Merge branch 'master' of https://github.com/jamesagnew/hapi-fhir

example-projects/hapi-fhir-jpaserver-cds-example/pom.xml

@@ -224,13 +224,17 @@
 		</pluginManagement>
 
 		<plugins>
-			<!-- Tell Maven which Java source version you want to use -->
+
+			<!--
+			The CQF-Ruler project has some OWASP dependency security failures which we don't want
+			to cause the whole build to fail. TODO: investigate these
+			-->
 			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
+				<groupId>org.owasp</groupId>
-				<artifactId>maven-compiler-plugin</artifactId>
+				<artifactId>dependency-check-maven</artifactId>
 				<configuration>
-					<source>1.7</source>
+					<failBuildOnCVSS>99</failBuildOnCVSS>
-					<target>1.7</target>
+					<failOnError>false</failOnError>
 				</configuration>
 			</plugin>
 

hapi-fhir-base/pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-base</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<url>http://jamesagnew.github.io/hapi-fhir/</url>
 
@@ -150,6 +150,21 @@
 				</executions>
 			</plugin>
 			-->
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Import-Package>
+							<!--required when using servers-->
+							ca.uhn.fhir.rest.api.server;resolution:=optional,
+							ca.uhn.fhir.model.api;resolution:=optional,
+							*
+						</Import-Package>
+					</instructions>
+				</configuration>
+			</plugin>
 		</plugins>
 		<resources>
 			<resource>

hapi-fhir-client/pom.xml

@@ -9,7 +9,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-client</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR - Client Framework</name>
 
@@ -69,6 +69,18 @@
 					<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+					</instructions>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 

hapi-fhir-converter/pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-converter</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<dependencies>
 		<dependency>
@@ -134,5 +134,21 @@
 				<filtering>false</filtering>
 			</resource>
 		</resources>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Import-Package>
+							ca.uhn.fhir.rest.server*;resolution:=optional,
+							javax.servlet.http;resolution:=optional,
+							*
+						</Import-Package>
+					</instructions>
+				</configuration>
+			</plugin>
+		</plugins>
 	</build>
 </project>

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

@@ -60,6 +60,9 @@ public class DaoConfig {
 	 * update setter javadoc if default changes
 	 */
 	private boolean myAllowExternalReferences = false;
+	/**
+	 * update setter javadoc if default changes
+	 */
 	private boolean myAllowContainsSearches = true;
 
 	/**
@@ -137,6 +140,7 @@ public class DaoConfig {
 		myTreatReferencesAsLogical.add(theTreatReferencesAsLogical);
 	}
 
+
 	/**
 	 * Specifies the highest number that a client is permitted to use in a
 	 * <code>Cache-Control: nostore, max-results=NNN</code>
@@ -376,9 +380,9 @@ public class DaoConfig {
 	 * of higher importance than raw write performance
 	 * </p>
 	 * <p>
-	 *    Note that this setting also has an impact on sorting (i.e. using the
+	 * Note that this setting also has an impact on sorting (i.e. using the
-	 *    <code>_sort</code> parameter on searches): If the server is configured
+	 * <code>_sort</code> parameter on searches): If the server is configured
-	 *    to not index missing field.
+	 * to not index missing field.
 	 * </p>
 	 */
 	public void setIndexMissingFields(IndexEnabledEnum theIndexMissingFields) {
@@ -650,6 +654,26 @@ public class DaoConfig {
 		return this;
 	}
 
+	/**
+	 * If enabled, the server will support the use of :contains searches,
+	 * which are helpful but can have adverse effects on performance.
+	 *
+	 * Default is <code>true</code>
+	 */
+	public boolean isAllowContainsSearches() {
+		return myAllowContainsSearches;
+	}
+
+	/**
+	 * If enabled, the server will support the use of :contains searches,
+	 * which are helpful but can have adverse effects on performance.
+	 *
+	 * Default is <code>true</code>
+	 */
+	public void setAllowContainsSearches(boolean theAllowContainsSearches) {
+		this.myAllowContainsSearches = theAllowContainsSearches;
+	}
+
 	/**
 	 * If set to <code>true</code> (default is <code>false</code>) the server will allow
 	 * resources to have references to external servers. For example if this server is
@@ -1099,16 +1123,6 @@ public class DaoConfig {
 
 	}
 
-	public boolean allowContainsSearches() {
-
-		return myAllowContainsSearches;
-	}
-
-	public void setAllowContainsSearches(boolean myAllowContainsSearches) {
-
-		this.myAllowContainsSearches = myAllowContainsSearches;
-	}
-
 	public enum IndexEnabledEnum {
 		ENABLED,
 		DISABLED

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

@@ -20,29 +20,32 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import javax.persistence.EntityManager;
 import java.util.Collection;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
-import javax.persistence.EntityManager;
-
-import org.hl7.fhir.instance.model.api.IBaseResource;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.Include;
-import ca.uhn.fhir.rest.param.DateRangeParam;
-
 public interface ISearchBuilder {
 
 	Iterator<Long> createQuery(SearchParameterMap theParams, String theSearchUuid);
 
-	void setType(Class<? extends IBaseResource> theResourceType, String theResourceName);
-
 	void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation, EntityManager theEntityManager,
-			FhirContext theContext, IDao theDao);
+									FhirContext theContext, IDao theDao);
 
 	Set<Long> loadReverseIncludes(IDao theCallingDao, FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode,
-			DateRangeParam theLastUpdated);
+											DateRangeParam theLastUpdated);
+
+	/**
+	 * How many results may be fetched at once
+	 */
+	void setFetchSize(int theFetchSize);
+
+	void setType(Class<? extends IBaseResource> theResourceType, String theResourceName);
 
 }

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

@@ -28,8 +28,6 @@ import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
 import ca.uhn.fhir.jpa.util.BaseIterator;
-import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
-import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.model.api.*;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
@@ -45,7 +43,9 @@ import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.param.*;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.Lists;
@@ -59,6 +59,9 @@ import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.tuple.Pair;
 import org.hibernate.ScrollMode;
 import org.hibernate.ScrollableResults;
+import org.hibernate.engine.spi.EntityKey;
+import org.hibernate.engine.spi.PersistenceContext;
+import org.hibernate.internal.SessionImpl;
 import org.hibernate.query.Query;
 import org.hl7.fhir.dstu3.model.BaseResource;
 import org.hl7.fhir.instance.model.api.IAnyResource;
@@ -104,6 +107,7 @@ public class SearchBuilder implements ISearchBuilder {
 	private ISearchParamRegistry mySearchParamRegistry;
 	private String mySearchUuid;
 	private IHapiTerminologySvc myTerminologySvc;
+	private int myFetchSize;
 
 	/**
 	 * Constructor
@@ -1091,10 +1095,10 @@ public class SearchBuilder implements ISearchBuilder {
 		} else if (theParameter instanceof StringParam) {
 			StringParam id = (StringParam) theParameter;
 			rawSearchTerm = id.getValue();
-			if ((id.isContains()) &&
+			if (id.isContains()) {
-				(!myCallingDao.getConfig().allowContainsSearches()))
+				if (!myCallingDao.getConfig().isAllowContainsSearches()) {
-			{
+					throw new MethodNotAllowedException(":contains modifier is disabled on this server");
-				throw new MethodNotAllowedException(":contains modifier is disabled on this server");
+				}
 			}
 		} else if (theParameter instanceof IPrimitiveDatatype<?>) {
 			IPrimitiveDatatype<?> id = (IPrimitiveDatatype<?>) theParameter;
@@ -1109,18 +1113,11 @@ public class SearchBuilder implements ISearchBuilder {
 		}
 
 		String likeExpression = BaseHapiFhirDao.normalizeString(rawSearchTerm);
-		if (myCallingDao.getConfig().allowContainsSearches()) {
+		if (theParameter instanceof StringParam &&
-			if (theParameter instanceof StringParam) {
+			((StringParam) theParameter).isContains() &&
-				if (((StringParam) theParameter).isContains()) {
+			myCallingDao.getConfig().isAllowContainsSearches()) {
-					likeExpression = createLeftAndRightMatchLikeExpression(likeExpression);
+			likeExpression = createLeftAndRightMatchLikeExpression(likeExpression);
-				} else {
+		} else {
-					likeExpression = createLeftMatchLikeExpression(likeExpression);
-				}
-			} else {
-				likeExpression = createLeftMatchLikeExpression(likeExpression);
-			}
-		}
-		else {
 			likeExpression = createLeftMatchLikeExpression(likeExpression);
 		}
 
@@ -1933,6 +1930,11 @@ public class SearchBuilder implements ISearchBuilder {
 		}
 	}
 
+	@Override
+	public void setFetchSize(int theFetchSize) {
+		myFetchSize = theFetchSize;
+	}
+
 	@Override
 	public void setType(Class<? extends IBaseResource> theResourceType, String theResourceName) {
 		myResourceType = theResourceType;
@@ -2020,14 +2022,14 @@ public class SearchBuilder implements ISearchBuilder {
 		return lastUpdatedPredicates;
 	}
 
-	private static String createLeftMatchLikeExpression(String likeExpression) {
-		return likeExpression.replace("%", "[%]") + "%";
-	}
-
 	private static String createLeftAndRightMatchLikeExpression(String likeExpression) {
 		return "%" + likeExpression.replace("%", "[%]") + "%";
 	}
 
+	private static String createLeftMatchLikeExpression(String likeExpression) {
+		return likeExpression.replace("%", "[%]") + "%";
+	}
+
 	private static Predicate createResourceLinkPathPredicate(IDao theCallingDao, FhirContext theContext, String theParamName, From<?, ? extends ResourceLink> theFrom,
 																				String theResourceType) {
 		RuntimeResourceDefinition resourceDef = theContext.getResourceDefinition(theResourceType);
@@ -2188,6 +2190,7 @@ public class SearchBuilder implements ISearchBuilder {
 				final TypedQuery<Long> query = createQuery(mySort, maximumResults);
 
 				Query<Long> hibernateQuery = (Query<Long>) query;
+				hibernateQuery.setFetchSize(myFetchSize);
 				ScrollableResults scroll = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
 				myResultsIterator = new ScrollableResultsIterator(scroll);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java

@@ -206,6 +206,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		Class<? extends IBaseResource> resourceTypeClass = myContext.getResourceDefinition(theResourceType).getImplementingClass();
 		final ISearchBuilder sb = theCallingDao.newSearchBuilder();
 		sb.setType(resourceTypeClass, theResourceType);
+		sb.setFetchSize(mySyncSize);
 
 		final Integer loadSynchronousUpTo;
 		if (theCacheControlDirective != null && theCacheControlDirective.isNoStore()) {
@@ -233,7 +234,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				public SimpleBundleProvider doInTransaction(TransactionStatus theStatus) {
 
 					// Load the results synchronously
-					final List<Long> pids = new ArrayList<Long>();
+					final List<Long> pids = new ArrayList<>();
 
 					Iterator<Long> resultIter = sb.createQuery(theParams, searchUuid);
 					while (resultIter.hasNext()) {
@@ -458,8 +459,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		private final SearchParameterMap myParams;
 		private final String myResourceType;
 		private final Search mySearch;
-		private final ArrayList<Long> mySyncedPids = new ArrayList<Long>();
+		private final ArrayList<Long> mySyncedPids = new ArrayList<>();
-		private final ArrayList<Long> myUnsyncedPids = new ArrayList<Long>();
+		private final ArrayList<Long> myUnsyncedPids = new ArrayList<>();
 		private boolean myAbortRequested;
 		private int myCountSaved = 0;
 		private String mySearchUuid;
@@ -503,7 +504,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		 * It is called automatically by the thread pool.
 		 */
 		@Override
-		public Void call() throws Exception {
+		public Void call() {
 			StopWatch sw = new StopWatch();
 
 			try {
@@ -631,10 +632,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			boolean keepWaiting;
 			do {
 				synchronized (mySyncedPids) {
-					keepWaiting = false;
+					keepWaiting = mySyncedPids.size() < theToIndex && mySearch.getStatus() == SearchStatusEnum.LOADING;
-					if (mySyncedPids.size() < theToIndex && mySearch.getStatus() == SearchStatusEnum.LOADING) {
-						keepWaiting = true;
-					}
 				}
 				if (keepWaiting) {
 					ourLog.info("Waiting, as we only have {} results", mySyncedPids.size());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java

@@ -11,6 +11,7 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.*;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -54,6 +55,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 	public void afterResetSearchSize() {
 		myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
 		myDaoConfig.setFetchSizeDefaultMaximum(new DaoConfig().getFetchSizeDefaultMaximum());
+		myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
 	}
 
 	@Before
@@ -1404,43 +1406,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		}
 	}
 
-	/**
-	 * See #819
-	 */
-	@Test
-	public void testSearchTokenWithNotModifier() {
-		String male, female;
-		{
-			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue("001");
-			patient.addName().setFamily("Tester").addGiven("Joe");
-			patient.setGender(AdministrativeGender.MALE);
-			male = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
-		}
-		{
-			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue("002");
-			patient.addName().setFamily("Tester").addGiven("Jane");
-			patient.setGender(AdministrativeGender.FEMALE);
-			female = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
-		}
-
-		List<String> patients;
-		SearchParameterMap params;
-
-		params = new SearchParameterMap();
-		params.add(Patient.SP_GENDER, new TokenParam(null, "male"));
-		params.setLoadSynchronous(true);
-		patients = toUnqualifiedVersionlessIdValues(myPatientDao.search(params));
-		assertThat(patients, contains(male));
-
-		params = new SearchParameterMap();
-		params.add(Patient.SP_GENDER, new TokenParam(null, "male").setModifier(TokenParamModifier.NOT));
-		params.setLoadSynchronous(true);
-		patients = toUnqualifiedVersionlessIdValues(myPatientDao.search(params));
-		assertThat(patients, contains(female));
-	}
-
 	@Test
 	public void testSearchNumberParam() {
 		ImmunizationRecommendation e1 = new ImmunizationRecommendation();
@@ -2122,6 +2087,43 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		}
 	}
 
+	/**
+	 * See #819
+	 */
+	@Test
+	public void testSearchTokenWithNotModifier() {
+		String male, female;
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
+			patient.addName().setFamily("Tester").addGiven("Joe");
+			patient.setGender(AdministrativeGender.MALE);
+			male = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
+		}
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
+			patient.addName().setFamily("Tester").addGiven("Jane");
+			patient.setGender(AdministrativeGender.FEMALE);
+			female = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
+		}
+
+		List<String> patients;
+		SearchParameterMap params;
+
+		params = new SearchParameterMap();
+		params.add(Patient.SP_GENDER, new TokenParam(null, "male"));
+		params.setLoadSynchronous(true);
+		patients = toUnqualifiedVersionlessIdValues(myPatientDao.search(params));
+		assertThat(patients, contains(male));
+
+		params = new SearchParameterMap();
+		params.add(Patient.SP_GENDER, new TokenParam(null, "male").setModifier(TokenParamModifier.NOT));
+		params.setLoadSynchronous(true);
+		patients = toUnqualifiedVersionlessIdValues(myPatientDao.search(params));
+		assertThat(patients, contains(female));
+	}
+
 	@Test
 	public void testSearchTokenWrongParam() {
 		Patient p1 = new Patient();
@@ -2257,6 +2259,67 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testSearchWithContains() {
+
+		Patient pt1 = new Patient();
+		pt1.addName().setFamily("ABCDEFGHIJK");
+		String pt1id = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
+
+		Patient pt2 = new Patient();
+		pt2.addName().setFamily("FGHIJK");
+		String pt2id = myPatientDao.create(pt2).getId().toUnqualifiedVersionless().getValue();
+
+		Patient pt3 = new Patient();
+		pt3.addName().setFamily("ZZZZZ");
+		myPatientDao.create(pt3).getId().toUnqualifiedVersionless().getValue();
+
+
+		List<String> ids;
+		SearchParameterMap map;
+		IBundleProvider results;
+
+		// Contains = true
+		map = new SearchParameterMap();
+		map.add(Patient.SP_NAME, new StringParam("FGHIJK").setContains(true));
+		map.setLoadSynchronous(true);
+		results = myPatientDao.search(map);
+		ids = toUnqualifiedVersionlessIdValues(results);
+		assertThat(ids, containsInAnyOrder(pt1id, pt2id));
+
+		// Contains = false
+		map = new SearchParameterMap();
+		map.add(Patient.SP_NAME, new StringParam("FGHIJK").setContains(false));
+		map.setLoadSynchronous(true);
+		results = myPatientDao.search(map);
+		ids = toUnqualifiedVersionlessIdValues(results);
+		assertThat(ids, containsInAnyOrder(pt2id));
+
+		// No contains
+		map = new SearchParameterMap();
+		map.add(Patient.SP_NAME, new StringParam("FGHIJK"));
+		map.setLoadSynchronous(true);
+		results = myPatientDao.search(map);
+		ids = toUnqualifiedVersionlessIdValues(results);
+		assertThat(ids, containsInAnyOrder(pt2id));
+	}
+
+	@Test
+	public void testSearchWithContainsDisabled() {
+		myDaoConfig.setAllowContainsSearches(false);
+
+		SearchParameterMap map = new SearchParameterMap();
+		map.setLoadSynchronous(true);
+		map.add(Patient.SP_NAME, new StringParam("FGHIJK").setContains(true));
+
+		try {
+			myPatientDao.search(map);
+			fail();
+		} catch (MethodNotAllowedException e) {
+			assertEquals(":contains modifier is disabled on this server", e.getMessage());
+		}
+	}
+
 	@Test
 	public void testSearchWithDate() {
 		IIdType orgId = myOrganizationDao.create(new Organization(), mySrd).getId();

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -68,6 +68,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		retVal.getTreatBaseUrlsAsLocal().add("https://fhirtest.uhn.ca/baseDstu2");
 		retVal.setCountSearchResultsUpTo(TestR4Config.COUNT_SEARCH_RESULTS_UP_TO);
 		retVal.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
+		retVal.setFetchSizeDefaultMaximum(10000);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -57,6 +57,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		retVal.getTreatBaseUrlsAsLocal().add("https://fhirtest.uhn.ca/baseDstu3");
 		retVal.setCountSearchResultsUpTo(TestR4Config.COUNT_SEARCH_RESULTS_UP_TO);
 		retVal.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
+		retVal.setFetchSizeDefaultMaximum(10000);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java

@@ -58,6 +58,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 		retVal.getTreatBaseUrlsAsLocal().add("https://fhirtest.uhn.ca/baseR4");
 		retVal.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
 		retVal.setCountSearchResultsUpTo(TestR4Config.COUNT_SEARCH_RESULTS_UP_TO);
+		retVal.setFetchSizeDefaultMaximum(10000);
 		return retVal;
 	}
 

hapi-fhir-structures-dstu2.1/pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR Structures - DSTU2.1 (2016May)</name>
 
@@ -273,6 +273,22 @@
 					<fork>true</fork>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+						<Import-Package>
+							javax.servlet*;resolution:=optional,
+							*
+						</Import-Package>
+					</instructions>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/hapi/validation/DefaultProfileValidationSupport.java

@@ -2,6 +2,7 @@ package org.hl7.fhir.dstu2016may.hapi.validation;
 
 import ca.uhn.fhir.context.FhirContext;
 import org.apache.commons.io.Charsets;
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.dstu2016may.model.*;
 import org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent;
@@ -68,8 +69,8 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 		Map<String, CodeSystem> codeSystems = myCodeSystems;
 		Map<String, ValueSet> valueSets = myValueSets;
 		if (codeSystems == null) {
-			codeSystems = new HashMap<String, CodeSystem>();
+			codeSystems = new HashMap<>();
-			valueSets = new HashMap<String, ValueSet>();
+			valueSets = new HashMap<>();
 
 			loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/dstu2016may/model/valueset/valuesets.xml");
 			loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/dstu2016may/model/valueset/v2-tables.xml");
@@ -155,27 +156,33 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 
 	private void loadCodeSystems(FhirContext theContext, Map<String, CodeSystem> theCodeSystems, Map<String, ValueSet> theValueSets, String theClasspath) {
 		ourLog.info("Loading CodeSystem/ValueSet from classpath: {}", theClasspath);
-		InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
+		InputStream inputStream = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
-		if (valuesetText != null) {
+		InputStreamReader reader = null;
-			InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);
+		if (inputStream != null) {
+			try {
+				reader = new InputStreamReader(inputStream, Charsets.UTF_8);
 
-			Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
+				Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
-			for (BundleEntryComponent next : bundle.getEntry()) {
+				for (BundleEntryComponent next : bundle.getEntry()) {
-				if (next.getResource() instanceof CodeSystem) {
+					if (next.getResource() instanceof CodeSystem) {
-					CodeSystem nextValueSet = (CodeSystem) next.getResource();
+						CodeSystem nextValueSet = (CodeSystem) next.getResource();
-					nextValueSet.getText().setDivAsString("");
+						nextValueSet.getText().setDivAsString("");
-					String system = nextValueSet.getUrl();
+						String system = nextValueSet.getUrl();
-					if (isNotBlank(system)) {
+						if (isNotBlank(system)) {
-						theCodeSystems.put(system, nextValueSet);
+							theCodeSystems.put(system, nextValueSet);
-					}
+						}
-				} else if (next.getResource() instanceof ValueSet) {
+					} else if (next.getResource() instanceof ValueSet) {
-					ValueSet nextValueSet = (ValueSet) next.getResource();
+						ValueSet nextValueSet = (ValueSet) next.getResource();
-					nextValueSet.getText().setDivAsString("");
+						nextValueSet.getText().setDivAsString("");
-					String system = nextValueSet.getUrl();
+						String system = nextValueSet.getUrl();
-					if (isNotBlank(system)) {
+						if (isNotBlank(system)) {
-						theValueSets.put(system, nextValueSet);
+							theValueSets.put(system, nextValueSet);
+						}
 					}
 				}
+			} finally {
+				IOUtils.closeQuietly(reader);
+				IOUtils.closeQuietly(inputStream);
 			}
 		} else {
 			ourLog.warn("Unable to load resource: {}", theClasspath);

hapi-fhir-structures-dstu2/pom.xml

@@ -9,7 +9,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-structures-dstu2</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)</name>
 
@@ -361,6 +361,22 @@
 					</execution>
 				</executions>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+						<Import-Package>
+							javax.servlet*;resolution:=optional,
+							*
+						</Import-Package>
+					</instructions>
+				</configuration>
+			</plugin>
 		</plugins>
 		<pluginManagement>
 			<plugins>

hapi-fhir-structures-dstu3/pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-structures-dstu3</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR Structures - DSTU3</name>
 
@@ -28,6 +28,18 @@
 
 	<build>
 		<plugins>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+					</instructions>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>org.jacoco</groupId>
 				<artifactId>jacoco-maven-plugin</artifactId>
@@ -272,5 +284,4 @@
 			<scope>test</scope>
 		</dependency>
 	</dependencies>
-
 </project>

hapi-fhir-structures-hl7org-dstu2/pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR Structures - HL7.org DSTU2</name>
 
@@ -272,6 +272,22 @@
 					<fork>true</fork>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+						<Import-Package>
+							javax.servlet*;resolution:=optional,
+							*
+						</Import-Package>
+					</instructions>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 

hapi-fhir-structures-r4/pom.xml

@@ -1,5 +1,5 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+			xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-structures-r4</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR Structures - FHIR R4</name>
 
@@ -29,11 +29,11 @@
 		<!-- 
 		Optional dependencies from RI codebase
 		-->
-      <dependency>
+		<dependency>
-         <groupId>org.codehaus.woodstox</groupId>
+			<groupId>org.codehaus.woodstox</groupId>
-         <artifactId>woodstox-core-asl</artifactId>
+			<artifactId>woodstox-core-asl</artifactId>
-         <scope>test</scope>
+			<scope>test</scope>
-      </dependency>
+		</dependency>
 		<dependency>
 			<groupId>es.nitaur.markdown</groupId>
 			<artifactId>txtmark</artifactId>
@@ -262,6 +262,18 @@
 					<fork>true</fork>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+					</instructions>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/ctx/DefaultProfileValidationSupport.java

@@ -2,6 +2,7 @@ package org.hl7.fhir.r4.hapi.ctx;
 
 import ca.uhn.fhir.context.FhirContext;
 import org.apache.commons.io.Charsets;
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -141,27 +142,33 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 
   private void loadCodeSystems(FhirContext theContext, Map<String, CodeSystem> theCodeSystems, Map<String, ValueSet> theValueSets, String theClasspath) {
     ourLog.info("Loading CodeSystem/ValueSet from classpath: {}", theClasspath);
-    InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
+    InputStream inputStream = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
-    if (valuesetText != null) {
+    InputStreamReader reader = null;
-      InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);
+    if (inputStream != null) {
+      try {
+        reader = new InputStreamReader(inputStream, Charsets.UTF_8);
 
-      Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
+        Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
-      for (BundleEntryComponent next : bundle.getEntry()) {
+        for (BundleEntryComponent next : bundle.getEntry()) {
-        if (next.getResource() instanceof CodeSystem) {
+          if (next.getResource() instanceof CodeSystem) {
-          CodeSystem nextValueSet = (CodeSystem) next.getResource();
+            CodeSystem nextValueSet = (CodeSystem) next.getResource();
-          nextValueSet.getText().setDivAsString("");
+            nextValueSet.getText().setDivAsString("");
-          String system = nextValueSet.getUrl();
+            String system = nextValueSet.getUrl();
-          if (isNotBlank(system)) {
+            if (isNotBlank(system)) {
-            theCodeSystems.put(system, nextValueSet);
+              theCodeSystems.put(system, nextValueSet);
-          }
+            }
-        } else if (next.getResource() instanceof ValueSet) {
+          } else if (next.getResource() instanceof ValueSet) {
-          ValueSet nextValueSet = (ValueSet) next.getResource();
+            ValueSet nextValueSet = (ValueSet) next.getResource();
-          nextValueSet.getText().setDivAsString("");
+            nextValueSet.getText().setDivAsString("");
-          String system = nextValueSet.getUrl();
+            String system = nextValueSet.getUrl();
-          if (isNotBlank(system)) {
+            if (isNotBlank(system)) {
-            theValueSets.put(system, nextValueSet);
+              theValueSets.put(system, nextValueSet);
+            }
           }
         }
+      } finally {
+        IOUtils.closeQuietly(reader);
+        IOUtils.closeQuietly(inputStream);
       }
     } else {
       ourLog.warn("Unable to load resource: {}", theClasspath);

hapi-fhir-utilities/pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-utilities</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR - Utilities</name>
 
@@ -122,6 +122,11 @@
 					<fork>true</fork>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+			</plugin>
 		</plugins>
 	</build>
 

hapi-fhir-validation-resources-dstu2.1/pom.xml

@@ -9,7 +9,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-validation-resources-dstu2.1</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR - Validation Resources DSTU2.1 (2016May)</name>
 
@@ -20,6 +20,20 @@
 				<filtering>false</filtering>
 			</resource>
 		</resources>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+					</instructions>
+				</configuration>
+			</plugin>
+		</plugins>
 	</build>
 
 </project>

hapi-fhir-validation-resources-dstu2/pom.xml

@@ -9,7 +9,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR - Validation Resources (DSTU2)</name>
 
@@ -20,6 +20,20 @@
 				<filtering>false</filtering>
 			</resource>
 		</resources>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+					</instructions>
+				</configuration>
+			</plugin>
+		</plugins>
 	</build>
 
