Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/plugins/serializers/rdfxml.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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 from rdflib.plugins.serializers.xmlwriter import XMLWriter
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2
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3 from rdflib.namespace import Namespace, RDF, RDFS # , split_uri
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4
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5 from rdflib.term import URIRef, Literal, BNode
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6 from rdflib.util import first, more_than
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7 from rdflib.collection import Collection
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8 from rdflib.serializer import Serializer
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9
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10 # from rdflib.exceptions import Error
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11
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12 from rdflib.py3compat import b
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13
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14 from xml.sax.saxutils import quoteattr, escape
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15 import xml.dom.minidom
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16
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17 from .xmlwriter import ESCAPE_ENTITIES
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18
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19 __all__ = ['fix', 'XMLSerializer', 'PrettyXMLSerializer']
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20
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21
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22 class XMLSerializer(Serializer):
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23
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24 def __init__(self, store):
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25 super(XMLSerializer, self).__init__(store)
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26
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27 def __bindings(self):
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28 store = self.store
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29 nm = store.namespace_manager
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30 bindings = {}
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31
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32 for predicate in set(store.predicates()):
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33 prefix, namespace, name = nm.compute_qname(predicate)
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34 bindings[prefix] = URIRef(namespace)
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35
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36 RDFNS = URIRef("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
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37
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38 if "rdf" in bindings:
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39 assert bindings["rdf"] == RDFNS
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40 else:
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41 bindings["rdf"] = RDFNS
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42
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43 for prefix, namespace in bindings.items():
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44 yield prefix, namespace
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45
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46 def serialize(self, stream, base=None, encoding=None, **args):
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47 self.base = base
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48 self.__stream = stream
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49 self.__serialized = {}
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50 encoding = self.encoding
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51 self.write = write = lambda uni: stream.write(
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52 uni.encode(encoding, 'replace'))
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53
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54 # startDocument
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55 write('<?xml version="1.0" encoding="%s"?>\n' % self.encoding)
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56
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57 # startRDF
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58 write('<rdf:RDF\n')
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59
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60 # If provided, write xml:base attribute for the RDF
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61 if "xml_base" in args:
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62 write(' xml:base="%s"\n' % args['xml_base'])
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63 # TODO:
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64 # assert(
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65 # namespaces["http://www.w3.org/1999/02/22-rdf-syntax-ns#"]=='rdf')
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66 bindings = list(self.__bindings())
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67 bindings.sort()
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68
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69 for prefix, namespace in bindings:
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70 if prefix:
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71 write(' xmlns:%s="%s"\n' % (prefix, namespace))
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72 else:
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73 write(' xmlns="%s"\n' % namespace)
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74 write('>\n')
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75
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76 # write out triples by subject
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77 for subject in self.store.subjects():
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78 self.subject(subject, 1)
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79
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80 # endRDF
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81 write("</rdf:RDF>\n")
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82
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83 # Set to None so that the memory can get garbage collected.
