Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib_jsonld/parser.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 # -*- coding: utf-8 -*-
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2 """
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3 This parser will interpret a JSON-LD document as an RDF Graph. 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, Parser
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10 >>> register('json-ld', Parser, 'rdflib_jsonld.parser', 'JsonLDParser')
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11
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12 >>> from rdflib import Graph, URIRef, Literal
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13 >>> test_json = '''
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14 ... {
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15 ... "@context": {
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16 ... "dc": "http://purl.org/dc/terms/",
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17 ... "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
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18 ... "rdfs": "http://www.w3.org/2000/01/rdf-schema#"
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19 ... },
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20 ... "@id": "http://example.org/about",
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21 ... "dc:title": {
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22 ... "@language": "en",
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23 ... "@value": "Someone's Homepage"
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24 ... }
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25 ... }
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26 ... '''
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27 >>> g = Graph().parse(data=test_json, format='json-ld')
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28 >>> list(g) == [(URIRef('http://example.org/about'),
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29 ... URIRef('http://purl.org/dc/terms/title'),
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30 ... Literal("Someone's Homepage", lang='en'))]
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31 True
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32
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33 """
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34 # NOTE: This code reads the entire JSON object into memory before parsing, but
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35 # we should consider streaming the input to deal with arbitrarily large graphs.
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36
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37 import warnings
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38 from rdflib.graph import ConjunctiveGraph
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39 from rdflib.parser import Parser, URLInputSource
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40 from rdflib.namespace import RDF, XSD
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41 from rdflib.term import URIRef, BNode, Literal
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42
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43 from .context import Context, Term, UNDEF
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44 from .util import source_to_json, VOCAB_DELIMS, context_from_urlinputsource
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45 from .keys import CONTEXT, GRAPH, ID, INDEX, LANG, LIST, REV, SET, TYPE, VALUE, VOCAB
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46
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47 __all__ = ['JsonLDParser', 'to_rdf']
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48
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49
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50 TYPE_TERM = Term(str(RDF.type), TYPE, VOCAB)
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51
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52 ALLOW_LISTS_OF_LISTS = True # NOTE: Not allowed in JSON-LD 1.0
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53
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54
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55 class JsonLDParser(Parser):
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56 def __init__(self):
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57 super(JsonLDParser, self).__init__()
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58
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59 def parse(self, source, sink, **kwargs):
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60 # TODO: docstring w. args and return value
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61 encoding = kwargs.get('encoding') or 'utf-8'
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62 if encoding not in ('utf-8', 'utf-16'):
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63 warnings.warn("JSON should be encoded as unicode. " +
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64 "Given encoding was: %s" % encoding)
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65
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66 base = kwargs.get('base') or sink.absolutize(
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67 source.getPublicId() or source.getSystemId() or "")
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68 context_data = kwargs.get('context')
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69 if not context_data and isinstance(source, URLInputSource):
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70 context_data = context_from_urlinputsource(source)
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71 produce_generalized_rdf = kwargs.get('produce_generalized_rdf', False)
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72
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73 data = source_to_json(source)
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74 conj_sink = ConjunctiveGraph(
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75 store=sink.store, identifier=sink.identifier)
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76 to_rdf(data, conj_sink, base, context_data)
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77
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78
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79 def to_rdf(data, graph, base=None, context_data=None,
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80 produce_generalized_rdf=False,
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81 allow_lists_of_lists=None):
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82 # TODO: docstring w. args and return value
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83 context=Context(base=base)
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84 if context_data:
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85 context.load(context_data)
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86 parser = Parser(generalized_rdf=produce_generalized_rdf,
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87 allow_lists_of_lists=allow_lists_of_lists)
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88 return parser.parse(data, context, graph)
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89
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90
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91 class Parser(object):
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92
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93 def __init__(self, generalized_rdf=False, allow_lists_of_lists=None):
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94 self.generalized_rdf = generalized_rdf
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95 self.allow_lists_of_lists = (allow_lists_of_lists
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96 if allow_lists_of_lists is not None else ALLOW_LISTS_OF_LISTS)
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97
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98 def parse(self, data, context, graph):
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99 topcontext = False
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100
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101 if isinstance(data, list):
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102 resources = data
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103 elif isinstance(data, dict):
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104 l_ctx = data.get(CONTEXT)
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105 if l_ctx:
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106 context.load(l_ctx, context.base)
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107 topcontext = True
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108 resources = data
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109 if not isinstance(resources, list):
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110 resources = [resources]
