Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib_jsonld/serializer.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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1 # -*- coding: utf-8 -*-
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2 """
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3 This serialiser will output an RDF Graph as a JSON-LD formatted document. See:
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4
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5 http://json-ld.org/
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6
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7 Example usage::
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8
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9 >>> from rdflib.plugin import register, Serializer
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10 >>> register('json-ld', Serializer, 'rdflib_jsonld.serializer', 'JsonLDSerializer')
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11
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12 >>> from rdflib import Graph
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13
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14 >>> testrdf = '''
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15 ... @prefix dc: <http://purl.org/dc/terms/> .
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16 ... <http://example.org/about>
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17 ... dc:title "Someone's Homepage"@en .
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18 ... '''
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19
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20 >>> g = Graph().parse(data=testrdf, format='n3')
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21
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22 >>> print((g.serialize(format='json-ld', indent=4).decode()))
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23 [
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24 {
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25 "@id": "http://example.org/about",
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26 "http://purl.org/dc/terms/title": [
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27 {
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28 "@language": "en",
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29 "@value": "Someone's Homepage"
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30 }
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31 ]
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32 }
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33 ]
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34
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35 """
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36
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37 # NOTE: This code writes the entire JSON object into memory before serialising,
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38 # but we should consider streaming the output to deal with arbitrarily large
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39 # graphs.
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40
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41 import warnings
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42
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43 from rdflib.serializer import Serializer
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44 from rdflib.graph import Graph
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45 from rdflib.term import URIRef, Literal, BNode
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46 from rdflib.namespace import RDF, XSD
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47
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48 from .context import Context, UNDEF
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49 from .util import json
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50 from .keys import CONTEXT, GRAPH, ID, VOCAB, LIST, SET, LANG
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51
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52 __all__ = ['JsonLDSerializer', 'from_rdf']
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53
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54
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55 PLAIN_LITERAL_TYPES = set([XSD.boolean, XSD.integer, XSD.double, XSD.string])
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56
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57
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58 class JsonLDSerializer(Serializer):
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59 def __init__(self, store):
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60 super(JsonLDSerializer, self).__init__(store)
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61
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62 def serialize(self, stream, base=None, encoding=None, **kwargs):
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63 # TODO: docstring w. args and return value
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64 encoding = encoding or 'utf-8'
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65 if encoding not in ('utf-8', 'utf-16'):
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66 warnings.warn("JSON should be encoded as unicode. " +
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67 "Given encoding was: %s" % encoding)
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68
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69 context_data = kwargs.get('context')
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70 use_native_types = kwargs.get('use_native_types', False),
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71 use_rdf_type = kwargs.get('use_rdf_type', False)
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72 auto_compact = kwargs.get('auto_compact', False)
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73
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74 indent = kwargs.get('indent', 2)
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75 separators = kwargs.get('separators', (',', ': '))
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76 sort_keys = kwargs.get('sort_keys', True)
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77 ensure_ascii = kwargs.get('ensure_ascii', False)
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78
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79 obj = from_rdf(self.store, context_data, base,
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80 use_native_types, use_rdf_type,
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81 auto_compact=auto_compact)
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82
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83 data = json.dumps(obj, indent=indent, separators=separators,
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84 sort_keys=sort_keys, ensure_ascii=ensure_ascii)
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85
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86 stream.write(data.encode(encoding, 'replace'))
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87
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88
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89 def from_rdf(graph, context_data=None, base=None,
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90 use_native_types=False, use_rdf_type=False,
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91 auto_compact=False, startnode=None, index=False):
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92 # TODO: docstring w. args and return value
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93 # TODO: support for index and startnode
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94
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95 if not context_data and auto_compact:
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96 context_data = dict(
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97 (pfx, str(ns))
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98 for (pfx, ns) in graph.namespaces() if pfx and
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99 str(ns) != "http://www.w3.org/XML/1998/namespace")
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100
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101 if isinstance(context_data, Context):
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102 context = context_data
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103 context_data = context.to_dict()
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104 else:
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105 context = Context(context_data, base=base)
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106
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107 converter = Converter(context, use_native_types, use_rdf_type)
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108 result = converter.convert(graph)
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109
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110 if converter.context.active:
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111 if isinstance(result, list):
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112 result = {context.get_key(GRAPH): result}
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113 result[CONTEXT] = context_data
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114
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115 return result
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116
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117
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118 class Converter(object):
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119
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120 def __init__(self, context, use_native_types, use_rdf_type):
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121 self.context = context
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122 self.use_native_types = context.active or use_native_types
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123 self.use_rdf_type = use_rdf_type
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124
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125 def convert(self, graph):
