Add mode to parser to force it to not encode certain elements when serializing

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

@@ -91,6 +91,10 @@ public abstract class BaseParser implements IParser {
 	private boolean mySummaryMode;
 	private boolean mySuppressNarratives;
 
+	private Set<String> myDontEncodeElements;
+
+	private boolean myDontEncodeElementsIncludesStars;
+
 	/**
 	 * Constructor
 	 * 
@@ -605,6 +609,21 @@ public abstract class BaseParser implements IParser {
 		return theValues;
 	}
 
+	@Override
+	public void setDontEncodeElements(Set<String> theDontEncodeElements) {
+		myDontEncodeElementsIncludesStars = false;
+		if (theDontEncodeElements == null || theDontEncodeElements.isEmpty()) {
+			myDontEncodeElements = null;
+		} else {
+			myDontEncodeElements = theDontEncodeElements;
+			for (String next : theDontEncodeElements) {
+				if (next.startsWith("*.")) {
+					myDontEncodeElementsIncludesStars = true;
+				}
+			}
+		}
+	}
+
 	@Override
 	public void setEncodeElements(Set<String> theEncodeElements) {
 		myEncodeElementsIncludesStars = false;
@@ -676,6 +695,38 @@ public abstract class BaseParser implements IParser {
 		return isSummaryMode() || isSuppressNarratives();
 	}
 
+	protected boolean shouldEncodeResourceId(IBaseResource theResource) {
+		boolean retVal = true;
+		if (isOmitResourceId()) {
+			retVal = false;
+		} else {
+			if (myDontEncodeElements != null) {
+				String resourceName = myContext.getResourceDefinition(theResource).getName();
+				if (myDontEncodeElements.contains(resourceName + ".id")) {
+					retVal = false;
+				} else if (myDontEncodeElements.contains("*.id")) {
+					retVal = false;
+				}
+			}
+		}
+		return retVal;
+	}
+
+	/**
+	 * Used for DSTU2 only
+	 */
+	protected boolean shouldEncodeResourceMeta(IResource theResource) {
+		if (myDontEncodeElements != null) {
+			String resourceName = myContext.getResourceDefinition(theResource).getName();
+			if (myDontEncodeElements.contains(resourceName + ".meta")) {
+				return false;
+			} else if (myDontEncodeElements.contains("*.meta")) {
+				return false;
+			}
+		}
+		return true;
+	}
+
 	private String subsetDescription() {
 		return "Resource encoded in summary mode";
 	}
@@ -770,32 +821,46 @@ public abstract class BaseParser implements IParser {
 			}
 		}
 
-		private boolean checkIfParentShouldBeEncodedAndBuildPath(StringBuilder theB, boolean theStarPass) {
+		private boolean checkIfParentShouldBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
+			return checkIfPathMatches(thePathBuilder, theStarPass, myEncodeElementsAppliesToResourceTypes, myEncodeElements, true);
+		}
+
+		private boolean checkIfParentShouldNotBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
+			return checkIfPathMatches(thePathBuilder, theStarPass, null, myDontEncodeElements, false);
+		}
+
+		private boolean checkIfPathMatches(StringBuilder thePathBuilder, boolean theStarPass, Set<String> theResourceTypes, Set<String> theElements, boolean theCheckingForWhitelist) {
 			if (myResDef != null) {
-				if (myEncodeElementsAppliesToResourceTypes != null) {
+				if (theResourceTypes != null) {
-					if (!myEncodeElementsAppliesToResourceTypes.contains(myResDef.getName())) {
+					if (!theResourceTypes.contains(myResDef.getName())) {
 						return true;
 					}
 				}
 				if (theStarPass) {
-					theB.append('*');
+					thePathBuilder.append('*');
 				} else {
-					theB.append(myResDef.getName());
+					thePathBuilder.append(myResDef.getName());
 				}
-				if (myEncodeElements.contains(theB.toString())) {
+				if (theElements.contains(thePathBuilder.toString())) {
 					return true;
 				} else {
 					return false;
 				}
 			} else if (myParent != null) {
-				if (myParent.checkIfParentShouldBeEncodedAndBuildPath(theB, theStarPass)) {
+				boolean parentCheck;
+				if (theCheckingForWhitelist) {
+					parentCheck = myParent.checkIfParentShouldBeEncodedAndBuildPath(thePathBuilder, theStarPass);
+				} else {
+					parentCheck = myParent.checkIfParentShouldNotBeEncodedAndBuildPath(thePathBuilder, theStarPass);
+				}
+				if (parentCheck) {
 					return true;
 				}
 
