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annotate planemo/lib/python3.7/site-packages/prov/serializers/provrdf.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 """PROV-RDF serializers for ProvDocument
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2 """
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3 from __future__ import (absolute_import, division, print_function,
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4 unicode_literals)
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5
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6 import base64
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7 from collections import OrderedDict
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8 import datetime
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9 import io
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10
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11 import dateutil.parser
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12 import six
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13
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14 from rdflib.term import URIRef, BNode
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15 from rdflib.term import Literal as RDFLiteral
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16 from rdflib.graph import ConjunctiveGraph
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17 from rdflib.namespace import RDF, RDFS, XSD
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18
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19 import prov.model as pm
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20 from prov.constants import (
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21 PROV, PROV_ID_ATTRIBUTES_MAP, PROV_N_MAP, PROV_BASE_CLS, XSD_QNAME,
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22 PROV_END, PROV_START, PROV_USAGE, PROV_GENERATION, PROV_DERIVATION, PROV_INVALIDATION,
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23 PROV_ALTERNATE, PROV_MENTION, PROV_DELEGATION, PROV_ACTIVITY, PROV_ATTR_STARTTIME,
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24 PROV_ATTR_ENDTIME, PROV_LOCATION, PROV_ATTR_TIME, PROV_ROLE, PROV_COMMUNICATION,
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25 PROV_ATTR_INFORMANT, PROV_ATTR_RESPONSIBLE, PROV_ATTR_TRIGGER, PROV_ATTR_ENDER,
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26 PROV_ATTR_STARTER, PROV_ATTR_USED_ENTITY)
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27 from prov.serializers import Serializer, Error
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28
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29
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30 __author__ = 'Satrajit S. Ghosh'
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31 __email__ = 'satra@mit.edu'
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32
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33
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34 class ProvRDFException(Error):
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35 pass
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36
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37
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38 class AnonymousIDGenerator:
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39 def __init__(self):
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40 self._cache = {}
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41 self._count = 0
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42
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43 def get_anon_id(self, obj, local_prefix="id"):
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44 if obj not in self._cache:
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45 self._count += 1
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46 self._cache[obj] = pm.Identifier(
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47 '_:%s%d' % (local_prefix, self._count)
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48 ).uri
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49 return self._cache[obj]
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50
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51
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52 # Reverse map for prov.model.XSD_DATATYPE_PARSERS
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53 LITERAL_XSDTYPE_MAP = {
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54 float: XSD['double'],
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55 int: XSD['int'],
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56 six.text_type: XSD['string'],
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57 # boolean, string values are supported natively by PROV-RDF
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58 # datetime values are converted separately
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59 }
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60
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61 # Add long on Python 2
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62 if six.integer_types[-1] not in LITERAL_XSDTYPE_MAP:
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63 LITERAL_XSDTYPE_MAP[six.integer_types[-1]] = XSD['long']
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64
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65
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66 def attr2rdf(attr):
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67 return URIRef(PROV[PROV_ID_ATTRIBUTES_MAP[attr].split('prov:')[1]].uri)
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68
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69
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70 def valid_qualified_name(bundle, value, xsd_qname=False):
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71 if value is None:
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72 return None
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73 qualified_name = bundle.valid_qualified_name(value)
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74 return qualified_name if not xsd_qname else XSD_QNAME(qualified_name)
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75
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76
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77 class ProvRDFSerializer(Serializer):
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78 """
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79 PROV-O serializer for :class:`~prov.model.ProvDocument`
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80 """
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81
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82 def serialize(self, stream=None, rdf_format='trig', **kwargs):
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83 """
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84 Serializes a :class:`~prov.model.ProvDocument` instance to
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85 `PROV-O <https://www.w3.org/TR/prov-o/>`_.
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86
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87 :param stream: Where to save the output.
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88 :param rdf_format: The RDF format of the output, default to TRiG.
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89 """
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90 container = self.encode_document(self.document)
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91 newargs = kwargs.copy()
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92 newargs['format'] = rdf_format
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93
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94 if six.PY2:
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95 buf = io.BytesIO()
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96 try:
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97 container.serialize(buf, **newargs)
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98 buf.seek(0, 0)
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99 # Right now this is a bytestream. If the object to stream to is
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100 # a text object is must be decoded. We assume utf-8 here which
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101 # should be fine for almost every case.
