[(master)] Merge remote-tracking branch 'upstream/master'

.gitignore

@@ -141,6 +141,8 @@ local.properties
 **/.target
 **/.project
 **/.classpath
+**/.factorypath
+**/.springBeans
 
 
 # PDT-specific

appveyor.yml

@@ -0,0 +1,7 @@
+version: 1.0.{build}
+image: Visual Studio 2017
+cache:
+  - C:\maven\
+  - C:\Users\appveyor\.m2
+build_script:
+   - cmd: mvn -P MINPARALLEL,ALLMODULES install

examples/pom.xml

@@ -92,6 +92,12 @@
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-web</artifactId>
 		</dependency>
+
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>slf4j-simple</artifactId>
+		</dependency>
+
 	</dependencies>
 
 	<reporting>

hapi-deployable-pom/pom.xml

@@ -116,10 +116,10 @@
 							<artifactId>spring-jcl</artifactId>
 						</dependency>
 					</ignoredDependencies>
-					<ignoredResources>
+					<ignoredResourcePatterns>
-						<ignoredResource>changelog.txt</ignoredResource>
+						<ignoredResourcePattern>changelog.txt</ignoredResourcePattern>
 						<ignoredResource>javac.bat</ignoredResource>
-					</ignoredResources>
+					</ignoredResourcePatterns>
 				</configuration>
 			</plugin>
 		</plugins>

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

@@ -43,7 +43,7 @@ public abstract class BaseParser implements IParser {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
 
 	private ContainedResources myContainedResources;
-
+	private boolean myEncodeElementsAppliesToChildResourcesOnly;
 	private FhirContext myContext;
 	private Set<String> myDontEncodeElements;
 	private boolean myDontEncodeElementsIncludesStars;
@@ -556,6 +556,16 @@ public abstract class BaseParser implements IParser {
 			&& theIncludedResource == false;
 	}
 
+	@Override
+	public boolean isEncodeElementsAppliesToChildResourcesOnly() {
+		return myEncodeElementsAppliesToChildResourcesOnly;
+	}
+
+	@Override
+	public void setEncodeElementsAppliesToChildResourcesOnly(boolean theEncodeElementsAppliesToChildResourcesOnly) {
+		myEncodeElementsAppliesToChildResourcesOnly = theEncodeElementsAppliesToChildResourcesOnly;
+	}
+
 	@Override
 	public boolean isOmitResourceId() {
 		return myOmitResourceId;
@@ -1051,7 +1061,13 @@ public abstract class BaseParser implements IParser {
 		}
 
 		private boolean checkIfParentShouldBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
-			return checkIfPathMatchesForEncoding(thePathBuilder, theStarPass, myEncodeElementsAppliesToResourceTypes, myEncodeElements, true);
+			Set<String> encodeElements = myEncodeElements;
+			if (encodeElements != null && encodeElements.isEmpty() == false) {
+				if (isEncodeElementsAppliesToChildResourcesOnly() && !mySubResource) {
+					encodeElements = null;
+				}
+			}
+			return checkIfPathMatchesForEncoding(thePathBuilder, theStarPass, myEncodeElementsAppliesToResourceTypes, encodeElements, true);
 		}
 
 		private boolean checkIfParentShouldNotBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
@@ -1070,6 +1086,9 @@ public abstract class BaseParser implements IParser {
 				} else {
 					thePathBuilder.append(myResDef.getName());
 				}
+				if (theElements == null) {
+					return true;
+				}
 				if (theElements.contains(thePathBuilder.toString())) {
 					return true;
 				}

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

@@ -206,6 +206,22 @@ public interface IParser {
 	 */
 	void setEncodeElements(Set<String> theEncodeElements);
 
+	/**
+	 * If set to <code>true</code> (default is false), the values supplied
+	 * to {@link #setEncodeElements(Set)} will not be applied to the root
+	 * resource (typically a Bundle), but will be applied to any sub-resources
+	 * contained within it (i.e. search result resources in that bundle)
+	 */
+	void setEncodeElementsAppliesToChildResourcesOnly(boolean theEncodeElementsAppliesToChildResourcesOnly);
+
+	/**
+	 * If set to <code>true</code> (default is false), the values supplied
+	 * to {@link #setEncodeElements(Set)} will not be applied to the root
+	 * resource (typically a Bundle), but will be applied to any sub-resources
+	 * contained within it (i.e. search result resources in that bundle)
+	 */
+	boolean isEncodeElementsAppliesToChildResourcesOnly();
+
 	/**
 	 * If provided, tells the parse which resource types to apply {@link #setEncodeElements(Set) encode elements} to. Any
 	 * resource types not specified here will be encoded completely, with no elements excluded.

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BinaryUtil.java

@@ -19,12 +19,13 @@ public class BinaryUtil {
 	public static IBaseReference getSecurityContext(FhirContext theCtx, IBaseBinary theBinary) {
 		RuntimeResourceDefinition def = theCtx.getResourceDefinition("Binary");
 		BaseRuntimeChildDefinition child = def.getChildByName("securityContext");
-
-		List<IBase> values = child.getAccessor().getValues(theBinary);
 		IBaseReference retVal = null;
+		if (child != null) {
+			List<IBase> values = child.getAccessor().getValues(theBinary);
 			if (values.size() > 0) {
 				retVal = (IBaseReference) values.get(0);
 			}
+		}
 		return retVal;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/PortUtil.java

@@ -21,12 +21,14 @@ package ca.uhn.fhir.util;
  */
 
 import java.net.ServerSocket;
+import java.util.LinkedHashSet;
 
 /**
  * Provides server ports
  */
 @CoverageIgnore
 public class PortUtil {
+	private static LinkedHashSet<Integer> ourPorts = new LinkedHashSet<>();
 
 	/*
 	 * Non instantiable
@@ -41,9 +43,13 @@ public class PortUtil {
 	public static int findFreePort() {
 		ServerSocket server;
 		try {
+			int port;
+			do {
 				server = new ServerSocket(0);
-			int port = server.getLocalPort();
+				port = server.getLocalPort();
 				server.close();
+			} while (!ourPorts.add(port));
+
 			Thread.sleep(500);
 			return port;
 		} catch (Exception e) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TestUtil.java

@@ -30,8 +30,10 @@ import org.slf4j.LoggerFactory;
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
 import java.util.Arrays;
+import java.util.List;
 import java.util.Locale;
 import java.util.TimeZone;
+import java.util.concurrent.atomic.AtomicInteger;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 
@@ -123,6 +125,27 @@ public class TestUtil {
 		ourLog.info("Tests are using time zone: {}", TimeZone.getDefault().getID());
 	}
 
+
+	/**
+	 * <b>THIS IS FOR UNIT TESTS ONLY - DO NOT CALL THIS METHOD FROM USER CODE</b>
+	 * <p>
+	 * Wait for an atomicinteger to hit a given site and fail if it never does
+	 */
+	public static void waitForSize(int theTarget, AtomicInteger theInteger) {
+		long start = System.currentTimeMillis();
+		while (theInteger.get() != theTarget && (System.currentTimeMillis() - start) <= 15000) {
+			try {
+				Thread.sleep(50);
+			} catch (InterruptedException theE) {
+				throw new Error(theE);
+			}
+		}
+		if ((System.currentTimeMillis() - start) >= 15000) {
+			throw new IllegalStateException("Size " + theInteger.get() + " is != target " + theTarget);
+		}
+	}
+
+
 	/**
 	 * <b>THIS IS FOR UNIT TESTS ONLY - DO NOT CALL THIS METHOD FROM USER CODE</b>
 	 * <p>

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirDbConfig.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.demo;
 
 import java.util.Properties;
 
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
@@ -23,6 +24,7 @@ public class FhirDbConfig {
 		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
 		extraProperties.put("hibernate.cache.use_structured_entries", "false");
 		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", "target/lucenefiles");
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/interceptor/AdditionalRequestHeadersInterceptor.java

@@ -0,0 +1,96 @@
+package ca.uhn.fhir.rest.client.interceptor;
+
+import ca.uhn.fhir.rest.client.api.IClientInterceptor;
+import ca.uhn.fhir.rest.client.api.IHttpRequest;
+import ca.uhn.fhir.rest.client.api.IHttpResponse;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+/**
+ * This interceptor adds arbitrary header values to requests made by the client.
+ */
+public class AdditionalRequestHeadersInterceptor implements IClientInterceptor {
+	private final Map<String, List<String>> additionalHttpHeaders = new HashMap<>();
+
+	public AdditionalRequestHeadersInterceptor() {
+		this(new HashMap<String, List<String>>());
+	}
+
+	public AdditionalRequestHeadersInterceptor(Map<String, List<String>> additionalHttpHeaders) {
+		super();
+		if (additionalHttpHeaders != null) {
+			this.additionalHttpHeaders.putAll(additionalHttpHeaders);
+		}
+	}
+
+	/**
+	 * Adds the given header value.
+	 * Note that {@code headerName} and {@code headerValue} cannot be null.
+	 * @param headerName the name of the header
+	 * @param headerValue the value to add for the header
+	 * @throws NullPointerException if either parameter is {@code null}
+	 */
+	public void addHeaderValue(String headerName, String headerValue) {
+		Objects.requireNonNull(headerName, "headerName cannot be null");
+		Objects.requireNonNull(headerValue, "headerValue cannot be null");
+
+		getHeaderValues(headerName).add(headerValue);
+	}
+
+	/**
+	 * Adds the list of header values for the given header.
+	 * Note that {@code headerName} and {@code headerValues} cannot be null.
+	 * @param headerName the name of the header
+	 * @param headerValues the list of values to add for the header
+	 * @throws NullPointerException if either parameter is {@code null}
+	 */
+	public void addAllHeaderValues(String headerName, List<String> headerValues) {
+		Objects.requireNonNull(headerName, "headerName cannot be null");
+		Objects.requireNonNull(headerValues, "headerValues cannot be null");
+
+		getHeaderValues(headerName).addAll(headerValues);
+	}
+
+	/**
+	 * Gets the header values list for a given header.
+	 * If the header doesn't have any values, an empty list will be returned.
+	 * @param headerName the name of the header
+	 * @return the list of values for the header
+	 */
+	private List<String> getHeaderValues(String headerName) {
+		if (additionalHttpHeaders.get(headerName) == null) {
+			additionalHttpHeaders.put(headerName, new ArrayList<String>());
+		}
+		return additionalHttpHeaders.get(headerName);
+	}
+
+	/**
+	 * Adds the additional header values to the HTTP request.
+	 * @param theRequest the HTTP request
+	 */
+	@Override
+	public void interceptRequest(IHttpRequest theRequest) {
+		for (Map.Entry<String, List<String>> header : additionalHttpHeaders.entrySet()) {
+			for (String headerValue : header.getValue()) {
+				if (headerValue != null) {
+					theRequest.addHeader(header.getKey(), headerValue);
+				}
+			}
+		}
+	}
+
+	/**
+	 * Does nothing since this interceptor is not concerned with the response.
+	 * @param theResponse the HTTP response
+	 * @throws IOException
+	 */
+	@Override
+	public void interceptResponse(IHttpResponse theResponse) throws IOException {
+		// Do nothing. This interceptor is not concerned with the response.
+	}
+}

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/interceptor/SimpleRequestHeaderInterceptor.java

@@ -32,6 +32,8 @@ import org.apache.commons.lang3.Validate;
 /**
  * This interceptor adds an arbitrary header to requests made by this client. Both the
  * header name and the header value are specified by the calling code.
+ *
+ * @see AdditionalRequestHeadersInterceptor for a more advanced version of this interceptor which can add multiple headers
  */
 public class SimpleRequestHeaderInterceptor implements IClientInterceptor {
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java

@@ -26,20 +26,8 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
-import org.apache.lucene.analysis.core.LowerCaseFilterFactory;
-import org.apache.lucene.analysis.core.StopFilterFactory;
-import org.apache.lucene.analysis.miscellaneous.WordDelimiterFilterFactory;
-import org.apache.lucene.analysis.ngram.EdgeNGramFilterFactory;
-import org.apache.lucene.analysis.ngram.NGramFilterFactory;
-import org.apache.lucene.analysis.pattern.PatternTokenizerFactory;
-import org.apache.lucene.analysis.phonetic.PhoneticFilterFactory;
-import org.apache.lucene.analysis.snowball.SnowballPorterFilterFactory;
-import org.apache.lucene.analysis.standard.StandardFilterFactory;
-import org.apache.lucene.analysis.standard.StandardTokenizerFactory;
-import org.hibernate.annotations.ColumnDefault;
 import org.hibernate.annotations.OptimisticLock;
 import org.hibernate.search.annotations.*;
-import org.hibernate.search.annotations.Parameter;
 
 import javax.persistence.*;
 import javax.persistence.Index;
@@ -61,53 +49,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 	@Index(name = "IDX_RES_TYPE", columnList = "RES_TYPE"),
 	@Index(name = "IDX_INDEXSTATUS", columnList = "SP_INDEX_STATUS")
 })
-@AnalyzerDefs({
-	@AnalyzerDef(name = "autocompleteEdgeAnalyzer",
-		tokenizer = @TokenizerDef(factory = PatternTokenizerFactory.class, params = {
-			@Parameter(name = "pattern", value = "(.*)"),
-			@Parameter(name = "group", value = "1")
-		}),
-		filters = {
-			@TokenFilterDef(factory = LowerCaseFilterFactory.class),
-			@TokenFilterDef(factory = StopFilterFactory.class),
-			@TokenFilterDef(factory = EdgeNGramFilterFactory.class, params = {
-				@Parameter(name = "minGramSize", value = "3"),
-				@Parameter(name = "maxGramSize", value = "50")
-			}),
-		}),
-	@AnalyzerDef(name = "autocompletePhoneticAnalyzer",
-		tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
-		filters = {
-			@TokenFilterDef(factory = StandardFilterFactory.class),
-			@TokenFilterDef(factory = StopFilterFactory.class),
-			@TokenFilterDef(factory = PhoneticFilterFactory.class, params = {
-				@Parameter(name = "encoder", value = "DoubleMetaphone")
-			}),
-			@TokenFilterDef(factory = SnowballPorterFilterFactory.class, params = {
-				@Parameter(name = "language", value = "English")
-			})
-		}),
-	@AnalyzerDef(name = "autocompleteNGramAnalyzer",
-		tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
-		filters = {
-			@TokenFilterDef(factory = WordDelimiterFilterFactory.class),
-			@TokenFilterDef(factory = LowerCaseFilterFactory.class),
-			@TokenFilterDef(factory = NGramFilterFactory.class, params = {
-				@Parameter(name = "minGramSize", value = "3"),
-				@Parameter(name = "maxGramSize", value = "20")
-			}),
-		}),
-	@AnalyzerDef(name = "standardAnalyzer",
-		tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
-		filters = {
-			@TokenFilterDef(factory = LowerCaseFilterFactory.class),
-		}),
-	@AnalyzerDef(name = "exactAnalyzer",
-		tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
-		filters = {
-		})
-}
-)
 //@formatter:on
 public class ResourceTable extends BaseHasResource implements Serializable {
 	static final int RESTYPE_LEN = 30;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java

