def test_biolink_rdf(self):
""" Test the rdf generator for the biolink model """
self.single_file_generator('ttl', RDFGenerator, serialize_args=dict(
context=["https://w3id.org/linkml/meta.context.jsonld"]), comparator=compare_rdf)
# Validate the RDF against the Biolink ShEx
if SKIP_SHEX_VALIDATION:
print(f'* test_biolink_rdf: {SKIP_SHEX_VALIDATION_REASON}')
else:
g = Graph()
g.load(env.expected_path('biolink_model.ttl'), format='ttl')
focus = BIOLINK_NS.biolink_model
start = METAMODEL_NAMESPACE.SchemaDefinition
results = ShExEvaluator(g, env.expected_path('biolink_model.shexj'), focus, start).evaluate(debug=False)
self.assertTrue(self._evaluate_shex_results(results))
def test_biolink_correct_rdf(self):
""" Test some conforming RDF """
self.single_file_generator('shexj', ShExGenerator, format='json') # Make sure ShEx is current
shex_file = env.expected_path('biolink-model.shexj')
focus = "http://identifiers.org/drugbank:DB00005"
start = BIOLINK_NS.Drug
evaluator = ShExEvaluator(None, shex_file, focus, start)
rdf_file = env.input_path('probe.ttl')
results = evaluator.evaluate(rdf_file, debug=False)
self.assertTrue(self._evaluate_shex_results(results))
def test_biolink_shex_incorrect_rdf(self):
""" Test some non-conforming RDF """
self.single_file_generator('shexj', ShExGenerator, format='json')
shex_file = env.expected_path('biolink-model.shexj')
focus = "http://identifiers.org/drugbank:DB00005"
start = BIOLINK_NS.Drug
evaluator = ShExEvaluator(None, shex_file, focus, start)
# incorrect.ttl has 16 error lines (more or less).
rdf_file = env.temp_file_path('incorrect.ttl')
errs_file = env.temp_file_path('incorrect.errs')
results = evaluator.evaluate(rdf_file)
self.assertFalse(self._evaluate_shex_results(results, printit=False))
self.assertEqual(1, len(results))
self.assertTrue('Unmatched triples in CLOSED shape' in results[0].reason)
ntabs = results[0].reason.count('\n\t')
self.assertEqual(13, ntabs)
if not os.path.exists(errs_file):
with open(errs_file, 'w') as f:
f.write(shex_results_as_string(results[0]))