Accurately reflect codesystem URL

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

@@ -1538,9 +1538,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 				codeSystem = new TermCodeSystem();
 			}
 			codeSystem.setResource(theCodeSystemVersion.getResource());
-			codeSystem.setCodeSystemUri(theSystemUri);
-			codeSystem.setName(theSystemName);
-			myCodeSystemDao.save(codeSystem);
 		} else {
 			if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemVersion.getResource().getId())) {
 				String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
@@ -1548,6 +1545,11 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 				throw new UnprocessableEntityException(msg);
 			}
 		}
+
+		codeSystem.setCodeSystemUri(theSystemUri);
+		codeSystem.setName(theSystemName);
+		codeSystem = myCodeSystemDao.save(codeSystem);
+
 		theCodeSystemVersion.setCodeSystem(codeSystem);
 
 		theCodeSystemVersion.setCodeSystemDisplayName(theSystemName);
@@ -1626,6 +1628,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.MANDATORY)
 	public void storeNewCodeSystemVersionIfNeeded(CodeSystem theCodeSystem, ResourceTable theResourceEntity) {
 		if (theCodeSystem != null && isNotBlank(theCodeSystem.getUrl())) {
 			String codeSystemUrl = theCodeSystem.getUrl();
@@ -1633,20 +1636,13 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 				ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", theResourceEntity.getIdDt().getValue(), theCodeSystem.getContentElement().getValueAsString());
 
 				Long codeSystemResourcePid = getCodeSystemResourcePid(theCodeSystem.getIdElement());
-				TermCodeSystemVersion persCs = myCodeSystemVersionDao.findCurrentVersionForCodeSystemResourcePid(codeSystemResourcePid);
+				TermCodeSystemVersion persCs = new TermCodeSystemVersion();
-				if (persCs != null) {
-					ourLog.info("Code system version already exists in database");
-				} else {
 
-					persCs = new TermCodeSystemVersion();
+				populateCodeSystemVersionProperties(persCs, theCodeSystem, theResourceEntity);
-					populateCodeSystemVersionProperties(persCs, theCodeSystem, theResourceEntity);
-
-					persCs.getConcepts().addAll(toPersistedConcepts(theCodeSystem.getConcept(), persCs));
-					ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
-					storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, theCodeSystem.getName(), theCodeSystem.getVersion(), persCs);
-
-				}
 
+				persCs.getConcepts().addAll(toPersistedConcepts(theCodeSystem.getConcept(), persCs));
+				ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
+				storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, theCodeSystem.getName(), theCodeSystem.getVersion(), persCs);
 			}
 		}
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java

@@ -612,6 +612,59 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
 		}
 	}
 
+	@Test
+	public void testExpandValueSetBasedOnCodeSystemWithChangedUrl() throws IOException {
+
+		CodeSystem cs = new CodeSystem();
+		cs.setId("CodeSystem/CS");
+		cs.setContent(CodeSystemContentMode.COMPLETE);
+		cs.setUrl("http://foo1");
+		cs.addConcept().setCode("foo1").setDisplay("foo1");
+		ourClient.update().resource(cs).execute();
+
+		ValueSet vs = new ValueSet();
+		vs.setId("ValueSet/VS179789");
+		vs.setUrl("http://bar");
+		vs.getCompose().addInclude().setSystem("http://foo1").addConcept().setCode("foo1");
+		ourClient.update().resource(vs).execute();
+
+		ValueSet expanded = ourClient
+			.operation()
+			.onInstance(new IdType("ValueSet/VS179789"))
+			.named("$expand")
+			.withNoParameters(Parameters.class)
+			.returnResourceType(ValueSet.class)
+				.execute();
+		ourLog.info("Expanded: {}",myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
+		assertEquals(1, expanded.getExpansion().getContains().size());
+
+		// Update the CodeSystem URL and Codes
+		cs = new CodeSystem();
+		cs.setId("CodeSystem/CS");
+		cs.setContent(CodeSystemContentMode.COMPLETE);
+		cs.setUrl("http://foo2");
+		cs.addConcept().setCode("foo2").setDisplay("foo2");
+		ourClient.update().resource(cs).execute();
+
+		vs = new ValueSet();
+		vs.setId("ValueSet/VS179789");
+		vs.setUrl("http://bar");
+		vs.getCompose().addInclude().setSystem("http://foo2").addConcept().setCode("foo2");
+		ourClient.update().resource(vs).execute();
+
+		expanded = ourClient
+			.operation()
+			.onInstance(new IdType("ValueSet/VS179789"))
+			.named("$expand")
+			.withNoParameters(Parameters.class)
+			.returnResourceType(ValueSet.class)
+			.execute();
+		ourLog.info("Expanded: {}",myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
+		assertEquals(1, expanded.getExpansion().getContains().size());
+	}
+
+
+
 	/**
 	 * #516
 	 */

