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annotate planemo/lib/python3.7/site-packages/prov/model.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 """Python implementation of the W3C Provenance Data Model (PROV-DM), including
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2 support for PROV-JSON import/export
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3
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4 References:
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5
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6 PROV-DM: http://www.w3.org/TR/prov-dm/
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7 PROV-JSON: https://provenance.ecs.soton.ac.uk/prov-json/
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8 """
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9 from __future__ import (absolute_import, division, print_function,
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10 unicode_literals)
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11
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12 from collections import defaultdict
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13 from copy import deepcopy
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14 import datetime
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15 import io
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16 import itertools
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17 import logging
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18 import os
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19 import shutil
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20 import tempfile
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21
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22 import dateutil.parser
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23 from prov import Error, serializers
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24 from prov.constants import *
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25 from prov.identifier import Identifier, QualifiedName, Namespace
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26 from six.moves.urllib.parse import urlparse
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27
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28
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29 __author__ = 'Trung Dong Huynh'
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30 __email__ = 'trungdong@donggiang.com'
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31
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32
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33 logger = logging.getLogger(__name__)
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34
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35
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36 # Data Types
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37 def _ensure_datetime(value):
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38 if isinstance(value, six.string_types):
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39 return dateutil.parser.parse(value)
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40 else:
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41 return value
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42
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43
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44 def parse_xsd_datetime(value):
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45 try:
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46 return dateutil.parser.parse(value)
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47 except ValueError:
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48 pass
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49 return None
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50
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51
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52 def parse_boolean(value):
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53 if value.lower() in ("false", "0"):
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54 return False
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55 elif value.lower() in ("true", "1"):
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56 return True
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57 else:
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58 return None
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59
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60 DATATYPE_PARSERS = {
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61 datetime.datetime: parse_xsd_datetime,
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62 }
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63
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64
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65 # Mappings for XSD datatypes to Python standard types
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66 XSD_DATATYPE_PARSERS = {
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67 XSD_STRING: six.text_type,
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68 XSD_DOUBLE: float,
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69 # long on Python 2, int on Python 3
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70 XSD_LONG: six.integer_types[-1],
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71 XSD_INT: int,
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72 XSD_BOOLEAN: parse_boolean,
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73 XSD_DATETIME: parse_xsd_datetime,
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74 XSD_ANYURI: Identifier
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75 }
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76
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77
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78 def parse_xsd_types(value, datatype):
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79 return (
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80 XSD_DATATYPE_PARSERS[datatype](value)
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81 if datatype in XSD_DATATYPE_PARSERS else None
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82 )
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83
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84
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85 def first(a_set):
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86 return next(iter(a_set), None)
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87
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88
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89 def _ensure_multiline_string_triple_quoted(value):
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90 # converting the value to a string
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91 s = six.text_type(value)
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92 # Escaping any double quote
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93 s = s.replace('"', '\\"')
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94 if '\n' in s:
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95 return '"""%s"""' % s
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96 else:
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97 return '"%s"' % s
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98
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99
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100 def encoding_provn_value(value):
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101 if isinstance(value, six.string_types):
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102 return _ensure_multiline_string_triple_quoted(value)
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103 elif isinstance(value, datetime.datetime):
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104 return u'"{0}" %% xsd:dateTime'.format(value.isoformat())
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105 elif isinstance(value, float):
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106 return u'"%g" %%%% xsd:float' % value
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107 elif isinstance(value, bool):
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108 return u'"%i" %%%% xsd:boolean' % value
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109 else:
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110 # TODO: QName export
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111 return six.text_type(value)
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112
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113
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114 @six.python_2_unicode_compatible
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115 class Literal(object):
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116 def __init__(self, value, datatype=None, langtag=None):
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117 self._value = six.text_type(value) # value is always a string
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118 if langtag:
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119 if datatype is None:
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120 logger.debug(
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121 'Assuming prov:InternationalizedString as the type of '
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122 '"%s"@%s' % (value, langtag)
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123 )
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124 datatype = PROV["InternationalizedString"]
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125 # PROV JSON states that the type field must not be set when
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126 # using the lang attribute and PROV XML requires it to be an
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127 # internationalized string.
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128 elif datatype != PROV["InternationalizedString"]:
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129 logger.warn(
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130 'Invalid data type (%s) for "%s"@%s, overridden as '
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131 'prov:InternationalizedString.' %
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132 (datatype, value, langtag)
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133 )
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134 datatype = PROV["InternationalizedString"]
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135 self._datatype = datatype
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136 # langtag is always a string
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137 self._langtag = six.text_type(langtag) if langtag is not None else None
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138
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139 def __str__(self):
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140 return self.provn_representation()
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141
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142 def __repr__(self):
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143 return u'<Literal: %s>' % self.provn_representation()
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144
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145 def __eq__(self, other):
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146 return (
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147 (self._value == other.value and
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148 self._datatype == other.datatype and
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149 self._langtag == other.langtag)
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150 if isinstance(other, Literal) else False
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151 )
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152
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153 def __ne__(self, other):
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154 return not (self == other)
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155
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156 def __hash__(self):
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157 return hash((self._value, self._datatype, self._langtag))
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158
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159 @property
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160 def value(self):
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161 return self._value
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162
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163 @property
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164 def datatype(self):
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165 return self._datatype
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166
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167 @property
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168 def langtag(self):
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169 return self._langtag
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170
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171 def has_no_langtag(self):
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172 return self._langtag is None
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173
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174 def provn_representation(self):
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175 if self._langtag:
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176 # a language tag can only go with prov:InternationalizedString
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177 return '%s@%s' % (
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178 _ensure_multiline_string_triple_quoted(self._value),
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179 six.text_type(self._langtag)
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180 )
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181 else:
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182 return '%s %%%% %s' % (
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183 _ensure_multiline_string_triple_quoted(self._value),
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184 six.text_type(self._datatype)
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185 )
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186
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187
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188 # Exceptions and warnings
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189 class ProvException(Error):
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190 """Base class for PROV model exceptions."""
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191 pass
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192
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193
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194 class ProvWarning(Warning):
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195 """Base class for PROV model warnings."""
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196 pass
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197
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198
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199 @six.python_2_unicode_compatible
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200 class ProvExceptionInvalidQualifiedName(ProvException):
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201 """Exception for an invalid qualified identifier name."""
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202
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203 qname = None
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204 """Intended qualified name."""
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205
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206 def __init__(self, qname):
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207 """
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208 Constructor.
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209
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210 :param qname: Invalid qualified name.
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211 """
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212 self.qname = qname
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213
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214 def __str__(self):
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215 return u'Invalid Qualified Name: %s' % self.qname
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216
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217
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218 @six.python_2_unicode_compatible
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219 class ProvElementIdentifierRequired(ProvException):
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220 """Exception for a missing element identifier."""
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221
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222 def __str__(self):
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223 return u'An identifier is missing. All PROV elements require a valid ' \
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224 u'identifier.'
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225
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226
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227 # PROV records
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228 @six.python_2_unicode_compatible
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229 class ProvRecord(object):
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230 """Base class for PROV records."""
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231
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232 FORMAL_ATTRIBUTES = ()
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233
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234 _prov_type = None
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235 """PROV type of record."""
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236
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237 def __init__(self, bundle, identifier, attributes=None):
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238 """
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239 Constructor.
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240
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241 :param bundle: Bundle for the PROV record.
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242 :param identifier: (Unique) identifier of the record.
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243 :param attributes: Attributes to associate with the record (default: None).
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244 """
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245 self._bundle = bundle
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246 self._identifier = identifier
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247 self._attributes = defaultdict(set)
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248 if attributes:
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249 self.add_attributes(attributes)
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250
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251 def __hash__(self):
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252 return hash(
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253 (self.get_type(), self._identifier, frozenset(self.attributes))
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254 )
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255
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256 def copy(self):
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257 """
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258 Return an exact copy of this record.
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259 """
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260 return PROV_REC_CLS[self.get_type()](
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261 self._bundle, self.identifier, self.attributes
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262 )
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263
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264 def get_type(self):
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265 """Returns the PROV type of the record."""
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266 return self._prov_type
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267
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268 def get_asserted_types(self):
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269 """Returns the set of all asserted PROV types of this record."""
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270 return self._attributes[PROV_TYPE]
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271
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272 def add_asserted_type(self, type_identifier):
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273 """
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274 Adds a PROV type assertion to the record.
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275
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276 :param type_identifier: PROV namespace identifier to add.
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277 """
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278 self._attributes[PROV_TYPE].add(type_identifier)
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279
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280 def get_attribute(self, attr_name):
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281 """
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282 Returns the attribute of the given name.
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283
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284 :param attr_name: Name of the attribute.
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285 :return: Tuple (name, value)
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286 """
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287 attr_name = self._bundle.valid_qualified_name(attr_name)
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288 return self._attributes[attr_name]
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289
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290 @property
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291 def identifier(self):
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292 """Record's identifier."""
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293 return self._identifier
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294
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295 @property
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296 def attributes(self):
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297 """
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298 All record attributes.
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299
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300 :return: List of tuples (name, value)
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301 """
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302 return [
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303 (attr_name, value)
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304 for attr_name, values in self._attributes.items()
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305 for value in values
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306 ]
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307
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308 @property
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309 def args(self):
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310 """
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311 All values of the record's formal attributes.
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312
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313 :return: Tuple
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314 """
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315 return tuple(
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316 first(self._attributes[attr_name])
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317 for attr_name in self.FORMAL_ATTRIBUTES
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318 )
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319
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320 @property
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321 def formal_attributes(self):
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322 """
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323 All names and values of the record's formal attributes.
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324
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325 :return: Tuple of tuples (name, value)
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326 """
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327 return tuple(
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328 (attr_name, first(self._attributes[attr_name]))
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329 for attr_name in self.FORMAL_ATTRIBUTES
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330 )
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331
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332 @property
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333 def extra_attributes(self):
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334 """
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335 All names and values of the record's attributes that are not formal
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336 attributes.
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337
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338 :return: Tuple of tuples (name, value)
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339 """
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340 return [
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341 (attr_name, attr_value) for attr_name, attr_value in self.attributes
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342 if attr_name not in self.FORMAL_ATTRIBUTES
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343 ]
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344
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345 @property
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346 def bundle(self):
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347 """
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348 Bundle of the record.
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349
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350 :return: :py:class:`ProvBundle`
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351 """
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352 return self._bundle
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353
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354 @property
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355 def label(self):
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356 """Identifying label of the record."""
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357 return first(self._attributes[PROV_LABEL]) \
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358 if self._attributes[PROV_LABEL] else self._identifier
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359
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360 @property
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361 def value(self):
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362 """Value of the record."""
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363 return self._attributes[PROV_VALUE]
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364
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365 # Handling attributes
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366 def _auto_literal_conversion(self, literal):
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367 # This method normalise datatype for literals
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368
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369 if isinstance(literal, ProvRecord):
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370 # Use the QName of the record as the literal
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371 literal = literal.identifier
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372
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373 if isinstance(literal, str):
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374 return six.text_type(literal)
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375 elif isinstance(literal, QualifiedName):
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376 return self._bundle.valid_qualified_name(literal)
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377 elif isinstance(literal, Literal) and literal.has_no_langtag():
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378 if literal.datatype:
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379 # try convert generic Literal object to Python standard type
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380 # this is to match JSON decoding's literal conversion
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381 value = parse_xsd_types(literal.value, literal.datatype)
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382 else:
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383 # A literal with no datatype nor langtag defined
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384 # try auto-converting the value
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385 value = self._auto_literal_conversion(literal.value)
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386 if value is not None:
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387 return value
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388
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389 # No conversion possible, return the original value
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390 return literal
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391
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392 def add_attributes(self, attributes):
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393 """
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394 Add attributes to the record.
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395
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396 :param attributes: Dictionary of attributes, with keys being qualified
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397 identifiers. Alternatively an iterable of tuples (key, value) with the
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398 keys satisfying the same condition.
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guerler
parents:
diff changeset
399 """
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guerler
parents:
diff changeset
400 if attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
401 if isinstance(attributes, dict):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
402 # Converting the dictionary into a list of tuples
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guerler
parents:
diff changeset
403 # (i.e. attribute-value pairs)
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parents:
diff changeset
404 attributes = attributes.items()
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parents:
diff changeset
405
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parents:
diff changeset
406 # Check if one of the attributes specifies that the current type
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
407 # is a collection. In that case multiple attributes of the same
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guerler
parents:
diff changeset
408 # type are allowed.