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102 if isinstance(stream, io.TextIOBase):
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103 stream.write(buf.read().decode('utf-8'))
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104 else:
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105 stream.write(buf.read())
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106 finally:
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107 buf.close()
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108 else:
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109 buf = io.BytesIO()
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110 try:
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111 container.serialize(buf, **newargs)
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112 buf.seek(0, 0)
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113 # Right now this is a bytestream. If the object to stream to is
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114 # a text object is must be decoded. We assume utf-8 here which
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115 # should be fine for almost every case.
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116 if isinstance(stream, io.TextIOBase):
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117 stream.write(buf.read().decode('utf-8'))
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118 else:
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119 stream.write(buf.read())
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120 finally:
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121 buf.close()
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122
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123 def deserialize(self, stream, rdf_format='trig', **kwargs):
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124 """
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125 Deserialize from the `PROV-O <https://www.w3.org/TR/prov-o/>`_
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126 representation to a :class:`~prov.model.ProvDocument` instance.
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127
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128 :param stream: Input data.
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129 :param rdf_format: The RDF format of the input data, default: TRiG.
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130 """
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131 newargs = kwargs.copy()
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132 newargs['format'] = rdf_format
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133 container = ConjunctiveGraph()
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134 container.parse(stream, **newargs)
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135 document = pm.ProvDocument()
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136 self.document = document
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137 self.decode_document(container, document)
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138 return document
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139
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140 def valid_identifier(self, value):
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141 return self.document.valid_qualified_name(value)
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142
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143 def encode_rdf_representation(self, value):
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144 if isinstance(value, URIRef):
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145 return value
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146 elif isinstance(value, pm.Literal):
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147 return literal_rdf_representation(value)
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148 elif isinstance(value, datetime.datetime):
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149 return RDFLiteral(value.isoformat(), datatype=XSD['dateTime'])
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150 elif isinstance(value, pm.QualifiedName):
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151 return URIRef(value.uri)
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152 elif isinstance(value, pm.Identifier):
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153 return RDFLiteral(value.uri, datatype=XSD['anyURI'])
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154 elif type(value) in LITERAL_XSDTYPE_MAP:
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155 return RDFLiteral(value, datatype=LITERAL_XSDTYPE_MAP[type(value)])
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156 else:
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157 return RDFLiteral(value)
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158
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159 def decode_rdf_representation(self, literal, graph):
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160 if isinstance(literal, RDFLiteral):
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161 value = literal.value if literal.value is not None else literal
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162 datatype = literal.datatype if hasattr(literal, 'datatype') else None
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163 langtag = literal.language if hasattr(literal, 'language') else None
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164 if datatype and 'XMLLiteral' in datatype:
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165 value = literal
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166 if datatype and 'base64Binary' in datatype:
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167 value = base64.standard_b64encode(value)
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168 if datatype == XSD['QName']:
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169 return pm.Literal(literal, datatype=XSD_QNAME)
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170 if datatype == XSD['dateTime']:
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171 return dateutil.parser.parse(literal)
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172 if datatype == XSD['gYear']:
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173 return pm.Literal(dateutil.parser.parse(literal).year,
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174 datatype=self.valid_identifier(datatype))
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175 if datatype == XSD['gYearMonth']:
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176 parsed_info = dateutil.parser.parse(literal)
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177 return pm.Literal('{0}-{1:02d}'.format(parsed_info.year, parsed_info.month),
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178 datatype=self.valid_identifier(datatype))
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179 else:
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180 # The literal of standard Python types is not converted here
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181 # It will be automatically converted when added to a record by
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182 # _auto_literal_conversion()
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183 return pm.Literal(value, self.valid_identifier(datatype), langtag)
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184 elif isinstance(literal, URIRef):
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185 rval = self.valid_identifier(literal)
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186 if rval is None:
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187 prefix, iri, _ = graph.namespace_manager.compute_qname(literal)
