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comparison 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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0:d30785e31577 1:56ad4e20f292
1 from __future__ import (absolute_import, division, print_function,
2 unicode_literals)
3
4 import unittest
5 from prov.model import ProvDocument
6 from prov.tests.utility import RoundTripTestCase
7 from prov.tests.test_model import (TestStatementsBase,
8 TestAttributesBase, TestQualifiedNamesBase)
9 import os
10 from glob import glob
11 import logging
12 logger = logging.getLogger(__name__)
13
14 from prov.tests import examples
15 import prov.model as pm
16
17 import rdflib as rl
18 from rdflib.compare import graph_diff
19 from io import BytesIO, StringIO
20
21
22 def find_diff(g_rdf, g0_rdf):
23 graphs_equal = True
24 in_both, in_first, in_second = graph_diff(g_rdf, g0_rdf)
25 g1 = sorted(in_first.serialize(format='nt').splitlines())[1:]
26 g2 = sorted(in_second.serialize(format='nt').splitlines())[1:]
27 # Compare literals
28 if len(g1) != len(g2):
29 graphs_equal = False
30 matching_indices = [[], []]
31 for idx in range(len(g1)):
32 g1_stmt = list(rl.ConjunctiveGraph().parse(BytesIO(g1[idx]),
33 format='nt'))[0]
34 match_found = False
35 for idx2 in range(len(g2)):
36 if idx2 in matching_indices[1]:
37 continue
38 g2_stmt = list(rl.ConjunctiveGraph().parse(BytesIO(g2[idx2]),
39 format='nt'))[0]
40 try:
41 all_match = all([g1_stmt[i].eq(g2_stmt[i]) for i in range(3)])
42 except TypeError as e:
43 #logger.info(e, g1_stmt, g2_stmt)
44 all_match = False
45 if all_match:
46 matching_indices[0].append(idx)
47 matching_indices[1].append(idx2)
48 match_found = True
49 break
50 if not match_found:
51 graphs_equal = False
52 in_first2 = rl.ConjunctiveGraph()
53 for idx in range(len(g1)):
54 if idx in matching_indices[0]:
55 in_both.parse(BytesIO(g1[idx]), format='nt')
56 else:
57 in_first2.parse(BytesIO(g1[idx]), format='nt')
58 in_second2 = rl.ConjunctiveGraph()
59 for idx in range(len(g2)):
60 if not idx in matching_indices[1]:
61 in_second2.parse(BytesIO(g2[idx]), format='nt')
62 #logger.info(in_first2)
63 #logger.info(in_second2)
64 return graphs_equal, in_both, in_first2, in_second2
65
66
67 class TestExamplesBase(object):
68 """This is the base class for testing support for all the examples provided
69 in prov.tests.examples.
70 It is not runnable and needs to be included in a subclass of
71 RoundTripTestCase.
72 """
73 def test_all_examples(self):
74 counter = 0
75 for name, graph in examples.tests:
76 if name in ['datatypes']:
77 logger.info('%d. Skipping the %s example', counter, name)
78 continue
79 counter += 1
80 logger.info('%d. Testing the %s example', counter, name)
81 g = graph()
82 self.do_tests(g)
83
84
85 class TestJSONExamplesBase(object):
86 """This is the base class for testing support for all the examples provided
87 in prov.tests.examples.
88 It is not runnable and needs to be included in a subclass of
89 RoundTripTestCase.
90 """
91 def test_all_examples(self):
92 counter = 0
93 for name, graph in examples.tests:
94 if name in ['datatypes']:
95 logger.info('%d. Skipping the %s example', counter, name)
96 continue
97 counter += 1
98 logger.info('%d. Testing the %s example', counter, name)
99 g = graph()
100 self.do_tests(g)
101
102
103 class TestStatementsBase2(TestStatementsBase):
104 @unittest.expectedFailure
105 def test_scruffy_end_1(self):
106 TestStatementsBase.test_scruffy_end_1()
107 @unittest.expectedFailure
108 def test_scruffy_end_2(self):
109 TestStatementsBase.test_scruffy_end_2()
110 @unittest.expectedFailure
111 def test_scruffy_end_3(self):
112 TestStatementsBase.test_scruffy_end_3()
113 @unittest.expectedFailure
114 def test_scruffy_end_4(self):
115 TestStatementsBase.test_scruffy_end_4()
116 @unittest.expectedFailure
117 def test_scruffy_generation_1(self):
118 TestStatementsBase.test_scruffy_generation_1()
119 @unittest.expectedFailure
120 def test_scruffy_generation_2(self):
121 TestStatementsBase.test_scruffy_generation_2()
122 @unittest.expectedFailure
123 def test_scruffy_invalidation_1(self):
124 TestStatementsBase.test_scruffy_invalidation_1()
125 @unittest.expectedFailure