@@ -52,16 +52,12 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
-import org.apache.lucene.analysis.core.WhitespaceTokenizerFactory;
 import org.hibernate.search.annotations.Analyze;
 import org.hibernate.search.annotations.Analyzer;
-import org.hibernate.search.annotations.AnalyzerDef;
-import org.hibernate.search.annotations.AnalyzerDefs;
 import org.hibernate.search.annotations.Field;
 import org.hibernate.search.annotations.Fields;
 import org.hibernate.search.annotations.Indexed;
 import org.hibernate.search.annotations.Store;
-import org.hibernate.search.annotations.TokenizerDef;
 
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
 import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
@@ -73,12 +69,6 @@ import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
 }, indexes= {
 	@Index(name = "IDX_CONCEPT_INDEXSTATUS", columnList="INDEX_STATUS") 
 })
-@AnalyzerDefs({
-	@AnalyzerDef(name = "conceptParentPidsAnalyzer",
-		tokenizer = @TokenizerDef(factory = WhitespaceTokenizerFactory.class),
-		filters = {
-		})
-})
 public class TermConcept implements Serializable {
 	private static final int MAX_DESC_LENGTH = 400;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);

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

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.jpa.search;
+
+import org.apache.lucene.analysis.core.LowerCaseFilterFactory;
+import org.apache.lucene.analysis.core.StopFilterFactory;
+import org.apache.lucene.analysis.core.WhitespaceTokenizerFactory;
+import org.apache.lucene.analysis.miscellaneous.WordDelimiterFilterFactory;
+import org.apache.lucene.analysis.ngram.EdgeNGramFilterFactory;
+import org.apache.lucene.analysis.ngram.NGramFilterFactory;
+import org.apache.lucene.analysis.pattern.PatternTokenizerFactory;
+import org.apache.lucene.analysis.phonetic.PhoneticFilterFactory;
+import org.apache.lucene.analysis.snowball.SnowballPorterFilterFactory;
+import org.apache.lucene.analysis.standard.StandardFilterFactory;
+import org.apache.lucene.analysis.standard.StandardTokenizerFactory;
+import org.hibernate.search.annotations.Factory;
+import org.hibernate.search.cfg.SearchMapping;
+
+/**
+ * Factory for defining the analysers.
+ */
+public class LuceneSearchMappingFactory {
+	@Factory
+	public SearchMapping getSearchMapping() {
+		SearchMapping mapping = new SearchMapping();
+
+		mapping.analyzerDef("autocompleteEdgeAnalyzer", PatternTokenizerFactory.class)
+				.tokenizerParam("pattern", "(.*)")
+				.tokenizerParam("group", "1")
+				.filter(LowerCaseFilterFactory.class)
+				.filter(StopFilterFactory.class)
+				.filter(EdgeNGramFilterFactory.class)
+				.param("minGramSize", "3")
+				.param("maxGramSize", "50")
+			.analyzerDef("autocompletePhoneticAnalyzer", StandardTokenizerFactory.class)
+				.filter(StandardFilterFactory.class)
+				.filter(StopFilterFactory.class)
+				.filter(PhoneticFilterFactory.class)
+				.param("encoder", "DoubleMetaphone")
+				.filter(SnowballPorterFilterFactory.class)
+				.param("language", "English")
+			.analyzerDef("autocompleteNGramAnalyzer", StandardTokenizerFactory.class)
+				.filter(WordDelimiterFilterFactory.class)
+				.filter(LowerCaseFilterFactory.class)
+				.filter(NGramFilterFactory.class)
+				.param("minGramSize", "3")
+				.param("maxGramSize", "20")
+			.analyzerDef("standardAnalyzer", StandardTokenizerFactory.class)
+				.filter(LowerCaseFilterFactory.class)
+			.analyzerDef("exactAnalyzer", StandardTokenizerFactory.class)
+			.analyzerDef("conceptParentPidsAnalyzer", WhitespaceTokenizerFactory.class);
+
+		return mapping;
+	}
+}

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

@@ -19,39 +19,51 @@ package ca.uhn.fhir.jpa.search;
  * limitations under the License.
  * #L%family
  */
-import java.util.*;
-import java.util.concurrent.*;
-
-import javax.persistence.EntityManager;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.IDao;
+import ca.uhn.fhir.jpa.dao.ISearchBuilder;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import ca.uhn.fhir.jpa.dao.data.ISearchDao;
+import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
+import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
+import ca.uhn.fhir.jpa.entity.*;
+import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.SimpleBundleProvider;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.method.PageMethodBinding;
+import com.google.common.annotations.VisibleForTesting;
+import com.google.common.collect.Lists;
 import org.apache.commons.lang3.ObjectUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.exception.ExceptionUtils;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.domain.*;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Pageable;
 import org.springframework.scheduling.concurrent.CustomizableThreadFactory;
-import org.springframework.transaction.*;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionDefinition;
+import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
-import org.springframework.transaction.support.*;
+import org.springframework.transaction.support.TransactionCallback;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionTemplate;
 
-import com.google.common.annotations.VisibleForTesting;
+import javax.persistence.EntityManager;
-import com.google.common.collect.Lists;
+import java.util.*;
-
+import java.util.concurrent.*;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.dao.*;
-import ca.uhn.fhir.jpa.dao.data.*;
-import ca.uhn.fhir.jpa.entity.*;
-import ca.uhn.fhir.jpa.util.StopWatch;
-import ca.uhn.fhir.model.api.Include;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.server.SimpleBundleProvider;
-import ca.uhn.fhir.rest.server.exceptions.*;
-import ca.uhn.fhir.rest.server.method.PageMethodBinding;
 
 public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 	public static final int DEFAULT_SYNC_SIZE = 250;
@@ -420,6 +432,19 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		}
 	}
 
+	/**
+	 * A search task is a Callable task that runs in
+	 * a thread pool to handle an individual search. One instance
+	 * is created for any requested search and runs from the
+	 * beginning to the end of the search.
+	 *
+	 * Understand:
+	 * This class executes in its own thread separate from the
+	 * web server client thread that made the request. We do that
+	 * so that we can return to the client as soon as possible,
+	 * but keep the search going in the background (and have
+	 * the next page of results ready to go when the client asks).
+	 */
 	public class SearchTask implements Callable<Void> {
 
 		private final IDao myCallingDao;
@@ -434,6 +459,9 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		private int myCountSaved = 0;
 		private String mySearchUuid;
 
+		/**
+		 * Constructor
+		 */
 		public SearchTask(Search theSearch, IDao theCallingDao, SearchParameterMap theParams, String theResourceType, String theSearchUuid) {
 			mySearch = theSearch;
 			myCallingDao = theCallingDao;
@@ -443,6 +471,11 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			mySearchUuid = theSearchUuid;
 		}
 
+		/**
+		 * This method is called by the server HTTP thread, and
+		 * will block until at least one page of results have been
+		 * fetched from the DB, and will never block after that.
+		 */
 		public Integer awaitInitialSync() {
 			ourLog.trace("Awaiting initial sync");
 			do {
@@ -451,6 +484,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 						break;
 					}
 				} catch (InterruptedException e) {
+					// Shouldn't happen
 					throw new InternalErrorException(e);
 				}
 			} while (mySearch.getStatus() == SearchStatusEnum.LOADING);
@@ -459,11 +493,16 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			return mySearch.getTotalCount();
 		}
 
+		/**
+		 * This is the method which actually performs the search.
+		 * It is called automatically by the thread pool.
+		 */
 		@Override
 		public Void call() throws Exception {
 			StopWatch sw = new StopWatch();
 
 			try {
+				// Create an initial search in the DB and give it an ID
 				saveSearch();
 
 				TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
@@ -480,7 +519,9 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			} catch (Throwable t) {
 
 				/*
-				 * Don't print a stack trace for client errors.. that's just noisy
+				 * Don't print a stack trace for client errors (i.e. requests that
+				 * aren't valid because the client screwed up).. that's just noise
+				 * in the logs and who needs that.
 				 */
 				boolean logged = false;
 				if (t instanceof BaseServerResponseException) {
@@ -535,13 +576,27 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			Class<? extends IBaseResource> resourceTypeClass = myContext.getResourceDefinition(myResourceType).getImplementingClass();
 			ISearchBuilder sb = myCallingDao.newSearchBuilder();
 			sb.setType(resourceTypeClass, myResourceType);
-			Iterator<Long> theResultIter = sb.createQuery(myParams, mySearchUuid);
+			Iterator<Long> theResultIterator = sb.createQuery(myParams, mySearchUuid);
 
-			while (theResultIter.hasNext()) {
+			while (theResultIterator.hasNext()) {
-				myUnsyncedPids.add(theResultIter.next());
+				myUnsyncedPids.add(theResultIterator.next());
-				if (myUnsyncedPids.size() >= mySyncSize) {
+
-					saveUnsynced(theResultIter);
+				boolean shouldSync = myUnsyncedPids.size() >= mySyncSize;
+
+				if (myDaoConfig.getCountSearchResultsUpTo() != null &&
+					myDaoConfig.getCountSearchResultsUpTo() > 0 &&
+					myDaoConfig.getCountSearchResultsUpTo() < myUnsyncedPids.size()) {
+					shouldSync = false;
 				}
+
+				if (myUnsyncedPids.size() > 50000) {
+					shouldSync = true;
+				}
+
+				if (shouldSync) {
+					saveUnsynced(theResultIterator);
+				}
+
 				if (myLoadingThrottleForUnitTests != null) {
 					try {
 						Thread.sleep(myLoadingThrottleForUnitTests);
@@ -549,9 +604,12 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 						// ignore
 					}
 				}
+
+				// Check if an abort got requested
 				Validate.isTrue(myAbortRequested == false, "Abort has been requested");
+
 			}
-			saveUnsynced(theResultIter);
+			saveUnsynced(theResultIterator);
 		}
 
 		public CountDownLatch getCompletionLatch() {
@@ -648,11 +706,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 							mySearch.setStatus(SearchStatusEnum.FINISHED);
 						}
 					}
-					mySearch.setNumFound(myCountSaved);
-					doSaveSearch();
 
-				}
+					mySearch.setNumFound(myCountSaved);
-			});
 
 					int numSynced;
 					synchronized (mySyncedPids) {
@@ -664,6 +719,12 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 						myDaoConfig.getCountSearchResultsUpTo() <= numSynced) {
 						myInitialCollectionLatch.countDown();
 					}
+
+					doSaveSearch();
+
+				}
+			});
+
 		}
 
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java

@@ -1,7 +1,7 @@
 package ca.uhn.fhir.jpa.config;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.subscription.email.SubscriptionEmailInterceptor;
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import org.apache.commons.dbcp2.BasicDataSource;
@@ -60,6 +60,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");
 		extraProperties.put("hibernate.dialect", "org.hibernate.dialect.DerbyTenSevenDialect");
+		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "ram");
 		extraProperties.put("hibernate.search.lucene_version","LUCENE_CURRENT");
 		return extraProperties;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java

@@ -1,5 +1,15 @@
 package ca.uhn.fhir.jpa.config;
 
+import java.sql.Connection;
+import java.sql.SQLException;
+import java.util.Properties;
+import java.util.concurrent.TimeUnit;
+
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
+
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
+import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.subscription.email.IEmailSender;
 import ca.uhn.fhir.jpa.subscription.email.JavaMailEmailSender;
@@ -141,6 +151,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");
 		extraProperties.put("hibernate.dialect", "org.hibernate.dialect.DerbyTenSevenDialect");
+		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "ram");
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
 		extraProperties.put("hibernate.search.autoregister_listeners", "true");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.config;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import net.ttddyy.dsproxy.listener.ThreadQueryCountHolder;
@@ -125,6 +126,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");
 		extraProperties.put("hibernate.dialect", "org.hibernate.dialect.DerbyTenSevenDialect");
+		extraProperties.put("hibernate.search.model_mapping", ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "ram");
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
 		extraProperties.put("hibernate.search.autoregister_listeners", "true");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java

@@ -56,6 +56,30 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		myDaoConfig.setTreatReferencesAsLogical(new DaoConfig().getTreatReferencesAsLogical());
 	}
 
+	/**
+	 * See #773
+	 */
+	@Test
+	public void testDeleteResourceWithOutboundDeletedResources() {
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
+
+		Organization org = new Organization();
+		org.setId("ORG");
+		org.setName("ORG");
+		myOrganizationDao.update(org);
+
+		Patient pat = new Patient();
+		pat.setId("PAT");
+		pat.setActive(true);
+		pat.setManagingOrganization(new ResourceReferenceDt("Organization/ORG"));
+		myPatientDao.update(pat);
+
+		myOrganizationDao.delete(new IdDt("Organization/ORG"));
+
+		myPatientDao.delete(new IdDt("Patient/PAT"));
+	}
+
+
 	private void assertGone(IIdType theId) {
 		try {
 			assertNotGone(theId);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -55,6 +55,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	public final void after() {
 		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
 		myDaoConfig.setTreatReferencesAsLogical(new DaoConfig().getTreatReferencesAsLogical());
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(new DaoConfig().isEnforceReferentialIntegrityOnDelete());
 	}
 
 	private void assertGone(IIdType theId) {
@@ -98,6 +99,29 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	}
 
 
+	/**
+	 * See #773
+	 */
+	@Test
+	public void testDeleteResourceWithOutboundDeletedResources() {
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
+
+		Organization org = new Organization();
+		org.setId("ORG");
+		org.setName("ORG");
+		myOrganizationDao.update(org);
+
+		Patient pat = new Patient();
+		pat.setId("PAT");
+		pat.setActive(true);
+		pat.setManagingOrganization(new Reference("Organization/ORG"));
+		myPatientDao.update(pat);
+
+		myOrganizationDao.delete(new IdType("Organization/ORG"));
+
+		myPatientDao.delete(new IdType("Patient/PAT"));
+	}
+
 
