Fix validation issue

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/validation/DefaultProfileValidationSupport.java

@@ -223,14 +223,32 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
 		CodeSystem cs = fetchCodeSystem(theContext, theCodeSystem);
 		if (cs != null) {
-			for (ConceptDefinitionComponent next : cs.getConcept()) {
+			CodeValidationResult retVal = testIfConceptIsInList(theCode, cs.getConcept());
-				if (next.getCode().equals(theCode)) {
+			
-					return new CodeValidationResult(next);
+			if (retVal != null) {
-				}
+				return retVal;
 			}
 		}
 
 		return new CodeValidationResult(IssueSeverity.INFORMATION, "Unknown code: " + theCodeSystem + " / " + theCode);
 	}
 
+	private CodeValidationResult testIfConceptIsInList(String theCode, List<ConceptDefinitionComponent> conceptList) {
+		CodeValidationResult retVal = null;
+		for (ConceptDefinitionComponent next : conceptList) {
+			if (next.getCode().equals(theCode)) {
+				retVal = new CodeValidationResult(next);
+				break;
+			}
+
+			// recurse
+			retVal = testIfConceptIsInList(theCode, next.getConcept());
+			if (retVal != null) {
+				break;
+			}
+		}
+		
+		return retVal;
+	}
+
 }

hapi-fhir-structures-dstu3/src/test/java/org/hl7/fhir/dstu3/hapi/validation/ResourceValidatorDstu3Test.java

@@ -6,10 +6,12 @@ import static org.hamcrest.Matchers.stringContainsInOrder;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 
+import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.Condition;
@@ -35,61 +37,58 @@ public class ResourceValidatorDstu3Test {
 
 	private static FhirContext ourCtx = FhirContext.forDstu3();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceValidatorDstu3Test.class);
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
-	
 	/**
-	 * Make sure that the elements that appear in all resources (meta, language, extension, etc)
+	 * Make sure that the elements that appear in all resources (meta, language, extension, etc) all appear in the correct order
-	 * all appear in the correct order
 	 */
 	@Test
 	public void testValidateResourceWithResourceElements() {
 
-      XmlParserDstu3Test.TestPatientFor327 patient = new XmlParserDstu3Test.TestPatientFor327();
+		XmlParserDstu3Test.TestPatientFor327 patient = new XmlParserDstu3Test.TestPatientFor327();
-      patient.setBirthDate(new Date());
+		patient.setBirthDate(new Date());
-      patient.setId("123");
+		patient.setId("123");
-      patient.getText().setDivAsString("<div>FOO</div>");
+		patient.getText().setDivAsString("<div>FOO</div>");
-      patient.getText().setStatus(NarrativeStatus.GENERATED);
+		patient.getText().setStatus(NarrativeStatus.GENERATED);
-      patient.getLanguageElement().setValue("en");
+		patient.getLanguageElement().setValue("en");
-      patient.addExtension().setUrl("http://foo").setValue(new StringType("MOD"));
+		patient.addExtension().setUrl("http://foo").setValue(new StringType("MOD"));
-      patient.getMeta().setLastUpdated(new Date());
+		patient.getMeta().setLastUpdated(new Date());
 
-      List<Reference> conditions = new ArrayList<Reference>();
+		List<Reference> conditions = new ArrayList<Reference>();
-      Condition condition = new Condition();
+		Condition condition = new Condition();
-      condition.getPatient().setReference("Patient/123");
+		condition.getPatient().setReference("Patient/123");
-      condition.addBodySite().setText("BODY SITE");
+		condition.addBodySite().setText("BODY SITE");
-      condition.getCode().setText("CODE");
+		condition.getCode().setText("CODE");
-      condition.setVerificationStatus(ConditionVerificationStatus.CONFIRMED);
+		condition.setVerificationStatus(ConditionVerificationStatus.CONFIRMED);
 		conditions.add(new Reference(condition));
-      patient.setCondition(conditions);
+		patient.setCondition(conditions);
-      patient.addIdentifier().setSystem("http://foo").setValue("123");
+		patient.addIdentifier().setSystem("http://foo").setValue("123");
-      
+
-      String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
 		ourLog.info(encoded);
 