 </project>

hapi-fhir-validation-resources-dstu3/pom.xml

@@ -9,7 +9,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR - Validation Resources (DSTU3)</name>
 
@@ -34,6 +34,20 @@
 				<filtering>false</filtering>
 			</resource>
 		</resources>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+					</instructions>
+				</configuration>
+			</plugin>
+		</plugins>
 	</build>
 
 </project>

hapi-fhir-validation-resources-r4/pom.xml

@@ -9,7 +9,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-validation-resources-r4</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR - Validation Resources (FHIR R4)</name>
 
@@ -34,6 +34,20 @@
 				<filtering>false</filtering>
 			</resource>
 		</resources>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+					</instructions>
+				</configuration>
+			</plugin>
+		</plugins>
 	</build>
 
 </project>

hapi-fhir-validation/pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>hapi-fhir-validation</artifactId>
-	<packaging>jar</packaging>
+	<packaging>bundle</packaging>
 
 	<name>HAPI FHIR - Validation</name>
 
@@ -246,6 +246,18 @@
 					<fork>true</fork>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Fragment-Host>
+							ca.uhn.hapi.fhir.hapi-fhir-base
+						</Fragment-Host>
+					</instructions>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 

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

@@ -2,7 +2,7 @@ package org.hl7.fhir.dstu3.hapi.validation;
 
 import ca.uhn.fhir.context.FhirContext;
 import org.apache.commons.io.Charsets;
-import org.apache.commons.lang.WordUtils;
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
@@ -24,243 +24,249 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class DefaultProfileValidationSupport implements IValidationSupport {
 
-  private static final String URL_PREFIX_VALUE_SET = "http://hl7.org/fhir/ValueSet/";
+	private static final String URL_PREFIX_VALUE_SET = "http://hl7.org/fhir/ValueSet/";
-  private static final String URL_PREFIX_STRUCTURE_DEFINITION = "http://hl7.org/fhir/StructureDefinition/";
+	private static final String URL_PREFIX_STRUCTURE_DEFINITION = "http://hl7.org/fhir/StructureDefinition/";
-  private static final String URL_PREFIX_STRUCTURE_DEFINITION_BASE = "http://hl7.org/fhir/";
+	private static final String URL_PREFIX_STRUCTURE_DEFINITION_BASE = "http://hl7.org/fhir/";
 
-  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DefaultProfileValidationSupport.class);
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DefaultProfileValidationSupport.class);
 
-  private Map<String, CodeSystem> myCodeSystems;
+	private Map<String, CodeSystem> myCodeSystems;
-  private Map<String, StructureDefinition> myStructureDefinitions;
+	private Map<String, StructureDefinition> myStructureDefinitions;
-  private Map<String, ValueSet> myValueSets;
+	private Map<String, ValueSet> myValueSets;
 
-  @Override
+	@Override
-  public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
+	public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
-    ValueSetExpansionComponent retVal = new ValueSetExpansionComponent();
+		ValueSetExpansionComponent retVal = new ValueSetExpansionComponent();
 
-    Set<String> wantCodes = new HashSet<String>();
+		Set<String> wantCodes = new HashSet<>();
-    for (ConceptReferenceComponent next : theInclude.getConcept()) {
+		for (ConceptReferenceComponent next : theInclude.getConcept()) {
-      wantCodes.add(next.getCode());
+			wantCodes.add(next.getCode());
-    }
+		}
 
-    CodeSystem system = fetchCodeSystem(theContext, theInclude.getSystem());
+		CodeSystem system = fetchCodeSystem(theContext, theInclude.getSystem());
-    for (ConceptDefinitionComponent next : system.getConcept()) {
+		for (ConceptDefinitionComponent next : system.getConcept()) {
-      if (wantCodes.isEmpty() || wantCodes.contains(next.getCode())) {
+			if (wantCodes.isEmpty() || wantCodes.contains(next.getCode())) {
-        retVal.addContains().setSystem(theInclude.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
+				retVal.addContains().setSystem(theInclude.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
-      }
+			}
-    }
+		}
 
-    return retVal;
+		return retVal;
-  }
+	}
 
-  @Override
+	@Override
-  public List<IBaseResource> fetchAllConformanceResources(FhirContext theContext) {
+	public List<IBaseResource> fetchAllConformanceResources(FhirContext theContext) {
-    ArrayList<IBaseResource> retVal = new ArrayList<>();
+		ArrayList<IBaseResource> retVal = new ArrayList<>();
-    retVal.addAll(myCodeSystems.values());
+		retVal.addAll(myCodeSystems.values());
-    retVal.addAll(myStructureDefinitions.values());
+		retVal.addAll(myStructureDefinitions.values());
-    retVal.addAll(myValueSets.values());
+		retVal.addAll(myValueSets.values());
-    return retVal;
+		return retVal;
-  }
+	}
 
-  @Override
+	@Override
-  public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
+	public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
-    return new ArrayList<StructureDefinition>(provideStructureDefinitionMap(theContext).values());
+		return new ArrayList<StructureDefinition>(provideStructureDefinitionMap(theContext).values());
-  }
+	}
 
-  @Override
+	@Override
-  public CodeSystem fetchCodeSystem(FhirContext theContext, String theSystem) {
+	public CodeSystem fetchCodeSystem(FhirContext theContext, String theSystem) {
-    return (CodeSystem) fetchCodeSystemOrValueSet(theContext, theSystem, true);
+		return (CodeSystem) fetchCodeSystemOrValueSet(theContext, theSystem, true);
-  }
+	}
 
-  private DomainResource fetchCodeSystemOrValueSet(FhirContext theContext, String theSystem, boolean codeSystem) {
+	private DomainResource fetchCodeSystemOrValueSet(FhirContext theContext, String theSystem, boolean codeSystem) {
-    synchronized (this) {
+		synchronized (this) {
-      Map<String, CodeSystem> codeSystems = myCodeSystems;
+			Map<String, CodeSystem> codeSystems = myCodeSystems;
-      Map<String, ValueSet> valueSets = myValueSets;
+			Map<String, ValueSet> valueSets = myValueSets;
-      if (codeSystems == null || valueSets == null) {
+			if (codeSystems == null || valueSets == null) {
-        codeSystems = new HashMap<String, CodeSystem>();
+				codeSystems = new HashMap<String, CodeSystem>();
-        valueSets = new HashMap<String, ValueSet>();
+				valueSets = new HashMap<String, ValueSet>();
 
-        loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/dstu3/model/valueset/valuesets.xml");
+				loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/dstu3/model/valueset/valuesets.xml");
-        loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/dstu3/model/valueset/v2-tables.xml");
+				loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/dstu3/model/valueset/v2-tables.xml");
-        loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/dstu3/model/valueset/v3-codesystems.xml");
+				loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/dstu3/model/valueset/v3-codesystems.xml");
 
-        myCodeSystems = codeSystems;
+				myCodeSystems = codeSystems;
-        myValueSets = valueSets;
+				myValueSets = valueSets;
-      }
+			}
 
-      if (codeSystem) {
+			if (codeSystem) {
-        return codeSystems.get(theSystem);
+				return codeSystems.get(theSystem);
-      } else {
+			} else {
-        return valueSets.get(theSystem);
+				return valueSets.get(theSystem);
-      }
+			}
-    }
+		}
-  }
+	}
 
-  @SuppressWarnings("unchecked")
+	@SuppressWarnings("unchecked")
-  @Override
+	@Override
-  public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
+	public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
-    Validate.notBlank(theUri, "theUri must not be null or blank");
+		Validate.notBlank(theUri, "theUri must not be null or blank");
 
-    if (theClass.equals(StructureDefinition.class)) {
+		if (theClass.equals(StructureDefinition.class)) {
-      return (T) fetchStructureDefinition(theContext, theUri);
+			return (T) fetchStructureDefinition(theContext, theUri);
-    }
+		}
 
-    if (theClass.equals(ValueSet.class) || theUri.startsWith(URL_PREFIX_VALUE_SET)) {
+		if (theClass.equals(ValueSet.class) || theUri.startsWith(URL_PREFIX_VALUE_SET)) {
-      return (T) fetchValueSet(theContext, theUri);
+			return (T) fetchValueSet(theContext, theUri);
-    }
+		}
 
-    return null;
+		return null;
-  }
+	}
 
-  @Override
+	@Override
-  public StructureDefinition fetchStructureDefinition(FhirContext theContext, String theUrl) {
+	public StructureDefinition fetchStructureDefinition(FhirContext theContext, String theUrl) {
-    String url = theUrl;
+		String url = theUrl;
-    if (url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) {
+		if (url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) {
-      // no change
+			// no change
-    } else if (url.indexOf('/') == -1) {
+		} else if (url.indexOf('/') == -1) {
-      url = URL_PREFIX_STRUCTURE_DEFINITION + url;
+			url = URL_PREFIX_STRUCTURE_DEFINITION + url;
-    } else if (StringUtils.countMatches(url, '/') == 1) {
+		} else if (StringUtils.countMatches(url, '/') == 1) {
-      url = URL_PREFIX_STRUCTURE_DEFINITION_BASE + url;
+			url = URL_PREFIX_STRUCTURE_DEFINITION_BASE + url;
-    }
+		}
-	  Map<String, StructureDefinition> map = provideStructureDefinitionMap(theContext);
+		Map<String, StructureDefinition> map = provideStructureDefinitionMap(theContext);
-	  StructureDefinition retVal = map.get(url);
+		StructureDefinition retVal = map.get(url);
 
-	  if (retVal == null && url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) {
+		if (retVal == null && url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) {
-	  		String tryUrl = URL_PREFIX_STRUCTURE_DEFINITION + StringUtils.capitalize(url.substring(URL_PREFIX_STRUCTURE_DEFINITION.length()));
+			String tryUrl = URL_PREFIX_STRUCTURE_DEFINITION + StringUtils.capitalize(url.substring(URL_PREFIX_STRUCTURE_DEFINITION.length()));
-		  retVal = map.get(tryUrl);
+			retVal = map.get(tryUrl);
-	  }
+		}
 
-	  return retVal;
+		return retVal;
-  }
+	}
 
-  ValueSet fetchValueSet(FhirContext theContext, String theSystem) {
+	ValueSet fetchValueSet(FhirContext theContext, String theSystem) {
-    return (ValueSet) fetchCodeSystemOrValueSet(theContext, theSystem, false);
+		return (ValueSet) fetchCodeSystemOrValueSet(theContext, theSystem, false);
-  }
+	}
 
-  public void flush() {
+	public void flush() {
-    myCodeSystems = null;
+		myCodeSystems = null;
-    myStructureDefinitions = null;
+		myStructureDefinitions = null;
-  }
+	}
 
-  @Override
+	@Override
-  public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
+	public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
-    CodeSystem cs = fetchCodeSystem(theContext, theSystem);
+		CodeSystem cs = fetchCodeSystem(theContext, theSystem);
-    return cs != null && cs.getContent() != CodeSystemContentMode.NOTPRESENT;
+		return cs != null && cs.getContent() != CodeSystemContentMode.NOTPRESENT;
-  }
+	}
 
-  private void loadCodeSystems(FhirContext theContext, Map<String, CodeSystem> theCodeSystems, Map<String, ValueSet> theValueSets, String theClasspath) {
+	private void loadCodeSystems(FhirContext theContext, Map<String, CodeSystem> theCodeSystems, Map<String, ValueSet> theValueSets, String theClasspath) {
-    ourLog.info("Loading CodeSystem/ValueSet from classpath: {}", theClasspath);
+		ourLog.info("Loading CodeSystem/ValueSet from classpath: {}", theClasspath);
-    InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
+		InputStream inputStream = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
-    if (valuesetText != null) {
+		InputStreamReader reader = null;
-      InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);
+		if (inputStream != null) {
+			try {
+				reader = new InputStreamReader(inputStream, Charsets.UTF_8);
 
-      Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
+				Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
-      for (BundleEntryComponent next : bundle.getEntry()) {
+				for (BundleEntryComponent next : bundle.getEntry()) {
-        if (next.getResource() instanceof CodeSystem) {
+					if (next.getResource() instanceof CodeSystem) {
-          CodeSystem nextValueSet = (CodeSystem) next.getResource();
+						CodeSystem nextValueSet = (CodeSystem) next.getResource();
-          nextValueSet.getText().setDivAsString("");
+						nextValueSet.getText().setDivAsString("");
-          String system = nextValueSet.getUrl();
+						String system = nextValueSet.getUrl();
-          if (isNotBlank(system)) {
+						if (isNotBlank(system)) {
-            theCodeSystems.put(system, nextValueSet);
+							theCodeSystems.put(system, nextValueSet);
-          }
+						}
-        } else if (next.getResource() instanceof ValueSet) {
+					} else if (next.getResource() instanceof ValueSet) {
-          ValueSet nextValueSet = (ValueSet) next.getResource();
+						ValueSet nextValueSet = (ValueSet) next.getResource();
-          nextValueSet.getText().setDivAsString("");
+						nextValueSet.getText().setDivAsString("");
-          String system = nextValueSet.getUrl();
+						String system = nextValueSet.getUrl();
-          if (isNotBlank(system)) {
+						if (isNotBlank(system)) {
-            theValueSets.put(system, nextValueSet);
+							theValueSets.put(system, nextValueSet);
-          }
+						}
-        }
+					}
-      }
+				}
-    } else {
+			} finally {
-      ourLog.warn("Unable to load resource: {}", theClasspath);
+				IOUtils.closeQuietly(reader);
-    }
+				IOUtils.closeQuietly(inputStream);
-  }
+			}
+		} else {
+			ourLog.warn("Unable to load resource: {}", theClasspath);
+		}
+	}
 
-  private void loadStructureDefinitions(FhirContext theContext, Map<String, StructureDefinition> theCodeSystems, String theClasspath) {
+	private void loadStructureDefinitions(FhirContext theContext, Map<String, StructureDefinition> theCodeSystems, String theClasspath) {
-    ourLog.info("Loading structure definitions from classpath: {}", theClasspath);
+		ourLog.info("Loading structure definitions from classpath: {}", theClasspath);
-    InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
+		InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
-    if (valuesetText != null) {
+		if (valuesetText != null) {
-      InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);
+			InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);
 
-      Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
+			Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
-      for (BundleEntryComponent next : bundle.getEntry()) {
+			for (BundleEntryComponent next : bundle.getEntry()) {
-        if (next.getResource() instanceof StructureDefinition) {
+				if (next.getResource() instanceof StructureDefinition) {
-          StructureDefinition nextSd = (StructureDefinition) next.getResource();
+					StructureDefinition nextSd = (StructureDefinition) next.getResource();
-          nextSd.getText().setDivAsString("");
+					nextSd.getText().setDivAsString("");
-          String system = nextSd.getUrl();
+					String system = nextSd.getUrl();
-          if (isNotBlank(system)) {
+					if (isNotBlank(system)) {
-            theCodeSystems.put(system, nextSd);
+						theCodeSystems.put(system, nextSd);
-          }
+					}
-        }
+				}
-      }
+			}
-    } else {
+		} else {
-      ourLog.warn("Unable to load resource: {}", theClasspath);
+			ourLog.warn("Unable to load resource: {}", theClasspath);
-    }
+		}
-  }
+	}
 
-  private Map<String, StructureDefinition> provideStructureDefinitionMap(FhirContext theContext) {
+	private Map<String, StructureDefinition> provideStructureDefinitionMap(FhirContext theContext) {
-    Map<String, StructureDefinition> structureDefinitions = myStructureDefinitions;
+		Map<String, StructureDefinition> structureDefinitions = myStructureDefinitions;
-    if (structureDefinitions == null) {
+		if (structureDefinitions == null) {
-      structureDefinitions = new HashMap<String, StructureDefinition>();
+			structureDefinitions = new HashMap<String, StructureDefinition>();
 
-      loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/dstu3/model/profile/profiles-resources.xml");
+			loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/dstu3/model/profile/profiles-resources.xml");
-      loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/dstu3/model/profile/profiles-types.xml");
+			loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/dstu3/model/profile/profiles-types.xml");
-      loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/dstu3/model/profile/profiles-others.xml");
+			loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/dstu3/model/profile/profiles-others.xml");
 
-      myStructureDefinitions = structureDefinitions;
+			myStructureDefinitions = structureDefinitions;
-    }
+		}
-    return structureDefinitions;
+		return structureDefinitions;
-  }
+	}
 
-  private CodeValidationResult testIfConceptIsInList(String theCode, List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive) {
+	private CodeValidationResult testIfConceptIsInList(String theCode, List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive) {
-    String code = theCode;
+		String code = theCode;
-    if (theCaseSensitive == false) {
+		if (theCaseSensitive == false) {
-      code = code.toUpperCase();
+			code = code.toUpperCase();
-    }
+		}
 
-    return testIfConceptIsInListInner(conceptList, theCaseSensitive, code);
+		return testIfConceptIsInListInner(conceptList, theCaseSensitive, code);
-  }
+	}
 
-  private CodeValidationResult testIfConceptIsInListInner(List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive, String code) {
+	private CodeValidationResult testIfConceptIsInListInner(List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive, String code) {
-    CodeValidationResult retVal = null;
+		CodeValidationResult retVal = null;
-    for (ConceptDefinitionComponent next : conceptList) {
+		for (ConceptDefinitionComponent next : conceptList) {
-      String nextCandidate = next.getCode();
+			String nextCandidate = next.getCode();
-      if (theCaseSensitive == false) {
+			if (theCaseSensitive == false) {
-        nextCandidate = nextCandidate.toUpperCase();
+				nextCandidate = nextCandidate.toUpperCase();
-      }
+			}
-      if (nextCandidate.equals(code)) {
+			if (nextCandidate.equals(code)) {
-        retVal = new CodeValidationResult(next);
+				retVal = new CodeValidationResult(next);
-        break;
+				break;
-      }
+			}
 
-      // recurse
+			// recurse
-      retVal = testIfConceptIsInList(code, next.getConcept(), theCaseSensitive);
+			retVal = testIfConceptIsInList(code, next.getConcept(), theCaseSensitive);
-      if (retVal != null) {
+			if (retVal != null) {
-        break;
+				break;
-      }
+			}
-    }
+		}
 
-    return retVal;
+		return retVal;
-  }
+	}
 
-  @Override
+	@Override
-  public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
-    CodeSystem cs = fetchCodeSystem(theContext, theCodeSystem);
+		CodeSystem cs = fetchCodeSystem(theContext, theCodeSystem);
-    if (cs != null) {
+		if (cs != null) {
-      boolean caseSensitive = true;
+			boolean caseSensitive = true;
-      if (cs.hasCaseSensitive()) {
+			if (cs.hasCaseSensitive()) {
-        caseSensitive = cs.getCaseSensitive();
+				caseSensitive = cs.getCaseSensitive();
-      }
+			}
 
-      CodeValidationResult retVal = testIfConceptIsInList(theCode, cs.getConcept(), caseSensitive);
+			CodeValidationResult retVal = testIfConceptIsInList(theCode, cs.getConcept(), caseSensitive);
 
-      if (retVal != null) {
+			if (retVal != null) {
-        return retVal;
+				return retVal;
-      }
+			}
-    }
+		}
 
-    return new CodeValidationResult(IssueSeverity.WARNING, "Unknown code: " + theCodeSystem + " / " + theCode);
+		return new CodeValidationResult(IssueSeverity.WARNING, "Unknown code: " + theCodeSystem + " / " + theCode);
-  }
+	}
 
 }

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

@@ -2,6 +2,7 @@ package org.hl7.fhir.instance.hapi.validation;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.Bundle;
 import org.hl7.fhir.instance.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.instance.model.CodeType;
@@ -44,9 +45,9 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 			if (valueSets == null) {
 				valueSets = new HashMap<String, ValueSet>();
 
-				loadCodeSystems(theContext, valueSets, "/org/hl7/fhir/instance/model/valueset/valuesets.xml");
+				loadValueSets(theContext, valueSets, "/org/hl7/fhir/instance/model/valueset/valuesets.xml");
-				loadCodeSystems(theContext, valueSets, "/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
+				loadValueSets(theContext, valueSets, "/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
-				loadCodeSystems(theContext, valueSets, "/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
+				loadValueSets(theContext, valueSets, "/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
 
 				myCodeSystems = valueSets;
 			}
@@ -108,26 +109,34 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 		return false;
 	}
 
-	private void loadCodeSystems(FhirContext theContext, Map<String, ValueSet> codeSystems, String file) {
+	private void loadValueSets(FhirContext theContext, Map<String, ValueSet> theValueSets, String theFile) {
-		InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(file);
+		InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theFile);
-		if (valuesetText != null) {
+		try {
-			InputStreamReader reader;
+			if (valuesetText != null) {
-			try {
+				InputStreamReader reader = null;
-				reader = new InputStreamReader(valuesetText, "UTF-8");
+				try {
-			} catch (UnsupportedEncodingException e) {
+					reader = new InputStreamReader(valuesetText, "UTF-8");
-				// Shouldn't happen!
-				throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
-			}
 
-			FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
+					FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
-			Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
+					Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
-			for (BundleEntryComponent next : bundle.getEntry()) {
+					for (BundleEntryComponent next : bundle.getEntry()) {
-				ValueSet nextValueSet = (ValueSet) next.getResource();
+						ValueSet nextValueSet = (ValueSet) next.getResource();
-				String system = nextValueSet.getCodeSystem().getSystem();
+						String system = nextValueSet.getCodeSystem().getSystem();
-				if (isNotBlank(system)) {
+						if (isNotBlank(system)) {
-					codeSystems.put(system, nextValueSet);
+							theValueSets.put(system, nextValueSet);
+						}
+					}
+
+				} catch (UnsupportedEncodingException e) {
+					// Shouldn't happen!
+					throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
+				} finally {
+					IOUtils.closeQuietly(reader);
 				}
+
 			}
+		} finally {
+			IOUtils.closeQuietly(valuesetText);
 		}
 	}
 
@@ -136,7 +145,7 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 		ValueSet vs = fetchCodeSystem(theContext, theCodeSystem);
 		if (vs != null) {
 			for (ValueSet.ConceptDefinitionComponent nextConcept : vs.getCodeSystem().getConcept()) {
-				if (nextConcept.getCode().equals(theCode)){
+				if (nextConcept.getCode().equals(theCode)) {
 					ValueSet.ConceptDefinitionComponent component = new ValueSet.ConceptDefinitionComponent(new CodeType(theCode));
 					return new CodeValidationResult(component);
 				}

osgi/hapi-fhir-karaf-features/pom.xml

@@ -0,0 +1,218 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+			xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-deployable-pom</artifactId>
+		<version>3.3.0-SNAPSHOT</version>
+		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
+	</parent>
+
+	<groupId>ca.uhn.hapi.fhir.karaf</groupId>
+	<artifactId>hapi-fhir</artifactId>
+	<packaging>pom</packaging>
+	<name>HAPI FHIR - Apache Karaf :: Features</name>
+
+	<properties>
+		<features.file>features.xml</features.file>
+		<pax-logging-version>1.8.6</pax-logging-version>
+		<felix-framework-version>3.2.2</felix-framework-version>
+	</properties>
+
+	<dependencies>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-base</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu2</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu3</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-r4</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu2.1</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-r4</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-converter</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<!-- The validate plugin will export these provided dependencies bundles export packages first -->
+
+		<dependency>
+			<groupId>org.osgi</groupId>
+			<artifactId>org.osgi.core</artifactId>
+			<version>4.3.1</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.ops4j.pax.logging</groupId>
+			<artifactId>pax-logging-api</artifactId>
+			<version>${pax-logging-version}</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.ops4j.pax.logging</groupId>
+			<artifactId>pax-logging-service</artifactId>
+			<version>${pax-logging-version}</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.felix</groupId>
+			<artifactId>org.apache.felix.framework</artifactId>
+			<version>${felix-framework-version}</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.felix</groupId>
+			<artifactId>org.apache.felix.configadmin</artifactId>
+			<version>1.8.8</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.aries.blueprint</groupId>
+			<artifactId>org.apache.aries.blueprint.api</artifactId>
+			<version>1.0.1</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.aries.blueprint</groupId>
+			<artifactId>org.apache.aries.blueprint.core</artifactId>
+			<version>1.0.1</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.karaf.shell</groupId>
+			<artifactId>org.apache.karaf.shell.core</artifactId>
+			<version>${apache_karaf_version}</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.karaf.features</groupId>
+			<artifactId>framework</artifactId>
+			<version>${apache_karaf_version}</version>
+			<type>kar</type>
+			<scope>provided</scope>
+		</dependency>
+	</dependencies>
+
+	<build>
+		<resources>
+			<resource>
+				<directory>src/main/resources</directory>
+				<filtering>true</filtering>
+			</resource>
+		</resources>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-resources-plugin</artifactId>
+				<version>3.0.2</version>
+				<executions>
+					<execution>
+						<id>filter</id>
+						<phase>generate-resources</phase>
+						<goals>
+							<goal>resources</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>build-helper-maven-plugin</artifactId>
+				<executions>
+					<execution>
+						<id>attach-artifacts</id>
+						<phase>package</phase>
+						<goals>
+							<goal>attach-artifact</goal>
+						</goals>
+						<configuration>
+							<artifacts>
+								<artifact>
+									<file>target/classes/features.xml</file>
+									<type>xml</type>
+									<classifier>features</classifier>
+								</artifact>
+							</artifacts>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.karaf.tooling</groupId>
+				<artifactId>karaf-maven-plugin</artifactId>
+				<version>${apache_karaf_version}</version>
+				<configuration>
+					<descriptors>
+						<descriptor>file://${project.build.directory}/classes/${features.file}</descriptor>
+						<descriptor>mvn:org.apache.karaf.features/enterprise/${apache_karaf_version}/xml/features</descriptor>
+					</descriptors>
+					<distribution>org.apache.karaf.features:framework</distribution>
+					<javase>1.8</javase>
+					<framework>
+						<feature>framework</feature>
+					</framework>
+					<features>
+						<feature>hapi-fhir*</feature>
+					</features>
+				</configuration>
+				<executions>
+					<execution>
+						<id>validate</id>
+						<phase>process-resources</phase>
+						<goals>
+							<goal>verify</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
+	</build>
+</project>