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188 ns = self.document.add_namespace(prefix, iri)
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189 rval = pm.QualifiedName(ns, literal.replace(ns.uri, ''))
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190 return rval
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191 else:
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192 # simple type, just return it
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193 return literal
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194
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195 def encode_document(self, document):
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196 container = self.encode_container(document)
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197 for item in document.bundles:
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198 # encoding the sub-bundle
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199 bundle = self.encode_container(item, identifier=item.identifier.uri)
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200 container.addN(bundle.quads())
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201 return container
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202
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203 def encode_container(self, bundle, container=None, identifier=None):
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204 if container is None:
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205 container = ConjunctiveGraph(identifier=identifier)
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206 nm = container.namespace_manager
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207 nm.bind('prov', PROV.uri)
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208
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209 for namespace in bundle.namespaces:
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210 container.bind(namespace.prefix, namespace.uri)
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211
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212 id_generator = AnonymousIDGenerator()
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213 real_or_anon_id = lambda record: record._identifier.uri if \
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214 record._identifier else id_generator.get_anon_id(record)
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215
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216 for record in bundle._records:
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217 rec_type = record.get_type()
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218 if hasattr(record, 'identifier') and record.identifier:
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219 identifier = URIRef(six.text_type(real_or_anon_id(record)))
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220 container.add((identifier, RDF.type, URIRef(rec_type.uri)))
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221 else:
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222 identifier = None
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223 if record.attributes:
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224 bnode = None
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225 formal_objects = []
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226 used_objects = []
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227 all_attributes = list(record.formal_attributes) + list(record.attributes)
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228 formal_qualifiers = False
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229 for attrid, (attr, value) in enumerate(list(record.formal_attributes)):
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230 if (identifier is not None and value is not None) or \
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231 (identifier is None and value is not None and attrid > 1):
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232 formal_qualifiers = True
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233 has_qualifiers = len(record.extra_attributes) > 0 or formal_qualifiers
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234 for idx, (attr, value) in enumerate(all_attributes):
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235 if record.is_relation():
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236 pred = URIRef(PROV[PROV_N_MAP[rec_type]].uri)
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237 # create bnode relation
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238 if bnode is None:
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239 valid_formal_indices = set()
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240 for idx, (key, val) in enumerate(record.formal_attributes):
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241 formal_objects.append(key)
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242 if val:
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243 valid_formal_indices.add(idx)
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244 used_objects = [record.formal_attributes[0][0]]
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245 subj = None
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246 if record.formal_attributes[0][1]:
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247 subj = URIRef(record.formal_attributes[0][1].uri)
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248 if identifier is None and subj is not None:
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249 try:
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250 obj_val = record.formal_attributes[1][1]
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251 obj_attr = URIRef(record.formal_attributes[1][0].uri)
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parents:
diff changeset
252 # TODO: Why is obj_attr above not used anywhere?
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parents:
diff changeset
253 except IndexError:
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254 obj_val = None
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parents:
diff changeset
255 if obj_val and (rec_type not in {PROV_END,
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parents:
diff changeset
256 PROV_START,
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parents:
diff changeset
257 PROV_USAGE,
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parents:
diff changeset
258 PROV_GENERATION,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
259 PROV_DERIVATION,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
260 PROV_INVALIDATION} or
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parents:
diff changeset
261 (valid_formal_indices == {0, 1} and
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262 len(record.extra_attributes) == 0)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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263 used_objects.append(record.formal_attributes[1][0])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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264 obj_val = self.encode_rdf_representation(obj_val)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
265 if rec_type == PROV_ALTERNATE:
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diff changeset
266 subj, obj_val = obj_val, subj
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parents:
diff changeset
267 container.add((subj, pred, obj_val))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
268 if rec_type == PROV_MENTION:
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parents:
diff changeset
269 if record.formal_attributes[2][1]:
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diff changeset
270 used_objects.append(record.formal_attributes[2][0])
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diff changeset
