Merge branch 'master' into 963_jpa_performance

.travis.yml

@@ -4,10 +4,11 @@
 
 # Use VM based build environment
 sudo: required
+dist: trusty
 
 language: java
 jdk:
-  - oraclejdk8
+  - oraclejdk9
 env:
   global:
     - MAVEN_OPTS="-Xmx1024m"
@@ -25,5 +26,4 @@ before_script:
 script:
 #  - mvn -e -B clean install && cd hapi-fhir-ra && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID clean test jacoco:report coveralls:report
 #  - mvn -Dci=true -e -B -P ALLMODULES,NOPARALLEL,ERRORPRONE clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report 
-  - mvn -Dci=true -e -B -P ALLMODULES,REDUCED_JPA_TESTS,ERRORPRONE_JDK8,JACOCO clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report 
-
+  - mvn -Dci=true -e -B -P ALLMODULES,REDUCED_JPA_TESTS,ERRORPRONE,JACOCO clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report

README.md

@@ -1,21 +1,19 @@
-hapi-fhir
+HAPI FHIR
 =========
 
 HAPI FHIR - Java API for HL7 FHIR Clients and Servers
 
 [![Coverage Status](https://coveralls.io/repos/jamesagnew/hapi-fhir/badge.svg?branch=master&service=github)](https://coveralls.io/github/jamesagnew/hapi-fhir?branch=master)
 [![Maven Central](https://maven-badges.herokuapp.com/maven-central/ca.uhn.hapi.fhir/hapi-fhir-base/badge.svg)](http://search.maven.org/#search|ga|1|ca.uhn.hapi.fhir)
-[![Dependency Status](https://www.versioneye.com/user/projects/55e1d0d9c6d8f2001c00043e/badge.svg?style=flat)](https://www.versioneye.com/user/projects/55e1d0d9c6d8f2001c00043e)
 [![License](https://img.shields.io/badge/license-apache%202.0-60C060.svg)](http://jamesagnew.github.io/hapi-fhir/license.html)
 
 * Linux Build: [![Build Status](https://travis-ci.org/jamesagnew/hapi-fhir.svg?branch=master)](https://travis-ci.org/jamesagnew/hapi-fhir)
 * Windows Build: <a href="https://ci.appveyor.com/project/jamesagnew/hapi-fhir"><img src="https://ci.appveyor.com/api/projects/status/github/jamesagnew/hapi-fhir?branch=master&svg=true"></a>
 
-
 Complete project documentation is available here:
 http://jamesagnew.github.io/hapi-fhir/
 
 A demonstration of this project is available here:
-http://fhirtest.uhn.ca/
+http://hapi.fhir.org/
 
 This project is Open Source, licensed under the Apache Software License 2.0.

appveyor.yml

@@ -4,4 +4,6 @@ cache:
   - C:\maven\
   - C:\Users\appveyor\.m2\repository
 build_script:
-   - cmd: mvn -P MINPARALLEL,ALLMODULES clean install
+  - SET JAVA_HOME=C:\Program Files\Java\jdk10
+  - SET PATH=C:\Program Files\Java\jdk10\bin;%PATH%
+  - cmd: mvn -P MINPARALLEL,ALLMODULES,REDUCED_JPA_TESTS clean install

example-projects/hapi-fhir-base-example-embedded-ws/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 

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

@@ -10,7 +10,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 

example-projects/hapi-fhir-jpaserver-cds-example/src/test/java/ca/uhn/fhir/jpa/cds/example/CdsExampleTests.java

@@ -14,6 +14,7 @@ import org.junit.AfterClass;
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.junit.Ignore;
 
 import java.io.*;
 import java.net.HttpURLConnection;
@@ -188,7 +189,8 @@ public class CdsExampleTests {
 		Assert.assertTrue(procedureRequest.getDoNotPerform());
 	}
 
-	//@Test
+	@Test
+	@Ignore
 	public void CdsHooksPatientViewTest() throws IOException {
 		putResource("cds-bcs-library.json", "patient-view");
 		putResource("cds-bcs-patient.json", "Patient-6532");

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

@@ -10,7 +10,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 	   <relativePath>../../pom.xml</relativePath>
 	</parent>
 

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

@@ -10,7 +10,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>2.1-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 	
@@ -26,28 +26,28 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-base</artifactId>
-			<version>2.1-SNAPSHOT</version>
+			<version>${project.version}</version>
 		</dependency>
 
 		<!-- This dependency includes the JPA server itself, which is packaged separately from the rest of HAPI FHIR -->
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-base</artifactId>
-			<version>2.1-SNAPSHOT</version>
+			<version>${project.version}</version>
 		</dependency>
 
 		<!-- This dependency is used for the "FHIR Tester" web app overlay -->
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-testpage-overlay</artifactId>
-			<version>2.1-SNAPSHOT</version>
+			<version>${project.version}</version>
 			<type>war</type>
 			<scope>provided</scope>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-testpage-overlay</artifactId>
-			<version>2.1-SNAPSHOT</version>
+			<version>${project.version}</version>
 			<classifier>classes</classifier>
 			<scope>provided</scope>
 		</dependency>

example-projects/hapi-fhir-jpaserver-example-postgres/readme.intellij.txt

@@ -1,6 +1,8 @@
 Running hapi-fhir-jpaserver-example in Tomcat from IntelliJ
 
 Install Tomcat.
+Install mvn
+run `mvn clean install`
 
 Make sure you have Tomcat set up in IntelliJ.
 File->Settings->Build, Execution, Deployment->Application Servers
@@ -26,6 +28,6 @@ Select your server, and click the green triangle (or the bug if you want to debu
 Wait for the console output to stop
 
 Point your browser (or fiddler, or what have you) to 
-http://localhost:8080/hapi/base/Patient
+http://localhost:8080/hapi/baseDstu3/Patient
 
 You should get an empty bundle back.

