feat(core): transaction referential integrity check improvements

core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/repository/RepositoryTransactionContext.java

@@ -20,13 +20,15 @@
 
 import java.io.IOException;
 import java.util.*;
+import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import org.eclipse.xtext.util.Pair;
 import org.eclipse.xtext.util.Tuples;
 
 import com.b2international.commons.CompareUtils;
 import com.b2international.commons.exceptions.AlreadyExistsException;
+import com.b2international.commons.exceptions.BadRequestException;
 import com.b2international.commons.exceptions.ConflictException;
 import com.b2international.commons.exceptions.CycleDetectedException;
 import com.b2international.index.Index;
@@ -304,11 +306,34 @@
 		if (!ensurePresent.isEmpty()) {
 			// check if any of the listed IDs are already present in the index and if NOT, report ComponentNotFoundException for the first registered ID (same behavior as before with explicit checks)
 			for (Class<? extends Revision> type : ensurePresent.keySet()) {
-				final Collection<String> idsToCheck = ensurePresent.get(type).stream().filter(id -> !IComponent.ROOT_ID.equals(id)).toList();
-				final Map<String, ?> existingComponents = Maps.uniqueIndex(fetchComponents(idsToCheck, type), Revision::getId);
-				for (String idToCheck : idsToCheck) {
-					if (!existingComponents.containsKey(idToCheck)) {
-						throw new ComponentNotFoundException(DocumentMapping.getDocType(type), idToCheck).toBadRequestException();
+				final Set<String> idsToCheck = ensurePresent.get(type).stream().filter(id -> !IComponent.ROOT_ID.equals(id)).collect(Collectors.toSet());
+
+				// first check if there are any deletion that are present in the ID set, if yes, then those IDs won't be available anymore, report a transaction error
+				var deletedIds = staging.getRemovedObjects(Revision.class)
+					.map(Revision::getId)
+					.filter(idsToCheck::contains)
+					.collect(Collectors.toSet());
+
+				if (!deletedIds.isEmpty()) {
+					throw new BadRequestException("Transaction would delete components that are still referenced by other components.")
+						.withAdditionalInfo(Map.of("ids", deletedIds));
+				}
+
+				// then remove all new/changed objects that are already present in the tx staging area, those can be considered ensured
+				staging.getNewObjects(Revision.class)
+					.map(Revision::getId)
+					.forEach(idsToCheck::remove);
+				staging.getChangedObjects(Revision.class)
+					.map(Revision::getId)
+					.forEach(idsToCheck::remove);
+
+				// then if there are any remaining IDs to check, fetch them from the store
+				if (!idsToCheck.isEmpty()) {
+					final Map<String, ?> existingComponents = Maps.uniqueIndex(fetchComponents(idsToCheck, type), Revision::getId);				
+					for (String idToCheck : idsToCheck) {
+						if (!existingComponents.containsKey(idToCheck)) {
+							throw new ComponentNotFoundException(DocumentMapping.getDocType(type), idToCheck).toBadRequestException();
+						}
 					}
 				}
 			}

snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/core/domain/refset/SnomedReferenceSetMember.java

@@ -231,7 +231,7 @@ public Request<TransactionContext, String> toCreateRequest(String containerId) {
 		return SnomedRequests.prepareNewMember()
 				.setId(getId())
 				.setActive(isActive())
-				.setReferencedComponentId(containerId)
+				.setReferencedComponentId(containerId != null ? containerId : getReferencedComponentId())
 				.setRefsetId(getRefsetId())
 				.setModuleId(getModuleId())
 				.setProperties(getProperties())

snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/core/store/SnomedComponentBuilder.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2011-2021 B2i Healthcare, https://b2ihealthcare.com
+ * Copyright 2011-2024 B2i Healthcare, https://b2ihealthcare.com
  * 
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -102,7 +102,7 @@ public void init(CB component, TransactionContext context) {
 
 		// check that the module does exist in the system
 		if (!id.equals(moduleId)) {
-			context.lookup(moduleId, SnomedConceptDocument.class);
+			context.ensurePresent(SnomedConceptDocument.class, moduleId);
 		}
 
 		if (effectiveTime == null) {

snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/core/store/SnomedConceptBuilder.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2011-2021 B2i Healthcare, https://b2ihealthcare.com
+ * Copyright 2011-2024 B2i Healthcare, https://b2ihealthcare.com
  * 
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -59,7 +59,7 @@ protected SnomedConceptDocument.Builder create() {
 	public void init(SnomedConceptDocument.Builder component, TransactionContext context) {
 		super.init(component, context);
 		// check that the definitionStatus concept does exist before using it in this concept
-		context.lookup(definitionStatusId, SnomedConceptDocument.class);
+		context.ensurePresent(SnomedConceptDocument.class, definitionStatusId);
 		component.definitionStatusId(definitionStatusId);
 		component.exhaustive(exhaustive);
 	}

snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/core/store/SnomedDescriptionBuilder.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2011-2020 B2i Healthcare, https://b2ihealthcare.com
+ * Copyright 2011-2024 B2i Healthcare, https://b2ihealthcare.com
  * 
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -89,12 +89,18 @@ public SnomedDescriptionBuilder withConcept(String concept) {
 	@Override
 	public void init(SnomedDescriptionIndexEntry.Builder component, TransactionContext context) {
 		super.init(component, context);
-		component.caseSignificanceId(context.lookup(caseSignificanceId, SnomedConceptDocument.class).getId());
-		component.typeId(context.lookup(type, SnomedConceptDocument.class).getId());
+		context.ensurePresent(SnomedConceptDocument.class, caseSignificanceId);
+		component.caseSignificanceId(caseSignificanceId);
+
+		context.ensurePresent(SnomedConceptDocument.class, type);
+		component.typeId(type);
+
 		component.term(term);
 		component.languageCode(languageCode);
+
 		if (concept != null) {
-			component.conceptId(context.lookup(concept, SnomedConceptDocument.class).getId());
+			context.ensurePresent(SnomedConceptDocument.class, concept);
+			component.conceptId(concept);
 		}
 	}
 

snomed/com.b2international.snowowl.snomed.datastore/src/com/b2international/snowowl/snomed/core/store/SnomedRelationshipBuilder.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2011-2021 B2i Healthcare, https://b2ihealthcare.com
+ * Copyright 2011-2024 B2i Healthcare, https://b2ihealthcare.com
  * 
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -141,28 +141,31 @@ protected SnomedRelationshipIndexEntry.Builder create() {
 		return SnomedRelationshipIndexEntry.builder();
 	}
 
-	private String ensureConceptExists(final String conceptId, final TransactionContext context) {
-		return context.lookup(conceptId, SnomedConceptDocument.class).getId();
-	}
-
 	@Override
 	public void init(final SnomedRelationshipIndexEntry.Builder component, final TransactionContext context) {
 		super.init(component, context);
 
-		if (sourceId != null) { 
-			component.sourceId(ensureConceptExists(sourceId, context)); 
+		if (sourceId != null) {
+			context.ensurePresent(SnomedConceptDocument.class, sourceId);
+			component.sourceId(sourceId); 
 		}
 
 		if (destinationId != null) { 
-			component.destinationId(ensureConceptExists(destinationId, context)); 
+			context.ensurePresent(SnomedConceptDocument.class, destinationId);
+			component.destinationId(destinationId); 
 		}
 
-		component.typeId(ensureConceptExists(typeId, context));
+		context.ensurePresent(SnomedConceptDocument.class, typeId);
+		component.typeId(typeId);
 		component.destinationNegated(destinationNegated);
 		component.value(value);
 		component.relationshipGroup(relationshipGroup);
 		component.unionGroup(unionGroup);
-		component.characteristicTypeId(ensureConceptExists(characteristicTypeId, context));
-		component.modifierId(ensureConceptExists(modifierId, context));
+
+		context.ensurePresent(SnomedConceptDocument.class, characteristicTypeId);
+		component.characteristicTypeId(characteristicTypeId);
+
+		context.ensurePresent(SnomedConceptDocument.class, modifierId);
+		component.modifierId(modifierId);
 	}
 }

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

@@ -17,30 +17,19 @@
 
 import static com.google.common.collect.Sets.newHashSet;
 
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
+import java.util.*;
 import java.util.Map.Entry;
-import java.util.Optional;
-import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import jakarta.validation.constraints.NotNull;
-import jakarta.validation.constraints.Size;
-
 import com.b2international.collections.PrimitiveSets;
 import com.b2international.commons.exceptions.BadRequestException;
 import com.b2international.snowowl.core.domain.TransactionContext;
 import com.b2international.snowowl.core.events.Request;
 import com.b2international.snowowl.core.exceptions.ComponentNotFoundException;
 import com.b2international.snowowl.snomed.common.SnomedConstants.Concepts;
 import com.b2international.snowowl.snomed.common.SnomedRf2Headers;
-import com.b2international.snowowl.snomed.core.domain.Acceptability;
-import com.b2international.snowowl.snomed.core.domain.ConstantIdStrategy;
-import com.b2international.snowowl.snomed.core.domain.SnomedConcept;
-import com.b2international.snowowl.snomed.core.domain.SnomedConcepts;
-import com.b2international.snowowl.snomed.core.domain.SubclassDefinitionStatus;
+import com.b2international.snowowl.snomed.core.domain.*;
 import com.b2international.snowowl.snomed.core.domain.refset.SnomedRefSetType;
 import com.b2international.snowowl.snomed.core.store.SnomedComponents;
 import com.b2international.snowowl.snomed.datastore.SnomedRefSetUtil;
@@ -50,6 +39,9 @@
 import com.google.common.collect.ImmutableSet;
 import com.google.common.collect.Multiset;
 
+import jakarta.validation.constraints.NotNull;
+import jakarta.validation.constraints.Size;
+
 /**
  * @since 4.5
  */