SO-6106: "Sub...PropertyOf" support for axiom-relationship conversions

cis/com.b2international.snowowl.snomed.cis.product/.launch/snow-owl-cis.launch

@@ -158,7 +158,7 @@
         <setEntry value="org.objectweb.asm@default:default"/>
         <setEntry value="org.objenesis@default:default"/>
         <setEntry value="org.reactivestreams.reactive-streams@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.w3c.css.sac@default:default"/>
         <setEntry value="org.yaml.snakeyaml@default:default"/>
         <setEntry value="slf4j.api@default:default"/>

core/com.b2international.snowowl.core.rest.tests/.launch/core-e2e-tests.launch

@@ -193,7 +193,7 @@
         <setEntry value="org.protege.editor.owl@default:default"/>
         <setEntry value="org.reactivestreams.reactive-streams@default:default"/>
         <setEntry value="org.semanticweb.owl.owlapi@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.yaml.snakeyaml@default:default"/>
         <setEntry value="slf4j.api@default:default"/>
     </setAttribute>

fhir/com.b2international.snowowl.fhir.rest.tests/.launch/fhir-api-tests.launch

@@ -194,7 +194,7 @@
         <setEntry value="org.protege.editor.owl@default:default"/>
         <setEntry value="org.reactivestreams.reactive-streams@default:default"/>
         <setEntry value="org.semanticweb.owl.owlapi@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.w3c.dom.events@default:default"/>
         <setEntry value="org.yaml.snakeyaml@default:default"/>
         <setEntry value="slf4j.api@default:default"/>

fhir/com.b2international.snowowl.fhir.rest.tests/.launch/fhir-unit-tests.launch

@@ -171,7 +171,7 @@
         <setEntry value="org.protege.editor.owl@default:default"/>
         <setEntry value="org.reactivestreams.reactive-streams@default:default"/>
         <setEntry value="org.semanticweb.owl.owlapi@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.w3c.css.sac@default:default"/>
         <setEntry value="org.w3c.dom.events@default:default"/>
         <setEntry value="org.w3c.dom.smil@default:default"/>

fhir/com.b2international.snowowl.fhir.rest/.launch/fhir-api-server.launch

@@ -180,7 +180,7 @@
         <setEntry value="org.sat4j.core@default:default"/>
         <setEntry value="org.sat4j.pb@default:default"/>
         <setEntry value="org.semanticweb.owl.owlapi@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.tukaani.xz@default:default"/>
         <setEntry value="org.yaml.snakeyaml@default:default"/>
         <setEntry value="slf4j.api@default:default"/>

pom.xml

@@ -35,7 +35,7 @@
 		<fastutil.version>8.3.1</fastutil.version>
 		<jaxb.api.version>2.3.0</jaxb.api.version>
 		<javax.activation.version>1.2.0</javax.activation.version>
-		<snomed.owl.toolkit.version>3.0.6</snomed.owl.toolkit.version>
+		<snomed.owl.toolkit.version>3.0.106</snomed.owl.toolkit.version>
 		<failsafe.version>2.3.1</failsafe.version>
 		<osgi.versionRange>[3.16.0,3.17.0]</osgi.versionRange>
 
@@ -626,7 +626,7 @@
 			<scope>provided</scope>
 		</dependency>
 		<dependency>
-    		<groupId>org.snomed.otf</groupId>
+    		<groupId>com.b2international</groupId>
 			<artifactId>snomed-owl-toolkit</artifactId>
 			<version>${snomed.owl.toolkit.version}</version>
 			<classifier>bundle</classifier>

releng/com.b2international.snowowl.server.update/.launch/snow-owl-oss.launch

@@ -148,7 +148,7 @@
         <setEntry value="org.reactivestreams.reactive-streams@default:default"/>
         <setEntry value="org.semanticweb.elk@default:default"/>
         <setEntry value="org.semanticweb.owl.owlapi@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.yaml.snakeyaml@default:default"/>
         <setEntry value="slf4j.api@default:default"/>
         <setEntry value="stax2-api@default:default"/>

snomed/com.b2international.snowowl.snomed.common/src/com/b2international/snowowl/snomed/common/SnomedConstants.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2011-2023 B2i Healthcare Pte Ltd, http://b2i.sg
+ * Copyright 2011-2024 B2i Healthcare Pte Ltd, http://b2i.sg
  * 
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -274,6 +274,9 @@ private Concepts() { }
 		public static final String CONCEPT_MODEL_OBJECT_ATTRIBUTE = "762705008";
 		public static final String CONCEPT_MODEL_DATA_ATTRIBUTE = "762706009";
 