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parents:
diff changeset
409 if PROV_ATTR_COLLECTION in [_i[0] for _i in attributes]:
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parents:
diff changeset
410 is_collection = True
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parents:
diff changeset
411 else:
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diff changeset
412 is_collection = False
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guerler
parents:
diff changeset
413
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parents:
diff changeset
414 for attr_name, original_value in attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
415 if original_value is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
416 continue
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parents:
diff changeset
417
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guerler
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diff changeset
418 # make sure the attribute name is valid
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diff changeset
419 attr = self._bundle.valid_qualified_name(attr_name)
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diff changeset
420 if attr is None:
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421 raise ProvExceptionInvalidQualifiedName(attr_name)
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parents:
diff changeset
422
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423 if attr in PROV_ATTRIBUTE_QNAMES:
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parents:
diff changeset
424 # Expecting a qualified name
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425 qname = original_value.identifier \
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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426 if isinstance(original_value, ProvRecord) \
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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427 else original_value
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428 value = self._bundle.valid_qualified_name(qname)
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guerler
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diff changeset
429 elif attr in PROV_ATTRIBUTE_LITERALS:
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diff changeset
430 value = original_value \
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431 if isinstance(original_value, datetime.datetime) \
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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432 else parse_xsd_datetime(original_value)
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diff changeset
433 else:
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434 value = self._auto_literal_conversion(original_value)
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435
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436 if value is None:
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parents:
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437 raise ProvException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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438 'Invalid value for attribute %s: %s' %
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parents:
diff changeset
439 (attr, original_value)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
440 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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441
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442 if not is_collection and attr in PROV_ATTRIBUTES and \
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
443 self._attributes[attr]:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
444 existing_value = first(self._attributes[attr])
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445 is_not_same_value = True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
446 try:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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447 is_not_same_value = value != existing_value
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guerler
parents:
diff changeset
448 except TypeError:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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449 # Cannot compare them
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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450 pass # consider them different values
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guerler
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diff changeset
451
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parents:
diff changeset
452 if is_not_same_value:
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453 raise ProvException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
454 'Cannot have more than one value for attribute %s'
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guerler
parents:
diff changeset
455 % attr
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guerler
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diff changeset
456 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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457 else:
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guerler
parents:
diff changeset
458 # Same value, ignore it
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diff changeset
459 continue
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diff changeset
460
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461 self._attributes[attr].add(value)
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462
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463 def __eq__(self, other):
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diff changeset
464 if self.get_type() != other.get_type():
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diff changeset
465 return False
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diff changeset
466 if self._identifier and not (self._identifier == other._identifier):
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diff changeset
467 return False
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guerler
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diff changeset
468
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diff changeset
469 return set(self.attributes) == set(other.attributes)
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guerler
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diff changeset
470
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guerler
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diff changeset
471 def __str__(self):
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diff changeset
472 return self.get_provn()
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diff changeset
473
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diff changeset
474 def get_provn(self):
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diff changeset
475 """
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diff changeset
476 Returns the PROV-N representation of the record.
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guerler
parents:
diff changeset
477
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guerler
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diff changeset
478 :return: String
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
479 """
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diff changeset
480 items = []
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diff changeset
481
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guerler
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diff changeset
482 # Generating identifier
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diff changeset
483 relation_id = '' # default blank
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parents:
diff changeset
484 if self._identifier:
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parents:
diff changeset
485 identifier = six.text_type(self._identifier) # TODO: QName export
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guerler
parents:
diff changeset
486 if self.is_element():
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diff changeset
487 items.append(identifier)
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diff changeset
488 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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489 # this is a relation
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490 # relations use ; to separate identifiers
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guerler
parents:
diff changeset
491 relation_id = identifier + '; '
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parents:
diff changeset
492
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guerler
parents:
diff changeset
493 # Writing out the formal attributes
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parents:
diff changeset
494 for attr in self.FORMAL_ATTRIBUTES:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
495 if attr in self._attributes and self._attributes[attr]:
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guerler
parents:
diff changeset
496 # Formal attributes always have single values
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diff changeset
497 value = first(self._attributes[attr])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
498 # TODO: QName export
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
499 items.append(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
500 value.isoformat() if isinstance(value, datetime.datetime)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
501 else six.text_type(value)
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guerler
parents:
diff changeset
502 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
503 else:
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parents:
diff changeset
504 items.append('-')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
505
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guerler
parents:
diff changeset
506 # Writing out the remaining attributes
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guerler
parents:
diff changeset
507 extra = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
508 for attr in self._attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
509 if attr not in self.FORMAL_ATTRIBUTES:
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guerler
parents:
diff changeset
510 for value in self._attributes[attr]:
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guerler
parents:
diff changeset
511 try:
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guerler
parents:
diff changeset
512 # try if there is a prov-n representation defined
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guerler
parents:
diff changeset
513 provn_represenation = value.provn_representation()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
514 except AttributeError:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
515 provn_represenation = encoding_provn_value(value)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
516 # TODO: QName export
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guerler
parents:
diff changeset
517 extra.append(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
518 '%s=%s' % (six.text_type(attr), provn_represenation)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
519 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
520
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
521 if extra:
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parents:
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522 items.append('[%s]' % ', '.join(extra))
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guerler
parents:
diff changeset
523 prov_n = '%s(%s%s)' % (
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guerler
parents:
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524 PROV_N_MAP[self.get_type()], relation_id, ', '.join(items)
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guerler
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diff changeset
525 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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diff changeset
526 return prov_n
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guerler
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diff changeset
527
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diff changeset
528 def is_element(self):
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diff changeset
529 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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530 True, if the record is an element, False otherwise.
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531
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532 :return: bool
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533 """
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534 return False
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535
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536 def is_relation(self):
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537 """
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538 True, if the record is a relation, False otherwise.
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539
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540 :return: bool
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541 """
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542 return False
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543
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544
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545 # Abstract classes for elements and relations
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546 class ProvElement(ProvRecord):
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547 """Provenance Element (nodes in the provenance graph)."""
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548
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549 def __init__(self, bundle, identifier, attributes=None):
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550 if identifier is None:
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551 # All types of PROV elements require a valid identifier
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552 raise ProvElementIdentifierRequired()
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553
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554 super(ProvElement, self).__init__(bundle, identifier, attributes)
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555
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556 def is_element(self):
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557 """
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558 True, if the record is an element, False otherwise.
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559
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560 :return: bool
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561 """
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562 return True
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563
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564 def __repr__(self):
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565 return '<%s: %s>' % (self.__class__.__name__, self._identifier)
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566
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567
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568 class ProvRelation(ProvRecord):
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569 """Provenance Relationship (edge between nodes)."""
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570
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571 def is_relation(self):
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572 """
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573 True, if the record is a relation, False otherwise.
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574
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575 :return: bool
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576 """
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577 return True
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578
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579 def __repr__(self):
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580 identifier = ' %s' % self._identifier if self._identifier else ''
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581 element_1, element_2 = [
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582 qname for _, qname in self.formal_attributes[:2]
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583 ]
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584 return '<%s:%s (%s, %s)>' % (
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585 self.__class__.__name__, identifier, element_1, element_2
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586 )
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587
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588
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589 # Component 1: Entities and Activities
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590 class ProvEntity(ProvElement):
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591 """Provenance Entity element"""
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592
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593 _prov_type = PROV_ENTITY
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594
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595 # Convenient assertions that take the current ProvEntity as the first
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596 # (formal) argument
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597 def wasGeneratedBy(self, activity, time=None, attributes=None):
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598 """
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599 Creates a new generation record to this entity.
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600
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601 :param activity: Activity or string identifier of the activity involved in
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602 the generation (default: None).
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603 :param time: Optional time for the generation (default: None).
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604 Either a :py:class:`datetime.datetime` object or a string that can be
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605 parsed by :py:func:`dateutil.parser`.
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606 :param attributes: Optional other attributes as a dictionary or list
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607 of tuples to be added to the record optionally (default: None).
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608 """
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609 self._bundle.generation(
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610 self, activity, time, other_attributes=attributes
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611 )
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612 return self
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613
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614 def wasInvalidatedBy(self, activity, time=None, attributes=None):
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615 """
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616 Creates a new invalidation record for this entity.
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617
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618 :param activity: Activity or string identifier of the activity involved in
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619 the invalidation (default: None).
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620 :param time: Optional time for the invalidation (default: None).
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621 Either a :py:class:`datetime.datetime` object or a string that can be
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622 parsed by :py:func:`dateutil.parser`.
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623 :param attributes: Optional other attributes as a dictionary or list
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624 of tuples to be added to the record optionally (default: None).
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625 """
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626 self._bundle.invalidation(
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627 self, activity, time, other_attributes=attributes
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628 )
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629 return self
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630
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631 def wasDerivedFrom(self, usedEntity, activity=None, generation=None,
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632 usage=None, attributes=None):
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633 """
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634 Creates a new derivation record for this entity from a used entity.
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635
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636 :param usedEntity: Entity or a string identifier for the used entity.
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637 :param activity: Activity or string identifier of the activity involved in
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638 the derivation (default: None).
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639 :param generation: Optionally extra activity to state qualified derivation
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640 through an internal generation (default: None).
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641 :param usage: Optionally extra entity to state qualified derivation through
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642 an internal usage (default: None).
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643 :param attributes: Optional other attributes as a dictionary or list
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644 of tuples to be added to the record optionally (default: None).
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645 """
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646 self._bundle.derivation(
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647 self, usedEntity, activity, generation, usage,
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648 other_attributes=attributes
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649 )
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650 return self
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651
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652 def wasAttributedTo(self, agent, attributes=None):
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653 """
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654 Creates a new attribution record between this entity and an agent.
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655
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656 :param agent: Agent or string identifier of the agent involved in the
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657 attribution.
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658 :param attributes: Optional other attributes as a dictionary or list
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659 of tuples to be added to the record optionally (default: None).
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660 """
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661 self._bundle.attribution(self, agent, other_attributes=attributes)
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662 return self
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663
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664 def alternateOf(self, alternate2):
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diff changeset
665 """
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parents:
diff changeset
666 Creates a new alternate record between this and another entity.
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diff changeset
667
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diff changeset
668 :param alternate2: Entity or a string identifier for the second entity.
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diff changeset
669 """
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diff changeset
670 self._bundle.alternate(self, alternate2)
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diff changeset
671 return self
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diff changeset
672
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diff changeset
673 def specializationOf(self, generalEntity):
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diff changeset
674 """
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parents:
diff changeset
675 Creates a new specialisation record for this from a general entity.
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676
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diff changeset
677 :param generalEntity: Entity or a string identifier for the general entity.
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678 """
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diff changeset
679 self._bundle.specialization(self, generalEntity)
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diff changeset
680 return self
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681
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682 def hadMember(self, entity):
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diff changeset
683 """
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diff changeset
684 Creates a new membership record to an entity for a collection.
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685
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diff changeset
686 :param entity: Entity to be added to the collection.
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687 """
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688 self._bundle.membership(self, entity)
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689 return self
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690
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691
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692 class ProvActivity(ProvElement):
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693 """Provenance Activity element."""
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694
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695 FORMAL_ATTRIBUTES = (PROV_ATTR_STARTTIME, PROV_ATTR_ENDTIME)
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696
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697 _prov_type = PROV_ACTIVITY
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diff changeset
698
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699 # Convenient methods
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700 def set_time(self, startTime=None, endTime=None):
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701 """
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702 Sets the time this activity took place.
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703
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704 :param startTime: Start time for the activity.
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diff changeset
705 Either a :py:class:`datetime.datetime` object or a string that can be
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diff changeset
706 parsed by :py:func:`dateutil.parser`.
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707 :param endTime: Start time for the activity.
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diff changeset
708 Either a :py:class:`datetime.datetime` object or a string that can be
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parents:
diff changeset
709 parsed by :py:func:`dateutil.parser`.
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710 """
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711 if startTime is not None:
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diff changeset
712 self._attributes[PROV_ATTR_STARTTIME] = {startTime}
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713 if endTime is not None:
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714 self._attributes[PROV_ATTR_ENDTIME] = {endTime}
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715
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716 def get_startTime(self):
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717 """
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718 Returns the time the activity started.
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diff changeset
719
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720 :return: :py:class:`datetime.datetime`
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721 """
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722 values = self._attributes[PROV_ATTR_STARTTIME]
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diff changeset
723 return first(values) if values else None
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724
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725 def get_endTime(self):
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726 """
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diff changeset
727 Returns the time the activity ended.
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diff changeset
728
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diff changeset
729 :return: :py:class:`datetime.datetime`
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730 """
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731 values = self._attributes[PROV_ATTR_ENDTIME]
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732 return first(values) if values else None
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diff changeset
733
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diff changeset
734 # Convenient assertions that take the current ProvActivity as the first
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parents:
diff changeset
735 # (formal) argument
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736 def used(self, entity, time=None, attributes=None):
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diff changeset
737 """
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diff changeset
738 Creates a new usage record for this activity.
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diff changeset
739
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diff changeset
740 :param entity: Entity or string identifier of the entity involved in
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741 the usage relationship (default: None).
