Merge pull request #1291 from b2ihealthcare/issue/SO-6101-annotation-…

…properties-in-delegateontology fix(snomed.reasoner): Add support for annotation properties in DelegateOntology as well
b2ihealthcare · May 8, 2024 · 2d5ed54 · 2d5ed54
2 parents 297f06a + 0acc688
commit 2d5ed54
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Showing 3 changed files with 100 additions and 5 deletions.
diff --git a/.../b2international/snowowl/snomed/core/rest/classification/SnomedClassificationApiTest.java b/.../b2international/snowowl/snomed/core/rest/classification/SnomedClassificationApiTest.java
@@ -17,6 +17,7 @@
 
 import static com.b2international.snowowl.snomed.core.rest.SnomedClassificationRestRequests.*;
 import static com.b2international.snowowl.snomed.core.rest.SnomedComponentRestRequests.createComponent;
+import static com.b2international.snowowl.snomed.core.rest.SnomedComponentRestRequests.deleteComponent;
 import static com.b2international.snowowl.snomed.core.rest.SnomedComponentRestRequests.getComponent;
 import static com.b2international.snowowl.snomed.core.rest.SnomedRestFixtures.*;
 import static com.b2international.snowowl.test.commons.codesystem.CodeSystemRestRequests.createCodeSystem;
@@ -588,9 +589,13 @@ public void issue_SO_4985_testExtensionModuleChange() throws Exception {
 	public void issue_SO_6106_testSubAnnotationPropertyOfAxiomClassification() throws Exception {
 		String parentConceptId = createNewConcept(branchPath);
 		String childConceptId = createNewConcept(branchPath, parentConceptId);
+
+		SnomedConcept childConcept = getConcept(childConceptId, "relationships()");
+		childConcept.getRelationships()
+			.forEach(r -> deleteComponent(branchPath, SnomedComponentType.RELATIONSHIP, r.getId(), false));
 
 		createNewRefSetMember(branchPath, childConceptId, Concepts.REFSET_OWL_AXIOM, Map.of(
-			SnomedRf2Headers.FIELD_OWL_EXPRESSION, "SubAnnotationPropertyOf(: " + childConceptId + " :" + parentConceptId + ")"));
+			SnomedRf2Headers.FIELD_OWL_EXPRESSION, String.format("SubAnnotationPropertyOf(:%s :%s)", childConceptId, parentConceptId)));
 
 		String classificationId = getClassificationJobId(beginClassification(branchPath));
 		waitForClassificationJob(branchPath, classificationId)

diff --git a/.../com/b2international/snowowl/snomed/datastore/index/taxonomy/ReasonerTaxonomyBuilder.java b/.../com/b2international/snowowl/snomed/datastore/index/taxonomy/ReasonerTaxonomyBuilder.java
@@ -719,13 +719,14 @@ public ReasonerTaxonomyBuilder addActiveAxioms(final RevisionSearcher searcher)
 				final StringTokenizer tok = new StringTokenizer(expression.toLowerCase(Locale.ENGLISH), "(): ");
 				boolean isSubPropertyOf = false;
 
-				// OWL axiom types that we are expecting here, four of which requires special handling:
+				// OWL axiom types that we are expecting here, five of which requires special handling:
 				// 
 				// [ ] SubClassOf(...)
 				// [ ] EquivalentClasses(...)
 				// [+] SubObjectPropertyOf(ObjectPropertyChain(:246093002 :738774007) :246093002)
 				// [+] SubObjectPropertyOf(:x :y)
 				// [+] SubDataPropertyOf(:x :y)
+				// [+] SubAnnotationPropertyOf(:x :y)
 				// [+] TransitiveObjectProperty(:774081006)
 				// [ ] ReflexiveObjectProperty(...)
 				try {
@@ -750,7 +751,7 @@ public ReasonerTaxonomyBuilder addActiveAxioms(final RevisionSearcher searcher)
 						isSubPropertyOf = true;
 					}
 