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126 # TODO: bug in rdflib dataset parsing (nquads et al):
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127 # plain triples end up in separate unnamed graphs (rdflib issue #436)
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128 if graph.context_aware:
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129 default_graph = Graph()
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130 graphs = [default_graph]
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131 for g in graph.contexts():
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132 if isinstance(g.identifier, URIRef):
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133 graphs.append(g)
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134 else:
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135 default_graph += g
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136 else:
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137 graphs = [graph]
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138
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139 context = self.context
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140
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141 objs = []
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142 for g in graphs:
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143 obj = {}
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144 graphname = None
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145
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146 if isinstance(g.identifier, URIRef):
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147 graphname = context.shrink_iri(g.identifier)
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148 obj[context.id_key] = graphname
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149
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150 nodes = self.from_graph(g)
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151
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152 if not graphname and len(nodes) == 1:
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153 obj.update(nodes[0])
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154 else:
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155 if not nodes:
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156 continue
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157 obj[context.graph_key] = nodes
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158
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159 if objs and objs[0].get(context.get_key(ID)) == graphname:
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160 objs[0].update(obj)
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161 else:
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162 objs.append(obj)
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163
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164 if len(graphs) == 1 and len(objs) == 1 and not self.context.active:
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165 default = objs[0]
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166 items = default.get(context.graph_key)
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167 if len(default) == 1 and items:
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168 objs = items
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169 elif len(objs) == 1 and self.context.active:
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170 objs = objs[0]
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171
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172 return objs
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173
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174 def from_graph(self, graph):
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175 nodemap = {}
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176
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177 for s in set(graph.subjects()):
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178 ## only iri:s and unreferenced (rest will be promoted to top if needed)
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179 if isinstance(s, URIRef) or (isinstance(s, BNode)
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180 and not any(graph.subjects(None, s))):
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181 self.process_subject(graph, s, nodemap)
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182
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183 return list(nodemap.values())
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184
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185 def process_subject(self, graph, s, nodemap):
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186 if isinstance(s, URIRef):
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187 node_id = self.context.shrink_iri(s)
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188 elif isinstance(s, BNode):
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189 node_id = s.n3()
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190 else:
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191 node_id = None
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192
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193 #used_as_object = any(graph.subjects(None, s))
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194 if node_id in nodemap:
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195 return None
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196
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197 node = {}
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198 node[self.context.id_key] = node_id
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199 nodemap[node_id] = node
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200
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201 for p, o in graph.predicate_objects(s):
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202 self.add_to_node(graph, s, p, o, node, nodemap)
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203
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204 return node
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205
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206 def add_to_node(self, graph, s, p, o, s_node, nodemap):
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207 context = self.context
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208
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209 if isinstance(o, Literal):
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210 datatype = str(o.datatype) if o.datatype else None
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211 language = o.language
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212 term = context.find_term(str(p), datatype, language=language)
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213 else:
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214 containers = [LIST, None] if graph.value(o, RDF.first) else [None]
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215 for container in containers:
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216 for coercion in (ID, VOCAB, UNDEF):
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217 term = context.find_term(str(p), coercion, container)
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218 if term:
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219 break
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220 if term:
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221 break
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222
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223 node = None
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224 use_set = not context.active
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225
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226 if term:
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227 p_key = term.name
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228
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229 if term.type:
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230 node = self.type_coerce(o, term.type)
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231 elif term.language and o.language == term.language:
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232 node = str(o)
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233 elif context.language and (
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234 term.language is None and o.language is None):
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235 node = str(o)
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236
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237 if term.container == SET:
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238 use_set = True
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239 elif term.container == LIST:
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240 node = [self.type_coerce(v, term.type) or self.to_raw_value(graph, s, v, nodemap)
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241 for v in self.to_collection(graph, o)]
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242 elif term.container == LANG and language:
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243 value = s_node.setdefault(p_key, {})
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244 values = value.get(language)
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245 node = str(o)
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246 if values:
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247 if not isinstance(values, list):
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248 value[language] = values = [values]
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249 values.append(node)
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250 else:
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251 value[language] = node
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252 return
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253
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254 else:
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255 p_key = context.to_symbol(p)
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256 # TODO: for coercing curies - quite clumsy; unify to_symbol and find_term?