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742 :param time: Optional time for the usage (default: None).
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diff changeset
743 Either a :py:class:`datetime.datetime` object or a string that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
744 parsed by :py:func:`dateutil.parser`.
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diff changeset
745 :param attributes: Optional other attributes as a dictionary or list
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diff changeset
746 of tuples to be added to the record optionally (default: None).
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diff changeset
747 """
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diff changeset
748 self._bundle.usage(self, entity, time, other_attributes=attributes)
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diff changeset
749 return self
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750
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diff changeset
751 def wasInformedBy(self, informant, attributes=None):
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diff changeset
752 """
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diff changeset
753 Creates a new communication record for this activity.
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diff changeset
754
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diff changeset
755 :param informant: The informing activity (relationship source).
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diff changeset
756 :param attributes: Optional other attributes as a dictionary or list
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diff changeset
757 of tuples to be added to the record optionally (default: None).
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758 """
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759 self._bundle.communication(
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diff changeset
760 self, informant, other_attributes=attributes
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diff changeset
761 )
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762 return self
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diff changeset
763
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diff changeset
764 def wasStartedBy(self, trigger, starter=None, time=None, attributes=None):
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diff changeset
765 """
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diff changeset
766 Creates a new start record for this activity. The activity did not exist
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diff changeset
767 before the start by the trigger.
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diff changeset
768
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diff changeset
769 :param trigger: Entity triggering the start of this activity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
770 :param starter: Optionally extra activity to state a qualified start
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parents:
diff changeset
771 through which the trigger entity for the start is generated
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diff changeset
772 (default: None).
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diff changeset
773 :param time: Optional time for the start (default: None).
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parents:
diff changeset
774 Either a :py:class:`datetime.datetime` object or a string that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
775 parsed by :py:func:`dateutil.parser`.
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guerler
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diff changeset
776 :param attributes: Optional other attributes as a dictionary or list
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diff changeset
777 of tuples to be added to the record optionally (default: None).
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778 """
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diff changeset
779 self._bundle.start(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
780 self, trigger, starter, time, other_attributes=attributes
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parents:
diff changeset
781 )
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782 return self
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783
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784 def wasEndedBy(self, trigger, ender=None, time=None, attributes=None):
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diff changeset
785 """
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diff changeset
786 Creates a new end record for this activity.
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guerler
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diff changeset
787
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diff changeset
788 :param trigger: Entity triggering the end of this activity.
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diff changeset
789 :param ender: Optionally extra activity to state a qualified end through
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diff changeset
790 which the trigger entity for the end is generated (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
791 :param time: Optional time for the end (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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792 Either a :py:class:`datetime.datetime` object or a string that can be
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793 parsed by :py:func:`dateutil.parser`.
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794 :param attributes: Optional other attributes as a dictionary or list
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795 of tuples to be added to the record optionally (default: None).
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796 """
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797 self._bundle.end(
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798 self, trigger, ender, time, other_attributes=attributes
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799 )
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800 return self
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801
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802 def wasAssociatedWith(self, agent, plan=None, attributes=None):
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803 """
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804 Creates a new association record for this activity.
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805
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806 :param agent: Agent or string identifier of the agent involved in the
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diff changeset
807 association (default: None).
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808 :param plan: Optionally extra entity to state qualified association through
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809 an internal plan (default: None).
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810 :param attributes: Optional other attributes as a dictionary or list
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811 of tuples to be added to the record optionally (default: None).
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812 """
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813 self._bundle.association(
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814 self, agent, plan, other_attributes=attributes
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815 )
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816 return self
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817
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818
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819 class ProvGeneration(ProvRelation):
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820 """Provenance Generation relationship."""
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821
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822 FORMAL_ATTRIBUTES = (PROV_ATTR_ENTITY, PROV_ATTR_ACTIVITY, PROV_ATTR_TIME)
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823
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824 _prov_type = PROV_GENERATION
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825
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826
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827 class ProvUsage(ProvRelation):
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828 """Provenance Usage relationship."""
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829
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830 FORMAL_ATTRIBUTES = (PROV_ATTR_ACTIVITY, PROV_ATTR_ENTITY, PROV_ATTR_TIME)
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831
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832 _prov_type = PROV_USAGE
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833
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834
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835 class ProvCommunication(ProvRelation):
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836 """Provenance Communication relationship."""
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837
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838 FORMAL_ATTRIBUTES = (PROV_ATTR_INFORMED, PROV_ATTR_INFORMANT)
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839
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840 _prov_type = PROV_COMMUNICATION
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841
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842
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843 class ProvStart(ProvRelation):
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844 """Provenance Start relationship."""
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845
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846 FORMAL_ATTRIBUTES = (PROV_ATTR_ACTIVITY, PROV_ATTR_TRIGGER,
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847 PROV_ATTR_STARTER, PROV_ATTR_TIME)
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848
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849 _prov_type = PROV_START
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850
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851
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852 class ProvEnd(ProvRelation):
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853 """Provenance End relationship."""
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854
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855 FORMAL_ATTRIBUTES = (PROV_ATTR_ACTIVITY, PROV_ATTR_TRIGGER,
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856 PROV_ATTR_ENDER, PROV_ATTR_TIME)
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857
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858 _prov_type = PROV_END
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859
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860
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861 class ProvInvalidation(ProvRelation):
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862 """Provenance Invalidation relationship."""
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863
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864 FORMAL_ATTRIBUTES = (PROV_ATTR_ENTITY, PROV_ATTR_ACTIVITY, PROV_ATTR_TIME)
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865
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866 _prov_type = PROV_INVALIDATION
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867
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868
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869 # Component 2: Derivations
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870 class ProvDerivation(ProvRelation):
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871 """Provenance Derivation relationship."""
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872
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873 FORMAL_ATTRIBUTES = (PROV_ATTR_GENERATED_ENTITY, PROV_ATTR_USED_ENTITY,
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874 PROV_ATTR_ACTIVITY, PROV_ATTR_GENERATION,
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875 PROV_ATTR_USAGE)
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876
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877 _prov_type = PROV_DERIVATION
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878
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879
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880 # Component 3: Agents, Responsibility, and Influence
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881 class ProvAgent(ProvElement):
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882 """Provenance Agent element."""
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883
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884 _prov_type = PROV_AGENT
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885
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886 # Convenient assertions that take the current ProvAgent as the first
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887 # (formal) argument
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888 def actedOnBehalfOf(self, responsible, activity=None, attributes=None):
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889 """
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890 Creates a new delegation record on behalf of this agent.
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891
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892 :param responsible: Agent the responsibility is delegated to.
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893 :param activity: Optionally extra activity to state qualified delegation
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894 internally (default: None).
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895 :param attributes: Optional other attributes as a dictionary or list
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896 of tuples to be added to the record optionally (default: None).
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897 """
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898 self._bundle.delegation(
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899 self, responsible, activity, other_attributes=attributes
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900 )
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901 return self
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902
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903
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904 class ProvAttribution(ProvRelation):
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905 """Provenance Attribution relationship."""
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906
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907 FORMAL_ATTRIBUTES = (PROV_ATTR_ENTITY, PROV_ATTR_AGENT)
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908
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909 _prov_type = PROV_ATTRIBUTION
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910
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911
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912 class ProvAssociation(ProvRelation):
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913 """Provenance Association relationship."""
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914
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915 FORMAL_ATTRIBUTES = (PROV_ATTR_ACTIVITY, PROV_ATTR_AGENT, PROV_ATTR_PLAN)
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916
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917 _prov_type = PROV_ASSOCIATION
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918
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919
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920 class ProvDelegation(ProvRelation):
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921 """Provenance Delegation relationship."""
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922
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923 FORMAL_ATTRIBUTES = (PROV_ATTR_DELEGATE, PROV_ATTR_RESPONSIBLE,
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924 PROV_ATTR_ACTIVITY)
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925
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926 _prov_type = PROV_DELEGATION
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927
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928
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929 class ProvInfluence(ProvRelation):
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930 """Provenance Influence relationship."""
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diff changeset
931
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932 FORMAL_ATTRIBUTES = (PROV_ATTR_INFLUENCEE, PROV_ATTR_INFLUENCER)
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933
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934 _prov_type = PROV_INFLUENCE
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935
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936
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937 # Component 5: Alternate Entities
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938 class ProvSpecialization(ProvRelation):
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939 """Provenance Specialization relationship."""
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940
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941 FORMAL_ATTRIBUTES = (PROV_ATTR_SPECIFIC_ENTITY, PROV_ATTR_GENERAL_ENTITY)
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942
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943 _prov_type = PROV_SPECIALIZATION
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944
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945
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946 class ProvAlternate(ProvRelation):
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947 """Provenance Alternate relationship."""
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948
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949 FORMAL_ATTRIBUTES = (PROV_ATTR_ALTERNATE1, PROV_ATTR_ALTERNATE2)
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950
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951 _prov_type = PROV_ALTERNATE
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952
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953
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954 class ProvMention(ProvSpecialization):
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955 """Provenance Mention relationship (specific Specialization)."""
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956
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957 FORMAL_ATTRIBUTES = (PROV_ATTR_SPECIFIC_ENTITY, PROV_ATTR_GENERAL_ENTITY,
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958 PROV_ATTR_BUNDLE)
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959
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960 _prov_type = PROV_MENTION
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961
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962
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963 # Component 6: Collections
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964 class ProvMembership(ProvRelation):
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965 """Provenance Membership relationship."""
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966
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967 FORMAL_ATTRIBUTES = (PROV_ATTR_COLLECTION, PROV_ATTR_ENTITY)
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968
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969 _prov_type = PROV_MEMBERSHIP
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970
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971
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972 # Class mappings from PROV record type
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973 PROV_REC_CLS = {
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974 PROV_ENTITY: ProvEntity,
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975 PROV_ACTIVITY: ProvActivity,
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976 PROV_GENERATION: ProvGeneration,
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977 PROV_USAGE: ProvUsage,
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978 PROV_COMMUNICATION: ProvCommunication,
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979 PROV_START: ProvStart,
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980 PROV_END: ProvEnd,
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981 PROV_INVALIDATION: ProvInvalidation,
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982 PROV_DERIVATION: ProvDerivation,
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983 PROV_AGENT: ProvAgent,
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984 PROV_ATTRIBUTION: ProvAttribution,
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985 PROV_ASSOCIATION: ProvAssociation,
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986 PROV_DELEGATION: ProvDelegation,
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987 PROV_INFLUENCE: ProvInfluence,
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988 PROV_SPECIALIZATION: ProvSpecialization,
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989 PROV_ALTERNATE: ProvAlternate,
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990 PROV_MENTION: ProvMention,
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991 PROV_MEMBERSHIP: ProvMembership,
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992 }
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993
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994
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995 DEFAULT_NAMESPACES = {'prov': PROV, 'xsd': XSD, 'xsi': XSI}
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996
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997
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998 # Bundle
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999 class NamespaceManager(dict):
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1000 """Manages namespaces for PROV documents and bundles."""
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1001
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1002 parent = None
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1003 """Parent :py:class:`NamespaceManager` this manager one is a child of."""
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1004
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1005 def __init__(self, namespaces=None, default=None, parent=None):
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1006 """
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1007 Constructor.
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1008
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1009 :param namespaces: Optional namespaces to add to the manager
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1010 (default: None).
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1011 :param default: Optional default namespace to use (default: None).
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1012 :param parent: Optional parent :py:class:`NamespaceManager` to make this
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1013 namespace manager a child of (default: None).
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1014 """
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1015 dict.__init__(self)
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1016 self._default_namespaces = DEFAULT_NAMESPACES
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1017 self.update(self._default_namespaces)
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1018 self._namespaces = {}
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1019
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1020 if default is not None:
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1021 self.set_default_namespace(default)
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1022 else:
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1023 self._default = None
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1024 self.parent = parent
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1025 # TODO check if default is in the default namespaces
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1026 self._anon_id_count = 0
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1027 self._uri_map = dict()
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1028 self._rename_map = dict()
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1029 self._prefix_renamed_map = dict()
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1030 self.add_namespaces(namespaces)
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1031
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1032 def get_namespace(self, uri):
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1033 """
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1034 Returns the namespace prefix for the given URI.
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1035
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1036 :param uri: Namespace URI.
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1037 :return: :py:class:`~prov.identifier.Namespace`.
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1038 """
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1039 for namespace in self.values():
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1040 if uri == namespace._uri:
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1041 return namespace
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1042 return None
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1043
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1044 def get_registered_namespaces(self):
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1045 """
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1046 Returns all registered namespaces.
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1047
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1048 :return: Iterable of :py:class:`~prov.identifier.Namespace`.
