Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/prov/serializers/provjson.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 from __future__ import (absolute_import, division, print_function,
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2 unicode_literals)
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3
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4 from collections import defaultdict
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5 import datetime
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6 import io
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7 import json
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8
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9 from prov.serializers import Serializer, Error
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10 from prov.constants import *
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11 from prov.model import (Literal, Identifier, QualifiedName,
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12 Namespace, ProvDocument, ProvBundle, first,
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13 parse_xsd_datetime)
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14
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15 import logging
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16 logger = logging.getLogger(__name__)
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17
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18 __author__ = 'Trung Dong Huynh'
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19 __email__ = 'trungdong@donggiang.com'
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20
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21
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22 class ProvJSONException(Error):
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23 pass
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24
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25
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26 class AnonymousIDGenerator:
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27 def __init__(self):
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28 self._cache = {}
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29 self._count = 0
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30
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31 def get_anon_id(self, obj, local_prefix='id'):
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32 if obj not in self._cache:
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33 self._count += 1
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34 self._cache[obj] = Identifier(
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35 '_:%s%d' % (local_prefix, self._count)
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36 )
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37 return self._cache[obj]
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38
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39
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40 # Reverse map for prov.model.XSD_DATATYPE_PARSERS
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41 LITERAL_XSDTYPE_MAP = {
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42 float: 'xsd:double',
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43 int: 'xsd:int'
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44 # boolean, string values are supported natively by PROV-JSON
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45 # datetime values are converted separately
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46 }
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47
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48 # Add long on Python 2
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49 if six.integer_types[-1] not in LITERAL_XSDTYPE_MAP:
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50 LITERAL_XSDTYPE_MAP[six.integer_types[-1]] = 'xsd:long'
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51
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52
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53 class ProvJSONSerializer(Serializer):
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54 """
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55 PROV-JSON serializer for :class:`~prov.model.ProvDocument`
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56 """
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57 def serialize(self, stream, **kwargs):
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58 """
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59 Serializes a :class:`~prov.model.ProvDocument` instance to
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60 `PROV-JSON <https://provenance.ecs.soton.ac.uk/prov-json/>`_.
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61
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62 :param stream: Where to save the output.
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63 """
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64 if six.PY2:
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65 buf = io.BytesIO()
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66 try:
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67 json.dump(self.document, buf, cls=ProvJSONEncoder,
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68 **kwargs)
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69 buf.seek(0, 0)
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70 # Right now this is a bytestream. If the object to stream to is
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71 # a text object is must be decoded. We assume utf-8 here which
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72 # should be fine for almost every case.
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73 if isinstance(stream, io.TextIOBase):
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74 stream.write(buf.read().decode('utf-8'))
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75 else:
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76 stream.write(buf.read())
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77 finally:
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78 buf.close()
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79 else:
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80 buf = io.StringIO()
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81 try:
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82 json.dump(self.document, buf, cls=ProvJSONEncoder,
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83 **kwargs)
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84 buf.seek(0, 0)
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85 # Right now this is a bytestream. If the object to stream to is
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86 # a text object is must be decoded. We assume utf-8 here which
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87 # should be fine for almost every case.
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88 if isinstance(stream, io.TextIOBase):
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89 stream.write(buf.read())
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90 else:
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91 stream.write(buf.read().encode('utf-8'))
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92 finally:
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93 buf.close()
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94
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95 def deserialize(self, stream, **kwargs):
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96 """
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97 Deserialize from the `PROV JSON
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98 <https://provenance.ecs.soton.ac.uk/prov-json/>`_ representation to a
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99 :class:`~prov.model.ProvDocument` instance.
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100
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101 :param stream: Input data.