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

@@ -21,6 +21,7 @@ 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;
+import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 
 /**
  * This class isn't used by default by the example, but 
@@ -84,7 +85,7 @@ 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.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");

example-projects/hapi-fhir-jpaserver-example-postgres/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java

@@ -18,7 +18,7 @@ import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.server.ETagSupportEnum;
-import ca.uhn.fhir.rest.server.EncodingEnum;
+import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;

example-projects/hapi-fhir-standalone-overlay-example/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 	<artifactId>hapi-fhir-standalone-overlay-example</artifactId>

examples/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -96,6 +96,7 @@
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-simple</artifactId>
+			<version>${slf4j_version}</version>
 		</dependency>
 
 	</dependencies>

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-android/src/test/java/ca/uhn/fhir/android/BuiltJarDstu2IT.java

@@ -72,6 +72,7 @@ public class BuiltJarDstu2IT {
 	 * android uses) and see if this passes
 	 */
 	@SuppressWarnings("deprecation")
+	@Test
 	public void testClient() {
 		FhirContext ctx = FhirContext.forDstu2();
 		try {

hapi-fhir-android/src/test/java/ca/uhn/fhir/android/client/GenericClientDstu3IT.java

@@ -190,7 +190,7 @@ public class GenericClientDstu3IT {
 	@Test
 	public void testClientFailures() throws Exception {
 		ResponseBody body = mock(ResponseBody.class);
-		when(body.source()).thenThrow(IllegalStateException.class, RuntimeException.class, Exception.class);
+		when(body.source()).thenThrow(IllegalStateException.class, RuntimeException.class);
 		
 		myHttpResponse = new Response.Builder()
 				.request(myRequest)
@@ -216,12 +216,6 @@ public class GenericClientDstu3IT {
 			assertEquals("java.lang.RuntimeException", e.toString());
 		}
 
-		try {
-			client.read().resource(Patient.class).withId("1").execute();
-			fail();
-		} catch (FhirClientConnectionException e) {
-			assertEquals("java.lang.Exception", e.getMessage());
-		}
 	}
 
 

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeResourceDefinition.java

@@ -185,14 +185,29 @@ public class RuntimeResourceDefinition extends BaseRuntimeElementCompositeDefini
 		});
 		mySearchParams = Collections.unmodifiableList(searchParams);
 
-		Map<String, List<RuntimeSearchParam>> compartmentNameToSearchParams = new HashMap<String, List<RuntimeSearchParam>>();
+		Map<String, List<RuntimeSearchParam>> compartmentNameToSearchParams = new HashMap<>();
 		for (RuntimeSearchParam next : searchParams) {
 			if (next.getProvidesMembershipInCompartments() != null) {
 				for (String nextCompartment : next.getProvidesMembershipInCompartments()) {
 					if (!compartmentNameToSearchParams.containsKey(nextCompartment)) {
-						compartmentNameToSearchParams.put(nextCompartment, new ArrayList<RuntimeSearchParam>());
+						compartmentNameToSearchParams.put(nextCompartment, new ArrayList<>());
+					}
+					List<RuntimeSearchParam> searchParamsForCompartment = compartmentNameToSearchParams.get(nextCompartment);
+					searchParamsForCompartment.add(next);
+
+					/*
+					 * If one search parameter marks an SP as making a resource
+					 * a part of a compartment, let's also denote all other
+					 * SPs with the same path the same way. This behaviour is
+					 * used by AuthorizationInterceptor
+					 */
+					for (RuntimeSearchParam nextAlternate : searchParams) {
+						if (nextAlternate.getPath().equals(next.getPath())) {
+							if (!nextAlternate.getName().equals(next.getName())) {
+								searchParamsForCompartment.add(nextAlternate);
+							}
+						}
 					}
-					compartmentNameToSearchParams.get(nextCompartment).add(next);
 				}
 			}
 		}

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeSearchParam.java

@@ -5,6 +5,10 @@ import static org.apache.commons.lang3.StringUtils.trim;
 
 import java.util.*;
 
+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.hl7.fhir.instance.model.api.IIdType;
 
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
@@ -38,6 +42,18 @@ public class RuntimeSearchParam {
 	private final RestSearchParameterTypeEnum myParamType;
 	private final String myPath;
 	private final Set<String> myTargets;
+
+	@Override
+	public String toString() {
+		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
+			.append("base", myBase)
+			.append("name", myName)
+			.append("path", myPath)
+			.append("id", myId)
+			.append("uri", myUri)
+			.toString();
+	}
+
 	private final Set<String> myProvidesMembershipInCompartments;
 	private final RuntimeSearchParamStatusEnum myStatus;
 	private final String myUri;
@@ -55,9 +71,36 @@ public class RuntimeSearchParam {
 		this(theId, theUri, theName, theDescription, thePath, theParamType, theCompositeOf, theProvidesMembershipInCompartments, theTargets, theStatus, null);
 	}
 
+	@Override
+	public boolean equals(Object theO) {
+		if (this == theO) return true;
+
+		if (theO == null || getClass() != theO.getClass()) return false;
+
+		RuntimeSearchParam that = (RuntimeSearchParam) theO;
+
+		return new EqualsBuilder()
+			.append(getId(), that.getId())
+			.append(getName(), that.getName())
+			.append(getPath(), that.getPath())
+			.append(getUri(), that.getUri())
+			.isEquals();
+	}
+
+	@Override
+	public int hashCode() {
+		return new HashCodeBuilder(17, 37)
+			.append(getId())
+			.append(getName())
+			.append(getPath())
+			.append(getUri())
+			.toHashCode();
+	}
+
 	public RuntimeSearchParam(IIdType theId, String theUri, String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, List<RuntimeSearchParam> theCompositeOf,
-			Set<String> theProvidesMembershipInCompartments, Set<String> theTargets, RuntimeSearchParamStatusEnum theStatus, Collection<String> theBase) {
+									  Set<String> theProvidesMembershipInCompartments, Set<String> theTargets, RuntimeSearchParamStatusEnum theStatus, Collection<String> theBase) {
 		super();
+
 		myId = theId;
 		myUri = theUri;
 		myName = theName;

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

@@ -274,6 +274,7 @@ public class Constants {
 		corsAllowedHeaders.add("Content-Type");
 		corsAllowedHeaders.add("Origin");
 		corsAllowedHeaders.add("Prefer");
+		corsAllowedHeaders.add("X-FHIR-Starter");
 		corsAllowedHeaders.add("X-Requested-With");
 		CORS_ALLOWED_HEADERS = Collections.unmodifiableSet(corsAllowedHeaders);
 

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

@@ -1757,8 +1757,8 @@ public class XmlUtil {
 
 	private static void throwUnitTestExceptionIfConfiguredToDoSo() throws FactoryConfigurationError, XMLStreamException {
 		if (ourNextException != null) {
-			if (ourNextException instanceof FactoryConfigurationError) {
-				throw ((FactoryConfigurationError)ourNextException);
+			if (ourNextException instanceof javax.xml.stream.FactoryConfigurationError) {
+				throw ((javax.xml.stream.FactoryConfigurationError)ourNextException);
 			}
 			throw (XMLStreamException)ourNextException;
 		}