126 def test_scruffy_invalidation_2(self):
127 TestStatementsBase.test_scruffy_invalidation_2()
128 @unittest.expectedFailure
129 def test_scruffy_start_1(self):
130 TestStatementsBase.test_scruffy_start_1()
131 @unittest.expectedFailure
132 def test_scruffy_start_2(self):
133 TestStatementsBase.test_scruffy_start_2()
134 @unittest.expectedFailure
135 def test_scruffy_start_3(self):
136 TestStatementsBase.test_scruffy_start_3()
137 @unittest.expectedFailure
138 def test_scruffy_start_4(self):
139 TestStatementsBase.test_scruffy_start_4()
140 @unittest.expectedFailure
141 def test_scruffy_usage_1(self):
142 TestStatementsBase.test_scruffy_usage_1()
143 @unittest.expectedFailure
144 def test_scruffy_usage_2(self):
145 TestStatementsBase.test_scruffy_usage_2()
146
147
148 class TestAttributesBase2(TestAttributesBase):
149 @unittest.expectedFailure
150 def test_entity_with_multiple_attribute(self):
151 TestAttributesBase.test_entity_with_multiple_attribute()
152 @unittest.expectedFailure
153 def test_entity_with_multiple_value_attribute(self):
154 TestAttributesBase.test_entity_with_multiple_value_attribute()
155 @unittest.expectedFailure
156 def test_entity_with_one_type_attribute_8(self):
157 TestAttributesBase.test_entity_with_one_type_attribute_8()
158
159
160 class AllTestsBase(TestExamplesBase,
161 TestStatementsBase2,
162 TestQualifiedNamesBase,
163 TestAttributesBase2
164 ):
165 """This is a test to include all available tests.
166 """
167 pass
168
169
170 class TestRDFSerializer(unittest.TestCase):
171 def test_decoding_unicode_value(self):
172 unicode_char = u'\u2019'
173 rdf_content = u'''
174 @prefix ex: <http://www.example.org/> .
175 @prefix prov: <http://www.w3.org/ns/prov#> .
176 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
177 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
178 @prefix xml: <http://www.w3.org/XML/1998/namespace> .
179 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
180
181 ex:unicode_char a prov:Entity ;
182 rdfs:label "%s"^^xsd:string .
183 ''' % unicode_char
184 prov_doc = ProvDocument.deserialize(content=rdf_content,
185 format='rdf', rdf_format='turtle')
186 e1 = prov_doc.get_record('ex:unicode_char')[0]
187 self.assertIn(unicode_char, e1.get_attribute('prov:label'))
188
189 def test_json_to_ttl_match(self):
190 json_files = sorted(
191 glob(os.path.join(os.path.dirname(__file__), 'json', '*.json')))
192
193 # invalid round trip files
194 skip = list(range(352, 380))
195
196 # invalid literal set representation e.g., set((1, True))
197 skip_match = [5, 6, 7, 8, 15, 27, 28, 29, 75, 76, 77, 78, 79, 80, 260,
198 261, 262, 263, 264,
199 306, 313, 315, 317, 322, 323, 324, 325, 330, 332, 344,
200 346, 382, 389, 395, 397,
201 ]
202 errors = []
203 for idx, fname in enumerate(json_files):
204 _, ttl_file = os.path.split(fname)
205 ttl_file = os.path.join(os.path.dirname(__file__), 'rdf',
206 ttl_file.replace('json', 'ttl'))
207 try:
208 g = pm.ProvDocument.deserialize(fname)
209 if len(g.bundles) == 0:
210 format = 'turtle'
211 else:
212 format = 'trig'
213 if format == 'trig':
214 ttl_file = ttl_file.replace('ttl', 'trig')
215
216 with open(ttl_file, 'rb') as fp:
217 g_rdf = rl.ConjunctiveGraph().parse(fp, format=format)
218 g0_rdf = rl.ConjunctiveGraph().parse(
219 StringIO(g.serialize(format='rdf', rdf_format=format)),
220 format=format)
221 if idx not in skip_match:
222 match, _, in_first, in_second = find_diff(g_rdf, g0_rdf)
223 self.assertTrue(match)
224 else:
225 logger.info('Skipping match: %s' % fname)
226 if idx in skip:
227 logger.info('Skipping deserialization: %s' % fname)
228 continue
229 g1 = pm.ProvDocument.deserialize(
230 content=g.serialize(format='rdf', rdf_format=format),
231 format='rdf', rdf_format=format)
232 except Exception as e:
233 #logger.info(e)
234 errors.append((e, idx, fname, in_first, in_second))
235 self.assertFalse(errors)
236
237
238 class RoundTripRDFTests(RoundTripTestCase, AllTestsBase):
239 FORMAT = 'rdf'
240
241 if __name__ == "__main__":
242 suite = unittest.TestSuite()
243 for method in dir(TestRDFSerializer):
244 if method.startswith("test"):
245 suite.addTest(TestRDFSerializer(method))
246 unittest.TextTestRunner().run(suite)