Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/prov/serializers/provxml.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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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 import datetime
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5 import logging
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6 from lxml import etree
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7 import io
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8 import warnings
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9 import prov
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10 import prov.identifier
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11 from prov.model import DEFAULT_NAMESPACES, sorted_attributes
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12 from prov.constants import * # NOQA
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13
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14
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15 __author__ = 'Lion Krischer'
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16 __email__ = 'krischer@geophysik.uni-muenchen.de'
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17
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18 logger = logging.getLogger(__name__)
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19
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20 # Create a dictionary containing all top-level PROV XML elements for an easy
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21 # mapping.
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22 FULL_NAMES_MAP = dict(PROV_N_MAP)
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23 FULL_NAMES_MAP.update(ADDITIONAL_N_MAP)
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24 # Inverse mapping.
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25 FULL_PROV_RECORD_IDS_MAP = dict((FULL_NAMES_MAP[rec_type_id], rec_type_id) for
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26 rec_type_id in FULL_NAMES_MAP)
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27
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28 XML_XSD_URI = 'http://www.w3.org/2001/XMLSchema'
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29
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30
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31 class ProvXMLException(prov.Error):
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32 pass
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33
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34
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35 class ProvXMLSerializer(prov.serializers.Serializer):
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36 """PROV-XML serializer for :class:`~prov.model.ProvDocument`
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37 """
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38 def serialize(self, stream, force_types=False, **kwargs):
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39 """
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40 Serializes a :class:`~prov.model.ProvDocument` instance to `PROV-XML
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41 <http://www.w3.org/TR/prov-xml/>`_.
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42
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43 :param stream: Where to save the output.
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44 :type force_types: boolean, optional
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45 :param force_types: Will force xsd:types to be written for most
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46 attributes mainly PROV-"attributes", e.g. tags not in the
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47 PROV namespace. Off by default meaning xsd:type attributes will
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48 only be set for prov:type, prov:location, and prov:value as is
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49 done in the official PROV-XML specification. Furthermore the
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50 types will always be set if the Python type requires it. False
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51 is a good default and it should rarely require changing.
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52 """
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53 xml_root = self.serialize_bundle(bundle=self.document,
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54 force_types=force_types)
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55 for bundle in self.document.bundles:
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56 self.serialize_bundle(bundle=bundle, element=xml_root,
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57 force_types=force_types)
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58 # No encoding must be specified when writing to String object which
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59 # does not have the concept of an encoding as it should already
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60 # represent unicode code points.
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61 et = etree.ElementTree(xml_root)
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62 if isinstance(stream, io.TextIOBase):
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63 stream.write(etree.tostring(et, xml_declaration=True,
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64 pretty_print=True).decode('utf-8'))
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65 else:
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66 et.write(stream, pretty_print=True, xml_declaration=True,
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67 encoding="UTF-8")
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68
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69 def serialize_bundle(self, bundle, element=None, force_types=False):
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70 """
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71 Serializes a bundle or document to PROV XML.
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72
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73 :param bundle: The bundle or document.
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74 :param element: The XML element to write to. Will be created if None.
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75 :type force_types: boolean, optional
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76 :param force_types: Will force xsd:types to be written for most
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77 attributes mainly PROV-"attributes", e.g. tags not in the
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78 PROV namespace. Off by default meaning xsd:type attributes will
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79 only be set for prov:type, prov:location, and prov:value as is
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80 done in the official PROV-XML specification. Furthermore the
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81 types will always be set if the Python type requires it. False
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82 is a good default and it should rarely require changing.
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83 """
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84 # Build the namespace map for lxml and attach it to the root XML
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85 # element. No dictionary comprehension in Python 2.6!