 				if (myDef != null) {
-					theB.append('.');
+					thePathBuilder.append('.');
-					theB.append(myDef.getElementName());
+					thePathBuilder.append(myDef.getElementName());
-					return myEncodeElements.contains(theB.toString());
+					return theElements.contains(thePathBuilder.toString());
 				}
 			}
 
@@ -815,13 +880,19 @@ public abstract class BaseParser implements IParser {
 		}
 
 		public boolean shouldBeEncoded() {
-			if (myEncodeElements == null) {
+			boolean retVal = true;
-				return true;
+			if (myEncodeElements != null) {
-			}
+				retVal = checkIfParentShouldBeEncodedAndBuildPath(new StringBuilder(), false);
-			boolean retVal = checkIfParentShouldBeEncodedAndBuildPath(new StringBuilder(), false);
 				if (retVal == false && myEncodeElementsIncludesStars) {
 					retVal = checkIfParentShouldBeEncodedAndBuildPath(new StringBuilder(), true);
 				}
+			}
+			if (retVal && myDontEncodeElements != null) {
+				retVal = !checkIfParentShouldNotBeEncodedAndBuildPath(new StringBuilder(), false);
+				if (retVal && myDontEncodeElementsIncludesStars) {
+					retVal = !checkIfParentShouldNotBeEncodedAndBuildPath(new StringBuilder(), true);
+				}
+			}
 			return retVal;
 		}
 	}

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

@@ -215,18 +215,41 @@ public interface IParser {
 	 */
 	TagList parseTagList(String theString);
 
+	/**
+	 * If provided, specifies the elements which should NOT be encoded. Valid values for this
+	 * field would include:
+	 * <ul>
+	 * <li><b>Patient</b> - Don't encode patient and all its children</li>
+	 * <li><b>Patient.name</b> - Don't encode the patient's name</li>
+	 * <li><b>Patient.name.family</b> - Don't encode the patient's family name</li>
+	 * <li><b>*.text</b> - Don't encode the text element on any resource (only the very first position may contain a wildcard)</li>
+	 * </ul>
+	 * <p>
+	 * DSTU2 note: Note that values including meta, such as <code>Patient.meta</code>
+	 * will work for DSTU2 parsers, but values with subelements on meta such
+	 * as <code>Patient.meta.lastUpdated</code> will only work in 
+	 * DSTU3+ mode.
+	 * </p>
+	 * 
+	 * @param theDontEncodeElements
+	 *           The elements to encode
+	 * @see #setEncodeElements(Set)
+	 */
+	void setDontEncodeElements(Set<String> theDontEncodeElements);
+
 	/**
 	 * If provided, specifies the elements which should be encoded, to the exclusion of all others. Valid values for this
 	 * field would include:
 	 * <ul>
 	 * <li><b>Patient</b> - Encode patient and all its children</li>
-	 * <li><b>Patient.name</b> - Encoding only the patient's name</li>
+	 * <li><b>Patient.name</b> - Encode only the patient's name</li>
 	 * <li><b>Patient.name.family</b> - Encode only the patient's family name</li>
 	 * <li><b>*.text</b> - Encode the text element on any resource (only the very first position may contain a wildcard)</li>
 	 * </ul>
 	 * 
 	 * @param theEncodeElements
 	 *           The elements to encode
+	 * @see #setDontEncodeElements(Set)
 	 */
 	void setEncodeElements(Set<String> theEncodeElements);
 

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

@@ -800,7 +800,7 @@ public class JsonParser extends BaseParser implements IParser {
 		}
 
 		if (!theContainedResource) {
-			if (isOmitResourceId()) {
+			if (super.shouldEncodeResourceId(theResource) == false) {
 				resourceId = null;
 			} else if (getEncodeForceResourceId() != null) {
 				resourceId = getEncodeForceResourceId();
@@ -847,7 +847,7 @@ public class JsonParser extends BaseParser implements IParser {
 				versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
 			}
 