osgi/hapi-fhir-karaf-features/src/main/resources/features.xml

@@ -0,0 +1,135 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--
+
+ HAPI FHIR - Apache Karaf Features
+
+ Copyright (C) 2014 - 2018 University Health Network
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+   http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+-->
+<features name='hapi-fhir-${project.version}' xmlns="http://karaf.apache.org/xmlns/features/v1.3.0">
+
+  <feature name='hapi-fhir' version='${project.version}' start-level='50'>
+	  <feature prerequisite="true">wrap</feature>
+	  <bundle dependency='true'>mvn:com.google.code.gson/gson/${gson_version}</bundle>
+	  <bundle dependency='true'>mvn:org.apache.commons/commons-lang3/${commons_lang3_version}</bundle>
+	  <bundle dependency='true'>mvn:commons-codec/commons-codec/${commons_codec_version}</bundle>
+	  <bundle dependency='true'>mvn:commons-io/commons-io/${commons_io_version}</bundle>
+	  <bundle dependency='true'>mvn:com.google.guava/guava/${guava_version}</bundle>
+	  <bundle dependency='true'>wrap:mvn:com.google.errorprone/error_prone_annotations/${error_prone_annotations_version}</bundle>
+	  <bundle dependency='true'>mvn:org.codehaus.woodstox/stax2-api/${stax2_api_version}</bundle>
+	  <bundle dependency='true'>mvn:org.codehaus.woodstox/woodstox-core-asl/${woodstox_core_asl_version}</bundle>
+	  <bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-base/${project.version}</bundle>
+  </feature>
+
+	<feature name='hapi-fhir-client' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir</feature>
+		<bundle dependency='true'>mvn:org.apache.httpcomponents/httpcore-osgi/${httpcore_version}</bundle>
+		<bundle dependency='true'>mvn:org.apache.httpcomponents/httpclient-osgi/${httpclient_version}</bundle>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-client/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-utilities' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir</feature>
+		<bundle dependency='true'>mvn:com.google.code.gson/gson/${gson_version}</bundle>
+		<bundle dependency='true'>mvn:commons-codec/commons-codec/${commons_codec_version}</bundle>
+		<bundle dependency='true'>mvn:commons-io/commons-io/${commons_io_version}</bundle>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-utilities/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-dstu2' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir</feature>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-structures-dstu2/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-hl7org-dstu2' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir</feature>
+		<feature version='${project.version}'>hapi-fhir-utilities</feature>
+		<bundle dependency='true'>
+			mvn:org.apache.servicemix.bundles/org.apache.servicemix.bundles.saxon/${servicemix_saxon_version}
+		</bundle>
+		<bundle dependency='true'>
+			mvn:org.apache.servicemix.bundles/org.apache.servicemix.bundles.xmlresolver/${servicemix_xmlresolver_version}
+		</bundle>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-structures-hl7org-dstu2/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-dstu2.1' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir</feature>
+		<feature version='${project.version}'>hapi-fhir-utilities</feature>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-structures-dstu2.1/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-dstu3' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir</feature>
+		<feature version='${project.version}'>hapi-fhir-utilities</feature>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-structures-dstu3/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-r4' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir</feature>
+		<feature version='${project.version}'>hapi-fhir-utilities</feature>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-structures-r4/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-ph-schematron' version='${project.version}' start-level='50'>
+		<bundle dependency='true'>
+			mvn:org.apache.servicemix.bundles/org.apache.servicemix.bundles.saxon/${servicemix_saxon_version}
+		</bundle>
+		<bundle dependency='true'>
+			mvn:org.apache.servicemix.bundles/org.apache.servicemix.bundles.xmlresolver/${servicemix_xmlresolver_version}
+		</bundle>
+		<bundle dependency='true'>mvn:com.google.code.findbugs/jsr305/${jsr305_version}</bundle>
+		<bundle>mvn:com.phloc/phloc-schematron/${phloc_schematron_version}</bundle>
+		<bundle>mvn:com.phloc/phloc-commons/${phloc_commons_version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-validation' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir</feature>
+		<feature version='${project.version}'>hapi-fhir-utilities</feature>
+		<feature version='${project.version}'>hapi-fhir-ph-schematron</feature>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-converter/${project.version}</bundle>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-validation/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-validation-dstu2' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir-validation</feature>
+		<feature version='${project.version}'>hapi-fhir-dstu2</feature>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-validation-resources-dstu2/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-validation-hl7org-dstu2' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir-validation</feature>
+		<feature version='${project.version}'>hapi-fhir-hl7org-dstu2</feature>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-validation-resources-dstu2/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-validation-dstu2.1' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir-validation</feature>
+		<feature version='${project.version}'>hapi-fhir-dstu2.1</feature>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-validation-resources-dstu2.1/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-validation-dstu3' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir-validation</feature>
+		<feature version='${project.version}'>hapi-fhir-dstu3</feature>
+		<feature version='${project.version}'>hapi-fhir-r4</feature>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-validation-resources-dstu3/${project.version}</bundle>
+	</feature>
+
+	<feature name='hapi-fhir-validation-r4' version='${project.version}' start-level='50'>
+		<feature version='${project.version}'>hapi-fhir-validation</feature>
+		<feature version='${project.version}'>hapi-fhir-r4</feature>
+		<bundle>mvn:ca.uhn.hapi.fhir/hapi-fhir-validation-resources-r4/${project.version}</bundle>
+	</feature>
+</features>

osgi/hapi-fhir-karaf-integration-tests/pom.xml

@@ -0,0 +1,181 @@
+<!--
+  Licensed to the Apache Software Foundation (ASF) under one or more
+  contributor license agreements.  See the NOTICE file distributed with
+  this work for additional information regarding copyright ownership.
+  The ASF licenses this file to You under the Apache License, Version 2.0
+  (the "License"); you may not use this file except in compliance with
+  the License.  You may obtain a copy of the License at
+
+  http://www.apache.org/licenses/LICENSE-2.0
+
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+   <modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-deployable-pom</artifactId>
+		<version>3.3.0-SNAPSHOT</version>
+		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
+	</parent>
+
+   <artifactId>hapi-fhir-karaf-integration-tests</artifactId>
+   <packaging>jar</packaging>
+   <name>HAPI-FHIR Apache Karaf Integration Tests</name>
+
+   <description>
+      Integration tests for the HAPI-FHIR Apache Karaf features
+   </description>
+
+   <properties>
+		<pax.exam.version>4.9.1</pax.exam.version>
+   </properties>
+
+   <dependencies>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-base</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-client</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu2</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu3</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-r4</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu2.1</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-r4</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+
+      <!-- karaf test -->
+      <dependency>
+         <groupId>org.ops4j.pax.exam</groupId>
+         <artifactId>pax-exam-container-karaf</artifactId>
+         <version>${pax.exam.version}</version>
+         <scope>test</scope>
+      </dependency>
+      <dependency>
+         <groupId>org.ops4j.pax.exam</groupId>
+         <artifactId>pax-exam-junit4</artifactId>
+         <version>${pax.exam.version}</version>
+         <scope>test</scope>
+      </dependency>
+		<dependency>
+			<groupId>org.xmlunit</groupId>
+			<artifactId>xmlunit-core</artifactId>
+			<scope>test</scope>
+		</dependency>
+      <dependency>
+         <groupId>org.apache.karaf</groupId>
+         <artifactId>apache-karaf</artifactId>
+         <version>${apache_karaf_version}</version>
+         <scope>test</scope>
+         <type>tar.gz</type>
+      </dependency>
+      <dependency>
+         <groupId>org.apache.karaf.shell</groupId>
+         <artifactId>org.apache.karaf.shell.console</artifactId>
+         <version>${apache_karaf_version}</version>
+         <scope>test</scope>
+      </dependency>
+      <dependency>
+			<groupId>ca.uhn.hapi.fhir.karaf</groupId>
+			<artifactId>hapi-fhir</artifactId>
+         <version>${project.version}</version>
+         <classifier>features</classifier>
+         <type>xml</type>
+         <scope>test</scope>
+      </dependency>
+      <dependency>
+         <groupId>org.apache.karaf.features</groupId>
+         <artifactId>enterprise</artifactId>
+         <version>${apache_karaf_version}</version>
+         <classifier>features</classifier>
+         <type>xml</type>
+         <scope>test</scope>
+      </dependency>
+		<dependency>
+			<groupId>org.apache.servicemix.bundles</groupId>
+			<artifactId>org.apache.servicemix.bundles.hamcrest</artifactId>
+			<version>1.3_1</version>
+			<scope>runtime</scope>
+		</dependency>
+   </dependencies>
+
+   <build>
+      <plugins>
+         <plugin>
+            <groupId>org.apache.servicemix.tooling</groupId>
+            <artifactId>depends-maven-plugin</artifactId>
+            <version>1.2</version>
+            <executions>
+               <execution>
+                  <id>generate-depends-file</id>
+                  <goals>
+                     <goal>generate-depends-file</goal>
+                  </goals>
+               </execution>
+            </executions>
+         </plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<configuration>
+					<forkCount>1</forkCount>
+					<reuseForks>false</reuseForks>
+				</configuration>
+			</plugin>
+      </plugins>
+   </build>
+</project>

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/PaxExamOptions.java

@@ -0,0 +1,142 @@
+package ca.uhn.fhir.tests.integration.karaf;
+
+import org.ops4j.pax.exam.Option;
+import org.ops4j.pax.exam.karaf.options.LogLevelOption;
+import org.ops4j.pax.exam.options.DefaultCompositeOption;
+
+import java.io.File;
+
+import static org.ops4j.pax.exam.CoreOptions.maven;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.configureConsole;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.karafDistributionConfiguration;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.keepRuntimeFolder;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.logLevel;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.features;
+
+public enum PaxExamOptions {
+   KARAF(
+           karafDistributionConfiguration()
+                   .frameworkUrl(
+                           maven()
+                                   .groupId("org.apache.karaf")
+                                   .artifactId("apache-karaf")
+                                   .versionAsInProject()
+                                   .type("zip"))
+                   .name("Apache Karaf")
+                   .useDeployFolder(false)
+                   .unpackDirectory(new File("target/paxexam/unpack/")),
+           keepRuntimeFolder(),
+           configureConsole().ignoreLocalConsole(),
+           logLevel(LogLevelOption.LogLevel.INFO)
+   ),
+	WRAP(
+		features(
+			maven()
+				.groupId("org.apache.karaf.features")
+				.artifactId("enterprise")
+				.type("xml")
+				.classifier("features")
+				.versionAsInProject(),
+			"wrap")
+	),
+	HAPI_FHIR_CLIENT(
+		features(
+			maven()
+				.groupId("ca.uhn.hapi.fhir.karaf")
+				.artifactId("hapi-fhir")
+				.type("xml")
+				.classifier("features")
+				.versionAsInProject(),
+			"hapi-fhir-client")
+	),
+	HAPI_FHIR_HL7ORG_DSTU2(
+		features(
+			maven()
+				.groupId("ca.uhn.hapi.fhir.karaf")
+				.artifactId("hapi-fhir")
+				.type("xml")
+				.classifier("features")
+				.versionAsInProject(),
+			"hapi-fhir-hl7org-dstu2")
+	),
+	HAPI_FHIR_DSTU2_1(
+		features(
+			maven()
+				.groupId("ca.uhn.hapi.fhir.karaf")
+				.artifactId("hapi-fhir")
+				.type("xml")
+				.classifier("features")
+				.versionAsInProject(),
+			"hapi-fhir-dstu2.1")
+	),
+   HAPI_FHIR_DSTU3(
+           features(
+                   maven()
+                           .groupId("ca.uhn.hapi.fhir.karaf")
+                           .artifactId("hapi-fhir")
+                           .type("xml")
+                           .classifier("features")
+                           .versionAsInProject(),
+                   "hapi-fhir-dstu3")
+   ),
+	HAPI_FHIR_R4(
+		features(
+			maven()
+				.groupId("ca.uhn.hapi.fhir.karaf")
+				.artifactId("hapi-fhir")
+				.type("xml")
+				.classifier("features")
+				.versionAsInProject(),
+			"hapi-fhir-r4")
+	),
+	HAPI_FHIR_VALIDATION_DSTU2(
+		features(
+			maven()
+				.groupId("ca.uhn.hapi.fhir.karaf")
+				.artifactId("hapi-fhir")
+				.type("xml")
+				.classifier("features")
+				.versionAsInProject(),
+			"hapi-fhir-validation-dstu2")
+	),
+	HAPI_FHIR_VALIDATION_HL7ORG_DSTU2(
+		features(
+			maven()
+				.groupId("ca.uhn.hapi.fhir.karaf")
+				.artifactId("hapi-fhir")
+				.type("xml")
+				.classifier("features")
+				.versionAsInProject(),
+			"hapi-fhir-validation-hl7org-dstu2")
+	),
+	HAPI_FHIR_VALIDATION_DSTU3(
+		features(
+			maven()
+				.groupId("ca.uhn.hapi.fhir.karaf")
+				.artifactId("hapi-fhir")
+				.type("xml")
+				.classifier("features")
+				.versionAsInProject(),
+			"hapi-fhir-validation-dstu3")
+	),
+	HAPI_FHIR_VALIDATION_R4(
+		features(
+			maven()
+				.groupId("ca.uhn.hapi.fhir.karaf")
+				.artifactId("hapi-fhir")
+				.type("xml")
+				.classifier("features")
+				.versionAsInProject(),
+			"hapi-fhir-validation-r4")
+	);
+
+   private final Option[] options;
+
+   PaxExamOptions(Option... options) {
+      this.options = options;
+   }
+
+   public Option option() {
+      return new DefaultCompositeOption(options);
+   }
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/client/FhirClientTest.java

@@ -0,0 +1,63 @@
+package ca.uhn.fhir.tests.integration.karaf.client;
+
+import java.io.IOException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.PreferReturnEnum;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.ops4j.pax.exam.Configuration;
+import org.ops4j.pax.exam.Option;
+import org.ops4j.pax.exam.junit.PaxExam;
+import org.ops4j.pax.exam.spi.reactors.ExamReactorStrategy;
+import org.ops4j.pax.exam.spi.reactors.PerClass;
+
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.HAPI_FHIR_CLIENT;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.HAPI_FHIR_DSTU3;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.KARAF;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.WRAP;
+import static org.ops4j.pax.exam.CoreOptions.mavenBundle;
+import static org.ops4j.pax.exam.CoreOptions.options;
+import static org.ops4j.pax.exam.CoreOptions.when;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.debugConfiguration;
+
+/**
+ * Useful docs about this test: https://ops4j1.jira.com/wiki/display/paxexam/FAQ
+ */
+@RunWith(PaxExam.class)
+@ExamReactorStrategy(PerClass.class)
+@Ignore(value = "Relies on external service being up and running")
+public class FhirClientTest {
+
+	private FhirContext fhirContext = FhirContext.forDstu3();
+	private IGenericClient client   = fhirContext.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3");
+	private final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirClientTest.class);
+
+	@Configuration
+	public Option[] config() throws IOException {
+		return options(
+			KARAF.option(),
+			HAPI_FHIR_CLIENT.option(),
+			HAPI_FHIR_DSTU3.option(),
+			mavenBundle().groupId("org.apache.servicemix.bundles").artifactId("org.apache.servicemix.bundles.hamcrest").versionAsInProject(),
+			WRAP.option(),
+			when(false)
+				.useOptions(
+					debugConfiguration("5005", true))
+		);
+	}
+
+	@Test
+	public void createPatient() throws Exception {
+		Patient patient = new Patient();
+		patient.setId("PATIENTID");
+		patient.getMeta().addProfile("http://BAR");
+		patient.addName().addGiven("GIVEN");
+		MethodOutcome execute = client.create().resource(patient).prefer(PreferReturnEnum.REPRESENTATION).execute();
+		ourLog.info(execute.toString());
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu2/Dstu2ResourceValidatorDstu2Test.java

@@ -0,0 +1,331 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu2;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.List;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.ExtensionDt;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
+import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Condition;
+import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.dstu2.valueset.ConditionVerificationStatusEnum;
+import ca.uhn.fhir.model.dstu2.valueset.NarrativeStatusEnum;
+import ca.uhn.fhir.model.primitive.DateDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.parser.StrictErrorHandler;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.SchemaBaseValidator;
+import ca.uhn.fhir.validation.ValidationFailureException;
+import ca.uhn.fhir.validation.ValidationResult;
+import ca.uhn.fhir.validation.schematron.SchematronBaseValidator;
+import org.apache.commons.io.IOUtils;
+import org.hamcrest.Matcher;
+import org.hamcrest.Matchers;
+import org.hamcrest.core.StringContains;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.ops4j.pax.exam.Configuration;
+import org.ops4j.pax.exam.Option;
+import org.ops4j.pax.exam.junit.PaxExam;
+import org.ops4j.pax.exam.spi.reactors.ExamReactorStrategy;
+import org.ops4j.pax.exam.spi.reactors.PerClass;
+
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.HAPI_FHIR_VALIDATION_DSTU2;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.KARAF;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.WRAP;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.not;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.ops4j.pax.exam.CoreOptions.mavenBundle;
+import static org.ops4j.pax.exam.CoreOptions.options;
+import static org.ops4j.pax.exam.CoreOptions.when;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.debugConfiguration;
+
+
+/**
+ * Useful docs about this test: https://ops4j1.jira.com/wiki/display/paxexam/FAQ
+ */
+@RunWith(PaxExam.class)
+@ExamReactorStrategy(PerClass.class)
+public class Dstu2ResourceValidatorDstu2Test {
+
+	private FhirContext ourCtx = FhirContext.forDstu2();
+	private final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Dstu2ResourceValidatorDstu2Test.class);
+
+   @Configuration
+   public Option[] config() throws IOException {
+      return options(
+      	KARAF.option(),
+			WRAP.option(),
+			HAPI_FHIR_VALIDATION_DSTU2.option(),
+			mavenBundle().groupId("org.apache.servicemix.bundles").artifactId("org.apache.servicemix.bundles.hamcrest").versionAsInProject(),
+			when(false)
+         	.useOptions(
+            	debugConfiguration("5005", true))
+      );
+   }
+
+	private FhirValidator createFhirValidator() {
+		FhirValidator val = ourCtx.newValidator();
+		val.setValidateAgainstStandardSchema(true);
+		val.setValidateAgainstStandardSchematron(true);
+		return val;
+	}
+
+	private String logOperationOutcome(ValidationResult result) {
+		OperationOutcome operationOutcome = (OperationOutcome) result.toOperationOutcome();
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(operationOutcome);
+		ourLog.info(encoded);
+		return encoded;
+	}
+
+	/**
+	 * See issue #50
+	 */
+	@Test()
+	public void testOutOfBoundsDate() {
+		Patient p = new Patient();
+		p.setBirthDate(new DateDt("2000-12-31"));
+
+		// Put in an invalid date
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new StrictErrorHandler());
+
+		String encoded = parser.setPrettyPrint(true).encodeResourceToString(p).replace("2000-12-31", "2000-15-31");
+		ourLog.info(encoded);
+
+		assertThat(encoded, StringContains.containsString("2000-15-31"));
+
+		ValidationResult result = ourCtx.newValidator().validateWithResult(encoded);
+		String resultString = parser.setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
+		ourLog.info(resultString);
+
+		assertEquals(2, ((OperationOutcome)result.toOperationOutcome()).getIssue().size());
+		assertThat(resultString, StringContains.containsString("cvc-pattern-valid"));
+
+		try {
+			parser.parseResource(encoded);
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Invalid attribute value \"2000-15-31\": Invalid date/time format: \"2000-15-31\"", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testSchemaBundleValidatorIsSuccessful() throws IOException {
+		String res = IOUtils.toString(getClass().getClassLoader().getResourceAsStream("bundle-example.json"), StandardCharsets.UTF_8);
+		Bundle b = ourCtx.newJsonParser().parseResource(Bundle.class, res);
+
+		ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(b));
+
+		FhirValidator val = createFhirValidator();
+
+		ValidationResult result = val.validateWithResult(b);
+
+		OperationOutcome operationOutcome = (OperationOutcome) result.toOperationOutcome();
+
+		assertTrue(result.toString(), result.isSuccessful());
+		assertNotNull(operationOutcome);
+		assertEquals(1, operationOutcome.getIssue().size());
+	}
+
+	@SuppressWarnings("deprecation")
+	@Test
+	public void testSchemaResourceValidator() throws IOException {
+		String res = IOUtils.toString(getClass().getClassLoader().getResourceAsStream("patient-example-dicom.json"));
+		Patient p = ourCtx.newJsonParser().parseResource(Patient.class, res);
+
+		ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p));
+
+		FhirValidator val = ourCtx.newValidator();
+		val.setValidateAgainstStandardSchema(true);
+		val.setValidateAgainstStandardSchematron(false);
+
+		val.validate(p);
+
+		p.getAnimal().getBreed().setText("The Breed");
+		try {
+			val.validate(p);
+			fail();
+		} catch (ValidationFailureException e) {
+			OperationOutcome operationOutcome = (OperationOutcome) e.getOperationOutcome();
+			ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(operationOutcome));
+			assertEquals(1, operationOutcome.getIssue().size());
+			assertThat(operationOutcome.getIssueFirstRep().getDetailsElement().getValue(), containsString("cvc-complex-type"));
+		}
+	}
+
+	/**
+	 * Make sure that the elements that appear in all resources (meta, language, extension, etc)
+	 * all appear in the correct order
+	 */
+	@Test
+	public void testValidateResourceWithResourceElements() {
+		TestPatientFor327 patient = new TestPatientFor327();
+		patient.setBirthDate(new Date(), TemporalPrecisionEnum.DAY);
+		patient.setId("123");
+		patient.getText().setDiv("<div>FOO</div>");
+		patient.getText().setStatus(NarrativeStatusEnum.GENERATED);
+		patient.getLanguage().setValue("en");
+		patient.addUndeclaredExtension(true, "http://foo").setValue(new StringDt("MOD"));
+		ResourceMetadataKeyEnum.UPDATED.put(patient, new InstantDt(new Date()));
+
+		List<ResourceReferenceDt> conditions = new ArrayList<ResourceReferenceDt>();
+		Condition condition = new Condition();
+		condition.getPatient().setReference("Patient/123");
+		condition.addBodySite().setText("BODY SITE");
+		condition.getCode().setText("CODE");
+		condition.setVerificationStatus(ConditionVerificationStatusEnum.CONFIRMED);
+		conditions.add(new ResourceReferenceDt(condition));
+		patient.setCondition(conditions);
+		patient.addIdentifier().setSystem("http://foo").setValue("123");
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+
+		FhirValidator val = createFhirValidator();
+		ValidationResult result = val.validateWithResult(encoded);
+
+		String messageString = logOperationOutcome(result);
+
+		assertTrue(result.isSuccessful());
+
+		assertThat(messageString, containsString("No issues"));
+
+	}
+
+	/**
+	 * 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() {
+		PatientProfileDstu2 myPatient = new PatientProfileDstu2();
+		myPatient.setColorPrimary(new CodeableConceptDt("http://example.com#animalColor", "furry-grey"));
+		myPatient.setColorSecondary(new CodeableConceptDt("http://example.com#animalColor", "furry-white"));
+		myPatient.setOwningOrganization(new ResourceReferenceDt("Organization/2.25.79433498044103547197447759549862032393"));
+		myPatient.addName().addFamily("FamilyName");
+		myPatient.addUndeclaredExtension(new ExtensionDt().setUrl("http://foo.com/example").setValue(new StringDt("String Extension")));
+
+		IParser p = FhirContext.forDstu2().newJsonParser().setPrettyPrint(true);
+		String messageString = p.encodeResourceToString(myPatient);
+		ourLog.info(messageString);
+
+		//@formatter:off
+		assertThat(messageString, stringContainsInOrder(
+			"meta",
+			"String Extension",
+			"Organization/2.25.79433498044103547197447759549862032393",
+			"furry-grey",
+			"furry-white",
+			"FamilyName"
+		));
+		assertThat(messageString, not(stringContainsInOrder(
+			"extension",
+			"meta"
+		)));
+		//@formatter:on
+
+		FhirValidator val = ourCtx.newValidator();
+		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+
+		ValidationResult result = val.validateWithResult(messageString);
+
+		logOperationOutcome(result);
+
+		assertTrue(result.isSuccessful());
+
+		assertThat(messageString, containsString("valueReference"));
+		assertThat(messageString, not(containsString("valueResource")));
+	}
+
+	private Matcher<? super String> stringContainsInOrder(java.lang.String... substrings) {
+		return Matchers.stringContainsInOrder(Arrays.asList(substrings));
+	}
+
+	/**
+	 * 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 testValidateWithExtensionsXml() {
+		PatientProfileDstu2 myPatient = new PatientProfileDstu2();
+		myPatient.setColorPrimary(new CodeableConceptDt("http://example.com#animalColor", "furry-grey"));
+		myPatient.setColorSecondary(new CodeableConceptDt("http://example.com#animalColor", "furry-white"));
+		myPatient.setOwningOrganization(new ResourceReferenceDt("Organization/2.25.79433498044103547197447759549862032393"));
+		myPatient.addName().addFamily("FamilyName");
+		myPatient.addUndeclaredExtension(new ExtensionDt().setUrl("http://foo.com/example").setValue(new StringDt("String Extension")));
+
+		IParser p = FhirContext.forDstu2().newXmlParser().setPrettyPrint(true);
+		String messageString = p.encodeResourceToString(myPatient);
+		ourLog.info(messageString);
+
+		//@formatter:off
+		assertThat(messageString, stringContainsInOrder(
+			"meta",
+			"Organization/2.25.79433498044103547197447759549862032393",
+			"furry-grey",
+			"furry-white",
+			"String Extension",
+			"FamilyName"
+		));
+		assertThat(messageString, not(stringContainsInOrder(
+			"extension",
+			"meta"
+		)));
+		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));
+
+		ValidationResult result = val.validateWithResult(messageString);
+
+		logOperationOutcome(result);
+
+		assertTrue(result.isSuccessful());
+
+		assertThat(messageString, containsString("valueReference"));
+		assertThat(messageString, not(containsString("valueResource")));
+	}
+
+	@ResourceDef(name = "Patient")
+	public static class TestPatientFor327 extends Patient {
+
+		private static final long serialVersionUID = 1L;
+
+		@Child(name = "testCondition")
+		@ca.uhn.fhir.model.api.annotation.Extension(url = "testCondition", definedLocally = true, isModifier = false)
+		private List<ResourceReferenceDt> testConditions = null;
+
+		public List<ResourceReferenceDt> getConditions() {
+			return this.testConditions;
+		}
+
+		public void setCondition(List<ResourceReferenceDt> ref) {
+			this.testConditions = ref;
+		}
+	}
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu2/PatientProfileDstu2.java

@@ -0,0 +1,72 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu2;
+
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
+import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.util.ElementUtil;
+
+@ResourceDef(name="Patient", profile = "http://ahr.copa.inso.tuwien.ac.at/StructureDefinition/Patient")
+public class PatientProfileDstu2 extends Patient {
+
+	private static final long serialVersionUID = 1L;
+
+	@Child(name="owner", min=0, max=1)
+    @Extension(url="http://ahr.copa.inso.tuwien.ac.at/StructureDefinition/Patient#owningOrganization", definedLocally=false, isModifier=false)
+    @Description(shortDefinition="The organization that owns this animal")
+    private ResourceReferenceDt owningOrganization;
+
+    public ResourceReferenceDt getOwningOrganization() {
+        if (owningOrganization == null) {
+            owningOrganization = new ResourceReferenceDt();
+        }
+        return owningOrganization;
+    }
+
+    public PatientProfileDstu2 setOwningOrganization(ResourceReferenceDt owningOrganization) {
+        this.owningOrganization = owningOrganization;
+        return this;
+    }
+
+    @Child(name="colorPrimary", min=0, max=1)
+    @Extension(url="http://ahr.copa.inso.tuwien.ac.at/StructureDefinition/Patient#animal-colorPrimary", definedLocally=false, isModifier=false)
+    @Description(shortDefinition="The animals primary color")
+    private CodeableConceptDt colorPrimary;
+
+    @Child(name="colorSecondary", min=0, max=1)
+    @Extension(url="http://ahr.copa.inso.tuwien.ac.at/StructureDefinition/Patient#animal-colorSecondary", definedLocally=false, isModifier=false)
+    @Description(shortDefinition="The animals secondary color")
+    private CodeableConceptDt colorSecondary;
+
+    public CodeableConceptDt getColorPrimary() {
+        if (this.colorPrimary == null) {
+            return new CodeableConceptDt();
+        }
+        return colorPrimary;
+    }
+
+    public void setColorPrimary(CodeableConceptDt colorPrimary) {
+        this.colorPrimary = colorPrimary;
+    }
+
+    public CodeableConceptDt getColorSecondary() {
+        if (this.colorSecondary == null) {
+            return new CodeableConceptDt();
+        }
+        return colorSecondary;
+    }
+
+    public void setColorSecondary(CodeableConceptDt colorSecondary) {
+        this.colorSecondary = colorSecondary;
+    }
+
+    @Override
+    public boolean isEmpty() {
+        return super.isEmpty() && ElementUtil.isEmpty(owningOrganization) &&  ElementUtil.isEmpty(colorPrimary)
+                && ElementUtil.isEmpty(colorSecondary) ;
+    }
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu21/PatientWithExtendedContactDstu3.java