 	@Before
 	public void beforeDisableResultReuse() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderInterceptorDstu3Test.java

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.jpa.provider.dstu3;
 
 import ca.uhn.fhir.jpa.provider.r4.ResourceProviderInterceptorR4Test;
-import ca.uhn.fhir.model.dstu2.resource.Conformance;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
@@ -61,8 +60,8 @@ public class ResourceProviderInterceptorDstu3Test extends BaseResourceProviderDs
 	public void before() throws Exception {
 		super.before();
 
-		myServerInterceptor = mock(IServerInterceptor.class);
+		myServerInterceptor = mock(IServerInterceptor.class, withSettings().verboseLogging());
-		myDaoInterceptor = mock(IServerInterceptor.class);
+		myDaoInterceptor = mock(IServerInterceptor.class, withSettings().verboseLogging());
 
 		resetServerInterceptor();
 
@@ -125,6 +124,8 @@ public class ResourceProviderInterceptorDstu3Test extends BaseResourceProviderDs
 	public void testCreateResourceInTransaction() throws IOException, ServletException {
 		String methodName = "testCreateResourceInTransaction";
 
+		ourLog.info("** Starting {}", methodName);
+
 		Patient pt = new Patient();
 		pt.addName().setFamily(methodName);
 
@@ -140,6 +141,11 @@ public class ResourceProviderInterceptorDstu3Test extends BaseResourceProviderDs
 
 		resetServerInterceptor();
 
+		ArgumentCaptor<ActionRequestDetails> ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
+		ArgumentCaptor<RestOperationTypeEnum> opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
+		verify(myDaoInterceptor, times(0)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
+		verify(myServerInterceptor, times(0)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
+
 		HttpPost post = new HttpPost(ourServerBase + "/");
 		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
 		CloseableHttpResponse response = ourHttpClient.execute(post);
@@ -153,8 +159,8 @@ public class ResourceProviderInterceptorDstu3Test extends BaseResourceProviderDs
 		 * Server Interceptor
 		 */
 
-		ArgumentCaptor<ActionRequestDetails> ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
+		ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
-		ArgumentCaptor<RestOperationTypeEnum> opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
+		opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
 		verify(myServerInterceptor, times(2)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
 		assertEquals(RestOperationTypeEnum.TRANSACTION, opTypeCaptor.getAllValues().get(0));
 		assertEquals(null, ardCaptor.getAllValues().get(0).getResourceType());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -3149,17 +3149,19 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			.count(1)
 			.execute();
 
-		ourLog.info("** Done searching with count of 1");
+		ourLog.info("** Done searching in {}ms with count of 1", sw.getMillis());
 
 		ourLog.info(myCapturingInterceptor.getLastResponse().getAllHeaders().toString());
 		assertThat(myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE), Matchers.<String>empty());
 		assertThat(myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE.toLowerCase()),Matchers.<String>empty());
 
-		assertThat(sw.getMillis(), lessThan(1000L));
+		String msg = "Total is " + found.getTotalElement().getValue() + " and took " + sw.getMillis() + " millis";
 
 		// If this fails under load, try increasing the throttle above
-		assertEquals(null, found.getTotalElement().getValue());
+		assertEquals(msg,null, found.getTotalElement().getValue());
-		assertEquals(1, found.getEntry().size());
+		assertEquals(msg, 1, found.getEntry().size());
+		assertThat(msg, sw.getMillis(), lessThan(1000L));
+
 	}
 
 	@Test
@@ -3214,11 +3216,10 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		assertThat(myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE), Matchers.<String>empty());
 		assertThat(myCapturingInterceptor.getLastResponse().getHeaders(Constants.HEADER_X_CACHE.toLowerCase()),Matchers.<String>empty());
 
-		assertThat(sw.getMillis(), lessThan(1000L));
-
 		// If this fails under load, try increasing the throttle above
 		assertEquals(null, found.getTotalElement().getValue());
 		assertEquals(1, found.getEntry().size());
+		assertThat(sw.getMillis(), lessThan(1000L));
 	}
 
 	@Test

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java

@@ -5,6 +5,7 @@ import java.util.Properties;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.jpa.HibernatePersistenceProvider;
@@ -80,6 +81,7 @@ public class FhirServerConfig extends BaseJavaConfigDstu3 {
 		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
 		extraProperties.put("hibernate.cache.use_structured_entries", "false");
 		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", "target/lucenefiles");
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu2.java

@@ -1,10 +1,9 @@
 package ca.uhn.fhir.jpa.demo;
 
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
-import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
-import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
@@ -80,6 +79,7 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
 		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
 		extraProperties.put("hibernate.cache.use_structured_entries", "false");
 		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", "target/lucenefiles");
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

hapi-fhir-jpaserver-examples/hapi-fhir-jpaserver-example-postgres/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java

@@ -84,6 +84,7 @@ public class FhirServerConfig extends BaseJavaConfigDstu3 {
 		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
 		extraProperties.put("hibernate.cache.use_structured_entries", "false");
 		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.model_mapping", SearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", "target/lucenefiles");
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu2Config.java

@@ -2,6 +2,7 @@ package ca.uhn.fhirtest.config;
 
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
@@ -111,6 +112,7 @@ public class TdlDstu2Config extends BaseJavaConfigDstu2 {
 		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
 		extraProperties.put("hibernate.cache.use_structured_entries", "false");
 		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider" ,"filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", myFhirLuceneLocation);
 		extraProperties.put("hibernate.search.lucene_version","LUCENE_CURRENT");

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu3Config.java

@@ -5,6 +5,7 @@ import java.util.Properties;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.dialect.DerbyTenSevenDialect;
@@ -13,7 +14,6 @@ import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.DependsOn;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Lazy;
 import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
@@ -94,6 +94,7 @@ public class TdlDstu3Config extends BaseJavaConfigDstu3 {
 		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
 		extraProperties.put("hibernate.cache.use_structured_entries", "false");
 		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", myFhirLuceneLocation);
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

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

@@ -2,6 +2,7 @@ package ca.uhn.fhirtest.config;
 
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
@@ -65,6 +66,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		retVal.setAllowExternalReferences(true);
 		retVal.getTreatBaseUrlsAsLocal().add("http://fhirtest.uhn.ca/baseDstu2");
 		retVal.getTreatBaseUrlsAsLocal().add("https://fhirtest.uhn.ca/baseDstu2");
+		retVal.setCountSearchResultsUpTo(TestR4Config.COUNT_SEARCH_RESULTS_UP_TO);
 		return retVal;
 	}
 
@@ -115,6 +117,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
 		extraProperties.put("hibernate.cache.use_structured_entries", "false");
 		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", myFhirLuceneLocation);
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

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

@@ -5,6 +5,7 @@ import java.util.Properties;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.dialect.DerbyTenSevenDialect;
@@ -54,6 +55,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		retVal.setAllowExternalReferences(true);
 		retVal.getTreatBaseUrlsAsLocal().add("http://fhirtest.uhn.ca/baseDstu3");
 		retVal.getTreatBaseUrlsAsLocal().add("https://fhirtest.uhn.ca/baseDstu3");
+		retVal.setCountSearchResultsUpTo(TestR4Config.COUNT_SEARCH_RESULTS_UP_TO);
 		return retVal;
 	}
 
@@ -112,6 +114,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
 		extraProperties.put("hibernate.cache.use_structured_entries", "false");
 		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", myFhirLuceneLocation);
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

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

@@ -5,11 +5,11 @@ import java.util.Properties;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.dialect.DerbyTenSevenDialect;
 import org.hibernate.dialect.PostgreSQL94Dialect;
-import org.hibernate.dialect.PostgreSQL95Dialect;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Value;
@@ -110,6 +110,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
 		extraProperties.put("hibernate.cache.use_structured_entries", "false");
 		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", myFhirLuceneLocation);
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServerUtils.java

@@ -86,10 +86,41 @@ public class RestfulServerUtils {
 			}
 		}
 		if (elements != null && elements.size() > 0) {
-			Set<String> newElements = new HashSet<String>();
+			Set<String> newElements = new HashSet<>();
 			for (String next : elements) {
 				newElements.add("*." + next);
 			}
+
+			/*
+			 * We try to be smart about what the user is asking for
+			 * when they include an _elements parameter. If we're responding
+			 * to something that returns a Bundle (e.g. a search) we assume
+			 * the elements don't apply to the Bundle itself, unless
+			 * the client has explicitly scoped the Bundle
+			 * (i.e. with Bundle.total or something like that)
+			 */
+			switch (theRequestDetails.getRestOperationType()) {
+				case SEARCH_SYSTEM:
+				case SEARCH_TYPE:
+				case HISTORY_SYSTEM:
+				case HISTORY_TYPE:
+				case HISTORY_INSTANCE:
+				case GET_PAGE:
+					boolean haveExplicitBundleElement = false;
+					for (String next : newElements) {
+						if (next.startsWith("Bundle.")) {
+							haveExplicitBundleElement = true;
+							break;
+						}
+					}
+					if (!haveExplicitBundleElement) {
+						parser.setEncodeElementsAppliesToChildResourcesOnly(true);
+					}
+					break;
+				default:
+					break;
+			}
+
 			parser.setEncodeElements(newElements);
 			parser.setEncodeElementsAppliesToResourceTypes(elementsAppliesTo);
 		}
@@ -147,6 +178,19 @@ public class RestfulServerUtils {
 				b.append(theBundleType.getCode());
 			}
 
+			String paramName = Constants.PARAM_ELEMENTS;
+			String[] params = theRequestParameters.get(paramName);
+			if (params != null) {
+				for (String nextValue : params) {
+					if (isNotBlank(nextValue)) {
+						b.append('&');
+						b.append(paramName);
+						b.append('=');
+						b.append(UrlUtil.escape(nextValue));
+					}
+				}
+			}
+
 			return b.toString();
 		} catch (UnsupportedEncodingException e) {
 			throw new Error("UTF-8 not supported", e);// should not happen
@@ -587,10 +631,12 @@ public class RestfulServerUtils {
 			response.addHeader(Constants.HEADER_CONTENT_DISPOSITION, "Attachment;");
 
 			IBaseReference securityContext = BinaryUtil.getSecurityContext(theServer.getFhirContext(), bin);
+			if (securityContext != null) {
 				String securityContextRef = securityContext.getReferenceElement().getValue();
 				if (isNotBlank(securityContextRef)) {
 					response.addHeader(Constants.HEADER_X_SECURITY_CONTEXT, securityContextRef);
 				}
+			}
 
 			return response.sendAttachmentResponse(bin, theStausCode, contentType);
 		}

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseResourceReturningMethodBinding.java

@@ -332,7 +332,7 @@ public abstract class BaseResourceReturningMethodBinding extends BaseMethodBindi
 		}
 
 		bundleFactory.addRootPropertiesToBundle(theResult.getUuid(), serverBase, theLinkSelf, linkPrev, linkNext, theResult.size(), theBundleType, theResult.getPublished());
-		bundleFactory.addResourcesToBundle(new ArrayList<IBaseResource>(resourceList), theBundleType, serverBase, theServer.getBundleInclusionRule(), theIncludes);
+		bundleFactory.addResourcesToBundle(new ArrayList<>(resourceList), theBundleType, serverBase, theServer.getBundleInclusionRule(), theIncludes);
 
 		if (theServer.getPagingProvider() != null) {
 			int limit;

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml

@@ -0,0 +1,118 @@
+<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">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-fhir-spring-boot</artifactId>
+		<version>3.1.0-SNAPSHOT</version>
+	</parent>
+
+	<artifactId>hapi-fhir-spring-boot-autoconfigure</artifactId>
+
+	<packaging>jar</packaging>
+
+	<dependencies>
+		<!-- Compile dependencies -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-autoconfigure</artifactId>
+		</dependency>
+
+		<!-- Optional dependencies -->
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-base</artifactId>
+			<version>${project.version}</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-server</artifactId>
+			<version>${project.version}</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-base</artifactId>
+			<version>${project.version}</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jaxrsserver-base</artifactId>
+			<version>${project.version}</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-client</artifactId>
+			<version>${project.version}</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-client-okhttp</artifactId>
+			<version>${project.version}</version>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>javax.servlet</groupId>
+			<artifactId>javax.servlet-api</artifactId>
+			<optional>true</optional>
+		</dependency>
+
+		<!-- @ConfigurationProperties annotation processing (metadata for IDEs) -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-configuration-processor</artifactId>
+			<optional>true</optional>
+		</dependency>
+
+		<!-- Test dependencies -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-test</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-web</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>com.h2database</groupId>
+			<artifactId>h2</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>log4j-over-slf4j</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
+			<version>${project.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu2.1</artifactId>
+			<version>${project.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
+			<version>${project.version}</version>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+
+</project>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/src/main/java/ca/uhn/fhir/spring/boot/autoconfigure/FhirAutoConfiguration.java