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257 key_term = context.terms.get(p_key)
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258 if key_term and (key_term.type or key_term.container):
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259 p_key = p
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260 if not term and p == RDF.type and not self.use_rdf_type:
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261 if isinstance(o, URIRef):
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262 node = context.to_symbol(o)
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263 p_key = context.type_key
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264
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265 if node is None:
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266 node = self.to_raw_value(graph, s, o, nodemap)
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267
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268 value = s_node.get(p_key)
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269 if value:
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270 if not isinstance(value, list):
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271 value = [value]
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272 value.append(node)
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273 elif use_set:
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274 value = [node]
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275 else:
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276 value = node
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277 s_node[p_key] = value
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278
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279 def type_coerce(self, o, coerce_type):
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280 if coerce_type == ID:
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281 if isinstance(o, URIRef):
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282 return self.context.shrink_iri(o)
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283 elif isinstance(o, BNode):
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284 return o.n3()
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285 else:
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286 return o
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287 elif coerce_type == VOCAB and isinstance(o, URIRef):
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288 return self.context.to_symbol(o)
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289 elif isinstance(o, Literal) and str(o.datatype) == coerce_type:
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290 return o
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291 else:
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292 return None
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293
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294 def to_raw_value(self, graph, s, o, nodemap):
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295 context = self.context
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296 coll = self.to_collection(graph, o)
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297 if coll is not None:
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298 coll = [self.to_raw_value(graph, s, lo, nodemap)
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299 for lo in self.to_collection(graph, o)]
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300 return {context.list_key: coll}
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301 elif isinstance(o, BNode):
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302 embed = False # TODO: self.context.active or using startnode and only one ref
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303 onode = self.process_subject(graph, o, nodemap)
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304 if onode:
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305 if embed and not any(s2 for s2 in graph.subjects(None, o) if s2 != s):
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306 return onode
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307 else:
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308 nodemap[onode[context.id_key]] = onode
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309 return {context.id_key: o.n3()}
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310 elif isinstance(o, URIRef):
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311 # TODO: embed if o != startnode (else reverse)
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312 return {context.id_key: context.shrink_iri(o)}
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313 elif isinstance(o, Literal):
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314 # TODO: if compact
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315 native = self.use_native_types and o.datatype in PLAIN_LITERAL_TYPES
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316 if native:
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317 v = o.toPython()
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318 else:
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319 v = str(o)
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320 if o.datatype:
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321 if native:
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322 if self.context.active:
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323 return v
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324 else:
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325 return {context.value_key: v}
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326 return {context.type_key: context.to_symbol(o.datatype),
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327 context.value_key: v}
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328 elif o.language and o.language != context.language:
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329 return {context.lang_key: o.language,
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330 context.value_key: v}
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331 elif not context.active or context.language and not o.language:
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332 return {context.value_key: v}
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333 else:
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334 return v
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335
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336 def to_collection(self, graph, l):
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337 if l != RDF.nil and not graph.value(l, RDF.first):
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338 return None
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339 list_nodes = []
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340 chain = set([l])
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341 while l:
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342 if l == RDF.nil:
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343 return list_nodes
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344 if isinstance(l, URIRef):
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345 return None
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346 first, rest = None, None
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347 for p, o in graph.predicate_objects(l):
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348 if not first and p == RDF.first:
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349 first = o
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350 elif not rest and p == RDF.rest:
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351 rest = o
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352 elif p != RDF.type or o != RDF.List:
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353 return None
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354 list_nodes.append(first)
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355 l = rest
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356 if l in chain:
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357 return None
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358 chain.add(l)
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359