Fix minor bugs detected while writing the documentation of SimPhoNy v…

…4.0.0rc3 (#813)

* Fixed minor bugs related to ontology restrictions and compositions, attributes, relationships, classes and individuals.

* Fixed minor bug in `host` and `sparql` functions.

simphony_osp/interfaces/sqlalchemy/interface.py

@@ -44,7 +44,7 @@ def open(self, configuration: str, create: bool = False):
             )
 
         self.base = Graph("SQLAlchemy", identifier=self._identifier)
-        self.base.open(configuration, create=True)
+        self.base.open(configuration, create=create)
         self._uri = configuration
 
     def close(self) -> None:

simphony_osp/interfaces/sqlite/interface.py

@@ -27,6 +27,8 @@ def open(self, configuration: str, create: bool = False):
             raise FileNotFoundError(
                 f"Database file {configuration} does not " f"exist."
             )
-        return super().open(configuration="sqlite:///" + configuration)
+        return super().open(
+            configuration="sqlite:///" + configuration, create=create
+        )
 
     # ↑ ---------------- ↑

simphony_osp/ontology/attribute.py

@@ -4,7 +4,7 @@
 import logging
 from typing import TYPE_CHECKING, Any, Iterable, Iterator, Optional
 
-from rdflib import OWL, RDFS, Literal, URIRef
+from rdflib import OWL, RDF, RDFS, Literal, URIRef
 from rdflib.term import Identifier
 
 from simphony_osp.ontology.entity import OntologyEntity
@@ -165,20 +165,29 @@ def _get_subclasses(self) -> Iterator[OntologyAttribute]:
         """
         yield self
 
-        def closure(node, graph):
-            yield from graph.subjects(RDFS.subPropertyOf, node)
-
-        for x in self.session.graph.transitiveClosure(
-            closure, self.identifier
-        ):
-            try:
-                yield self.session.from_identifier_typed(
-                    x, typing=OntologyAttribute
+        if self.identifier == OWL.topDataProperty:
+            yield from (
+                self.session.from_identifier_typed(s, typing=OntologyAttribute)
+                for s in self.session.graph.subjects(
+                    RDF.type, OWL.DatatypeProperty
                 )
-            except TypeError:
-                pass
-        # The filter makes sure that `OntologyAnnotation` and
-        #  `OntologyRelationship` objects are not superclasses, as
-        #  `RDFS.subPropertyOf` is used to establish class hierarchies of
-        #  rdf:Property, owl:DatatypeProperty, owl:ObjectProperty and
-        #  owl:AnnotationProperty.
+            )
+        else:
+
+            def closure(node, graph):
+                yield from graph.subjects(RDFS.subPropertyOf, node)
+
+            for x in self.session.graph.transitiveClosure(
+                closure, self.identifier
+            ):
+                try:
+                    yield self.session.from_identifier_typed(
+                        x, typing=OntologyAttribute
+                    )
+                except TypeError:
+                    pass
+            # The filter makes sure that `OntologyAnnotation` and
+            #  `OntologyRelationship` objects are not superclasses, as
+            #  `RDFS.subPropertyOf` is used to establish class hierarchies of
+            #  rdf:Property, owl:DatatypeProperty, owl:ObjectProperty and
+            #  owl:AnnotationProperty.

simphony_osp/ontology/composition.py

@@ -42,7 +42,7 @@ def operator(self) -> OPERATOR:
         Returns:
             The operator Enum.
         """
-        operator, _ = self._get_operator_and_operands
+        operator, _ = self._get_operator_and_operands()
         return operator
 
     @property
@@ -54,7 +54,7 @@ def operands(
         Returns:
             The operands.
         """
-        _, operands = self._get_operator_and_operands
+        _, operands = self._get_operator_and_operands()
         return tuple(operands)
 
     def __str__(self) -> str:

simphony_osp/ontology/individual.py

@@ -1121,7 +1121,7 @@ def __getitem__(
     def __setitem__(
         self,
         rel: Union[OntologyPredicate, str],
-        values: Optional[Union[PredicateValue, Set[PredicateValue]]],
+        values: Optional[Union[PredicateValue, Iterable[PredicateValue]]],
     ) -> None:
         """Manages object, data and annotation properties.
 
@@ -1178,7 +1178,9 @@ def __setitem__(
 
         values = values or set()
         values = (
-            {values} if not isinstance(values, (Set, MutableSet)) else values
+            {values}
+            if not isinstance(values, (Tuple, Set, MutableSet))
+            else set(values)
         )
         # Apparently instances of MutableSet are not instances of Set.
 

simphony_osp/ontology/oclass.py

@@ -22,6 +22,7 @@
 from rdflib.term import Identifier, Node
 
 from simphony_osp.ontology.attribute import OntologyAttribute
+from simphony_osp.ontology.composition import Composition
 from simphony_osp.ontology.entity import OntologyEntity
 from simphony_osp.ontology.restriction import Restriction
 from simphony_osp.utils.cache import lru_cache_timestamp
@@ -232,10 +233,10 @@ def _compute_axioms(
         for o in self.session.graph.objects(identifier, predicate):
             if not isinstance(o, BNode):
                 continue
-            try:
+            if (o, RDF_type, OWL_Restriction) in self.session.graph:
                 axioms.add(self.session.from_identifier_typed(o, Restriction))
-            except (KeyError, TypeError):
-                pass
+            elif (o, RDF_type, OWL.Class) in self.session.graph:
+                axioms.add(self.session.from_identifier_typed(o, Composition))
         return frozenset(axioms)
 