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102 """
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103 if not isinstance(stream, io.TextIOBase):
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104 buf = io.StringIO(stream.read().decode('utf-8'))
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105 stream = buf
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106 return json.load(stream, cls=ProvJSONDecoder, **kwargs)
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107
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108
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109 class ProvJSONEncoder(json.JSONEncoder):
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110 def default(self, o):
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111 if isinstance(o, ProvDocument):
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112 return encode_json_document(o)
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113 else:
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114 return super(ProvJSONEncoder, self).encode(o)
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115
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116
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117 class ProvJSONDecoder(json.JSONDecoder):
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118 def decode(self, s, *args, **kwargs):
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119 container = super(ProvJSONDecoder, self).decode(s, *args, **kwargs)
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120 document = ProvDocument()
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121 decode_json_document(container, document)
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122 return document
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123
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124
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125 # Encoding/decoding functions
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126 def valid_qualified_name(bundle, value):
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127 if value is None:
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128 return None
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129 qualified_name = bundle.valid_qualified_name(value)
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130 return qualified_name
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131
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132
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133 def encode_json_document(document):
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134 container = encode_json_container(document)
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135 for bundle in document.bundles:
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136 # encoding the sub-bundle
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137 bundle_json = encode_json_container(bundle)
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138 container['bundle'][six.text_type(bundle.identifier)] = bundle_json
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139 return container
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140
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141
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142 def encode_json_container(bundle):
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143 container = defaultdict(dict)
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144 prefixes = {}
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145 for namespace in bundle._namespaces.get_registered_namespaces():
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146 prefixes[namespace.prefix] = namespace.uri
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147 if bundle._namespaces._default:
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148 prefixes['default'] = bundle._namespaces._default.uri
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149 if prefixes:
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150 container['prefix'] = prefixes
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151
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152 id_generator = AnonymousIDGenerator()
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153
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154 def real_or_anon_id(r):
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155 return r._identifier if r._identifier else id_generator.get_anon_id(r)
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156
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157 for record in bundle._records:
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158 rec_type = record.get_type()
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159 rec_label = PROV_N_MAP[rec_type]
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160 identifier = six.text_type(real_or_anon_id(record))
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161
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162 record_json = {}
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163 if record._attributes:
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164 for (attr, values) in record._attributes.items():
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165 if not values:
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166 continue
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167 attr_name = six.text_type(attr)
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168 if attr in PROV_ATTRIBUTE_QNAMES:
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169 # TODO: QName export
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170 record_json[attr_name] = six.text_type(first(values))
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171 elif attr in PROV_ATTRIBUTE_LITERALS:
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172 record_json[attr_name] = first(values).isoformat()
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173 else:
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174 if len(values) == 1:
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175 # single value
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176 record_json[attr_name] = encode_json_representation(
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177 first(values)
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178 )
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179 else:
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180 # multiple values
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181 record_json[attr_name] = list(
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182 encode_json_representation(value)
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183 for value in values
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184 )
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185 # Check if the container already has the id of the record
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186 if identifier not in container[rec_label]:
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187 # this is the first instance, just put in the new record
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188 container[rec_label][identifier] = record_json
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189 else:
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190 # the container already has some record(s) of the same identifier
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191 # check if this is the second instance
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192 current_content = container[rec_label][identifier]
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193 if hasattr(current_content, 'items'):
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194 # this is a dict, make it a singleton list
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195 container[rec_label][identifier] = [current_content]
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196 # now append the new record to the list
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197 container[rec_label][identifier].append(record_json)
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198
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199 return container
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200
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201
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202 def decode_json_document(content, document):
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203 bundles = dict()
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204 if 'bundle' in content:
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205 bundles = content['bundle']
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206 del content['bundle']
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207
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208 decode_json_container(content, document)
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209
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210 for bundle_id, bundle_content in bundles.items():
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211 bundle = ProvBundle(document=document)
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212 decode_json_container(bundle_content, bundle)
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213 document.add_bundle(bundle, bundle.valid_qualified_name(bundle_id))
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214
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215
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216 def decode_json_container(jc, bundle):
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217 if 'prefix' in jc:
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218 prefixes = jc['prefix']
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219 for prefix, uri in prefixes.items():
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220 if prefix != 'default':
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221 bundle.add_namespace(Namespace(prefix, uri))
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222 else:
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223 bundle.set_default_namespace(uri)
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224 del jc['prefix']
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225
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226 for rec_type_str in jc:
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227 rec_type = PROV_RECORD_IDS_MAP[rec_type_str]
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228 for rec_id, content in jc[rec_type_str].items():
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229 if hasattr(content, 'items'): # it is a dict
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230 # There is only one element, create a singleton list
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231 elements = [content]
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232 else:
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233 # expect it to be a list of dictionaries
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234 elements = content
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235
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236 for element in elements:
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237 attributes = dict()
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238 other_attributes = []
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239 # this is for the multiple-entity membership hack to come
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240 membership_extra_members = None
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241 for attr_name, values in element.items():
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242 attr = (
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243 PROV_ATTRIBUTES_ID_MAP[attr_name]
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244 if attr_name in PROV_ATTRIBUTES_ID_MAP
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245 else valid_qualified_name(bundle, attr_name)
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246 )
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247 if attr in PROV_ATTRIBUTES:
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248 if isinstance(values, list):
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249 # only one value is allowed
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250 if len(values) > 1:
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251 # unless it is the membership hack
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252 if rec_type == PROV_MEMBERSHIP and \
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253 attr == PROV_ATTR_ENTITY:
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254 # This is a membership relation with
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255 # multiple entities
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256 # HACK: create multiple membership
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257 # relations, one for each entity
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258
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259 # Store all the extra entities
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260 membership_extra_members = values[1:]
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261 # Create the first membership relation as
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262 # normal for the first entity
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263 value = values[0]
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264 else:
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265 error_msg = (
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266 'The prov package does not support PROV'
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267 ' attributes having multiple values.'
