Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/prov/tests/test_rdf.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 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 unittest
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5 from prov.model import ProvDocument
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6 from prov.tests.utility import RoundTripTestCase
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7 from prov.tests.test_model import (TestStatementsBase,
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8 TestAttributesBase, TestQualifiedNamesBase)
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9 import os
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10 from glob import glob
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11 import logging
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12 logger = logging.getLogger(__name__)
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13
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14 from prov.tests import examples
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15 import prov.model as pm
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16
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17 import rdflib as rl
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18 from rdflib.compare import graph_diff
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19 from io import BytesIO, StringIO
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20
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21
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22 def find_diff(g_rdf, g0_rdf):
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23 graphs_equal = True
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24 in_both, in_first, in_second = graph_diff(g_rdf, g0_rdf)
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25 g1 = sorted(in_first.serialize(format='nt').splitlines())[1:]
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26 g2 = sorted(in_second.serialize(format='nt').splitlines())[1:]
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27 # Compare literals
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28 if len(g1) != len(g2):
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29 graphs_equal = False
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30 matching_indices = [[], []]
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31 for idx in range(len(g1)):
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32 g1_stmt = list(rl.ConjunctiveGraph().parse(BytesIO(g1[idx]),
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33 format='nt'))[0]
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34 match_found = False
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35 for idx2 in range(len(g2)):
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36 if idx2 in matching_indices[1]:
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37 continue
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38 g2_stmt = list(rl.ConjunctiveGraph().parse(BytesIO(g2[idx2]),
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39 format='nt'))[0]
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40 try:
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41 all_match = all([g1_stmt[i].eq(g2_stmt[i]) for i in range(3)])
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42 except TypeError as e:
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43 #logger.info(e, g1_stmt, g2_stmt)
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44 all_match = False
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45 if all_match:
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46 matching_indices[0].append(idx)
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47 matching_indices[1].append(idx2)
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48 match_found = True
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49 break
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50 if not match_found:
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51 graphs_equal = False
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52 in_first2 = rl.ConjunctiveGraph()
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53 for idx in range(len(g1)):
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54 if idx in matching_indices[0]:
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55 in_both.parse(BytesIO(g1[idx]), format='nt')
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56 else:
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57 in_first2.parse(BytesIO(g1[idx]), format='nt')
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58 in_second2 = rl.ConjunctiveGraph()
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59 for idx in range(len(g2)):
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60 if not idx in matching_indices[1]:
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61 in_second2.parse(BytesIO(g2[idx]), format='nt')
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62 #logger.info(in_first2)
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63 #logger.info(in_second2)
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64 return graphs_equal, in_both, in_first2, in_second2
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65
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66
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67 class TestExamplesBase(object):
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68 """This is the base class for testing support for all the examples provided
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69 in prov.tests.examples.
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70 It is not runnable and needs to be included in a subclass of
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71 RoundTripTestCase.
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72 """
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73 def test_all_examples(self):
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74 counter = 0
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75 for name, graph in examples.tests:
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76 if name in ['datatypes']:
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77 logger.info('%d. Skipping the %s example', counter, name)
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78 continue
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79 counter += 1
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80 logger.info('%d. Testing the %s example', counter, name)
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81 g = graph()
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82 self.do_tests(g)
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83
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84
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85 class TestJSONExamplesBase(object):
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86 """This is the base class for testing support for all the examples provided
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87 in prov.tests.examples.
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88 It is not runnable and needs to be included in a subclass of
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89 RoundTripTestCase.
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90 """
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91 def test_all_examples(self):
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92 counter = 0
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93 for name, graph in examples.tests:
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94 if name in ['datatypes']:
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95 logger.info('%d. Skipping the %s example', counter, name)
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96 continue
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97 counter += 1
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98 logger.info('%d. Testing the %s example', counter, name)
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99 g = graph()
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100 self.do_tests(g)
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101
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102
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103 class TestStatementsBase2(TestStatementsBase):
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104 @unittest.expectedFailure
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105 def test_scruffy_end_1(self):
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106 TestStatementsBase.test_scruffy_end_1()
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107 @unittest.expectedFailure
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108 def test_scruffy_end_2(self):
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109 TestStatementsBase.test_scruffy_end_2()
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110 @unittest.expectedFailure
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111 def test_scruffy_end_3(self):
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112 TestStatementsBase.test_scruffy_end_3()
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113 @unittest.expectedFailure
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114 def test_scruffy_end_4(self):
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115 TestStatementsBase.test_scruffy_end_4()
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116 @unittest.expectedFailure
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117 def test_scruffy_generation_1(self):
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118 TestStatementsBase.test_scruffy_generation_1()
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119 @unittest.expectedFailure
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120 def test_scruffy_generation_2(self):
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121 TestStatementsBase.test_scruffy_generation_2()
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122 @unittest.expectedFailure
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123 def test_scruffy_invalidation_1(self):
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124 TestStatementsBase.test_scruffy_invalidation_1()
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125 @unittest.expectedFailure
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126 def test_scruffy_invalidation_2(self):
