def test_annotation_annotation(self):
self.assertEqual(
a1,
Annotation(RDFS.comment, "Outer", [
Annotation(RDFS.comment, "Middle 1"),
Annotation(RDFS.label, "Middle 2",
[Annotation(RDFS.comment, "Inner")])
]).to_functional(self.w).getvalue())
def test_ontology_document(self):
doc = OntologyDocument()
self.assertEqual(expected([]), str(doc.to_functional().getvalue()))
doc.ontology.iri = "http://snomed.info/sct/"
self.assertEqual(expected(['<http://snomed.info/sct/>']), str(doc.to_functional().getvalue()))
doc.ontology.version = "http://snomed.info/sct/version/201802017"
self.assertEqual(expected(['<http://snomed.info/sct/> <http://snomed.info/sct/version/201802017>']),
doc.to_functional().getvalue())
doc.prefixes(RDFS, owl=OWL, rdf=RDF)
self.assertEqual('''Prefix( xml: = <http://www.w3.org/XML/1998/namespace> )
Prefix( rdf: = <http://www.w3.org/1999/02/22-rdf-syntax-ns#> )
Prefix( rdfs: = <http://www.w3.org/2000/01/rdf-schema#> )
Prefix( xsd: = <http://www.w3.org/2001/XMLSchema#> )
Prefix( owl: = <http://www.w3.org/2002/07/owl#> )
Prefix( : = <http://www.w3.org/2000/01/rdf-schema#> )
Ontology( <http://snomed.info/sct/> <http://snomed.info/sct/version/201802017> )''', str(doc.to_functional()))
doc.ontology.imports(SKOS)
doc.ontology.imports("http://example.org/dep")
doc.ontology.annotations.append(Annotation(RDFS.label, "foo"))
self.assertEqual('''Prefix( xml: = <http://www.w3.org/XML/1998/namespace> )
Prefix( rdf: = <http://www.w3.org/1999/02/22-rdf-syntax-ns#> )
Prefix( rdfs: = <http://www.w3.org/2000/01/rdf-schema#> )
Prefix( xsd: = <http://www.w3.org/2001/XMLSchema#> )
Prefix( owl: = <http://www.w3.org/2002/07/owl#> )
Prefix( : = <http://www.w3.org/2000/01/rdf-schema#> )
Ontology( <http://snomed.info/sct/> <http://snomed.info/sct/version/201802017>
Import( <http://www.w3.org/2004/02/skos/core#> )
Import( <http://example.org/dep> )
Annotation( :label "foo" )
)''', str(doc.to_functional()))
def test_annotatable_constructor(self):
""" A single annotation should get transformed into a list by the annotation constructor """
@dataclass
class Foo(Annotatable):
annotations: List[Annotation] = empty_list()
a = Annotation(RDFS.comment, "Not a list")
x = Foo(a)
self.assertEqual(x.annotations, [a])
def test_classassertion(self):
self.assertEqual('ClassAssertion( a:GriffinFamilyMember a:Peter_Griffin )',
ClassAssertion(A.GriffinFamilyMember, A.Peter_Griffin).to_functional(self.wa).getvalue())
self.wa.reset()
self.assertEqual("""ClassAssertion(
Annotation( rdfs:comment "It runs in..." )
a:GriffinFamilyMember a:Peter_Griffin
)""", ClassAssertion(A.GriffinFamilyMember, A.Peter_Griffin,
Annotation(RDFS.comment, "It runs in...")).to_functional(self.wa).getvalue())
def test_annotatable(self):
@dataclass
class Foo(Annotatable):
props: List[IRI] = empty_list()
annotations: List[Annotation] = empty_list()
def to_functional(self, w: FunctionalWriter) -> FunctionalWriter:
return self.annots(w, lambda: w.iter(self.props, indent=False))
self.assertEqual("Foo( )", Foo().to_functional(self.w).getvalue())
f = Foo(annotations=[Annotation(RDFS.comment, "t1")])
self.w.reset()
self.assertEqual("""Foo(
Annotation( rdfs:comment "t1" )
)""",
f.to_functional(self.w).getvalue())
self.w.reset()
f.props += [RDF.type, RDFS.label]