@@ -0,0 +1,287 @@
+package ca.uhn.fhir.spring.boot.autoconfigure;
+
+import java.util.List;
+
+import javax.servlet.ServletException;
+import javax.sql.DataSource;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jaxrs.server.AbstractJaxRsProvider;
+import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
+import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.provider.BaseJpaProvider;
+import ca.uhn.fhir.jpa.provider.BaseJpaSystemProvider;
+import ca.uhn.fhir.okhttp.client.OkHttpRestfulClientFactory;
+import ca.uhn.fhir.rest.client.apache.ApacheRestfulClientFactory;
+import ca.uhn.fhir.rest.client.api.IClientInterceptor;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.api.IRestfulClientFactory;
+import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
+import ca.uhn.fhir.rest.server.IPagingProvider;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
+import okhttp3.OkHttpClient;
+import org.apache.http.client.HttpClient;
+
+import org.springframework.beans.factory.ObjectProvider;
+import org.springframework.boot.autoconfigure.AutoConfigureAfter;
+import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnBean;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnClass;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingClass;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.boot.autoconfigure.condition.ResourceCondition;
+import org.springframework.boot.autoconfigure.domain.EntityScan;
+import org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration;
+import org.springframework.boot.autoconfigure.orm.jpa.HibernateJpaAutoConfiguration;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.boot.web.servlet.ServletRegistrationBean;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.core.annotation.AnnotationAwareOrderComparator;
+import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
+import org.springframework.util.CollectionUtils;
+
+/**
+ * {@link EnableAutoConfiguration Auto-configuration} for HAPI FHIR.
+ *
+ * @author Mathieu Ouellet
+ */
+@Configuration
+@AutoConfigureAfter({ DataSourceAutoConfiguration.class, HibernateJpaAutoConfiguration.class })
+@EnableConfigurationProperties(FhirProperties.class)
+public class FhirAutoConfiguration {
+
+    private final FhirProperties properties;
+
+    public FhirAutoConfiguration(FhirProperties properties) {
+        this.properties = properties;
+    }
+
+    @Bean
+    @ConditionalOnMissingBean
+    public FhirContext fhirContext() {
+        FhirContext fhirContext = new FhirContext(properties.getVersion());
+        return fhirContext;
+    }
+
+    @Configuration
+    @ConditionalOnClass(AbstractJaxRsProvider.class)
+    @EnableConfigurationProperties(FhirProperties.class)
+    @ConfigurationProperties("hapi.fhir.rest")
+    @SuppressWarnings("serial")
+    static class FhirRestfulServerConfiguration extends RestfulServer {
+
+        private final FhirProperties properties;
+
+        private final FhirContext fhirContext;
+
+        private final List<IResourceProvider> resourceProviders;
+
+        private final IPagingProvider pagingProvider;
+
+        private final List<IServerInterceptor> interceptors;
+
+        private final List<FhirRestfulServerCustomizer> customizers;
+
+        public FhirRestfulServerConfiguration(
+                FhirProperties properties,
+                FhirContext fhirContext,
+                ObjectProvider<List<IResourceProvider>> resourceProviders,
+                ObjectProvider<IPagingProvider> pagingProvider,
+                ObjectProvider<List<IServerInterceptor>> interceptors,
+                ObjectProvider<List<FhirRestfulServerCustomizer>> customizers) {
+            this.properties = properties;
+            this.fhirContext = fhirContext;
+            this.resourceProviders = resourceProviders.getIfAvailable();
+            this.pagingProvider = pagingProvider.getIfAvailable();
+            this.interceptors = interceptors.getIfAvailable();
+            this.customizers = customizers.getIfAvailable();
+        }
+
+        @Bean
+        public ServletRegistrationBean fhirServerRegistrationBean() {
+            ServletRegistrationBean registration = new ServletRegistrationBean(this, this.properties.getServer().getPath());
+            registration.setLoadOnStartup(1);
+            return registration;
+        }
+
+        @Override
+        protected void initialize() throws ServletException {
+            super.initialize();
+
+            setFhirContext(this.fhirContext);
+            setResourceProviders(this.resourceProviders);
+            setPagingProvider(this.pagingProvider);
+            setInterceptors(this.interceptors);
+
+            setServerAddressStrategy(new HardcodedServerAddressStrategy(this.properties.getServer().getPath()));
+
+            customize();
+        }
+
+        private void customize() {
+            if (this.customizers != null) {
+                AnnotationAwareOrderComparator.sort(this.customizers);
+                for (FhirRestfulServerCustomizer customizer : this.customizers) {
+                    customizer.customize(this);
+                }
+            }
+        }
+    }
+
+    @Configuration
+    @ConditionalOnClass(BaseJpaProvider.class)
+    @ConditionalOnBean(DataSource.class)
+    @EnableConfigurationProperties(FhirProperties.class)
+    static class FhirJpaServerConfiguration {
+
+        @Configuration
+        @EntityScan("ca.uhn.fhir.jpa.entity")
+        @EnableJpaRepositories(basePackages = "ca.uhn.fhir.jpa.dao.data")
+        static class FhirJpaDaoConfiguration {
+
+            @Bean
+            @ConditionalOnMissingBean
+            @ConfigurationProperties("hapi.fhir.jpa")
+            public DaoConfig fhirDaoConfig() {
+                DaoConfig fhirDaoConfig = new DaoConfig();
+                return fhirDaoConfig;
+            }
+        }
+
+        @Configuration
+        @ConditionalOnBean({ DaoConfig.class, RestfulServer.class })
+        @SuppressWarnings("rawtypes")
+        static class RestfulServerCustomizer implements FhirRestfulServerCustomizer {
+
+            private final BaseJpaSystemProvider systemProviders;
+
+            public RestfulServerCustomizer(ObjectProvider<BaseJpaSystemProvider> systemProviders) {
+                this.systemProviders = systemProviders.getIfAvailable();
+            }
+
+            @Override
+            public void customize(RestfulServer server) {
+                server.setPlainProviders(systemProviders);
+            }
+        }
+
+        @Configuration
+        @ConditionalOnMissingBean(type = "ca.uhn.fhir.jpa.config.BaseConfig")
+        @ConditionalOnProperty(name = "hapi.fhir.version", havingValue = "DSTU3")
+        static class Dstu3 extends BaseJavaConfigDstu3 {
+        }
+
+        @Configuration
+        @ConditionalOnMissingBean(type = "ca.uhn.fhir.jpa.config.BaseConfig")
+        @ConditionalOnProperty(name = "hapi.fhir.version", havingValue = "DSTU2")
+        static class Dstu2 extends BaseJavaConfigDstu2 {
+        }
+    }
+
+    @Configuration
+    @Conditional(FhirValidationConfiguration.SchemaAvailableCondition.class)
+    @ConditionalOnProperty(name = "hapi.fhir.validation.enabled", matchIfMissing = true)
+    static class FhirValidationConfiguration {
+
+        @Bean
+        @ConditionalOnMissingBean
+        public RequestValidatingInterceptor requestValidatingInterceptor() {
+            return new RequestValidatingInterceptor();
+        }
+
+        @Bean
+        @ConditionalOnMissingBean
+        @ConditionalOnProperty(name = "hapi.fhir.validation.request-only", havingValue = "false")
+        public ResponseValidatingInterceptor responseValidatingInterceptor() {
+            return new ResponseValidatingInterceptor();
+        }
+
+        static class SchemaAvailableCondition extends ResourceCondition {
+
+            SchemaAvailableCondition() {
+                super("ValidationSchema",
+                        "hapi.fhir.validation",
+                        "schema-location",
+                        "classpath:/org/hl7/fhir/instance/model/schema",
+                        "classpath:/org/hl7/fhir/dstu2016may/model/schema",
+                        "classpath:/org/hl7/fhir/dstu3/model/schema");
+            }
+        }
+    }
+
+    @Configuration
+    @ConditionalOnProperty("hapi.fhir.server.url")
+    @EnableConfigurationProperties(FhirProperties.class)
+    static class FhirRestfulClientConfiguration {
+
+        private final FhirProperties properties;
+
+        private final List<IClientInterceptor> clientInterceptors;
+
+        public FhirRestfulClientConfiguration(FhirProperties properties, ObjectProvider<List<IClientInterceptor>> clientInterceptors) {
+            this.properties = properties;
+            this.clientInterceptors = clientInterceptors.getIfAvailable();
+        }
+
+        @Bean
+        @ConditionalOnBean(IRestfulClientFactory.class)
+        public IGenericClient fhirClient(final IRestfulClientFactory clientFactory) {
+            IGenericClient fhirClient = clientFactory.newGenericClient(this.properties.getServer().getUrl());
+            if (!CollectionUtils.isEmpty(this.clientInterceptors)) {
+                for (IClientInterceptor interceptor : this.clientInterceptors) {
+                    fhirClient.registerInterceptor(interceptor);
+                }
+            }
+            return fhirClient;
+        }
+
+        @Configuration
+        @ConditionalOnClass(HttpClient.class)
+        @ConditionalOnMissingClass("okhttp3.OkHttpClient")
+        static class Apache {
+
+            private final FhirContext context;
+
+            public Apache(FhirContext context) {
+                this.context = context;
+            }
+
+            @Bean
+            @ConditionalOnMissingBean
+            @ConfigurationProperties("hapi.fhir.rest.client.apache")
+            public IRestfulClientFactory fhirRestfulClientFactory() {
+                ApacheRestfulClientFactory restfulClientFactory = new ApacheRestfulClientFactory(this.context);
+                return restfulClientFactory;
+            }
+        }
+
+        @Configuration
+        @ConditionalOnClass(OkHttpClient.class)
+        static class OkHttp {
+
+            private final FhirContext context;
+
+            public OkHttp(FhirContext context) {
+                this.context = context;
+            }
+
+            @Bean
+            @ConditionalOnMissingBean
+            @ConfigurationProperties("hapi.fhir.rest.client.okhttp")
+            public IRestfulClientFactory fhirRestfulClientFactory() {
+                OkHttpRestfulClientFactory restfulClientFactory = new OkHttpRestfulClientFactory(this.context);
+                return restfulClientFactory;
+            }
+        }
+    }
+
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/src/main/java/ca/uhn/fhir/spring/boot/autoconfigure/FhirProperties.java

@@ -0,0 +1,85 @@
+package ca.uhn.fhir.spring.boot.autoconfigure;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+@ConfigurationProperties(prefix = "hapi.fhir")
+public class FhirProperties {
+
+    private FhirVersionEnum version = FhirVersionEnum.DSTU2;
+
+    private Server server = new Server();
+
+    private Validation validation = new Validation();
+
+    public FhirVersionEnum getVersion() {
+        return version;
+    }
+
+    public void setVersion(FhirVersionEnum version) {
+        this.version = version;
+    }
+
+    public Server getServer() {
+        return server;
+    }
+
+    public void setServer(Server server) {
+        this.server = server;
+    }
+
+    public Validation getValidation() {
+        return validation;
+    }
+
+    public void setValidation(Validation validation) {
+        this.validation = validation;
+    }
+
+    public static class Server {
+
+        private String url;
+
+        private String path = "/fhir/*";
+
+        public String getUrl() {
+            return url;
+        }
+
+        public void setUrl(String url) {
+            this.url = url;
+        }
+
+        public String getPath() {
+            return path;
+        }
+
+        public void setPath(String path) {
+            this.path = path;
+        }
+    }
+
+    public static class Validation {
+
+        private boolean enabled = true;
+
+        private boolean requestOnly = true;
+
+        public boolean isEnabled() {
+            return enabled;
+        }
+
+        public void setEnabled(boolean enabled) {
+            this.enabled = enabled;
+        }
+
+        public boolean isRequestOnly() {
+            return requestOnly;
+        }
+
+        public void setRequestOnly(boolean requestOnly) {
+            this.requestOnly = requestOnly;
+        }
+    }
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/src/main/java/ca/uhn/fhir/spring/boot/autoconfigure/FhirRestfulServerCustomizer.java

@@ -0,0 +1,13 @@
+package ca.uhn.fhir.spring.boot.autoconfigure;
+
+import ca.uhn.fhir.rest.server.RestfulServer;
+
+@FunctionalInterface
+public interface FhirRestfulServerCustomizer {
+
+    /**
+     * Customize the server.
+     * @param server the server to customize
+     */
+    void customize(RestfulServer server);
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/src/main/resources/META-INF/spring.factories

@@ -0,0 +1 @@
+org.springframework.boot.autoconfigure.EnableAutoConfiguration=ca.uhn.fhir.spring.boot.autoconfigure.FhirAutoConfiguration

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/src/test/java/ca/uhn/fhir/spring/boot/autoconfigure/FhirAutoConfigurationTest.java