-			if (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) {
+			if (super.shouldEncodeResourceMeta(resource) && ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) {
 				theEventWriter.writeStartObject("meta");
 				writeOptionalTagWithTextNode(theEventWriter, "versionId", versionIdPart);
 				writeOptionalTagWithTextNode(theEventWriter, "lastUpdated", updated);

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

@@ -787,7 +787,7 @@ public class XmlParser extends BaseParser implements IParser {
 		}
 
 		if (!theIncludedResource) {
-			if (isOmitResourceId()) {
+			if (super.shouldEncodeResourceId(theResource) == false) {
 				resourceId = null;
 			} else if (getEncodeForceResourceId() != null) {
 				resourceId = getEncodeForceResourceId();
@@ -844,7 +844,7 @@ public class XmlParser extends BaseParser implements IParser {
 				List<IdDt> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
 				TagList tags = getMetaTagsForEncoding((resource));
 
-				if (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) {
+				if (super.shouldEncodeResourceMeta(resource) && ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) {
 					theEventWriter.writeStartElement("meta");
 					writeOptionalTagWithValue(theEventWriter, "versionId", versionIdPart);
 					if (updated != null) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java

@@ -68,6 +68,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
 
+import com.google.common.base.Charsets;
 import com.google.common.collect.ArrayListMultimap;
 
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
@@ -720,18 +721,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		ResourceEncodingEnum encoding = myConfig.getResourceEncoding();
 		theEntity.setEncoding(encoding);
 		theEntity.setFhirVersion(myContext.getVersion().getVersion());
-		try {
 		switch (encoding) {
 		case JSON:
-				theEntity.setResource(encoded.getBytes("UTF-8"));
+			theEntity.setResource(encoded.getBytes(Charsets.UTF_8));
 			break;
 		case JSONC:
 			theEntity.setResource(GZipUtil.compress(encoded));
 			break;
 		}
-		} catch (UnsupportedEncodingException e) {
-			throw new InternalErrorException(e);
-		}
 
 		Set<TagDefinition> allDefs = new HashSet<TagDefinition>();
 
@@ -1119,16 +1116,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			theEntity.setPublished(theUpdateTime);
 		}
 
-//		if (theUpdateHistory) {
-//			Long existingId = theEntity.getId();
-//			ResourceHistoryTable existingHistory = existingId != null ? myResourceHistoryTableDao.findForIdAndVersion(existingId, theEntity.getVersion()) : null;
-//			final ResourceHistoryTable historyEntry = theEntity.toHistory(existingHistory);
-//
-//			ourLog.info("Saving history entry for update {}", historyEntry.getIdDt());
-//			myResourceHistoryTableDao.save(historyEntry);
-//
-//		}
-
 		if (theUpdateVersion) {
 			theEntity.setVersion(theEntity.getVersion() + 1);
 		}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UpdateTest.java

@@ -31,6 +31,7 @@ import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.dstu3.model.UriType;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.mockito.ArgumentCaptor;
 
@@ -277,6 +278,25 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
 
 	}
 
+	@Test
+	@Ignore
+	public void testUpdateIgnoresIdenticalVersions() throws InterruptedException {
+		String methodName = "testUpdateIgnoresIdenticalVersions";
+		
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p1.addName().addFamily("Tester").addGiven(methodName);
+		IIdType p1id = myPatientDao.create(p1, new ServletRequestDetails()).getId();
+
+		IIdType p1id2 = myPatientDao.update(p1, mySrd).getId();
+		assertEquals(p1id.getValue(), p1id2.getValue());
+		
+		p1.addName().addGiven("NewGiven");
+		IIdType p1id3 = myPatientDao.update(p1, mySrd).getId();
+		assertNotEquals(p1id.getValue(), p1id3.getValue());
+		
+	}
+
 	@Test
 	public void testDuplicateProfilesIgnored() {
 		String name = "testDuplicateProfilesIgnored";