+		// Concept model attribute hierarchy roots, starting with INT 20240301
+		public static final String ANNOTATION_ATTRIBUTE = "1295447006";
+
 		// Concepts that require special care when classifying
 		public static final String ROLE_GROUP = "609096000";
 		public static final String PART_OF = "123005000";

snomed/com.b2international.snowowl.snomed.core.rest.tests/.launch/snomed-e2e-tests (cis).launch

@@ -210,7 +210,7 @@
         <setEntry value="org.reactivestreams.reactive-streams@default:default"/>
         <setEntry value="org.semanticweb.elk@default:default"/>
         <setEntry value="org.semanticweb.owl.owlapi@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.yaml.snakeyaml@default:default"/>
         <setEntry value="slf4j.api@default:default"/>
     </setAttribute>

snomed/com.b2international.snowowl.snomed.core.rest.tests/.launch/snomed-e2e-tests.launch

@@ -190,7 +190,7 @@
         <setEntry value="org.reactivestreams.reactive-streams@default:default"/>
         <setEntry value="org.semanticweb.elk@default:default"/>
         <setEntry value="org.semanticweb.owl.owlapi@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.yaml.snakeyaml@default:default"/>
         <setEntry value="slf4j.api@default:default"/>
     </setAttribute>

snomed/com.b2international.snowowl.snomed.datastore.tests/.launch/snomed-core-unit-tests.launch

@@ -162,7 +162,7 @@
         <setEntry value="org.protege.editor.owl@default:default"/>
         <setEntry value="org.reactivestreams.reactive-streams@default:default"/>
         <setEntry value="org.semanticweb.owl.owlapi@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.yaml.snakeyaml@default:default"/>
         <setEntry value="slf4j.api@default:default"/>
     </setAttribute>

snomed/com.b2international.snowowl.snomed.datastore.tests/src/com/b2international/snowowl/snomed/datastore/AllSnomedDatastoreTests.java

@@ -43,6 +43,8 @@
 import com.b2international.snowowl.snomed.datastore.internal.id.SnomedIdentifierTest;
 import com.b2international.snowowl.snomed.datastore.internal.id.reservations.ReservationImplTest;
 import com.b2international.snowowl.snomed.datastore.internal.id.reservations.SnomedIdentifierReservationServiceImplTest;
+import com.b2international.snowowl.snomed.datastore.request.SnomedOWLExpressionConverterTest;
+import com.b2international.snowowl.snomed.datastore.request.SnomedOWLRelationshipConverterTest;
 import com.b2international.snowowl.snomed.validation.SnomedQueryValidationRuleEvaluatorTest;
 
 /**
@@ -82,6 +84,8 @@
 	SnomedDescriptionUtilsTest.class,
 	// Validate Rule Evaluators
 	SnomedQueryValidationRuleEvaluatorTest.class,
+	SnomedOWLExpressionConverterTest.class,	
+	SnomedOWLRelationshipConverterTest.class,
 })
 public class AllSnomedDatastoreTests {
 

snomed/com.b2international.snowowl.snomed.datastore.tests/src/com/b2international/snowowl/snomed/datastore/request/SnomedOWLExpressionConverterTest.java