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86 nsmap = dict((ns.prefix, ns.uri) for ns in
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87 self.document._namespaces.get_registered_namespaces())
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88 if self.document._namespaces._default:
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89 nsmap[None] = self.document._namespaces._default.uri
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90 for namespace in bundle.namespaces:
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91 if namespace not in nsmap:
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92 nsmap[namespace.prefix] = namespace.uri
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93
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94 for key, value in DEFAULT_NAMESPACES.items():
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95 uri = value.uri
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96 if value.prefix == "xsd":
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97 # The XSD namespace for some reason has no hash at the end
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98 # for PROV XML, but for all other serializations it does.
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99 uri = uri.rstrip("#")
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100 nsmap[value.prefix] = uri
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101
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102 if element is not None:
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103 xml_bundle_root = etree.SubElement(
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104 element, _ns_prov("bundleContent"), nsmap=nsmap)
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105 else:
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106 xml_bundle_root = etree.Element(_ns_prov("document"), nsmap=nsmap)
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107
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108 if bundle.identifier:
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109 xml_bundle_root.attrib[_ns_prov("id")] = \
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110 six.text_type(bundle.identifier)
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111
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112 for record in bundle._records:
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113 rec_type = record.get_type()
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114 identifier = six.text_type(record._identifier) \
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115 if record._identifier else None
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116
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117 if identifier:
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118 attrs = {_ns_prov("id"): identifier}
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119 else:
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120 attrs = None
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121
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122 # Derive the record label from its attributes which is sometimes
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123 # needed.
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124 attributes = list(record.attributes)
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125 rec_label = self._derive_record_label(rec_type, attributes)
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126
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127 elem = etree.SubElement(xml_bundle_root,
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128 _ns_prov(rec_label), attrs)
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129
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130 for attr, value in sorted_attributes(rec_type, attributes):
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131 subelem = etree.SubElement(
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132 elem, _ns(attr.namespace.uri, attr.localpart))
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133 if isinstance(value, prov.model.Literal):
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134 if value.datatype not in \
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135 [None, PROV["InternationalizedString"]]:
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136 subelem.attrib[_ns_xsi("type")] = "%s:%s" % (
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137 value.datatype.namespace.prefix,
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138 value.datatype.localpart)
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139 if value.langtag is not None:
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140 subelem.attrib[_ns_xml("lang")] = value.langtag
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141 v = value.value
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142 elif isinstance(value, prov.model.QualifiedName):
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143 if attr not in PROV_ATTRIBUTE_QNAMES:
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144 subelem.attrib[_ns_xsi("type")] = "xsd:QName"
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145 v = six.text_type(value)
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146 elif isinstance(value, datetime.datetime):
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147 v = value.isoformat()
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148 else:
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149 v = six.text_type(value)
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150
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151 # xsd type inference.
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152 #
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153 # This is a bit messy and there are all kinds of special
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154 # rules but it appears to get the job done.
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155 #
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156 # If it is a type element and does not yet have an
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157 # associated xsi type, try to infer it from the value.
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158 # The not startswith("prov:") check is a little bit hacky to
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159 # avoid type interference when the type is a standard prov
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160 # type.
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161 #
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162 # To enable a mapping of Python types to XML and back,
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163 # the XSD type must be written for these types.
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164 ALWAYS_CHECK = [bool, datetime.datetime, float,
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165 prov.identifier.Identifier]
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166 # Add long and int on Python 2, only int on Python 3.
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167 ALWAYS_CHECK.extend(six.integer_types)
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168 ALWAYS_CHECK = tuple(ALWAYS_CHECK)
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169 if (force_types or
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170 type(value) in ALWAYS_CHECK or
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171 attr in [PROV_TYPE, PROV_LOCATION, PROV_VALUE]) and \
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172 _ns_xsi("type") not in subelem.attrib and \
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173 not six.text_type(value).startswith("prov:") and \
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174 not (attr in PROV_ATTRIBUTE_QNAMES and v) and \
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175 attr not in [PROV_ATTR_TIME, PROV_LABEL]:
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176 xsd_type = None
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177 if isinstance(value, bool):
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178 xsd_type = XSD_BOOLEAN
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179 v = v.lower()
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180 elif isinstance(value, six.string_types):
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181 xsd_type = XSD_STRING
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182 elif isinstance(value, float):
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183 xsd_type = XSD_DOUBLE
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184 elif isinstance(value, six.integer_types):
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185 xsd_type = XSD_INT
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186 elif isinstance(value, datetime.datetime):
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187 # Exception of the exception, while technically
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188 # still correct, do not write XSD dateTime type for
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189 # attributes in the PROV namespaces as the type is
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190 # already declared in the XSD and PROV XML also does
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191 # not specify it in the docs.