271 obj_val = self.encode_rdf_representation(record.formal_attributes[2][1])
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272 container.add((subj, URIRef(PROV['asInBundle'].uri), obj_val))
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273 has_qualifiers = False
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diff changeset
274 if rec_type in [PROV_ALTERNATE]:
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parents:
diff changeset
275 continue
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276 if subj and (has_qualifiers or identifier):
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277 qualifier = rec_type._localpart
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278 rec_uri = rec_type.uri
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parents:
diff changeset
279 for attr_name, val in record.extra_attributes:
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280 if attr_name == PROV['type']:
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281 if PROV['Revision'] == val or \
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282 PROV['Quotation'] == val or \
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283 PROV['PrimarySource'] == val:
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parents:
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284 qualifier = val._localpart
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parents:
diff changeset
285 rec_uri = val.uri
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parents:
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286 if identifier is not None:
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diff changeset
287 container.remove((identifier,
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288 RDF.type,
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289 URIRef(rec_type.uri)))
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parents:
diff changeset
290 QRole = URIRef(PROV['qualified' + qualifier].uri)
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291 if identifier is not None:
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diff changeset
292 container.add((subj, QRole, identifier))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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293 else:
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294 bnode = identifier = BNode()
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diff changeset
295 container.add((subj, QRole, identifier))
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parents:
diff changeset
296 container.add(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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297 (identifier, RDF.type, URIRef(rec_uri))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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298 ) # reset identifier to BNode
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diff changeset
299 if value is not None and attr not in used_objects:
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parents:
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300 if attr in formal_objects:
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parents:
diff changeset
301 pred = attr2rdf(attr)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
302 elif attr == PROV['role']:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
303 pred = URIRef(PROV['hadRole'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
304 elif attr == PROV['plan']:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
305 pred = URIRef(PROV['hadPlan'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
306 elif attr == PROV['type']:
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diff changeset
307 pred = RDF.type
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
308 elif attr == PROV['label']:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
309 pred = RDFS.label
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
310 elif isinstance(attr, pm.QualifiedName):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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311 pred = URIRef(attr.uri)
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diff changeset
312 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
313 pred = self.encode_rdf_representation(attr)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
314 if PROV['plan'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
315 pred = URIRef(PROV['hadPlan'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
316 if PROV['informant'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
317 pred = URIRef(PROV['activity'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
318 if PROV['responsible'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
319 pred = URIRef(PROV['agent'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
320 if rec_type == PROV_DELEGATION and PROV['activity'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
321 pred = URIRef(PROV['hadActivity'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
322 if (rec_type in [PROV_END, PROV_START] and PROV['trigger'].uri in pred) or\
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
323 (rec_type in [PROV_USAGE] and PROV['used'].uri in pred):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
324 pred = URIRef(PROV['entity'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
325 if rec_type in [PROV_GENERATION, PROV_END,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
326 PROV_START, PROV_USAGE,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
327 PROV_INVALIDATION]:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
328 if PROV['time'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
329 pred = URIRef(PROV['atTime'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
330 if PROV['ender'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
331 pred = URIRef(PROV['hadActivity'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
332 if PROV['starter'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
333 pred = URIRef(PROV['hadActivity'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
334 if PROV['location'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
335 pred = URIRef(PROV['atLocation'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
336 if rec_type in [PROV_ACTIVITY]:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
337 if PROV_ATTR_STARTTIME in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
338 pred = URIRef(PROV['startedAtTime'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
339 if PROV_ATTR_ENDTIME in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
340 pred = URIRef(PROV['endedAtTime'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
341 if rec_type == PROV_DERIVATION:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
342 if PROV['activity'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
343 pred = URIRef(PROV['hadActivity'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
344 if PROV['generation'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
345 pred = URIRef(PROV['hadGeneration'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
346 if PROV['usage'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
347 pred = URIRef(PROV['hadUsage'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
348 if PROV['usedEntity'].uri in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
349 pred = URIRef(PROV['entity'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
350 container.add((identifier, pred,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
351 self.encode_rdf_representation(value)))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
352 continue
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
353 if value is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
354 continue
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
