subjects
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90
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91 def preprocess(self):
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92 for triple in self.store.triples((None, None, None)):
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93 self.preprocessTriple(triple)
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94
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95 def preprocessTriple(self, xxx_todo_changeme):
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96 (s, p, o) = xxx_todo_changeme
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97 self._references[o]+=1
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98 self._subjects[s] = True
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99
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100 def reset(self):
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101 self.depth = 0
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102 self.lists = {}
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103 self.namespaces = {}
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104 self._references = defaultdict(int)
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105 self._serialized = {}
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106 self._subjects = {}
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107 self._topLevels = {}
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108
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109 for prefix, ns in self.store.namespaces():
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110 self.addNamespace(prefix, ns)
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111
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112 def buildPredicateHash(self, subject):
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113 """
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114 Build a hash key by predicate to a list of objects for the given
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115 subject
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116 """
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117 properties = {}
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118 for s, p, o in self.store.triples((subject, None, None)):
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119 oList = properties.get(p, [])
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120 oList.append(o)
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121 properties[p] = oList
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122 return properties
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123
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124 def sortProperties(self, properties):
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125 """Take a hash from predicate uris to lists of values.
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126 Sort the lists of values. Return a sorted list of properties."""
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127 # Sort object lists
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128 for prop, objects in list(properties.items()):
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129 objects.sort(key=cmp_to_key(_object_comparator))
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130
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131 # Make sorted list of properties
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132 propList = []
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133 seen = {}
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134 for prop in self.predicateOrder:
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135 if (prop in properties) and (prop not in seen):
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136 propList.append(prop)
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137 seen[prop] = True
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138 props = list(properties.keys())
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139 props.sort()
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140 for prop in props:
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141 if prop not in seen:
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142 propList.append(prop)
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143 seen[prop] = True
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144 return propList
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145
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146 def subjectDone(self, subject):
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147 """Mark a subject as done."""
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148 self._serialized[subject] = True
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149
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150 def indent(self, modifier=0):
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151 """Returns indent string multiplied by the depth"""
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152 return (self.depth + modifier) * self.indentString
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153
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154 def write(self, text):
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155 """Write text in given encoding."""
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156 self.stream.write(text.encode(self.encoding, 'replace'))
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157
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158
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159 SUBJECT = 0
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160 VERB = 1
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161 OBJECT = 2
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162
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163 _GEN_QNAME_FOR_DT = False
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164 _SPACIOUS_OUTPUT = False
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165
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166
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167 class TurtleSerializer(RecursiveSerializer):
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168
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169 short_name = "turtle"
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170 indentString = ' '
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171
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172 def __init__(self, store):
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173 self._ns_rewrite = {}
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174 super(TurtleSerializer, self).__init__(store)
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175 self.keywords = {
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176 RDF.type: 'a'
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177 }
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178 self.reset()
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179 self.stream = None
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180 self._spacious = _SPACIOUS_OUTPUT
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181
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182 def addNamespace(self, prefix, namespace):
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183 # Turtle does not support prefix that start with _
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184 # if they occur in the graph, rewrite to p_blah
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185 # this is more complicated since we need to make sure p_blah
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186 # does not already exist. And we register namespaces as we go, i.e.
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187 # we may first see a triple with prefix _9 - rewrite it to p_9
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188 # and then later find a triple with a "real" p_9 prefix
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189
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190 # so we need to keep track of ns rewrites we made so far.
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191
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192 if (prefix > '' and prefix[0] == '_') \
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193 or self.namespaces.get(prefix, namespace) != namespace:
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194
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195 if prefix not in self._ns_rewrite:
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196 p = "p" + prefix
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197 while p in self.namespaces:
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198 p = "p" + p
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199 self._ns_rewrite[prefix] = p
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200
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201 prefix = self._ns_rewrite.get(prefix, prefix)
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202
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203 super(TurtleSerializer, self).addNamespace(prefix, namespace)
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204 return prefix
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205
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206 def reset(self):
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207 super(TurtleSerializer, self).reset()
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208 self._shortNames = {}
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209 self._started = False
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210 self._ns_rewrite = {}
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211
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212 def serialize(self, stream, base=None, encoding=None,
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213 spacious=None, **args):
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214 self.reset()
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215 self.stream = stream
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216 self.base = base
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217
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218 if spacious is not None:
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219 self._spacious = spacious
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220
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221 self.preprocess()
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222 subjects_list = self.orderSubjects()
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223
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224 self.startDocument()
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225
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226 firstTime = True
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227 for subject in subjects_list:
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228 if self.isDone(subject):
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229 continue
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230 if firstTime:
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231 firstTime = False
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232 if self.statement(subject) and not firstTime:
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233 self.write('\n')
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234
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235 self.endDocument()
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236 stream.write("\n".encode('ascii'))
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237
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238 def preprocessTriple(self, triple):
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239 super(TurtleSerializer, self).preprocessTriple(triple)
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240 for i, node in enumerate(triple):
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241 if node in self.keywords:
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242 continue
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243 # Don't use generated prefixes for subjects and objects
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244 self.getQName(node, gen_prefix=(i == VERB))
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245 if isinstance(node, Literal) and node.datatype:
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246 self.getQName(node.datatype, gen_prefix=_GEN_QNAME_FOR_DT)
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247 p = triple[1]
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248 if isinstance(p, BNode): # hmm - when is P ever a bnode?
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249 self._references[p]+=1
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250
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251 def getQName(self, uri, gen_prefix=True):
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252 if not isinstance(uri, URIRef):
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253 return None
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254
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255 parts = None
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256
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257 try:
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258 parts = self.store.compute_qname(uri, generate=gen_prefix)
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259 except:
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260
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261 # is the uri a namespace in itself?