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -166,13 +166,22 @@
 			<artifactId>thymeleaf-spring4</artifactId>
 		</dependency>
 
+		<!-- Dependencies for Schematron -->
 		<dependency>
 			<groupId>com.helger</groupId>
 			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
-					<artifactId>Saxon-HE</artifactId>
-					<groupId>net.sf.saxon</groupId>
+					<groupId>org.glassfish.jaxb</groupId>
+					<artifactId>jaxb-runtime</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.glassfish.jaxb</groupId>
+					<artifactId>jaxb-core</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>com.sun.istack</groupId>
+					<artifactId>istack-commons-runtime</artifactId>
 				</exclusion>
 			</exclusions>
 		</dependency>
@@ -180,18 +189,17 @@
 			<groupId>com.helger</groupId>
 			<artifactId>ph-commons</artifactId>
 		</dependency>
-
-		<!--
-		These have been added as explicit dependencies
-		as JDK9 no longer includes them by default
-		-->
 		<dependency>
 			<groupId>javax.xml.bind</groupId>
 			<artifactId>jaxb-api</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.glassfish.jaxb</groupId>
-			<artifactId>jaxb-runtime</artifactId>
+			<groupId>com.sun.xml.bind</groupId>
+			<artifactId>jaxb-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.sun.xml.bind</groupId>
+			<artifactId>jaxb-impl</artifactId>
 		</dependency>
 
 

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ExportConceptMapToCsvCommand.java

@@ -23,23 +23,23 @@ package ca.uhn.fhir.cli;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVPrinter;
 import org.apache.commons.csv.QuoteMode;
-import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.convertors.VersionConvertor_30_40;
+import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
 import org.hl7.fhir.r4.model.ConceptMap.SourceElementComponent;
 
-import java.io.BufferedWriter;
 import java.io.IOException;
 import java.io.Writer;
 import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.ExecutionException;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 
@@ -72,11 +72,11 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
 	}
 
 	@Override
-	protected void process() throws ParseException {
+	protected void process() throws ExecutionException {
 		searchForConceptMapByUrl();
 	}
 
-	private void searchForConceptMapByUrl() {
+	private void searchForConceptMapByUrl() throws ExecutionException {
 		ourLog.info("Searching for ConceptMap with specified URL (i.e. ConceptMap.url): {}", conceptMapUrl);
 		if (fhirVersion == FhirVersionEnum.DSTU3) {
 			org.hl7.fhir.dstu3.model.Bundle response = client
@@ -111,61 +111,26 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
 		}
 	}
 
-	private void convertConceptMapToCsv(org.hl7.fhir.dstu3.model.ConceptMap theConceptMap) {
-		ourLog.info("Exporting ConceptMap to CSV...");
-		BufferedWriter bufferedWriter = null;
-		CSVPrinter csvPrinter = null;
+	private void convertConceptMapToCsv(org.hl7.fhir.dstu3.model.ConceptMap theConceptMap) throws ExecutionException {
 		try {
-			bufferedWriter = Files.newBufferedWriter(Paths.get(file));
-			csvPrinter = new CSVPrinter(
-				bufferedWriter,
-				CSVFormat
-					.DEFAULT
-					.withRecordSeparator("\n")
-					.withHeader(Header.class));
-
-			for (org.hl7.fhir.dstu3.model.ConceptMap.ConceptMapGroupComponent group : theConceptMap.getGroup()) {
-				for (org.hl7.fhir.dstu3.model.ConceptMap.SourceElementComponent element : group.getElement()) {
-					for (org.hl7.fhir.dstu3.model.ConceptMap.TargetElementComponent target : element.getTarget()) {
-
-						List<String> columns = new ArrayList<>();
-						columns.add(defaultString(group.getSource()));
-						columns.add(defaultString(group.getSourceVersion()));
-						columns.add(defaultString(group.getTarget()));
-						columns.add(defaultString(group.getTargetVersion()));
-						columns.add(defaultString(element.getCode()));
-						columns.add(defaultString(element.getDisplay()));
-						columns.add(defaultString(target.getCode()));
-						columns.add(defaultString(target.getDisplay()));
-						columns.add(defaultString(target.getEquivalence().toCode()));
-						columns.add(defaultString(target.getComment()));
-
-						csvPrinter.print(columns);
-					}
-				}
-			}
-		} catch (IOException ioe) {
-			throw new InternalErrorException(ioe);
-		} finally {
-			IOUtils.closeQuietly(csvPrinter);
-			IOUtils.closeQuietly(bufferedWriter);
+			convertConceptMapToCsv(VersionConvertor_30_40.convertConceptMap(theConceptMap));
+		} catch (FHIRException fe) {
+			throw new ExecutionException(fe);
 		}
-		ourLog.info("Finished exporting to {}", file);
 	}
 
 	private void convertConceptMapToCsv(ConceptMap theConceptMap) {
 		ourLog.info("Exporting ConceptMap to CSV...");
-		Writer writer = null;
-		CSVPrinter csvPrinter = null;
-		try {
-			writer = Files.newBufferedWriter(Paths.get(file));
-			csvPrinter = new CSVPrinter(
+		try (
+			Writer writer = Files.newBufferedWriter(Paths.get(file));
+			CSVPrinter csvPrinter = new CSVPrinter(
 				writer,
 				CSVFormat
 					.DEFAULT
 					.withRecordSeparator("\n")
-					.withHeader(Header.class).withQuoteMode(QuoteMode.ALL));
-
+					.withHeader(Header.class)
+					.withQuoteMode(QuoteMode.ALL));
+		) {
 			for (ConceptMapGroupComponent group : theConceptMap.getGroup()) {
 				for (SourceElementComponent element : group.getElement()) {
 					for (ConceptMap.TargetElementComponent target : element.getTarget()) {
@@ -188,10 +153,8 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
 			}
 		} catch (IOException ioe) {
 			throw new InternalErrorException(ioe);
-		} finally {
-			IOUtils.closeQuietly(csvPrinter);
-			IOUtils.closeQuietly(writer);
 		}
+
 		ourLog.info("Finished exporting to {}", file);
 	}
 }

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommand.java

@@ -25,11 +25,9 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVParser;
 import org.apache.commons.csv.CSVRecord;
-import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.model.ConceptMap;
@@ -43,7 +41,10 @@ import java.io.IOException;
 import java.io.Reader;
 import java.nio.file.Files;
 import java.nio.file.Paths;
-import java.util.*;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.Map;
+import java.util.Set;
 import java.util.concurrent.ExecutionException;
 
 import static org.apache.commons.lang3.StringUtils.*;
@@ -96,7 +97,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 	}
 