-					// Collect the OWL axiom only if it is not of type "Sub<Object|Data>PropertyOf"
+					// Collect the OWL axiom only if it is not of type "Sub<Object|Data|Annotation>PropertyOf"
 					if (!isSubPropertyOf) {
 						axioms.add(expression);
 					}
@@ -787,7 +788,7 @@ public ReasonerTaxonomyBuilder addActiveAxioms(final RevisionSearcher searcher)
 
 						if (isSubPropertyOf) {
 							/*
-							 * XXX: Register "Sub<Object|Data>PropertyOf" axioms as "stated parents", so that we
+							 * XXX: Register "Sub<Object|Data|Annotation>PropertyOf" axioms as "stated parents", so that we
 							 * can create both the original axiom _and_ a SubClassOf axiom for a (punted)
 							 * OWL class representing the property concept.
 							 */

diff --git a/...d.reasoner/src/com/b2international/snowowl/snomed/reasoner/ontology/DelegateOntology.java b/...d.reasoner/src/com/b2international/snowowl/snomed/reasoner/ontology/DelegateOntology.java
@@ -81,6 +81,8 @@ public final class DelegateOntology extends DelegateOntologyStub implements OWLM
 	private static final long PRE_2018_OBJECT_ATTRIBUTE = Long.parseLong(Concepts.CONCEPT_MODEL_ATTRIBUTE);
 	private static final long PRE_2018_DATA_ATTRIBUTE = Long.parseLong(Concepts.SG_CONCRETE_DOMAIN_ATTRIBUTE);
 
+	private static final long ANNOTATION_ATTRIBUTE = Long.parseLong(Concepts.ANNOTATION_ATTRIBUTE);
+
 	private static final long IS_A = Long.parseLong(Concepts.IS_A);
 	private static final long ROLE_GROUP = Long.parseLong(Concepts.ROLE_GROUP);
 
@@ -237,6 +239,52 @@ private long nextApplicableParentId() {
 			return -1L;
 		}
 	}
+
+	private final class SubAnnotationPropertyOfAxiomIterator extends AbstractIterator<OWLSubAnnotationPropertyOfAxiom> {
+		private final LongIterator childIterator;
+
+		private long childId = -1L;
+		private LongIterator parentIterator;
+
+		public SubAnnotationPropertyOfAxiomIterator(final LongIterator childIterator) {
+			this.childIterator = childIterator;
+		}
+
+		@Override
+		protected OWLSubAnnotationPropertyOfAxiom computeNext() {
+			final long parentId = nextApplicableParentId(); 
+			if (parentId == -1L) {
+				return endOfData();
+			}
+
+			final OWLAnnotationProperty childProperty = getConceptAnnotationProperty(childId);
+			final OWLAnnotationProperty parentProperty = getConceptAnnotationProperty(parentId);
+			return getOWLSubAnnotationPropertyOfAxiom(childProperty, parentProperty);	
+		}
+
+		private long nextApplicableParentId() {
+			// Check if there are more parents to return for the current value of "childId"
+			if (parentIterator != null) {
+				while (parentIterator.hasNext()) {
+					return parentIterator.next();
+				}
+			}
+
+			// Otherwise, look for the next child which has parents
+			while (childIterator.hasNext()) {
+				childId = childIterator.next();
+				parentIterator = taxonomy.getStatedAncestors()
+						.getDestinations(childId, true)
+						.iterator();
+
+				while (parentIterator.hasNext()) {
+					return parentIterator.next();
+				}
+			}
+
+			return -1L;
+		}
+	}
 
 	private final class SubClassOfAxiomIterator extends AbstractIterator<OWLSubClassOfAxiom> {
 		private final LongIterator childIterator;
@@ -376,6 +424,7 @@ private static DefaultPrefixManager createPrefixManager() {
 
 	private final long objectAttributeId;
 	private final long dataAttributeId;
+	private final long annotationAttributeId;
 	private final LongSet neverGroupedIds;
 
 	public DelegateOntology(final OWLOntologyManager manager, 
@@ -400,6 +449,12 @@ public DelegateOntology(final OWLOntologyManager manager,
 			dataAttributeId = PRE_2018_DATA_ATTRIBUTE;
 		}
 
+		if (taxonomy.getConceptMap().getInternalId(ANNOTATION_ATTRIBUTE) != -1) {
+			annotationAttributeId = ANNOTATION_ATTRIBUTE;
+		} else {
+			annotationAttributeId = -1L;
+		}
+
 		if (!taxonomy.getNeverGroupedTypeIds().isEmpty()) {
 			this.neverGroupedIds = taxonomy.getNeverGroupedTypeIds();
 		} else {
@@ -539,6 +594,7 @@ public Iterator<OWLLogicalAxiom> iterator() {
 						objectAttributeSubClassOfAxioms(),
 						dataAttributeSubPropertyOfAxioms(),
 						dataAttributeSubClassOfAxioms(),
+						annotationAttributeSubClassOfAxioms(),
 						disjointUnionAxioms());
 			}
 