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268 )
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269 logger.error(error_msg)
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270 raise ProvJSONException(error_msg)
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271 else:
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272 value = values[0]
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273 else:
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274 value = values
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275 value = (
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276 valid_qualified_name(bundle, value)
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277 if attr in PROV_ATTRIBUTE_QNAMES
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278 else parse_xsd_datetime(value)
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279 )
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280 attributes[attr] = value
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281 else:
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282 if isinstance(values, list):
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283 other_attributes.extend(
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284 (
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285 attr,
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286 decode_json_representation(value, bundle)
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287 )
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288 for value in values
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289 )
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290 else:
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291 # single value
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292 other_attributes.append(
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293 (
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294 attr,
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295 decode_json_representation(values, bundle)
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296 )
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297 )
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298 bundle.new_record(
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299 rec_type, rec_id, attributes, other_attributes
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300 )
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301 # HACK: creating extra (unidentified) membership relations
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302 if membership_extra_members:
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303 collection = attributes[PROV_ATTR_COLLECTION]
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304 for member in membership_extra_members:
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305 bundle.membership(
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306 collection, valid_qualified_name(bundle, member)
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307 )
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308
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309
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310 def encode_json_representation(value):
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311 if isinstance(value, Literal):
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312 return literal_json_representation(value)
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313 elif isinstance(value, datetime.datetime):
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314 return {'$': value.isoformat(), 'type': 'xsd:dateTime'}
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315 elif isinstance(value, QualifiedName):
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316 # TODO Manage prefix in the whole structure consistently
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317 # TODO QName export
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318 return {'$': str(value), 'type': PROV_QUALIFIEDNAME._str}
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319 elif isinstance(value, Identifier):
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320 return {'$': value.uri, 'type': 'xsd:anyURI'}
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321 elif type(value) in LITERAL_XSDTYPE_MAP:
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322 return {'$': value, 'type': LITERAL_XSDTYPE_MAP[type(value)]}
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323 else:
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324 return value
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325
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326
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327 def decode_json_representation(literal, bundle):
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328 if isinstance(literal, dict):
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329 # complex type
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330 value = literal['$']
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331 datatype = literal['type'] if 'type' in literal else None
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332 datatype = valid_qualified_name(bundle, datatype)
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333 langtag = literal['lang'] if 'lang' in literal else None
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334 if datatype == XSD_ANYURI:
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335 return Identifier(value)
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336 elif datatype == PROV_QUALIFIEDNAME:
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337 return valid_qualified_name(bundle, value)
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338 else:
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339 # The literal of standard Python types is not converted here
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340 # It will be automatically converted when added to a record by
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341 # _auto_literal_conversion()
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342 return Literal(value, datatype, langtag)
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343 else:
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344 # simple type, just return it
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345 return literal
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346
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347
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348 def literal_json_representation(literal):
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349 # TODO: QName export
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350 value, datatype, langtag = literal.value, literal.datatype, literal.langtag
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351 if langtag:
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352 return {'$': value, 'lang': langtag}
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353 else:
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354 return {'$': value, 'type': six.text_type(datatype)}