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192 if attr.namespace.prefix != "prov" \
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193 or "time" not in attr.localpart.lower():
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194 xsd_type = XSD_DATETIME
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195 elif isinstance(value, prov.identifier.Identifier):
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196 xsd_type = XSD_ANYURI
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197
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198 if xsd_type is not None:
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199 subelem.attrib[_ns_xsi("type")] = \
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200 six.text_type(xsd_type)
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201
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202 if attr in PROV_ATTRIBUTE_QNAMES and v:
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203 subelem.attrib[_ns_prov("ref")] = v
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204 else:
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205 subelem.text = v
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206 return xml_bundle_root
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207
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208 def deserialize(self, stream, **kwargs):
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209 """
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210 Deserialize from `PROV-XML <http://www.w3.org/TR/prov-xml/>`_
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211 representation to a :class:`~prov.model.ProvDocument` instance.
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212
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213 :param stream: Input data.
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214 """
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215 if isinstance(stream, io.TextIOBase):
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216 with io.BytesIO() as buf:
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217 buf.write(stream.read().encode('utf-8'))
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218 buf.seek(0, 0)
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219 xml_doc = etree.parse(buf).getroot()
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220 else:
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221 xml_doc = etree.parse(stream).getroot()
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222
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223 # Remove all comments.
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224 for c in xml_doc.xpath("//comment()"):
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225 p = c.getparent()
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226 p.remove(c)
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227
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228 document = prov.model.ProvDocument()
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229 self.deserialize_subtree(xml_doc, document)
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230 return document
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231
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232 def deserialize_subtree(self, xml_doc, bundle):
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233 """
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234 Deserialize an etree element containing a PROV document or a bundle
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235 and write it to the provided internal object.
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236
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237 :param xml_doc: An etree element containing the information to read.
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238 :param bundle: The bundle object to write to.
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239 """
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240
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241 for element in xml_doc:
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242 qname = etree.QName(element)
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243 if qname.namespace != DEFAULT_NAMESPACES["prov"].uri:
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244 raise ProvXMLException("Non PROV element discovered in "
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245 "document or bundle.")
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246 # Ignore the <prov:other> element storing non-PROV information.
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247 if qname.localname == "other":
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248 warnings.warn(
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249 "Document contains non-PROV information in "
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250 "<prov:other>. It will be ignored in this package.",
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251 UserWarning)
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252 continue
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253
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254 id_tag = _ns_prov("id")
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255 rec_id = element.attrib[id_tag] if id_tag in element.attrib \
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256 else None
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257
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258 if rec_id is not None:
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259 # Try to make a qualified name out of it!
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260 rec_id = xml_qname_to_QualifiedName(element, rec_id)
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261
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262 # Recursively read bundles.
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263 if qname.localname == "bundleContent":
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264 b = bundle.bundle(identifier=rec_id)
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265 self.deserialize_subtree(element, b)
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266 continue
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267
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268 attributes = _extract_attributes(element)
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269
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270 # Map the record type to its base type.
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271 q_prov_name = FULL_PROV_RECORD_IDS_MAP[qname.localname]
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272 rec_type = PROV_BASE_CLS[q_prov_name]
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273
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274 if _ns_xsi("type") in element.attrib:
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275 value = xml_qname_to_QualifiedName(
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276 element, element.attrib[_ns_xsi("type")]
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277 )
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278 attributes.append((PROV["type"], value))
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279
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280 rec = bundle.new_record(rec_type, rec_id, attributes)
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281
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282 # Add the actual type in case a base type has been used.