f.props.append(OWL.Ontology)
self.assertEqual(
"""Foo(
Annotation( rdfs:comment "t1" )
rdf:type
rdfs:label
owl:Ontology
)""",
f.to_functional(self.w).getvalue())
self.w.reset()
f.annotations[0].annotations.append(
Annotation(RDFS.comment, "This is great"))
self.assertEqual(
"""Foo(
Annotation(
Annotation( rdfs:comment "This is great" )
rdfs:comment "t1"
)
rdf:type
rdfs:label
owl:Ontology
)""",
f.to_functional(self.w).getvalue())
def test_annotation_domain_range(self):
self.assertEqual(
a2d,
AnnotationPropertyDomain(
RDFS.comment, RDFS.Resource).to_functional(self.w).getvalue())
self.w.reset()
self.assertEqual(
a2r,
AnnotationPropertyRange(RDFS.comment, XSD.string,
[Annotation(RDFS.comment, "test")
]).to_functional(self.w).getvalue())
def test_differentindividuals(self):
self.assertEqual('DifferentIndividuals( a:Peter a:Peter_Griffin )',
DifferentIndividuals(A.Peter, A.Peter_Griffin).to_functional(self.wa).getvalue())
with self.assertRaises(ValueError):
# Only one individual
DifferentIndividuals(A.Peter).to_functional(self.wa)
self.wa.reset()
self.assertEqual("""DifferentIndividuals(
Annotation( rdfs:comment "We know better" )
a:Alex a:Bob a:Charlie
)""", DifferentIndividuals(A.Alex, A.Bob, A.Charlie,
annotations=Annotation(RDFS.comment, "We know better")).to_functional(self.wa).getvalue())
def test_sameindividual(self):
self.assertEqual('SameIndividual( a:Peter a:Peter_Griffin )',
SameIndividual(A.Peter, A.Peter_Griffin).to_functional(self.wa).getvalue())
with self.assertRaises(ValueError):
# Only one individual
SameIndividual(A.Peter).to_functional(self.wa)
self.wa.reset()
self.assertEqual("""SameIndividual(
Annotation( rdfs:comment "Many aliases" )
a:Alex a:Bob a:Charlie
)""", SameIndividual(A.Alex, A.Bob, A.Charlie,
annotations=Annotation(RDFS.comment, "Many aliases")).to_functional(self.wa).getvalue())
def test_differentindividuals_rdf(self):
g = Graph()
g.bind('owl', str(OWL))
DifferentIndividuals(A.Alex, A.Bob).to_rdf(g)
self.assertEqual("""@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<http://example.org/a#Alex> a owl:NamedIndividual ;
owl:differentFrom <http://example.org/a#Bob> .
<http://example.org/a#Bob> a owl:NamedIndividual .""", g.serialize(format="turtle").decode().strip())
g = Graph(namespace_manager=g.namespace_manager)
DifferentIndividuals(A.Alex, A.Bob, A.Fred, A.Joe).to_rdf(g)
print(g.serialize(format="turtle").decode())
g = Graph(namespace_manager=g.namespace_manager)
DifferentIndividuals(A.Alex, A.Bob, annotations=[Annotation(RDFS.label, "Test")]).to_rdf(g)
print(g.serialize(format="turtle").decode())
def annotation(
self, prop: AnnotationProperty.types(), value: AnnotationValue.types()
) -> "Ontology":
self.annotations.append(Annotation(prop, value))
return self
def test_annotation_anon(self):
self.assertEqual(
"Annotation( rdfs:label _:12345 )",
Annotation(RDFS.label, '_:12345').to_functional(self.w).getvalue())
def test_annotation_IRI(self):
self.assertEqual(
"Annotation( rdfs:label rdfs:Resource )",
Annotation(RDFS.label,
RDFS.Resource).to_functional(self.w).getvalue())
def test_basic_annotation(self):
self.assertEqual(
'Annotation( rdfs:label "This is a test" )',
Annotation(RDFS.label,
"This is a test").to_functional(self.w).getvalue())