355 if isinstance(value, pm.ProvRecord):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
356 obj = URIRef(six.text_type(real_or_anon_id(value)))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
357 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
358 # Assuming this is a datetime value
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
359 obj = self.encode_rdf_representation(value)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
360 if attr == PROV['location']:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
361 pred = URIRef(PROV['atLocation'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
362 if False and isinstance(value, (URIRef, pm.QualifiedName)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
363 if isinstance(value, pm.QualifiedName):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
364 value = URIRef(value.uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
365 container.add((identifier, pred, value))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
366 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
367 container.add((identifier, pred,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
368 self.encode_rdf_representation(obj)))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
369 continue
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
370 if attr == PROV['type']:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
371 pred = RDF.type
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
372 elif attr == PROV['label']:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
373 pred = RDFS.label
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
374 elif attr == PROV_ATTR_STARTTIME:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
375 pred = URIRef(PROV['startedAtTime'].uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
376 elif attr == PROV_ATTR_ENDTIME:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
377 pred = URIRef(PROV['endedAtTime'].uri)
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guerler
parents:
diff changeset
378 else:
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guerler
parents:
diff changeset
379 pred = self.encode_rdf_representation(attr)
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guerler
parents:
diff changeset
380 container.add((identifier, pred, obj))
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guerler
parents:
diff changeset
381 return container
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guerler
parents:
diff changeset
382
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guerler
parents:
diff changeset
383 def decode_document(self, content, document):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
384 for prefix, url in content.namespaces():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
385 document.add_namespace(prefix, six.text_type(url))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
386 if hasattr(content, 'contexts'):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
387 for graph in content.contexts():
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guerler
parents:
diff changeset
388 if isinstance(graph.identifier, BNode):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
389 self.decode_container(graph, document)
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guerler
parents:
diff changeset
390 else:
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guerler
parents:
diff changeset
391 bundle_id = six.text_type(graph.identifier)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
392 bundle = document.bundle(bundle_id)
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guerler
parents:
diff changeset
393 self.decode_container(graph, bundle)
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guerler
parents:
diff changeset
394 else:
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guerler
parents:
diff changeset
395 self.decode_container(content, document)
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guerler
parents:
diff changeset
396
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guerler
parents:
diff changeset
397 def decode_container(self, graph, bundle):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
398 ids = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
399 PROV_CLS_MAP = {}
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guerler
parents:
diff changeset
400 formal_attributes = {}
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guerler
parents:
diff changeset
401 unique_sets = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
402 for key, val in PROV_BASE_CLS.items():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
403 PROV_CLS_MAP[key.uri] = PROV_BASE_CLS[key]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
404 relation_mapper = {URIRef(PROV['alternateOf'].uri): 'alternate',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
405 URIRef(PROV['actedOnBehalfOf'].uri): 'delegation',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
406 URIRef(PROV['specializationOf'].uri): 'specialization',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
407 URIRef(PROV['mentionOf'].uri): 'mention',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
408 URIRef(PROV['wasAssociatedWith'].uri): 'association',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
409 URIRef(PROV['wasDerivedFrom'].uri): 'derivation',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
410 URIRef(PROV['wasAttributedTo'].uri): 'attribution',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
411 URIRef(PROV['wasInformedBy'].uri): 'communication',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
412 URIRef(PROV['wasGeneratedBy'].uri): 'generation',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
413 URIRef(PROV['wasInfluencedBy'].uri): 'influence',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
414 URIRef(PROV['wasInvalidatedBy'].uri): 'invalidation',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
415 URIRef(PROV['wasEndedBy'].uri): 'end',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
416 URIRef(PROV['wasStartedBy'].uri): 'start',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
417 URIRef(PROV['hadMember'].uri): 'membership',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
418 URIRef(PROV['used'].uri): 'usage',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
419 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
420 predicate_mapper = {RDFS.label: pm.PROV['label'],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
421 URIRef(PROV['atLocation'].uri): PROV_LOCATION,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
422 URIRef(PROV['startedAtTime'].uri): PROV_ATTR_STARTTIME,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
423 URIRef(PROV['endedAtTime'].uri): PROV_ATTR_ENDTIME,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
424 URIRef(PROV['atTime'].uri): PROV_ATTR_TIME,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
425 URIRef(PROV['hadRole'].uri): PROV_ROLE,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
426 URIRef(PROV['hadPlan'].uri): pm.PROV_ATTR_PLAN,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
427 URIRef(PROV['hadUsage'].uri): pm.PROV_ATTR_USAGE,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
428 URIRef(PROV['hadGeneration'].uri): pm.PROV_ATTR_GENERATION,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
429 URIRef(PROV['hadActivity'].uri): pm.PROV_ATTR_ACTIVITY,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
430 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
431 other_attributes = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
432 for stmt in graph.triples((None, RDF.type, None)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
433 id = six.text_type(stmt[0])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
434 obj = six.text_type(stmt[2])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
435 if obj in PROV_CLS_MAP:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