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127 TestStatementsBase.test_scruffy_invalidation_2()
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128 @unittest.expectedFailure
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129 def test_scruffy_start_1(self):
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130 TestStatementsBase.test_scruffy_start_1()
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131 @unittest.expectedFailure
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132 def test_scruffy_start_2(self):
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133 TestStatementsBase.test_scruffy_start_2()
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134 @unittest.expectedFailure
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135 def test_scruffy_start_3(self):
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136 TestStatementsBase.test_scruffy_start_3()
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137 @unittest.expectedFailure
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138 def test_scruffy_start_4(self):
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139 TestStatementsBase.test_scruffy_start_4()
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140 @unittest.expectedFailure
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141 def test_scruffy_usage_1(self):
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142 TestStatementsBase.test_scruffy_usage_1()
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143 @unittest.expectedFailure
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144 def test_scruffy_usage_2(self):
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145 TestStatementsBase.test_scruffy_usage_2()
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146
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147
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148 class TestAttributesBase2(TestAttributesBase):
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149 @unittest.expectedFailure
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150 def test_entity_with_multiple_attribute(self):
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151 TestAttributesBase.test_entity_with_multiple_attribute()
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152 @unittest.expectedFailure
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153 def test_entity_with_multiple_value_attribute(self):
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154 TestAttributesBase.test_entity_with_multiple_value_attribute()
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155 @unittest.expectedFailure
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156 def test_entity_with_one_type_attribute_8(self):
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157 TestAttributesBase.test_entity_with_one_type_attribute_8()
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158
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159
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160 class AllTestsBase(TestExamplesBase,
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161 TestStatementsBase2,
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162 TestQualifiedNamesBase,
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163 TestAttributesBase2
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164 ):
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165 """This is a test to include all available tests.
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166 """
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167 pass
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168
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169
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170 class TestRDFSerializer(unittest.TestCase):
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171 def test_decoding_unicode_value(self):
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172 unicode_char = u'\u2019'
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173 rdf_content = u'''
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174 @prefix ex: <http://www.example.org/> .
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175 @prefix prov: <http://www.w3.org/ns/prov#> .
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176 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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177 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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178 @prefix xml: <http://www.w3.org/XML/1998/namespace> .
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179 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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180
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181 ex:unicode_char a prov:Entity ;
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182 rdfs:label "%s"^^xsd:string .
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183 ''' % unicode_char
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184 prov_doc = ProvDocument.deserialize(content=rdf_content,
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185 format='rdf', rdf_format='turtle')
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186 e1 = prov_doc.get_record('ex:unicode_char')[0]
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187 self.assertIn(unicode_char, e1.get_attribute('prov:label'))
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188
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189 def test_json_to_ttl_match(self):
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190 json_files = sorted(
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191 glob(os.path.join(os.path.dirname(__file__), 'json', '*.json')))
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192
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193 # invalid round trip files
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194 skip = list(range(352, 380))
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195
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196 # invalid literal set representation e.g., set((1, True))
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197 skip_match = [5, 6, 7, 8, 15, 27, 28, 29, 75, 76, 77, 78, 79, 80, 260,
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198 261, 262, 263, 264,
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199 306, 313, 315, 317, 322, 323, 324, 325, 330, 332, 344,
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200 346, 382, 389, 395, 397,
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201 ]
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202 errors = []
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203 for idx, fname in enumerate(json_files):
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204 _, ttl_file = os.path.split(fname)
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205 ttl_file = os.path.join(os.path.dirname(__file__), 'rdf',
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206 ttl_file.replace('json', 'ttl'))
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207 try:
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208 g = pm.ProvDocument.deserialize(fname)
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209 if len(g.bundles) == 0:
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210 format = 'turtle'
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211 else:
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212 format = 'trig'
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213 if format == 'trig':
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214 ttl_file = ttl_file.replace('ttl', 'trig')
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215
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216 with open(ttl_file, 'rb') as fp:
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217 g_rdf = rl.ConjunctiveGraph().parse(fp, format=format)
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218 g0_rdf = rl.ConjunctiveGraph().parse(
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219 StringIO(g.serialize(format='rdf', rdf_format=format)),
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220 format=format)
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221 if idx not in skip_match:
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222 match, _, in_first, in_second = find_diff(g_rdf, g0_rdf)
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223 self.assertTrue(match)
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224 else:
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225 logger.info('Skipping match: %s' % fname)
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226 if idx in skip:
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227 logger.info('Skipping deserialization: %s' % fname)
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228 continue
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229 g1 = pm.ProvDocument.deserialize(
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230 content=g.serialize(format='rdf', rdf_format=format),
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231 format='rdf', rdf_format=format)
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232 except Exception as e:
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233 #logger.info(e)
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234 errors.append((e, idx, fname, in_first, in_second))
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235 self.assertFalse(errors)
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236
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237
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238 class RoundTripRDFTests(RoundTripTestCase, AllTestsBase):
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239 FORMAT = 'rdf'
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240
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241 if __name__ == "__main__":
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242 suite = unittest.TestSuite()
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243 for method in dir(TestRDFSerializer):
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244 if method.startswith("test"):
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245 suite.addTest(TestRDFSerializer(method))
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246 unittest.TextTestRunner().run(suite)