@@ -0,0 +1,171 @@
+package ca.uhn.fhir.spring.boot.autoconfigure;
+
+import java.net.URL;
+import java.net.URLClassLoader;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.okhttp.client.OkHttpRestfulClientFactory;
+import ca.uhn.fhir.rest.client.apache.ApacheRestfulClientFactory;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.spring.boot.autoconfigure.FhirAutoConfiguration.FhirJpaServerConfiguration.Dstu3;
+import org.assertj.core.util.Arrays;
+import org.junit.After;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.ExpectedException;
+
+import org.springframework.beans.factory.NoSuchBeanDefinitionException;
+import org.springframework.boot.autoconfigure.context.PropertyPlaceholderAutoConfiguration;
+import org.springframework.boot.autoconfigure.jdbc.EmbeddedDataSourceConfiguration;
+import org.springframework.boot.autoconfigure.orm.jpa.HibernateJpaAutoConfiguration;
+import org.springframework.boot.test.util.EnvironmentTestUtils;
+import org.springframework.boot.web.servlet.ServletRegistrationBean;
+import org.springframework.context.annotation.AnnotationConfigApplicationContext;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+/**
+ * Tests for {@link FhirAutoConfiguration}.
+ *
+ * @author Mathieu Ouellet
+ */
+public class FhirAutoConfigurationTest {
+
+    @Rule
+    public final ExpectedException thrown = ExpectedException.none();
+
+    private AnnotationConfigApplicationContext context;
+
+    @After
+    public void close() {
+        if (this.context != null) {
+            this.context.close();
+        }
+    }
+
+    @Test
+    public void withFhirContext() throws Exception {
+        load();
+        assertThat(this.context.getBeansOfType(FhirContext.class)).hasSize(1);
+    }
+
+    @Test
+    public void withFhirVersion() throws Exception {
+        load("hapi.fhir.version:DSTU3");
+        assertThat(this.context.getBean(FhirContext.class).getVersion()).isEqualTo(FhirVersionEnum.DSTU3.getVersionImplementation());
+    }
+
+    @Test
+    public void withRestfulServer() {
+        load("hapi.fhir.server.path:/hapi-fhir/*");
+        assertThat(this.context.getBeansOfType(ServletRegistrationBean.class)).hasSize(1);
+        assertThat(this.context.getBeansOfType(RestfulServer.class)).hasSize(1);
+        assertThat(this.context.getBean(ServletRegistrationBean.class).getUrlMappings()).contains("/hapi-fhir/*");
+    }
+
+    @Test
+    public void withJpaServer() {
+        load(
+                Arrays.array(
+                        EmbeddedDataSourceConfiguration.class,
+                        HibernateJpaAutoConfiguration.class,
+                        PropertyPlaceholderAutoConfiguration.class,
+                        FhirAutoConfiguration.class),
+                "hapi.fhir.version:DSTU3",
+                "spring.jpa.properties.hibernate.search.default.indexBase:target/lucenefiles",
+			  		 "spring.jpa.properties.hibernate.search.model_mapping:ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory");
+        assertThat(this.context.getBeansOfType(DaoConfig.class)).hasSize(1);
+        assertThat(this.context.getBeansOfType(Dstu3.class)).hasSize(1);
+    }
+
+    @Test
+    public void withNoValidation() {
+        load("hapi.fhir.validation.enabled:false");
+        this.thrown.expect(NoSuchBeanDefinitionException.class);
+        this.context.getBean(RequestValidatingInterceptor.class);
+    }
+
+    @Test
+    public void withValidation() {
+        load();
+        assertThat(this.context.getBeansOfType(IServerInterceptor.class)).hasSize(1);
+    }
+
+    @Test
+    public void withValidations() {
+        load("hapi.fhir.validation.request-only=false");
+        assertThat(this.context.getBeansOfType(IServerInterceptor.class)).hasSize(2);
+    }
+
+    @Test
+    public void withCustomValidationSchemaLocation() {
+        load("hapi.fhir.validation.schema-location:custom-schema-location");
+        assertThat(this.context.getBeansOfType(IServerInterceptor.class)).hasSize(1);
+    }
+
+    @Test
+    public void withApacheHttpClient() {
+        load(new HidePackagesClassLoader("okhttp3"), "hapi.fhir.server.url:http://localhost:8080");
+        assertThat(this.context.getBeansOfType(ApacheRestfulClientFactory.class)).hasSize(1);
+        assertThat(this.context.getBeansOfType(OkHttpRestfulClientFactory.class)).hasSize(0);
+    }
+
+    @Test
+    public void withOkHttpClient() {
+        load("hapi.fhir.server.url:http://localhost:8080");
+        assertThat(this.context.getBeansOfType(OkHttpRestfulClientFactory.class)).hasSize(1);
+        assertThat(this.context.getBeansOfType(ApacheRestfulClientFactory.class)).hasSize(0);
+    }
+
+    private void load(String... environment) {
+        load(new Class<?>[] { FhirAutoConfiguration.class }, null, environment);
+    }
+
+    private void load(ClassLoader classLoader, String... environment) {
+        load(new Class<?>[] { FhirAutoConfiguration.class }, classLoader, environment);
+    }
+
+    private void load(Class<?>[] configs, String... environment) {
+        load(configs, null, environment);
+    }
+
+    private void load(Class<?>[] configs, ClassLoader classLoader, String... environment) {
+        AnnotationConfigApplicationContext applicationContext = new AnnotationConfigApplicationContext();
+        EnvironmentTestUtils.addEnvironment(applicationContext, environment);
+        if (classLoader != null) {
+            applicationContext.setClassLoader(classLoader);
+        }
+        if (configs != null) {
+            applicationContext.register(configs);
+        }
+        applicationContext.refresh();
+        this.context = applicationContext;
+    }
+
+    private static final class HidePackagesClassLoader extends URLClassLoader {
+
+        private final String[] hiddenPackages;
+
+        private HidePackagesClassLoader(String... hiddenPackages) {
+            super(new URL[0], FhirAutoConfigurationTest.class.getClassLoader());
+            this.hiddenPackages = hiddenPackages;
+        }
+
+        @Override
+        protected Class<?> loadClass(String name, boolean resolve)
+                throws ClassNotFoundException {
+            for (String hiddenPackage : this.hiddenPackages) {
+                if (name.startsWith(hiddenPackage)) {
+                    throw new ClassNotFoundException();
+                }
+            }
+            return super.loadClass(name, resolve);
+        }
+
+    }
+
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/src/test/resources/application.yml

@@ -0,0 +1,13 @@
+spring:
+  jpa:
+    hibernate:
+      ddl-auto: update
+    properties:
+      hibernate.jdbc.batch_size: 20
+      hibernate.cache.use_query_cache: false
+      hibernate.cache.use_second_level_cache: false
+      hibernate.cache.use_structured_entries: false
+      hibernate.cache.use_minimal_puts: false
+      hibernate.search.default.directory_provider: filesystem
+      hibernate.search.default.indexBase: target/lucenefiles
+      hibernate.search.lucene_version: LUCENE_CURRENT

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/src/test/resources/logback-test.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration>
+	<include resource="org/springframework/boot/logging/logback/base.xml"/>
+</configuration>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml

@@ -0,0 +1,64 @@
+<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">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
+		<version>3.1.0-SNAPSHOT</version>
+	</parent>
+
+	<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>
+
+	<packaging>jar</packaging>
+
+	<dependencies>
+		<!-- Compile -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-web</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-actuator</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-spring-boot-starter</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-client</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<!-- Optional -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-configuration-processor</artifactId>
+			<optional>true</optional>
+		</dependency>
+		<!-- Test -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-test</artifactId>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.springframework.boot</groupId>
+				<artifactId>spring-boot-maven-plugin</artifactId>
+			</plugin>
+		</plugins>
+	</build>
+
+
+</project>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/src/main/java/sample/fhir/client/SampleApacheRestfulClientApplication.java

@@ -0,0 +1,37 @@
+package sample.fhir.client;
+
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import org.hl7.fhir.dstu3.model.CapabilityStatement;
+
+import org.springframework.boot.CommandLineRunner;
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.context.annotation.Bean;
+
+@SpringBootApplication
+public class SampleApacheRestfulClientApplication {
+
+    public static void main(String[] args) {
+        SpringApplication.run(SampleApacheRestfulClientApplication.class, args);
+    }
+
+    @Bean
+    public LoggingInterceptor loggingInterceptor() {
+        return new LoggingInterceptor(true);
+    }
+
+    @Bean
+    public CommandLineRunner runner(final IGenericClient fhirClient) {
+        return new CommandLineRunner() {
+
+            @Override
+            public void run(String... args) throws Exception {
+                fhirClient.capabilities()
+                        .ofType(CapabilityStatement.class)
+                        .execute();
+            }
+        };
+    }
+
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/src/main/resources/application.yml

@@ -0,0 +1,13 @@
+server:
+  port: 8888
+hapi:
+  fhir:
+    version: dstu3
+    server:
+      url: http://localhost:8080/fhir
+management:
+  security:
+    enabled: false
+logging:
+  level:
+    ca.uhn.fhir.jaxrs: debug

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml

@@ -0,0 +1,64 @@
+<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">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
+		<version>3.1.0-SNAPSHOT</version>
+	</parent>
+
+	<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>
+
+	<packaging>jar</packaging>
+
+	<dependencies>
+		<!-- Compile -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-web</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-actuator</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-spring-boot-starter</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-client-okhttp</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<!-- Optional -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-configuration-processor</artifactId>
+			<optional>true</optional>
+		</dependency>
+		<!-- Test -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-test</artifactId>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.springframework.boot</groupId>
+				<artifactId>spring-boot-maven-plugin</artifactId>
+			</plugin>
+		</plugins>
+	</build>
+
+
+</project>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/src/main/java/sample/fhir/client/SampleOkHttpRestfulClientApplication.java

@@ -0,0 +1,37 @@
+package sample.fhir.client;
+
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import org.hl7.fhir.dstu3.model.CapabilityStatement;
+
+import org.springframework.boot.CommandLineRunner;
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.context.annotation.Bean;
+
+@SpringBootApplication
+public class SampleOkHttpRestfulClientApplication {
+
+    public static void main(String[] args) {
+        SpringApplication.run(SampleOkHttpRestfulClientApplication.class, args);
+    }
+
+    @Bean
+    public LoggingInterceptor loggingInterceptor() {
+        return new LoggingInterceptor(true);
+    }
+
+    @Bean
+    public CommandLineRunner runner(final IGenericClient fhirClient) {
+        return new CommandLineRunner() {
+
+            @Override
+            public void run(String... args) throws Exception {
+                fhirClient.capabilities()
+                        .ofType(CapabilityStatement.class)
+                        .execute();
+            }
+        };
+    }
+
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/src/main/resources/application.yml

@@ -0,0 +1,13 @@
+server:
+  port: 8888
+hapi:
+  fhir:
+    version: dstu3
+    server:
+      url: http://localhost:8080/fhir
+management:
+  security:
+    enabled: false
+logging:
+  level:
+    ca.uhn.fhir.jaxrs: debug

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml

@@ -0,0 +1,67 @@
+<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">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
+		<version>3.1.0-SNAPSHOT</version>
+	</parent>
+
+	<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>
+
+	<packaging>jar</packaging>
+
+	<dependencies>
+		<!-- Compile -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-web</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-actuator</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-jersey</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-spring-boot-starter</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jaxrsserver-base</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<!-- Optional -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-configuration-processor</artifactId>
+			<optional>true</optional>
+		</dependency>
+		<!-- Test -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-test</artifactId>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.springframework.boot</groupId>
+				<artifactId>spring-boot-maven-plugin</artifactId>
+			</plugin>
+		</plugins>
+	</build>
+
+</project>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/src/main/java/sample/fhir/server/jersey/SampleJerseyRestfulServerApplication.java

@@ -0,0 +1,20 @@
+package sample.fhir.server.jersey;
+
+import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.context.annotation.Bean;
+
+@SpringBootApplication
+public class SampleJerseyRestfulServerApplication {
+
+    public static void main(String[] args) {
+        SpringApplication.run(SampleJerseyRestfulServerApplication.class, args);
+    }
+
+    @Bean
+    public LoggingInterceptor loggingInterceptor() {
+        return new LoggingInterceptor();
+    }
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/src/main/java/sample/fhir/server/jersey/provider/PatientResourceProvider.java

@@ -0,0 +1,73 @@
+package sample.fhir.server.jersey.provider;
+
+import java.util.concurrent.ConcurrentHashMap;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jaxrs.server.AbstractJaxRsResourceProvider;
+import ca.uhn.fhir.rest.annotation.Create;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Read;
+import ca.uhn.fhir.rest.annotation.ResourceParam;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import org.hl7.fhir.dstu3.model.HumanName;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.Patient;
+
+import org.springframework.stereotype.Component;
+
+@Component
+public class PatientResourceProvider extends AbstractJaxRsResourceProvider<Patient> {
+
+    private static Long counter = 1L;
+
+    private static final ConcurrentHashMap<String, Patient> patients = new ConcurrentHashMap<>();
+
+    static {
+        patients.put(String.valueOf(counter), createPatient("Van Houte"));
+        patients.put(String.valueOf(counter), createPatient("Agnew"));
+        for (int i = 0; i < 20; i++) {
+            patients.put(String.valueOf(counter), createPatient("Random Patient " + counter));
+        }
+    }
+
+    public PatientResourceProvider(FhirContext fhirContext) {
+        super(fhirContext);
+    }
+
+    @Read
+    public Patient find(@IdParam final IdType theId) {
+        if (patients.containsKey(theId.getIdPart())) {
+            return patients.get(theId.getIdPart());
+        } else {
+            throw new ResourceNotFoundException(theId);
+        }
+    }
+
+    @Create
+    public MethodOutcome createPatient(@ResourceParam Patient patient) {
+
+        patient.setId(createId(counter, 1L));
+        patients.put(String.valueOf(counter), patient);
+
+        return new MethodOutcome(patient.getIdElement());
+    }
+
+    @Override
+    public Class<Patient> getResourceType() {
+        return Patient.class;
+    }
+
+    private static IdType createId(final Long id, final Long theVersionId) {
+        return new IdType("Patient", "" + id, "" + theVersionId);
+    }
+
+    private static Patient createPatient(final String name) {
+        final Patient patient = new Patient();
+        patient.getName().add(new HumanName().setFamily(name));
+        patient.setId(createId(counter, 1L));
+        counter++;
+        return patient;
+    }
+
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/src/main/resources/application.yml

@@ -0,0 +1,21 @@
+hapi:
+  fhir:
+    version: dstu3
+    server:
+      path: /fhir/*
+    rest:
+      server-name: hapi-fhir-spring-boot-sample-server-jersey
+      server-version: 1.0.0
+      implementation-description: Spring Boot Jersey Server Sample
+      default-response-encoding: json
+      e-tag-support: enabled
+      default-pretty-print: true
+    validation:
+      enabled: true
+      request-only: true
+management:
+  security:
+    enabled: false
+logging:
+  level:
+    ca.uhn.fhir.jaxrs: debug

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/src/test/java/sample/fhir/server/jersey/SampleJerseyRestfulServerApplicationTest.java

@@ -0,0 +1,41 @@
+package sample.fhir.server.jersey;
+
+import org.junit.Test;
+import org.junit.runner.RunWith;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.context.SpringBootTest.WebEnvironment;
+import org.springframework.boot.test.web.client.TestRestTemplate;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+@RunWith(SpringRunner.class)
+@SpringBootTest(webEnvironment = WebEnvironment.RANDOM_PORT)
+public class SampleJerseyRestfulServerApplicationTest {
+
+    @Autowired
+    private TestRestTemplate restTemplate;
+
+    @Test
+    public void metadata() {
+        ResponseEntity<String> entity = this.restTemplate.getForEntity(
+                "/fhir/metadata",
+                String.class);
+        assertThat(entity.getStatusCode()).isEqualTo(HttpStatus.OK);
+        assertThat(entity.getBody()).contains("\"status\": \"active\"");
+    }
+
+    @Test
+    public void patientResource() {
+        ResponseEntity<String> entity = this.restTemplate.getForEntity(
+                "/fhir/Patient/1",
+                String.class);
+        assertThat(entity.getStatusCode()).isEqualTo(HttpStatus.OK);
+        assertThat(entity.getBody()).contains("\"family\": \"Van Houte\"");
+    }
+
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jpa/pom.xml

@@ -0,0 +1,75 @@
+<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">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
+		<version>3.1.0-SNAPSHOT</version>
+	</parent>
+
+	<artifactId>hapi-fhir-spring-boot-sample-server-jpa</artifactId>
+
+	<packaging>jar</packaging>
+
+	<dependencies>
+		<!-- Compile -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-web</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-actuator</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-jersey</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-data-jpa</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-spring-boot-starter</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-base</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jaxrsserver-base</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>com.h2database</groupId>
+			<artifactId>h2</artifactId>
+		</dependency>
+		<!-- Optional -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-configuration-processor</artifactId>
+			<optional>true</optional>
+		</dependency>
+		<!-- Test -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-test</artifactId>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.springframework.boot</groupId>
+				<artifactId>spring-boot-maven-plugin</artifactId>
+			</plugin>
+		</plugins>
+	</build>
+
+</project>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jpa/src/main/java/sample/fhir/server/jpa/SampleJpaRestfulServerApplication.java