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1049 """
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1050 return self._namespaces.values()
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1051
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1052 def set_default_namespace(self, uri):
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diff changeset
1053 """
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diff changeset
1054 Sets the default namespace to the one of a given URI.
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parents:
diff changeset
1055
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diff changeset
1056 :param uri: Namespace URI.
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parents:
diff changeset
1057 """
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diff changeset
1058 self._default = Namespace('', uri)
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parents:
diff changeset
1059 self[''] = self._default
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diff changeset
1060
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diff changeset
1061 def get_default_namespace(self):
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diff changeset
1062 """
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diff changeset
1063 Returns the default namespace.
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diff changeset
1064
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1065 :return: :py:class:`~prov.identifier.Namespace`
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diff changeset
1066 """
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1067 return self._default
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diff changeset
1068
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1069 def add_namespace(self, namespace):
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diff changeset
1070 """
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diff changeset
1071 Adds a namespace (if not available, yet).
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diff changeset
1072
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1073 :param namespace: :py:class:`~prov.identifier.Namespace` to add.
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1074 """
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1075 if namespace in self.values():
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diff changeset
1076 # no need to do anything
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1077 return namespace
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1078 if namespace in self._rename_map:
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parents:
diff changeset
1079 # already renamed and added
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1080 return self._rename_map[namespace]
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diff changeset
1081
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diff changeset
1082 # Checking if the URI has been defined and use the existing namespace
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diff changeset
1083 # instead
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1084 uri = namespace.uri
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diff changeset
1085 prefix = namespace.prefix
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diff changeset
1086
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1087 if uri in self._uri_map:
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diff changeset
1088 existing_ns = self._uri_map[uri]
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diff changeset
1089 self._rename_map[namespace] = existing_ns
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1090 self._prefix_renamed_map[prefix] = existing_ns
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diff changeset
1091 return existing_ns
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1092
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1093 if prefix in self:
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diff changeset
1094 # Conflicting prefix
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1095 new_prefix = self._get_unused_prefix(prefix)
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1096 new_namespace = Namespace(new_prefix, namespace.uri)
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diff changeset
1097 self._rename_map[namespace] = new_namespace
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diff changeset
1098 # TODO: What if the prefix is already in the map and point to a
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diff changeset
1099 # different Namespace? Raise an exception?
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diff changeset
1100 self._prefix_renamed_map[prefix] = new_namespace
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diff changeset
1101 prefix = new_prefix
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1102 namespace = new_namespace
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diff changeset
1103
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1104 # Only now add the namespace to the registry
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diff changeset
1105 self._namespaces[prefix] = namespace
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diff changeset
1106 self[prefix] = namespace
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diff changeset
1107 self._uri_map[uri] = namespace
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1108
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1109 return namespace
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1110
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1111 def add_namespaces(self, namespaces):
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1112 """
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1113 Add multiple namespaces into this manager.
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1114
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1115 :param namespaces: A collection of namespace(s) to add.
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1116 :type namespaces: List of :py:class:`~prov.identifier.Namespace` or
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1117 dict of {prefix: uri}.
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1118 :returns: None
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1119 """
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1120 if isinstance(namespaces, dict):
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diff changeset
1121 # expecting a dictionary of {prefix: uri},
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1122 # convert it to a list of Namespace
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1123 namespaces = [
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1124 Namespace(prefix, uri) for prefix, uri in namespaces.items()
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1125 ]
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1126 if namespaces:
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1127 for ns in namespaces:
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diff changeset
1128 self.add_namespace(ns)
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1129
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1130 def valid_qualified_name(self, qname):
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1131 """
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1132 Resolves an identifier to a valid qualified name.
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1133
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1134 :param qname: Qualified name as :py:class:`~prov.identifier.QualifiedName`
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1135 or a tuple (namespace, identifier).
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1136 :return: :py:class:`~prov.identifier.QualifiedName` or None in case of
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diff changeset
1137 failure.
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1138 """
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1139 if not qname:
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1140 return None
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1141
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1142 if isinstance(qname, QualifiedName):
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diff changeset
1143 # Register the namespace if it has not been registered before
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1144 namespace = qname.namespace
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1145 prefix = namespace.prefix
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1146 local_part = qname.localpart
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1147 if not prefix:
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1148 # the namespace is a default namespace
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1149 if self._default == namespace:
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1150 # the same default namespace is defined
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diff changeset
1151 new_qname = self._default[local_part]
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1152 elif self._default is None:
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diff changeset
1153 # no default namespace is defined, reused the one given
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diff changeset
1154 self._default = namespace
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1155 return qname # no change, return the original
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1156 else:
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1157 # different default namespace,
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diff changeset
1158 # use the 'dn' prefix for the new namespace
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1159 dn_namespace = Namespace('dn', namespace.uri)
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1160 dn_namespace = self.add_namespace(dn_namespace)
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diff changeset
1161 new_qname = dn_namespace[local_part]
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diff changeset
1162 elif prefix in self and self[prefix] == namespace:
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diff changeset
1163 # No need to add the namespace
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diff changeset
1164 existing_ns = self[prefix]
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1165 if existing_ns is namespace:
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1166 return qname
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1167 else:
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1168 # reuse the existing namespace
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diff changeset
1169 new_qname = existing_ns[local_part]
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1170 else:
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1171 # Do not reuse the namespace object
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1172 ns = self.add_namespace(deepcopy(namespace))
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diff changeset
1173 # minting the same Qualified Name from the namespace's copy
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diff changeset
1174 new_qname = ns[qname.localpart]
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parents:
diff changeset
1175 # returning the new qname
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1176 return new_qname
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1177
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1178 # Trying to guess from here
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1179 if not isinstance(qname, (six.string_types, Identifier)):
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parents:
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1180 # Only proceed for string or URI values
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diff changeset
1181 return None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1182 # Try to generate a Qualified Name
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1183 str_value = \
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1184 qname.uri if isinstance(qname, Identifier) else six.text_type(qname)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1185 if str_value.startswith('_:'):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1186 # this is a blank node ID
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guerler
parents:
diff changeset
1187 return None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1188 elif ':' in str_value:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1189 # check if the identifier contains a registered prefix
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1190 prefix, local_part = str_value.split(':', 1)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1191 if prefix in self:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1192 # return a new QualifiedName
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1193 return self[prefix][local_part]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1194 if prefix in self._prefix_renamed_map:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1195 # return a new QualifiedName
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1196 return self._prefix_renamed_map[prefix][local_part]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1197 else:
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guerler
parents:
diff changeset
1198 # treat as a URI (with the first part as its scheme)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1199 # check if the URI can be compacted
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1200 for namespace in self.values():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1201 if str_value.startswith(namespace.uri):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1202 # create a QName with the namespace
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1203 return namespace[str_value.replace(namespace.uri, '')]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1204 elif self._default:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1205 # create and return an identifier in the default namespace
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1206 return self._default[qname]
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guerler
parents:
diff changeset
1207
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guerler
parents:
diff changeset
1208 if self.parent:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1209 # all attempts have failed so far
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guerler
parents:
diff changeset
1210 # now delegate this to the parent NamespaceManager
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1211 return self.parent.valid_qualified_name(qname)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1212
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1213 # Default to FAIL
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1214 return None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1215
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1216 def get_anonymous_identifier(self, local_prefix='id'):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1217 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1218 Returns an anonymous identifier (without a namespace prefix).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1219
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1220 :param local_prefix: Optional local namespace prefix as a string
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1221 (default: 'id').
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1222 :return: :py:class:`~prov.identifier.Identifier`
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1223 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1224 self._anon_id_count += 1
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1225 return Identifier('_:%s%d' % (local_prefix, self._anon_id_count))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1226
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1227 def _get_unused_prefix(self, original_prefix):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1228 if original_prefix not in self:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1229 return original_prefix
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1230 count = 1
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1231 while True:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1232 new_prefix = '_'.join((original_prefix, six.text_type(count)))
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1233 if new_prefix in self:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1234 count += 1
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1235 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1236 return new_prefix
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guerler
parents:
diff changeset
1237
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guerler
parents:
diff changeset
1238
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1239 class ProvBundle(object):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1240 """PROV Bundle"""
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guerler
parents:
diff changeset
1241
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1242 def __init__(self, records=None, identifier=None, namespaces=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1243 document=None):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1244 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1245 Constructor.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1246
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1247 :param records: Optional iterable of records to add to the bundle
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1248 (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1249 :param identifier: Optional identifier of the bundle (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1250 :param namespaces: Optional iterable of :py:class:`~prov.identifier.Namespace`s
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1251 to set the document up with (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1252 :param document: Optional document to add to the bundle (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1253 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1254 # Initializing bundle-specific attributes
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1255 self._identifier = identifier
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1256 self._records = list()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1257 self._id_map = defaultdict(list)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1258 self._document = document
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1259 self._namespaces = NamespaceManager(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1260 namespaces,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1261 parent=(document._namespaces if document is not None else None)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1262 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1263 if records:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1264 for record in records:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1265 self.add_record(record)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1266
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1267 def __repr__(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1268 return '<%s: %s>' % (self.__class__.__name__, self._identifier)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1269
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1270 @property
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1271 def namespaces(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1272 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1273 Returns the set of registered namespaces.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1274
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1275 :return: Set of :py:class:`~prov.identifier.Namespace`.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1276 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1277 return set(self._namespaces.get_registered_namespaces())
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1278
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1279 @property
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1280 def default_ns_uri(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1281 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1282 Returns the default namespace's URI, if any.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1283
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1284 :return: URI as string.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1285 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1286 default_ns = self._namespaces.get_default_namespace()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1287 return default_ns.uri if default_ns else None
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1288
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1289 @property
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1290 def document(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1291 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1292 Returns the parent document, if any.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1293
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1294 :return: :py:class:`ProvDocument`.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1295 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1296 return self._document
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1297
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1298 @property
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1299 def identifier(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1300 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1301 Returns the bundle's identifier
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1302 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1303 return self._identifier
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1304
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1305 @property
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1306 def records(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1307 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1308 Returns the list of all records in the current bundle
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1309 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1310 return list(self._records)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1311
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1312 # Bundle configurations
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diff changeset
1313 def set_default_namespace(self, uri):
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diff changeset
1314 """
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diff changeset
1315 Sets the default namespace through a given URI.
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diff changeset
1316
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diff changeset
1317 :param uri: Namespace URI.
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diff changeset
1318 """
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diff changeset
1319 self._namespaces.set_default_namespace(uri)
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parents:
diff changeset
1320
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diff changeset
1321 def get_default_namespace(self):
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diff changeset
1322 """
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diff changeset
1323 Returns the default namespace.
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parents:
diff changeset
1324
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diff changeset
1325 :return: :py:class:`~prov.identifier.Namespace`
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diff changeset
1326 """
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diff changeset
1327 return self._namespaces.get_default_namespace()
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parents:
diff changeset
1328
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diff changeset
1329 def add_namespace(self, namespace_or_prefix, uri=None):
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diff changeset
1330 """
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diff changeset
1331 Adds a namespace (if not available, yet).
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diff changeset
1332
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diff changeset
1333 :param namespace_or_prefix: :py:class:`~prov.identifier.Namespace` or its
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diff changeset
1334 prefix as a string to add.
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diff changeset
1335 :param uri: Namespace URI (default: None). Must be present if only a
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diff changeset
1336 prefix is given in the previous parameter.
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1337 """
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diff changeset
1338 if uri is None:
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diff changeset
1339 return self._namespaces.add_namespace(namespace_or_prefix)
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diff changeset
1340 else:
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diff changeset
1341 return self._namespaces.add_namespace(
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diff changeset
1342 Namespace(namespace_or_prefix, uri)
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diff changeset
1343 )
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diff changeset
1344
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diff changeset
1345 def get_registered_namespaces(self):
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diff changeset
1346 """
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diff changeset
1347 Returns all registered namespaces.
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diff changeset
1348
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diff changeset
1349 :return: Iterable of :py:class:`~prov.identifier.Namespace`.
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1350 """
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diff changeset
1351 return self._namespaces.get_registered_namespaces()
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diff changeset
1352
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1353 def valid_qualified_name(self, identifier):
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diff changeset
1354 return self._namespaces.valid_qualified_name(identifier)
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diff changeset
1355
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diff changeset
1356 def get_records(self, class_or_type_or_tuple=None):
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diff changeset
1357 """
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diff changeset
1358 Returns all records. Returned records may be filtered by the optional
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diff changeset
1359 argument.
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diff changeset
1360
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1361 :param class_or_type_or_tuple: A filter on the type for which records are
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diff changeset
1362 to be returned (default: None). The filter checks by the type of the
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diff changeset
1363 record using the `isinstance` check on the record.
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diff changeset
1364 :return: List of :py:class:`ProvRecord` objects.