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/ValidationSupportChain.java

@@ -49,7 +49,9 @@ public class ValidationSupportChain implements IValidationSupport {
 	@Override
 	public ValueSetExpander.ValueSetExpansionOutcome expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
 		for (IValidationSupport next : myChain) {
-			if (next.isCodeSystemSupported(theCtx, theInclude.getSystem())) {
+			boolean codeSystemSupported = next.isCodeSystemSupported(theCtx, theInclude.getSystem());
+			ourLog.trace("Support {} supports: {}", next, codeSystemSupported);
+			if (codeSystemSupported) {
 				ValueSetExpander.ValueSetExpansionOutcome expansion = next.expandValueSet(theCtx, theInclude);
 				if (expansion != null) {
 					return expansion;
@@ -57,7 +59,7 @@ public class ValidationSupportChain implements IValidationSupport {
 			}
 		}
 
-		throw new InvalidRequestException("unable to find code system " + theInclude.getSystem());
+		throw new InvalidRequestException("Unable to find code system " + theInclude.getSystem());
 	}
 
 	@Override

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/QuestionnaireResponseValidatorR4Test.java

@@ -633,6 +633,57 @@ public class QuestionnaireResponseValidatorR4Test {
 
 	}
 
+
+	@Test
+	public void testOpenchoiceAnswerWithOptions() {
+		String questionnaireRef = "http://example.com/Questionnaire/q1";
+
+		List<Questionnaire.QuestionnaireItemAnswerOptionComponent> options = new ArrayList<>();
+		options.add(new Questionnaire.QuestionnaireItemAnswerOptionComponent().setValue(new Coding("http://foo", "foo", "FOOOO")));
+		options.add(new Questionnaire.QuestionnaireItemAnswerOptionComponent().setValue(new Coding("http://bar", "bar", "FOOOO")));
+
+		Questionnaire q = new Questionnaire();
+		QuestionnaireItemComponent item = q.addItem();
+		item.setLinkId("link0")
+			.setRequired(true)
+			.setType(QuestionnaireItemType.OPENCHOICE)
+			.setAnswerOption(options);
+		when(myValSupport.fetchResource(any(FhirContext.class), eq(Questionnaire.class), eq(questionnaireRef))).thenReturn(q);
+
+		QuestionnaireResponse qa;
+		ValidationResult errors;
+
+		qa = new QuestionnaireResponse();
+		qa.getText().setDiv(new XhtmlNode().setValue("<div>AA</div>")).setStatus(Narrative.NarrativeStatus.GENERATED);
+		qa.setStatus(QuestionnaireResponseStatus.COMPLETED);
+		qa.getQuestionnaireElement().setValue(questionnaireRef);
+		qa.addItem().setLinkId("link0").addAnswer().setValue(new Coding().setSystem("http://foo").setCode("foo"));
+		errors = myVal.validateWithResult(qa);
+		ourLog.info(errors.toString());
+		assertEquals(true, errors.isSuccessful());
+
+		qa = new QuestionnaireResponse();
+		qa.getText().setDiv(new XhtmlNode().setValue("<div>AA</div>")).setStatus(Narrative.NarrativeStatus.GENERATED);
+		qa.setStatus(QuestionnaireResponseStatus.COMPLETED);
+		qa.getQuestionnaireElement().setValue(questionnaireRef);
+		qa.addItem().setLinkId("link0").addAnswer().setValue(new StringType("Hello"));
+		errors = myVal.validateWithResult(qa);
+		ourLog.info(errors.toString());
+		assertEquals(true, errors.isSuccessful());
+
+		qa = new QuestionnaireResponse();
+		qa.getText().setDiv(new XhtmlNode().setValue("<div>AA</div>")).setStatus(Narrative.NarrativeStatus.GENERATED);
+		qa.setStatus(QuestionnaireResponseStatus.COMPLETED);
+		qa.getQuestionnaireElement().setValue(questionnaireRef);
+		qa.addItem().setLinkId("link0").addAnswer().setValue(new Coding().setSystem("http://foo").setCode("hello"));
+		errors = myVal.validateWithResult(qa);
+		ourLog.info(errors.toString());
+		// This is set in InstanceValidator#validateAnswerCode
+		assertEquals(false, errors.isSuccessful());
+
+	}
+
+
 	@Test
 	public void testUnexpectedAnswer() {
 		Questionnaire q = new Questionnaire();

src/changes/changes.xml

@@ -137,6 +137,11 @@
 				Fix a failure in FhirTerser#visit when fields in model classes being visited contain custom subclasses of the
 				expected type.
 			</action>
+			<action type="fix">
+				Updating an existing CodeSystem resource with a content mode of COMPLETE did not cause the
+				terminology service to accurately reflect the new CodeSystem URL and/or concepts. This is now
+				corrected.
+			</action>
 		</release>
 		<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
 			<action type="fix">