@@ -0,0 +1,12 @@
+package sample.fhir.server.jpa;
+
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+
+@SpringBootApplication
+public class SampleJpaRestfulServerApplication {
+
+    public static void main(String[] args) {
+        SpringApplication.run(SampleJpaRestfulServerApplication.class, args);
+    }
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jpa/src/main/resources/application.yml

@@ -0,0 +1,39 @@
+spring:
+  jpa:
+    hibernate:
+      ddl-auto: create-drop
+    properties:
+      hibernate.jdbc.batch_size: 20
+      hibernate.cache.use_query_cache: false
+      hibernate.cache.use_second_level_cache: false
+      hibernate.cache.use_structured_entries: false
+      hibernate.cache.use_minimal_puts: false
+      hibernate.search.default.directory_provider: filesystem
+      hibernate.search.default.indexBase: target/lucenefiles
+      hibernate.search.lucene_version: LUCENE_CURRENT
+      hibernate.search.model_mapping: ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory
+
+  h2:
+    console:
+      enabled: true
+hapi:
+  fhir:
+    version: dstu3
+    server:
+      path: /fhir/*
+    rest:
+      server-name: hapi-fhir-spring-boot-sample-server-jpa
+      server-version: 1.0.0
+      implementation-description: Spring Boot Jpa Server Sample
+      default-response-encoding: json
+      e-tag-support: enabled
+      default-pretty-print: true
+    validation:
+      enabled: true
+      request-only: true
+    jpa:
+      scheduling-disabled: true
+      subscription-enabled: false
+management:
+  security:
+    enabled: false

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jpa/src/test/java/sample/fhir/server/jpa/SampleJpaRestfulServerApplicationTest.java

@@ -0,0 +1,41 @@
+package sample.fhir.server.jpa;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.context.embedded.LocalServerPort;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.context.SpringBootTest.WebEnvironment;
+import org.springframework.test.context.junit4.SpringRunner;
+
+@RunWith(SpringRunner.class)
+@SpringBootTest(webEnvironment = WebEnvironment.RANDOM_PORT)
+public class SampleJpaRestfulServerApplicationTest {
+
+    @Autowired
+    FhirContext fhirContext;
+
+    @LocalServerPort
+    int port;
+
+    @Test
+    public void createAndRead() {
+        IGenericClient client = fhirContext.newRestfulGenericClient("http://localhost:" + port + "/fhir");
+
+        Patient patient = new Patient();
+        patient.addName().setFamily("Test");
+        IIdType id = client.create().resource(patient).execute().getId();
+
+        System.out.println(id);
+
+        Patient result = client.read().resource(Patient.class).withId(id).execute();
+
+        System.out.println(result);
+    }
+
+}

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml

@@ -0,0 +1,21 @@
+<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">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-fhir-spring-boot</artifactId>
+		<version>3.1.0-SNAPSHOT</version>
+	</parent>
+
+	<artifactId>hapi-fhir-spring-boot-samples</artifactId>
+	<packaging>pom</packaging>
+
+	<modules>
+		<module>hapi-fhir-spring-boot-sample-client-apache</module>
+		<module>hapi-fhir-spring-boot-sample-client-okhttp</module>
+		<module>hapi-fhir-spring-boot-sample-server-jersey</module>
+		<module>hapi-fhir-spring-boot-sample-server-jpa</module>
+	</modules>
+
+</project>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml

@@ -0,0 +1,27 @@
+<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">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-fhir-spring-boot</artifactId>
+		<version>3.1.0-SNAPSHOT</version>
+	</parent>
+
+	<artifactId>hapi-fhir-spring-boot-starter</artifactId>
+
+	<packaging>jar</packaging>
+
+	<dependencies>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-spring-boot-autoconfigure</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+	</dependencies>
+
+</project>

hapi-fhir-spring-boot/pom.xml

@@ -0,0 +1,21 @@
+<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">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-fhir</artifactId>
+		<version>3.1.0-SNAPSHOT</version>
+		<relativePath>../pom.xml</relativePath>
+	</parent>
+
+	<artifactId>hapi-fhir-spring-boot</artifactId>
+	<packaging>pom</packaging>
+
+	<modules>
+		<module>hapi-fhir-spring-boot-autoconfigure</module>
+		<module>hapi-fhir-spring-boot-starter</module>
+		<module>hapi-fhir-spring-boot-samples</module>
+	</modules>
+
+</project>

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2_1Test.java

@@ -1499,7 +1499,7 @@ public class JsonParserDstu2_1Test {
 
 		String val = ourCtx.newJsonParser().encodeResourceToString(patient);
 
-		String expected = "{\"resourceType\":\"Binary\",\"id\":\"11\",\"contentType\":\"foo\",\"content\":\"AQIDBA==\"}";
+		String expected = "{\"resourceType\":\"Binary\",\"id\":\"11\",\"meta\":{\"versionId\":\"22\"},\"contentType\":\"foo\",\"content\":\"AQIDBA==\"}";
 		ourLog.info("Expected: {}", expected);
 		ourLog.info("Actual  : {}", val);
 		assertEquals(expected, val);

hapi-fhir-structures-dstu3/pom.xml

@@ -70,13 +70,6 @@
 					<skipUpdateLicense>true</skipUpdateLicense>
 				</configuration>
 			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-compiler-plugin</artifactId>
-				<configuration>
-					<fork>true</fork>
-				</configuration>
-			</plugin>
 		</plugins>
 	</build>
 

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/context/FhirContextDstu3Test.java

@@ -1,13 +1,8 @@
 package ca.uhn.fhir.context;
 
-import static org.junit.Assert.*;
+import ca.uhn.fhir.rest.client.MyPatientWithExtensions;
-
+import ca.uhn.fhir.util.OperationOutcomeUtil;
-import java.util.ArrayList;
+import ca.uhn.fhir.util.TestUtil;
-import java.util.Collections;
-import java.util.List;
-import java.util.concurrent.CountDownLatch;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
 import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.Reference;
@@ -15,19 +10,21 @@ import org.hl7.fhir.dstu3.model.StructureDefinition;
 import org.junit.AfterClass;
 import org.junit.Test;
 
-import ca.uhn.fhir.rest.client.MyPatientWithExtensions;
+import java.util.ArrayList;
-import ca.uhn.fhir.util.TestUtil;
+import java.util.Collections;
+import java.util.List;
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import static org.junit.Assert.*;
 
 public class FhirContextDstu3Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirContextDstu3Test.class);
 
 	private static FhirContext ourCtx = FhirContext.forDstu3();
 
-	@AfterClass
-	public static void afterClassClearContext() {
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-		
 	@SuppressWarnings("deprecation")
 	@Test
 	public void testAutoDetectVersion() {
@@ -35,6 +32,17 @@ public class FhirContextDstu3Test {
 		assertEquals(FhirVersionEnum.DSTU3, ctx.getVersion().getVersion());
 	}
 
+	@Test
+	public void testCustomTypeDoesntBecomeDefault() {
+		FhirContext ctx = FhirContext.forDstu3();
+
+		MyPatientWithExtensions pt = new MyPatientWithExtensions();
+		pt.addName().addGiven("FOO");
+		ctx.newXmlParser().encodeResourceToString(pt);
+
+		assertEquals(Patient.class, ctx.getResourceDefinition("Patient").getImplementingClass());
+	}
+
 	/**
 	 * See #344
 	 */
@@ -56,37 +64,6 @@ public class FhirContextDstu3Test {
 		assertEquals(StructureDefinition.class, ourCtx.getResourceDefinition("structuredefinition").getImplementingClass());
 	}
 
-	@Test
-	public void testCustomTypeDoesntBecomeDefault() {
-		FhirContext ctx = FhirContext.forDstu3();
-		
-		MyPatientWithExtensions pt = new MyPatientWithExtensions();
-		pt.addName().addGiven("FOO");
-		ctx.newXmlParser().encodeResourceToString(pt);
-		
-		assertEquals(Patient.class, ctx.getResourceDefinition("Patient").getImplementingClass());
-	}
-	
-	@Test
-	public void testQueryBoundCode() {
-		RuntimeResourceDefinition patientType = ourCtx.getResourceDefinition(Patient.class);
-		String childName = "gender";
-		BaseRuntimeChildDatatypeDefinition genderChild = (BaseRuntimeChildDatatypeDefinition) patientType.getChildByName(childName);
-		ourLog.trace(genderChild.getClass().getName());
-		
-		assertEquals(AdministrativeGender.class, genderChild.getBoundEnumType());
-	}
-	
-	@Test
-	public void testQueryNonBoundCode() {
-		RuntimeResourceDefinition patientType = ourCtx.getResourceDefinition(Patient.class);
-		String childName = "name";
-		BaseRuntimeChildDatatypeDefinition genderChild = (BaseRuntimeChildDatatypeDefinition) patientType.getChildByName(childName);
-		ourLog.trace(genderChild.getClass().getName());
-		
-		assertEquals(null, genderChild.getBoundEnumType());
-	}
-
 	@Test
 	public void testInitialisationThreadSafety() {
 		final FhirContext ctx = FhirContext.forDstu3();
@@ -126,4 +103,54 @@ public class FhirContextDstu3Test {
 
 		assertTrue("failed with exception(s): " + exceptions, exceptions.isEmpty());
 	}
+
+	/**
+	 * See #794
+	 */
+	@Test
+	public void testInitializeThreadSafety2() throws InterruptedException {
+		final FhirContext dstu3FhirContext = FhirContext.forDstu3();
+
+		final AtomicInteger count = new AtomicInteger();
+
+		for (int i = 0; i < 10; i++) {
+			new Thread(new Runnable() {
+				@Override
+				public void run() {
+					OperationOutcomeUtil.newInstance(dstu3FhirContext);
+					ourLog.info("Have finished {}", count.incrementAndGet());
+				}
+			}).start();
+		}
+
+		TestUtil.waitForSize(10, count);
+
+	}
+
+	@Test
+	public void testQueryBoundCode() {
+		RuntimeResourceDefinition patientType = ourCtx.getResourceDefinition(Patient.class);
+		String childName = "gender";
+		BaseRuntimeChildDatatypeDefinition genderChild = (BaseRuntimeChildDatatypeDefinition) patientType.getChildByName(childName);
+		ourLog.trace(genderChild.getClass().getName());
+
+		assertEquals(AdministrativeGender.class, genderChild.getBoundEnumType());
+	}
+
+	@Test
+	public void testQueryNonBoundCode() {
+		RuntimeResourceDefinition patientType = ourCtx.getResourceDefinition(Patient.class);
+		String childName = "name";
+		BaseRuntimeChildDatatypeDefinition genderChild = (BaseRuntimeChildDatatypeDefinition) patientType.getChildByName(childName);
+		ourLog.trace(genderChild.getClass().getName());
+
+		assertEquals(null, genderChild.getBoundEnumType());
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+
 }

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

@@ -1,41 +1,26 @@
 package ca.uhn.fhir.parser;
 
-import static org.hamcrest.Matchers.contains;
+import ca.uhn.fhir.context.FhirContext;
-import static org.hamcrest.Matchers.containsString;
+import ca.uhn.fhir.model.api.annotation.Child;
-import static org.hamcrest.Matchers.empty;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import static org.hamcrest.Matchers.not;
+import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
-import static org.hamcrest.Matchers.startsWith;
+import ca.uhn.fhir.parser.FooMessageHeaderWithExplicitField.FooMessageSourceComponent;
-import static org.hamcrest.Matchers.stringContainsInOrder;
+import ca.uhn.fhir.parser.IParserErrorHandler.IParseLocation;
-import static org.junit.Assert.assertArrayEquals;
+import ca.uhn.fhir.parser.PatientWithCustomCompositeExtension.FooParentExtension;
-import static org.junit.Assert.assertEquals;
+import ca.uhn.fhir.util.TestUtil;
-import static org.junit.Assert.assertFalse;
+import com.google.common.collect.Sets;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.times;
-import static org.mockito.Mockito.verify;
-
-import java.io.IOException;
-import java.io.StringReader;
-import java.nio.charset.StandardCharsets;
-import java.text.SimpleDateFormat;
-import java.util.*;
-
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringUtils;
 import org.hamcrest.collection.IsEmptyCollection;
 import org.hamcrest.core.StringContains;
 import org.hamcrest.text.StringContainsInOrder;
-import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Address.AddressUse;
 import org.hl7.fhir.dstu3.model.Address.AddressUseEnumFactory;
-import org.hl7.fhir.dstu3.model.Bundle.*;
+import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.dstu3.model.Bundle.BundleLinkComponent;
+import org.hl7.fhir.dstu3.model.Bundle.BundleType;
 import org.hl7.fhir.dstu3.model.ContactPoint.ContactPointSystem;
 import org.hl7.fhir.dstu3.model.DiagnosticReport.DiagnosticReportStatus;
 import org.hl7.fhir.dstu3.model.ElementDefinition.ElementDefinitionBindingComponent;
@@ -52,27 +37,27 @@ import org.junit.*;
 import org.mockito.ArgumentCaptor;
 import org.xmlunit.builder.DiffBuilder;
 import org.xmlunit.builder.Input;
-import org.xmlunit.diff.*;
+import org.xmlunit.diff.ComparisonControllers;
+import org.xmlunit.diff.DefaultNodeMatcher;
+import org.xmlunit.diff.Diff;
+import org.xmlunit.diff.ElementSelectors;
 
-import com.google.common.collect.Sets;
+import java.io.IOException;
+import java.io.StringReader;
+import java.nio.charset.StandardCharsets;
+import java.text.SimpleDateFormat;
+import java.util.*;
 
-import ca.uhn.fhir.context.FhirContext;
+import static org.hamcrest.Matchers.contains;
-import ca.uhn.fhir.model.api.annotation.Child;
+import static org.hamcrest.Matchers.*;
-import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import static org.hamcrest.Matchers.startsWith;
-import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
+import static org.junit.Assert.*;
-import ca.uhn.fhir.parser.FooMessageHeaderWithExplicitField.FooMessageSourceComponent;
+import static org.mockito.Matchers.any;
-import ca.uhn.fhir.parser.IParserErrorHandler.IParseLocation;
+import static org.mockito.Mockito.*;
-import ca.uhn.fhir.parser.PatientWithCustomCompositeExtension.FooParentExtension;
-import ca.uhn.fhir.rest.client.api.IGenericClient;
-import ca.uhn.fhir.util.TestUtil;
-import ca.uhn.fhir.validation.IValidationContext;
-import ca.uhn.fhir.validation.SingleValidationMessage;
-import ca.uhn.fhir.validation.ValidationContext;
-import ca.uhn.fhir.validation.ValidationResult;
 
 public class XmlParserDstu3Test {
-	private static FhirContext ourCtx = FhirContext.forDstu3();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu3Test.class);
+	private static FhirContext ourCtx = FhirContext.forDstu3();
 
