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.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 void storeNewCodeSystemVersionIfNeeded(
  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 void storeNewCodeSystemVersionIfNeeded(
  }
  }
 
+ 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.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.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 @@ private IIdType createLargeCodeSystem(String theVersion) {
  return id;
  }
 
+ @Test
+ public void testCodeSystemWithDuplicateCode() {
+ CodeSystem cs = new CodeSystem();
+ cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+ cs.setUrl("http:https://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:https://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);