 	@Override
-	protected void parseAdditionalParameters(CommandLine theCommandLine) throws ParseException {
+	protected void parseAdditionalParameters(CommandLine theCommandLine) {
 		sourceValueSet = theCommandLine.getOptionValue(SOURCE_VALUE_SET_PARAM);
 		if (isBlank(sourceValueSet)) {
 			ourLog.info("Source value set is not specified (i.e. ConceptMap.sourceUri).");
@@ -113,11 +114,11 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 	}
 
 	@Override
-	protected void process() throws ParseException, ExecutionException {
+	protected void process() throws ExecutionException {
 		searchForConceptMapByUrl();
 	}
 
-	private void searchForConceptMapByUrl() throws ParseException, ExecutionException {
+	private void searchForConceptMapByUrl() throws ExecutionException {
 		if (fhirVersion == FhirVersionEnum.DSTU3) {
 			org.hl7.fhir.dstu3.model.ConceptMap conceptMap = convertCsvToConceptMapDstu3();
 
@@ -153,7 +154,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 		}
 	}
 
-	private org.hl7.fhir.dstu3.model.ConceptMap convertCsvToConceptMapDstu3() throws ParseException, ExecutionException {
+	private org.hl7.fhir.dstu3.model.ConceptMap convertCsvToConceptMapDstu3() throws ExecutionException {
 		try {
 			return VersionConvertor_30_40.convertConceptMap(convertCsvToConceptMapR4());
 		} catch (FHIRException fe) {
@@ -161,14 +162,12 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 		}
 	}
 
-	private ConceptMap convertCsvToConceptMapR4() throws ParseException, ExecutionException {
+	private ConceptMap convertCsvToConceptMapR4() throws ExecutionException {
 		ourLog.info("Converting CSV to ConceptMap...");
 		ConceptMap retVal = new ConceptMap();
-		Reader reader = null;
-		CSVParser csvParser = null;
-		try {
-			reader = Files.newBufferedReader(Paths.get(file));
-			csvParser = new CSVParser(
+		try (
+			Reader reader = Files.newBufferedReader(Paths.get(file));
+			CSVParser csvParser = new CSVParser(
 				reader,
 				CSVFormat
 					.DEFAULT
@@ -178,7 +177,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 					.withIgnoreHeaderCase()
 					.withIgnoreEmptyLines()
 					.withTrim());
-
+		) {
 			retVal.setUrl(conceptMapUrl);
 
 			if (isNotBlank(sourceValueSet)) {
@@ -278,9 +277,6 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 			}
 		} catch (IOException e) {
 			throw new InternalErrorException(e);
-		} finally {
-			IOUtils.closeQuietly(csvParser);
-			IOUtils.closeQuietly(reader);
 		}
 
 		ourLog.info("Finished converting CSV to ConceptMap.");

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ExportConceptMapToCsvCommandDstu3Test.java