 	@After
 	public void after() {
@@ -83,21 +68,24 @@ public class XmlParserDstu3Test {
 	}
 
 	@Test
-	public void testEncodeBinaryWithSecurityContext() {
+	public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
-		Binary bin = new Binary();
+		String refVal = "http://my.org/FooBar";
-		bin.setContentType("text/plain");
-		bin.setContent("Now is the time".getBytes());
-		Reference securityContext = new Reference();
-		securityContext.setReference("DiagnosticReport/1");
-		bin.setSecurityContext(securityContext);
-		String encoded = ourCtx.newXmlParser().encodeResourceToString(bin);
-		ourLog.info(encoded);
-		assertThat(encoded, containsString("Binary"));
-		assertThat(encoded, containsString("<contentType value=\"text/plain\"/>"));
-		assertThat(encoded, containsString("<securityContext><reference value=\"DiagnosticReport/1\"/></securityContext>"));
-		assertThat(encoded, containsString("<content value=\"Tm93IGlzIHRoZSB0aW1l\"/>"));
-	}
 
+		Patient fhirPat = new Patient();
+		fhirPat.addExtension().setUrl("x1").setValue(new Reference(refVal));
+
+		IParser parser = ourCtx.newXmlParser();
+
+		String output = parser.encodeResourceToString(fhirPat);
+		System.out.println("output: " + output);
+
+		// Deserialize then check that valueReference value is still correct
+		fhirPat = parser.parseResource(Patient.class, output);
+
+		List<Extension> extlst = fhirPat.getExtensionsByUrl("x1");
+		Assert.assertEquals(1, extlst.size());
+		Assert.assertEquals(refVal, ((Reference) extlst.get(0).getValue()).getReference());
+	}
 
 	/**
 	 * See #544
@@ -977,6 +965,22 @@ public class XmlParserDstu3Test {
 		assertEquals("<Binary xmlns=\"http://hl7.org/fhir\"><content value=\"AQIDBA==\"/></Binary>", output);
 	}
 
+	@Test
+	public void testEncodeBinaryWithSecurityContext() {
+		Binary bin = new Binary();
+		bin.setContentType("text/plain");
+		bin.setContent("Now is the time".getBytes());
+		Reference securityContext = new Reference();
+		securityContext.setReference("DiagnosticReport/1");
+		bin.setSecurityContext(securityContext);
+		String encoded = ourCtx.newXmlParser().encodeResourceToString(bin);
+		ourLog.info(encoded);
+		assertThat(encoded, containsString("Binary"));
+		assertThat(encoded, containsString("<contentType value=\"text/plain\"/>"));
+		assertThat(encoded, containsString("<securityContext><reference value=\"DiagnosticReport/1\"/></securityContext>"));
+		assertThat(encoded, containsString("<content value=\"Tm93IGlzIHRoZSB0aW1l\"/>"));
+	}
+
 	@Test
 	public void testEncodeBundleWithContained() {
 		DiagnosticReport rpt = new DiagnosticReport();
@@ -1872,7 +1876,7 @@ public class XmlParserDstu3Test {
 
 		{
 			IParser p = ourCtx.newXmlParser();
-			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
+			p.setEncodeElements(new HashSet<>(Arrays.asList("Patient.name", "Bundle.entry")));
 			p.setPrettyPrint(true);
 			String out = p.encodeResourceToString(bundle);
 			ourLog.info(out);
@@ -1908,6 +1912,31 @@ public class XmlParserDstu3Test {
 
 	}
 
+	@Test
+	public void testEncodeWithEncodeElementsAppliesToChildResourcesOnly() throws Exception {
+		Patient patient = new Patient();
+		patient.getMeta().addProfile("http://profile");
+		patient.addName().setFamily("FAMILY");
+		patient.addAddress().addLine("LINE1");
+
+		Bundle bundle = new Bundle();
+		bundle.setTotal(100);
+		bundle.addEntry().setResource(patient);
+
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setEncodeElements(new HashSet<>(Arrays.asList("Patient.name")));
+			p.setEncodeElementsAppliesToChildResourcesOnly(true);
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(bundle);
+			ourLog.info(out);
+			assertThat(out, containsString("total"));
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, not(containsString("address")));
+		}
+	}
+
 	@Test
 	public void testEncodeWithNarrative() {
 		Patient p = new Patient();
@@ -2835,7 +2864,7 @@ public class XmlParserDstu3Test {
 
 	/**
 	 * See #426
-	 * 
+	 * <p>
 	 * Value type of FOO isn't a valid datatype
 	 */
 	@Test
@@ -2934,6 +2963,30 @@ public class XmlParserDstu3Test {
 		assertEquals("value", capt.getValue());
 	}
 
+	@Test
+	public void testParseMetaUpdatedDate() {
+
+		String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
+			"   <id value=\"e2ee823b-ee4d-472d-b79d-495c23f16b99\"/>\n" +
+			"   <meta>\n" +
+			"      <lastUpdated value=\"2015-06-22T15:48:57.554-04:00\"/>\n" +
+			"   </meta>\n" +
+			"   <type value=\"searchset\"/>\n" +
+			"   <base value=\"http://localhost:58109/fhir/context\"/>\n" +
+			"   <total value=\"0\"/>\n" +
+			"   <link>\n" +
+			"      <relation value=\"self\"/>\n" +
+			"      <url value=\"http://localhost:58109/fhir/context/Patient?_pretty=true\"/>\n" +
+			"   </link>\n" +
+			"</Bundle>";
+
+		Bundle b = ourCtx.newXmlParser().parseResource(Bundle.class, input);
+
+		InstantType updated = b.getMeta().getLastUpdatedElement();
+		assertEquals("2015-06-22T15:48:57.554-04:00", updated.getValueAsString());
+
+	}
+
 	@Test
 	public void testParseMetadata() throws Exception {
 
@@ -2987,43 +3040,6 @@ public class XmlParserDstu3Test {
 
 	}
 
-	public static void compareXml(String content, String reEncoded) {
-		Diff d = DiffBuilder.compare(Input.fromString(content))
-				.withTest(Input.fromString(reEncoded))
-				.withNodeMatcher(new DefaultNodeMatcher(ElementSelectors.byNameAndText))
-				.checkForSimilar()
-				.ignoreWhitespace() // this is working with newest Saxon 9.8.0-2 (not worked with 9.7.0-15
-				.ignoreComments() // this is not working even with newest Saxon 9.8.0-2
-				.withComparisonController(ComparisonControllers.Default)
-				.build();
-
-		assertTrue(d.toString(), !d.hasDifferences());
-	}
-
-	@Test
-	public void testParseMetaUpdatedDate() {
-
-		String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
-				"   <id value=\"e2ee823b-ee4d-472d-b79d-495c23f16b99\"/>\n" +
-				"   <meta>\n" +
-				"      <lastUpdated value=\"2015-06-22T15:48:57.554-04:00\"/>\n" +
-				"   </meta>\n" +
-				"   <type value=\"searchset\"/>\n" +
-				"   <base value=\"http://localhost:58109/fhir/context\"/>\n" +
-				"   <total value=\"0\"/>\n" +
-				"   <link>\n" +
-				"      <relation value=\"self\"/>\n" +
-				"      <url value=\"http://localhost:58109/fhir/context/Patient?_pretty=true\"/>\n" +
-				"   </link>\n" +
-				"</Bundle>";
-
-		Bundle b = ourCtx.newXmlParser().parseResource(Bundle.class, input);
-
-		InstantType updated = b.getMeta().getLastUpdatedElement();
-		assertEquals("2015-06-22T15:48:57.554-04:00", updated.getValueAsString());
-
-	}
-
 	// TODO: this should work
 	@Test
 	@Ignore
@@ -3094,40 +3110,6 @@ public class XmlParserDstu3Test {
 		assertEquals("Patient", reincarnatedPatient.getIdElement().getResourceType());
 	}
 
-	/**
-	 * See #344
-	 */
-	@Test
-	public void testParserIsCaseSensitive() {
-		Observation obs = new Observation();
-		SampledData data = new SampledData();
-		data.setData("1 2 3");
-		data.setOrigin((SimpleQuantity) new SimpleQuantity().setValue(0L));
-		data.setPeriod(1000L);
-		obs.setValue(data);
-
-		IParser p = ourCtx.newXmlParser().setPrettyPrint(true).setParserErrorHandler(new StrictErrorHandler());
-		String encoded = p.encodeResourceToString(obs);
-		ourLog.info(encoded);
-
-		p.parseResource(encoded);
-
-		try {
-			p.parseResource(encoded.replace("Observation", "observation"));
-			fail();
-		} catch (DataFormatException e) {
-			assertEquals("DataFormatException at [[row,col {unknown-source}]: [1,1]]: Unknown resource type 'observation': Resource names are case sensitive, found similar name: 'Observation'",
-					e.getMessage());
-		}
-
-		try {
-			p.parseResource(encoded.replace("valueSampledData", "valueSampleddata"));
-			fail();
-		} catch (DataFormatException e) {
-			assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Unknown element 'valueSampleddata' found during parse", e.getMessage());
-		}
-	}
-
 	@Test(expected = DataFormatException.class)
 	public void testParseWithInvalidLocalRef() throws IOException {
 		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
@@ -3226,6 +3208,40 @@ public class XmlParserDstu3Test {
 
 	}
 
+	/**
+	 * See #344
+	 */
+	@Test
+	public void testParserIsCaseSensitive() {
+		Observation obs = new Observation();
+		SampledData data = new SampledData();
+		data.setData("1 2 3");
+		data.setOrigin((SimpleQuantity) new SimpleQuantity().setValue(0L));
+		data.setPeriod(1000L);
+		obs.setValue(data);
+
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true).setParserErrorHandler(new StrictErrorHandler());
+		String encoded = p.encodeResourceToString(obs);
+		ourLog.info(encoded);
+
+		p.parseResource(encoded);
+
+		try {
+			p.parseResource(encoded.replace("Observation", "observation"));
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("DataFormatException at [[row,col {unknown-source}]: [1,1]]: Unknown resource type 'observation': Resource names are case sensitive, found similar name: 'Observation'",
+				e.getMessage());
+		}
+
+		try {
+			p.parseResource(encoded.replace("valueSampledData", "valueSampleddata"));
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Unknown element 'valueSampleddata' found during parse", e.getMessage());
+		}
+	}
+
 	/**
 	 * See #551
 	 */
@@ -3245,7 +3261,7 @@ public class XmlParserDstu3Test {
 
 	/**
 	 * See #339
-	 * 
+	 * <p>
 	 * https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
 	 */
 	@Test
@@ -3275,35 +3291,22 @@ public class XmlParserDstu3Test {
 
 	}
 
-	@Test
-	public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
-		String refVal = "http://my.org/FooBar";
-
-		Patient fhirPat = new Patient();
-		fhirPat.addExtension().setUrl("x1").setValue(new Reference(refVal));
-
-		IParser parser = ourCtx.newXmlParser();
-
-		String output = parser.encodeResourceToString(fhirPat);
-		System.out.println("output: " + output);
-
-		// Deserialize then check that valueReference value is still correct
-		fhirPat = parser.parseResource(Patient.class, output);
-
-		List<Extension> extlst = fhirPat.getExtensionsByUrl("x1");
-		Assert.assertEquals(1, extlst.size());
-		Assert.assertEquals(refVal, ((Reference) extlst.get(0).getValue()).getReference());
-	}
-
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
-	public static void main(String[] args) {
+	public static void compareXml(String content, String reEncoded) {
-		IGenericClient c = ourCtx.newRestfulGenericClient("http://fhir-dev.healthintersections.com.au/open");
+		Diff d = DiffBuilder.compare(Input.fromString(content))
-		// c.registerInterceptor(new LoggingInterceptor(true));
+			.withTest(Input.fromString(reEncoded))
-		c.read().resource("Patient").withId("324").execute();
+			.withNodeMatcher(new DefaultNodeMatcher(ElementSelectors.byNameAndText))
+			.checkForSimilar()
+			.ignoreWhitespace() // this is working with newest Saxon 9.8.0-2 (not worked with 9.7.0-15
+			.ignoreComments() // this is not working even with newest Saxon 9.8.0-2
+			.withComparisonController(ComparisonControllers.Default)
+			.build();
+
+		assertTrue(d.toString(), !d.hasDifferences());
 	}
 
 	@ResourceDef(name = "Patient")

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/SearchR4Test.java

@@ -1,32 +1,5 @@
 package ca.uhn.fhir.rest.server;
 
-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.fail;
-
-import java.io.IOException;
-import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.TimeUnit;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.http.client.ClientProtocolException;
-import org.apache.http.client.methods.CloseableHttpResponse;
-import org.apache.http.client.methods.HttpGet;
-import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.impl.client.HttpClientBuilder;
-import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
-import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.servlet.ServletHandler;
-import org.eclipse.jetty.servlet.ServletHolder;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.*;
-import org.junit.*;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.annotation.RequiredParam;
 import ca.uhn.fhir.rest.annotation.Search;
@@ -38,15 +11,46 @@ import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.gclient.StringClientParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.util.*;
+import ca.uhn.fhir.util.PortUtil;
+import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.util.UrlUtil;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.HumanName;
+import org.hl7.fhir.r4.model.OperationOutcome;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.not;
+import static org.junit.Assert.*;
 
 public class SearchR4Test {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchR4Test.class);
 	private static CloseableHttpClient ourClient;
 	private static FhirContext ourCtx = FhirContext.forR4();
 	private static TokenAndListParam ourIdentifiers;
 	private static String ourLastMethod;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchR4Test.class);
 	private static int ourPort;
 
 	private static Server ourServer;
@@ -57,74 +61,63 @@ public class SearchR4Test {
 		ourIdentifiers = null;
 	}
 
