Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/prov/tests/test_model.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """
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2 Created on Jan 25, 2012
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3
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4 @author: Trung Dong Huynh
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5 """
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6 from __future__ import (absolute_import, division, print_function,
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7 unicode_literals)
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8
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9 import unittest
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10 import logging
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11 import os
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12
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13 from prov.model import ProvDocument, ProvBundle, ProvException, first, Literal
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14 from prov.tests import examples
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15 from prov.tests.attributes import TestAttributesBase
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16 from prov.tests.qnames import TestQualifiedNamesBase
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17 from prov.tests.statements import TestStatementsBase
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18 from prov.tests.utility import RoundTripTestCase
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19
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20 logger = logging.getLogger(__name__)
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21
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22
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23 EX_URI = 'http://www.example.org/'
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24 EX2_URI = 'http://www.example2.org/'
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25
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26
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27 class TestExamplesBase(object):
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28 """This is the base class for testing support for all the examples provided
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29 in prov.tests.examples.
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30 It is not runnable and needs to be included in a subclass of
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31 RoundTripTestCase.
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32 """
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33 def test_all_examples(self):
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34 counter = 0
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35 for name, graph in examples.tests:
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36 counter += 1
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37 logger.info('%d. Testing the %s example', counter, name)
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38 g = graph()
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39 self.do_tests(g)
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40
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41
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42 class TestLoadingProvToolboxJSON(unittest.TestCase):
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43 def setUp(self):
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44 self.json_path = os.path.dirname(os.path.abspath(__file__)) + '/json/'
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45 filenames = os.listdir(self.json_path)
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46 self.fails = []
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47 for filename in filenames:
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48 if filename.endswith('.json'):
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49 with open(self.json_path + filename) as json_file:
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50 try:
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51 g1 = ProvDocument.deserialize(json_file)
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52 json_str = g1.serialize(indent=4)
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53 g2 = ProvDocument.deserialize(content=json_str)
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54 self.assertEqual(
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55 g1, g2,
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56 'Round-trip JSON encoding/decoding failed: %s.'
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57 % filename
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58 )
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59 except:
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60 self.fails.append(filename)
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61
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62 def test_loading_all_json(self):
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63 # self.assertFalse(fails, 'Failed to load/round-trip %d JSON files (%s)' % (len(fails), ', '.join(fails)))
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64
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65 # Code for debugging the failed tests
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66 for filename in self.fails:
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67 # Reload the failed files
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68 filepath = self.json_path + filename
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69 # os.rename(json_path + filename, json_path + filename + '-fail')
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70 with open(filepath) as json_file:
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71 logger.info("Loading %s...", filepath)
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72 g1 = ProvDocument.deserialize(json_file)
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73 json_str = g1.serialize(indent=4)
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74 g2 = ProvDocument.deserialize(content=json_str)
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75 self.assertEqual(
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76 g1, g2,
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77 'Round-trip JSON encoding/decoding failed: %s.'
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78 % filename
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79 )
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80
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81
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82 class TestFlattening(unittest.TestCase):
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83 def test_flattening(self):
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84 for name, graph in examples.tests:
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85 logger.info('Testing flattening of the %s example', name)
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86 document = graph()
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87 flattened = document.flattened()
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88 flattened_records = set(flattened.get_records())
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89 # counting all the records:
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90 n_records = 0
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91 for record in document.get_records():
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92 n_records += 1
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93 self.assertIn(record, flattened_records)
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94 for bundle in document.bundles:
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95 for record in bundle.get_records():
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96 n_records += 1
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97 self.assertIn(record, flattened_records)
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98 self.assertEqual(n_records, len(flattened.get_records()))
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99
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100
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101 class TestUnification(unittest.TestCase):
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102 def test_unifying(self):
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103 # This is a very trivial test just to exercise the unified() function
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104 # TODO: Create a proper unification test
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105 json_path = os.path.dirname(os.path.abspath(__file__)) + '/unification/'
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106 filenames = os.listdir(json_path)
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107 for filename in filenames:
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108 if not filename.endswith('.json'):
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109 continue
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110 filepath = json_path + filename
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111 with open(filepath) as json_file:
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112 logger.info('Testing unifying: %s', filename)
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113 logger.debug("Loading %s...", filepath)
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114 document = ProvDocument.deserialize(json_file)
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115 flattened = document.flattened()
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116 unified = flattened.unified()
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117 self.assertLess(
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118 len(unified.get_records()),
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119 len(flattened.get_records())
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120 )
