Mercurial > repos > shellac > guppy_basecaller

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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0
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1 from __future__ import (absolute_import, division, print_function,
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2 unicode_literals)
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3
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4 import io
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5 import unittest
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6
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7 from prov.model import *
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8 from prov.dot import prov_to_dot
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9 from prov.serializers import Registry
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10 from prov.tests.examples import primer_example, primer_example_alternate
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11
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12
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13 EX_NS = Namespace('ex', 'http://example.org/')
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14 EX2_NS = Namespace('ex2', 'http://example2.org/')
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15 EX_OTHER_NS = Namespace('other', 'http://exceptions.example.org/')
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16
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17
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18 def add_label(record):
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19 record.add_attributes(
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20 [('prov:label', Literal("hello"))]
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21 )
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22
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23
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24 def add_labels(record):
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25 record.add_attributes([
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26 ('prov:label', Literal("hello")),
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27 ('prov:label', Literal("bye", langtag="en")),
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28 ('prov:label', Literal("bonjour", langtag="fr"))
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29 ])
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30
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31
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32 def add_types(record):
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33 record.add_attributes([
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34 ('prov:type', 'a'),
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35 ('prov:type', 1),
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36 ('prov:type', 1.0),
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37 ('prov:type', True),
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38 ('prov:type', EX_NS['abc']),
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39 ('prov:type', datetime.datetime.now()),
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40 ('prov:type', Literal('http://boiled-egg.example.com',
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41 datatype=XSD_ANYURI)),
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42 ])
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43
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44
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45 def add_locations(record):
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46 record.add_attributes([
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47 ('prov:Location', "Southampton"),
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48 ('prov:Location', 1),
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49 ('prov:Location', 1.0),
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50 ('prov:Location', True),
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51 ('prov:Location', EX_NS['london']),
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52 ('prov:Location', datetime.datetime.now()),
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53 ('prov:Location', EX_NS.uri + "london"),
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54 ('prov:Location', Literal(2002, datatype=XSD['gYear'])),
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55 ])
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56
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57
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58 def add_value(record):
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59 record.add_attributes([
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60 ('prov:value', EX_NS['avalue'])
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61 ])
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62
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63
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64 def add_further_attributes(record):
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65 record.add_attributes([
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66 (EX_NS['tag1'], "hello"),
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67 (EX_NS['tag2'], "bye"),
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68 (EX2_NS['tag3'], "hi"),
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69 (EX_NS['tag1'], "hello\nover\nmore\nlines"),
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70 ])
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71
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72
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73 def add_further_attributes0(record):
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74 record.add_attributes([
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75 (EX_NS['tag1'], "hello"),
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76 (EX_NS['tag2'], "bye"),
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77 (EX_NS['tag2'], Literal("hola", langtag="es")),
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78 (EX2_NS['tag3'], "hi"),
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79 (EX_NS['tag'], 1),
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80 # long on python 2, int on python 3
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81 (EX_NS['tag'], six.integer_types[-1](1)),
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82 (EX_NS['tag'], Literal(1, datatype=XSD_SHORT)),
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83 (EX_NS['tag'], Literal(1, datatype=XSD_DOUBLE)),
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84 (EX_NS['tag'], 1.0),
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85 (EX_NS['tag'], True),
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86 (EX_NS['tag'], EX_NS.uri + "southampton"),
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87 ])
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88
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89 add_further_attributes_with_qnames(record)
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90
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91
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92 def add_further_attributes_with_qnames(record):
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93 record.add_attributes([
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94 (EX_NS['tag'], EX2_NS['newyork']),
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95 (EX_NS['tag'], EX_NS['london']),
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96 ])
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97
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98
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99 class TestExtras(unittest.TestCase):
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100 def test_dot(self):
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101 # This is naive, since we can't programatically check the output is
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102 # correct
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103 document = ProvDocument()
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104
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105 bundle1 = ProvBundle(identifier=EX_NS['bundle1'])
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106 bundle1.usage(
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107 activity=EX_NS['a1'], entity=EX_NS['e1'], identifier=EX_NS['use1']
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108 )
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109 bundle1.entity(
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110 identifier=EX_NS['e1'], other_attributes={PROV_ROLE: "sausage"}
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111 )
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112 bundle1.activity(identifier=EX_NS['a1'])
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113 document.activity(EX_NS['a2'])
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114
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115 bundle2 = ProvBundle(identifier=EX_NS['bundle2'])
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116 bundle2.usage(
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117 activity=EX_NS['aa1'], entity=EX_NS['ee1'],
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118 identifier=EX_NS['use2']
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119 )
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120 bundle2.entity(identifier=EX_NS['ee1'])
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121 bundle2.activity(identifier=EX_NS['aa1'])
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122
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123 document.add_bundle(bundle1)
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124 document.add_bundle(bundle2)
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125 prov_to_dot(document)
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126
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127 def test_extra_attributes(self):
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128
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129 document = ProvDocument()
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130
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131 inf = document.influence(
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132 EX_NS['a2'], EX_NS['a1'], identifier=EX_NS['inf7']
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133 )
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134 add_labels(inf)
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135 add_types(inf)
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136 add_further_attributes(inf)
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137
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138 self.assertEqual(
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139 len(inf.attributes),
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140 len(list(inf.formal_attributes) + inf.extra_attributes)
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141 )
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142
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143 def test_serialize_to_path(self):
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144 document = ProvDocument()