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84 # self.__serialized = None
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85 del self.__serialized
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86
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87 def subject(self, subject, depth=1):
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88 if not subject in self.__serialized:
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89 self.__serialized[subject] = 1
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90
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91 if isinstance(subject, (BNode, URIRef)):
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92 write = self.write
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93 indent = " " * depth
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94 element_name = "rdf:Description"
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95
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96 if isinstance(subject, BNode):
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97 write('%s<%s rdf:nodeID="%s"' % (
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98 indent, element_name, subject))
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99 else:
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100 uri = quoteattr(self.relativize(subject))
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101 write("%s<%s rdf:about=%s" % (indent, element_name, uri))
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102
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103 if (subject, None, None) in self.store:
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104 write(">\n")
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105
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106 for predicate, object in self.store.predicate_objects(
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107 subject):
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108 self.predicate(predicate, object, depth + 1)
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109 write("%s</%s>\n" % (indent, element_name))
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110
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111 else:
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112 write("/>\n")
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113
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114 def predicate(self, predicate, object, depth=1):
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115 write = self.write
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116 indent = " " * depth
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117 qname = self.store.namespace_manager.qname(predicate)
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118
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119 if isinstance(object, Literal):
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120 attributes = ""
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121
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122 if object.language:
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123 attributes += ' xml:lang="%s"' % object.language
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124
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125 if object.datatype:
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126 attributes += ' rdf:datatype="%s"' % object.datatype
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127
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128 write("%s<%s%s>%s</%s>\n" %
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129 (indent, qname, attributes,
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130 escape(object, ESCAPE_ENTITIES), qname))
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131 else:
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132
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133 if isinstance(object, BNode):
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134 write('%s<%s rdf:nodeID="%s"/>\n' %
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135 (indent, qname, object))
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136 else:
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137 write("%s<%s rdf:resource=%s/>\n" %
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138 (indent, qname, quoteattr(self.relativize(object))))
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139
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140 XMLLANG = "http://www.w3.org/XML/1998/namespacelang"
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141 XMLBASE = "http://www.w3.org/XML/1998/namespacebase"
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142 OWL_NS = Namespace('http://www.w3.org/2002/07/owl#')
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143
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144
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145 # TODO:
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146 def fix(val):
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147 "strip off _: from nodeIDs... as they are not valid NCNames"
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148 if val.startswith("_:"):
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149 return val[2:]
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150 else:
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151 return val
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152
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153
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154 class PrettyXMLSerializer(Serializer):
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155
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156 def __init__(self, store, max_depth=3):
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157 super(PrettyXMLSerializer, self).__init__(store)
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158 self.forceRDFAbout = set()
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159
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160 def serialize(self, stream, base=None, encoding=None, **args):
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161 self.__serialized = {}
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162 store = self.store
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163 self.base = base
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164 self.max_depth = args.get("max_depth", 3)
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165 assert self.max_depth > 0, "max_depth must be greater than 0"
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166
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167 self.nm = nm = store.namespace_manager
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168 self.writer = writer = XMLWriter(stream, nm, encoding)
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169 namespaces = {}
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170
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171 possible = set(store.predicates()).union(
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172 store.objects(None, RDF.type))
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173
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174 for predicate in possible:
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175 prefix, namespace, local = nm.compute_qname(predicate)
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176 namespaces[prefix] = namespace
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177
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178 namespaces["rdf"] = "http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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179
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180 writer.push(RDF.RDF)
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181
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182 if "xml_base" in args:
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183 writer.attribute(XMLBASE, args["xml_base"])
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184
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185 writer.namespaces(iter(namespaces.items()))
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186
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187 # Write out subjects that can not be inline
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188 for subject in store.subjects():
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189 if (None, None, subject) in store:
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190 if (subject, None, subject) in store:
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191 self.subject(subject, 1)
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192 else:
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193 self.subject(subject, 1)
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194
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195 # write out anything that has not yet been reached
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196 # write out BNodes last (to ensure they can be inlined where possible)
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197 bnodes = set()
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198
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199 for subject in store.subjects():
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200 if isinstance(subject, BNode):
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201 bnodes.add(subject)
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202 continue
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203 self.subject(subject, 1)
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204
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205 # now serialize only those BNodes that have not been serialized yet
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206 for bnode in bnodes:
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207 if bnode not in self.__serialized:
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208 self.subject(subject, 1)
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209
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210 writer.pop(RDF.RDF)
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211 stream.write(b("\n"))
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212
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213 # Set to None so that the memory can get garbage collected.