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java

@@ -16,6 +16,8 @@ import static org.mockito.Mockito.verify;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
 import java.util.List;
 import java.util.UUID;
 
@@ -27,6 +29,8 @@ import org.mockito.ArgumentCaptor;
 import org.mockito.Mockito;
 import org.mockito.internal.stubbing.answers.ThrowsException;
 
+import com.google.common.collect.Sets;
+
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
@@ -71,6 +75,7 @@ public class JsonParserDstu2Test {
 	private static final FhirContext ourCtx = FhirContext.forDstu2();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu2Test.class);
 
+	
 	/**
 	 * See #308
 	 */
@@ -510,6 +515,77 @@ public class JsonParserDstu2Test {
 		assertThat(json, not(containsString("\"id\"")));
 	}
 
+	@Test
+	public void testEncodeWithDontEncodeElements() throws Exception {
+		Patient patient = new Patient();
+		patient.setId("123");
+		
+		ArrayList<IdDt> list = new ArrayList<IdDt>();
+		list.add(new IdDt("http://profile"));
+		ResourceMetadataKeyEnum.PROFILES.put(patient, list);
+		patient.addName().addFamily("FAMILY").addGiven("GIVEN");
+		patient.addAddress().addLine("LINE1");
+		
+		{
+			IParser p = ourCtx.newJsonParser();
+			p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newJsonParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.meta", "Patient.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newJsonParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.name.family"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("GIVEN"));
+			assertThat(out, not(containsString("FAMILY")));
+		}
+		{
+			IParser p = ourCtx.newJsonParser();
+			p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newJsonParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.meta"));
+			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("id"));
+			assertThat(out, not(containsString("address")));
+			assertThat(out, not(containsString("meta")));
+		}
+	}
+
 	@Test
 	public void testEncodingNullExtension() {
 		Patient p = new Patient();

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java

@@ -38,6 +38,8 @@ import org.junit.Test;
 import org.mockito.ArgumentCaptor;
 import org.mockito.internal.stubbing.answers.ThrowsException;
 
+import com.google.common.collect.Sets;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.ExtensionDt;
@@ -1159,6 +1161,78 @@ public class XmlParserDstu2Test {
 	}
 
 	
+	@Test
+	public void testEncodeWithDontEncodeElements() throws Exception {
+		Patient patient = new Patient();
+		patient.setId("123");
+		
+		ArrayList<IdDt> list = new ArrayList<IdDt>();
+		list.add(new IdDt("http://profile"));
+		ResourceMetadataKeyEnum.PROFILES.put(patient, list);
+		patient.addName().addFamily("FAMILY").addGiven("GIVEN");
+		patient.addAddress().addLine("LINE1");
+		
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.meta", "Patient.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.name.family"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("GIVEN"));
+			assertThat(out, not(containsString("FAMILY")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.meta"));
+			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("id"));
+			assertThat(out, not(containsString("address")));
+			assertThat(out, not(containsString("meta")));
+		}
+	}
+
+
 	@Test
 	public void testMoreExtensions() throws Exception {
 

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

@@ -14,6 +14,8 @@ import static org.junit.Assert.fail;
 import java.io.IOException;
 import java.math.BigDecimal;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
 import java.util.List;
 import java.util.UUID;
 
@@ -54,6 +56,8 @@ import org.junit.Assert;
 import org.junit.Ignore;
 import org.junit.Test;
 
+import com.google.common.collect.Sets;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.server.Constants;
@@ -70,15 +74,6 @@ public class JsonParserDstu3Test {
 		ourCtx.setNarrativeGenerator(null);
 	}
 
-	@Test
-	public void testLinkage() {
-		Linkage l = new Linkage();
-		l.addItem().getResource().setDisplay("FOO");
-		String out = ourCtx.newXmlParser().encodeResourceToString(l);
-		ourLog.info(out);
-		assertEquals("<Linkage xmlns=\"http://hl7.org/fhir\"><item><resource><display value=\"FOO\"/></resource></item></Linkage>", out);
-	}
-	
 	@Test
 	public void testEncodeAndParseExtensions() throws Exception {
 