@@ -0,0 +1,283 @@
+package ca.uhn.fhir.cli;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.interceptor.VerboseLoggingInterceptor;
+import ca.uhn.fhir.util.PortUtil;
+import ca.uhn.fhir.util.TestUtil;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.dstu3.model.ConceptMap;
+import org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence;
+import org.hl7.fhir.dstu3.model.UriType;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+
+import static org.junit.Assert.assertEquals;
+
+public class ExportConceptMapToCsvCommandDstu3Test {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExportConceptMapToCsvCommandDstu3Test.class);
+	private static final String CM_URL = "http://example.com/conceptmap";
+	private static final String VS_URL_1 = "http://example.com/valueset/1";
+	private static final String VS_URL_2 = "http://example.com/valueset/2";
+	private static final String CS_URL_1 = "http://example.com/codesystem/1";
+	private static final String CS_URL_2 = "http://example.com/codesystem/2";
+	private static final String CS_URL_3 = "http://example.com/codesystem/3";
+	private static final String FILE = "./target/output.csv";
+
+	private static String ourBase;
+	private static IGenericClient ourClient;
+	private static FhirContext ourCtx = FhirContext.forDstu3();
+	private static int ourPort;
+	private static Server ourServer;
+	private static String ourVersion = "dstu3";
+
+	static {
+		System.setProperty("test", "true");
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		ServletHandler servletHandler = new ServletHandler();
+
+		RestfulServer restfulServer = new RestfulServer(ourCtx);
+		restfulServer.registerInterceptor(new VerboseLoggingInterceptor());
+		restfulServer.setResourceProviders(new HashMapResourceProviderConceptMapDstu3(ourCtx));
+
+		ServletHolder servletHolder = new ServletHolder(restfulServer);
+		servletHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(servletHandler);
+
+		ourServer.start();
+
+		ourBase = "http://localhost:" + ourPort;
+
+		ourClient = ourCtx.newRestfulGenericClient(ourBase);
+
+		ourClient.create().resource(createConceptMap()).execute();
+	}
+
+	@Test
+	public void testExportConceptMapToCsvCommand() throws IOException {
+		ourLog.info("ConceptMap:\n" + ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createConceptMap()));
+
+		App.main(new String[] {"export-conceptmap-to-csv",
+			"-v", ourVersion,
+			"-t", ourBase,
+			"-u", CM_URL,
+			"-f", FILE,
+			"-l"});
+
+		String expected = "\"SOURCE_CODE_SYSTEM\",\"SOURCE_CODE_SYSTEM_VERSION\",\"TARGET_CODE_SYSTEM\",\"TARGET_CODE_SYSTEM_VERSION\",\"SOURCE_CODE\",\"SOURCE_DISPLAY\",\"TARGET_CODE\",\"TARGET_DISPLAY\",\"EQUIVALENCE\",\"COMMENT\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1a\",\"Display 1a\",\"Code 2a\",\"Display 2a\",\"equal\",\"2a This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1b\",\"Display 1b\",\"Code 2b\",\"Display 2b\",\"equal\",\"2b This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1c\",\"Display 1c\",\"Code 2c\",\"Display 2c\",\"equal\",\"2c This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1d\",\"Display 1d\",\"Code 2d\",\"Display 2d\",\"equal\",\"2d This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1a\",\"Display 1a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1b\",\"Display 1b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1c\",\"Display 1c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
+			"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1d\",\"Display 1d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2a\",\"Display 2a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2b\",\"Display 2b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2c\",\"Display 2c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
+			"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2d\",\"Display 2d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n";
+		String result = IOUtils.toString(new FileInputStream(FILE), Charsets.UTF_8);
+		assertEquals(expected, result);
+
+		FileUtils.deleteQuietly(new File(FILE));
+	}
+
+	static ConceptMap createConceptMap() {
+		ConceptMap conceptMap = new ConceptMap();
+		conceptMap
+			.setUrl(CM_URL)
+			.setSource(new UriType(VS_URL_1))
+			.setTarget(new UriType(VS_URL_2));
+
+		ConceptMap.ConceptMapGroupComponent group = conceptMap.addGroup();
+		group
+			.setSource(CS_URL_1)
+			.setSourceVersion("Version 1s")
+			.setTarget(CS_URL_2)
+			.setTargetVersion("Version 2t");
+
+		ConceptMap.SourceElementComponent element = group.addElement();
+		element
+			.setCode("Code 1a")
+			.setDisplay("Display 1a");
+
+		ConceptMap.TargetElementComponent target = element.addTarget();
+		target
+			.setCode("Code 2a")
+			.setDisplay("Display 2a")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("2a This is a comment.");
+
+		element = group.addElement();
+		element
+			.setCode("Code 1b")
+			.setDisplay("Display 1b");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 2b")
+			.setDisplay("Display 2b")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("2b This is a comment.");
+
+		element = group.addElement();
+		element
+			.setCode("Code 1c")
+			.setDisplay("Display 1c");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 2c")
+			.setDisplay("Display 2c")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("2c This is a comment.");
+
+		element = group.addElement();
+		element
+			.setCode("Code 1d")
+			.setDisplay("Display 1d");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 2d")
+			.setDisplay("Display 2d")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("2d This is a comment.");
+
+		group = conceptMap.addGroup();
+		group
+			.setSource(CS_URL_1)
+			.setSourceVersion("Version 1s")
+			.setTarget(CS_URL_3)
+			.setTargetVersion("Version 3t");
+
+		element = group.addElement();
+		element
+			.setCode("Code 1a")
+			.setDisplay("Display 1a");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 3a")
+			.setDisplay("Display 3a")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("3a This is a comment.");
+
+		element = group.addElement();
+		element
+			.setCode("Code 1b")
+			.setDisplay("Display 1b");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 3b")
+			.setDisplay("Display 3b")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("3b This is a comment.");
+
+		element = group.addElement();
+		element
+			.setCode("Code 1c")
+			.setDisplay("Display 1c");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 3c")
+			.setDisplay("Display 3c")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("3c This is a comment.");
+
+		element = group.addElement();
+		element
+			.setCode("Code 1d")
+			.setDisplay("Display 1d");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 3d")
+			.setDisplay("Display 3d")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("3d This is a comment.");
+
+		group = conceptMap.addGroup();
+		group
+			.setSource(CS_URL_2)
+			.setSourceVersion("Version 2s")
+			.setTarget(CS_URL_3)
+			.setTargetVersion("Version 3t");
+
+		element = group.addElement();
+		element
+			.setCode("Code 2a")
+			.setDisplay("Display 2a");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 3a")
+			.setDisplay("Display 3a")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("3a This is a comment.");
+
+		element = group.addElement();
+		element
+			.setCode("Code 2b")
+			.setDisplay("Display 2b");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 3b")
+			.setDisplay("Display 3b")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("3b This is a comment.");
+
+		element = group.addElement();
+		element
+			.setCode("Code 2c")
+			.setDisplay("Display 2c");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 3c")
+			.setDisplay("Display 3c")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("3c This is a comment.");
+
+		element = group.addElement();
+		element
+			.setCode("Code 2d")
+			.setDisplay("Display 2d");
+
+		target = element.addTarget();
+		target
+			.setCode("Code 3d")
+			.setDisplay("Display 3d")
+			.setEquivalence(ConceptMapEquivalence.EQUAL)
+			.setComment("3d This is a comment.");
+
+		return conceptMap;
+	}
+}

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ExportConceptMapToCsvCommandR4Test.java

@@ -25,8 +25,8 @@ import java.io.IOException;
 
 import static org.junit.Assert.assertEquals;
 
-public class ExportConceptMapToCsvCommandTest {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExportConceptMapToCsvCommandTest.class);
+public class ExportConceptMapToCsvCommandR4Test {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExportConceptMapToCsvCommandR4Test.class);
 	private static final String CM_URL = "http://example.com/conceptmap";
 	private static final String VS_URL_1 = "http://example.com/valueset/1";
 	private static final String VS_URL_2 = "http://example.com/valueset/2";
@@ -40,6 +40,7 @@ public class ExportConceptMapToCsvCommandTest {
 	private static FhirContext ourCtx = FhirContext.forR4();
 	private static int ourPort;
 	private static Server ourServer;
+	private static String ourVersion = "r4";
 
 	static {
 		System.setProperty("test", "true");
@@ -80,7 +81,7 @@ public class ExportConceptMapToCsvCommandTest {
 		ourLog.info("ConceptMap:\n" + ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createConceptMap()));
 
 		App.main(new String[] {"export-conceptmap-to-csv",
-			"-v", "r4",
+			"-v", ourVersion,
 			"-t", ourBase,
 			"-u", CM_URL,
 			"-f", FILE,

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HashMapResourceProviderConceptMapDstu3.java