@@ -0,0 +1,66 @@
+/*
+ * Copyright 2024 B2i Healthcare Ltd, http://b2ihealthcare.com
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package com.b2international.snowowl.snomed.datastore.request;
+
+import static org.junit.Assert.*;
+
+import java.util.List;
+
+import org.elasticsearch.core.Set;
+import org.junit.Test;
+
+import com.b2international.snowowl.snomed.common.SnomedConstants.Concepts;
+import com.b2international.snowowl.snomed.datastore.index.entry.SnomedOWLRelationshipDocument;
+import com.google.common.collect.Iterables;
+
+/**
+ * @since 7.24.3
+ */
+public class SnomedOWLExpressionConverterTest {
+
+	@Test
+	public void testSubObjectPropertyOf() {
+		testSubPropertyOf("SubObjectPropertyOf");
+	}
+
+	@Test
+	public void testSubDataPropertyOf() {
+		testSubPropertyOf("SubDataPropertyOf");
+	}
+
+	@Test
+	public void testSubAnnotationPropertyOf() {
+		testSubPropertyOf("SubAnnotationPropertyOf");
+	}
+
+	private void testSubPropertyOf(String subPropertyOfAxiom) {
+		SnomedOWLExpressionConverter converter = new SnomedOWLExpressionConverter(() -> Set.of());
+
+		// XXX: Using nonsensical but valid SCTIDs
+		SnomedOWLExpressionConverterResult converterResult = converter.toSnomedOWLRelationships(
+			Concepts.FINDING_SITE, 
+			String.format("%s(:%s :%s)", subPropertyOfAxiom, Concepts.FINDING_SITE, Concepts.AMBIGUOUS));
+
+		assertNull(converterResult.getGciAxiomRelationships());
+
+		final List<SnomedOWLRelationshipDocument> relationships = converterResult.getClassAxiomRelationships();
+		assertEquals(1, relationships.size());
+
+		final SnomedOWLRelationshipDocument relationship = Iterables.getOnlyElement(relationships);
+		assertEquals(Concepts.IS_A, relationship.getTypeId());
+		assertEquals(Concepts.AMBIGUOUS, relationship.getDestinationId());
+	}
+}

snomed/com.b2international.snowowl.snomed.datastore.tests/src/com/b2international/snowowl/snomed/datastore/request/SnomedOWLRelationshipConverterTest.java

@@ -0,0 +1,106 @@
+/*
+ * Copyright 2024 B2i Healthcare Ltd, http://b2ihealthcare.com
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package com.b2international.snowowl.snomed.datastore.request;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.Collection;
+import java.util.List;
+
+import org.elasticsearch.core.Set;
+import org.junit.Test;
+
+import com.b2international.snowowl.snomed.common.SnomedConstants.Concepts;
+import com.b2international.snowowl.snomed.datastore.index.entry.SnomedOWLRelationshipDocument;
+
+/**
+ * @since 7.24.3
+ */
+public class SnomedOWLRelationshipConverterTest {
+
+	@Test
+	public void testSubClassOf() {
+		testSubPropertyOf(
+			"SubClassOf", 
+			Set.of(),
+			Set.of(),
+			Set.of(),
+			Concepts.DEVICE
+		);
+	}
+
+	@Test
+	public void testSubObjectPropertyOf() {
+		testSubPropertyOf(
+			"SubObjectPropertyOf", 
+			Set.of(Long.parseLong(Concepts.CONCEPT_MODEL_OBJECT_ATTRIBUTE)),
+			Set.of(),
+			Set.of(),
+			Concepts.CONCEPT_MODEL_OBJECT_ATTRIBUTE
+		);
+	}
+
+	@Test
+	public void testSubDataPropertyOf() {
+		testSubPropertyOf(
+			"SubDataPropertyOf", 
+			Set.of(),
+			Set.of(Long.parseLong(Concepts.CONCEPT_MODEL_DATA_ATTRIBUTE)),
+			Set.of(),
+			Concepts.CONCEPT_MODEL_DATA_ATTRIBUTE
+		);
+	}
+
+	@Test
+	public void testSubAnnotationPropertyOf() {
+		testSubPropertyOf(
+			"SubAnnotationPropertyOf",
+			Set.of(),
+			Set.of(),
+			Set.of(Long.parseLong(Concepts.ANNOTATION_ATTRIBUTE)),
+			Concepts.ANNOTATION_ATTRIBUTE
+		);
+	}
+
+	private void testSubPropertyOf(
+		String subPropertyOfAxiom,
+		Collection<Long> objectAttributes,
+		Collection<Long> dataAttributes,
+		Collection<Long> annotationAttributes,
+		String destinationId
+	) {
+		SnomedOWLRelationshipConverter converter = new SnomedOWLRelationshipConverter(
+			Set.of(), 
+			objectAttributes, 
+			dataAttributes, 
+			annotationAttributes);
+
+		// XXX: Using nonsensical but valid SCTIDs
+		final List<SnomedOWLRelationshipDocument> owlRelationships = List.of(
+			SnomedOWLRelationshipDocument.create(Concepts.IS_A, destinationId, 0)
+		);
+
+		final String expectedExpression = String.format("%s(:%s :%s)", subPropertyOfAxiom, Concepts.FINDING_SITE, destinationId);
+		final String actualExpression = converter.fromSnomedOwlRelationships(
+			false,
+			true,
+			Concepts.FINDING_SITE, 
+			owlRelationships
+		);
+
+		assertEquals(expectedExpression, actualExpression);
+	}
+}

