def test_meta_output(self):
""" Generate a context AND a jsonld for the metamodel and make sure it parses as RDF """
jsonld_path = os.path.join(testscriptstempdir, 'metajson.jsonld')
rdf_path = os.path.join(testscriptstempdir, 'metardf.ttl')
meta_context_path = os.path.join(testscriptstempdir,
'metacontext.jsonld')
# Generate an image of the metamodel
gen = ContextGenerator(source_yaml_path)
base = gen.schema.id
if base[-1] not in '/#':
base += '/'
base += gen.schema.name
with open(meta_context_path, 'w') as tfile:
tfile.write(gen.serialize())
with open(jsonld_path, 'w') as tfile:
tfile.write(JSONLDGenerator(source_yaml_path, fmt=JSONLDGenerator.valid_formats[0])\
.serialize(context=meta_context_path))
g = Graph()
g.load(jsonld_path, format="json-ld")
g.serialize(rdf_path, format="ttl")
g.bind('meta', METAMODEL_NAMESPACE)
new_ttl = g.serialize(format="turtle").decode()
new_g = Graph()
new_g.parse(data=new_ttl, format="turtle")
self.check_size(g, new_g, URIRef(base), 11, 79, 11, "meta")
def end_schema(self, output: Optional[str] = None, context: str = METAMODEL_CONTEXT_URI, **_) -> None:
gen = JSONLDGenerator(self, fmt=JSONLDGenerator.valid_formats[0], emit_metadata=self.emit_metadata,
importmap=self.importmap)
# Iterate over permissible text strings making them URI compatible
for e in gen.schema.enums.values():
for pv in e.permissible_values.values():
pv.text = urlparse.quote(pv.text)
jsonld_str = gen.serialize(context=context)
graph = Graph()
graph.parse(data=jsonld_str, format="json-ld", base=self.namespaces._base, prefix=True)
if output:
with open(output, 'w') as outf:
outf.write(self._data(graph))
else:
print(self._data(graph))
def test_mappings_rdf(self):
""" Test the imported mappings in the biolink metamodel """
test_dir = self.env.temp_file_path('mappings_rdf_test', is_dir=True)
# Create the mappings json file
json_file = os.path.join(test_dir, 'mappings.jsonld')
json_str = JSONLDGenerator(env.meta_yaml, importmap=env.import_map).serialize()
with open(json_file, 'w') as f:
f.write(json_str)
# Create the mappings context file
context_file = os.path.join(test_dir, 'mappings.context.jsonld')
ContextGenerator(env.meta_yaml, importmap=env.import_map).serialize(output=context_file)
self.assertTrue(os.path.exists(context_file))
# Generate context and use it to create the RDF
self.single_file_generator('context.jsonld', ContextGenerator, filtr=ldcontext_metadata_filter, subdir='includes')
# Generate a copy of the JSON representation of the model
context_loc = json_file
context_args = {"context": ['file://' + LOCAL_METAMODEL_LDCONTEXT_FILE, 'file://' + context_loc]}
msg += self.single_file_generator('json', JSONLDGenerator, serialize_args=context_args,
filtr=json_metadata_context_filter, fail_if_expected_missing=False)
# Make a fresh copy of the RDF and validate it as well
msg += self.single_file_generator('ttl', RDFGenerator, serialize_args=context_args,
comparator=GeneratorTestCase.rdf_comparator, fail_if_expected_missing=False)
if msg:
self.fail(msg)
g = Graph()
rdf_file = os.path.join(sourcedir, 'meta_mappings.ttl')
g.load(rdf_file, format='turtle')
ns = PrefixLibrary()
ns.add_rdf(g)
ns['FULL'] = "http://example.org/fulluri/"
ns['EX'] = "http://example.org/mappings/"
ns['META'] = "https://w3id.org/biolink/biolinkml/meta/"
# Make sure that the expected triples got added
self.assertEqual({ns.EX.slot1_close, ns.FULL.slot1_close}, set(g.objects(ns.EX.s1, ns.SKOS.closeMatch)))
self.assertEqual({ns.EX.slot1, ns.FULL.slot1}, set(g.objects(ns.EX.s1, ns.SKOS.exactMatch)))
self.assertEqual(ns.EX.s3, g.value(ns.EX.s1, ns.META.deprecated_element_has_exact_replacement, any=False))
self.assertEqual(ns.EX.s4, g.value(ns.EX.s1, ns.META.deprecated_element_has_possible_replacement, any=False))
self.assertEqual({ns.EX.class1_close, ns.FULL.class1_close}, set(g.objects(ns.EX.C1, ns.SKOS.closeMatch)))
self.assertEqual({ns.EX.class1, ns.FULL.class1}, set(g.objects(ns.EX.C1, ns.SKOS.exactMatch)))
self.assertEqual(ns.EX.c2, g.value(ns.EX.C1, ns.META.deprecated_element_has_exact_replacement, any=False))
self.assertEqual(ns.EX.c3, g.value(ns.EX.C1, ns.META.deprecated_element_has_possible_replacement, any=False))
if DO_SHEX_VALIDATION:
EX = Namespace("http://example.org/mappings/")
focus = EX.testMetamodelMappings
start = METAMODEL_NAMESPACE.SchemaDefinition
results = ShExEvaluator(g, LOCAL_SHEXJ_FILE_NAME, focus, start).evaluate(debug=False)
self.assertTrue(self._evaluate_shex_results(results))
else:
print("*** RDF Model validation step was skipped. Set: tests.__init__.DO_SHEX_VALIDATION to run it")
