feat(rf2): validate and report incorrect non-sctids in container...

...component columns (eg. concept in case of a description file)
b2ihealthcare · May 1, 2024 · b297247 · b297247
1 parent 6c615e8
commit b297247
Show file tree

Hide file tree

Showing 4 changed files with 21 additions and 15 deletions.
diff --git a/...rnational/snowowl/snomed/datastore/request/rf2/importer/IgnoredRf2EffectiveTimeSlice.java b/...rnational/snowowl/snomed/datastore/request/rf2/importer/IgnoredRf2EffectiveTimeSlice.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2021 B2i Healthcare, https://b2ihealthcare.com
+ * Copyright 2021-2024 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.
@@ -45,7 +45,7 @@ public IgnoredRf2EffectiveTimeSlice(String effectiveTimeToIgnore, String message
 	}
 
 	@Override
-	public void register(String containerId, Rf2ContentType<?> type, String[] values, ImportDefectBuilder defectBuilder) {
+	public void register(long containerId, Rf2ContentType<?> type, String[] values, ImportDefectBuilder defectBuilder) {
 	}
 
 	@Override

diff --git a/...ternational/snowowl/snomed/datastore/request/rf2/importer/MapDBRf2EffectiveTimeSlice.java b/...ternational/snowowl/snomed/datastore/request/rf2/importer/MapDBRf2EffectiveTimeSlice.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2017-2023 B2i Healthcare, https://b2ihealthcare.com
+ * Copyright 2017-2024 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.
@@ -105,25 +105,24 @@ private <T extends SnomedComponent> T getComponent(String componentId) {
 	}
 
 	@Override
-	public void register(String containerId, Rf2ContentType<?> type, String[] values, ImportDefectBuilder defectBuilder) {
+	public void register(long containerId, Rf2ContentType<?> type, String[] values, ImportDefectBuilder defectBuilder) {
 
 		String[] valuesWithType = new String[values.length + 1];
 		valuesWithType[0] = type.getType();
 		System.arraycopy(values, 0, valuesWithType, 1, values.length);
 
 		final String componentId = values[0];
-		final long containerIdL = Long.parseLong(containerId);
 
 		// track refset members via membersByReferencedComponent map
 		if (Rf2RefSetContentType.class.isAssignableFrom(type.getClass())) {
-			if (!membersByReferencedComponent.containsKey(containerIdL)) {
-				membersByReferencedComponent.put(containerIdL, newHashSet());
+			if (!membersByReferencedComponent.containsKey(containerId)) {
+				membersByReferencedComponent.put(containerId, newHashSet());
 			}
-			membersByReferencedComponent.get(containerIdL).add(componentId);
+			membersByReferencedComponent.get(containerId).add(componentId);
 		} else {
 			// register other non-concept components in the dependency graph to force strongly connected subgraphs
-			if (!IComponent.ROOT_ID.equals(containerId)) {
-				registerDependencies(containerIdL, PrimitiveSets.newLongOpenHashSet(Long.parseLong(componentId)));
+			if (IComponent.ROOT_IDL != containerId) {
+				registerDependencies(containerId, PrimitiveSets.newLongOpenHashSet(Long.parseLong(componentId)));
 			}
 		}
 

diff --git a/...src/com/b2international/snowowl/snomed/datastore/request/rf2/importer/Rf2ContentType.java b/...src/com/b2international/snowowl/snomed/datastore/request/rf2/importer/Rf2ContentType.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2017-2021 B2i Healthcare, https://b2ihealthcare.com
+ * Copyright 2017-2024 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.
@@ -38,8 +38,15 @@ public interface Rf2ContentType<T extends SnomedComponent> {
 	default void register(String[] values, Rf2EffectiveTimeSlice slice, ImportDefectBuilder defectBuilder) {
 
 		final String containerId = getContainerId(values);
-		slice.register(containerId, this, values, defectBuilder);
-		slice.registerDependencies(getDependentComponentId(values), getDependencies(values));
+		try {
+			final long containerIdL = Long.parseLong(containerId);
+
+			slice.register(containerIdL, this, values, defectBuilder);
+			slice.registerDependencies(getDependentComponentId(values), getDependencies(values));
+		} catch (NumberFormatException e) {
+			defectBuilder.error("Non-SCTID (%s) present in container column of RF2 content type of '%s'", containerId, getType());
+			return;
+		}
 	}
 
 	default long getDependentComponentId(String[] values) {

diff --git a/.../b2international/snowowl/snomed/datastore/request/rf2/importer/Rf2EffectiveTimeSlice.java b/.../b2international/snowowl/snomed/datastore/request/rf2/importer/Rf2EffectiveTimeSlice.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2021-2023 B2i Healthcare, https://b2ihealthcare.com
+ * Copyright 2021-2024 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.
@@ -35,7 +35,7 @@ public interface Rf2EffectiveTimeSlice {
 
 	int BATCH_SIZE = 5000;
 
-	void register(String containerId, Rf2ContentType<?> type, String[] values, ImportDefectBuilder defectBuilder);
+	void register(long containerId, Rf2ContentType<?> type, String[] values, ImportDefectBuilder defectBuilder);
 
 	void registerDependencies(long componentId, LongSet dependencies);