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diff changeset
1365 """
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1366 results = list(self._records)
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diff changeset
1367 if class_or_type_or_tuple:
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parents:
diff changeset
1368 return filter(
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diff changeset
1369 lambda rec: isinstance(rec, class_or_type_or_tuple), results
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diff changeset
1370 )
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1371 else:
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diff changeset
1372 return results
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diff changeset
1373
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1374 def get_record(self, identifier):
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1375 """
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1376 Returns a specific record matching a given identifier.
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diff changeset
1377
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1378 :param identifier: Record identifier.
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diff changeset
1379 :return: :py:class:`ProvRecord`
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1380 """
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diff changeset
1381 # TODO: This will not work with the new _id_map, which is now a map of
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diff changeset
1382 # (QName, list(ProvRecord))
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diff changeset
1383 if identifier is None:
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1384 return None
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diff changeset
1385 valid_id = self.valid_qualified_name(identifier)
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diff changeset
1386 try:
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diff changeset
1387 return self._id_map[valid_id]
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diff changeset
1388 except KeyError:
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diff changeset
1389 # looking up the parent bundle
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diff changeset
1390 if self.is_bundle():
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diff changeset
1391 return self.document.get_record(valid_id)
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diff changeset
1392 else:
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diff changeset
1393 return None
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diff changeset
1394
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diff changeset
1395 # Miscellaneous functions
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diff changeset
1396 def is_document(self):
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diff changeset
1397 """
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diff changeset
1398 `True` if the object is a document, `False` otherwise.
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diff changeset
1399
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diff changeset
1400 :return: bool
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diff changeset
1401 """
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diff changeset
1402 return False
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diff changeset
1403
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diff changeset
1404 def is_bundle(self):
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diff changeset
1405 """
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diff changeset
1406 `True` if the object is a bundle, `False` otherwise.
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diff changeset
1407
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diff changeset
1408 :return: bool
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diff changeset
1409 """
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diff changeset
1410 return True
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diff changeset
1411
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diff changeset
1412 def has_bundles(self):
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diff changeset
1413 """
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diff changeset
1414 `True` if the object has at least one bundle, `False` otherwise.
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parents:
diff changeset
1415
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diff changeset
1416 :return: bool
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diff changeset
1417 """
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diff changeset
1418 return False
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diff changeset
1419
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diff changeset
1420 @property
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diff changeset
1421 def bundles(self):
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diff changeset
1422 """
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diff changeset
1423 Returns bundles contained in the document
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parents:
diff changeset
1424
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diff changeset
1425 :return: Iterable of :py:class:`ProvBundle`.
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diff changeset
1426 """
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diff changeset
1427 return frozenset()
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diff changeset
1428
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diff changeset
1429 def get_provn(self, _indent_level=0):
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parents:
diff changeset
1430 """
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diff changeset
1431 Returns the PROV-N representation of the bundle.
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parents:
diff changeset
1432
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diff changeset
1433 :return: String
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diff changeset
1434 """
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diff changeset
1435 indentation = '' + (' ' * _indent_level)
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parents:
diff changeset
1436 newline = '\n' + (' ' * (_indent_level + 1))
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parents:
diff changeset
1437
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diff changeset
1438 # if this is the document, start the document;
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diff changeset
1439 # otherwise, start the bundle
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diff changeset
1440 lines = ['document'] if self.is_document() \
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parents:
diff changeset
1441 else ['bundle %s' % self._identifier]
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parents:
diff changeset
1442
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diff changeset
1443 default_namespace = self._namespaces.get_default_namespace()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1444 if default_namespace:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1445 lines.append('default <%s>' % default_namespace.uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1446
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1447 registered_namespaces = self._namespaces.get_registered_namespaces()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1448 if registered_namespaces:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1449 lines.extend(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1450 ['prefix %s <%s>' % (namespace.prefix, namespace.uri)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1451 for namespace in registered_namespaces]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1452 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1453
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1454 if default_namespace or registered_namespaces:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1455 # a blank line between the prefixes and the assertions
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1456 lines.append('')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1457
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1458 # adding all the records
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1459 lines.extend([record.get_provn() for record in self._records])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1460 if self.is_document():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1461 # Print out bundles
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1462 lines.extend(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1463 bundle.get_provn(_indent_level + 1) for bundle in self.bundles
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1464 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1465 provn_str = newline.join(lines) + '\n'
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1466
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1467 # closing the structure
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1468 provn_str += indentation + (
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1469 'endDocument' if self.is_document() else 'endBundle'
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guerler
parents:
diff changeset
1470 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1471 return provn_str
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1472
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guerler
parents:
diff changeset
1473 def __eq__(self, other):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1474 if not isinstance(other, ProvBundle):
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guerler
parents:
diff changeset
1475 return False
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guerler
parents:
diff changeset
1476 other_records = set(other.get_records())
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1477 this_records = set(self.get_records())
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1478 if len(this_records) != len(other_records):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1479 return False
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1480 # check if all records for equality
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1481 for record_a in this_records:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1482 # Manually look for the record
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1483 found = False
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1484 for record_b in other_records:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1485 if record_a == record_b:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1486 other_records.remove(record_b)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1487 found = True
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1488 break
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1489 if not found:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1490 logger.debug(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1491 'Equality (ProvBundle): Could not find this record: %s',
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1492 six.text_type(record_a)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1493 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1494 return False
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1495 return True
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guerler
parents:
diff changeset
1496
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guerler
parents:
diff changeset
1497 def __ne__(self, other):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1498 return not (self == other)
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guerler
parents:
diff changeset
1499
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guerler
parents:
diff changeset
1500 __hash__ = None
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guerler
parents:
diff changeset
1501
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guerler
parents:
diff changeset
1502 # Transformations
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1503 def _unified_records(self):
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guerler
parents:
diff changeset
1504 """Returns a list of unified records."""
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1505 # TODO: Check unification rules in the PROV-CONSTRAINTS document
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1506 # This method simply merges the records having the same name
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1507 merged_records = dict()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1508 for identifier, records in self._id_map.items():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1509 if len(records) > 1:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1510 # more than one record having the same identifier
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1511 # merge the records
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1512 merged = records[0].copy()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1513 for record in records[1:]:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1514 merged.add_attributes(record.attributes)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1515 # map all of them to the merged record
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1516 for record in records:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1517 merged_records[record] = merged
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1518 if not merged_records:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1519 # No merging done, just return the list of original records
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1520 return list(self._records)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1521
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1522 added_merged_records = set()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1523 unified_records = list()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1524 for record in self._records:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1525 if record in merged_records:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1526 merged = merged_records[record]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1527 if merged not in added_merged_records:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1528 unified_records.append(merged)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1529 added_merged_records.add(merged)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1530 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1531 # add the original record
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1532 unified_records.append(record)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1533 return unified_records
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1534
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1535 def unified(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1536 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1537 Unifies all records in the bundle that haves same identifiers
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1538
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1539 :returns: :py:class:`ProvBundle` -- the new unified bundle.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1540 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1541 unified_records = self._unified_records()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1542 bundle = ProvBundle(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1543 records=unified_records, identifier=self.identifier
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1544 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1545 return bundle
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1546
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1547 def update(self, other):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1548 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1549 Append all the records of the *other* ProvBundle into this bundle.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1550
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1551 :param other: the other bundle whose records to be appended.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1552 :type other: :py:class:`ProvBundle`
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1553 :returns: None.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1554 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1555 if isinstance(other, ProvBundle):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1556 if other.is_document() and other.has_bundles():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1557 # Cannot add bundles to a bundle
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1558 raise ProvException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1559 'ProvBundle.update(): The other bundle is a document with '
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1560 'sub-bundle(s).'
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1561 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1562 for record in other.get_records():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1563 self.add_record(record)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1564 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1565 raise ProvException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1566 'ProvBundle.update(): The other bundle is not a ProvBundle '
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1567 'instance (%s)' % type(other)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1568 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1569
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1570 # Provenance statements
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1571 def _add_record(self, record):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1572 # IMPORTANT: All records need to be added to a bundle/document via this
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1573 # method. Otherwise, the _id_map dict will not be correctly updated
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1574 identifier = record.identifier
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1575 if identifier is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1576 self._id_map[identifier].append(record)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1577 self._records.append(record)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1578
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1579 def new_record(self, record_type, identifier, attributes=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1580 other_attributes=None):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1581 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1582 Creates a new record.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1583
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1584 :param record_type: Type of record (one of :py:const:`PROV_REC_CLS`).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1585 :param identifier: Identifier for new record.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1586 :param attributes: Attributes as a dictionary or list of tuples to be added
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1587 to the record optionally (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1588 :param other_attributes: Optional other attributes as a dictionary or list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1589 of tuples to be added to the record optionally (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1590 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1591 attr_list = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1592 if attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1593 if isinstance(attributes, dict):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1594 attr_list.extend(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1595 (attr, value) for attr, value in attributes.items()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1596 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1597 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1598 # expecting a list of attributes here
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1599 attr_list.extend(attributes)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1600 if other_attributes:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1601 attr_list.extend(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1602 other_attributes.items() if isinstance(other_attributes, dict)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1603 else other_attributes
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1604 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1605 new_record = PROV_REC_CLS[record_type](
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1606 self, self.valid_qualified_name(identifier), attr_list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1607 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1608 self._add_record(new_record)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1609 return new_record
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1610
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1611 def add_record(self, record):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1612 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1613 Adds a new record that to the bundle.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1614
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1615 :param record: :py:class:`ProvRecord` to be added.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1616 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1617 return self.new_record(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1618 record.get_type(), record.identifier, record.formal_attributes,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1619 record.extra_attributes
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1620 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1621
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1622 def entity(self, identifier, other_attributes=None):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1623 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1624 Creates a new entity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1625
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1626 :param identifier: Identifier for new entity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1627 :param other_attributes: Optional other attributes as a dictionary or list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1628 of tuples to be added to the record optionally (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1629 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1630 return self.new_record(PROV_ENTITY, identifier, None, other_attributes)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1631
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1632 def activity(self, identifier, startTime=None, endTime=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1633 other_attributes=None):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1634 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1635 Creates a new activity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1636
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1637 :param identifier: Identifier for new activity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1638 :param startTime: Optional start time for the activity (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1639 Either a :py:class:`datetime.datetime` object or a string that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1640 parsed by :py:func:`dateutil.parser`.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1641 :param endTime: Optional start time for the activity (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1642 Either a :py:class:`datetime.datetime` object or a string that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1643 parsed by :py:func:`dateutil.parser`.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1644 :param other_attributes: Optional other attributes as a dictionary or list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1645 of tuples to be added to the record optionally (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1646 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1647 return self.new_record(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1648 PROV_ACTIVITY, identifier, {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1649 PROV_ATTR_STARTTIME: _ensure_datetime(startTime),
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1650 PROV_ATTR_ENDTIME: _ensure_datetime(endTime)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1651 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1652 other_attributes
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1653 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1654
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1655 def generation(self, entity, activity=None, time=None, identifier=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1656 other_attributes=None):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1657 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1658 Creates a new generation record for an entity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1659
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1660 :param entity: Entity or a string identifier for the entity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1661 :param activity: Activity or string identifier of the activity involved in
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1662 the generation (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1663 :param time: Optional time for the generation (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1664 Either a :py:class:`datetime.datetime` object or a string that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1665 parsed by :py:func:`dateutil.parser`.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1666 :param identifier: Identifier for new generation record.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1667 :param other_attributes: Optional other attributes as a dictionary or list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1668 of tuples to be added to the record optionally (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1669 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1670 return self.new_record(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1671 PROV_GENERATION, identifier, {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1672 PROV_ATTR_ENTITY: entity,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1673 PROV_ATTR_ACTIVITY: activity,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1674 PROV_ATTR_TIME: _ensure_datetime(time)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1675 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1676 other_attributes
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1677 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1678
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1679 def usage(self, activity, entity=None, time=None, identifier=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1680 other_attributes=None):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1681 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1682 Creates a new usage record for an activity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1683
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1684 :param activity: Activity or a string identifier for the entity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1685 :param entity: Entity or string identifier of the entity involved in
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1686 the usage relationship (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1687 :param time: Optional time for the usage (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1688 Either a :py:class:`datetime.datetime` object or a string that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1689 parsed by :py:func:`dateutil.parser`.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1690 :param identifier: Identifier for new usage record.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1691 :param other_attributes: Optional other attributes as a dictionary or list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1692 of tuples to be added to the record optionally (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1693 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1694 return self.new_record(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1695 PROV_USAGE, identifier, {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1696 PROV_ATTR_ACTIVITY: activity,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1697 PROV_ATTR_ENTITY: entity,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1698 PROV_ATTR_TIME: _ensure_datetime(time)},
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1699 other_attributes
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1700 )
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diff changeset
1701
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diff changeset
1702 def start(self, activity, trigger=None, starter=None, time=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1703 identifier=None, other_attributes=None):
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parents:
diff changeset
1704 """
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parents:
diff changeset
1705 Creates a new start record for an activity.
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parents:
diff changeset
1706
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diff changeset
1707 :param activity: Activity or a string identifier for the entity.