@@ -0,0 +1,127 @@
+package ca.uhn.fhir.cli;
+
+/*-
+ * #%L
+ * HAPI FHIR - Server Framework
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.provider.AbstractHashMapResourceProvider;
+import com.google.common.base.Charsets;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.utils.URLEncodedUtils;
+import org.hl7.fhir.dstu3.model.ConceptMap;
+import org.hl7.fhir.dstu3.model.IdType;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.TreeMap;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+/**
+ * This is a subclass to implement FHIR operations specific to DSTU3 ConceptMap
+ * resources. Its superclass, {@link AbstractHashMapResourceProvider}, is a simple
+ * implementation of the resource provider interface that uses a HashMap to
+ * store all resources in memory.
+ * <p>
+ * This subclass currently supports the following FHIR operations:
+ * </p>
+ * <ul>
+ * <li>Search for DSTU3 ConceptMap resources by ConceptMap.url</li>
+ * <li>Conditional update for DSTU3 ConceptMap resources by ConceptMap.url</li>
+ * </ul>
+ */
+public class HashMapResourceProviderConceptMapDstu3 extends AbstractHashMapResourceProvider<ConceptMap> {
+	@SuppressWarnings("unchecked")
+	public HashMapResourceProviderConceptMapDstu3(FhirContext theFhirContext) {
+		super(theFhirContext, ConceptMap.class);
+
+		FhirVersionEnum fhirVersion = theFhirContext.getVersion().getVersion();
+		if (fhirVersion != FhirVersionEnum.DSTU3) {
+			throw new IllegalStateException("Requires FHIR version DSTU3. Unsupported FHIR version provided: " + fhirVersion);
+		}
+
+
+	}
+
+	@Search
+	public List<ConceptMap> searchByUrl(
+		@RequiredParam(name=ConceptMap.SP_URL) String theConceptMapUrl) {
+
+		List<ConceptMap> retVal = new ArrayList<>();
+
+		for (TreeMap<Long, ConceptMap> next : myIdToVersionToResourceMap.values()) {
+			if (!next.isEmpty()) {
+				ConceptMap conceptMap = next.lastEntry().getValue();
+				if (theConceptMapUrl.equals(conceptMap.getUrl()))
+				retVal.add(conceptMap);
+				break;
+			}
+		}
+
+		return retVal;
+	}
+
+	@Update
+	public MethodOutcome updateConceptMapConditional(
+		@ResourceParam ConceptMap theConceptMap,
+		@IdParam IdType theId,
+		@ConditionalUrlParam String theConditional) {
+
+		MethodOutcome methodOutcome = new MethodOutcome();
+
+		if (theConditional != null) {
+
+			String url = null;
+
+			try {
+				List<NameValuePair> params = URLEncodedUtils.parse(new URI(theConditional), Charsets.UTF_8);
+				for (NameValuePair param : params) {
+					if (param.getName().equalsIgnoreCase("url")) {
+						url = param.getValue();
+						break;
+					}
+				}
+			} catch (URISyntaxException urise) {
+				throw new InvalidRequestException(urise);
+			}
+
+			if (isNotBlank(url)) {
+				List<ConceptMap> conceptMaps = searchByUrl(url);
+
+				if (!conceptMaps.isEmpty()) {
+					methodOutcome = update(conceptMaps.get(0));
+				} else {
+					methodOutcome = create(theConceptMap);
+				}
+			}
+
+		} else {
+			methodOutcome = update(theConceptMap);
+		}
+
+		return methodOutcome;
+	}
+}