@@ -0,0 +1,60 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu21;
+
+import java.util.ArrayList;
+import java.util.List;
+import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.dstu2016may.model.Identifier;
+import org.hl7.fhir.dstu2016may.model.Patient;
+
+@ResourceDef(name = "Patient")
+public class PatientWithExtendedContactDstu3 extends Patient {
+
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * A contact party (e.g. guardian, partner, friend) for the patient.
+	 */
+	@Child(name = "contact", type = {}, order = Child.REPLACE_PARENT, min = 0, max = Child.MAX_UNLIMITED, modifier = false, summary = false)
+	@Description(shortDefinition = "A contact party (e.g. guardian, partner, friend) for the patient", formalDefinition = "A contact party (e.g. guardian, partner, friend) for the patient.")
+	protected List<CustomContactComponent> customContact;
+
+	public List<CustomContactComponent> getCustomContact() {
+		if (customContact == null) {
+			customContact = new ArrayList<CustomContactComponent>();
+		}
+		return customContact;
+	}
+
+	@Block()
+	public static class CustomContactComponent extends ContactComponent {
+
+		private static final long serialVersionUID = 1L;
+		@Child(name = "contact-eyecolour", type = { Identifier.class }, modifier = true)
+		@Description(shortDefinition = "Application ID")
+		@Extension(url = "http://foo.com/contact-eyecolour", definedLocally = false, isModifier = false)
+		private Identifier myEyeColour;
+
+		/*
+		 * Get messageHeaderApplicationId
+		 */
+		public Identifier getEyeColour() {
+			if (myEyeColour == null) {
+				myEyeColour = new Identifier();
+			}
+			return myEyeColour;
+		}
+
+		/*
+		 * Set messageHeaderApplicationId
+		 */
+		public void setEyeColour(Identifier messageHeaderApplicationId) {
+			this.myEyeColour = messageHeaderApplicationId;
+		}
+
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu2hl7org/FhirInstanceValidatorTest.java

@@ -0,0 +1,136 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu2hl7org;
+
+import java.io.IOException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.ValidationResult;
+import org.hl7.fhir.instance.hapi.validation.DefaultProfileValidationSupport;
+import org.hl7.fhir.instance.hapi.validation.FhirInstanceValidator;
+import org.hl7.fhir.instance.model.DateType;
+import org.hl7.fhir.instance.model.Observation;
+import org.hl7.fhir.instance.model.QuestionnaireResponse;
+import org.hl7.fhir.instance.model.StringType;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.ops4j.pax.exam.Configuration;
+import org.ops4j.pax.exam.Option;
+import org.ops4j.pax.exam.junit.PaxExam;
+import org.ops4j.pax.exam.spi.reactors.ExamReactorStrategy;
+import org.ops4j.pax.exam.spi.reactors.PerClass;
+
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.HAPI_FHIR_VALIDATION_HL7ORG_DSTU2;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.KARAF;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.WRAP;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.not;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+import static org.ops4j.pax.exam.CoreOptions.mavenBundle;
+import static org.ops4j.pax.exam.CoreOptions.options;
+import static org.ops4j.pax.exam.CoreOptions.when;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.debugConfiguration;
+
+/**
+ * Useful docs about this test: https://ops4j1.jira.com/wiki/display/paxexam/FAQ
+ */
+@RunWith(PaxExam.class)
+@ExamReactorStrategy(PerClass.class)
+public class FhirInstanceValidatorTest {
+   private FhirInstanceValidator ourValidator = new FhirInstanceValidator(new DefaultProfileValidationSupport());
+   private FhirContext ourCtxHl7OrgDstu2 = FhirContext.forDstu2Hl7Org();
+   private final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidatorTest.class);
+
+	@Configuration
+	public Option[] config() throws IOException {
+		return options(
+			KARAF.option(),
+			WRAP.option(),
+			HAPI_FHIR_VALIDATION_HL7ORG_DSTU2.option(),
+			mavenBundle().groupId("org.apache.servicemix.bundles").artifactId("org.apache.servicemix.bundles.hamcrest").versionAsInProject(),
+			when(false)
+				.useOptions(
+					debugConfiguration("5005", true))
+		);
+	}
+
+	@Test
+	public void testQuestionnaireResponse() {
+		QuestionnaireResponse qr = new QuestionnaireResponse();
+		qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
+		qr.getGroup().addGroup().addQuestion().setLinkId("foo");
+		qr.getGroup().addQuestion().setLinkId("bar");
+
+		FhirValidator val = ourCtxHl7OrgDstu2.newValidator();
+
+		val.registerValidatorModule(ourValidator);
+
+		ValidationResult result = val.validateWithResult(qr);
+
+		String encoded = ourCtxHl7OrgDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
+		ourLog.info(encoded);
+
+		assertTrue(result.isSuccessful());
+	}
+
+	@Test
+	public void testObservation() {
+		Observation o = new Observation();
+		o.addIdentifier().setSystem("http://acme.org").setValue("1234");
+		o.setStatus(Observation.ObservationStatus.FINAL);
+		o.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
+		o.getEncounter().setReference("Encounter/1234");
+
+		FhirValidator val = ourCtxHl7OrgDstu2.newValidator();
+
+		val.registerValidatorModule(ourValidator);
+
+		ValidationResult result = val.validateWithResult(o);
+
+		String encoded = ourCtxHl7OrgDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
+		ourLog.info(encoded);
+
+		assertTrue(result.isSuccessful());
+	}
+
+	@Test
+	public void testParametersWithTwoParameters() {
+		org.hl7.fhir.instance.model.Patient patient = new org.hl7.fhir.instance.model.Patient();
+		patient.addName().addGiven("James");
+		patient.setBirthDateElement(new DateType("2011-02-02"));
+
+		org.hl7.fhir.instance.model.Parameters input = new org.hl7.fhir.instance.model.Parameters();
+		input.addParameter().setName("mode").setValue(new StringType("create"));
+		input.addParameter().setName("resource").setResource(patient);
+
+		FhirValidator val = ourCtxHl7OrgDstu2.newValidator();
+
+		val.registerValidatorModule(ourValidator);
+
+		ValidationResult result = val.validateWithResult(input);
+
+		String encoded = ourCtxHl7OrgDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
+		ourLog.info(encoded);
+
+		assertTrue(result.isSuccessful());
+		assertThat(encoded, not(containsString("A parameter must have a value or a resource, but not both")));
+	}
+
+	@Test
+	public void testParametersHl7OrgDstu2() {
+		org.hl7.fhir.instance.model.Patient patient = new org.hl7.fhir.instance.model.Patient();
+		patient.addName().addGiven("James");
+		patient.setBirthDateElement(new DateType("2011-02-02"));
+
+		org.hl7.fhir.instance.model.Parameters input = new org.hl7.fhir.instance.model.Parameters();
+		input.addParameter().setName("resource").setResource(patient);
+
+		FhirValidator val = ourCtxHl7OrgDstu2.newValidator();
+
+		val.registerValidatorModule(ourValidator);
+
+		ValidationResult result = val.validateWithResult(input);
+
+		ourLog.info(ourCtxHl7OrgDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome()));
+		assertTrue(result.isSuccessful());
+	}
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu2hl7org/MyObservationWithExtensions.java

@@ -0,0 +1,106 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu2hl7org;
+
+import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.util.ElementUtil;
+import org.hl7.fhir.instance.model.Attachment;
+import org.hl7.fhir.instance.model.BackboneElement;
+import org.hl7.fhir.instance.model.DateType;
+import org.hl7.fhir.instance.model.Patient;
+import org.hl7.fhir.instance.model.StringType;
+import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
+
+
+@ResourceDef(name="Patient")
+public class MyObservationWithExtensions extends Patient {
+	
+	@Extension(url = "urn:patientext:att", definedLocally = false, isModifier = false)
+	@Child(name = "extAtt", order = 0)
+	private Attachment myExtAtt;
+
+	@Extension(url = "urn:patientext:moreext", definedLocally = false, isModifier = false)
+	@Child(name = "moreExt", order = 1)
+	private MoreExt myMoreExt;
+
+	@Extension(url = "urn:modext", definedLocally = false, isModifier = true)
+	@Child(name = "modExt", order = 2)
+	private DateType myModExt;
+
+	public Attachment getExtAtt() {
+		return myExtAtt;
+	}
+
+	public MoreExt getMoreExt() {
+		return myMoreExt;
+	}
+
+	public void setMoreExt(MoreExt theMoreExt) {
+		myMoreExt = theMoreExt;
+	}
+
+	public DateType getModExt() {
+		return myModExt;
+	}
+
+	public void setModExt(DateType theModExt) {
+		myModExt = theModExt;
+	}
+
+	public void setExtAtt(Attachment theExtAtt) {
+		myExtAtt = theExtAtt;
+	}
+
+	@Override
+	public boolean isEmpty() {
+		return super.isEmpty() && ElementUtil.isEmpty(myExtAtt, myModExt, myMoreExt);
+	}
+
+	/**
+	 * Block class for child element: <b>Observation.referenceRange</b> (Provides guide for interpretation)
+	 * 
+	 * <p>
+	 * <b>Definition:</b> Guidance on how to interpret the value by comparison to a normal or recommended range
+	 * </p>
+	 */
+	@Block(name = "Observation.someExtensions")
+	public static class MoreExt extends BackboneElement implements IBaseBackboneElement {
+
+		@Extension(url = "urn:patientext:moreext:1", definedLocally = false, isModifier = false)
+		@Child(name = "str1", order = 0)
+		private StringType myStr1;
+
+		@Extension(url = "urn:patientext:moreext:2", definedLocally = false, isModifier = false)
+		@Child(name = "str2", order = 1)
+		private StringType myStr2;
+
+		public StringType getStr1() {
+			return myStr1;
+		}
+
+		public void setStr1(StringType theStr1) {
+			myStr1 = theStr1;
+		}
+
+		public StringType getStr2() {
+			return myStr2;
+		}
+
+		public void setStr2(StringType theStr2) {
+			myStr2 = theStr2;
+		}
+
+		@Override
+		public boolean isEmpty() {
+			return ElementUtil.isEmpty(myStr1, myStr2);
+		}
+
+		@Override
+		public BackboneElement copy() {
+			throw new UnsupportedOperationException();
+		}
+
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu2hl7org/MyOrganizationDstu2.java

@@ -0,0 +1,11 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu2hl7org;
+
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.instance.model.Organization;
+
+@ResourceDef()
+public class MyOrganizationDstu2 extends Organization {
+
+	private static final long serialVersionUID = 1L;
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu2hl7org/MyPatientHl7Org.java

@@ -0,0 +1,64 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu2hl7org;
+
+import java.util.ArrayList;
+import java.util.List;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.instance.model.DateTimeType;
+import org.hl7.fhir.instance.model.Patient;
+import org.hl7.fhir.instance.model.Reference;
+import org.hl7.fhir.instance.model.StringType;
+
+
+@ResourceDef()
+public class MyPatientHl7Org extends Patient {
+	
+	private static final long serialVersionUID = 1L;
+
+	@Child(name="petName")	
+	@Extension(url="http://example.com/dontuse#petname", definedLocally=false, isModifier=false)
+	@Description(shortDefinition="The name of the patient's favourite pet")
+	private StringType myPetName;
+	
+	@Child(name="importantDates", max=Child.MAX_UNLIMITED)	
+	@Extension(url="http://example.com/dontuse#importantDates", definedLocally=false, isModifier=true)
+	@Description(shortDefinition="Some dates of note for the patient")
+	private List<DateTimeType> myImportantDates;
+	
+	@Child(name="managingOrganization", order=Child.REPLACE_PARENT, min=0, max=1, type={
+			MyOrganizationDstu2.class	})
+		@Description(
+			shortDefinition="Organization that is the custodian of the patient record",
+			formalDefinition="Organization that is the custodian of the patient record"
+		)
+	private Reference myManagingOrganization;
+	
+	
+	@Override
+	public boolean isEmpty() {
+		return super.isEmpty() && myPetName.isEmpty();
+	}
+	
+	
+	public List<DateTimeType> getImportantDates() {
+		if (myImportantDates==null) {
+			myImportantDates = new ArrayList<DateTimeType>();
+		}
+		return myImportantDates;
+	}
+
+	public StringType getPetName() {
+		return myPetName;
+	}
+
+	public void setImportantDates(List<DateTimeType> theImportantDates) {
+		myImportantDates = theImportantDates;
+	}
+
+	public void setPetName(StringType thePetName) {
+		myPetName = thePetName;
+	}
+	
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu2hl7org/MyPatientWithOneDeclaredEnumerationExtension.java

@@ -0,0 +1,26 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu2hl7org;
+
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.instance.model.Address.AddressUse;
+import org.hl7.fhir.instance.model.Enumeration;
+import org.hl7.fhir.instance.model.Patient;
+
+@ResourceDef(name = "Patient")
+public class MyPatientWithOneDeclaredEnumerationExtension extends Patient {
+
+	private static final long serialVersionUID = 1L;
+
+	@Child(order = 0, name = "foo")
+	@ca.uhn.fhir.model.api.annotation.Extension(url = "urn:foo", definedLocally = true, isModifier = false)
+	private Enumeration<AddressUse> myFoo;
+
+	public Enumeration<AddressUse> getFoo() {
+		return myFoo;
+	}
+
+	public void setFoo(Enumeration<AddressUse> theFoo) {
+		myFoo = theFoo;
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu2hl7org/ResourceWithExtensionsA.java

@@ -0,0 +1,206 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu2hl7org;
+
+import java.util.List;
+import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.instance.model.BackboneElement;
+import org.hl7.fhir.instance.model.CodeableConcept;
+import org.hl7.fhir.instance.model.DateType;
+import org.hl7.fhir.instance.model.DomainResource;
+import org.hl7.fhir.instance.model.Identifier;
+import org.hl7.fhir.instance.model.ResourceType;
+import org.hl7.fhir.instance.model.StringType;
+
+@ResourceDef(name = "ResourceWithExtensionsA", id="0001")
+public class ResourceWithExtensionsA extends DomainResource {
+
+	/*
+	 * NB: several unit tests depend on the structure here
+	 * so check the unit tests immediately after any changes 
+	 */
+	
+
+	private static final long serialVersionUID = 1L;
+
+	@Child(name = "foo1", type = StringType.class, order = 0, min = 0, max = Child.MAX_UNLIMITED)
+	@Extension(url = "http://foo/#f1", definedLocally=true, isModifier=false)
+	private List<StringType> myFoo1;
+
+	@Child(name = "foo2", type = StringType.class, order = 1, min = 0, max = 1)
+	@Extension(url = "http://foo/#f2", definedLocally=true, isModifier=true)
+	private StringType myFoo2;
+
+	@Child(name = "bar1", type = Bar1.class, order = 2, min = 1, max = Child.MAX_UNLIMITED)
+	@Extension(url = "http://bar/#b1", definedLocally=true, isModifier=false)
+	private List<Bar1> myBar1;
+	
+	@Child(name = "bar2", type = Bar1.class, order = 3, min = 1, max = Child.MAX_UNLIMITED)
+	@Extension(url = "http://bar/#b2", definedLocally=true, isModifier=false)
+	private Bar1 myBar2;
+	
+	@Child(name="baz", type = CodeableConcept.class, order = 4)
+    @Extension(url= "http://baz/#baz", definedLocally=true, isModifier=false)
+    @Description(shortDefinition = "Contains a codeable concept")
+	private CodeableConcept myBaz;
+
+	@Child(name = "identifier", type = Identifier.class, order = 0, min = 0, max = Child.MAX_UNLIMITED)
+	private List<Identifier> myIdentifier;
+
+	public List<Bar1> getBar1() {
+		return myBar1;
+	}
+
+	public Bar1 getBar2() {
+		return myBar2;
+	}
+
+	public List<StringType> getFoo1() {
+		return myFoo1;
+	}
+
+	public StringType getFoo2() {
+		return myFoo2;
+	}
+
+	public CodeableConcept getBaz() { return myBaz; }
+
+	public List<Identifier> getIdentifier() {
+		return myIdentifier;
+	}
+
+	public void setBar1(List<Bar1> theBar1) {
+		myBar1 = theBar1;
+	}
+
+	public void setBar2(Bar1 theBar2) {
+		myBar2 = theBar2;
+	}
+
+	public void setFoo1(List<StringType> theFoo1) {
+		myFoo1 = theFoo1;
+	}
+
+	public void setFoo2(StringType theFoo2) {
+		myFoo2 = theFoo2;
+	}
+
+	public void setBaz(CodeableConcept myBaz) { this.myBaz = myBaz; }
+
+	public void setIdentifier(List<Identifier> theValue) {
+		myIdentifier = theValue;
+	}
+
+	@Block(name = "Bar1")
+	public static class Bar1 extends BackboneElement {
+
+		public Bar1() {
+			super();
+		}
+		
+		@Child(name = "bar11", type = DateType.class, order = 0, min = 0, max = Child.MAX_UNLIMITED)
+		@Extension(url = "http://bar/#b1/1", definedLocally=true, isModifier=false)
+		private List<DateType> myBar11;
+
+		@Child(name = "bar12", type = DateType.class, order = 1, min = 0, max = Child.MAX_UNLIMITED)
+		@Extension(url = "http://bar/#b1/2", definedLocally=true, isModifier=false)
+		private List<Bar2> myBar12;
+
+		@Override
+		public boolean isEmpty() {
+			return false; // not implemented
+		}
+
+		public List<DateType> getBar11() {
+			return myBar11;
+		}
+
+		public List<Bar2> getBar12() {
+			return myBar12;
+		}
+
+		public void setBar11(List<DateType> theBar11) {
+			myBar11 = theBar11;
+		}
+
+		public void setBar12(List<Bar2> theBar12) {
+			myBar12 = theBar12;
+		}
+		
+
+		@Override
+		public BackboneElement copy() {
+			// TODO Auto-generated method stub
+			return null;
+		}
+
+
+
+	}
+
+	@Block(name = "Bar2")
+	public static class Bar2 extends BackboneElement {
+
+		@Child(name = "bar121", type = DateType.class, order = 0, min = 0, max = Child.MAX_UNLIMITED)
+		@Extension(url = "http://bar/#b1/2/1", definedLocally=true, isModifier=false)
+		private List<DateType> myBar121;
+
+		@Child(name = "bar122", type = DateType.class, order = 1, min = 0, max = Child.MAX_UNLIMITED)
+		@Extension(url = "http://bar/#b1/2/2", definedLocally=true, isModifier=false)
+		private List<DateType> myBar122;
+
+		@Override
+		public boolean isEmpty() {
+			return false; // not implemented
+		}
+
+
+		public List<DateType> getBar121() {
+			return myBar121;
+		}
+
+		public List<DateType> getBar122() {
+			return myBar122;
+		}
+
+		public void setBar121(List<DateType> theBar121) {
+			myBar121 = theBar121;
+		}
+
+		public void setBar122(List<DateType> theBar122) {
+			myBar122 = theBar122;
+		}
+
+		@Override
+		public BackboneElement copy() {
+			// TODO Auto-generated method stub
+			return null;
+		}
+
+
+
+	}
+
+	@Override
+	public boolean isEmpty() {
+		return false; // not implemented
+	}
+
+
+	@Override
+	public DomainResource copy() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public ResourceType getResourceType() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/CustomDiagnosticReport.java

@@ -0,0 +1,13 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu3;
+
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.dstu3.model.DiagnosticReport;
+
+@ResourceDef(name = "DiagnosticReport", profile = CustomDiagnosticReport.PROFILE)
+public class CustomDiagnosticReport extends DiagnosticReport {
+
+	public static final String PROFILE = "http://custom_DiagnosticReport";
+
+	private static final long serialVersionUID = 1L;
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/CustomObservation.java

@@ -0,0 +1,13 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu3;
+
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.dstu3.model.Observation;
+
+@ResourceDef(name = "Observation", profile = CustomObservation.PROFILE)
+public class CustomObservation extends Observation {
+
+	public static final String PROFILE = "http://custom_Observation";
+	
+	private static final long serialVersionUID = 1L;
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/CustomPatientDstu3.java

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu3;
+
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.dstu3.model.BooleanType;
+import org.hl7.fhir.dstu3.model.Patient;
+
+@ResourceDef(name = "Patient", profile = "Patient")
+public class CustomPatientDstu3 extends Patient {
+
+
+    private static final long serialVersionUID = 1L;
+
+    @Child(name = "homeless", order = 1)
+    @Extension(url = "/StructureDefinition/homeless", definedLocally = true, isModifier = false)
+    @Description(shortDefinition = "The patient being homeless, true if homeless")
+    private BooleanType homeless;
+
+
+    public BooleanType getHomeless() {
+        return homeless;
+    }
+
+    public void setHomeless(final BooleanType homeless) {
+        this.homeless = homeless;
+    }
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/FooMessageHeader.java

@@ -0,0 +1,46 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu3;
+
+import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.dstu3.model.Identifier;
+import org.hl7.fhir.dstu3.model.MessageHeader;
+import org.hl7.fhir.exceptions.FHIRException;
+
+@ResourceDef(name = "MessageHeader")
+public class FooMessageHeader extends MessageHeader {
+
+	private static final long serialVersionUID = 1L;
+
+	@Block()
+	public static class FooMessageSourceComponent extends MessageSourceComponent {
+
+		private static final long serialVersionUID = 1L;
+		@Child(name = "ext-messageheader-application-id", type = Identifier.class, modifier = true)
+		@Description(shortDefinition = "Message Header Application ID")
+		@Extension(url = "http://foo", definedLocally = false, isModifier = false)
+		private Identifier messageHeaderApplicationId;
+
+		/*
+		 * Get messageHeaderApplicationId
+		 */
+		public Identifier getMessageHeaderApplicationId() throws FHIRException {
+
+			if (messageHeaderApplicationId == null) {
+				messageHeaderApplicationId = new Identifier();
+			}
+			return messageHeaderApplicationId;
+		}
+
+		/*
+		 * Set messageHeaderApplicationId
+		 */
+		public void setmessageHeaderApplicationId(Identifier messageHeaderApplicationId) {
+			this.messageHeaderApplicationId = messageHeaderApplicationId;
+		}
+
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/FooMessageHeaderWithExplicitField.java

@@ -0,0 +1,57 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu3;
+
+import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.dstu3.model.Identifier;
+import org.hl7.fhir.dstu3.model.MessageHeader;
+import org.hl7.fhir.exceptions.FHIRException;
+
+@ResourceDef(name = "FooMessageHeader")
+public class FooMessageHeaderWithExplicitField extends MessageHeader {
+
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * The source application from which this message originated.
+	 */
+	@Child(name = "source", type = {}, order = Child.REPLACE_PARENT, min = 1, max = 1, modifier = false, summary = true)
+	@Description(shortDefinition = "Message Source Application", formalDefinition = "The source application from which this message originated.")
+	protected FooMessageSourceComponent source;
+
+	public void setSourceNew(FooMessageSourceComponent theSource) {
+		source = theSource;
+	}
+
+	@Block()
+	public static class FooMessageSourceComponent extends MessageSourceComponent {
+
+		private static final long serialVersionUID = 1L;
+		@Child(name = "ext-messageheader-application-id", type = Identifier.class, modifier = true)
+		@Description(shortDefinition = "Message Header Application ID")
+		@Extension(url = "http://foo", definedLocally = false, isModifier = false)
+		private Identifier messageHeaderApplicationId;
+
+		/*
+		 * Get messageHeaderApplicationId
+		 */
+		public Identifier getMessageHeaderApplicationId() throws FHIRException {
+
+			if (messageHeaderApplicationId == null) {
+				messageHeaderApplicationId = new Identifier();
+			}
+			return messageHeaderApplicationId;
+		}
+
+		/*
+		 * Set messageHeaderApplicationId
+		 */
+		public void setmessageHeaderApplicationId(Identifier messageHeaderApplicationId) {
+			this.messageHeaderApplicationId = messageHeaderApplicationId;
+		}
+
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/MyPatientWithCustomUrlExtension.java

@@ -0,0 +1,52 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu3;
+
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.StringType;
+
+@ResourceDef()
+public class MyPatientWithCustomUrlExtension extends Patient {
+
+    private static final long serialVersionUID = 1L;
+
+    @Child(name = "petName")
+    @Extension(url = "/petname", definedLocally = false, isModifier = false)
+    @Description(shortDefinition = "The name of the patient's favourite pet")
+    private StringType myPetName;
+
+    @Child(name = "customid")
+    @Extension(url = "/customid", definedLocally = false, isModifier = false)
+    @Description(shortDefinition = "The customid of the patient's ")
+    private IdType myCustomId;
+
+    public StringType getPetName() {
+        if (myPetName == null) {
+            myPetName = new StringType();
+        }
+        return myPetName;
+    }
+
+    public void setPetName(final StringType thePetName) {
+        myPetName = thePetName;
+    }
+
+    @Override
+    public boolean isEmpty() {
+        return super.isEmpty() && getCustomId().isEmpty() && getPetName().isEmpty();
+    }
+
+    public IdType getCustomId() {
+        if (myCustomId == null) {
+            myCustomId = new IdType();
+        }
+        return myCustomId;
+    }
+
+    public void setCustomId(final IdType myCustomId) {
+        this.myCustomId = myCustomId;
+    }
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/MyPatientWithOneDeclaredEnumerationExtensionDstu3.java