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145 document.serialize("output.json")
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146 os.remove('output.json')
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147
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148 document.serialize("http://netloc/outputmyprov/submit.php")
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149
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150 def test_bundle_no_id(self):
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151 document = ProvDocument()
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152
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153 def test():
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154 bundle = ProvBundle()
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155 document.add_bundle(bundle)
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156
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157 self.assertRaises(ProvException, test)
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158
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159 def test_use_set_time_helpers(self):
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160 dt = datetime.datetime.now()
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161 document1 = ProvDocument()
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162 document1.activity(EX_NS['a8'], startTime=dt, endTime=dt)
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163
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164 document2 = ProvDocument()
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165 a = document2.activity(EX_NS['a8'])
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166 a.set_time(startTime=dt, endTime=dt)
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167
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168 self.assertEqual(document1, document2)
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169 self.assertEqual(a.get_startTime(), dt)
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170 self.assertEqual(a.get_endTime(), dt)
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171
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172 def test_bundle_add_garbage(self):
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173 document = ProvDocument()
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174
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175 def test():
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176 document.add_bundle(
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177 document.entity(EX_NS['entity_trying_to_be_a_bundle'])
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178 )
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179
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180 self.assertRaises(ProvException, test)
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181
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182 def test():
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183 bundle = ProvBundle()
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184 document.add_bundle(bundle)
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185
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186 self.assertRaises(ProvException, test)
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187
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188 def test_bundle_equality_garbage(self):
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189 document = ProvBundle()
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190 self.assertNotEqual(document, 1)
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191
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192 def test_bundle_is_bundle(self):
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193 document = ProvBundle()
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194 self.assertTrue(document.is_bundle())
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195
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196 def test_bundle_get_record_by_id(self):
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197 document = ProvDocument()
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198 self.assertEqual(document.get_record(None), None)
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199
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200 # record = document.entity(identifier=EX_NS['e1'])
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201 # self.assertEqual(document.get_record(EX_NS['e1']), record)
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202 #
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203 # bundle = document.bundle(EX_NS['b'])
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204 # self.assertEqual(bundle.get_record(EX_NS['e1']), record)
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205
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206 def test_bundle_get_records(self):
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207 document = ProvDocument()
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208
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209 document.entity(identifier=EX_NS['e1'])
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210 document.agent(identifier=EX_NS['e1'])
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211 self.assertEqual(len(list(document.get_records(ProvAgent))), 1)
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212 self.assertEqual(len(document.get_records()), 2)
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213
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214 def test_bundle_name_clash(self):
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215 document = ProvDocument()
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216
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217 def test():
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218 document.bundle(EX_NS['indistinct'])
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219 document.bundle(EX_NS['indistinct'])
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220
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221 self.assertRaises(ProvException, test)
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222
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223 document = ProvDocument()
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224
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225 def test():
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226 document.bundle(EX_NS['indistinct'])
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227 bundle = ProvBundle(identifier=EX_NS['indistinct'])
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228 document.add_bundle(bundle)
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229
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230 self.assertRaises(ProvException, test)
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231
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232 def test_document_helper_methods(self):
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233 document = ProvDocument()
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234 self.assertFalse(document.is_bundle())
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235 self.assertFalse(document.has_bundles())
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236 document.bundle(EX_NS['b'])
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237 self.assertTrue(document.has_bundles())
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238 self.assertEqual(u'<ProvDocument>', str(document))
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239
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240 def test_reading_and_writing_to_file_like_objects(self):
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241 """
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242 Tests reading and writing to and from file like objects.
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243 """
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244 # Create some random document.
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245 document = ProvDocument()
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246 document.entity(EX2_NS["test"])
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247
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248 objects = [io.BytesIO, io.StringIO]
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249
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250 Registry.load_serializers()
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251 formats = Registry.serializers.keys()
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252
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253 for obj in objects:
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254 for format in formats:
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255 try:
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256 buf = obj()
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257 document.serialize(destination=buf, format=format)
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258 buf.seek(0, 0)
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259 new_document = ProvDocument.deserialize(source=buf,
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260 format=format)
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261 self.assertEqual(document, new_document)
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262 except NotImplementedError:
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263 # Some serializers might not implement serialize or
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264 # deserialize method
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265 pass # and this is fine in the context of this test
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266 finally:
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267 buf.close()
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268
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269 # def test_document_unification(self):
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270 # # TODO: Improve testing of this...
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271 # document = ProvDocument()
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272 # bundle = document.bundle(identifier=EX_NS['b'])
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273 # e1 = bundle.entity(EX_NS['e'])
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274 # e2 = bundle.entity(EX_NS['e'])
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275 # unified = document.unified()
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276 #
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277 # self.assertEqual(len(unified._bundles[0]._records), 1)
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278
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279 def test_primer_alternate(self):
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280 g1 = primer_example()
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281 g2 = primer_example_alternate()
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282 self.assertEqual(g1, g2)
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283
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284
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285 if __name__ == '__main__':
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286 unittest.main()