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommandDstu3Test.java

@@ -0,0 +1,367 @@
+package ca.uhn.fhir.cli;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.interceptor.VerboseLoggingInterceptor;
+import ca.uhn.fhir.util.PortUtil;
+import ca.uhn.fhir.util.TestUtil;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.ConceptMap;
+import org.hl7.fhir.dstu3.model.ConceptMap.ConceptMapGroupComponent;
+import org.hl7.fhir.dstu3.model.ConceptMap.SourceElementComponent;
+import org.hl7.fhir.dstu3.model.ConceptMap.TargetElementComponent;
+import org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import java.io.File;
+
+import static org.junit.Assert.*;
+
+public class ImportCsvToConceptMapCommandDstu3Test {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ImportCsvToConceptMapCommandDstu3Test.class);
+	private static final String CM_URL = "http://example.com/conceptmap";
+	private static final String VS_URL_1 = "http://example.com/valueset/1";
+	private static final String VS_URL_2 = "http://example.com/valueset/2";
+	private static final String CS_URL_1 = "http://example.com/codesystem/1";
+	private static final String CS_URL_2 = "http://example.com/codesystem/2";
+	private static final String CS_URL_3 = "http://example.com/codesystem/3";
+	private static final String FILENAME = "import-csv-to-conceptmap-command-test-input.csv";
+
+	private static String file;
+	private static String ourBase;
+	private static IGenericClient ourClient;
+	private static FhirContext ourCtx = FhirContext.forDstu3();
+	private static int ourPort;
+	private static Server ourServer;
+	private static String ourVersion = "dstu3";
+
+	private static RestfulServer restfulServer;
+
+	private static HashMapResourceProviderConceptMapDstu3 hashMapResourceProviderConceptMapDstu3;
+
+	static {
+		System.setProperty("test", "true");
+	}
+
+	@After
+	public void afterClearResourceProvider() {
+		HashMapResourceProviderConceptMapDstu3 resourceProvider = (HashMapResourceProviderConceptMapDstu3) restfulServer.getResourceProviders().iterator().next();
+		resourceProvider.clear();
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		ServletHandler servletHandler = new ServletHandler();
+
+		restfulServer = new RestfulServer(ourCtx);
+		restfulServer.registerInterceptor(new VerboseLoggingInterceptor());
+		restfulServer.setResourceProviders(new HashMapResourceProviderConceptMapDstu3(ourCtx));
+
+		ServletHolder servletHolder = new ServletHolder(restfulServer);
+		servletHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(servletHandler);
+
+		ourServer.start();
+
+		ourBase = "http://localhost:" + ourPort;
+
+		ourClient = ourCtx.newRestfulGenericClient(ourBase);
+	}
+
+	@Test
+	public void testConditionalUpdateResultsInCreate() {
+		ConceptMap conceptMap = ExportConceptMapToCsvCommandDstu3Test.createConceptMap();
+		String conceptMapUrl = conceptMap.getUrl();
+
+		ourLog.info("Searching for existing ConceptMap with specified URL (i.e. ConceptMap.url): {}", conceptMapUrl);
+		MethodOutcome methodOutcome = ourClient
+			.update()
+			.resource(conceptMap)
+			.conditional()
+			.where(ConceptMap.URL.matches().value(conceptMapUrl))
+			.execute();
+
+		assertEquals(Boolean.TRUE, methodOutcome.getCreated());
+	}
+
+	@Test
+	public void testConditionalUpdateResultsInUpdate() {
+		ConceptMap conceptMap = ExportConceptMapToCsvCommandDstu3Test.createConceptMap();
+		ourClient.create().resource(conceptMap).execute();
+		String conceptMapUrl = conceptMap.getUrl();
+
+		ourLog.info("Searching for existing ConceptMap with specified URL (i.e. ConceptMap.url): {}", conceptMapUrl);
+		MethodOutcome methodOutcome = ourClient
+			.update()
+			.resource(conceptMap)
+			.conditional()
+			.where(ConceptMap.URL.matches().value(conceptMapUrl))
+			.execute();
+
+		assertNull(methodOutcome.getCreated());
+	}
+
+	@Test
+	public void testNonConditionalUpdate() {
+		ConceptMap conceptMap = ExportConceptMapToCsvCommandDstu3Test.createConceptMap();
+		ourClient.create().resource(conceptMap).execute();
+
+		Bundle response = ourClient
+			.search()
+			.forResource(ConceptMap.class)
+			.where(ConceptMap.URL.matches().value(CM_URL))
+			.returnBundle(Bundle.class)
+			.execute();
+
+		ConceptMap resultConceptMap = (ConceptMap) response.getEntryFirstRep().getResource();
+
+		MethodOutcome methodOutcome = ourClient
+			.update()
+			.resource(resultConceptMap)
+			.withId(resultConceptMap.getIdElement())
+			.execute();
+
+		assertNull(methodOutcome.getCreated());
+	}
+
+	@Test
+	public void testImportCsvToConceptMapCommand() throws FHIRException {
+		ClassLoader classLoader = getClass().getClassLoader();
+		File fileToImport = new File(classLoader.getResource(FILENAME).getFile());
+		ImportCsvToConceptMapCommandDstu3Test.file = fileToImport.getAbsolutePath();
+
+		App.main(new String[] {"import-csv-to-conceptmap",
+			"-v", ourVersion,
+			"-t", ourBase,
+			"-u", CM_URL,
+			"-i", VS_URL_1,
+			"-o", VS_URL_2,
+			"-f", file,
+			"-l"});
+
+		Bundle response = ourClient
+			.search()
+			.forResource(ConceptMap.class)
+			.where(ConceptMap.URL.matches().value(CM_URL))
+			.returnBundle(Bundle.class)
+			.execute();
+
+		ConceptMap conceptMap = (ConceptMap) response.getEntryFirstRep().getResource();
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
+
+		assertEquals("http://localhost:" + ourPort + "/ConceptMap/1/_history/1", conceptMap.getId());
+
+		assertEquals(CM_URL, conceptMap.getUrl());
+		assertEquals(VS_URL_1, conceptMap.getSourceUriType().getValueAsString());
+		assertEquals(VS_URL_2, conceptMap.getTargetUriType().getValueAsString());
+
+		assertEquals(3, conceptMap.getGroup().size());
+
+		ConceptMapGroupComponent group = conceptMap.getGroup().get(0);
+		assertEquals(CS_URL_1, group.getSource());
+		assertEquals("Version 1s", group.getSourceVersion());
+		assertEquals(CS_URL_2, group.getTarget());
+		assertEquals("Version 2t", group.getTargetVersion());
+
+		assertEquals(4, group.getElement().size());
+
+		SourceElementComponent source = group.getElement().get(0);
+		assertEquals("Code 1a", source.getCode());
+		assertEquals("Display 1a", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		TargetElementComponent target = source.getTarget().get(0);
+		assertEquals("Code 2a", target.getCode());
+		assertEquals("Display 2a", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("2a This is a comment.", target.getComment());
+
+		source = group.getElement().get(1);
+		assertEquals("Code 1b", source.getCode());
+		assertEquals("Display 1b", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 2b", target.getCode());
+		assertEquals("Display 2b", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("2b This is a comment.", target.getComment());
+
+		source = group.getElement().get(2);
+		assertEquals("Code 1c", source.getCode());
+		assertEquals("Display 1c", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 2c", target.getCode());
+		assertEquals("Display 2c", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("2c This is a comment.", target.getComment());
+
+		source = group.getElement().get(3);
+		assertEquals("Code 1d", source.getCode());
+		assertEquals("Display 1d", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 2d", target.getCode());
+		assertEquals("Display 2d", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("2d This is a comment.", target.getComment());
+
+		group = conceptMap.getGroup().get(1);
+		assertEquals(CS_URL_1, group.getSource());
+		assertEquals("Version 1s", group.getSourceVersion());
+		assertEquals(CS_URL_3, group.getTarget());
+		assertEquals("Version 3t", group.getTargetVersion());
+
+		assertEquals(4, group.getElement().size());
+
+		source = group.getElement().get(0);
+		assertEquals("Code 1a", source.getCode());
+		assertEquals("Display 1a", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 3a", target.getCode());
+		assertEquals("Display 3a", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("3a This is a comment.", target.getComment());
+
+		source = group.getElement().get(1);
+		assertEquals("Code 1b", source.getCode());
+		assertEquals("Display 1b", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 3b", target.getCode());
+		assertEquals("Display 3b", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("3b This is a comment.", target.getComment());
+
+		source = group.getElement().get(2);
+		assertEquals("Code 1c", source.getCode());
+		assertEquals("Display 1c", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 3c", target.getCode());
+		assertEquals("Display 3c", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("3c This is a comment.", target.getComment());
+
+		source = group.getElement().get(3);
+		assertEquals("Code 1d", source.getCode());
+		assertEquals("Display 1d", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 3d", target.getCode());
+		assertEquals("Display 3d", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("3d This is a comment.", target.getComment());
+
+		group = conceptMap.getGroup().get(2);
+		assertEquals(CS_URL_2, group.getSource());
+		assertEquals("Version 2s", group.getSourceVersion());
+		assertEquals(CS_URL_3, group.getTarget());
+		assertEquals("Version 3t", group.getTargetVersion());
+
+		assertEquals(4, group.getElement().size());
+
+		source = group.getElement().get(0);
+		assertEquals("Code 2a", source.getCode());
+		assertEquals("Display 2a", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 3a", target.getCode());
+		assertEquals("Display 3a", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("3a This is a comment.", target.getComment());
+
+		source = group.getElement().get(1);
+		assertEquals("Code 2b", source.getCode());
+		assertEquals("Display 2b", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 3b", target.getCode());
+		assertEquals("Display 3b", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("3b This is a comment.", target.getComment());
+
+		source = group.getElement().get(2);
+		assertEquals("Code 2c", source.getCode());
+		assertEquals("Display 2c", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 3c", target.getCode());
+		assertEquals("Display 3c", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("3c This is a comment.", target.getComment());
+
+		source = group.getElement().get(3);
+		assertEquals("Code 2d", source.getCode());
+		assertEquals("Display 2d", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		target = source.getTarget().get(0);
+		assertEquals("Code 3d", target.getCode());
+		assertEquals("Display 3d", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
+		assertEquals("3d This is a comment.", target.getComment());
+
+		App.main(new String[] {"import-csv-to-conceptmap",
+			"-v", ourVersion,
+			"-t", ourBase,
+			"-u", CM_URL,
+			"-i", VS_URL_1,
+			"-o", VS_URL_2,
+			"-f", file,
+			"-l"});
+
+		response = ourClient
+			.search()
+			.forResource(ConceptMap.class)
+			.where(ConceptMap.URL.matches().value(CM_URL))
+			.returnBundle(Bundle.class)
+			.execute();
+
+		conceptMap = (ConceptMap) response.getEntryFirstRep().getResource();
+
+		assertEquals("http://localhost:" + ourPort + "/ConceptMap/1/_history/2", conceptMap.getId());
+	}
+}

