Merge pull request #73 from dice-group/issues-solving

fixing issue with OWLNothing + new parameter for `OWLReasoner.instances`

owlapy/abstracts/abstract_owl_reasoner.py

@@ -201,13 +201,14 @@ def object_property_values(self, ind: OWLNamedIndividual, pe: OWLObjectPropertyE
         pass
 
     @abstractmethod
-    def instances(self, ce: OWLClassExpression, direct: bool = False) -> Iterable[OWLNamedIndividual]:
+    def instances(self, ce: OWLClassExpression, direct: bool = False, timeout: int = 1000) -> Iterable[OWLNamedIndividual]:
         """Gets the individuals which are instances of the specified class expression.
 
         Args:
             ce: The class expression whose instances are to be retrieved.
             direct: Specifies if the direct instances should be retrieved (True), or if all instances should be
                 retrieved (False).
+            timeout: Time limit in seconds until results must be returned, else empty set is returned.
 
         Returns:
             If direct is True, each named individual j where the set of reasoner axioms entails

owlapy/owl_reasoner.py

@@ -1,6 +1,8 @@
 """OWL Reasoner"""
 import operator
 import logging
+import threading
+
 import owlready2
 
 from collections import defaultdict
@@ -35,6 +37,18 @@
 _P = TypeVar('_P', bound=OWLPropertyExpression)
 
 
+def run_with_timeout(func, timeout, args=(), kwargs={}):
+    result = [None]
+    thread = threading.Thread(target=lambda: result.append(func(*args, **kwargs)))
+    thread.start()
+    thread.join(timeout)
+    if thread.is_alive():
+        print(f"{func.__self__.__class__.__name__}.instances timed out! Timeout limit is currently set to {timeout} "
+              f"seconds\nReturning empty results...")
+        return []
+    return result[-1]
+
+
 class OntologyReasoner(AbstractOWLReasonerEx):
     __slots__ = '_ontology', '_world'
     # TODO: CD: We will remove owlready2 from owlapy
@@ -198,7 +212,7 @@ def object_property_values(self, ind: OWLNamedIndividual, pe: OWLObjectPropertyE
         else:
             raise NotImplementedError(pe)
 
-    def instances(self, ce: OWLClassExpression, direct: bool = False) -> Iterable[OWLNamedIndividual]:
+    def _instances(self, ce: OWLClassExpression, direct: bool = False) -> Iterable[OWLNamedIndividual]:
         if direct:
             if isinstance(ce, OWLClass):
                 c_x: owlready2.ThingClass = self._world[ce.str]
@@ -226,6 +240,9 @@ def instances(self, ce: OWLClassExpression, direct: bool = False) -> Iterable[OW
             else:
                 raise NotImplementedError("instances for complex class expressions not implemented", ce)
 
+    def instances(self, ce: OWLClassExpression, direct: bool = False, timeout: int = 1000):
+        return run_with_timeout(self._instances, timeout, (ce, direct))
+
     def _sub_classes_recursive(self, ce: OWLClassExpression, seen_set: Set, only_named: bool = True) \
             -> Iterable[OWLClassExpression]:
 
@@ -690,14 +707,17 @@ def object_property_values(self, ind: OWLNamedIndividual, pe: OWLObjectPropertyE
             -> Iterable[OWLNamedIndividual]:
         yield from self._base_reasoner.object_property_values(ind, pe, direct)
 
-    def instances(self, ce: OWLClassExpression, direct: bool = False) -> Iterable[OWLNamedIndividual]:
+    def _instances(self, ce: OWLClassExpression, direct: bool = False) -> Iterable[OWLNamedIndividual]:
         if direct:
             if not self.__warned & 2:
                 logger.warning("direct not implemented")
                 self.__warned |= 2
         temp = self._find_instances(ce)
         yield from temp
 
+    def instances(self, ce: OWLClassExpression, direct: bool = False, timeout: int = 1000):
+        return run_with_timeout(self._instances, timeout, (ce, direct))
+
     def sub_classes(self, ce: OWLClassExpression, direct: bool = False, only_named: bool = True) \
             -> Iterable[OWLClassExpression]:
         yield from self._base_reasoner.sub_classes(ce, direct=direct, only_named=only_named)
@@ -1216,10 +1236,9 @@ def __init__(self, ontology: Union[SyncOntology, str], reasoner="HermiT"):
         else:
             raise NotImplementedError("Not implemented")
 
+        self.reasoner = reasoner
 
-        self.reasoner=reasoner
-
-    def instances(self, ce: OWLClassExpression, direct=False) -> Set[OWLNamedIndividual]:
+    def _instances(self, ce: OWLClassExpression, direct=False) -> Set[OWLNamedIndividual]:
         """
         Get the instances for a given class expression using HermiT.
 
@@ -1230,12 +1249,15 @@ def instances(self, ce: OWLClassExpression, direct=False) -> Set[OWLNamedIndivid
         Returns:
             set: A set of individuals classified by the given class expression.
         """
-        mapped_ce=self.mapper.map_(ce)
+        mapped_ce = self.mapper.map_(ce)
         instances = self._owlapi_reasoner.getInstances(mapped_ce, direct)
         flattended_instances = instances.getFlattened()
         assert str(type(flattended_instances)) == "<java class 'java.util.LinkedHashSet'>"
         return {self.mapper.map_(ind) for ind in flattended_instances}
 
+    def instances(self, ce: OWLClassExpression, direct: bool = False, timeout: int = 1000):
+        return run_with_timeout(self._instances, timeout, (ce, direct))
+
     def equivalent_classes(self, ce: OWLClassExpression) -> List[OWLClassExpression]:
         """
         Gets the set of named classes that are equivalent to the specified class expression with

owlapy/owlapi_mapper.py

@@ -3,8 +3,7 @@
 import jpype.imports
 
 from owlapy import owl_expression_to_manchester, manchester_to_owl_expression
-from owlapy.class_expression import OWLClassExpression, OWLDataOneOf, OWLFacetRestriction, OWLDatatypeRestriction, \
-    OWLNothing, OWLClass
+from owlapy.class_expression import OWLClassExpression, OWLDataOneOf, OWLFacetRestriction, OWLDatatypeRestriction
 from owlapy.iri import IRI
 from owlapy.owl_axiom import OWLDeclarationAxiom, OWLAnnotation, OWLAnnotationProperty, OWLClassAssertionAxiom, \
     OWLDataPropertyAssertionAxiom, OWLDataPropertyDomainAxiom, OWLDataPropertyRangeAxiom, OWLObjectPropertyDomainAxiom, \
@@ -111,6 +110,7 @@ def __init__(self, ontology: _SO):
         ontology_set.add(self.ontology)
         bidi_provider = BidirectionalShortFormProviderAdapter(self.manager, ontology_set, SimpleShortFormProvider())
         entity_checker = ShortFormEntityChecker(bidi_provider)
+        bidi_provider.add(self.manager.getOWLDataFactory().getOWLNothing())
         self.parser = ManchesterOWLSyntaxClassExpressionParser(self.manager.getOWLDataFactory(), entity_checker)
         self.renderer = ManchesterOWLSyntaxOWLObjectRendererImpl()
 
@@ -152,8 +152,6 @@ def _(self, e):
 
     @map_.register
     def _(self, e: OWLClassExpression):
-        if isinstance(e, OWLClass) and e.str == OWLNothing.str:
-            return OWLClassImpl(self.map_(e.iri))
         return self.parser.parse(owl_expression_to_manchester(e))
 
     @map_.register(OWLAnonymousClassExpressionImpl)