 		FhirValidator val = ourCtx.newValidator();
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
 		val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
 		val.registerValidatorModule(new FhirInstanceValidator());
-        
+
 		ValidationResult result = val.validateWithResult(encoded);
-		
+
 		OperationOutcome operationOutcome = (OperationOutcome) result.toOperationOutcome();
 		String ooencoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(operationOutcome);
 		ourLog.info(ooencoded);
 
 		assertTrue(result.isSuccessful());
-		
+
 		assertThat(ooencoded, containsString("No issues"));
 	}
 
 	/**
-	 * See
+	 * See https://groups.google.com/d/msgid/hapi-fhir/a266083f-6454-4cf0-a431-c6500f052bea%40googlegroups.com?utm_medium= email&utm_source=footer
-	 * https://groups.google.com/d/msgid/hapi-fhir/a266083f-6454-4cf0-a431-c6500f052bea%40googlegroups.com?utm_medium=
-	 * email&utm_source=footer
 	 */
 	@Test
 	public void testValidateWithExtensionsXml() {
@@ -104,7 +103,7 @@ public class ResourceValidatorDstu3Test {
 		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
 		String messageString = p.encodeResourceToString(myPatient);
 		ourLog.info(messageString);
-		
+
 		//@formatter:off
 		assertThat(messageString, stringContainsInOrder(
 			"meta",
@@ -121,12 +120,12 @@ public class ResourceValidatorDstu3Test {
 		assertThat(messageString, containsString("url=\"http://ahr.copa.inso.tuwien.ac.at/StructureDefinition/Patient#animal-colorSecondary\""));
 		assertThat(messageString, containsString("url=\"http://foo.com/example\""));
 		//@formatter:on
-		
+
 		FhirValidator val = ourCtx.newValidator();
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
 		val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
 		val.registerValidatorModule(new FhirInstanceValidator());
-        
+
 		ValidationResult result = val.validateWithResult(messageString);
 
 		OperationOutcome operationOutcome = (OperationOutcome) result.toOperationOutcome();
@@ -134,15 +133,32 @@ public class ResourceValidatorDstu3Test {
 		ourLog.info(encoded);
 
 		assertTrue(result.isSuccessful());
-		
+
 		assertThat(messageString, containsString("valueReference"));
 		assertThat(messageString, not(containsString("valueResource")));
 	}
 
 	/**
-	 * See
+	 * Per email from Jon Zammit
-	 * https://groups.google.com/d/msgid/hapi-fhir/a266083f-6454-4cf0-a431-c6500f052bea%40googlegroups.com?utm_medium=
+	 */
-	 * email&utm_source=footer
+	@Test
+	public void testValidateQuestionnaire() throws IOException {
+		String input = IOUtils.toString(getClass().getResourceAsStream("/questionnaire_jon_z_20160506.xml"));
+
+		FhirValidator val = ourCtx.newValidator();
+		val.registerValidatorModule(new FhirInstanceValidator());
+
+		ValidationResult result = val.validateWithResult(input);
+
+		OperationOutcome operationOutcome = (OperationOutcome) result.toOperationOutcome();
+		String ooencoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(operationOutcome);
+		ourLog.info(ooencoded);
+
+		assertTrue(result.isSuccessful());
+	}
+
+	/**
+	 * See https://groups.google.com/d/msgid/hapi-fhir/a266083f-6454-4cf0-a431-c6500f052bea%40googlegroups.com?utm_medium= email&utm_source=footer
 	 */
 	@Test
 	public void testValidateWithExtensionsJson() {
@@ -177,7 +193,7 @@ public class ResourceValidatorDstu3Test {
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
 		val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
 		val.registerValidatorModule(new FhirInstanceValidator());
-        
+
 		ValidationResult result = val.validateWithResult(messageString);
 
 		OperationOutcome operationOutcome = (OperationOutcome) result.toOperationOutcome();
@@ -185,7 +201,7 @@ public class ResourceValidatorDstu3Test {
 		ourLog.info(encoded);
 
 		assertTrue(result.isSuccessful());
-		
+
 		assertThat(messageString, containsString("valueReference"));
 		assertThat(messageString, not(containsString("valueResource")));
 	}

src/changes/changes.xml

@@ -107,6 +107,12 @@
 				Properly handle null arrays when parsing JSON resources. Thanks to Subhro for
 				fixing this and providing a pull request!
 			</action>
+			<action type="fix">
+				STU3 validator failed to validate codes where the
+				code was a child code within the code system that contained it
+				(i.e. not a top level code). Thanks to Jon
+				Zammit for reporting!
+			</action>
 		</release>
 		<release version="1.5" date="2016-04-20">
 			<action type="fix" issue="339">