@@ -0,0 +1,66 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu3;
+
+import java.util.List;
+import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.dstu3.model.Address.AddressUse;
+import org.hl7.fhir.dstu3.model.Enumeration;
+import org.hl7.fhir.dstu3.model.Identifier;
+import org.hl7.fhir.dstu3.model.Patient;
+
+@ResourceDef(name = "Patient")
+public class MyPatientWithOneDeclaredEnumerationExtensionDstu3 extends Patient {
+
+	private static final long serialVersionUID = 1L;
+
+	@Child(order = 0, name = "foo")
+	@Extension(url = "urn:foo", definedLocally = true, isModifier = false)
+	private Enumeration<AddressUse> myFoo;
+
+   /**
+    * A contact party (e.g. guardian, partner, friend) for the patient.
+    */
+   @Child(name = "contact", type = {}, order=Child.REPLACE_PARENT, min=0, max=Child.MAX_UNLIMITED, modifier=false, summary=false)
+   @Description(shortDefinition="A contact party (e.g. guardian, partner, friend) for the patient", formalDefinition="A contact party (e.g. guardian, partner, friend) for the patient." )
+   protected List<ContactComponent> contact;
+
+	public Enumeration<AddressUse> getFoo() {
+		return myFoo;
+	}
+
+	public void setFoo(Enumeration<AddressUse> theFoo) {
+		myFoo = theFoo;
+	}
+
+	@Block()
+	public static class MessageSourceComponent extends ContactComponent {
+
+		private static final long serialVersionUID = 1L;
+		@Child(name = "contact-eyecolour", type = { Identifier.class }, modifier = true)
+		@Description(shortDefinition = "Application ID")
+		@Extension(url = "http://foo.com/contact-eyecolour", definedLocally = false, isModifier = false)
+		private Identifier myEyeColour;
+
+		/*
+		 * Get messageHeaderApplicationId
+		 */
+		public Identifier getEyeColour() {
+			if (myEyeColour == null) {
+				myEyeColour = new Identifier();
+			}
+			return myEyeColour;
+		}
+
+		/*
+		 * Set messageHeaderApplicationId
+		 */
+		public void setEyeColour(Identifier messageHeaderApplicationId) {
+			this.myEyeColour = messageHeaderApplicationId;
+		}
+
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/PatientProfileDstu3.java

@@ -0,0 +1,72 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu3;
+
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.util.ElementUtil;
+import org.hl7.fhir.dstu3.model.CodeableConcept;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.Reference;
+
+@ResourceDef(name="Patient", profile = "http://hl7.org/fhir/StructureDefinition/Patient")
+public class PatientProfileDstu3 extends Patient {
+
+	private static final long serialVersionUID = 1L;
+
+	@Child(name="owner", min=0, max=1)
+    @Extension(url="http://ahr.copa.inso.tuwien.ac.at/StructureDefinition/Patient#owningOrganization", definedLocally=false, isModifier=false)
+    @Description(shortDefinition="The organization that owns this animal")
+    private Reference owningOrganization;
+
+    public Reference getOwningOrganization() {
+        if (owningOrganization == null) {
+            owningOrganization = new Reference();
+        }
+        return owningOrganization;
+    }
+
+    public PatientProfileDstu3 setOwningOrganization(Reference owningOrganization) {
+        this.owningOrganization = owningOrganization;
+        return this;
+    }
+
+    @Child(name="colorPrimary", min=0, max=1)
+    @Extension(url="http://ahr.copa.inso.tuwien.ac.at/StructureDefinition/Patient#animal-colorPrimary", definedLocally=false, isModifier=false)
+    @Description(shortDefinition="The animals primary color")
+    private CodeableConcept colorPrimary;
+
+    @Child(name="colorSecondary", min=0, max=1)
+    @Extension(url="http://ahr.copa.inso.tuwien.ac.at/StructureDefinition/Patient#animal-colorSecondary", definedLocally=false, isModifier=false)
+    @Description(shortDefinition="The animals secondary color")
+    private CodeableConcept colorSecondary;
+
+    public CodeableConcept getColorPrimary() {
+        if (this.colorPrimary == null) {
+            return new CodeableConcept();
+        }
+        return colorPrimary;
+    }
+
+    public void setColorPrimary(CodeableConcept colorPrimary) {
+        this.colorPrimary = colorPrimary;
+    }
+
+    public CodeableConcept getColorSecondary() {
+        if (this.colorSecondary == null) {
+            return new CodeableConcept();
+        }
+        return colorSecondary;
+    }
+
+    public void setColorSecondary(CodeableConcept colorSecondary) {
+        this.colorSecondary = colorSecondary;
+    }
+
+    @Override
+    public boolean isEmpty() {
+        return super.isEmpty() && ElementUtil.isEmpty(owningOrganization) &&  ElementUtil.isEmpty(colorPrimary)
+                && ElementUtil.isEmpty(colorSecondary) ;
+    }
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/PatientWithCustomCompositeExtension.java

@@ -0,0 +1,81 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu3;
+
+import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.util.ElementUtil;
+import org.hl7.fhir.dstu3.model.BackboneElement;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.StringType;
+
+@ResourceDef(name = "Patient")
+public class PatientWithCustomCompositeExtension extends Patient {
+
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * A custom extension
+	 */
+	@Child(name = "foo")
+	@Extension(url="http://acme.org/fooParent", definedLocally = false, isModifier = false)
+	protected FooParentExtension fooParentExtension;
+
+	public FooParentExtension getFooParentExtension() {
+		return fooParentExtension;
+	}
+
+	@Override
+	public boolean isEmpty() {
+		return super.isEmpty() && ElementUtil.isEmpty(fooParentExtension);
+	}
+
+	public void setFooParentExtension(FooParentExtension theFooParentExtension) {
+		fooParentExtension = theFooParentExtension;
+	}
+
+	@Block
+	public static class FooParentExtension extends BackboneElement {
+
+		private static final long serialVersionUID = 4522090347756045145L;
+
+		@Child(name = "childA")
+		@Extension(url = "http://acme.org/fooChildA", definedLocally = false, isModifier = false)
+		private StringType myChildA;
+
+		@Child(name = "childB")
+		@Extension(url = "http://acme.org/fooChildB", definedLocally = false, isModifier = false)
+		private StringType myChildB;
+
+		@Override
+		public FooParentExtension copy() {
+			FooParentExtension copy = new FooParentExtension();
+			copy.myChildA = myChildA;
+			copy.myChildB = myChildB;
+			return copy;
+		}
+
+		@Override
+		public boolean isEmpty() {
+			return super.isEmpty() && ElementUtil.isEmpty(myChildA, myChildB);
+		}
+
+		public StringType getChildA() {
+			return myChildA;
+		}
+
+		public StringType getChildB() {
+			return myChildB;
+		}
+
+		public void setChildA(StringType theChildA) {
+			myChildA = theChildA;
+		}
+
+		public void setChildB(StringType theChildB) {
+			myChildB = theChildB;
+		}
+
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/ResourceValidatorDstu3FeatureTest.java

@@ -0,0 +1,410 @@
+package ca.uhn.fhir.tests.integration.karaf.dstu3;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.parser.StrictErrorHandler;
+import ca.uhn.fhir.validation.*;
+import ca.uhn.fhir.validation.schematron.SchematronBaseValidator;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.Validate;
+import org.hamcrest.core.StringContains;
+import org.hl7.fhir.dstu3.conformance.ProfileUtilities;
+import org.hl7.fhir.dstu3.context.IWorkerContext;
+import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
+import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
+import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
+import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.utilities.validation.ValidationMessage;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.ops4j.pax.exam.Configuration;
+import org.ops4j.pax.exam.Option;
+import org.ops4j.pax.exam.junit.PaxExam;
+import org.ops4j.pax.exam.spi.reactors.ExamReactorStrategy;
+import org.ops4j.pax.exam.spi.reactors.PerClass;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.List;
+
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.HAPI_FHIR_VALIDATION_DSTU3;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.KARAF;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.WRAP;
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
+import static org.ops4j.pax.exam.CoreOptions.mavenBundle;
+import static org.ops4j.pax.exam.CoreOptions.options;
+import static org.ops4j.pax.exam.CoreOptions.when;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.debugConfiguration;
+
+/**
+ * Useful docs about this test: https://ops4j1.jira.com/wiki/display/paxexam/FAQ
+ */
+@RunWith(PaxExam.class)
+@ExamReactorStrategy(PerClass.class)
+public class ResourceValidatorDstu3FeatureTest {
+
+	private final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceValidatorDstu3FeatureTest.class);
+	private FhirContext ourCtx = FhirContext.forDstu3();
+
+	@Configuration
+	public Option[] config() throws IOException {
+		return options(
+			KARAF.option(),
+			HAPI_FHIR_VALIDATION_DSTU3.option(),
+			mavenBundle().groupId("org.apache.servicemix.bundles").artifactId("org.apache.servicemix.bundles.hamcrest").versionAsInProject(),
+			WRAP.option(),
+			when(false)
+				.useOptions(
+					debugConfiguration("5005", true))
+		);
+	}
+
+
+	private List<SingleValidationMessage> logResultsAndReturnNonInformationalOnes(ValidationResult theOutput) {
+		List<SingleValidationMessage> retVal = new ArrayList<>();
+
+		int index = 0;
+		for (SingleValidationMessage next : theOutput.getMessages()) {
+			ourLog.info("Result {}: {} - {} - {}",
+				new Object[]{index, next.getSeverity(), next.getLocationString(), next.getMessage()});
+			index++;
+
+			if (next.getSeverity() != ResultSeverityEnum.INFORMATION) {
+				retVal.add(next);
+			}
+		}
+
+		return retVal;
+	}
+
+	/**
+	 * See issue #50
+	 */
+	@Test
+	public void testOutOfBoundsDate() {
+		Patient p = new Patient();
+		p.setBirthDateElement(new DateType("2000-12-31"));
+
+		// Put in an invalid date
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new StrictErrorHandler());
+
+		String encoded = parser.setPrettyPrint(true).encodeResourceToString(p).replace("2000-12-31", "2000-15-31");
+		ourLog.info(encoded);
+
+		assertThat(encoded, StringContains.containsString("2000-15-31"));
+
+		ValidationResult result = ourCtx.newValidator().validateWithResult(encoded);
+		String resultString = parser.setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
+		ourLog.info(resultString);
+
+		assertEquals(2, ((OperationOutcome) result.toOperationOutcome()).getIssue().size());
+		assertThat(resultString, StringContains.containsString("cvc-pattern-valid"));
+
+		try {
+			parser.parseResource(encoded);
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Invalid attribute value \"2000-15-31\": Invalid date/time format: \"2000-15-31\"", e.getMessage());
+		}
+	}
+	@Test
+	public void testValidateCareTeamXsd() {
+		CareTeam careTeam = new CareTeam();
+		careTeam
+			.addParticipant()
+			.setMember(new Reference("http://example.com/Practitioner/1647bbb2-3b12-43cc-923c-a475f817e881"))
+			.setOnBehalfOf(new Reference("Organization/5859a28f-01e7-42d8-a8ba-48b31679a828"));
+
+		IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
+		String encoded = parser.encodeResourceToString(careTeam);
+
+		ourLog.info(encoded);
+
+		FhirValidator val = ourCtx.newValidator();
+
+		ValidationResult result = val.validateWithResult(encoded);
+		String resultString = parser.setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
+		ourLog.info(resultString);
+
+		assertThat(resultString, containsString("No issues detected during validation"));
+
+	}
+
+	@Test
+	public void testValidateCodeableConceptContainingOnlyBadCode() {
+		Patient p = new Patient();
+		p.getMaritalStatus().addCoding().setSystem("http://hl7.org/fhir/v3/MaritalStatus").setCode("FOO");
+
+		FhirValidator val = ourCtx.newValidator();
+		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		val.registerValidatorModule(new FhirInstanceValidator());
+
+		ValidationResult output = val.validateWithResult(p);
+		List<SingleValidationMessage> all = logResultsAndReturnNonInformationalOnes(output);
+
+		assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/marital-status (http://hl7.org/fhir/ValueSet/marital-status, and a code should come from this value set unless it has no suitable code) (codes = http://hl7.org/fhir/v3/MaritalStatus#FOO)", output.getMessages().get(0).getMessage());
+		assertEquals(ResultSeverityEnum.WARNING, output.getMessages().get(0).getSeverity());
+	}
+
+	@Test
+	public void testValidateCodeableConceptContainingOnlyGoodCode() {
+		Patient p = new Patient();
+		p.getMaritalStatus().addCoding().setSystem("http://hl7.org/fhir/v3/MaritalStatus").setCode("M");
+
+		FhirValidator val = ourCtx.newValidator();
+		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		val.registerValidatorModule(new FhirInstanceValidator());
+
+		ValidationResult output = val.validateWithResult(p);
+		List<SingleValidationMessage> all = logResultsAndReturnNonInformationalOnes(output);
+		assertEquals(0, all.size());
+		assertEquals(0, output.getMessages().size());
+	}
+
+	@Test
+	public void testValidateJsonNumericId() {
+		String input = "{\"resourceType\": \"Patient\",\n" +
+			"  \"id\": 123,\n" +
+			"  \"meta\": {\n" +
+			"    \"versionId\": \"29\",\n" +
+			"    \"lastUpdated\": \"2015-12-22T19:53:11.000Z\"\n" +
+			"  },\n" +
+			"  \"communication\": {\n" +
+			"    \"language\": {\n" +
+			"      \"coding\": [\n" +
+			"        {\n" +
+			"          \"system\": \"urn:ietf:bcp:47\",\n" +
+			"          \"code\": \"hi\",\n" +
+			"          \"display\": \"Hindi\",\n" +
+			"          \"userSelected\": false\n" +
+			"        }],\n" +
+			"      \"text\": \"Hindi\"\n" +
+			"    },\n" +
+			"    \"preferred\": true\n" +
+			"  }\n" +
+			"}";
+
+		FhirValidator val = ourCtx.newValidator();
+		val.registerValidatorModule(new FhirInstanceValidator());
+		ValidationResult output = val.validateWithResult(input);
+
+		OperationOutcome operationOutcome = (OperationOutcome) output.toOperationOutcome();
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(operationOutcome);
+//		ourLog.info(encoded);
+
+		assertThat(encoded, containsString("Error parsing JSON: the primitive value must be a string"));
+
+	}
+
+	@Test
+	public void testValidateQuestionnaireWithCanonicalUrl() {
+		String input = "{\n" +
+			"  \"resourceType\": \"Questionnaire\",\n" +
+			"  \"url\": \"http://some.example.url\",\n" +
+			"  \"status\": \"active\",\n" +
+			"  \"subjectType\": [\n" +
+			"    \"Patient\"\n" +
+			"  ],\n" +
+			"  \"item\": [\n" +
+			"    {\n" +
+			"      \"linkId\": \"example-question\",\n" +
+			"      \"text\": \"Is the sky blue?\",\n" +
+			"      \"type\": \"choice\",\n" +
+			"      \"options\": {\n" +
+			"        \"reference\": \"http://loinc.org/vs/LL3044-6\"\n" +
+			"      }\n" +
+			"    }\n" +
+			"  ]\n" +
+			"}";
+
+		Questionnaire q = new Questionnaire();
+		q = ourCtx.newJsonParser().parseResource(Questionnaire.class, input);
+
+		FhirValidator val = ourCtx.newValidator();
+		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		val.registerValidatorModule(new FhirInstanceValidator());
+
+		ValidationResult result = val.validateWithResult(q);
+
+		OperationOutcome operationOutcome = (OperationOutcome) result.toOperationOutcome();
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(operationOutcome);
+		ourLog.info(encoded);
+
+	}
+
+	/**
+	 * Make sure that the elements that appear in all resources (meta, language, extension, etc) all appear in the correct order
+	 */
+	@Test
+	public void testValidateResourceWithResourceElements() {
+		TestPatientFor327 patient = new TestPatientFor327();
+		patient.setBirthDate(new Date());
+		patient.setId("123");
+		patient.getText().setDivAsString("<div>FOO</div>");
+		patient.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
+		patient.getLanguageElement().setValue("en");
+		patient.addExtension().setUrl("http://foo").setValue(new StringType("MOD"));
+		patient.getMeta().setLastUpdated(new Date());
+
+		List<Reference> conditions = new ArrayList<Reference>();
+		Condition condition = new Condition();
+		condition.getSubject().setReference("Patient/123");
+		condition.addBodySite().setText("BODY SITE");
+		condition.getCode().setText("CODE");
+		condition.setClinicalStatus(Condition.ConditionClinicalStatus.ACTIVE);
+		condition.setVerificationStatus(Condition.ConditionVerificationStatus.CONFIRMED);
+		conditions.add(new Reference(condition));
+		patient.setCondition(conditions);
+		patient.addIdentifier().setSystem("http://foo").setValue("123");
+
+		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("Unknown extension http://foo"));
+	}
+
+	/**
+	 * 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() {
+		PatientProfileDstu3 myPatient = new PatientProfileDstu3();
+		myPatient.setId("1");
+		myPatient.setColorPrimary(new CodeableConcept().addCoding(new Coding().setSystem("http://example.com#animalColor").setCode("furry-grey")));
+		myPatient.setColorSecondary(new CodeableConcept().addCoding(new Coding().setSystem("http://example.com#animalColor").setCode("furry-white")));
+		myPatient.setOwningOrganization(new Reference("Organization/2.25.79433498044103547197447759549862032393"));
+		myPatient.addName().setFamily("FamilyName");
+		myPatient.addExtension().setUrl("http://foo.com/example").setValue(new StringType("String Extension"));
+
+		IParser p = ourCtx.newJsonParser().setPrettyPrint(true);
+		String messageString = p.encodeResourceToString(myPatient);
+//		ourLog.info(messageString);
+
+		String[] strings = {"meta",
+			"String Extension",
+			"Organization/2.25.79433498044103547197447759549862032393",
+			"furry-grey",
+			"furry-white",
+			"FamilyName"};
+		assertThat(messageString, stringContainsInOrder(
+			Arrays.asList(strings)
+		));
+		String[] strings1 = {"extension",
+			"meta"};
+		assertThat(messageString, not(stringContainsInOrder(
+			Arrays.asList(strings1)
+		)));
+
+		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();
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(operationOutcome);
+		ourLog.info(encoded);
+
+		assertTrue(result.isSuccessful());
+
+		assertThat(messageString, containsString("valueReference"));
+		assertThat(messageString, not(containsString("valueResource")));
+	}
+
+	/**
+	 * 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 testValidateWithExtensionsXml() {
+		PatientProfileDstu3 myPatient = new PatientProfileDstu3();
+		myPatient.setId("1");
+		myPatient.setColorPrimary(new CodeableConcept().addCoding(new Coding().setSystem("http://example.com#animalColor").setCode("furry-grey")));
+		myPatient.setColorSecondary(new CodeableConcept().addCoding(new Coding().setSystem("http://example.com#animalColor").setCode("furry-white")));
+		myPatient.setOwningOrganization(new Reference("Organization/2.25.79433498044103547197447759549862032393"));
+		myPatient.addName().setFamily("FamilyName");
+		myPatient.addExtension().setUrl("http://foo.com/example").setValue(new StringType("String Extension"));
+
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String messageString = p.encodeResourceToString(myPatient);
+		ourLog.info(messageString);
+
+		//@formatter:off
+		String[] strings = {"meta",
+			"Organization/2.25.79433498044103547197447759549862032393",
+			"furry-grey",
+			"furry-white",
+			"String Extension",
+			"FamilyName"};
+		assertThat(messageString, stringContainsInOrder(
+			Arrays.asList(strings)
+		));
+		String[] strings1 = {"extension",
+			"meta"};
+		assertThat(messageString, not(stringContainsInOrder(
+			Arrays.asList(strings1)
+		)));
+		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();
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(operationOutcome);
+		ourLog.info(encoded);
+
+		assertTrue(result.isSuccessful());
+
+		assertThat(messageString, containsString("valueReference"));
+		assertThat(messageString, not(containsString("valueResource")));
+	}
+
+	@ResourceDef(name = "Patient")
+	public static class TestPatientFor327 extends Patient {
+
+		private static final long serialVersionUID = 1L;
+
+		@Child(name = "testCondition")
+		@ca.uhn.fhir.model.api.annotation.Extension(url = "testCondition", definedLocally = true, isModifier = false)
+		private List<Reference> testConditions = null;
+
+		public List<Reference> getConditions() {
+			return this.testConditions;
+		}
+
+		public void setCondition(List<Reference> ref) {
+			this.testConditions = ref;
+		}
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/r4/FhirInstanceValidatorR4Test.java

@@ -0,0 +1,114 @@
+package ca.uhn.fhir.tests.integration.karaf.r4;
+
+import java.io.IOException;
+import java.util.List;
+import ca.uhn.fhir.context.FhirContext;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
+import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
+import org.hl7.fhir.r4.model.Base;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.model.StructureDefinition;
+import org.hl7.fhir.r4.utils.FHIRPathEngine;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.ops4j.pax.exam.Configuration;
+import org.ops4j.pax.exam.Option;
+import org.ops4j.pax.exam.junit.PaxExam;
+import org.ops4j.pax.exam.spi.reactors.ExamReactorStrategy;
+import org.ops4j.pax.exam.spi.reactors.PerClass;
+
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.HAPI_FHIR_VALIDATION_R4;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.KARAF;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.WRAP;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.ops4j.pax.exam.CoreOptions.mavenBundle;
+import static org.ops4j.pax.exam.CoreOptions.options;
+import static org.ops4j.pax.exam.CoreOptions.when;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.debugConfiguration;
+
+/**
+ * Useful docs about this test: https://ops4j1.jira.com/wiki/display/paxexam/FAQ
+ */
+@RunWith(PaxExam.class)
+@ExamReactorStrategy(PerClass.class)
+public class FhirInstanceValidatorR4Test {
+
+	private FhirContext ourCtx = FhirContext.forR4();
+	private FHIRPathEngine ourEngine = new FHIRPathEngine(new HapiWorkerContext(ourCtx, new DefaultProfileValidationSupport()));
+	private final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidatorR4Test.class);
+
+	@Configuration
+	public Option[] config() throws IOException {
+		return options(
+			KARAF.option(),
+			HAPI_FHIR_VALIDATION_R4.option(),
+			mavenBundle().groupId("org.apache.servicemix.bundles").artifactId("org.apache.servicemix.bundles.hamcrest").versionAsInProject(),
+			WRAP.option(),
+			when(false)
+				.useOptions(
+					debugConfiguration("5005", true))
+		);
+	}
+
+	@Test
+	public void testAs() throws Exception {
+		Observation obs = new Observation();
+		obs.setValue(new StringType("FOO"));
+
+		List<Base> value = ourEngine.evaluate(obs, "Observation.value.as(String)");
+		assertEquals(1, value.size());
+		assertEquals("FOO", ((StringType)value.get(0)).getValue());
+	}
+
+	@Test
+	public void testExistsWithNoValue() throws FHIRException {
+		Patient patient = new Patient();
+		patient.setDeceased(new BooleanType());
+		List<Base> eval = ourEngine.evaluate(patient, "Patient.deceased.exists()");
+		ourLog.info(eval.toString());
+		assertFalse(((BooleanType)eval.get(0)).getValue());
+	}
+
+	@Test
+	public void testExistsWithValue() throws FHIRException {
+		Patient patient = new Patient();
+		patient.setDeceased(new BooleanType(false));
+		List<Base> eval = ourEngine.evaluate(patient, "Patient.deceased.exists()");
+		ourLog.info(eval.toString());
+		assertTrue(((BooleanType)eval.get(0)).getValue());
+	}
+
+	@Test
+	public void testConcatenation() throws FHIRException {
+		String exp = "Patient.name.family & '.'";
+
+		Patient p = new Patient();
+		p.addName().setFamily("TEST");
+		String result = ourEngine.evaluateToString(p, exp);
+		assertEquals("TEST.", result);
+	}
+
+	@Test
+	public void testConcatenationFunction() throws FHIRException {
+		String exp = "element.first().path.startsWith(%resource.type) and element.tail().all(path.startsWith(%resource.type&'.'))";
+
+		StructureDefinition sd = new StructureDefinition();
+		StructureDefinition.StructureDefinitionDifferentialComponent diff = sd.getDifferential();
+
+		diff.addElement().setPath("Patient.name");
+
+
+		Patient p = new Patient();
+		p.addName().setFamily("TEST");
+		List<Base> result = ourEngine.evaluate(null, p, diff, exp);
+		ourLog.info(result.toString());
+//		assertEquals("TEST.", result);
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/r4/R4JsonParserTest.java