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214 self.__serialized = None
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215
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216 def subject(self, subject, depth=1):
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217 store = self.store
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218 writer = self.writer
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219
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220 if subject in self.forceRDFAbout:
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221 writer.push(RDF.Description)
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222 writer.attribute(RDF.about, self.relativize(subject))
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223 writer.pop(RDF.Description)
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224 self.forceRDFAbout.remove(subject)
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225
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226 elif not subject in self.__serialized:
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227 self.__serialized[subject] = 1
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228 type = first(store.objects(subject, RDF.type))
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229
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230 try:
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231 self.nm.qname(type)
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232 except:
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233 type = None
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234
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235 element = type or RDF.Description
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236 writer.push(element)
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237
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238 if isinstance(subject, BNode):
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239 def subj_as_obj_more_than(ceil):
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240 return True
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241 # more_than(store.triples((None, None, subject)), ceil)
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242
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243 # here we only include BNode labels if they are referenced
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244 # more than once (this reduces the use of redundant BNode
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245 # identifiers)
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246 if subj_as_obj_more_than(1):
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247 writer.attribute(RDF.nodeID, fix(subject))
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248
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249 else:
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250 writer.attribute(RDF.about, self.relativize(subject))
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251
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252 if (subject, None, None) in store:
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253 for predicate, object in store.predicate_objects(subject):
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254 if not (predicate == RDF.type and object == type):
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255 self.predicate(predicate, object, depth + 1)
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256
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257 writer.pop(element)
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258
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259 elif subject in self.forceRDFAbout:
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260 writer.push(RDF.Description)
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261 writer.attribute(RDF.about, self.relativize(subject))
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262 writer.pop(RDF.Description)
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263 self.forceRDFAbout.remove(subject)
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264
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265 def predicate(self, predicate, object, depth=1):
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266 writer = self.writer
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267 store = self.store
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268 writer.push(predicate)
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269
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270 if isinstance(object, Literal):
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271 if object.language:
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272 writer.attribute(XMLLANG, object.language)
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273
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274 if (object.datatype == RDF.XMLLiteral and
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275 isinstance(object.value, xml.dom.minidom.Document)):
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276 writer.attribute(RDF.parseType, "Literal")
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277 writer.text("")
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278 writer.stream.write(object)
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279 else:
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280 if object.datatype:
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281 writer.attribute(RDF.datatype, object.datatype)
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282 writer.text(object)
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283
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284 elif object in self.__serialized or not (object, None, None) in store:
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285
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286 if isinstance(object, BNode):
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287 if more_than(store.triples((None, None, object)), 0):
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288 writer.attribute(RDF.nodeID, fix(object))
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289 else:
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290 writer.attribute(RDF.resource, self.relativize(object))
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291
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292 else:
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293 if first(store.objects(object, RDF.first)): # may not have type
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294 # RDF.List
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295
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296 self.__serialized[object] = 1
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297
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298 # Warn that any assertions on object other than
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299 # RDF.first and RDF.rest are ignored... including RDF.List
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300 import warnings
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301 warnings.warn(
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302 "Assertions on %s other than RDF.first " % repr(object) +
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303 "and RDF.rest are ignored ... including RDF.List",
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304 UserWarning, stacklevel=2)
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305 writer.attribute(RDF.parseType, "Collection")
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306
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307 col = Collection(store, object)
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308
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309 for item in col:
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310
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311 if isinstance(item, URIRef):
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312 self.forceRDFAbout.add(item)
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313 self.subject(item)
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314
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315 if not isinstance(item, URIRef):
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316 self.__serialized[item] = 1
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317 else:
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318 if first(store.triples_choices(
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319 (object, RDF.type, [OWL_NS.Class, RDFS.Class]))) \
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320 and isinstance(object, URIRef):
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321 writer.attribute(RDF.resource, self.relativize(object))
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322
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323 elif depth <= self.max_depth:
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324 self.subject(object, depth + 1)
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325
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326 elif isinstance(object, BNode):
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327
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328 if not object in self.__serialized \
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329 and (object, None, None) in store \
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330 and len(list(store.subjects(object=object))) == 1:
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331 # inline blank nodes if they haven't been serialized yet
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332 # and are only referenced once (regardless of depth)
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333 self.subject(object, depth + 1)
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334 else:
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335 writer.attribute(RDF.nodeID, fix(object))
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336
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337 else:
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338 writer.attribute(RDF.resource, self.relativize(object))
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339
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340 writer.pop(predicate)