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guerler
parents:
diff changeset
1708 :param trigger: Entity triggering the start of this activity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1709 :param starter: Optionally extra activity to state a qualified start
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1710 through which the trigger entity for the start is generated
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1711 (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1712 :param time: Optional time for the start (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1713 Either a :py:class:`datetime.datetime` object or a string that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1714 parsed by :py:func:`dateutil.parser`.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1715 :param identifier: Identifier for new start record.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1716 :param other_attributes: Optional other attributes as a dictionary or list
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parents:
diff changeset
1717 of tuples to be added to the record optionally (default: None).
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parents:
diff changeset
1718 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1719 return self.new_record(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1720 PROV_START, identifier, {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1721 PROV_ATTR_ACTIVITY: activity,
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parents:
diff changeset
1722 PROV_ATTR_TRIGGER: trigger,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1723 PROV_ATTR_STARTER: starter,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1724 PROV_ATTR_TIME: _ensure_datetime(time)
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parents:
diff changeset
1725 },
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parents:
diff changeset
1726 other_attributes
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parents:
diff changeset
1727 )
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parents:
diff changeset
1728
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parents:
diff changeset
1729 def end(self, activity, trigger=None, ender=None, time=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1730 identifier=None, other_attributes=None):
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parents:
diff changeset
1731 """
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parents:
diff changeset
1732 Creates a new end record for an activity.
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parents:
diff changeset
1733
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parents:
diff changeset
1734 :param activity: Activity or a string identifier for the entity.
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parents:
diff changeset
1735 :param trigger: trigger: Entity triggering the end of this activity.
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parents:
diff changeset
1736 :param ender: Optionally extra activity to state a qualified end
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parents:
diff changeset
1737 through which the trigger entity for the end is generated
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parents:
diff changeset
1738 (default: None).
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parents:
diff changeset
1739 :param time: Optional time for the end (default: None).
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parents:
diff changeset
1740 Either a :py:class:`datetime.datetime` object or a string that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1741 parsed by :py:func:`dateutil.parser`.
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parents:
diff changeset
1742 :param identifier: Identifier for new end record.
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parents:
diff changeset
1743 :param other_attributes: Optional other attributes as a dictionary or list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1744 of tuples to be added to the record optionally (default: None).
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parents:
diff changeset
1745 """
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parents:
diff changeset
1746 return self.new_record(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1747 PROV_END, identifier, {
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parents:
diff changeset
1748 PROV_ATTR_ACTIVITY: activity,
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parents:
diff changeset
1749 PROV_ATTR_TRIGGER: trigger,
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parents:
diff changeset
1750 PROV_ATTR_ENDER: ender,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1751 PROV_ATTR_TIME: _ensure_datetime(time)
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parents:
diff changeset
1752 },
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parents:
diff changeset
1753 other_attributes
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parents:
diff changeset
1754 )
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parents:
diff changeset
1755
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diff changeset
1756 def invalidation(self, entity, activity=None, time=None, identifier=None,
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parents:
diff changeset
1757 other_attributes=None):
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parents:
diff changeset
1758 """
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parents:
diff changeset
1759 Creates a new invalidation record for an entity.
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guerler
parents:
diff changeset
1760
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diff changeset
1761 :param entity: Entity or a string identifier for the entity.
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parents:
diff changeset
1762 :param activity: Activity or string identifier of the activity involved in
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1763 the invalidation (default: None).
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parents:
diff changeset
1764 :param time: Optional time for the invalidation (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1765 Either a :py:class:`datetime.datetime` object or a string that can be
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1766 parsed by :py:func:`dateutil.parser`.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1767 :param identifier: Identifier for new invalidation record.
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guerler
parents:
diff changeset
1768 :param other_attributes: Optional other attributes as a dictionary or list
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parents:
diff changeset
1769 of tuples to be added to the record optionally (default: None).
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parents:
diff changeset
1770 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1771 return self.new_record(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1772 PROV_INVALIDATION, identifier, {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1773 PROV_ATTR_ENTITY: entity,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1774 PROV_ATTR_ACTIVITY: activity,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1775 PROV_ATTR_TIME: _ensure_datetime(time)
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parents:
diff changeset
1776 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1777 other_attributes
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parents:
diff changeset
1778 )
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parents:
diff changeset
1779
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parents:
diff changeset
1780 def communication(self, informed, informant, identifier=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1781 other_attributes=None):
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parents:
diff changeset
1782 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1783 Creates a new communication record for an entity.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1784
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parents:
diff changeset
1785 :param informed: The informed activity (relationship destination).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1786 :param informant: The informing activity (relationship source).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1787 :param identifier: Identifier for new communication record.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1788 :param other_attributes: Optional other attributes as a dictionary or list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1789 of tuples to be added to the record optionally (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1790 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1791 return self.new_record(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1792 PROV_COMMUNICATION, identifier, {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1793 PROV_ATTR_INFORMED: informed,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1794 PROV_ATTR_INFORMANT: informant
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parents:
diff changeset
1795 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1796 other_attributes
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parents:
diff changeset
1797 )
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parents:
diff changeset
1798
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1799 def agent(self, identifier, other_attributes=None):
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guerler
parents:
diff changeset
1800 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1801 Creates a new agent.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1802
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1803 :param identifier: Identifier for new agent.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1804 :param other_attributes: Optional other attributes as a dictionary or list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1805 of tuples to be added to the record optionally (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1806 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1807 return self.new_record(PROV_AGENT, identifier, None, other_attributes)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1808
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1809 def attribution(self, entity, agent, identifier=None,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1810 other_attributes=None):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1811 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1812 Creates a new attribution record between an entity and an agent.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1813
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1814 :param entity: Entity or a string identifier for the entity (relationship
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1815 source).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1816 :param agent: Agent or string identifier of the agent involved in the
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1817 attribution (relationship destination).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1818 :param identifier: Identifier for new attribution record.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1819 :param other_attributes: Optional other attributes as a dictionary or list
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1820 of tuples to be added to the record optionally (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1821 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1822 return self.new_record(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1823 PROV_ATTRIBUTION, identifier, {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1824 PROV_ATTR_ENTITY: entity,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1825 PROV_ATTR_AGENT: agent
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guerler
parents:
diff changeset
1826 },
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parents:
diff changeset
1827 other_attributes
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diff changeset
1828 )
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parents:
diff changeset
1829
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diff changeset
1830 def association(self, activity, agent=None, plan=None, identifier=None,
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diff changeset
1831 other_attributes=None):
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diff changeset
1832 """
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parents:
diff changeset
1833 Creates a new association record for an activity.
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parents:
diff changeset
1834
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diff changeset
1835 :param activity: Activity or a string identifier for the activity.
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parents:
diff changeset
1836 :param agent: Agent or string identifier of the agent involved in the
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parents:
diff changeset
1837 association (default: None).
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parents:
diff changeset
1838 :param plan: Optionally extra entity to state qualified association through
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parents:
diff changeset
1839 an internal plan (default: None).
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parents:
diff changeset
1840 :param identifier: Identifier for new association record.
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parents:
diff changeset
1841 :param other_attributes: Optional other attributes as a dictionary or list
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parents:
diff changeset
1842 of tuples to be added to the record optionally (default: None).
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parents:
diff changeset
1843 """
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parents:
diff changeset
1844 return self.new_record(
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parents:
diff changeset
1845 PROV_ASSOCIATION, identifier, {
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parents:
diff changeset
1846 PROV_ATTR_ACTIVITY: activity,
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parents:
diff changeset
1847 PROV_ATTR_AGENT: agent,
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parents:
diff changeset
1848 PROV_ATTR_PLAN: plan
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parents:
diff changeset
1849 },
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diff changeset
1850 other_attributes
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diff changeset
1851 )
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parents:
diff changeset
1852
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1853 def delegation(self, delegate, responsible, activity=None, identifier=None,
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parents:
diff changeset
1854 other_attributes=None):
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diff changeset
1855 """
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parents:
diff changeset
1856 Creates a new delegation record on behalf of an agent.
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parents:
diff changeset
1857
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1858 :param delegate: Agent delegating the responsibility (relationship source).
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parents:
diff changeset
1859 :param responsible: Agent the responsibility is delegated to (relationship
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parents:
diff changeset
1860 destination).
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diff changeset
1861 :param activity: Optionally extra activity to state qualified delegation
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parents:
diff changeset
1862 internally (default: None).
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parents:
diff changeset
1863 :param identifier: Identifier for new association record.
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parents:
diff changeset
1864 :param other_attributes: Optional other attributes as a dictionary or list
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parents:
diff changeset
1865 of tuples to be added to the record optionally (default: None).
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diff changeset
1866 """
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parents:
diff changeset
1867 return self.new_record(
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diff changeset
1868 PROV_DELEGATION, identifier, {
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parents:
diff changeset
1869 PROV_ATTR_DELEGATE: delegate,
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parents:
diff changeset
1870 PROV_ATTR_RESPONSIBLE: responsible,
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parents:
diff changeset
1871 PROV_ATTR_ACTIVITY: activity
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parents:
diff changeset
1872 },
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diff changeset
1873 other_attributes
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diff changeset
1874 )
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parents:
diff changeset
1875
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1876 def influence(self, influencee, influencer, identifier=None,
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1877 other_attributes=None):
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diff changeset
1878 """
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diff changeset
1879 Creates a new influence record between two entities, activities or agents.
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diff changeset
1880
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1881 :param influencee: Influenced entity, activity or agent (relationship
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diff changeset
1882 source).
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diff changeset
1883 :param influencer: Influencing entity, activity or agent (relationship
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diff changeset
1884 destination).
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diff changeset
1885 :param identifier: Identifier for new influence record.
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diff changeset
1886 :param other_attributes: Optional other attributes as a dictionary or list
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diff changeset
1887 of tuples to be added to the record optionally (default: None).
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diff changeset
1888 """
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1889 return self.new_record(
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diff changeset
1890 PROV_INFLUENCE, identifier, {
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diff changeset
1891 PROV_ATTR_INFLUENCEE: influencee,
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diff changeset
1892 PROV_ATTR_INFLUENCER: influencer
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diff changeset
1893 },
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diff changeset
1894 other_attributes
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diff changeset
1895 )
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diff changeset
1896
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1897 def derivation(self, generatedEntity, usedEntity, activity=None,
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diff changeset
1898 generation=None, usage=None,
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diff changeset
1899 identifier=None, other_attributes=None):
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diff changeset
1900 """
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diff changeset
1901 Creates a new derivation record for a generated entity from a used entity.
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diff changeset
1902
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diff changeset
1903 :param generatedEntity: Entity or a string identifier for the generated
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diff changeset
1904 entity (relationship source).
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diff changeset
1905 :param usedEntity: Entity or a string identifier for the used entity
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diff changeset
1906 (relationship destination).
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diff changeset
1907 :param activity: Activity or string identifier of the activity involved in
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diff changeset
1908 the derivation (default: None).
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diff changeset
1909 :param generation: Optionally extra activity to state qualified generation
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diff changeset
1910 through a generation (default: None).
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1911 :param usage: XXX (default: None).
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diff changeset
1912 :param identifier: Identifier for new derivation record.
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diff changeset
1913 :param other_attributes: Optional other attributes as a dictionary or list
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diff changeset
1914 of tuples to be added to the record optionally (default: None).
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diff changeset
1915 """
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diff changeset
1916 attributes = {PROV_ATTR_GENERATED_ENTITY: generatedEntity,
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diff changeset
1917 PROV_ATTR_USED_ENTITY: usedEntity,
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diff changeset
1918 PROV_ATTR_ACTIVITY: activity,
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diff changeset
1919 PROV_ATTR_GENERATION: generation,
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diff changeset
1920 PROV_ATTR_USAGE: usage}
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diff changeset
1921 return self.new_record(
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diff changeset
1922 PROV_DERIVATION, identifier, attributes, other_attributes
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diff changeset
1923 )
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diff changeset
1924
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diff changeset
1925 def revision(self, generatedEntity, usedEntity, activity=None,
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diff changeset
1926 generation=None, usage=None,
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diff changeset
1927 identifier=None, other_attributes=None):
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diff changeset
1928 """
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diff changeset
1929 Creates a new revision record for a generated entity from a used entity.
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diff changeset
1930
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diff changeset
1931 :param generatedEntity: Entity or a string identifier for the generated
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diff changeset
1932 entity (relationship source).
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diff changeset
1933 :param usedEntity: Entity or a string identifier for the used entity
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diff changeset
1934 (relationship destination).