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283 if rec_type != q_prov_name:
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284 rec.add_asserted_type(q_prov_name)
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285 return bundle
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286
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287 def _derive_record_label(self, rec_type, attributes):
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288 """
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289 Helper function trying to derive the record label taking care of
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290 subtypes and what not. It will also remove the type declaration for
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291 the attributes if it was used to specialize the type.
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292
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293 :param rec_type: The type of records.
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294 :param attributes: The attributes of the record.
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295 """
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296 rec_label = FULL_NAMES_MAP[rec_type]
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297
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298 for key, value in list(attributes):
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299 if key != PROV_TYPE:
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300 continue
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301 if isinstance(value, prov.model.Literal):
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302 value = value.value
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303 if value in PROV_BASE_CLS and PROV_BASE_CLS[value] != value:
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304 attributes.remove((key, value))
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305 rec_label = FULL_NAMES_MAP[value]
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306 break
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307 return rec_label
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308
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309
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310 def _extract_attributes(element):
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311 """
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312 Extract the PROV attributes from an etree element.
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313
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314 :param element: The lxml.etree.Element instance.
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315 """
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316 attributes = []
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317 for subel in element:
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318 sqname = etree.QName(subel)
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319 _t = xml_qname_to_QualifiedName(
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320 subel, "%s:%s" % (subel.prefix, sqname.localname)
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321 )
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322
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323 for key, value in subel.attrib.items():
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324 if key == _ns_xsi("type"):
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325 datatype = xml_qname_to_QualifiedName(subel, value)
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326 if datatype == XSD_QNAME:
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327 _v = xml_qname_to_QualifiedName(subel, subel.text)
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328 else:
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329 _v = prov.model.Literal(subel.text, datatype)
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330 elif key == _ns_prov("ref"):
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331 _v = xml_qname_to_QualifiedName(subel, value)
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332 elif key == _ns_xml("lang"):
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333 _v = prov.model.Literal(subel.text, langtag=value)
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334 else:
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335 warnings.warn(
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336 "The element '%s' contains an attribute %s='%s' "
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337 "which is not representable in the prov module's "
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338 "internal data model and will thus be ignored." %
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339 (_t, six.text_type(key), six.text_type(value)),
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340 UserWarning)
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341
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342 if not subel.attrib:
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343 _v = subel.text
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344
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345 attributes.append((_t, _v))
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346
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347 return attributes
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348
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349
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350 def xml_qname_to_QualifiedName(element, qname_str):
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351 if ':' in qname_str:
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352 prefix, localpart = qname_str.split(':', 1)
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353 if prefix in element.nsmap:
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354 ns_uri = element.nsmap[prefix]
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355 if ns_uri == XML_XSD_URI:
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356 ns = XSD # use the standard xsd namespace (i.e. with #)
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357 elif ns_uri == PROV.uri:
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358 ns = PROV
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359 else:
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360 ns = Namespace(prefix, ns_uri)
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361 return ns[localpart]
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362 # case 1: no colon
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363 # case 2: unknown prefix
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364 if None in element.nsmap:
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365 ns_uri = element.nsmap[None]
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366 ns = Namespace('', ns_uri)
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367 return ns[qname_str]
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368 # no default namespace
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369 raise ProvXMLException(
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370 'Could not create a valid QualifiedName for "%s"' % qname_str
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371 )
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372
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373
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374 def _ns(ns, tag):
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375 return "{%s}%s" % (ns, tag)
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376
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377
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378 def _ns_prov(tag):
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379 return _ns(DEFAULT_NAMESPACES['prov'].uri, tag)
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380
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381
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382 def _ns_xsi(tag):
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383 return _ns(DEFAULT_NAMESPACES['xsi'].uri, tag)
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384
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385
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386 def _ns_xml(tag):
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387 NS_XML = "http://www.w3.org/XML/1998/namespace"
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388 return _ns(NS_XML, tag)