Preserve contained resource meta when encoding to dao (#1311)

* Preserve contained resource meta when encoding with: parser.setDontEncodeElements(ResourceMetaParams.EXCLUDE_ELEMENTS_IN_ENCODED)

* - Correct so security, lastUpdated and versionId is not encoded
- Added test

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java

@@ -47,6 +47,8 @@ public abstract class BaseParser implements IParser {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
 
+	private static final Set<String> notEncodeForContainedResource = new HashSet<>(Arrays.asList("security", "versionId", "lastUpdated"));
+
 	private ContainedResources myContainedResources;
 	private boolean myEncodeElementsAppliesToChildResourcesOnly;
 	private FhirContext myContext;
@@ -161,7 +163,7 @@ public abstract class BaseParser implements IParser {
 							 */
 							if (myNext.getDef().getElementName().equals("id")) {
 								myNext = null;
-							} else if (!myNext.shouldBeEncoded()) {
+							} else if (!myNext.shouldBeEncoded(theContainedResource)) {
 								myNext = null;
 							} else if (isSummaryMode() && !myNext.getDef().isSummary()) {
 								myNext = null;
@@ -176,7 +178,6 @@ public abstract class BaseParser implements IParser {
 									myNext = null;
 								}
 							}
-
 						} while (myNext == null);
 
 						myHasNext = true;
@@ -1157,7 +1158,7 @@ public abstract class BaseParser implements IParser {
 			return myParent;
 		}
 
-		public boolean shouldBeEncoded() {
+		public boolean shouldBeEncoded(boolean theContainedResource) {
 			boolean retVal = true;
 			if (myEncodeElements != null) {
 				retVal = checkIfParentShouldBeEncodedAndBuildPath();
@@ -1165,6 +1166,9 @@ public abstract class BaseParser implements IParser {
 			if (retVal && myDontEncodeElements != null) {
 				retVal = !checkIfParentShouldNotBeEncodedAndBuildPath();
 			}
+			if (theContainedResource) {
+				retVal = !notEncodeForContainedResource.contains(myDef.getElementName());
+			}
 
 			return retVal;
 		}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java

@@ -24,8 +24,8 @@ import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.Bundle.BundleType;
 import org.hl7.fhir.dstu3.model.CapabilityStatement.UnknownContentCode;
-import org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus;
 import org.hl7.fhir.dstu3.model.Enumeration;
+import org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus;
 import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse;
 import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
@@ -48,6 +48,7 @@ import static org.junit.Assert.*;
 import static org.mockito.Matchers.any;
 import static org.mockito.Matchers.eq;
 import static org.mockito.Matchers.isNull;
+import static org.mockito.Mockito.nullable;
 import static org.mockito.Mockito.*;
 
 public class JsonParserDstu3Test {
@@ -2384,6 +2385,45 @@ public class JsonParserDstu3Test {
 		assertTrue(result.isSuccessful());
 	}
 
+	@Test
+	public void encodeResourceToString_withEXCLUDE_ELEMENTS_IN_ENCODED_metaKeptInContainedResource() {
+		// Arrange
+		Organization containedOrganization = new Organization();
+		containedOrganization.getMeta().addProfile(UUID.randomUUID().toString());
+		containedOrganization.getMeta().setLastUpdated(new Date());
+		containedOrganization.getMeta().setVersionId(UUID.randomUUID().toString());
+		containedOrganization.getMeta().setSecurity(Arrays.asList(new Coding(UUID.randomUUID().toString(), UUID.randomUUID().toString(), UUID.randomUUID().toString())));
+		containedOrganization.getMeta().setTag(Arrays.asList(new Coding(UUID.randomUUID().toString(), UUID.randomUUID().toString(), UUID.randomUUID().toString())));
+
+		Patient patient = new Patient();
+		patient.setId(UUID.randomUUID().toString());
+		patient.getMeta().addProfile(UUID.randomUUID().toString());
+		patient.setGeneralPractitioner(Arrays.asList(new Reference(containedOrganization)));
+
+		HashSet<String> excludeElementsInEncoded = new HashSet<>(); // ResourceMetaParams.EXCLUDE_ELEMENTS_IN_ENCODED
+		excludeElementsInEncoded.add("id");
+		excludeElementsInEncoded.add("*.meta");
+
+		IParser parser = ourCtx.newJsonParser();
+		parser.setDontEncodeElements(excludeElementsInEncoded);
+
+		// Act
+		String encodedPatient = parser.encodeResourceToString(patient);
+
+		// Assert
+		Patient parsedPatient = (Patient) parser.parseResource(encodedPatient);
+		assertNull(parsedPatient.getId());
+		assertTrue(parsedPatient.getMeta().isEmpty());
+
+		Resource containedResource = parsedPatient.getContained().get(0);
+		assertNotNull(containedResource.getMeta());
+		assertNull(containedResource.getMeta().getVersionId());
+		assertNull(containedResource.getMeta().getLastUpdated());
+		assertTrue(containedResource.getMeta().getSecurity().isEmpty());
+		assertEquals(1, containedResource.getMeta().getProfile().size());
+		assertEquals(1, containedResource.getMeta().getTag().size());
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();