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111
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112 if context.vocab:
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113 graph.bind(None, context.vocab)
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114 for name, term in list(context.terms.items()):
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115 if term.id and term.id.endswith(VOCAB_DELIMS):
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116 graph.bind(name, term.id)
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117
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118 for node in resources:
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119 self._add_to_graph(graph, graph, context, node, topcontext)
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120
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121 return graph
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122
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123
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124 def _add_to_graph(self, dataset, graph, context, node, topcontext=False):
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125 if not isinstance(node, dict) or context.get_value(node):
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126 return
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127
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128 if CONTEXT in node and not topcontext:
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129 l_ctx = node.get(CONTEXT)
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130 if l_ctx:
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131 context = context.subcontext(l_ctx)
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132 else:
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133 context = Context(base=context.doc_base)
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134
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135 id_val = context.get_id(node)
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136 if isinstance(id_val, str):
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137 subj = self._to_rdf_id(context, id_val)
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138 else:
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139 subj = BNode()
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140
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141 if subj is None:
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142 return None
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143
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144 for key, obj in list(node.items()):
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145 if key in (CONTEXT, ID, context.get_key(ID)):
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146 continue
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147 if key in (REV, context.get_key(REV)):
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148 for rkey, robj in list(obj.items()):
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149 self._key_to_graph(dataset, graph, context, subj, rkey, robj, True)
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150 else:
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151 self._key_to_graph(dataset, graph, context, subj, key, obj)
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152
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153 return subj
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154
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155
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156 def _key_to_graph(self, dataset, graph, context, subj, key, obj, reverse=False):
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157
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158 if isinstance(obj, list):
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159 obj_nodes = obj
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160 else:
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161 obj_nodes = [obj]
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162
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163 term = context.terms.get(key)
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164 if term:
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165 term_id = term.id
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166 if term.container == LIST:
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167 obj_nodes = [{LIST: obj_nodes}]
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168 elif isinstance(obj, dict):
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169 if term.container == INDEX:
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170 obj_nodes = []
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171 for values in list(obj.values()):
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172 if not isinstance(values, list):
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173 obj_nodes.append(values)
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174 else:
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175 obj_nodes += values
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176 elif term.container == LANG:
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177 obj_nodes = []
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178 for lang, values in list(obj.items()):
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179 if not isinstance(values, list):
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180 values = [values]
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181 for v in values:
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182 obj_nodes.append((v, lang))
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183 else:
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184 term_id = None
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185
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186 if TYPE in (key, term_id):
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187 term = TYPE_TERM
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188 elif GRAPH in (key, term_id):
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189 #assert graph.context_aware
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190 subgraph = dataset.get_context(subj)
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191 for onode in obj_nodes:
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192 self._add_to_graph(dataset, subgraph, context, onode)
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193 return
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194 elif SET in (key, term_id):
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195 for onode in obj_nodes:
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196 self._add_to_graph(dataset, graph, context, onode)
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197 return
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198
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199 pred_uri = term.id if term else context.expand(key)
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200
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201 flattened = []
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202 for obj in obj_nodes:
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203 if isinstance(obj, dict):
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204 objs = context.get_set(obj)
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205 if objs is not None:
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206 obj = objs
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207 if isinstance(obj, list):
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208 flattened += obj
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209 continue
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210 flattened.append(obj)
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211 obj_nodes = flattened
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212
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parents:
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213 if not pred_uri:
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214 return
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parents:
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215
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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216 if term and term.reverse:
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217 reverse = not reverse
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218
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219 bid = self._get_bnodeid(pred_uri)
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220 if bid:
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221 if not self.generalized_rdf:
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222 return