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diff changeset
1935 :param activity: Activity or string identifier of the activity involved in
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parents:
diff changeset
1936 the revision (default: None).
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diff changeset
1937 :param generation: Optionally to state qualified revision through a
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diff changeset
1938 generation activity (default: None).
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diff changeset
1939 :param usage: XXX (default: None).
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diff changeset
1940 :param identifier: Identifier for new revision record.
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diff changeset
1941 :param other_attributes: Optional other attributes as a dictionary or list
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diff changeset
1942 of tuples to be added to the record optionally (default: None).
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diff changeset
1943 """
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diff changeset
1944 record = self.derivation(
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diff changeset
1945 generatedEntity, usedEntity, activity, generation, usage,
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diff changeset
1946 identifier, other_attributes
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diff changeset
1947 )
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diff changeset
1948 record.add_asserted_type(PROV['Revision'])
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diff changeset
1949 return record
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diff changeset
1950
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diff changeset
1951 def quotation(self, generatedEntity, usedEntity, activity=None,
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diff changeset
1952 generation=None, usage=None,
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diff changeset
1953 identifier=None, other_attributes=None):
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diff changeset
1954 """
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diff changeset
1955 Creates a new quotation record for a generated entity from a used entity.
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1956
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1957 :param generatedEntity: Entity or a string identifier for the generated
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diff changeset
1958 entity (relationship source).
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1959 :param usedEntity: Entity or a string identifier for the used entity
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diff changeset
1960 (relationship destination).
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diff changeset
1961 :param activity: Activity or string identifier of the activity involved in
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diff changeset
1962 the quotation (default: None).
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1963 :param generation: Optionally to state qualified quotation through a
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parents:
diff changeset
1964 generation activity (default: None).
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diff changeset
1965 :param usage: XXX (default: None).
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diff changeset
1966 :param identifier: Identifier for new quotation record.
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diff changeset
1967 :param other_attributes: Optional other attributes as a dictionary or list
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diff changeset
1968 of tuples to be added to the record optionally (default: None).
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diff changeset
1969 """
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diff changeset
1970 record = self.derivation(
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diff changeset
1971 generatedEntity, usedEntity, activity, generation, usage,
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diff changeset
1972 identifier, other_attributes
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diff changeset
1973 )
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1974 record.add_asserted_type(PROV['Quotation'])
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diff changeset
1975 return record
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diff changeset
1976
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1977 def primary_source(self, generatedEntity, usedEntity, activity=None,
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1978 generation=None, usage=None,
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diff changeset
1979 identifier=None, other_attributes=None):
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diff changeset
1980 """
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diff changeset
1981 Creates a new primary source record for a generated entity from a used
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diff changeset
1982 entity.
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diff changeset
1983
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1984 :param generatedEntity: Entity or a string identifier for the generated
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diff changeset
1985 entity (relationship source).
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diff changeset
1986 :param usedEntity: Entity or a string identifier for the used entity
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diff changeset
1987 (relationship destination).
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1988 :param activity: Activity or string identifier of the activity involved in
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diff changeset
1989 the primary source (default: None).
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diff changeset
1990 :param generation: Optionally to state qualified primary source through a
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diff changeset
1991 generation activity (default: None).
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1992 :param usage: XXX (default: None).
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diff changeset
1993 :param identifier: Identifier for new primary source record.
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diff changeset
1994 :param other_attributes: Optional other attributes as a dictionary or list
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diff changeset
1995 of tuples to be added to the record optionally (default: None).
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diff changeset
1996 """
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1997 record = self.derivation(
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diff changeset
1998 generatedEntity, usedEntity, activity, generation, usage,
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diff changeset
1999 identifier, other_attributes
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diff changeset
2000 )
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diff changeset
2001 record.add_asserted_type(PROV['PrimarySource'])
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diff changeset
2002 return record
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diff changeset
2003
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2004 def specialization(self, specificEntity, generalEntity):
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diff changeset
2005 """
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diff changeset
2006 Creates a new specialisation record for a specific from a general entity.
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diff changeset
2007
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diff changeset
2008 :param specificEntity: Entity or a string identifier for the specific
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diff changeset
2009 entity (relationship source).
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2010 :param generalEntity: Entity or a string identifier for the general entity
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diff changeset
2011 (relationship destination).
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diff changeset
2012 """
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diff changeset
2013 return self.new_record(
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diff changeset
2014 PROV_SPECIALIZATION, None, {
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parents:
diff changeset
2015 PROV_ATTR_SPECIFIC_ENTITY: specificEntity,
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parents:
diff changeset
2016 PROV_ATTR_GENERAL_ENTITY: generalEntity
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diff changeset
2017 }
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parents:
diff changeset
2018 )
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diff changeset
2019
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diff changeset
2020 def alternate(self, alternate1, alternate2):
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diff changeset
2021 """
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diff changeset
2022 Creates a new alternate record between two entities.
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diff changeset
2023
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diff changeset
2024 :param alternate1: Entity or a string identifier for the first entity
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parents:
diff changeset
2025 (relationship source).
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diff changeset
2026 :param alternate2: Entity or a string identifier for the second entity
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parents:
diff changeset
2027 (relationship destination).
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diff changeset
2028 """
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diff changeset
2029 return self.new_record(
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parents:
diff changeset
2030 PROV_ALTERNATE, None, {
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diff changeset
2031 PROV_ATTR_ALTERNATE1: alternate1,
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parents:
diff changeset
2032 PROV_ATTR_ALTERNATE2: alternate2
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diff changeset
2033 },
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parents:
diff changeset
2034 )
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diff changeset
2035
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diff changeset
2036 def mention(self, specificEntity, generalEntity, bundle):
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parents:
diff changeset
2037 """
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parents:
diff changeset
2038 Creates a new mention record for a specific from a general entity.
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parents:
diff changeset
2039
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diff changeset
2040 :param specificEntity: Entity or a string identifier for the specific
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parents:
diff changeset
2041 entity (relationship source).
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parents:
diff changeset
2042 :param generalEntity: Entity or a string identifier for the general entity
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parents:
diff changeset
2043 (relationship destination).
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parents:
diff changeset
2044 :param bundle: XXX
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diff changeset
2045 """
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diff changeset
2046 return self.new_record(
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parents:
diff changeset
2047 PROV_MENTION, None, {
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parents:
diff changeset
2048 PROV_ATTR_SPECIFIC_ENTITY: specificEntity,
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parents:
diff changeset
2049 PROV_ATTR_GENERAL_ENTITY: generalEntity,
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parents:
diff changeset
2050 PROV_ATTR_BUNDLE: bundle
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parents:
diff changeset
2051 }
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parents:
diff changeset
2052 )
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parents:
diff changeset
2053
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parents:
diff changeset
2054 def collection(self, identifier, other_attributes=None):
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parents:
diff changeset
2055 """
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parents:
diff changeset
2056 Creates a new collection record for a particular record.
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parents:
diff changeset
2057
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parents:
diff changeset
2058 :param identifier: Identifier for new collection record.
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parents:
diff changeset
2059 :param other_attributes: Optional other attributes as a dictionary or list
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parents:
diff changeset
2060 of tuples to be added to the record optionally (default: None).
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parents:
diff changeset
2061 """
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diff changeset
2062 record = self.new_record(
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parents:
diff changeset
2063 PROV_ENTITY, identifier, None, other_attributes
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parents:
diff changeset
2064 )
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parents:
diff changeset
2065 record.add_asserted_type(PROV['Collection'])
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parents:
diff changeset
2066 return record
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parents:
diff changeset
2067
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parents:
diff changeset
2068 def membership(self, collection, entity):
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parents:
diff changeset
2069 """
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parents:
diff changeset
2070 Creates a new membership record for an entity to a collection.
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parents:
diff changeset
2071
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parents:
diff changeset
2072 :param collection: Collection the entity is to be added to.
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parents:
diff changeset
2073 :param entity: Entity to be added to the collection.
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parents:
diff changeset
2074 """
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parents:
diff changeset
2075 return self.new_record(
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parents:
diff changeset
2076 PROV_MEMBERSHIP, None, {
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parents:
diff changeset
2077 PROV_ATTR_COLLECTION: collection,
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parents:
diff changeset
2078 PROV_ATTR_ENTITY: entity
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parents:
diff changeset
2079 }
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parents:
diff changeset
2080 )
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parents:
diff changeset
2081
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parents:
diff changeset
2082 def plot(self, filename=None, show_nary=True, use_labels=False,
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parents:
diff changeset
2083 show_element_attributes=True, show_relation_attributes=True):
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parents:
diff changeset
2084 """
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parents:
diff changeset
2085 Convenience function to plot a PROV document.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2086
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parents:
diff changeset
2087 :param filename: The filename to save to. If not given, it will open
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2088 an interactive matplotlib plot. The filetype is determined from
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2089 the filename ending.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2090 :type filename: String
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2091 :param show_nary: Shows all elements in n-ary relations.
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parents:
diff changeset
2092 :type show_nary: bool
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parents:
diff changeset
2093 :param use_labels: Uses the `prov:label` property of an element as its
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2094 name (instead of its identifier).
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parents:
diff changeset
2095 :type use_labels: bool
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2096 :param show_element_attributes: Shows attributes of elements.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2097 :type show_element_attributes: bool
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2098 :param show_relation_attributes: Shows attributes of relations.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2099 :type show_relation_attributes: bool
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parents:
diff changeset
2100 """
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guerler
parents:
diff changeset
2101 # Lazy imports to have soft dependencies on pydot and matplotlib
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2102 # (imported even later).
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guerler
parents:
diff changeset
2103 from prov import dot
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2104
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parents:
diff changeset
2105 if filename:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2106 format = os.path.splitext(filename)[-1].lower().strip(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2107 os.path.extsep)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2108 else:
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parents:
diff changeset
2109 format = "png"
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parents:
diff changeset
2110 format = format.lower()
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parents:
diff changeset
2111 d = dot.prov_to_dot(self, show_nary=show_nary, use_labels=use_labels,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2112 show_element_attributes=show_element_attributes,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2113 show_relation_attributes=show_relation_attributes)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2114 method = "create_%s" % format
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2115 if not hasattr(d, method):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2116 raise ValueError("Format '%s' cannot be saved." % format)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2117 with io.BytesIO() as buf:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2118 buf.write(getattr(d, method)())
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guerler
parents:
diff changeset
2119
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parents:
diff changeset
2120 buf.seek(0, 0)
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parents:
diff changeset
2121 if filename:
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parents:
diff changeset
2122 with open(filename, "wb") as fh:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2123 fh.write(buf.read())
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parents:
diff changeset
2124 else:
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guerler
parents:
diff changeset
2125 # Use matplotlib to show the image as it likely is more
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2126 # widespread then PIL and works nicely in the ipython notebook.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2127 import matplotlib.pylab as plt
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2128 import matplotlib.image as mpimg
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guerler
parents:
diff changeset
2129
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parents:
diff changeset
2130 max_size = 30
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parents:
diff changeset
2131
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parents:
diff changeset
2132 img = mpimg.imread(buf)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2133 # pydot makes a border around the image. remove it.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2134 img = img[1:-1, 1:-1]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2135 size = (img.shape[1] / 100.0, img.shape[0] / 100.0)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2136 if max(size) > max_size:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2137 scale = max_size / max(size)
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parents:
diff changeset
2138 else:
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parents:
diff changeset
2139 scale = 1.0
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2140 size = (scale * size[0], scale * size[1])
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guerler
parents:
diff changeset
2141
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parents:
diff changeset
2142 plt.figure(figsize=size)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2143 plt.subplots_adjust(bottom=0, top=1, left=0, right=1)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2144 plt.xticks([])
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parents:
diff changeset
2145 plt.yticks([])
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parents:
diff changeset
2146 plt.imshow(img)
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parents:
diff changeset
2147 plt.axis("off")
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parents:
diff changeset
2148 plt.show()
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guerler
parents:
diff changeset
2149
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diff changeset
2150 # Aliases
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parents:
diff changeset
2151 wasGeneratedBy = generation
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2152 used = usage
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2153 wasStartedBy = start
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2154 wasEndedBy = end
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2155 wasInvalidatedBy = invalidation
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2156 wasInformedBy = communication
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2157 wasAttributedTo = attribution
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2158 wasAssociatedWith = association
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2159 actedOnBehalfOf = delegation
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2160 wasInfluencedBy = influence
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2161 wasDerivedFrom = derivation
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2162 wasRevisionOf = revision
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2163 wasQuotedFrom = quotation
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guerler
parents:
diff changeset
2164 hadPrimarySource = primary_source
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2165 alternateOf = alternate
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2166 specializationOf = specialization
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2167 mentionOf = mention
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2168 hadMember = membership
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2169
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2170
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guerler
parents:
diff changeset
2171 class ProvDocument(ProvBundle):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2172 """Provenance Document."""