436 if not isinstance(stmt[0], BNode) and self.valid_identifier(id) is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
437 prefix, iri, _ = graph.namespace_manager.compute_qname(id)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
438 self.document.add_namespace(prefix, iri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
439 try:
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guerler
parents:
diff changeset
440 prov_obj = PROV_CLS_MAP[obj]
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guerler
parents:
diff changeset
441 except AttributeError:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
442 prov_obj = None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
443 add_attr = True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
444 isderivation = pm.PROV['Revision'].uri in stmt[2] or \
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
445 pm.PROV['Quotation'].uri in stmt[2] or \
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
446 pm.PROV['PrimarySource'].uri in stmt[2]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
447 if id not in ids and prov_obj and (prov_obj.uri == obj or
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
448 isderivation or
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
449 isinstance(stmt[0], BNode)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
450 ids[id] = prov_obj
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
451 klass = pm.PROV_REC_CLS[prov_obj]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
452 formal_attributes[id] = OrderedDict([(key, None) for key in klass.FORMAL_ATTRIBUTES])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
453 unique_sets[id] = OrderedDict([(key, []) for key in klass.FORMAL_ATTRIBUTES])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
454 add_attr = False or ((isinstance(stmt[0], BNode) or isderivation) and prov_obj.uri != obj)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
455 if add_attr:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
456 if id not in other_attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
457 other_attributes[id] = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
458 obj_formatted = self.decode_rdf_representation(stmt[2], graph)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
459 other_attributes[id].append((pm.PROV['type'], obj_formatted))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
460 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
461 if id not in other_attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
462 other_attributes[id] = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
463 obj = self.decode_rdf_representation(stmt[2], graph)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
464 other_attributes[id].append((pm.PROV['type'], obj))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
465 for id, pred, obj in graph:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
466 id = six.text_type(id)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
467 if id not in other_attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
468 other_attributes[id] = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
469 if pred == RDF.type:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
470 continue
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
471 if pred in relation_mapper:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
472 if 'alternateOf' in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
473 getattr(bundle, relation_mapper[pred])(obj, id)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
474 elif 'mentionOf' in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
475 mentionBundle = None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
476 for stmt in graph.triples((URIRef(id), URIRef(pm.PROV['asInBundle'].uri), None)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
477 mentionBundle = stmt[2]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
478 getattr(bundle, relation_mapper[pred])(id, six.text_type(obj), mentionBundle)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
479 elif 'actedOnBehalfOf' in pred or 'wasAssociatedWith' in pred:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
480 qualifier = 'qualified' + relation_mapper[pred].upper()[0] + relation_mapper[pred][1:]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
481 qualifier_bnode = None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
482 for stmt in graph.triples((URIRef(id), URIRef(pm.PROV[qualifier].uri), None)):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
483 qualifier_bnode = stmt[2]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
484 if qualifier_bnode is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
485 getattr(bundle, relation_mapper[pred])(id, six.text_type(obj))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
486 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
487 fakeys = list(formal_attributes[six.text_type(qualifier_bnode)].keys())
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
488 formal_attributes[six.text_type(qualifier_bnode)][fakeys[0]] = id
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
489 formal_attributes[six.text_type(qualifier_bnode)][fakeys[1]] = six.text_type(obj)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
490 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
491 getattr(bundle, relation_mapper[pred])(id, six.text_type(obj))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
492 elif id in ids:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
493 obj1 = self.decode_rdf_representation(obj, graph)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
494 if obj is not None and obj1 is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
495 raise ValueError(('Error transforming', obj))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
496 pred_new = pred
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parents:
diff changeset
497 if pred in predicate_mapper:
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guerler
parents:
diff changeset
498 pred_new = predicate_mapper[pred]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
499 if ids[id] == PROV_COMMUNICATION and 'activity' in six.text_type(pred_new):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
500 pred_new = PROV_ATTR_INFORMANT
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
501 if ids[id] == PROV_DELEGATION and 'agent' in six.text_type(pred_new):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
502 pred_new = PROV_ATTR_RESPONSIBLE
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guerler
parents:
diff changeset
503 if ids[id] in [PROV_END, PROV_START] and 'entity' in six.text_type(pred_new):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
504 pred_new = PROV_ATTR_TRIGGER
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guerler
parents:
diff changeset
505 if ids[id] in [PROV_END] and 'activity' in six.text_type(pred_new):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
506 pred_new = PROV_ATTR_ENDER
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guerler
parents:
diff changeset
507 if ids[id] in [PROV_START] and 'activity' in six.text_type(pred_new):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
508 pred_new = PROV_ATTR_STARTER
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guerler
parents:
diff changeset
509 if ids[id] == PROV_DERIVATION and 'entity' in six.text_type(pred_new):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
510 pred_new = PROV_ATTR_USED_ENTITY
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guerler
parents:
diff changeset
511 if six.text_type(pred_new) in [val.uri for val in formal_attributes[id]]:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
512 qname_key = self.valid_identifier(pred_new)
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guerler
parents:
diff changeset