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223 pred = BNode(bid)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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224 else:
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225 pred = URIRef(pred_uri)
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parents:
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226 for obj_node in obj_nodes:
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227 obj = self._to_object(dataset, graph, context, term, obj_node)
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228 if obj is None:
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diff changeset
229 continue
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
230 if reverse:
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diff changeset
231 graph.add((obj, pred, subj))
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232 else:
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233 graph.add((subj, pred, obj))
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parents:
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234
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235
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
236 def _to_object(self, dataset, graph, context, term, node, inlist=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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237
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parents:
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238 if node is None:
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parents:
diff changeset
239 return
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parents:
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240
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parents:
diff changeset
241 if isinstance(node, tuple):
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parents:
diff changeset
242 value, lang = node
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
243 if value is None:
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parents:
diff changeset
244 return
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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245 return Literal(value, lang=lang)
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parents:
diff changeset
246
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parents:
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247 if isinstance(node, dict):
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248 node_list = context.get_list(node)
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parents:
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249 if node_list is not None:
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parents:
diff changeset
250 if inlist and not self.allow_lists_of_lists:
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parents:
diff changeset
251 return
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252 listref = self._add_list(dataset, graph, context, term, node_list)
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253 if listref:
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254 return listref
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255
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parents:
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256 else: # expand..
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257 if not term or not term.type:
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258 if isinstance(node, float):
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259 return Literal(node, datatype=XSD.double)
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260 if term and term.language is not UNDEF:
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261 lang = term.language
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262 else:
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263 lang = context.language
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264 return Literal(node, lang=lang)
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265 else:
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266 if term.type == ID:
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267 node = {ID: context.resolve(node)}
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268 elif term.type == VOCAB:
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269 node = {ID: context.expand(node) or context.resolve_iri(node)}
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270 else:
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271 node = {TYPE: term.type,
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272 VALUE: node}
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273
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274 lang = context.get_language(node)
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275 if lang or context.get_key(VALUE) in node or VALUE in node:
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276 value = context.get_value(node)
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277 if value is None:
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278 return None
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279 datatype = not lang and context.get_type(node) or None
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280 if lang:
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281 return Literal(value, lang=lang)
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282 elif datatype:
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283 return Literal(value, datatype=context.expand(datatype))
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284 else:
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285 return Literal(value)
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286 else:
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287 return self._add_to_graph(dataset, graph, context, node)
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288
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289
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290 def _to_rdf_id(self, context, id_val):
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291 bid = self._get_bnodeid(id_val)
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292 if bid:
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293 return BNode(bid)
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294 else:
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295 uri = context.resolve(id_val)
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296 if not self.generalized_rdf and ':' not in uri:
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297 return None
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298 return URIRef(uri)
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299
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300
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301 def _get_bnodeid(self, ref):
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302 if not ref.startswith('_:'):
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303 return
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304 bid = ref.split('_:', 1)[-1]
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305 return bid or None
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306
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307
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308 def _add_list(self, dataset, graph, context, term, node_list):
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309 if not isinstance(node_list, list):
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310 node_list = [node_list]
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311 first_subj = BNode()
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312 subj, rest = first_subj, None
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313 for node in node_list:
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314 if node is None:
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315 continue
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316 if rest:
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317 graph.add((subj, RDF.rest, rest))
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318 subj = rest
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319 obj = self._to_object(dataset, graph, context, term, node, inlist=True)
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320 if obj is None:
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321 continue
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322 graph.add((subj, RDF.first, obj))
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323 rest = BNode()
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324 if rest:
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325 graph.add((subj, RDF.rest, RDF.nil))
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326 return first_subj
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327 else:
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328 return RDF.nil