@@ -554,7 +610,10 @@ public Set<OWLAxiom> getAxioms() {
 		return new AbstractSet<OWLAxiom>() {
 			@Override
 			public Iterator<OWLAxiom> iterator() {
-				return Iterators.concat(conceptFsnAxioms(), getLogicalAxioms().iterator());
+				return Iterators.concat(
+					conceptFsnAxioms(), 
+					annotationAttributeSubPropertyOfAxioms(), 
+					getLogicalAxioms().iterator());
 			}
 
 			@Override
@@ -572,12 +631,14 @@ public int getLogicalAxiomCount() {
 				+ objectHierarchyCount()        // objectAttributeSubClassOfAxioms()
 				+ dataHierarchyCount()          // dataAttributeSubPropertyOfAxioms()
 				+ dataHierarchyCount()          // dataAttributeSubClassOfAxioms()
+				+ annotationHierarchyCount()    // annotationAttributeSubClassOfAxioms()
 				+ disjointUnionCount();         // disjointUnionAxioms()
 	}
 
 	@Override
 	public int getAxiomCount() {
 		return conceptFsnAxiomCount()           // conceptFsnAxioms()
+				+ annotationHierarchyCount()	// annotationAttributeSubPropertyOfAxioms()
 				+ getLogicalAxiomCount();
 	}
 
@@ -679,6 +740,18 @@ private int dataHierarchyCount() {
 		return hierarchyCount(dataAttributeId);
 	}
 
+	private Iterator<OWLSubAnnotationPropertyOfAxiom> annotationAttributeSubPropertyOfAxioms() {
+		return new SubAnnotationPropertyOfAxiomIterator(annotationAttributeIdIterator());
+	}
+
+	private Iterator<OWLSubClassOfAxiom> annotationAttributeSubClassOfAxioms() {
+		return new SubClassOfAxiomIterator(annotationAttributeIdIterator());
+	}
+
+	private int annotationHierarchyCount() {
+		return hierarchyCount(annotationAttributeId);
+	}
+
 	private int hierarchyCount(final long ancestorId) {
 		return getAllSubTypes(ancestorId).size();
 	}
@@ -726,6 +799,10 @@ private LongIterator objectAttributeIdIterator() {
 	private LongIterator dataAttributeIdIterator() {
 		return getAllSubTypes(dataAttributeId).iterator();
 	}
+
+	private LongIterator annotationAttributeIdIterator() {
+		return getAllSubTypes(annotationAttributeId).iterator();
+	}
 
 	private LongIterator exhaustiveIdIterator() {
 		return taxonomy.getExhaustiveConcepts().iterator();
@@ -786,6 +863,10 @@ private OWLObjectProperty getConceptObjectProperty(final long conceptId) {
 	private OWLDataProperty getConceptDataProperty(final long conceptId) {
 		return getOWLDataProperty(PREFIX_SCT + conceptId);
 	}
+
+	private OWLAnnotationProperty getConceptAnnotationProperty(final long conceptId) {
+		return getOWLAnnotationProperty(PREFIX_SCT + conceptId);
+	}
 
 	private OWLClassExpression getRelationshipExpression(final StatementFragment fragment) {
 		return fragment.map(
@@ -989,6 +1070,10 @@ private OWLDataProperty getOWLDataProperty(final String abbreviatedIRI) {
 		return getDataFactory().getOWLDataProperty(abbreviatedIRI, prefixManager);
 	}
 
+	private OWLAnnotationProperty getOWLAnnotationProperty(final String abbreviatedIRI) {
+		return getDataFactory().getOWLAnnotationProperty(abbreviatedIRI, prefixManager);
+	}
+
 	private OWLClassExpression getOWLObjectIntersectionOf(final Set<OWLClassExpression> conjuncts) {
 		if (conjuncts.size() > 1) {
 			return getDataFactory().getOWLObjectIntersectionOf(conjuncts);
@@ -1059,4 +1144,8 @@ private OWLSubObjectPropertyOfAxiom getOWLSubObjectPropertyOfAxiom(final OWLObje
 	private OWLSubDataPropertyOfAxiom getOWLSubDataPropertyOfAxiom(final OWLDataPropertyExpression child, final OWLDataPropertyExpression parent) {
 		return getDataFactory().getOWLSubDataPropertyOfAxiom(child, parent);
 	}
+
+	private OWLSubAnnotationPropertyOfAxiom getOWLSubAnnotationPropertyOfAxiom(final OWLAnnotationProperty child, final OWLAnnotationProperty parent) {
+		return getDataFactory().getOWLSubAnnotationPropertyOfAxiom(child, parent);
+	}
 }