@@ -0,0 +1,275 @@
+package ca.uhn.fhir.tests.integration.karaf.r4;
+
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
+import com.google.common.collect.Sets;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Extension;
+import org.hl7.fhir.r4.model.Medication;
+import org.hl7.fhir.r4.model.MedicationDispense;
+import org.hl7.fhir.r4.model.MedicationRequest;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.StringType;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.ops4j.pax.exam.Configuration;
+import org.ops4j.pax.exam.Option;
+import org.ops4j.pax.exam.junit.PaxExam;
+import org.ops4j.pax.exam.spi.reactors.ExamReactorStrategy;
+import org.ops4j.pax.exam.spi.reactors.PerClass;
+
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.HAPI_FHIR_R4;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.KARAF;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.WRAP;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.core.IsNot.not;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertThat;
+import static org.ops4j.pax.exam.CoreOptions.mavenBundle;
+import static org.ops4j.pax.exam.CoreOptions.options;
+import static org.ops4j.pax.exam.CoreOptions.when;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.debugConfiguration;
+
+
+/**
+ * Useful docs about this test: https://ops4j1.jira.com/wiki/display/paxexam/FAQ
+ */
+@RunWith(PaxExam.class)
+@ExamReactorStrategy(PerClass.class)
+public class R4JsonParserTest {
+
+	private final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(R4JsonParserTest.class);
+	private FhirContext ourCtx = FhirContext.forR4();
+
+   @Configuration
+   public Option[] config() throws IOException {
+      return options(
+      	KARAF.option(),
+			WRAP.option(),
+			HAPI_FHIR_R4.option(),
+			mavenBundle().groupId("org.apache.servicemix.bundles").artifactId("org.apache.servicemix.bundles.hamcrest").versionAsInProject(),
+			when(false)
+         	.useOptions(
+            	debugConfiguration("5005", true))
+      );
+   }
+
+	private Bundle createBundleWithPatient() {
+		Bundle b = new Bundle();
+		b.setId("BUNDLEID");
+		b.getMeta().addProfile("http://FOO");
+
+		Patient p = new Patient();
+		p.setId("PATIENTID");
+		p.getMeta().addProfile("http://BAR");
+		p.addName().addGiven("GIVEN");
+		b.addEntry().setResource(p);
+		return b;
+	}
+
+	/**
+	 * See #814
+	 */
+	@Test
+	public void testDuplicateContainedResourcesNotOutputtedTwice() {
+		MedicationDispense md = new MedicationDispense();
+
+		MedicationRequest mr = new MedicationRequest();
+		md.addAuthorizingPrescription().setResource(mr);
+
+		Medication med = new Medication();
+		md.setMedication(new Reference(med));
+		mr.setMedication(new Reference(med));
+
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(md);
+		ourLog.info(encoded);
+
+		int idx = encoded.indexOf("\"Medication\"");
+		assertNotEquals(-1, idx);
+
+		idx = encoded.indexOf("\"Medication\"", idx + 1);
+		assertEquals(-1, idx);
+
+	}
+
+	/**
+	 * See #814
+	 */
+	@Test
+	public void testDuplicateContainedResourcesNotOutputtedTwiceWithManualIds() {
+		MedicationDispense md = new MedicationDispense();
+
+		MedicationRequest mr = new MedicationRequest();
+		mr.setId("#MR");
+		md.addAuthorizingPrescription().setResource(mr);
+
+		Medication med = new Medication();
+		med.setId("#MED");
+		md.setMedication(new Reference(med));
+		mr.setMedication(new Reference(med));
+
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(md);
+		ourLog.info(encoded);
+
+		int idx = encoded.indexOf("\"Medication\"");
+		assertNotEquals(-1, idx);
+
+		idx = encoded.indexOf("\"Medication\"", idx + 1);
+		assertEquals(-1, idx);
+
+	}
+
+	@Test
+	public void testExcludeNothing() {
+		IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
+		Set<String> excludes = new HashSet<>();
+//		excludes.add("*.id");
+		parser.setDontEncodeElements(excludes);
+
+		Bundle b = createBundleWithPatient();
+
+		String encoded = parser.encodeResourceToString(b);
+		ourLog.info(encoded);
+
+		assertThat(encoded, containsString("BUNDLEID"));
+		assertThat(encoded, containsString("http://FOO"));
+		assertThat(encoded, containsString("PATIENTID"));
+		assertThat(encoded, containsString("http://BAR"));
+		assertThat(encoded, containsString("GIVEN"));
+
+		b = parser.parseResource(Bundle.class, encoded);
+
+		assertEquals("BUNDLEID", b.getIdElement().getIdPart());
+		assertEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
+		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
+	}
+
+	@Test
+	public void testExcludeRootStuff() {
+		IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
+		Set<String> excludes = new HashSet<>();
+		excludes.add("id");
+		excludes.add("meta");
+		parser.setDontEncodeElements(excludes);
+
+		Bundle b = createBundleWithPatient();
+
+		String encoded = parser.encodeResourceToString(b);
+		ourLog.info(encoded);
+
+		assertThat(encoded, not(containsString("BUNDLEID")));
+		assertThat(encoded, not(containsString("http://FOO")));
+		assertThat(encoded, (containsString("PATIENTID")));
+		assertThat(encoded, (containsString("http://BAR")));
+		assertThat(encoded, containsString("GIVEN"));
+
+		b = parser.parseResource(Bundle.class, encoded);
+
+		assertNotEquals("BUNDLEID", b.getIdElement().getIdPart());
+		assertEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
+		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
+	}
+
+	@Test
+	public void testExcludeStarDotStuff() {
+		IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
+		Set<String> excludes = new HashSet<>();
+		excludes.add("*.id");
+		excludes.add("*.meta");
+		parser.setDontEncodeElements(excludes);
+
+		Bundle b = createBundleWithPatient();
+
+		String encoded = parser.encodeResourceToString(b);
+		ourLog.info(encoded);
+
+		assertThat(encoded, not(containsString("BUNDLEID")));
+		assertThat(encoded, not(containsString("http://FOO")));
+		assertThat(encoded, not(containsString("PATIENTID")));
+		assertThat(encoded, not(containsString("http://BAR")));
+		assertThat(encoded, containsString("GIVEN"));
+
+		b = parser.parseResource(Bundle.class, encoded);
+
+		assertNotEquals("BUNDLEID", b.getIdElement().getIdPart());
+		assertNotEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
+		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
+	}
+
+	/**
+	 * Test that long JSON strings don't get broken up
+	 */
+	@Test
+	public void testNoBreakInLongString() {
+		String longString = StringUtils.leftPad("", 100000, 'A');
+
+		Patient p = new Patient();
+		p.addName().setFamily(longString);
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
+
+		assertThat(encoded, containsString(longString));
+	}
+
+	@Test
+	public void testParseAndEncodeExtensionWithValueWithExtension() {
+		String input = "{\n" +
+			"  \"resourceType\": \"Patient\",\n" +
+			"  \"extension\": [\n" +
+			"    {\n" +
+			"      \"url\": \"https://purl.org/elab/fhir/network/StructureDefinition/1/BirthWeight\",\n" +
+			"      \"_valueDecimal\": {\n" +
+			"        \"extension\": [\n" +
+			"          {\n" +
+			"            \"url\": \"http://www.hl7.org/fhir/extension-data-absent-reason.html\",\n" +
+			"            \"valueCoding\": {\n" +
+			"              \"system\": \"http://hl7.org/fhir/ValueSet/birthweight\",\n" +
+			"              \"code\": \"Underweight\",\n" +
+			"              \"userSelected\": false\n" +
+			"            }\n" +
+			"          }\n" +
+			"        ]\n" +
+			"      }\n" +
+			"    }\n" +
+			"  ],\n" +
+			"  \"identifier\": [\n" +
+			"    {\n" +
+			"      \"system\": \"https://purl.org/elab/fhir/network/StructureDefinition/1/EuroPrevallStudySubjects\",\n" +
+			"      \"value\": \"1\"\n" +
+			"    }\n" +
+			"  ],\n" +
+			"  \"gender\": \"female\"\n" +
+			"}";
+
+		IParser jsonParser = ourCtx.newJsonParser();
+		IParser xmlParser = ourCtx.newXmlParser();
+		jsonParser.setDontEncodeElements(Sets.newHashSet("id", "meta"));
+		xmlParser.setDontEncodeElements(Sets.newHashSet("id", "meta"));
+
+		Patient parsed = jsonParser.parseResource(Patient.class, input);
+
+		ourLog.info(jsonParser.setPrettyPrint(true).encodeResourceToString(parsed));
+		assertThat(xmlParser.encodeResourceToString(parsed), containsString("Underweight"));
+		assertThat(jsonParser.encodeResourceToString(parsed), containsString("Underweight"));
+
+	}
+
+	@Test
+	public void testParseExtensionOnPrimitive() throws IOException {
+		String input = IOUtils.toString(R4JsonParserTest.class.getResourceAsStream("/extension-on-line.txt"));
+		IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
+		Patient pt = parser.parseResource(Patient.class, input);
+
+		StringType line0 = pt.getAddressFirstRep().getLine().get(0);
+		assertEquals("535 Sheppard Avenue West, Unit 1907", line0.getValue());
+		Extension houseNumberExt = line0.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/iso21090-ADXP-houseNumber");
+		assertEquals("535", ((StringType) houseNumberExt.getValue()).getValue());
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/r4/R4XmlParserTest.java

@@ -0,0 +1,195 @@
+package ca.uhn.fhir.tests.integration.karaf.r4;
+
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
+import com.google.common.collect.Sets;
+import org.hamcrest.core.IsNot;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.ops4j.pax.exam.Configuration;
+import org.ops4j.pax.exam.Option;
+import org.ops4j.pax.exam.junit.PaxExam;
+import org.ops4j.pax.exam.spi.reactors.ExamReactorStrategy;
+import org.ops4j.pax.exam.spi.reactors.PerClass;
+
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.HAPI_FHIR_R4;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.KARAF;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.WRAP;
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertThat;
+import static org.ops4j.pax.exam.CoreOptions.mavenBundle;
+import static org.ops4j.pax.exam.CoreOptions.options;
+import static org.ops4j.pax.exam.CoreOptions.when;
+import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.debugConfiguration;
+
+
+/**
+ * Useful docs about this test: https://ops4j1.jira.com/wiki/display/paxexam/FAQ
+ */
+@RunWith(PaxExam.class)
+@ExamReactorStrategy(PerClass.class)
+public class R4XmlParserTest {
+
+	private final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(R4XmlParserTest.class);
+	private FhirContext ourCtx = FhirContext.forR4();
+
+   @Configuration
+   public Option[] config() throws IOException {
+      return options(
+      	KARAF.option(),
+			WRAP.option(),
+			HAPI_FHIR_R4.option(),
+			mavenBundle().groupId("org.apache.servicemix.bundles").artifactId("org.apache.servicemix.bundles.hamcrest").versionAsInProject(),
+			when(false)
+         	.useOptions(
+            	debugConfiguration("5005", true))
+      );
+   }
+	private Bundle createBundleWithPatient() {
+		Bundle b = new Bundle();
+		b.setId("BUNDLEID");
+		b.getMeta().addProfile("http://FOO");
+
+		Patient p = new Patient();
+		p.setId("PATIENTID");
+		p.getMeta().addProfile("http://BAR");
+		p.addName().addGiven("GIVEN");
+		b.addEntry().setResource(p);
+		return b;
+	}
+
+	@Test
+	public void testParseAndEncodeXmlNumericEntity() {
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+			"    <name>\n" +
+			"       <family value=\"A &#xA; B\"/>\n" +
+			"    </name>\n" +
+			"</Patient>";
+
+		Patient p = ourCtx.newXmlParser().parseResource(Patient.class, input);
+		assertEquals("A \n B", p.getNameFirstRep().getFamily());
+
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(output);
+
+	}
+
+	@Test
+	public void testExcludeNothing() {
+		IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
+		Set<String> excludes = new HashSet<>();
+//		excludes.add("*.id");
+		parser.setDontEncodeElements(excludes);
+
+		Bundle b = createBundleWithPatient();
+
+		String encoded = parser.encodeResourceToString(b);
+		ourLog.info(encoded);
+
+		assertThat(encoded, containsString("BUNDLEID"));
+		assertThat(encoded, containsString("http://FOO"));
+		assertThat(encoded, containsString("PATIENTID"));
+		assertThat(encoded, containsString("http://BAR"));
+		assertThat(encoded, containsString("GIVEN"));
+
+		b = parser.parseResource(Bundle.class, encoded);
+
+		assertEquals("BUNDLEID", b.getIdElement().getIdPart());
+		assertEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
+		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
+	}
+
+	@Test
+	public void testExcludeRootStuff() {
+		IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
+		Set<String> excludes = new HashSet<>();
+		excludes.add("id");
+		excludes.add("meta");
+		parser.setDontEncodeElements(excludes);
+
+		Bundle b = createBundleWithPatient();
+
+		String encoded = parser.encodeResourceToString(b);
+		ourLog.info(encoded);
+
+		assertThat(encoded, IsNot.not(containsString("BUNDLEID")));
+		assertThat(encoded, IsNot.not(containsString("http://FOO")));
+		assertThat(encoded, (containsString("PATIENTID")));
+		assertThat(encoded, (containsString("http://BAR")));
+		assertThat(encoded, containsString("GIVEN"));
+
+		b = parser.parseResource(Bundle.class, encoded);
+
+		assertNotEquals("BUNDLEID", b.getIdElement().getIdPart());
+		assertEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
+		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
+	}
+
+	@Test
+	public void testExcludeStarDotStuff() {
+		IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
+		Set<String> excludes = new HashSet<>();
+		excludes.add("*.id");
+		excludes.add("*.meta");
+		parser.setDontEncodeElements(excludes);
+
+		Bundle b = createBundleWithPatient();
+
+		String encoded = parser.encodeResourceToString(b);
+		ourLog.info(encoded);
+
+		assertThat(encoded, IsNot.not(containsString("BUNDLEID")));
+		assertThat(encoded, IsNot.not(containsString("http://FOO")));
+		assertThat(encoded, IsNot.not(containsString("PATIENTID")));
+		assertThat(encoded, IsNot.not(containsString("http://BAR")));
+		assertThat(encoded, containsString("GIVEN"));
+
+		b = parser.parseResource(Bundle.class, encoded);
+
+		assertNotEquals("BUNDLEID", b.getIdElement().getIdPart());
+		assertNotEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
+		assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
+	}
+
+	@Test
+	public void testParseAndEncodeExtensionWithValueWithExtension() {
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+			"    <extension url=\"https://purl.org/elab/fhir/network/StructureDefinition/1/BirthWeight\">\n" +
+			"       <valueDecimal>\n" +
+			"          <extension url=\"http://www.hl7.org/fhir/extension-data-absent-reason.html\">\n" +
+			"            <valueCoding>\n" +
+			"                <system value=\"http://hl7.org/fhir/ValueSet/birthweight\"/>\n" +
+			"                <code value=\"Underweight\"/>\n" +
+			"                <userSelected value=\"false\"/>\n" +
+			"            </valueCoding>\n" +
+			"          </extension>\n" +
+			"       </valueDecimal>\n" +
+			"    </extension>\n" +
+			"    <identifier>\n" +
+			"       <system value=\"https://purl.org/elab/fhir/network/StructureDefinition/1/EuroPrevallStudySubjects\"/>\n" +
+			"       <value value=\"1\"/>\n" +
+			"    </identifier>\n" +
+			"    <gender value=\"female\"/>\n" +
+			"</Patient>";
+
+		IParser xmlParser = ourCtx.newXmlParser();
+		IParser jsonParser = ourCtx.newJsonParser();
+		jsonParser.setDontEncodeElements(Sets.newHashSet("id", "meta"));
+		xmlParser.setDontEncodeElements(Sets.newHashSet("id", "meta"));
+
+		Patient parsed = xmlParser.parseResource(Patient.class, input);
+
+		ourLog.info(jsonParser.setPrettyPrint(true).encodeResourceToString(parsed));
+		assertThat(xmlParser.encodeResourceToString(parsed), containsString("Underweight"));
+		assertThat(jsonParser.encodeResourceToString(parsed), containsString("Underweight"));
+
+	}
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/bundle-example.json

@@ -0,0 +1,53 @@
+{
+  "resourceType": "Bundle",
+  "id": "example",
+  "meta": {
+    "versionId": "1",
+    "lastUpdated": "2014-08-18T01:43:30Z"
+  },
+  "type": "searchset",
+  "total": 3,
+  "link": [
+    {
+      "relation": "next",
+      "url": "https://example.com/base/MedicationOrder?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2"
+    },
+    {
+      "relation": "self",
+      "url": "https://example.com/base/MedicationOrder?patient=347&_include=MedicationOrder.medication"
+    }
+  ],
+  "entry": [
+    {
+		"fullUrl": "http://example.com/base/MedicationOrder/3123/_history/1",
+      "resource": {
+        "resourceType": "MedicationOrder",
+        "id": "3123",
+        "meta" : {
+        	"versionId" : "1",
+        	"lastUpdated" : "2014-08-16T05:31:17Z"
+        },
+        "patient": {
+          "reference": "Patient/347"
+        },
+        "medicationReference": {
+          "reference": "Medication/example"
+        }
+      },
+      "search": {
+        "mode": "match",
+        "score": 1
+      }
+    },
+    {
+		"fullUrl": "http://example.com/base/Medication/example",
+      "resource": {
+        "resourceType": "Medication",
+        "id": "example"
+      },
+      "search": {
+        "mode": "include"
+      }
+    }
+  ]
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/bundle_orion.xml

@@ -0,0 +1,72 @@
+<Bundle 
+    xmlns="http://hl7.org/fhir">
+    <id value="487d3669-0e1c-4867-b124-400d1849548d"></id>
+    <type value="searchset"></type>
+    <base value="http://localhost:19080/fhir/dstu1"></base>
+    <link>
+        <relation value="just trying add link"></relation>
+        <url value="blarion"></url>
+    </link>
+    <link>
+        <relation value="self"></relation>
+        <url value="http://localhost:19080/fhir/dstu1/Observation?subject.identifier=puppet|CLONE-AA102"></url>
+    </link>
+    <entry>
+        <link>
+            <relation value="orionhealth.edit"></relation>
+            <url value="Observation"></url>
+        </link>
+        <resource>
+            <Observation 
+                xmlns="http://hl7.org/fhir">
+                <id value="0d87f02c-da2c-4551-9ead-2956f0165a4f"></id>
+                <extension url="http://orionhealth.com/fhir/extensions#created-by"></extension>
+                <extension url="http://orionhealth.com/fhir/extensions#last-modified-by"></extension>
+                <extension url="http://orionhealth.com/fhir/extensions#received-instant">
+                    <valueInstant value="2015-06-25T17:08:47.190+12:00"></valueInstant>
+                </extension>
+                <code>
+                    <coding>
+                        <system value="http://loinc.org"></system>
+                        <code value="8867-4"></code>
+                    </coding>
+                </code>
+                <valueString value="observationValue"></valueString>
+                <status value="final"></status>
+                <reliability value="ok"></reliability>
+                <subject>
+                    <reference value="Patient/INGE6TSFFVAUCMJQGJAHA5LQOBSXI"></reference>
+                </subject>
+            </Observation>
+        </resource>
+    </entry>
+    <entry>
+        <link>
+            <relation value="orionhealth.edit"></relation>
+            <url value="Observation"></url>
+        </link>
+        <resource>
+            <Observation 
+                xmlns="http://hl7.org/fhir">
+                <id value="c54ac0cc-a99f-40aa-9541-c5aa853a2e88"></id>
+                <extension url="http://orionhealth.com/fhir/extensions#created-by"></extension>
+                <extension url="http://orionhealth.com/fhir/extensions#last-modified-by"></extension>
+                <extension url="http://orionhealth.com/fhir/extensions#received-instant">
+                    <valueInstant value="2015-06-25T17:08:47.190+12:00"></valueInstant>
+                </extension>
+                <code>
+                    <coding>
+                        <system value="http://loinc.org"></system>
+                        <code value="3141-9"></code>
+                    </coding>
+                </code>
+                <valueString value="observationValue"></valueString>
+                <status value="final"></status>
+                <reliability value="ok"></reliability>
+                <subject>
+                    <reference value="Patient/INGE6TSFFVAUCMJQGJAHA5LQOBSXI"></reference>
+                </subject>
+            </Observation>
+        </resource>
+    </entry>
+</Bundle>

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/bundle_with_contained_with_no_id.xml

@@ -0,0 +1,77 @@
+<Bundle xmlns="http://hl7.org/fhir">
+  <id value="fe7ff16d-8bdf-47a5-9de3-20165c6fe440" />
+  <meta>
+    <lastUpdated value="2016-08-25T12:17:12.159-04:00" />
+  </meta>
+  <type value="searchset" />
+  <total value="208" />
+  <link>
+    <relation value="self" />
+    <url value="http://foo.uhn.on.ca:25180/uhn-fhir-service-2.1/DiagnosticReport?_format=xml&amp;_include=DiagnosticReport%3Aencounter&amp;_include=Encounter%3AfacilityLocation&amp;_include=Observation%3Aperformer&amp;_include=DiagnosticReport%3Aresult&amp;_include=Encounter%3Alocation&amp;_include=Location.partOf&amp;_include=Encounter%3Aparticipant&amp;_include=DiagnosticReport%3Apatient&amp;subject%3Aidentifier=urn%3Aoid%3A2.16.840.1.113883.3.239.18.148%7C7000135" />
+  </link>
+ <entry>
+    <fullUrl value="http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-2.1/DiagnosticReport/7162221" />
+    <resource>
+      <DiagnosticReport xmlns="http://hl7.org/fhir">
+        <id value="7162221" />
+        <meta>
+          <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+          <profile value="http://fhir.uhn.ca/Profile/diagnosticreport" />
+        </meta>
+        <contained>
+          <Observation xmlns="http://hl7.org/fhir">
+            <meta>
+              <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+              <profile value="http://fhir.uhn.ca/Profile/observation" />
+            </meta>
+            <extension url="http://fhir.uhn.ca/Profile/observation#source_system_status">
+              <valueString value="F" />
+            </extension>
+            <status value="final" />
+            <code>
+              <coding>
+                <system value="urn:oid:1.3.6.1.4.1.12201.102.6" />
+                <code value="10017.1" />
+              </coding>
+              <text value="Date Dictated" />
+            </code>
+            <subject>
+              <reference value="Patient/5556918" />
+            </subject>
+            <issued value="2014-09-26T11:55:33.000-04:00" />
+            <valueString value="Fri, 26 Sep 2014" />
+            <interpretation>
+              <coding>
+                <system value="urn:uhn:qcpr:interpretation_codes" />
+                <code value="N" />
+              </coding>
+            </interpretation>
+          </Observation>
+        </contained>
+        <extension url="http://fhir.uhn.ca/Profile/diagnosticreport#source_system_status">
+          <valueString value="F" />
+        </extension>
+        <identifier>
+          <system value="urn:uhn:qcpr:order_ids" />
+          <value value="GI93#discharge_5677961273802d07ad7d079141525bba" />
+        </identifier>
+        <status value="final" />
+        <code>
+          <coding>
+            <system value="urn:oid:1.3.6.1.4.1.12201.102.5" />
+            <code value="5053" />
+          </coding>
+          <text value="Unscheduled Discharge Summary" />
+        </code>
+        <subject>
+          <reference value="Patient/5556918" />
+        </subject>
+        <encounter>
+          <reference value="Encounter/5885735" />
+        </encounter>
+        <effectiveDateTime value="2014-09-26T11:55:00-04:00" />
+        <issued value="2014-09-26T11:55:33.000-04:00" />
+      </DiagnosticReport>
+    </resource>
+  </entry>
+</Bundle>

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/bundle_with_invalid_contained_ref.xml

@@ -0,0 +1,50 @@
+<Bundle xmlns="http://hl7.org/fhir">
+  <id value="fe7ff16d-8bdf-47a5-9de3-20165c6fe440" />
+  <meta>
+    <lastUpdated value="2016-08-25T12:17:12.159-04:00" />
+  </meta>
+  <type value="searchset" />
+  <total value="208" />
+  <link>
+    <relation value="self" />
+    <url value="http://foo.uhn.on.ca:25180/uhn-fhir-service-2.1/DiagnosticReport?_format=xml&amp;_include=DiagnosticReport%3Aencounter&amp;_include=Encounter%3AfacilityLocation&amp;_include=Observation%3Aperformer&amp;_include=DiagnosticReport%3Aresult&amp;_include=Encounter%3Alocation&amp;_include=Location.partOf&amp;_include=Encounter%3Aparticipant&amp;_include=DiagnosticReport%3Apatient&amp;subject%3Aidentifier=urn%3Aoid%3A2.16.840.1.113883.3.239.18.148%7C7000135" />
+  </link>
+ <entry>
+    <fullUrl value="http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-2.1/DiagnosticReport/7162221" />
+    <resource>
+      <DiagnosticReport xmlns="http://hl7.org/fhir">
+        <id value="7162221" />
+        <meta>
+          <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+          <profile value="http://fhir.uhn.ca/Profile/diagnosticreport" />
+        </meta>
+        <extension url="http://fhir.uhn.ca/Profile/diagnosticreport#source_system_status">
+          <valueString value="F" />
+        </extension>
+        <identifier>
+          <system value="urn:uhn:qcpr:order_ids" />
+          <value value="GI93#discharge_5677961273802d07ad7d079141525bba" />
+        </identifier>
+        <status value="final" />
+        <code>
+          <coding>
+            <system value="urn:oid:1.3.6.1.4.1.12201.102.5" />
+            <code value="5053" />
+          </coding>
+          <text value="Unscheduled Discharge Summary" />
+        </code>
+        <subject>
+          <reference value="Patient/5556918" />
+        </subject>
+        <encounter>
+          <reference value="Encounter/5885735" />
+        </encounter>
+        <effectiveDateTime value="2014-09-26T11:55:00-04:00" />
+        <issued value="2014-09-26T11:55:33.000-04:00" />
+        <result>
+          <reference value="#1" />
+        </result>
+      </DiagnosticReport>
+    </resource>
+  </entry>
+</Bundle>