     @property
@@ -281,9 +282,6 @@ def _direct_attributes(
                     self.session.graph.value(
                         restriction_iri, OWL_someValuesFrom
                     ),
-                    self.session.graph.value(
-                        restriction_iri, OWL_allValuesFrom
-                    ),
                     self.session.graph.value(restriction_iri, OWL_hasValue),
                     self.session.graph.value(restriction_iri, OWL_cardinality)
                     != 0,
@@ -390,18 +388,30 @@ def _get_subclasses(self) -> Iterator[OntologyClass]:
         """
         yield self
 
-        def closure(node, graph):
-            yield from graph.subjects(RDFS_subClassOf, node)
+        if self.identifier == OWL_Thing:
+            for s in self.session.graph.subjects(RDF.type, OWL.Class):
+                try:
+                    yield self.session.from_identifier_typed(
+                        s, typing=OntologyClass
+                    )
+                except TypeError:
+                    pass
+            # The filter makes sure that `Restriction` and `Composition`
+            # objects are not returned.
+        else:
 
-        yield from filter(
-            lambda x: isinstance(x, OntologyClass),
-            (
-                self.session.from_identifier(x)
-                for x in self.session.graph.transitiveClosure(
-                    closure, self.identifier
-                )
-            ),
-        )
+            def closure(node, graph):
+                yield from graph.subjects(RDFS_subClassOf, node)
+
+            yield from filter(
+                lambda x: isinstance(x, OntologyClass),
+                (
+                    self.session.from_identifier(x)
+                    for x in self.session.graph.transitiveClosure(
+                        closure, self.identifier
+                    )
+                ),
+            )
 
     def _kwargs_to_attributes(
         self, kwargs: Mapping, _skip_checks: bool

simphony_osp/ontology/relationship.py

@@ -112,10 +112,7 @@ def _get_subclasses(self) -> Iterator[OntologyRelationship]:
         """
         yield self
 
-        def closure(node, graph):
-            yield from graph.subjects(RDFS.subPropertyOf, node)
-
-        if self.iri == OWL.topObjectProperty:
+        if self.identifier == OWL.topObjectProperty:
             yield from (
                 self.session.from_identifier_typed(
                     s, typing=OntologyRelationship
@@ -125,6 +122,10 @@ def closure(node, graph):
                 )
             )
         else:
+
+            def closure(node, graph):
+                yield from graph.subjects(RDFS.subPropertyOf, node)
+
             yield from (
                 self.session.from_identifier_typed(
                     x, typing=OntologyRelationship

simphony_osp/ontology/restriction.py

@@ -175,8 +175,11 @@ def _get_quantifier_and_target(
             (OWL.someValuesFrom, QUANTIFIER.SOME),
             (OWL.allValuesFrom, QUANTIFIER.ONLY),
             (OWL.cardinality, QUANTIFIER.EXACTLY),
+            (OWL.qualifiedCardinality, QUANTIFIER.EXACTLY),
             (OWL.minCardinality, QUANTIFIER.MIN),
+            (OWL.minQualifiedCardinality, QUANTIFIER.MIN),
             (OWL.maxCardinality, QUANTIFIER.MAX),
+            (OWL.maxQualifiedCardinality, QUANTIFIER.MAX),
             (OWL.hasValue, QUANTIFIER.VALUE),
         ]:
             x = self.session.graph.value(self.identifier, predicate)

simphony_osp/ontology/utils.py

@@ -168,7 +168,7 @@ def __xor__(self, other: set) -> set:
 
     def __iadd__(self, other: Any) -> DataStructureSet:
         """Return self+=other (equivalent to self|=other)."""
-        if isinstance(other, (Set, MutableSet)):
+        if isinstance(other, (Tuple, Set, MutableSet)):
             # Apparently instances of MutableSet are not instances of Set.
             self.update(other)
         else:
@@ -180,7 +180,7 @@ def __isub__(self, other: Any) -> DataStructureSet:
 
         Based on `difference_update`.
         """
-        if isinstance(other, (Set, MutableSet)):
+        if isinstance(other, (Tuple, Set, MutableSet)):
             # Apparently instances of MutableSet are not instances of Set.
             self.difference_update(other)
         else:

simphony_osp/tools/remote.py

@@ -11,7 +11,7 @@ def host(
     configuration_string: str = "",
     create: bool = False,
     hostname: str = "127.0.0.1",
-    port: int = "6537",
+    port: int = 6537,
     username: Optional[str] = None,
     password: Optional[str] = None,
     **kwargs: Union[

simphony_osp/tools/search.py

@@ -230,11 +230,16 @@ def criterion(individual):
     return find(criterion=criterion, root=root, rel=rel, find_all=True)
 
 
-def sparql(query: str, session: Optional[Session] = None) -> QueryResult:
+def sparql(
+    query: str, ontology: bool = False, session: Optional[Session] = None
+) -> QueryResult:
     """Performs a SPARQL query on a session.
 
     Args:
         query: A string with the SPARQL query to perform.
+        ontology: Whether to include the ontology in the query or not.
+            When the ontology is included, only read-only queries are
+            possible.
         session: The session on which the SPARQL query will be performed. If no
             session is specified, then the current default session is used.
             This means that, when no session is specified, inside session
@@ -248,4 +253,4 @@ def sparql(query: str, session: Optional[Session] = None) -> QueryResult:
         variable can be retrieved as follows: `row['variable']`.
     """
     session = session or Session.get_default_session()
-    return session.sparql(query)
+    return session.sparql(query, ontology=ontology)