def validate_owl2(fileloc: str) -> bool:
print(f"Validating {os.path.basename(fileloc)}")
# 1) convert the functional syntax to nn Ontology:
# Ontology = f(functional_repr)
with open(fileloc) as f:
func_repr = f.read()
logging.info('\n===== Original Input =====\n' + func_repr)
ontology_doc = to_python(func_repr)
if not ontology_doc:
return False
logging.info('\n===== Pass 1 Output =====\n' +
str(ontology_doc.to_functional()))
# 2) determine whether the RDF representation of the Ontology is what is expected
# g(f(functional_repr) == RDF
if do_rdf:
expected_rdf = Graph()
expected_rdf.load(fileloc.replace('.func', '.ttl'), format="turtle")
actual_rdf_graph = Graph()
actual_rdf_graph.add = lambda t: add(actual_rdf_graph, t)
ontology_doc.to_rdf(actual_rdf_graph)
rslts = compare_rdf(expected_rdf, actual_rdf_graph)
if rslts:
logging.info('\n========== pass 1 rdf output =================\n' +
actual_rdf_graph.serialize(format="turtle").decode())
logging.info('\n---------- expected rdf ------------\n' +
expected_rdf.serialize(format="turtle").decode())
print(rslts)
return False
# 3) convert the ontology back into functional syntax
# functional_repr_prime = f**-1(f(functional_repr))
ontology_2 = to_python(ontology_doc.to_functional().getvalue())
if not ontology_2:
logging.error(f"Failed to parse emitted functional syntax")
return False
logging.info('\n===== Pass 2 Output =====\n' +
str(ontology_2.to_functional()))
# 4) Convert the functional syntax back into an Ontology
# Ontology_prime = f(f**-1(f(functional_repr)))
if do_rdf:
roundtrip_rdf = Graph()
ontology_2.to_rdf(roundtrip_rdf)
logging.info('\n========== Round Trip RDF =================\n' +
roundtrip_rdf.serialize(format="turtle").decode())
# 5) Make sure that the RDF representation stll matches
# g(f(functional_repr)) == g(f(f**-1(f(functional_repr))
rslts = compare_rdf(expected_rdf, roundtrip_rdf)
if rslts:
print(rslts)
return False
return True
def verify(self, loc: Any) -> None:
self.maxDiff = None
doc = to_python(loc)
if os.path.exists(pizza_fun):
with open(pizza_fun) as f:
expected = f.read()
self.assertEqual(expected, str(doc.to_functional()))
else:
with open(pizza_fun, 'w') as f:
f.write(str(doc.to_functional()))
self.fail(f"{pizza_fun} written to disc - run test again")
def test_owlf_sample(self):
import os
from funowl.converters.functional_converter import to_python
from rdflib import Graph, SKOS, DCTERMS
clue = to_python(owlf)
g = Graph()
clue.to_rdf(g)
g.bind('skos', SKOS)
g.bind('dct', DCTERMS)
owlrdf = g.serialize(format='turtle').decode().strip()
# print(owlrdf)
self.assertEqual(expected.strip(), owlrdf)
def test_declaration(self):
parsed = to_python(text)
actual = str(parsed.to_functional())
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( pizza: = <http://www.co-ode.org/ontologies/pizza/pizza.owl#> )
Ontology( <http://www.co-ode.org/ontologies/pizza> <http://www.co-ode.org/ontologies/pizza/2.0.0>
Declaration( Class( pizza:American ) )
)""", actual)
def test_snomed(self):
doc = to_python('/Users/solbrig/data/terminology/snomedct/'
'SnomedCT_InternationalRF2_PRODUCTION_20190731T120000Z/Snapshot/Terminology/snomed.owl')
self.assertTrue(False, "Implement Me")
Prefix(document_ontology:=<https://loinc.org/document_ontology/#>)
Prefix(untitled-ontology-17:=<https://loinc.org/dmbaorto/ontologies/2019/5/untitled-ontology-17#>)
Ontology(<https://loinc.org/document_ontology/>
AnnotationAssertion(rdfs:label <https://loinc.org/document_ontology/#93024-8> "Pharmacist Consult note (D)"^^xsd:string)
AnnotationAssertion(document_ontology:hasCode <https://loinc.org/document_ontology/#93024-8> "93024-8"^^xsd:string)
SubClassOf(<https://loinc.org/document_ontology/#93024-8> document_ontology:Loincs)
SubClassOf(<https://loinc.org/document_ontology/#93024-8> ObjectSomeValuesFrom(document_ontology:document-kind document_ontology:LP173418-7))
SubClassOf(<https://loinc.org/document_ontology/#93024-8> ObjectSomeValuesFrom(document_ontology:document-role document_ontology:LP181523-4))
SubClassOf(<https://loinc.org/document_ontology/#93024-8> ObjectSomeValuesFrom(document_ontology:document-type-of-service document_ontology:LP173110-0))
)
"""
ontologydoc = to_python(owl_functional)
equivalents: Dict[ClassExpression, List[Axiom]] = dict()
# Convert all subclass expressions into the equivalents
for axiom in ontologydoc.ontology.axioms:
# Note that we can't use isinstance because of type cooercion
if issubclass(type(axiom), SubClassOf):
equivalents.setdefault(axiom.subClassExpression, []).append(axiom)
for class_expression, axioms in equivalents.items():
if len(axioms) == 1:
ontologydoc.ontology.equivalentClasses(class_expression,
axioms[0].superClassExpression)
else:
ontologydoc.ontology.equivalentClasses(
This is an example ontology that contains all constructs required for the various versions of the Pizza Tutorial
run by Manchester University
(see http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial).""",
lang="en")))
pizza.axioms.append(SubObjectPropertyOf(PIZZA.hasBase, PIZZA.hasIngredient))
pizza.axioms.append(InverseObjectProperties(PIZZA.hasBase, PIZZA.isBaseOf))
pizza.axioms.append(FunctionalObjectProperty(PIZZA.hasBase))
pizza.axioms.append(InverseFunctionalObjectProperty(PIZZA.hasBase))
pizza.axioms.append(ObjectPropertyDomain(PIZZA.hasBase, PIZZA.Pizza))
pizza.axioms.append(ObjectPropertyRange(PIZZA.hasBase, PIZZA.PizzaBase))
print(pizza_doc.to_functional().getvalue())
#%% md
## Ontologies in functional format can be read from files or URL's
#%%
from funowl.converters.functional_converter import to_python
from funowl.writers.FunctionalWriter import FunctionalWriter
pizza_doc = to_python(
"https://raw.githubusercontent.com/hsolbrig/funowl/master/tests/data/pizza.owl"
)
w = FunctionalWriter(g=pizza_doc.add_namespaces(Graph()))
for axiom in pizza_doc.ontology.axioms:
if isinstance(axiom, SubClassOf) and str(
axiom.subClassExpression) == 'pizza:AmericanHot':
w.add(axiom)
print(str(w))
def test_snomed(self):
start_time = time.time()
doc = to_python(os.path.join(datadir, 'ontology-after-conversion.owl'))
print("--- %s seconds ---" % (time.time() - start_time))
self.assertTrue(False, "Implement Me")