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/bundle_with_woven_obs.xml

@@ -0,0 +1,317 @@
+<Bundle xmlns="http://hl7.org/fhir">
+  <id value="fe7ff16d-8bdf-47a5-9de3-20165c6fe440" />
+  <meta>
+    <lastUpdated value="2016-08-25T12:17:12.159-04:00" />
+  </meta>
+  <type value="searchset" />
+  <total value="208" />
+  <link>
+    <relation value="self" />
+    <url value="http://foo.uhn.on.ca:25180/uhn-fhir-service-2.1/DiagnosticReport?_format=xml&amp;_include=DiagnosticReport%3Aencounter&amp;_include=Encounter%3AfacilityLocation&amp;_include=Observation%3Aperformer&amp;_include=DiagnosticReport%3Aresult&amp;_include=Encounter%3Alocation&amp;_include=Location.partOf&amp;_include=Encounter%3Aparticipant&amp;_include=DiagnosticReport%3Apatient&amp;subject%3Aidentifier=urn%3Aoid%3A2.16.840.1.113883.3.239.18.148%7C7000135" />
+  </link>
+ <entry>
+    <fullUrl value="http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-2.1/DiagnosticReport/7162221" />
+    <resource>
+      <DiagnosticReport xmlns="http://hl7.org/fhir">
+        <id value="7162221" />
+        <meta>
+          <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+          <profile value="http://fhir.uhn.ca/Profile/diagnosticreport" />
+        </meta>
+        <contained>
+          <Observation xmlns="http://hl7.org/fhir">
+            <id value="1" />
+            <meta>
+              <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+              <profile value="http://fhir.uhn.ca/Profile/observation" />
+            </meta>
+            <extension url="http://fhir.uhn.ca/Profile/observation#source_system_status">
+
+              <valueString value="F" />
+            </extension>
+            <status value="final" />
+            <code>
+              <coding>
+                <system value="urn:oid:1.3.6.1.4.1.12201.102.6" />
+                <code value="10017.1" />
+              </coding>
+              <text value="Date Dictated" />
+            </code>
+            <subject>
+              <reference value="Patient/5556918" />
+            </subject>
+            <issued value="2014-09-26T11:55:33.000-04:00" />
+            <valueString value="Fri, 26 Sep 2014" />
+            <interpretation>
+              <coding>
+                <system value="urn:uhn:qcpr:interpretation_codes" />
+                <code value="N" />
+              </coding>
+            </interpretation>
+          </Observation>
+        </contained>
+        <contained>
+          <Observation xmlns="http://hl7.org/fhir">
+            <id value="2" />
+            <meta>
+              <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+              <profile value="http://fhir.uhn.ca/Profile/observation" />
+            </meta>
+            <extension url="http://fhir.uhn.ca/Profile/observation#source_system_status">
+
+              <valueString value="F" />
+            </extension>
+            <status value="final" />
+            <code>
+              <coding>
+                <system value="urn:oid:1.3.6.1.4.1.12201.102.6" />
+                <code value="1126527.2" />
+              </coding>
+              <text value="Dictated by" />
+            </code>
+            <subject>
+              <reference value="Patient/5556918" />
+            </subject>
+            <issued value="2014-09-26T11:55:33.000-04:00" />
+            <performer>
+              <reference value="#3" />
+            </performer>
+            <valueString value="Gered Trystan King" />
+            <interpretation>
+              <coding>
+                <system value="urn:uhn:qcpr:interpretation_codes" />
+                <code value="normal" />
+              </coding>
+            </interpretation>
+          </Observation>
+        </contained>
+        <contained>
+          <Practitioner xmlns="http://hl7.org/fhir">
+            <id value="3" />
+            <identifier>
+              <system value="urn:uhn:qcpr:user_ids" />
+              <value value="160920" />
+            </identifier>
+            <name>
+              <family value="Gered Trystan King" />
+            </name>
+          </Practitioner>
+        </contained>
+        <contained>
+          <Observation xmlns="http://hl7.org/fhir">
+            <id value="4" />
+            <meta>
+              <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+              <profile value="http://fhir.uhn.ca/Profile/observation" />
+            </meta>
+            <extension url="http://fhir.uhn.ca/Profile/observation#source_system_status">
+
+              <valueString value="F" />
+            </extension>
+            <status value="final" />
+            <code>
+              <coding>
+                <system value="urn:oid:1.3.6.1.4.1.12201.102.6" />
+                <code value="14002.3" />
+              </coding>
+              <text value="Attending/Staff" />
+            </code>
+            <subject>
+              <reference value="Patient/5556918" />
+            </subject>
+            <issued value="2014-09-26T11:55:33.000-04:00" />
+            <performer>
+              <reference value="#5" />
+            </performer>
+            <valueString value="Gered Trystan King" />
+            <interpretation>
+              <coding>
+                <system value="urn:uhn:qcpr:interpretation_codes" />
+                <code value="normal" />
+              </coding>
+            </interpretation>
+          </Observation>
+        </contained>
+        <contained>
+          <Practitioner xmlns="http://hl7.org/fhir">
+            <id value="5" />
+            <identifier>
+              <system value="urn:uhn:qcpr:user_ids" />
+              <value value="160920" />
+            </identifier>
+            <name>
+              <family value="Gered Trystan King" />
+            </name>
+          </Practitioner>
+        </contained>
+        <contained>
+          <Observation xmlns="http://hl7.org/fhir">
+            <id value="6" />
+            <meta>
+              <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+              <profile value="http://fhir.uhn.ca/Profile/observation" />
+            </meta>
+            <extension url="http://fhir.uhn.ca/Profile/observation#source_system_status">
+
+              <valueString value="F" />
+            </extension>
+            <status value="final" />
+            <code>
+              <coding>
+                <system value="urn:oid:1.3.6.1.4.1.12201.102.6" />
+                <code value="10063.4" />
+              </coding>
+              <text value="Distribute Y/N?" />
+            </code>
+            <subject>
+              <reference value="Patient/5556918" />
+            </subject>
+            <issued value="2014-09-26T11:55:33.000-04:00" />
+            <valueString value="yes" />
+            <interpretation>
+              <coding>
+                <system value="urn:uhn:qcpr:interpretation_codes" />
+                <code value="N" />
+              </coding>
+            </interpretation>
+          </Observation>
+        </contained>
+        <contained>
+          <Observation xmlns="http://hl7.org/fhir">
+            <id value="7" />
+            <meta>
+              <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+              <profile value="http://fhir.uhn.ca/Profile/observation" />
+            </meta>
+            <extension url="http://fhir.uhn.ca/Profile/observation#source_system_status">
+
+              <valueString value="F" />
+            </extension>
+            <status value="final" />
+            <code>
+              <coding>
+                <system value="urn:oid:1.3.6.1.4.1.12201.102.6" />
+                <code value="14001.5" />
+              </coding>
+              <text value="Medical Records Report" />
+            </code>
+            <subject>
+              <reference value="Patient/5556918" />
+            </subject>
+            <issued value="2014-09-26T11:55:33.000-04:00" />
+            <valueString value="Medical Records Report" />
+          </Observation>
+        </contained>
+        <contained>
+          <Observation xmlns="http://hl7.org/fhir">
+            <id value="8" />
+            <meta>
+              <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+              <profile value="http://fhir.uhn.ca/Profile/observation" />
+            </meta>
+            <extension url="http://fhir.uhn.ca/Profile/observation#source_system_status">
+
+              <valueString value="F" />
+            </extension>
+            <status value="final" />
+            <code>
+              <coding>
+                <system value="urn:oid:1.3.6.1.4.1.12201.102.6" />
+                <code value="10060.6" />
+              </coding>
+              <text value="Report Type" />
+            </code>
+            <subject>
+              <reference value="Patient/5556918" />
+            </subject>
+            <issued value="2014-09-26T11:55:33.000-04:00" />
+            <valueString value="Unscheduled Discharge Summary" />
+            <interpretation>
+              <coding>
+                <system value="urn:uhn:qcpr:interpretation_codes" />
+                <code value="N" />
+              </coding>
+            </interpretation>
+          </Observation>
+        </contained>
+        <contained>
+          <Observation xmlns="http://hl7.org/fhir">
+            <id value="9" />
+            <meta>
+              <lastUpdated value="2014-09-26T11:55:33.000-04:00" />
+              <profile value="http://fhir.uhn.ca/Profile/observation" />
+            </meta>
+            <extension url="http://fhir.uhn.ca/Profile/observation#source_system_status">
+
+              <valueString value="F" />
+            </extension>
+            <status value="final" />
+            <code>
+              <coding>
+                <system value="urn:oid:1.3.6.1.4.1.12201.102.6" />
+                <code value="10064.7" />
+              </coding>
+              <text value="Review/Query?" />
+            </code>
+            <subject>
+              <reference value="Patient/5556918" />
+            </subject>
+            <issued value="2014-09-26T11:55:33.000-04:00" />
+            <valueString value="no" />
+            <interpretation>
+              <coding>
+                <system value="urn:uhn:qcpr:interpretation_codes" />
+                <code value="N" />
+              </coding>
+            </interpretation>
+          </Observation>
+        </contained>
+        <extension url="http://fhir.uhn.ca/Profile/diagnosticreport#source_system_status">
+
+          <valueString value="F" />
+        </extension>
+        <identifier>
+          <system value="urn:uhn:qcpr:order_ids" />
+          <value value="GI93#discharge_5677961273802d07ad7d079141525bba" />
+        </identifier>
+        <status value="final" />
+        <code>
+          <coding>
+            <system value="urn:oid:1.3.6.1.4.1.12201.102.5" />
+            <code value="5053" />
+          </coding>
+          <text value="Unscheduled Discharge Summary" />
+        </code>
+        <subject>
+          <reference value="Patient/5556918" />
+        </subject>
+        <context>
+          <reference value="Encounter/5885735" />
+        </context>
+        <effectiveDateTime value="2014-09-26T11:55:00-04:00" />
+        <issued value="2014-09-26T11:55:33.000-04:00" />
+        <result>
+          <reference value="#1" />
+        </result>
+        <result>
+          <reference value="#2" />
+        </result>
+        <result>
+          <reference value="#4" />
+        </result>
+        <result>
+          <reference value="#6" />
+        </result>
+        <result>
+          <reference value="#7" />
+        </result>
+        <result>
+          <reference value="#8" />
+        </result>
+        <result>
+          <reference value="#9" />
+        </result>
+      </DiagnosticReport>
+    </resource>
+  </entry>
+</Bundle>

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/dstu3/myconsent-resource.json

@@ -0,0 +1,55 @@
+{
+	"resourceType": "Consent",
+	"id": "consent-example-basic",
+	"text": {
+		"status": "generated",
+		"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n    <p>\n\tAuthorize Normal access for Treatment\n\t</p><p>\n    Patient &quot;P. van de Heuvel&quot; wishes to have all of the PHI collected at the Good Health Psychiatric Hospital \n   available for normal treatment use.\n   </p>\n   </div>"
+	},
+	"status": "active",
+	"patient": {
+		"reference": "Patient/f001",
+		"display": "P. van de Heuvel"
+	},
+	"period": {
+		"start": "1964-01-01",
+		"end": "2016-01-01"
+	},
+	"dateTime": "2016-05-11",
+	"organization": [
+		{
+			"reference": "Organization/Infoway",
+			"display": "Canada Infoway"
+		}
+	],
+	"sourceAttachment": {
+		"title": "The terms of the consent in lawyer speak."
+	},
+	"identifier": [
+		{
+			"use": "usual",
+			"type": {
+				"coding": [
+					{
+						"system": "http://hl7.org/fhir/v2/0203",
+						"code": "MR"
+					}
+				]
+			},
+			"system": "urn:oid:1.2.36.146.595.217.0.1",
+			"value": "12345",
+			"period": {
+				"start": "2001-05-06"
+			},
+			"assigner": {
+				"display": "Acme Healthcare"
+			}
+		}
+	],
+	"extension":[
+		{
+			"url" : "http://hl7.org/fhir/StructureDefinition/PruebaExtension",
+			"valueString" : "123456789"
+		}
+	],
+	"policyRule": "http://goodhealth.org/consent/policy/opt-in"
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/example-patient-general-hl7orgdstu2.json

@@ -0,0 +1,140 @@
+{
+    "resourceType":"Patient",
+    "text":{
+        "status":"generated",
+        "div":"<div>\n      <table>\n        <tbody>\n          <tr>\n            <td>Name</td>\n            <td>Peter James <b>Chalmers</b> (\"Jim\")</td>\n          </tr>\n          <tr>\n            <td>Address</td>\n            <td>534 Erewhon, Pleasantville, Vic, 3999</td>\n          </tr>\n          <tr>\n            <td>Contacts</td>\n            <td>Home: unknown. Work: (03) 5555 6473</td>\n          </tr>\n          <tr>\n            <td>Id</td>\n            <td>MRN: 12345 (Acme Healthcare)</td>\n          </tr>\n        </tbody>\n      </table>\n    </div>"
+    },
+    "extension":[
+        {
+            "url":"urn:patientext:att",
+            "valueAttachment":{
+                "contentType":"aaaa",
+                "data":"AAAA"
+            }
+        },
+        {
+            "url":"urn:patientext:moreext",
+            "extension":[
+                {
+                    "url":"urn:patientext:moreext:1",
+                    "valueString":"str1"
+                },
+                {
+                    "url":"urn:patientext:moreext:2",
+                    "valueString":"str2"
+                }
+            ]
+        }
+    ],
+    "modifierExtension":[
+        {
+            "url":"urn:modext",
+            "valueDate":"2011-01-02"
+        }
+    ],
+    "identifier":[
+        {
+            "use":"usual",
+            "system":"urn:oid:1.2.36.146.595.217.0.1",
+            "value":"12345",
+            "period":{
+                "start":"2001-05-06"
+            },
+            "assigner":{
+                "display":"Acme Healthcare"
+            }
+        }
+    ],
+    "active":true,
+    "name":[
+        {
+            "use":"official",
+            "family":[
+                "Chalmers"
+            ],
+            "given":[
+                "Peter",
+                "James"
+            ]
+        },
+        {
+            "use":"usual",
+            "given":[
+                "Jim"
+            ]
+        }
+    ],
+    "telecom":[
+        {
+            "use":"home"
+        },
+        {
+            "system":"phone",
+            "value":"(03) 5555 6473",
+            "use":"work"
+        }
+    ],
+    "gender":"male",
+    "birthDate":"1974-12-25",
+    "deceasedBoolean":false,
+    "address":[
+        {
+            "use":"home",
+            "line":[
+                "534 Erewhon St"
+            ],
+            "city":"PleasantVille",
+            "state":"Vic",
+            "postalCode":"3999"
+        },
+        {
+            "use":"old",
+            "line":[
+                "SecondAddress"
+            ]
+        }
+    ],
+    "contact":[
+        {
+            "relationship":[
+                {
+                    "coding":[
+                        {
+                            "system":"http://hl7.org/fhir/patient-contact-relationship",
+                            "code":"partner"
+                        }
+                    ]
+                }
+            ],
+            "name":{
+                "family":[
+                    "du",
+                    "Marché"
+                ],
+                "_family":[
+                    {
+                        "extension":[
+                            {
+                                "url":"http://hl7.org/fhir/Profile/iso-21090#qualifier",
+                                "valueCode":"VV"
+                            }
+                        ]
+                    },
+                    null
+                ],
+                "given":[
+                    "Bénédicte"
+                ]
+            },
+            "telecom":[
+                {
+                    "system":"phone",
+                    "value":"+33 (237) 998327"
+                }
+            ]
+        }
+    ],
+    "managingOrganization":{
+        "reference":"Organization/1"
+    }
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/example-patient-general-hl7orgdstu2.xml

@@ -0,0 +1,128 @@
+<Patient xmlns="http://hl7.org/fhir">
+  <text>
+    <status value="generated"/>
+    <div xmlns="http://www.w3.org/1999/xhtml">
+      <table>
+        <tbody>
+          <tr>
+            <td>Name</td>
+            <td>Peter James <b>Chalmers</b> (&quot;Jim&quot;)</td>
+          </tr>
+          <tr>
+            <td>Address</td>
+            <td>534 Erewhon, Pleasantville, Vic, 3999</td>
+          </tr>
+          <tr>
+            <td>Contacts</td>
+            <td>Home: unknown. Work: (03) 5555 6473</td>
+          </tr>
+          <tr>
+            <td>Id</td>
+            <td>MRN: 12345 (Acme Healthcare)</td>
+          </tr>
+        </tbody>
+      </table>
+    </div>
+  </text>
+
+  	<extension url="urn:patientext:att">
+		<valueAttachment>
+			<contentType value="aaaa"/>
+			<data value="AAAA"/>
+		</valueAttachment>
+	</extension>
+  
+  	<extension url="urn:patientext:moreext">
+  		<extension url="urn:patientext:moreext:1">
+  			<valueString value="str1"/>
+  		</extension>  		
+  		<extension url="urn:patientext:moreext:2">
+  			<valueString value="str2"/>
+  		</extension>
+  	</extension>
+  
+  	<modifierExtension url="urn:modext">
+  		<valueDate value="2011-01-02"/>
+  	</modifierExtension>
+  
+  <identifier>
+    <use value="usual"/>
+    <system value="urn:oid:1.2.36.146.595.217.0.1"/>
+    <value value="12345"/>
+    <period>
+      <start value="2001-05-06"/>
+    </period>
+    <assigner>
+      <display value="Acme Healthcare"/>
+    </assigner>
+  </identifier>
+
+  <active value="true"/>
+
+  <name>
+    <use value="official"/>
+    <family value="Chalmers"/>
+    <given value="Peter"/>
+    <given value="James"/>
+  </name>
+  <name>
+    <use value="usual"/>
+    <given value="Jim"/>
+  </name>
+
+  <telecom>
+    <use value="home"/>
+  </telecom>
+  <telecom>
+    <system value="phone"/>
+    <value value="(03) 5555 6473"/>
+    <use value="work"/>
+  </telecom>
+
+  <gender value="male"/>
+  <birthDate value="1974-12-25"/>
+  <deceasedBoolean value="false"/>
+
+  <address>
+    <use value="home"/>
+    <line value="534 Erewhon St"/>
+    <city value="PleasantVille"/>
+    <state value="Vic"/>
+    <postalCode value="3999"/>
+  </address>
+
+  <address>
+  	<use value="old"/>
+  	<line value="SecondAddress"/>
+  </address>
+
+  <contact>
+    <relationship>
+      <coding>
+        <system value="http://hl7.org/fhir/patient-contact-relationship"/>
+        <code value="partner"/>
+      </coding>
+    </relationship>
+
+    <name>
+      <family value="du">
+        <extension url="http://hl7.org/fhir/Profile/iso-21090#qualifier">
+          <valueCode value="VV"/>
+        </extension>
+      </family>
+      <family value="Marché"/>
+      <given value="Bénédicte"/>
+    </name>
+
+    <telecom>
+      <system value="phone"/>
+      <value value="+33 (237) 998327"/>
+    </telecom>
+  </contact>
+
+  <managingOrganization>
+    <reference value="Organization/1"/>
+  </managingOrganization>
+
+
+</Patient>

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/extension-on-line.txt

@@ -0,0 +1,58 @@
+{
+  "resourceType": "Patient",
+  "name": [
+    {
+      "family": "Doe",
+      "given": [
+        "John",
+        "W."
+      ]
+    }
+  ],
+  "gender": "male",
+  "birthDate": "2012-02-14",
+  "address": [
+    {
+      "use": "home",
+      "line": [
+        "535 Sheppard Avenue West, Unit 1907",
+        "RR 66, Station A, RPO 123"
+      ],
+      "_line": [
+        {
+          "extension": [
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/iso21090-ADXP-houseNumber",
+              "valueString": "535"
+            },
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/iso21090-ADXP-streetName",
+              "valueString": "Sheppard"
+            },
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/iso21090-ADXP-streetNameType",
+              "valueString": "Avenue"
+            },
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/iso21090-ADXP-direction",
+              "valueString": "West"
+            },
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/iso21090-ADXP-unitID",
+              "valueString": "1907"
+            },
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/iso21090-ADXP-postBox",
+              "valueString": "1234"
+            }
+          ]
+        }
+      ],
+      "city": "Toronto",
+      "state": "ON",
+      "postalCode": "M3H4X8"
+    }
+  ]
+}
+
+

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/patient-example-dicom.json

@@ -0,0 +1,60 @@
+{
+  "resourceType": "Patient",
+  "id": "dicom",
+  "text": {
+    "status": "generated",
+    "div": "<div> Patient MINT_TEST, ID = MINT1234. Age = 56y, Size =\n      1.83m, Weight = 72.58kg </div>"
+  },
+  "http://nema.org/fhir/extensions#0010:1010": [
+    {
+      "valueQuantity": {
+        "value": 56,
+        "units": "Y"
+      }
+    }
+  ],
+  "http://nema.org/fhir/extensions#0010:1020": [
+    {
+      "valueQuantity": {
+        "value": 1.83,
+        "units": "m"
+      }
+    }
+  ],
+  "http://nema.org/fhir/extensions#0010:1030": [
+    {
+      "valueQuantity": {
+        "value": 72.58,
+        "units": "kg"
+      }
+    }
+  ],
+  "identifier": [
+    {
+      "system": "http://nema.org/examples/patients",
+      "value": "MINT1234"
+    }
+  ],
+  "name": [
+    {
+      "family": [
+        "MINT_TEST"
+      ]
+    }
+  ],
+  "gender": "male",
+  "_gender": {
+    "http://nema.org/examples/extensions#gender": [
+      {
+        "valueCoding": {
+          "system": "http://nema.org/examples/gender",
+          "code": "M"
+        }
+      }
+    ]
+  },
+  "managingOrganization": {
+    "reference": "Organization/1"
+  },
+  "active": true
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/qr_jon.xml

@@ -0,0 +1,455 @@
+<QuestionnaireResponse xmlns="http://hl7.org/fhir">
+    <identifier>
+        <value value="1234567890"/>
+    </identifier>
+    <questionnaire>
+        <reference value="Questionnaire/q_jon"/>
+    </questionnaire>
+    <status value="completed"/>
+    <subject>
+        <reference value="http://fhirtest.uhn.ca/baseDstu3/Patient/proband"/>
+    </subject>
+    <author>
+        <reference value="http://fhirtest.uhn.ca/baseDstu3/Practitioner/f007"/>
+    </author>
+    <authored value="2016-01-08"/>
+    <item>
+        <linkId value="root"/>
+        <item>
+            <linkId value="g1"/>
+            <text value="CLINICAL INFORMATION"/>
+            <item>
+                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                    <valueString value="1.1"/>
+                </extension>
+                <linkId value="1.1"/>
+                <text value="Patient Clinical Information"/>
+                <answer>
+                    <valueString value="Previous chest X-RAY was suspicious. Heavy smoker, 15 pack years."/>
+                </answer>
+            </item>
+            <item>
+                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                    <valueString value="1.2"/>
+                </extension>
+                <linkId value="1.2"/>
+                <text value="Previous Examination (Date and Modality)"/>
+                <answer>
+                    <valueString value="Chest XR - September 23, 2015"/>
+                </answer>
+            </item>
+        </item>
+        <item>
+            <linkId value="g2"/>
+            <text value="IMAGING PROCEDURE DESCRIPTION"/>
+            <item>
+                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                    <valueString value="2.1"/>
+                </extension>
+                <linkId value="2.1"/>
+                <text value="Overall Image Quality:"/>
+                <answer>
+                    <valueCoding>
+                        <code value="2.1a"/>
+                        <display value="Adequate"/>
+                    </valueCoding>
+                </answer>
+            </item>
+            <item>
+                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                    <valueString value="2.2"/>
+                </extension>
+                <linkId value="2.2"/>
+                <text value="Intravenous Contrast Used?"/>
+                <answer>
+                    <valueBoolean value="false"/>
+                </answer>
+            </item>
+            <item>
+                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                    <valueString value="2.3"/>
+                </extension>
+                <linkId value="2.3"/>
+                <text value="Additional Comments"/>
+                <answer>
+                    <valueString value="n/a."/>
+                </answer>
+            </item>
+        </item>
+        <item>
+            <linkId value="g3"/>
+            <text value="FINDINGS"/>
+            <item>
+                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                    <valueString value="3"/>
+                </extension>
+                <linkId value="g3.0"/>
+                <text value="T Category"/>
+                <item>
+                    <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                        <valueString value="3.1"/>
+                    </extension>
+                    <linkId value="g3.1"/>
+                    <text value="Location of Main Nodule/Mass (Primary tumor, or Reference tumor)"/>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="3.1.1"/>
+                        </extension>
+                        <linkId value="q3.1.1"/>
+                        <text value="Location of main nodule/mass:"/>
+                        <answer>
+                            <valueCoding>
+                                <code value="3.1.1a"/>
+                                <display value="Peripheral"/>
+                            </valueCoding>
+                        </answer>
+                    </item>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="3.1.2"/>
+                        </extension>
+                        <linkId value="3.1.2"/>
+                        <answer>
+                            <valueString value="Right Upper Lung, Posterior segment."/>
+                        </answer>
+                    </item>
+                </item>
+                <item>
+                    <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                        <valueString value="3.2"/>
+                    </extension>
+                    <linkId value="g3.2"/>
+                    <text value="Size and characteristics of main nodule/mass"/>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="3.2.1"/>
+                        </extension>
+                        <linkId value="3.2.1"/>
+                        <text value="Size of the nodule/mass:"/>
+                        <answer>
+                            <valueCoding>
+                                <code value="3.2.1a"/>
+                                <display value="Solid nodule/mass"/>
+                            </valueCoding>
+                        </answer>
+                        <item><!-- Measurement, image, series, etc for all 3 answer choices goes here. Conditonal. -->
+                            <linkId value="g3.2.1"/>
+                            <item><!-- Group for answer choice a -->
+                                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-enableWhen"><!-- Note that this extension is at the group level. -->
+                                    <extension url="#question">
+                                        <valueString value="3.2.1"/>
+                                    </extension>
+                                    <extension url="#answer">
+                                        <valueCoding>
+                                            <code value="3.2.1a"/>
+                                        </valueCoding>
+                                    </extension>
+                                </extension>
+                                <linkId value="g3.2.1a"/>
+                                <item>
+                                    <linkId value="3.2.1a"/>
+                                    <text value="largest dimension:"/>
+                                    <answer>
+                                        <valueInteger value="20"/>
+                                    </answer>
+                                    <item>
+                                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl">
+                                            <valueCodeableConcept>
+                                                <coding>
+                                                    <system value="http://hl7.org/fhir/ValueSet/questionnaire-item-control"/>
+                                                    <code value="unit"/>
+                                                </coding>
+                                            </valueCodeableConcept>
+                                        </extension>
+                                        <text value="mm"/>
+                                    </item>
+                                </item>
+                                <item>
+                                    <linkId value="3.2.1a.image"/>
+                                    <text value="image"/>
+                                    <answer>
+                                        <valueString value="32"/>
+                                    </answer>
+                                </item>
+                                <item>
+                                    <linkId value="3.2.1a.series"/>
+                                    <text value="series"/>
+                                    <answer>
+                                        <valueString value="3"/>
+                                    </answer>
+                                </item>
+                            </item>    
+                        </item>
+                    </item>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="3.2.2"/>
+                        </extension>
+                        <linkId value="3.2.2"/>
+                        <text value="Plane in which the mass was measured:"/>
+                        <answer>
+                            <valueCoding>
+                                <code value="3.2.2a"/>
+                                <display value="Axial"/>
+                            </valueCoding>
+                        </answer>
+                    </item>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="3.2.3"/>
+                        </extension>
+                        <linkId value="3.2.3"/>
+                        <answer>
+                            <valueString value="Solid attenuation of mass, margins spiculated."/>
+                        </answer>
+                    </item>
+                </item>
+                <item>
+                    <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                        <valueString value="3.3"/>
+                    </extension>
+                    <linkId value="g3.3"/>
+                    <text value="Structures directly involved"/>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="3.3.1"/>
+                        </extension>
+                        <linkId value="3.3.1"/>
+                        <text value="State if there is bronchial involvement:"/>
+                        <answer>
+                            <valueCoding>
+                                <code value="3.3.1b"/>
+                                <display value="No"/>
+                            </valueCoding>
+                        </answer>
+                    </item>    
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="3.3.2"/>
+                        </extension>
+                        <linkId value="3.3.2"/>
+                        <text value="Is there direct involvement of any other anatomical structures?"/>
+                        <answer>
+                            <valueBoolean value="false"/>
+                        </answer>
+                    </item>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="3.3.3"/>
+                        </extension>
+                        <linkId value="3.3.3"/>
+                        <text value="Are there additional suspicious pulmonary nodules?"/>
+                        <answer>
+                            <valueBoolean value="false"/>
+                        </answer>
+                    </item>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="3.3.4"/>
+                        </extension>
+                        <linkId value="3.3.4"/>
+                        <text value="Other notable intrathoracic findings (eg lymphangitis carcinomatosis):"/>
+                        <answer>
+                            <valueString value="n/a"/>
+                        </answer>
+                    </item>
+                </item>
+            </item>
+            <item>
+                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                    <valueString value="4"/>
+                </extension>
+                <linkId value="4.0"/>
+                <text value="N Category"/>
+                <item>
+                    <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                        <valueString value="4.1"/>
+                    </extension>
+                    <linkId value="4.1"/>
+                    <text value="Are there enlarged lymph nodes?"/>
+                    <answer>
+                        <valueBoolean value="false"/>
+                    </answer>
+                </item>
+                <item>
+                    <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                        <valueString value="4.2"/>
+                    </extension>
+                    <linkId value="4.2"/>
+                    <text value="Other notable findings:"/>
+                    <answer>
+                        <valueString value="Liner / scar atelectasis lingua, anterior segment of right upper lobe and bilateral lower lobes."/>
+                    </answer>
+                </item>
+            </item>
+            <item>
+                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                    <valueString value="5"/>
+                </extension>
+                <linkId value="5.0"/>
+                <text value="M Category (Suspicious Extrathoracic Findings (M1b))"/>
+                <item>
+                    <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                        <valueString value="5.1"/>
+                    </extension>
+                    <linkId value="5.1"/>
+                    <text value="Are there suspicious extrathoracic findings?"/>
+                    <answer>
+                        <valueBoolean value="true"/>
+                    </answer>
+                    <item>
+                        <linkId value="g5.1.yes"/>
+                        <item>
+                            <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-enableWhen">
+                                <extension url="#question">
+                                    <valueString value="5.1"/>
+                                </extension>
+                                <extension url="#answer">
+                                    <valueBoolean value="true"/>
+                                </extension>
+                            </extension>
+                            <linkId value="5.1.yes"/>
+                            <text value="Applicable Structures and Descriptions:"/>
+                            <answer>
+                                <valueCoding>
+                                    <code value="5.1.yes.d"/>
+                                    <display value="Other"/>
+                                </valueCoding>
+                            </answer>
+                            <item>
+                                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-enableWhen">
+                                    <extension url="#question">
+                                        <valueString value="5.1.yes"/>
+                                    </extension>
+                                    <extension url="#answer">
+                                        <valueCoding>
+                                            <code value="5.1.yes.d"/>
+                                        </valueCoding>
+                                    </extension>
+                                </extension>
+                                <linkId value="5.1.yes.d.description"/>
+                                <text value="Description of structures:"/>
+                                <answer>
+                                    <valueString value="3 cm calcified thyroid nodule on TUL left."/>
+                                </answer>
+                            </item>
+                        </item>
+                    </item>
+                </item>
+            </item>
+            <item>
+                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                    <valueString value="6"/>
+                </extension>
+                <linkId value="6.0"/>
+                <text value="Additional Findings"/>
+                <item>
+                    <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                        <valueString value="6.1"/>
+                    </extension>
+                    <linkId value="6.1"/>
+                    <text value="Are there additional findings?"/>
+                    <answer>
+                        <valueBoolean value="true"/>
+                    </answer>
+                </item>
+                <item>
+                    <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                        <valueString value="6.2"/>
+                    </extension>
+                    <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-enableWhen">
+                        <extension url="#question">
+                            <valueString value="6.1"/>
+                        </extension>
+                        <extension url="#answer">
+                            <valueBoolean value="true"/>
+                        </extension>
+                    </extension>
+                    <linkId value="6.2"/>
+                    <text value="Findings and Descriptions:"/>
+                    <answer>
+                        <valueString value="Oligemic changes in right upper lobe from possible old pulmonary embolus."/>
+                    </answer>
+                </item>
+            </item>
+        </item>
+        <item>
+            <linkId value="g7"/>
+            <text value="IMPRESSIONS"/>
+            <item>
+                <linkId value="g7.1"/>
+                <item>
+                    <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                        <valueString value="7.1"/>
+                    </extension>
+                    <linkId value="7.1"/>
+                    <text value="Impression/Summary:"/>
+                    <answer>
+                        <valueString value="Spiculated mass in posterior segment of right upper lobe that has increasing size from 16 to 20 mm."/>
+                    </answer>
+                </item>
+            </item>
+            <item>
+                <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                    <valueString value="7.2"/>
+                </extension>
+                <linkId value="g7.2"/>
+                <text value="Radiologic Staging (TNM Version – 7th edition)"/>
+                <item>
+                    <linkId value="g7.20"/>
+                    <text value="If this is a biopsy proven carcinoma, the preliminary radiologic stage is:"/>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="i)"/>
+                        </extension>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-questionControl" >
+                            <valueCodeableConcept>
+                                <coding>
+                                    <code value="radio-button"/>
+                                    <display value="Radio Button"/>
+                                </coding>
+                            </valueCodeableConcept>
+                        </extension>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-choiceOrientation" >
+                            <valueCode value="horizontal"/>
+                        </extension>
+                        <linkId value="7.2i"/>
+                        <text value="Primary Tumour (T):"/>
+                        <answer>
+                            <valueCoding>
+                                <code value="T1a"/>
+                                <display value="T1a"/>
+                            </valueCoding>
+                        </answer>
+                    </item>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="ii)"/>
+                        </extension>
+                        <linkId value="7.2ii"/>
+                        <text value="Regional Lymph Nodes (N):"/>
+                        <answer>
+                            <valueCoding>
+                                <code value="N0"/>
+                                <display value="N0"/>
+                            </valueCoding>
+                        </answer>
+                    </item>
+                    <item>
+                        <extension url="http://hl7.org/fhir/StructureDefinition/questionnaire-label">
+                            <valueString value="iii)"/>
+                        </extension>
+                        <linkId value="7.2iii"/>
+                        <text value="Distant Metastasis (M):"/>
+                        <answer>
+                            <valueCoding>
+                                <code value="M0"/>
+                                <display value="M0"/>
+                            </valueCoding>
+                        </answer>
+                    </item>
+                </item>
+            </item>
+        </item>
+    </item>
+</QuestionnaireResponse>

