3164 updating code review points (#3165)

* 3164 updating code review points

* 3164 updating code review points

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3153-updating-unknowncodesystem-to-allow-warnings-to-be-registered-as-warnings.yaml

@@ -1,5 +1,6 @@
 ---
 type: fix
 issue: 3153
+jira: SMILE-3289
 title: "Updated UnknownCodeSystemWarningValidationSupport to allow the throwing of warnings if
 configured to do so."

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -161,6 +161,20 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 	}
 
+	private Observation createObservationForUnknownCodeSystemTest() {
+		Observation obs = new Observation();
+		obs.getMeta().addProfile("http://sd");
+		obs.getText().setDivAsString("<div>Hello</div>");
+		obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
+		obs.getCategoryFirstRep().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs");
+		obs.getCode().setText("hello");
+		obs.setSubject(new Reference("Patient/123"));
+		obs.addPerformer(new Reference("Practitioner/123"));
+		obs.setEffective(DateTimeType.now());
+		obs.setStatus(ObservationStatus.FINAL);
+		return obs;
+	}
+
 	/**
 	 * By default, an unknown code system should fail validation
 	 */
@@ -171,6 +185,32 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 		createStructureDefWithBindingToUnknownCs();
 
+		Observation obs = createObservationForUnknownCodeSystemTest();
+
+		OperationOutcome oo;
+		String encoded;
+
+		// Valid code
+		obs.setValue(new Quantity().setSystem("http://cs").setCode("code1").setValue(123));
+		oo = validateAndReturnOutcome(obs);
+		encoded = encode(oo);
+		ourLog.info(encoded);
+		assertTrue(oo.getIssueFirstRep().getDiagnostics().contains("No issues detected during validation"));
+
+		// Invalid code
+		obs.setValue(new Quantity().setSystem("http://cs").setCode("code99").setValue(123));
+		oo = validateAndReturnOutcome(obs);
+		encoded = encode(oo);
+		ourLog.info(encoded);
+		assertTrue(oo.getIssueFirstRep().getDiagnostics().contains("No issues detected during validation"));
+	}
+
+	@Test
+	public void testValidateCodeInValueSetWithUnknownCodeSystem_Error() {
+		myUnknownCodeSystemWarningValidationSupport.setNonExistentCodeSystemSeverity(IValidationSupport.IssueSeverity.ERROR);
+
+		createStructureDefWithBindingToUnknownCs();
+
 		Observation obs = new Observation();
 		obs.getMeta().addProfile("http://sd");
 		obs.getText().setDivAsString("<div>Hello</div>");
@@ -192,13 +232,15 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		ourLog.info(encoded);
 		assertTrue(oo.getIssueFirstRep().getDiagnostics().contains("No issues detected during validation"));
 
+
 		// Invalid code
 		obs.setValue(new Quantity().setSystem("http://cs").setCode("code99").setValue(123));
 		oo = validateAndReturnOutcome(obs);
 		encoded = encode(oo);
 		ourLog.info(encoded);
-		assertTrue(oo.getIssueFirstRep().getDiagnostics().contains("No issues detected during validation"));
+		assertTrue(oo.getIssueFirstRep()
-
+			.getDiagnostics().contains("The code provided (http://cs#code99) is not in the value set http://vs, and a code from this value set is required: Unknown code 'http://cs#code99' for in-memory expansion of ValueSet 'http://vs'")
+		);
 	}
 
 	public void createStructureDefWithBindingToUnknownCs() {

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/UnknownCodeSystemWarningValidationSupport.java

@@ -45,12 +45,15 @@ public class UnknownCodeSystemWarningValidationSupport extends BaseValidationSup
 	@Override
 	public CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
 		// filters out error/fatal
+		// NB: this is a secondary check. isCodeSystemSupported
+		// should prevent this from ever calling validate code here
+		// ... but should it ever get called, we'll return null
 		if (!canValidateCodeSystem(theValidationSupportContext, theCodeSystem)) {
 			return null;
 		}
 
 		CodeValidationResult result = new CodeValidationResult()
-			.setSeverity(myNonExistentCodeSystemSeverity); // will be warning or info
+			.setSeverity(myNonExistentCodeSystemSeverity); // will be warning or info (error/fatal filtered out above)
 
 		result.setMessage("No issues detected during validation");
 
@@ -89,15 +92,22 @@ public class UnknownCodeSystemWarningValidationSupport extends BaseValidationSup
 			case ERROR:
 			case FATAL:
 				return false;
+			case WARNING:
+			case INFORMATION:
+				return true;
 			default:
 				ourLog.info("Unknown issue severity " + myNonExistentCodeSystemSeverity.name()
 					+ ". Treating as INFO/WARNING");
-			case WARNING:
-			case INFORMATION:
 				return true;
 		}
 	}
 
+	/**
+	 * Determines if the code system can (and should) be validated.
+	 * @param theValidationSupportContext
+	 * @param theCodeSystem
+	 * @return
+	 */
 	private boolean canValidateCodeSystem(ValidationSupportContext theValidationSupportContext,
 													  String theCodeSystem) {
 		if (!allowNonExistentCodeSystems()) {