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2173
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guerler
parents:
diff changeset
2174 def __init__(self, records=None, namespaces=None):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2175 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2176 Constructor.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2177
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guerler
parents:
diff changeset
2178 :param records: Optional records to add to the document (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2179 :param namespaces: Optional iterable of :py:class:`~prov.identifier.Namespace`s
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2180 to set the document up with (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2181 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2182 ProvBundle.__init__(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2183 self, records=records, identifier=None, namespaces=namespaces
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guerler
parents:
diff changeset
2184 )
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guerler
parents:
diff changeset
2185 self._bundles = dict()
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guerler
parents:
diff changeset
2186
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guerler
parents:
diff changeset
2187 def __repr__(self):
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guerler
parents:
diff changeset
2188 return '<ProvDocument>'
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guerler
parents:
diff changeset
2189
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parents:
diff changeset
2190 def __eq__(self, other):
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guerler
parents:
diff changeset
2191 if not isinstance(other, ProvDocument):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2192 return False
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guerler
parents:
diff changeset
2193 # Comparing the documents' content
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2194 if not super(ProvDocument, self).__eq__(other):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2195 return False
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guerler
parents:
diff changeset
2196
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guerler
parents:
diff changeset
2197 # Comparing the documents' bundles
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2198 for b_id, bundle in self._bundles.items():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2199 if b_id not in other._bundles:
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guerler
parents:
diff changeset
2200 return False
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guerler
parents:
diff changeset
2201 other_bundle = other._bundles[b_id]
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guerler
parents:
diff changeset
2202 if bundle != other_bundle:
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guerler
parents:
diff changeset
2203 return False
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guerler
parents:
diff changeset
2204
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guerler
parents:
diff changeset
2205 # Everything is the same
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parents:
diff changeset
2206 return True
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guerler
parents:
diff changeset
2207
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diff changeset
2208 def is_document(self):
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parents:
diff changeset
2209 """
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guerler
parents:
diff changeset
2210 `True` if the object is a document, `False` otherwise.
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guerler
parents:
diff changeset
2211
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guerler
parents:
diff changeset
2212 :return: bool
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guerler
parents:
diff changeset
2213 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2214 return True
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guerler
parents:
diff changeset
2215
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guerler
parents:
diff changeset
2216 def is_bundle(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2217 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2218 `True` if the object is a bundle, `False` otherwise.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2219
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guerler
parents:
diff changeset
2220 :return: bool
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2221 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2222 return False
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2223
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2224 def has_bundles(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2225 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2226 `True` if the object has at least one bundle, `False` otherwise.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2227
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guerler
parents:
diff changeset
2228 :return: bool
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2229 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2230 return len(self._bundles) > 0
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2231
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2232 @property
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2233 def bundles(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2234 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2235 Returns bundles contained in the document
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2236
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2237 :return: Iterable of :py:class:`ProvBundle`.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2238 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2239 return self._bundles.values()
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guerler
parents:
diff changeset
2240
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guerler
parents:
diff changeset
2241 # Transformations
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2242 def flattened(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2243 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2244 Flattens the document by moving all the records in its bundles up
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2245 to the document level.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2246
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guerler
parents:
diff changeset
2247 :returns: :py:class:`ProvDocument` -- the (new) flattened document.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2248 """
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guerler
parents:
diff changeset
2249 if self._bundles:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2250 # Creating a new document for all the records
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2251 new_doc = ProvDocument()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2252 bundled_records = itertools.chain(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2253 *[b.get_records() for b in self._bundles.values()]
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guerler
parents:
diff changeset
2254 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2255 for record in itertools.chain(self._records, bundled_records):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2256 new_doc.add_record(record)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2257 return new_doc
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parents:
diff changeset
2258 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2259 # returning the same document
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2260 return self
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2261
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parents:
diff changeset
2262 def unified(self):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2263 """
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guerler
parents:
diff changeset
2264 Returns a new document containing all records having same identifiers
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2265 unified (including those inside bundles).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2266
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2267 :return: :py:class:`ProvDocument`
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2268 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2269 document = ProvDocument(self._unified_records())
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2270 document._namespaces = self._namespaces
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2271 for bundle in self.bundles:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2272 unified_bundle = bundle.unified()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2273 document.add_bundle(unified_bundle)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2274 return document
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guerler
parents:
diff changeset
2275
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parents:
diff changeset
2276 def update(self, other):
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parents:
diff changeset
2277 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2278 Append all the records of the *other* document/bundle into this document.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2279 Bundles having same identifiers will be merged.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2280
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guerler
parents:
diff changeset
2281 :param other: The other document/bundle whose records to be appended.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2282 :type other: :py:class:`ProvDocument` or :py:class:`ProvBundle`
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guerler
parents:
diff changeset
2283 :returns: None.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2284 """
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guerler
parents:
diff changeset
2285 if isinstance(other, ProvBundle):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2286 for record in other.get_records():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2287 self.add_record(record)
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guerler
parents:
diff changeset
2288 if other.has_bundles():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2289 for bundle in other.bundles:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2290 if bundle.identifier in self._bundles:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2291 self._bundles[bundle.identifier].update(bundle)
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guerler
parents:
diff changeset
2292 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2293 new_bundle = self.bundle(bundle.identifier)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2294 new_bundle.update(bundle)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2295 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2296 raise ProvException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2297 'ProvDocument.update(): The other is not a ProvDocument or '
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2298 'ProvBundle instance (%s)' % type(other)
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guerler
parents:
diff changeset
2299 )
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guerler
parents:
diff changeset
2300
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2301 # Bundle operations
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2302 def add_bundle(self, bundle, identifier=None):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2303 """
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guerler
parents:
diff changeset
2304 Add a bundle to the current document.
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guerler
parents:
diff changeset
2305
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guerler
parents:
diff changeset
2306 :param bundle: The bundle to add to the document.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2307 :type bundle: :py:class:`ProvBundle`
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2308 :param identifier: The (optional) identifier to use for the bundle
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2309 (default: None). If none given, use the identifier from the bundle
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2310 itself.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2311 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2312 if not isinstance(bundle, ProvBundle):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2313 raise ProvException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2314 'Only a ProvBundle instance can be added as a bundle in a '
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2315 'ProvDocument.'
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2316 )
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guerler
parents:
diff changeset
2317
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2318 if bundle.is_document():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2319 if bundle.has_bundles():
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2320 raise ProvException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2321 'Cannot add a document with nested bundles as a bundle.'
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2322 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2323 # Make it a new ProvBundle
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2324 new_bundle = ProvBundle(namespaces=bundle.namespaces)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2325 new_bundle.update(bundle)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2326 bundle = new_bundle
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2327
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2328 if identifier is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2329 identifier = bundle.identifier
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2330
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2331 if not identifier:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2332 raise ProvException('The provided bundle has no identifier')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2333
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2334 # Link the bundle namespace manager to the document's
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2335 bundle._namespaces.parent = self._namespaces
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2336
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2337 valid_id = bundle.valid_qualified_name(identifier)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2338 # IMPORTANT: Rewriting the bundle identifier for consistency
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2339 bundle._identifier = valid_id
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2340
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2341 if valid_id in self._bundles:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2342 raise ProvException('A bundle with that identifier already exists')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2343
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2344 self._bundles[valid_id] = bundle
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2345 bundle._document = self
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2346
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2347 def bundle(self, identifier):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2348 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2349 Returns a new bundle from the current document.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2350
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2351 :param identifier: The identifier to use for the bundle.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2352 :return: :py:class:`ProvBundle`
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2353 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2354 if identifier is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2355 raise ProvException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2356 'An identifier is required. Cannot create an unnamed bundle.'
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2357 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2358 valid_id = self.valid_qualified_name(identifier)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2359 if valid_id is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2360 raise ProvException(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2361 'The provided identifier "%s" is not valid' % identifier
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2362 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2363 if valid_id in self._bundles:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2364 raise ProvException('A bundle with that identifier already exists')
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2365 b = ProvBundle(identifier=valid_id, document=self)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2366 self._bundles[valid_id] = b
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2367 return b
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2368
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2369 # Serializing and deserializing
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2370 def serialize(self, destination=None, format='json', **args):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2371 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2372 Serialize the :py:class:`ProvDocument` to the destination.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2373
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2374 Available serializers can be queried by the value of
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2375 `:py:attr:~prov.serializers.Registry.serializers` after loading them via
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2376 `:py:func:~prov.serializers.Registry.load_serializers()`.
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guerler
parents:
diff changeset
2377
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guerler
parents:
diff changeset
2378 :param destination: Stream object to serialize the output to. Default is
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2379 `None`, which serializes as a string.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2380 :param format: Serialization format (default: 'json'), defaulting to
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2381 PROV-JSON.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2382 :return: Serialization in a string if no destination was given,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2383 None otherwise.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2384 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2385 serializer = serializers.get(format)(self)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2386 if destination is None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2387 stream = io.StringIO()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2388 serializer.serialize(stream, **args)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2389 return stream.getvalue()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2390 if hasattr(destination, "write"):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2391 stream = destination
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2392 serializer.serialize(stream, **args)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2393 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2394 location = destination
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2395 scheme, netloc, path, params, _query, fragment = urlparse(location)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2396 if netloc != "":
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2397 print("WARNING: not saving as location " +
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2398 "is not a local file reference")
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guerler
parents:
diff changeset
2399 return
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2400 fd, name = tempfile.mkstemp()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2401 stream = os.fdopen(fd, "wb")
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2402 serializer.serialize(stream, **args)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2403 stream.close()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2404 if hasattr(shutil, "move"):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2405 shutil.move(name, path)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2406 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2407 shutil.copy(name, path)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2408 os.remove(name)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2409
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2410 @staticmethod
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2411 def deserialize(source=None, content=None, format='json', **args):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2412 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2413 Deserialize the :py:class:`ProvDocument` from source (a stream or a
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2414 file path) or directly from a string content.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2415
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2416 Available serializers can be queried by the value of
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2417 `:py:attr:~prov.serializers.Registry.serializers` after loading them via
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2418 `:py:func:~prov.serializers.Registry.load_serializers()`.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2419
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2420 Note: Not all serializers support deserialization.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2421
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2422 :param source: Stream object to deserialize the PROV document from
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2423 (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2424 :param content: String to deserialize the PROV document from
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2425 (default: None).
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2426 :param format: Serialization format (default: 'json'), defaulting to
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2427 PROV-JSON.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2428 :return: :py:class:`ProvDocument`
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2429 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2430 serializer = serializers.get(format)()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2431
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2432 if content is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2433 # io.StringIO only accepts unicode strings
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2434 stream = io.StringIO(
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2435 content if not isinstance(content, six.binary_type)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2436 else content.decode()
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2437 )
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2438 return serializer.deserialize(stream, **args)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2439
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2440 if source is not None:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2441 if hasattr(source, "read"):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2442 return serializer.deserialize(source, **args)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2443 else:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2444 with open(source) as f:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2445 return serializer.deserialize(f, **args)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2446
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2447
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2448 def sorted_attributes(element, attributes):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2449 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2450 Helper function sorting attributes into the order required by PROV-XML.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2451
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2452 :param element: The prov element used to derive the type and the
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2453 attribute order for the type.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2454 :param attributes: The attributes to sort.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2455 """
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2456 attributes = list(attributes)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2457 order = list(PROV_REC_CLS[element].FORMAL_ATTRIBUTES)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2458
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2459 # Append label, location, role, type, and value attributes. This is
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2460 # universal amongst all elements.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2461 order.extend([PROV_LABEL, PROV_LOCATION, PROV_ROLE, PROV_TYPE,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2462 PROV_VALUE])
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2463
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2464 # Sort function. The PROV XML specification talks about alphabetical
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2465 # sorting. We now interpret it as sorting by tag including the prefix
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2466 # first and then sorting by the text, also including the namespace
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2467 # prefix if given.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2468 def sort_fct(x):
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2469 return (
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2470 six.text_type(x[0]),
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2471 six.text_type(x[1].value if hasattr(x[1], "value") else x[1])
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diff changeset
2472 )
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diff changeset
2473
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diff changeset
2474 sorted_elements = []
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2475 for item in order:
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2476 this_type_list = []
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2477 for e in list(attributes):
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2478 if e[0] != item:
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2479 continue
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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2480 this_type_list.append(e)
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2481 attributes.remove(e)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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2482 this_type_list.sort(key=sort_fct)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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2483 sorted_elements.extend(this_type_list)
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2484 # Add remaining attributes. According to the spec, the other attributes
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2485 # have a fixed alphabetical order.
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2486 attributes.sort(key=sort_fct)
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diff changeset
2487 sorted_elements.extend(attributes)
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2488
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diff changeset
2489 return sorted_elements