Add error checker for duplicate codesystem codes (#6014)

* Add error checker

* Add changelog

* Address review comment

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6014-add-codesystem-dupe-code-checker.yaml

@@ -0,0 +1,7 @@
+---
+type: add
+issue: 6014
+title: "When uploading an invalid CodeSystem to the JPA server containing
+  duplicate codes, the server responded with an unhelpful error message
+  referring to a database constraint error. This has been fixed so that 
+  a more informative error message is returned."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java

@@ -50,8 +50,10 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.ObjectUtil;
+import ca.uhn.fhir.util.UrlUtil;
 import ca.uhn.fhir.util.ValidateUtil;
 import jakarta.annotation.Nonnull;
 import jakarta.persistence.EntityManager;
@@ -294,6 +296,8 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 						theResourceEntity.getIdDt().getValue(),
 						theCodeSystem.getContentElement().getValueAsString());
 
+				detectDuplicatesInCodeSystem(theCodeSystem);
+
 				Long pid = (Long) theCodeSystem.getUserData(RESOURCE_PID_KEY);
 				assert pid != null;
 				JpaPid codeSystemResourcePid = JpaPid.fromId(pid);
@@ -339,6 +343,30 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		}
 	}
 
+	private static void detectDuplicatesInCodeSystem(CodeSystem theCodeSystem) {
+		detectDuplicatesInCodeSystem(theCodeSystem.getConcept(), new HashSet<>());
+	}
+
+	private static void detectDuplicatesInCodeSystem(
+			List<CodeSystem.ConceptDefinitionComponent> theCodeList, Set<String> theFoundCodesBuffer) {
+		for (var next : theCodeList) {
+			if (isNotBlank(next.getCode())) {
+				if (!theFoundCodesBuffer.add(next.getCode())) {
+					/*
+					 * Note: We could possibly modify this behaviour to be forgiving, and just
+					 * ignore duplicates. The only issue is that concepts can have properties,
+					 * designations, etc. and it could be dangerous to just pick one and ignore the
+					 * other. So the safer thing seems to be to just throw an error.
+					 */
+					throw new PreconditionFailedException(Msg.code(2528) + "Duplicate concept detected in CodeSystem: "
+							+ UrlUtil.sanitizeUrlPart(next.getCode()));
+				}
+			}
+			// Test child concepts within the parent concept
+			detectDuplicatesInCodeSystem(next.getConcept(), theFoundCodesBuffer);
+		}
+	}
+
 	@Override
 	@Transactional
 	public IIdType storeNewCodeSystemVersion(

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java

@@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
 import ca.uhn.fhir.jpa.test.Batch2JobHelper;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.CodeSystem;
@@ -20,6 +21,7 @@ import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.fail;
 
 public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
 
@@ -191,6 +193,46 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
 		return id;
 	}
 
+	@Test
+	public void testCodeSystemWithDuplicateCode() {
+		CodeSystem cs = new CodeSystem();
+		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		cs.setUrl("http://foo");
+		cs.setVersion("1.0");
+		cs.addConcept().setCode("CODE0").setDisplay("Code0");
+		cs.addConcept().setCode("CODE1").setDisplay("Code1");
+		cs.addConcept().setCode("CODE1").setDisplay("Code1");
+		cs.addConcept().setCode("CODE2").setDisplay("Code2");
+
+		try {
+			myCodeSystemDao.create(cs, mySrd);
+			fail();
+		} catch (PreconditionFailedException e) {
+			assertThat(e.getMessage()).contains("Duplicate concept detected in CodeSystem: CODE1");
+		}
+	}
+
+	@Test
+	public void testCodeSystemWithDuplicateCodeInChild() {
+		CodeSystem cs = new CodeSystem();
+		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		cs.setUrl("http://foo");
+		cs.setVersion("1.0");
+
+		CodeSystem.ConceptDefinitionComponent parent = cs.addConcept().setCode("CODE0").setDisplay("Code0");
+		parent.addConcept().setCode("CODE1").setDisplay("Code1");
+		parent.addConcept().setCode("CODE1").setDisplay("Code1");
+		cs.addConcept().setCode("CODE2").setDisplay("Code2");
+
+		try {
+			myCodeSystemDao.create(cs, mySrd);
+			fail();
+		} catch (PreconditionFailedException e) {
+			assertThat(e.getMessage()).contains("Duplicate concept detected in CodeSystem: CODE1");
+		}
+	}
+
+
 	@AfterAll
 	public static void afterClassClearContext() {
 		TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);