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/r4/bundle-with-no-type.json

@@ -0,0 +1,73 @@
+{
+  "resourceType": "Bundle",
+  "entry": [
+    {
+      "fullUrl": "http://localhost:5555/phr/baseDstu3/Person/PERSON1",
+      "resource": {
+        "resourceType": "Person",
+        "id": "PERSON1",
+        "meta": {
+          "versionId": "1",
+          "lastUpdated": "2017-08-17T16:19:40.109+03:00"
+        },
+        "identifier": [
+          {
+            "value": "081181-9984"
+          }
+        ],
+        "name": [
+          {
+            "text": "Anna Testi",
+            "family": "Testi",
+            "given": [
+              "Anna"
+            ]
+          },
+          {
+            "family": "asdfas"
+          }
+        ],
+        "telecom": [
+          {
+            "use": "home"
+          },
+          {
+            "system": "phone",
+            "value": "(044) 1234567",
+            "use": "work"
+          }
+        ],
+        "gender": "female",
+        "birthDate": "1981-11-08",
+        "address": [
+          {
+            "line": [
+              "Osuuspankkitie 2"
+            ],
+            "city": "Helsinki",
+            "postalCode": "00120",
+            "country": "Suomi"
+          },
+          {
+            "city": "Blo-49847020"
+          }
+        ],
+        "active": true,
+        "link": [
+          {
+            "target": {
+              "reference": "Patient/PATIENT1",
+              "display": "Anna Testi"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "PUT",
+        "url": "Person/PERSON1",
+        "ifMatch": "1"
+      }
+    }
+  ]
+}
+

osgi/hapi-fhir-karaf-integration-tests/src/test/resources/testscript-search.json

@@ -0,0 +1,298 @@
+{
+  "resourceType": "TestScript",
+  "id": "search",
+  "text": {
+    "status": "generated",
+    "div": "<div><p><b>Generated Narrative with Details</b></p><p><b>id</b>: search</p><p><b>name</b>: Read, Search and Conditional Create and Delete</p><p><b>description</b>: Test Script for testing search, read, and conditional create and delete</p><h3>Fixtures</h3><table><tr><td>-</td><td><b>Resource</b></td></tr><tr><td>*</td><td><a>Patient/patient-example.xml</a></td></tr></table><blockquote><p><b>variable</b></p><p><b>name</b>: V1</p><p><b>sourceId</b>: R1</p><p><b>headerField</b>: Location</p></blockquote><blockquote><p><b>variable</b></p><p><b>name</b>: V2</p><p><b>sourceId</b>: R3</p><p><b>path</b>: fhir:Patient/fhir:name/fhir:given/@value</p></blockquote><blockquote><p><b>setup</b></p><blockquote><p><b>action</b></p><h3>Operations</h3><table><tr><td>-</td><td><b>Type</b></td><td><b>Resource</b></td><td><b>Params</b></td></tr><tr><td>*</td><td>delete</td><td>Patient</td><td>given=John&amp;family=Doe</td></tr></table></blockquote></blockquote><blockquote><p><b>test</b></p><p><b>name</b>: Create</p><p><b>description</b>: Create, read, search, conditional create, conditional delete.</p><blockquote><p><b>metadata</b></p><h3>Links</h3><table><tr><td>-</td><td><b>Url</b></td><td><b>Description</b></td></tr><tr><td>*</td><td><a>http://hl7.org/implement/standards/FHIR-Develop/patient.html</a></td><td>FHIR Patient</td></tr></table><blockquote><p><b>operation</b></p><p><b>type</b>: create</p><p><b>resource</b>: Patient</p><p><b>description</b>: Conditional Create Operation</p><p><b>link</b>: <a>http://hl7-fhir.github.io/http.html#2.1.0.13.1</a></p><p><b>required</b>: true</p><p><b>validated</b>: true</p></blockquote><blockquote><p><b>operation</b></p><p><b>type</b>: delete</p><p><b>resource</b>: Patient</p><p><b>description</b>: Conditional Delete Operation</p><p><b>link</b>: <a>http://hl7-fhir.github.io/http.html#2.1.0.12.1</a></p><p><b>required</b>: true</p><p><b>validated</b>: true</p></blockquote><blockquote><p><b>operation</b></p><p><b>type</b>: read</p><p><b>resource</b>: Patient</p><p><b>description</b>: Patient Read Operation</p><p><b>link</b>: <a>http://hl7.org/implement/standards/FHIR-Develop/http.html#read</a></p><p><b>validated</b>: true</p></blockquote><blockquote><p><b>operation</b></p><p><b>type</b>: search</p><p><b>resource</b>: Patient</p><p><b>description</b>: Patient Search Operation</p><p><b>link</b>: <a>http://hl7-fhir.github.io/http.html#2.1.0.14</a></p><p><b>validated</b>: true</p></blockquote></blockquote><blockquote><p><b>action</b></p><h3>Operations</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Operations</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Operations</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Operations</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Operations</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Operations</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Operations</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>action</b></p><h3>Asserts</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote></blockquote></div>"
+  },
+  "url": "http://hl7.org/fhir/TestScript/search",
+  "name": "Read, Search and Conditional Create and Delete",
+  "status": "draft",
+  "description": "Test Script for testing search, read, and conditional create and delete",
+  "metadata": {
+    "capability": [
+      {
+        "required": true,
+        "description": "Patient Create and Read Operations",
+        "link": [
+          "http://hl7.org/implement/standards/FHIR-Develop/http.html#create",
+          "http://hl7.org/implement/standards/FHIR-Develop/http.html#read"
+        ],
+        "conformance": {
+          "reference": "Conformance/example"
+        }
+      },
+      {
+        "required": true,
+        "description": "Patient Conditional Delete Operation",
+        "link": [
+          "http://hl7-fhir.github.io/http.html#2.1.0.12.1"
+        ],
+        "conformance": {
+          "reference": "Conformance/example"
+        }
+      },
+      {
+        "required": true,
+        "description": "Patient Conditional Create Operation",
+        "link": [
+          "http://hl7-fhir.github.io/http.html#2.1.0.13.1"
+        ],
+        "conformance": {
+          "reference": "Conformance/example"
+        }
+      }
+    ]
+  },
+  "fixture": [
+    {
+      "id": "example-patient",
+      "resource": {
+        "reference": "Patient/example"
+      }
+    }
+  ],
+  "variable": [
+    {
+      "name": "V1",
+      "headerField": "Location",
+      "sourceId": "R1"
+    },
+    {
+      "name": "V2",
+      "path": "fhir:Patient/fhir:name/fhir:given/@value",
+      "sourceId": "R3"
+    },
+    {
+      "name": "DefaultValue",
+      "defaultValue": "Replace at Runtime"
+    }
+  ],
+  "setup": {
+    "action": [
+      {
+        "fhir_comments": [
+          "    Conditional Delete    "
+        ],
+        "operation": {
+          "type": {
+            "code": "delete"
+          },
+          "resource": "Patient",
+          "params": "given=John&family=Doe"
+        }
+      }
+    ]
+  },
+  "test": [
+    {
+      "id": "Test1",
+      "name": "Create",
+      "description": "Create, read, search, conditional create, conditional delete.",
+      "metadata": {
+        "link": [
+          {
+            "url": "http://hl7.org/implement/standards/FHIR-Develop/patient.html",
+            "description": "FHIR Patient"
+          }
+        ],
+        "capability": [
+          {
+            "validated": true,
+            "description": "Patient Search Operation",
+            "link": [
+              "http://hl7.org/implement/standards/FHIR-Develop/http.html#search"
+            ],
+            "conformance": {
+              "reference": "Conformance/example"
+            }
+          }
+        ]
+      },
+      "action": [
+        {
+          "fhir_comments": [
+            "    Create the patient using fixture    "
+          ],
+          "operation": {
+            "type": {
+              "code": "create"
+            },
+            "sourceId": "example-patient"
+          }
+        },
+        {
+          "assert": {
+            "responseCode": "201"
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Patient search by name.  Save the responseBody in 'F1' fixture.\n\t\t\t\tSave the responseHeader in H1    "
+          ],
+          "operation": {
+            "type": {
+              "code": "search"
+            },
+            "resource": "Patient",
+            "contentType": "json",
+            "params": "?given=John&family=Doe",
+            "responseId": "R1"
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Verify that the Location in response-header is valid    "
+          ],
+          "assert": {
+            "headerField": "Location",
+            "operator": "notEmpty",
+            "warningOnly": true
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Verify that the birthdate got persisted and is being returned properly    "
+          ],
+          "assert": {
+            "operator": "equals",
+            "path": "fhir:Patient/fhir:birthDate/@value",
+            "sourceId": "R1",
+            "value": "1974-12-31"
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Verify that the navigation links are valid    "
+          ],
+          "assert": {
+            "navigationLinks": true,
+            "warningOnly": true
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Use the Location returned earlier to grab the resource\n\t\t \t\tto verify that Location was pointing to correct resource.    "
+          ],
+          "operation": {
+            "type": {
+              "code": "search"
+            },
+            "accept": "json",
+            "responseId": "R2",
+            "url": "${V1}"
+          }
+        },
+        {
+          "assert": {
+            "contentType": "json"
+          }
+        },
+        {
+          "assert": {
+            "response": "okay"
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Search for the resource but this time using the birthdate\n\t\t\t\tas a search parameter to make sure search by birthDate works    "
+          ],
+          "operation": {
+            "type": {
+              "code": "search"
+            },
+            "resource": "Patient",
+            "accept": "json",
+            "params": "?given=John&family=Doe&birthdate=1974-12-31",
+            "responseId": "R3"
+          }
+        },
+        {
+          "assert": {
+            "contentType": "json"
+          }
+        },
+        {
+          "assert": {
+            "response": "okay"
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Verify that the birthDate matches expectations    "
+          ],
+          "assert": {
+            "compareToSourceId": "R2",
+            "compareToSourcePath": "fhir:Patient/fhir:birthDate/@value",
+            "path": "fhir:Patient/fhir:birthDate/@value",
+            "sourceId": "R3"
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Verify that the name matches expectations    "
+          ],
+          "assert": {
+            "path": "fhir:Patient/fhir:name/fhir:given/@value",
+            "sourceId": "R3",
+            "value": "John"
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Conditional Create    "
+          ],
+          "operation": {
+            "type": {
+              "code": "create"
+            },
+            "requestHeader": [
+              {
+                "field": "If-None-Exist",
+                "value": "Patient?given=John&Doe&birthdate=1974-12-31"
+              }
+            ],
+            "sourceId": "F1"
+          }
+        },
+        {
+          "fhir_comments": [
+            "    The response code of 200 verifies that the resource\n\t\t\t\talready exists and did not get created    "
+          ],
+          "assert": {
+            "responseCode": "200"
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Conditional Delete    "
+          ],
+          "operation": {
+            "type": {
+              "code": "delete"
+            },
+            "resource": "Patient",
+            "params": "?given=John&family=Doe&birthdate=1974-12-31"
+          }
+        },
+        {
+          "fhir_comments": [
+            "    Search again and make sure the patient has been deleted.\n\t\t \t\t This time perform read by id using variable    "
+          ],
+          "operation": {
+            "type": {
+              "code": "read"
+            },
+            "resource": "Patient",
+            "params": "/${V2}"
+          }
+        },
+        {
+          "assert": {
+            "responseCode": "410"
+          }
+        }
+      ]
+    }
+  ]
+}

pom.xml

@@ -1,5 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
+			xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
 	<parent>
 		<groupId>org.sonatype.oss</groupId>
@@ -411,6 +412,11 @@
 			<id>anthonys123</id>
 			<name>Anthony Sute</name>
 		</developer>
+		<developer>
+			<id>johnpoth</id>
+			<name>John Poth</name>
+			<organization>Red Hat</organization>
+		</developer>
 	</developers>
 
 	<licenses>
@@ -431,24 +437,38 @@
 		<scmPubCheckoutDirectory>${user.home}/sites/scm/hapi-fhir</scmPubCheckoutDirectory>
 
 		<!-- Dependency Versions -->
+		<apache_karaf_version>4.1.4</apache_karaf_version>
+		<commons_codec_version>1.10</commons_codec_version>
+		<commons_io_version>2.5</commons_io_version>
+		<commons_lang3_version>3.6</commons_lang3_version>
 		<derby_version>10.14.1.0</derby_version>
+		<error_prone_annotations_version>2.0.18</error_prone_annotations_version>
+		<guava_version>23.0</guava_version>
+		<gson_version>2.8.1</gson_version>
 		<jaxb_api_version>2.3.0</jaxb_api_version>
 		<jaxb_core_version>2.3.0</jaxb_core_version>
 		<jersey_version>2.25.1</jersey_version>
 		<jetty_version>9.4.8.v20171121</jetty_version>
+		<jsr305_version>3.0.2</jsr305_version>
 		<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
 		<hibernate_version>5.2.12.Final</hibernate_version>
 		<hibernate_validator_version>5.4.1.Final</hibernate_validator_version>
 		<!-- Update lucene version when you update hibernate-search version -->
 		<hibernate_search_version>5.7.1.Final</hibernate_search_version>
+		<httpcore_version>4.4.6</httpcore_version>
+		<httpclient_version>4.5.3</httpclient_version>
 		<lucene_version>5.5.4</lucene_version>
 		<maven_assembly_plugin_version>2.5.3</maven_assembly_plugin_version>
 		<maven_license_plugin_version>1.8</maven_license_plugin_version>
 		<phloc_schematron_version>2.7.1</phloc_schematron_version>
 		<phloc_commons_version>4.4.11</phloc_commons_version>
+		<servicemix_saxon_version>9.5.1-5_1</servicemix_saxon_version>
+		<servicemix_xmlresolver_version>1.2_5</servicemix_xmlresolver_version>
 		<spring_version>5.0.3.RELEASE</spring_version>
 		<spring-boot.version>1.5.6.RELEASE</spring-boot.version>
+		<stax2_api_version>3.1.4</stax2_api_version>
 		<thymeleaf-version>3.0.9.RELEASE</thymeleaf-version>
+		<woodstox_core_asl_version>4.4.1</woodstox_core_asl_version>
 
 		<!-- We are aiming to still work on a very old version of SLF4j even though we depend on the newest, just to be nice to users of the API. This version is tested in the hapi-fhir-cobertura. -->
 		<slf4j_target_version>1.6.0</slf4j_target_version>
@@ -532,7 +552,7 @@
 			<dependency>
 				<groupId>com.google.guava</groupId>
 				<artifactId>guava</artifactId>
-				<version>23.0</version>
+				<version>${guava_version}</version>
 			</dependency>
 			<dependency>
 				<groupId>com.google.guava</groupId>
@@ -567,12 +587,12 @@
 			<dependency>
 				<groupId>commons-codec</groupId>
 				<artifactId>commons-codec</artifactId>
-				<version>1.10</version>
+				<version>${commons_codec_version}</version>
 			</dependency>
 			<dependency>
 				<groupId>commons-io</groupId>
 				<artifactId>commons-io</artifactId>
-				<version>2.5</version>
+				<version>${commons_io_version}</version>
 			</dependency>
 			<dependency>
 				<groupId>directory-naming</groupId>
@@ -619,7 +639,7 @@
 			<dependency>
 				<groupId>com.google.code.gson</groupId>
 				<artifactId>gson</artifactId>
-				<version>2.8.1</version>
+				<version>${gson_version}</version>
 			</dependency>
 			<dependency>
 				<groupId>com.sun.xml.bind</groupId>
@@ -657,9 +677,9 @@
 				<version>2.0.1</version>
 			</dependency>
 			<dependency>
-	         <groupId>junit</groupId>
+				<groupId>junit</groupId>
-	         <artifactId>junit</artifactId>
+				<artifactId>junit</artifactId>
-	         <version>4.12</version>
+				<version>4.12</version>
 			</dependency>
 			<dependency>
 				<groupId>lt.velykis.maven.skins</groupId>
@@ -713,7 +733,7 @@
 			<dependency>
 				<groupId>org.apache.commons</groupId>
 				<artifactId>commons-lang3</artifactId>
-				<version>3.6</version>
+				<version>${commons_lang3_version}</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.derby</groupId>
@@ -733,7 +753,7 @@
 			<dependency>
 				<groupId>org.apache.httpcomponents</groupId>
 				<artifactId>httpclient</artifactId>
-				<version>4.5.3</version>
+				<version>${httpclient_version}</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.httpcomponents</groupId>
@@ -743,7 +763,7 @@
 			<dependency>
 				<groupId>org.apache.httpcomponents</groupId>
 				<artifactId>httpcore</artifactId>
-				<version>4.4.6</version>
+				<version>${httpcore_version}</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.lucene</groupId>
@@ -828,7 +848,7 @@
 			<dependency>
 				<groupId>org.codehaus.woodstox</groupId>
 				<artifactId>woodstox-core-asl</artifactId>
-				<version>4.4.1</version>
+				<version>${woodstox_core_asl_version}</version>
 			</dependency>
 			<dependency>
 				<groupId>org.ebaysf.web</groupId>
@@ -1127,7 +1147,7 @@
 				<plugin>
 					<groupId>org.apache.felix</groupId>
 					<artifactId>maven-bundle-plugin</artifactId>
-					<version>3.3.0</version>
+					<version>3.5.0</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
@@ -1301,7 +1321,8 @@
 				<plugin>
 					<groupId>org.jacoco</groupId>
 					<artifactId>
-						jacoco-maven-plugin</artifactId>
+						jacoco-maven-plugin
+					</artifactId>
 					<version>0.7.9</version>
 				</plugin>
 				<plugin>
@@ -1549,7 +1570,9 @@
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
-									<replacetoken>http://netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/css/bootstrap-responsive.min.css</replacetoken>
+									<replacetoken>
+										http://netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/css/bootstrap-responsive.min.css
+									</replacetoken>
 									<replacevalue>./css/bootstrap-responsive.min.css</replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
@@ -1559,8 +1582,10 @@
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
-									<replacetoken>http://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css</replacetoken>
+									<replacetoken>http://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css
-									<replacevalue>https://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css</replacevalue>
+									</replacetoken>
+									<replacevalue>https://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css
+									</replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
@@ -1604,28 +1629,35 @@
 								<echo>Adding Fontawesome</echo>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
-									<replacetoken><![CDATA[<a href="download.html" title="Download">Download</a>]]></replacetoken>
+									<replacetoken>
-									<replacevalue><![CDATA[<a href="download.html"  title="Download"><i class="fa fa-download"></i> Download</a>]]></replacevalue>
+										<![CDATA[<a href="download.html" title="Download">Download</a>]]></replacetoken>
+									<replacevalue>
+										<![CDATA[<a href="download.html"  title="Download"><i class="fa fa-download"></i> Download</a>]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
-									<replacetoken><![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project" class="externalLink">GitHub Project</a>]]></replacetoken>
+									<replacetoken>
-									<replacevalue><![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project"  class="externalLink"><i class="fa fa-github"></i> GitHub Project</a>]]></replacevalue>
+										<![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project" class="externalLink">GitHub Project</a>]]></replacetoken>
+									<replacevalue>
+										<![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project"  class="externalLink"><i class="fa fa-github"></i> GitHub Project</a>]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Test Servers <]]></replacetoken>
-									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-fire"></i>&nbsp;Test Servers&nbsp;<]]></replacevalue>
+									<replacevalue>
+										<![CDATA[data-toggle="dropdown"><i class="fa fa-fire"></i>&nbsp;Test Servers&nbsp;<]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Documentation <]]></replacetoken>
-									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-book"></i>&nbsp;Documentation&nbsp;<]]></replacevalue>
+									<replacevalue>
+										<![CDATA[data-toggle="dropdown"><i class="fa fa-book"></i>&nbsp;Documentation&nbsp;<]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Get Help <]]></replacetoken>
-									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-support"></i>&nbsp;Get Help&nbsp;<]]></replacevalue>
+									<replacevalue>
+										<![CDATA[data-toggle="dropdown"><i class="fa fa-support"></i>&nbsp;Get Help&nbsp;<]]></replacevalue>
 								</replace>
 								<echo>Changing Breadcrumbs</echo>
 								<replace dir="target/site" summary="true">
@@ -1802,21 +1834,6 @@
 					</execution>
 				</executions>
 			</plugin>
-			<plugin>
-			<groupId>org.owasp</groupId>
-			<artifactId>dependency-check-maven</artifactId>
-			<version>3.1.1</version>
-			<configuration>
-				<failBuildOnCVSS>8</failBuildOnCVSS>
-			</configuration>
-			<executions>
-				<execution>
-					<goals>
-						<goal>check</goal>
-					</goals>
-				</execution>
-			</executions>
-		</plugin>
 		</plugins>
 	</build>
 
@@ -1856,9 +1873,12 @@
 				<configuration>
 					<reportsDirectories>
 						<reportDirectory>${project.basedir}/hapi-fhir-base/target/surefire-reports/</reportDirectory>
-						<reportDirectory>${project.basedir}/hapi-fhir-structures-dstu/target/surefire-reports/</reportDirectory>
+						<reportDirectory>${project.basedir}/hapi-fhir-structures-dstu/target/surefire-reports/
-						<reportDirectory>${project.basedir}/hapi-fhir-structures-dstu2/target/surefire-reports/</reportDirectory>
+						</reportDirectory>
-						<reportDirectory>${project.basedir}/hapi-fhir-jpaserver-base/target/surefire-reports/</reportDirectory>
+						<reportDirectory>${project.basedir}/hapi-fhir-structures-dstu2/target/surefire-reports/
+						</reportDirectory>
+						<reportDirectory>${project.basedir}/hapi-fhir-jpaserver-base/target/surefire-reports/
+						</reportDirectory>
 					</reportsDirectories>
 				</configuration>
 			</plugin>
@@ -2000,6 +2020,8 @@
 				<module>hapi-fhir-cli</module>
 				<module>hapi-fhir-dist</module>
 				<module>examples</module>
+				<module>osgi/hapi-fhir-karaf-features</module>
+				<module>osgi/hapi-fhir-karaf-integration-tests</module>
 				<module>example-projects/hapi-fhir-base-example-embedded-ws</module>
 				<module>example-projects/hapi-fhir-standalone-overlay-example</module>
 				<module>example-projects/hapi-fhir-jpaserver-cds-example</module>
@@ -2075,6 +2097,28 @@
 				</plugins>
 			</build>
 		</profile>
+		<profile>
+			<id>OWASP</id>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.owasp</groupId>
+						<artifactId>dependency-check-maven</artifactId>
+						<version>3.1.1</version>
+						<configuration>
+							<failBuildOnCVSS>8</failBuildOnCVSS>
+						</configuration>
+						<executions>
+							<execution>
+								<goals>
+									<goal>check</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
 	</profiles>
 
 </project>

src/changes/changes.xml

@@ -41,6 +41,28 @@
 					</ul>
 				]]>
 			</action>
+			<action tyoe="add" issue="871">
+				A number of HAPI FHIR modules have been converted so that they now work
+				as OSGi modules. Unlike the previous OSGi module, which was a mega-JAR
+				with all of HAPI FHIR in it, this is simply the appropriate
+				OSGi manifest inside the existing JARs. Thanks to John Poth
+				for the Pull Request!
+				<![CDATA[
+				<br/><br/>
+				Note that this does not cover all modules in the project. Current support includes:
+				<ul>
+					<li>HAPI-FHIR structures DSTU2, HL7ORGDSTU2, DSTU2.1, DSTU3, R4</li>
+					<li>HAPI-FHIR Resource validation DSTU2, HL7ORGDSTU2, DSTU2.1, DSTU3, R4</li>
+					<li>Apache Karaf features for all the above</li>
+					<li> Integration Tests</li>
+				</ul>
+				Remaining work includes:
+				<ul>
+					<li>HAPI-FHIR Server support</li>
+					<li> HAPI-FHIR narrative support. This might be tricky as Thymeleaf doesn't support OSGi.</li>
+				</ul>
+				]]>
+			</action>
 			<action type="fix">
 				Fix a crash in the JSON parser when parsing extensions on repeatable
 				elements (e.g. Patient.address.line) where there is an extension on the
@@ -275,6 +297,13 @@
 				Suport for the :contains string search parameter modifier has been added to
 				the JPA server. Thanks to Anthony Sute for the pull request!
 			</action>
+			<action type="fix">
+				All instances of DefaultProfileValidationSupport (i.e. one for
+				each version of FHIR) have been fixed so that they explicitly
+				close any InputStreams they open in order to read the built-in
+				profile resources. Leaving these open caused resource starvation
+				in some cases under heavy load.
+			</action>
 		</release>
 		<release version="3.2.0" date="2018-01-13">
 			<action type="add">