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121
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122
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123 class TestBundleUpdate(unittest.TestCase):
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124 def test_bundle_update_simple(self):
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125 doc = ProvDocument()
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126 doc.set_default_namespace(EX_URI)
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127
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128 b1 = doc.bundle('b1')
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129 b1.entity('e')
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130
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131 b2 = doc.bundle('b2')
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132 b2.entity('e')
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133
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134 self.assertRaises(ProvException, lambda: b1.update(1))
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135 self.assertRaises(ProvException, lambda: b1.update(doc))
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136
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137 b1.update(b2)
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138 self.assertEqual(len(b1.get_records()), 2)
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139
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140 def test_document_update_simple(self):
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141 d1 = ProvDocument()
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142 d1.set_default_namespace(EX_URI)
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143 d1.entity('e')
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144
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145 b1 = d1.bundle('b1')
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146 b1.entity('e')
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147
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148 d2 = ProvDocument()
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149 d2.set_default_namespace(EX_URI)
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150 d2.entity('e')
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151
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152 b1 = d2.bundle('b1')
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153 b1.entity('e')
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154 b2 = d2.bundle('b2')
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155 b2.entity('e')
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156
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157 self.assertRaises(ProvException, lambda: d1.update(1))
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158
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159 d1.update(d2)
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160 self.assertEqual(len(d1.get_records()), 2)
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161 self.assertEqual(len(d1.bundles), 2)
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162
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163
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164 class TestAddBundle(unittest.TestCase):
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165 def document_1(self):
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166 d1 = ProvDocument()
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167 ns_ex = d1.add_namespace('ex', EX_URI)
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168 d1.entity(ns_ex['e1'])
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169 return d1
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170
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171 def document_2(self):
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172 d2 = ProvDocument()
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173 ns_ex = d2.add_namespace('ex', EX2_URI)
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174 d2.activity(ns_ex['a1'])
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175 return d2
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176
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177 def bundle_0(self):
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178 b = ProvBundle(namespaces={'ex': EX2_URI})
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179 return b
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180
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181 def test_add_bundle_simple(self):
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182 d1 = self.document_1()
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183 b0 = self.bundle_0()
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184
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185 def sub_test_1():
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186 d1.add_bundle(b0)
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187 self.assertRaises(ProvException, sub_test_1)
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188 self.assertFalse(d1.has_bundles())
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189
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190 d1.add_bundle(b0, 'ex:b0')
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191 self.assertTrue(d1.has_bundles())
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192 self.assertIn(b0, d1.bundles)
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193
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194 def sub_test_2():
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195 ex2_b0 = b0.identifier
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196 d1.add_bundle(ProvBundle(identifier=ex2_b0))
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197 self.assertRaises(ProvException, sub_test_2)
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198
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199 d1.add_bundle(ProvBundle(), 'ex:b0')
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200 self.assertEqual(len(d1.bundles), 2)
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201
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202 def test_add_bundle_document(self):
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203 d1 = self.document_1()
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204 d2 = self.document_2()
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205
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206 def sub_test_1():
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207 d1.add_bundle(d2)
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208 self.assertRaises(ProvException, sub_test_1)
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209
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210 ex2_b2 = d2.valid_qualified_name('ex:b2')
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211 d1.add_bundle(d2, 'ex:b2')
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212 self.assertEqual(ex2_b2, first(d1.bundles).identifier)
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213 self.assertNotIn(d2, d1.bundles)
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214 b2 = ProvBundle()
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215 b2.update(d2)
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216 self.assertIn(b2, d1.bundles)
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217
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218 class TestLiteralRepresentation(unittest.TestCase):
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219 def test_literal_provn_with_single_quotes(self):
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220 l = Literal('{"foo": "bar"}')
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221 string_rep = l.provn_representation()
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222 self.assertTrue('{\\"f' in string_rep)
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223
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224 def test_literal_provn_with_triple_quotes(self):
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225 l = Literal('"""foo\\nbar"""')
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226 string_rep = l.provn_representation()
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227 self.assertTrue('\\"\\"\\"f' in string_rep)
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228
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229 class AllTestsBase(TestExamplesBase, TestStatementsBase,
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230 TestAttributesBase, TestQualifiedNamesBase):
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231 """This is a test to include all available tests.
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232 """
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233 pass
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234
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235
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236 class RoundTripModelTest(RoundTripTestCase, AllTestsBase):
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237 def assertRoundTripEquivalence(self, prov_doc, msg=None):
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238 """Exercises prov.model without the actual serialization and PROV-N
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239 generation.
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240 """
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241 provn_content = prov_doc.get_provn()
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242 # Checking for self-equality
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243 self.assertEqual(
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244 prov_doc, prov_doc,
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245 'The document is not self-equal:\n' + provn_content)
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246
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247
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248 if __name__ == "__main__":
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249 unittest.main()