def test_uri_and_curie(self):
""" Compile a model of URI's and Curies and then test the various types """
self.single_file_generator('py',
PythonGenerator,
filtr=metadata_filter,
comparator=compare_python)
# Check that the interpretations are correct
self.single_file_generator(
'jsonld',
ContextGenerator,
filtr=ldcontext_metadata_filter,
comparator=lambda expected, actual: compare_rdf(
expected, actual, fmt="json-ld"))
self.single_file_generator('json',
JSONLDGenerator,
filtr=json_metadata_filter)
module = compile_python(env.expected_path(self.model_name + '.py'))
curie_obj = module.C1("ex:obj1",
hasCurie="ex:curie",
hasURI="http://example.org/test/uri",
hasNcName="A123",
id2="ex:id2")
instance_jsonld = loads('{ "ex": "http://example.org/test/inst#" }')
g = as_rdf(
curie_obj,
[env.input_path(self.model_name + '.jsonld'), instance_jsonld])
env.eval_single_file(env.expected_path('uriandcurie.ttl'),
g.serialize(format='ttl').decode(), lambda s: s,
compare_rdf)
def output_generator(dirname) -> None:
with open(os.path.join(dirname, 'issue_80.json'), 'w') as f:
f.write(as_json(example))
context = os.path.join(dirname, 'issue_80.context.jsonld')
with open(context, 'w') as f:
f.write(
ContextGenerator(
env.input_path('issue_80.yaml')).serialize())
with open(os.path.join(dirname, 'issue_80.ttl'), 'w') as f:
f.write(
as_rdf(
example,
contexts=context).serialize(format="turtle").decode())
def test_uriÎ_and_curie(self):
""" Compile a model of URI's and Curies and then test the various types """
self.single_file_generator('py',
PythonGenerator,
filtr=metadata_filter)
# Make sure the python is valid
with open(os.path.join(self.source_path,
self.model_name + '.py')) as f:
model = f.read()
spec = compile(model, 'test', 'exec')
module = ModuleType('test')
exec(spec, module.__dict__)
# Check that the interpretations are correct
msg = self.single_file_generator('jsonld',
ContextGenerator,
filtr=ldcontext_metadata_filter,
fail_if_expected_missing=False)
msg = self.single_file_generator('json',
JSONLDGenerator,
filtr=json_metadata_filter,
fail_if_expected_missing=False)
if msg:
self.fail(msg)
curie_obj = module.C1("ex:obj1",
hasCurie="ex:curie",
hasURI="http://example.org/test/uri",
hasNcName="A123",
id2="ex:id2")
instance_jsonld = loads('{ "ex": "http://example.org/test/inst#" }')
g = as_rdf(curie_obj, [
os.path.join(self.source_path, self.model_name + '.jsonld'),
instance_jsonld
])
self.rdf_comparator(
expected_rdf, g,
os.path.join(self.target_path, self.model_name + '.jsonld'))
def test_issue_80(self):
""" Make sure that types are generated as part of the output """
yaml_fname = os.path.join(sourcedir, 'issue_80.yaml')
python = PythonGenerator(yaml_fname).serialize()
print(self.header("Python"))
print(python)
spec = compile(python, 'test', 'exec')
module = ModuleType('test')
exec(spec, module.__dict__)
example = module.Person("http://example.org/person/17", "Fred Jones", 43)
# JSON Representation
print(self.header("JSON"))
print(as_json(example))
# Generate a context for this particular model
print(self.header("Context"))
context = ContextGenerator(yaml_fname).serialize()
print(context)
# RDF Representation
print(self.header("RDF"))
print(as_rdf(example, contexts=context).serialize(format="turtle").decode())
def test_nodeidentifier(self):
context = """{
"@context": {
"type": "@type",
"OIO": "http://www.geneontology.org/formats/oboInOwl#",
"dcterms": "http://purl.org/dc/terms/",
"metatype": "https://w3id.org/biolink/biolinkml/type/",
"owl": "http://www.w3.org/2002/07/owl#",
"pav": "http://purl.org/pav/",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"skos": "http://www.w3.org/2004/02/skos/core#",
"xsd": "http://www.w3.org/2001/XMLSchema#",
"s": {
"@id": "rdfs:subject"
},
"t": {
"@id": "rdfs:object"
}
}
}"""
EX = Namespace("http://example.org/tests/")
class Root(NodeIdentifier):
pass
class Child1(Root):
pass
class Child2(Root):
pass
class Desc1(Child1):
pass
class Unassoc(NodeIdentifier):
pass
@dataclass
class Pair(YAMLRoot):
s: Child1 = None
t: Child2 = None
def __post_init__(self):
if not isinstance(self.s, Child1):
self.s = Child1(self.s)
if not isinstance(self.t, Child2):
self.t = Child2(self.t)
super().__post_init__()
s = Desc1(EX.descendant1)
t = Child2(EX.child2)
y = Pair(s, t)
self.assertEqual(
"""{
"s": "http://example.org/tests/descendant1",
"t": "http://example.org/tests/child2"
}""", as_json(y))
self.assertEqual(
"""@prefix OIO: <http://www.geneontology.org/formats/oboInOwl#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix metatype: <https://w3id.org/biolink/biolinkml/type/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
[] a <biolink/biolinkml/tests/Pair> ;
rdfs:object "http://example.org/tests/child2" ;
rdfs:subject "http://example.org/tests/descendant1" .
""",
as_rdf(y, context).serialize(format="turtle").decode())
with self.assertRaises(ValueError):
y = Pair(s, s)
def add_to_graph(e: YAMLRoot, g: Optional[Graph] = None) -> Graph:
return as_rdf(e, context_jsonld, g)