-	@Test
+	private Bundle executeAndReturnLinkNext(HttpGet httpGet, EncodingEnum theExpectEncoding) throws IOException, ClientProtocolException {
-	public void testSearchNormal() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar");
 		CloseableHttpResponse status = ourClient.execute(httpGet);
+		Bundle bundle;
 		try {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseContent);
 			assertEquals(200, status.getStatusLine().getStatusCode());
-
+			EncodingEnum ct = EncodingEnum.forContentType(status.getEntity().getContentType().getValue().replaceAll(";.*", "").trim());
-			assertEquals("search", ourLastMethod);
+			assertEquals(theExpectEncoding, ct);
-
+			bundle = ct.newParser(ourCtx).parseResource(Bundle.class, responseContent);
-			assertEquals("foo", ourIdentifiers.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getSystem());
+			assertEquals(10, bundle.getEntry().size());
-			assertEquals("bar", ourIdentifiers.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
+			String linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
+			assertNotNull(linkNext);
 		} finally {
 			IOUtils.closeQuietly(status.getEntity().getContent());
 		}
-
+		return bundle;
 	}
 
 	@Test
-	public void testSearchWithInvalidChain() throws Exception {
+	public void testPagingPreservesElements() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier.chain=foo%7Cbar");
-		CloseableHttpResponse status = ourClient.execute(httpGet);
-		try {
-			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
-			ourLog.info(responseContent);
-			assertEquals(400, status.getStatusLine().getStatusCode());
-
-			OperationOutcome oo = (OperationOutcome) ourCtx.newJsonParser().parseResource(responseContent);
-			assertEquals(
-					"Invalid search parameter \"identifier.chain\". Parameter contains a chain (.chain) and chains are not supported for this parameter (chaining is only allowed on reference parameters)",
-					oo.getIssueFirstRep().getDiagnostics());
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
-		}
-
-	}
-
-	
-	@Test
-	public void testPagingPreservesEncodingJson() throws Exception {
 		HttpGet httpGet;
 		String linkNext;
 		Bundle bundle;
+		String linkSelf;
 
 		// Initial search
-		httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_format=json");
+		httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_elements=name");
 		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
+		assertThat(toJson(bundle), not(containsString("active")));
+		linkSelf = bundle.getLink(Constants.LINK_SELF).getUrl();
+		assertThat(linkSelf, containsString("_elements=name"));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_format=json"));
+		assertThat(linkNext, containsString("_elements=name"));
+
+		ourLog.info(toJson(bundle));
 
 		// Fetch the next page
 		httpGet = new HttpGet(linkNext);
 		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
+		assertThat(toJson(bundle), not(containsString("active")));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_format=json"));
+		assertThat(linkNext, containsString("_elements=name"));
 
 		// Fetch the next page
 		httpGet = new HttpGet(linkNext);
 		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
+		assertThat(toJson(bundle), not(containsString("active")));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_format=json"));
+		assertThat(linkNext, containsString("_elements=name"));
 
 		// Fetch the next page
 		httpGet = new HttpGet(linkNext);
 		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
+		assertThat(toJson(bundle), not(containsString("active")));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_format=json"));
+		assertThat(linkNext, containsString("_elements=name"));
 
 	}
 
@@ -161,34 +154,35 @@ public class SearchR4Test {
 	}
 
 	@Test
-	public void testPagingPreservesEncodingXml() throws Exception {
+	public void testPagingPreservesEncodingJson() throws Exception {
 		HttpGet httpGet;
 		String linkNext;
 		Bundle bundle;
 
 		// Initial search
-		httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_format=xml");
+		httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_format=json");
-		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
+		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
+		assertThat(toJson(bundle), containsString("active"));
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_format=xml"));
+		assertThat(linkNext, containsString("_format=json"));
 
 		// Fetch the next page
 		httpGet = new HttpGet(linkNext);
-		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
+		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_format=xml"));
+		assertThat(linkNext, containsString("_format=json"));
 
 		// Fetch the next page
 		httpGet = new HttpGet(linkNext);
-		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
+		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_format=xml"));
+		assertThat(linkNext, containsString("_format=json"));
 
 		// Fetch the next page
 		httpGet = new HttpGet(linkNext);
-		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
+		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
 		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
-		assertThat(linkNext, containsString("_format=xml"));
+		assertThat(linkNext, containsString("_format=json"));
 
 	}
 
@@ -260,25 +254,75 @@ public class SearchR4Test {
 
 	}
 
-	private Bundle executeAndReturnLinkNext(HttpGet httpGet, EncodingEnum theExpectEncoding) throws IOException, ClientProtocolException {
+	@Test
-		CloseableHttpResponse status = ourClient.execute(httpGet);
+	public void testPagingPreservesEncodingXml() throws Exception {
+		HttpGet httpGet;
+		String linkNext;
 		Bundle bundle;
+
+		// Initial search
+		httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_format=xml");
+		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
+		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
+		assertThat(linkNext, containsString("_format=xml"));
+
+		// Fetch the next page
+		httpGet = new HttpGet(linkNext);
+		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
+		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
+		assertThat(linkNext, containsString("_format=xml"));
+
+		// Fetch the next page
+		httpGet = new HttpGet(linkNext);
+		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
+		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
+		assertThat(linkNext, containsString("_format=xml"));
+
+		// Fetch the next page
+		httpGet = new HttpGet(linkNext);
+		bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
+		linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
+		assertThat(linkNext, containsString("_format=xml"));
+
+	}
+
+	@Test
+	public void testSearchNormal() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar");
+		CloseableHttpResponse status = ourClient.execute(httpGet);
 		try {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(responseContent);
 			assertEquals(200, status.getStatusLine().getStatusCode());
-			EncodingEnum ct = EncodingEnum.forContentType(status.getEntity().getContentType().getValue().replaceAll(";.*", "").trim());
+
-			assertEquals(theExpectEncoding, ct);
+			assertEquals("search", ourLastMethod);
-			bundle = ct.newParser(ourCtx).parseResource(Bundle.class, responseContent);
+
-			assertEquals(10, bundle.getEntry().size());
+			assertEquals("foo", ourIdentifiers.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getSystem());
-			String linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
+			assertEquals("bar", ourIdentifiers.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
-			assertNotNull(linkNext);
 		} finally {
 			IOUtils.closeQuietly(status.getEntity().getContent());
 		}
-		return bundle;
+
 	}
 
+	@Test
+	public void testSearchWithInvalidChain() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier.chain=foo%7Cbar");
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(400, status.getStatusLine().getStatusCode());
+
+			OperationOutcome oo = (OperationOutcome) ourCtx.newJsonParser().parseResource(responseContent);
+			assertEquals(
+				"Invalid search parameter \"identifier.chain\". Parameter contains a chain (.chain) and chains are not supported for this parameter (chaining is only allowed on reference parameters)",
+				oo.getIssueFirstRep().getDiagnostics());
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
 
 	@Test
 	public void testSearchWithPostAndInvalidParameters() throws Exception {
@@ -308,6 +352,10 @@ public class SearchR4Test {
 
 	}
 
+	private String toJson(Bundle theBundle) {
+		return ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(theBundle);
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() throws Exception {
 		ourServer.stop();
@@ -357,8 +405,9 @@ public class SearchR4Test {
 			for (int i = 0; i < 200; i++) {
 				Patient patient = new Patient();
 				patient.addName(new HumanName().setFamily("FAMILY"));
+				patient.setActive(true);
 				patient.getIdElement().setValue("Patient/" + i);
-				retVal.add((Patient) patient);
+				retVal.add(patient);
 			}
 			return retVal;
 		}

pom.xml

@@ -370,6 +370,14 @@
 			<id>malcolmm83</id>
 			<name>Malcolm McRoberts</name>
 		</developer>
+		<developer>
+			<id>mouellet</id>
+			<name>Mathieu Ouellet</name>
+		</developer>
+		<developer>
+			<id>JiajingLiang</id>
+			<name>Jiajing Liang</name>
+		</developer>
 	</developers>
 
 	<licenses>
@@ -403,6 +411,7 @@
 		<phloc_schematron_version>2.7.1</phloc_schematron_version>
 		<phloc_commons_version>4.4.11</phloc_commons_version>
 		<spring_version>5.0.0.RELEASE</spring_version>
+		<spring-boot.version>1.5.6.RELEASE</spring-boot.version>
 		<thymeleaf-version>3.0.7.RELEASE</thymeleaf-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. -->
@@ -970,6 +979,13 @@
 				<artifactId>spring-websocket</artifactId>
 				<version>${spring_version}</version>
 			</dependency>
+			<dependency>
+				<groupId>org.springframework.boot</groupId>
+				<artifactId>spring-boot-dependencies</artifactId>
+				<version>${spring-boot.version}</version>
+				<type>pom</type>
+				<scope>import</scope>
+			</dependency>
 			<dependency>
 				<groupId>org.thymeleaf</groupId>
 				<artifactId>thymeleaf</artifactId>
@@ -1032,7 +1048,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.6.2</version>
+					<version>3.7.0</version>
 					<configuration>
 						<source>1.7</source>
 						<target>1.7</target>
@@ -1045,6 +1061,10 @@
 						<testTarget>1.8</testTarget>
 						<forceJavacCompilerUse>true</forceJavacCompilerUse>
 						<encoding>UTF-8</encoding>
+
+						<fork>true</fork>
+						<meminitial>128m</meminitial>
+						<maxmem>1600m</maxmem>
 					</configuration>
 					<dependencies>
 						<dependency>
@@ -1880,6 +1900,7 @@
 				<module>example-projects/hapi-fhir-standalone-overlay-example</module>
 				<module>hapi-fhir-jacoco</module>
 				<module>hapi-fhir-igpacks</module>
+				<module>hapi-fhir-spring-boot</module>
 				<!--<module>hapi-fhir-osgi-core</module>-->
 			</modules>
 		</profile>

src/changes/changes.xml

@@ -154,7 +154,7 @@
 				JAX-RS client framework now supports the ability to
 				register your own JAX-RS Component Classes against the client,
 				as well as better documentation about thread safety. Thanks
-				to Sébastien Rivière for the pull request!
+				to Sébastien Rivière for the pull request!
 			</action>
 			<action type="fix" issue="717">
 				Processing of the If-Modified-Since header on FHIR read operations was reversed,
@@ -175,11 +175,43 @@
 				was not encoded correctly. Thanks to Malcolm McRoberts for the pull
 				request with fix and test case!
 			</action>
+			<action type="add">
+				Bundle resources did not have their version encoded when serializing
+				in FHIR resource (XML/JSON) format.
+			</action>
 			<action type="add">
 				The Binary resource endpoint now supports the `X-Security-Context` header when
 				reading or writing Binary contents using their native Content-Type (i.e exchanging
 				the raw binary with the server, as opposed to exchanging a FHIR resource).
 			</action>
+			<action type="fix">
+				When paging through multiple pages of search results, if the 
+				client had requested a subset of resources to be returned using the
+				<![CDATA[<code>_elements</code>]]> parameter, the elements list
+				was lost after the first page of results.
+				In addition, elements will not remove elements from
+				search/history Bundles (i.e. elements from the Bundle itself, as opposed
+				to elements in the entry resources) unless the Bundle elements are
+				explicitly listed, e.g. <![CDATA[<code>_include=Bundle.total</code>]]>.
+				Thanks to @parisni for reporting!
+			</action>
+			<action type="add" issue="743">
+				Add support for Spring Boot for initializing a number of parts of the library,
+				as well as several examples.
+				Thanks to Mathieu Ouellet for the contribution!
+			</action>
+			<action type="add" issue="747">
+				JPA server now has lucene index support moved to separate classes from the entity
+				classes in order to facilitate support for ElasticSearch. Thanks to Jiang Liang
+				for the pull request!
+			</action>
+			<action type="add" issue="755">
+				A new client interceptor has been added called
+				AdditionalRequestHeadersInterceptor, which allows 
+				a developer to add additional custom headers to a 
+				client requests.
+				Thanks to Clayton Bodendein for the pull request!
+			</action>
 		</release>
 		<release version="3.0.0" date="2017-09-27">
 			<action type="add">
@@ -545,7 +577,7 @@ Bundle bundle = client.search().forResource(Patient.class)
 			<action type="fix" issue="686">
 				Correct an issue in the validator (DSTU3/R4) where elements were not always
 				correctly validated if the element contained only a profiled extension. Thanks
-				to Sébastien Rivière for the pull request!
+				to Sébastien Rivière for the pull request!
 			</action>
 			<action type="add" issue="701">
 				Testing UI now has a dropdown for modifiers on token search. Thanks 
@@ -559,7 +591,7 @@ Bundle bundle = client.search().forResource(Patient.class)
 			</action>
 			<action type="fix" issue="695">
 				Extensions on ID datatypes were not parsed or serialized correctly. Thanks to
-				Stephen Rivière for the pull request!
+				Stephen Rivière for the pull request!
 			</action>
 			<action type="fix" issue="710">
 				Fix a bug in REST Hook Subscription interceptors which prevented subscriptions
@@ -880,7 +912,7 @@ Bundle bundle = client.search().forResource(Patient.class)
 			<action type="add">
 				DaoConfig#setAllowInlineMatchUrlReferences() now defaults to
 				<![CDATA[<code>true</code>]]> since inline conditional references
-				are now a part of the FHIR specification. Thanks to Jan Dědek for
+				are now a part of the FHIR specification. Thanks to Jan Dědek for
 				pointing this out!
 			</action>
 			<action type="add" issue="609">
@@ -1860,7 +1892,7 @@ Bundle bundle = client.search().forResource(Patient.class)
 			</action>
 			<action type="fix" issue="426">
 				Parser failed to parse resources containing an extension with a value type of
-				"id". Thanks to Raphael Mäder for reporting!  
+				"id". Thanks to Raphael Mäder for reporting!  
 			</action>
 			<action type="fix">
 				When committing a transaction in JPA server
@@ -2122,7 +2154,7 @@ Bundle bundle = client.search().forResource(Patient.class)
 				array instead of a string. Thanks to David Hay for reporting! 
 			</action>
 			<action type="add" issue="367">
-				Sébastien Rivière contributed an excellent pull request which adds a 
+				Sébastien Rivière contributed an excellent pull request which adds a 
 				number of enhancements to JAX-RS module:
 				<![CDATA[
 				<ul>