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262 pfx = self.store.store.prefix(uri)
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263
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264 if pfx is not None:
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265 parts = (pfx, uri, '')
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266 else:
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267 # nothing worked
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268 return None
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269
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270 prefix, namespace, local = parts
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271
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272 # QName cannot end with .
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273 if local.endswith("."): return None
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274
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275 prefix = self.addNamespace(prefix, namespace)
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276
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277 return '%s:%s' % (prefix, local)
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278
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279 def startDocument(self):
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280 self._started = True
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281 ns_list = sorted(self.namespaces.items())
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282 for prefix, uri in ns_list:
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283 self.write(self.indent() + '@prefix %s: <%s> .\n' % (prefix, uri))
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284 if ns_list and self._spacious:
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285 self.write('\n')
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286
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287 def endDocument(self):
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288 if self._spacious:
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289 self.write('\n')
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290
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291 def statement(self, subject):
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292 self.subjectDone(subject)
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293 return self.s_squared(subject) or self.s_default(subject)
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294
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295 def s_default(self, subject):
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296 self.write('\n' + self.indent())
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297 self.path(subject, SUBJECT)
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298 self.predicateList(subject)
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299 self.write(' .')
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300 return True
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301
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302 def s_squared(self, subject):
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303 if (self._references[subject] > 0) or not isinstance(subject, BNode):
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304 return False
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305 self.write('\n' + self.indent() + '[]')
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306 self.predicateList(subject)
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307 self.write(' .')
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308 return True
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309
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310 def path(self, node, position, newline=False):
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311 if not (self.p_squared(node, position, newline)
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312 or self.p_default(node, position, newline)):
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313 raise Error("Cannot serialize node '%s'" % (node, ))
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314
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315 def p_default(self, node, position, newline=False):
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316 if position != SUBJECT and not newline:
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317 self.write(' ')
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318 self.write(self.label(node, position))
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319 return True
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320
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321 def label(self, node, position):
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322 if node == RDF.nil:
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323 return '()'
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324 if position is VERB and node in self.keywords:
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325 return self.keywords[node]
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326 if isinstance(node, Literal):
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327 return node._literal_n3(
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328 use_plain=True,
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329 qname_callback=lambda dt: self.getQName(
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parents:
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330 dt, _GEN_QNAME_FOR_DT))
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331 else:
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332 node = self.relativize(node)
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333
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parents:
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334 return self.getQName(node, position == VERB) or node.n3()
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parents:
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335
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parents:
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336 def p_squared(self, node, position, newline=False):
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337 if (not isinstance(node, BNode)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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338 or node in self._serialized
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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339 or self._references[node] > 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
340 or position == SUBJECT):
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341 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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342
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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343 if not newline:
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344 self.write(' ')
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345
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parents:
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346 if self.isValidList(node):
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parents:
diff changeset
347 # this is a list
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diff changeset
348 self.write('(')
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parents:
diff changeset
349 self.depth += 1 # 2
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parents:
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350 self.doList(node)
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parents:
diff changeset
351 self.depth -= 1 # 2
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parents:
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352 self.write(' )')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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353 else:
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parents:
diff changeset
354 self.subjectDone(node)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
355 self.depth += 2
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parents:
diff changeset
356 # self.write('[\n' + self.indent())
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parents:
diff changeset
357 self.write('[')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
358 self.depth -= 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
359 # self.predicateList(node, newline=True)
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parents:
diff changeset
360 self.predicateList(node, newline=False)
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parents:
diff changeset
361 # self.write('\n' + self.indent() + ']')
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parents:
diff changeset
362 self.write(' ]')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
363 self.depth -= 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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364
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
365 return True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
366
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parents:
diff changeset
367 def isValidList(self, l):
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parents:
diff changeset
368 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
369 Checks if l is a valid RDF list, i.e. no nodes have other properties.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
370 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
371 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
372 if self.store.value(l, RDF.first) is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
373 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
374 except:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
375 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
376 while l:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
377 if l != RDF.nil and len(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
378 list(self.store.predicate_objects(l))) != 2:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
379 return False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
380 l = self.store.value(l, RDF.rest)
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parents:
diff changeset
381 return True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
382
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
383 def doList(self, l):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
384 while l:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
385 item = self.store.value(l, RDF.first)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
386 if item is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
387 self.path(item, OBJECT)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
388 self.subjectDone(l)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
389 l = self.store.value(l, RDF.rest)
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shellac
parents:
diff changeset
390
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
391 def predicateList(self, subject, newline=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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392 properties = self.buildPredicateHash(subject)
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393 propList = self.sortProperties(properties)
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394 if len(propList) == 0:
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395 return
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396 self.verb(propList[0], newline=newline)
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397 self.objectList(properties[propList[0]])
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398 for predicate in propList[1:]:
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399 self.write(' ;\n' + self.indent(1))
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400 self.verb(predicate, newline=True)
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401 self.objectList(properties[predicate])
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402
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403 def verb(self, node, newline=False):
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404 self.path(node, VERB, newline)
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405
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406 def objectList(self, objects):
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407 count = len(objects)
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408 if count == 0:
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409 return
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410 depthmod = (count == 1) and 0 or 1
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411 self.depth += depthmod
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412 self.path(objects[0], OBJECT)
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413 for obj in objects[1:]:
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414 self.write(',\n' + self.indent(1))
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415 self.path(obj, OBJECT, newline=True)
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416 self.depth -= depthmod