snomed/com.b2international.snowowl.snomed.datastore/META-INF/MANIFEST.MF

@@ -14,7 +14,7 @@ Require-Bundle: org.eclipse.core.runtime;bundle-version="3.9.0",
  org.eclipse.core.databinding;bundle-version="1.4.0",
  org.eclipse.core.expressions;bundle-version="3.4.400",
  com.fasterxml.jackson.dataformat.jackson-dataformat-csv;bundle-version="2.8.6",
- org.snomed.otf.snomed-owl-toolkit;bundle-version="3.0.2",
+ com.b2international.snomed-owl-toolkit,
  org.eclipse.xtext.xbase.lib,
  com.b2international.snowowl.snomed.cis;visibility:=reexport,
  com.b2international.snowowl.snomed.common;visibility:=reexport,

snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/datastore/request/SnomedOWLExpressionConverter.java

@@ -68,7 +68,9 @@ public final class SnomedOWLExpressionConverter {
 		"SubClassOf", 
 		"EquivalentClasses", 
 		"SubObjectPropertyOf", 
-		"SubDataPropertyOf");
+		"SubDataPropertyOf",
+		"SubAnnotationPropertyOf"
+	);
 
 	private final Supplier<AxiomRelationshipConversionService> conversionService;
 

snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/datastore/request/SnomedOWLRelationshipConverter.java

@@ -48,10 +48,21 @@ public final class SnomedOWLRelationshipConverter {
 
 	private final Supplier<AxiomRelationshipConversionService> conversionService;
 
-	public SnomedOWLRelationshipConverter(final Set<Long> ungroupedAttributes, final Collection<Long> objectAttributes, final Collection<Long> dataAttributes) {
+	public SnomedOWLRelationshipConverter(
+		final Set<Long> ungroupedAttributes, 
+		final Collection<Long> objectAttributes, 
+		final Collection<Long> dataAttributes,
+		final Collection<Long> annotationAttributes
+	) {
 		this.conversionService = Suppliers.memoize(() -> {
 			final Stopwatch stopwatch = Stopwatch.createStarted();
-			final AxiomRelationshipConversionService service = withTccl(() -> new AxiomRelationshipConversionService(ungroupedAttributes, objectAttributes, dataAttributes));
+			final AxiomRelationshipConversionService service = withTccl(() -> new AxiomRelationshipConversionService(
+				ungroupedAttributes, 
+				objectAttributes, 
+				dataAttributes,
+				annotationAttributes)
+			);
+
 			LOG.debug("SNOMED OWL Toolkit conversion service initialization took {}", TimeUtil.toString(stopwatch));
 			return service;
 		});

snomed/com.b2international.snowowl.snomed.reasoner.tests/.launch/snomed-reasoner-unit-tests.launch

@@ -151,7 +151,7 @@
         <setEntry value="org.protege.editor.owl@default:default"/>
         <setEntry value="org.reactivestreams.reactive-streams@default:default"/>
         <setEntry value="org.semanticweb.owl.owlapi@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.yaml.snakeyaml@default:default"/>
         <setEntry value="slf4j.api@default:default"/>
     </setAttribute>

snomed/com.b2international.snowowl.validation.snomed/.launch/validation-snomed-tests.launch

@@ -161,7 +161,7 @@
         <setEntry value="org.protege.editor.owl@default:default"/>
         <setEntry value="org.reactivestreams.reactive-streams@default:default"/>
         <setEntry value="org.semanticweb.owl.owlapi@default:default"/>
-        <setEntry value="org.snomed.otf.snomed-owl-toolkit@default:default"/>
+        <setEntry value="com.b2international.snomed-owl-toolkit@default:default"/>
         <setEntry value="org.w3c.dom.events@default:default"/>
         <setEntry value="org.yaml.snakeyaml@default:default"/>
         <setEntry value="slf4j.api@default:default"/>