513 formal_attributes[id][qname_key] = obj1
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guerler
parents:
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514 unique_sets[id][qname_key].append(obj1)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
515 if len(unique_sets[id][qname_key]) > 1:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
516 formal_attributes[id][qname_key] = None
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guerler
parents:
diff changeset
517 else:
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guerler
parents:
diff changeset
518 if 'qualified' not in six.text_type(pred_new) and \
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
519 'asInBundle' not in six.text_type(pred_new):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
520 other_attributes[id].append((six.text_type(pred_new), obj1))
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guerler
parents:
diff changeset
521 local_key = six.text_type(obj)
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guerler
parents:
diff changeset
522 if local_key in ids:
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guerler
parents:
diff changeset
523 if 'qualified' in pred:
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guerler
parents:
diff changeset
524 formal_attributes[local_key][list(formal_attributes[local_key].keys())[0]] = id
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guerler
parents:
diff changeset
525 for id in ids:
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guerler
parents:
diff changeset
526 attrs = None
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guerler
parents:
diff changeset
527 if id in other_attributes:
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guerler
parents:
diff changeset
528 attrs = other_attributes[id]
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guerler
parents:
diff changeset
529 items_to_walk = []
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guerler
parents:
diff changeset
530 for qname, values in unique_sets[id].items():
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guerler
parents:
diff changeset
531 if values and len(values) > 1:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
532 items_to_walk.append((qname, values))
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guerler
parents:
diff changeset
533 if items_to_walk:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
534 for subset in list(walk(items_to_walk)):
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guerler
parents:
diff changeset
535 for key, value in subset.items():
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guerler
parents:
diff changeset
536 formal_attributes[id][key] = value
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
537 bundle.new_record(ids[id], id, formal_attributes[id], attrs)
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guerler
parents:
diff changeset
538 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
539 bundle.new_record(ids[id], id, formal_attributes[id], attrs)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
540 ids[id] = None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
541 if attrs is not None:
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guerler
parents:
diff changeset
542 other_attributes[id] = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
543 for key, val in other_attributes.items():
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guerler
parents:
diff changeset
544 if val:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
545 ids[key].add_attributes(val)
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guerler
parents:
diff changeset
546
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guerler
parents:
diff changeset
547
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guerler
parents:
diff changeset
548 def walk(children, level=0, path=None, usename=True):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
549 """Generate all the full paths in a tree, as a dict.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
550
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guerler
parents:
diff changeset
551 :Example:
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guerler
parents:
diff changeset
552
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guerler
parents:
diff changeset
553 >>> from prov.serializers.provrdf import walk
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
554 >>> iterables = [('a', lambda: [1, 2]), ('b', lambda: [3, 4])]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
555 >>> [val['a'] for val in walk(iterables)]
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guerler
parents:
diff changeset
556 [1, 1, 2, 2]
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guerler
parents:
diff changeset
557 >>> [val['b'] for val in walk(iterables)]
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guerler
parents:
diff changeset
558 [3, 4, 3, 4]
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guerler
parents:
diff changeset
559 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
560 # Entry point
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guerler
parents:
diff changeset
561 if level == 0:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
562 path = {}
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
563 # Exit condition
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guerler
parents:
diff changeset
564 if not children:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
565 yield path.copy()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
566 return
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
567 # Tree recursion
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
568 head, tail = children[0], children[1:]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
569 name, func = head
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
570 for child in func:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
571 # We can use the arg name or the tree level as a key
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
572 if usename:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
573 path[name] = child
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
574 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
575 path[level] = child
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
576 # Recurse into the next level
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
577 for child_paths in walk(tail, level + 1, path, usename):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
578 yield child_paths
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
579
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
580
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
581 def literal_rdf_representation(literal):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
582 value = six.text_type(literal.value) if literal.value else literal
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
583 if literal.langtag:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
584 # a language tag can only go with prov:InternationalizedString
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
585 return RDFLiteral(value, lang=str(literal.langtag))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
586 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
587 datatype = literal.datatype
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
588 if 'base64Binary' in datatype.uri:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
589 if six.PY2:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
590 value = base64.standard_b64encode(value)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
591 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
592 value = literal.value.encode()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
593 return RDFLiteral(value, datatype=datatype.uri)