@@ -241,6 +236,7 @@ public class JsonParserDstu3Test {
 		assertEquals("sec_label2", tagList.get(1).getDisplay());
 	}
 
+	
 	@Test
 	public void testEncodeAndParseSecurityLabels() {
 		Patient p = new Patient();
@@ -474,6 +470,75 @@ public class JsonParserDstu3Test {
 		assertThat(json, not(containsString("\"id\"")));
 	}
 
+	@Test
+	public void testEncodeWithDontEncodeElements() throws Exception {
+		Patient patient = new Patient();
+		patient.setId("123");
+		
+		patient.getMeta().addProfile(("http://profile"));
+		patient.addName().addFamily("FAMILY").addGiven("GIVEN");
+		patient.addAddress().addLine("LINE1");
+		
+		{
+			IParser p = ourCtx.newJsonParser();
+			p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newJsonParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.meta", "Patient.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newJsonParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.name.family"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("GIVEN"));
+			assertThat(out, not(containsString("FAMILY")));
+		}
+		{
+			IParser p = ourCtx.newJsonParser();
+			p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newJsonParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.meta"));
+			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("id"));
+			assertThat(out, not(containsString("address")));
+			assertThat(out, not(containsString("meta")));
+		}
+	}
+
 	@Test
 	public void testEncodeWithNarrative() {
 		Patient p = new Patient();
@@ -547,6 +612,15 @@ public class JsonParserDstu3Test {
 
 	}
 
+	@Test
+	public void testLinkage() {
+		Linkage l = new Linkage();
+		l.addItem().getResource().setDisplay("FOO");
+		String out = ourCtx.newXmlParser().encodeResourceToString(l);
+		ourLog.info(out);
+		assertEquals("<Linkage xmlns=\"http://hl7.org/fhir\"><item><resource><display value=\"FOO\"/></resource></item></Linkage>", out);
+	}
+
 	// FIXME: this should pass
 	@Test
 	@Ignore

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java

@@ -85,6 +85,8 @@ import org.junit.Ignore;
 import org.junit.Test;
 import org.mockito.ArgumentCaptor;
 
+import com.google.common.collect.Sets;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.parser.IParserErrorHandler.IParseLocation;
@@ -101,6 +103,8 @@ public class XmlParserDstu3Test {
 	}
 
 	
+
+	
 	@Test
 	public void testBundleWithBinary() {
 		//@formatter:off
@@ -1018,9 +1022,10 @@ public class XmlParserDstu3Test {
 		assertThat(encoded, not(containsString("maritalStatus")));
 	}
 
-	@Test @Ignore
+	@Test
 	public void testEncodeWithEncodeElements() throws Exception {
 		Patient patient = new Patient();
+		patient.getMeta().addProfile("http://profile");
 		patient.addName().addFamily("FAMILY");
 		patient.addAddress().addLine("LINE1");
 		
@@ -1066,6 +1071,73 @@ public class XmlParserDstu3Test {
 		
 	}
 
+	@Test
+	public void testEncodeWithDontEncodeElements() throws Exception {
+		Patient patient = new Patient();
+		patient.setId("123");
+		patient.getMeta().addProfile("http://profile");
+		patient.addName().addFamily("FAMILY").addGiven("GIVEN");
+		patient.addAddress().addLine("LINE1");
+		
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.meta", "Patient.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.name.family"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("GIVEN"));
+			assertThat(out, not(containsString("FAMILY")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.meta"));
+			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("id"));
+			assertThat(out, not(containsString("address")));
+			assertThat(out, not(containsString("meta")));
+		}
+	}
 	
 	@Test
 	public void testEncodeWithNarrative() {

src/changes/changes.xml

@@ -241,6 +241,13 @@
 				first query. This should improve performance when searching against large
 				datasets.
 			</action>
+			<action type="add">
+				Parsers have new method 
+				<![CDATA[<code>setDontEncodeElements</code>]]>
+				which can be used to force the parser to not encode certain elements
+				in a resource when serializing. For example this can be used to omit
+				sensitive data or skip the resource metadata.
+			</action>
 		</release>
 		<release version="1.4" date="2016-02-04">
 			<action type="add">