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommandR4Test.java

@@ -10,13 +10,13 @@ import ca.uhn.fhir.util.TestUtil;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
-import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
 import org.hl7.fhir.r4.model.ConceptMap.SourceElementComponent;
 import org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent;
 import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
+import org.hl7.fhir.exceptions.FHIRException;
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
@@ -26,8 +26,8 @@ import java.io.File;
 
 import static org.junit.Assert.*;
 
-public class ImportCsvToConceptMapCommandTest {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ImportCsvToConceptMapCommandTest.class);
+public class ImportCsvToConceptMapCommandR4Test {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ImportCsvToConceptMapCommandR4Test.class);
 	private static final String CM_URL = "http://example.com/conceptmap";
 	private static final String VS_URL_1 = "http://example.com/valueset/1";
 	private static final String VS_URL_2 = "http://example.com/valueset/2";
@@ -42,6 +42,7 @@ public class ImportCsvToConceptMapCommandTest {
 	private static FhirContext ourCtx = FhirContext.forR4();
 	private static int ourPort;
 	private static Server ourServer;
+	private static String ourVersion = "r4";
 
 	private static RestfulServer restfulServer;
 
@@ -87,7 +88,7 @@ public class ImportCsvToConceptMapCommandTest {
 
 	@Test
 	public void testConditionalUpdateResultsInCreate() {
-		ConceptMap conceptMap = ExportConceptMapToCsvCommandTest.createConceptMap();
+		ConceptMap conceptMap = ExportConceptMapToCsvCommandR4Test.createConceptMap();
 		String conceptMapUrl = conceptMap.getUrl();
 
 		ourLog.info("Searching for existing ConceptMap with specified URL (i.e. ConceptMap.url): {}", conceptMapUrl);
@@ -104,7 +105,7 @@ public class ImportCsvToConceptMapCommandTest {
 
 	@Test
 	public void testConditionalUpdateResultsInUpdate() {
-		ConceptMap conceptMap = ExportConceptMapToCsvCommandTest.createConceptMap();
+		ConceptMap conceptMap = ExportConceptMapToCsvCommandR4Test.createConceptMap();
 		ourClient.create().resource(conceptMap).execute();
 		String conceptMapUrl = conceptMap.getUrl();
 
@@ -122,7 +123,7 @@ public class ImportCsvToConceptMapCommandTest {
 
 	@Test
 	public void testNonConditionalUpdate() {
-		ConceptMap conceptMap = ExportConceptMapToCsvCommandTest.createConceptMap();
+		ConceptMap conceptMap = ExportConceptMapToCsvCommandR4Test.createConceptMap();
 		ourClient.create().resource(conceptMap).execute();
 
 		Bundle response = ourClient
@@ -150,10 +151,10 @@ public class ImportCsvToConceptMapCommandTest {
 	public void testImportCsvToConceptMapCommand() throws FHIRException {
 		ClassLoader classLoader = getClass().getClassLoader();
 		File fileToImport = new File(classLoader.getResource(FILENAME).getFile());
-		ImportCsvToConceptMapCommandTest.file = fileToImport.getAbsolutePath();
+		ImportCsvToConceptMapCommandR4Test.file = fileToImport.getAbsolutePath();
 
 		App.main(new String[] {"import-csv-to-conceptmap",
-			"-v", "r4",
+			"-v", ourVersion,
 			"-t", ourBase,
 			"-u", CM_URL,
 			"-i", VS_URL_1,
@@ -349,7 +350,7 @@ public class ImportCsvToConceptMapCommandTest {
 		assertEquals("3d This is a comment.", target.getComment());
 
 		App.main(new String[] {"import-csv-to-conceptmap",
-			"-v", "r4",
+			"-v", ourVersion,
 			"-t", ourBase,
 			"-u", CM_URL,
 			"-i", VS_URL_1,

hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/import-csv-to-conceptmap-command-test-input.csv

@@ -1,13 +1,13 @@
-SOURCE_CODE_SYSTEM,SOURCE_CODE_SYSTEM_VERSION,TARGET_CODE_SYSTEM,TARGET_CODE_SYSTEM_VERSION,SOURCE_CODE,SOURCE_DISPLAY,TARGET_CODE,TARGET_DISPLAY,EQUIVALENCE,COMMENT
-http://example.com/codesystem/1,Version 1s,http://example.com/codesystem/2,Version 2t,Code 1a,Display 1a,Code 2a,Display 2a,equal,2a This is a comment.
-http://example.com/codesystem/1,Version 1s,http://example.com/codesystem/2,Version 2t,Code 1b,Display 1b,Code 2b,Display 2b,equal,2b This is a comment.
-http://example.com/codesystem/1,Version 1s,http://example.com/codesystem/2,Version 2t,Code 1c,Display 1c,Code 2c,Display 2c,equal,2c This is a comment.
-http://example.com/codesystem/1,Version 1s,http://example.com/codesystem/2,Version 2t,Code 1d,Display 1d,Code 2d,Display 2d,equal,2d This is a comment.
-http://example.com/codesystem/1,Version 1s,http://example.com/codesystem/3,Version 3t,Code 1a,Display 1a,Code 3a,Display 3a,equal,3a This is a comment.
-http://example.com/codesystem/1,Version 1s,http://example.com/codesystem/3,Version 3t,Code 1b,Display 1b,Code 3b,Display 3b,equal,3b This is a comment.
-http://example.com/codesystem/1,Version 1s,http://example.com/codesystem/3,Version 3t,Code 1c,Display 1c,Code 3c,Display 3c,equal,3c This is a comment.
-http://example.com/codesystem/1,Version 1s,http://example.com/codesystem/3,Version 3t,Code 1d,Display 1d,Code 3d,Display 3d,equal,3d This is a comment.
-http://example.com/codesystem/2,Version 2s,http://example.com/codesystem/3,Version 3t,Code 2a,Display 2a,Code 3a,Display 3a,equal,3a This is a comment.
-http://example.com/codesystem/2,Version 2s,http://example.com/codesystem/3,Version 3t,Code 2b,Display 2b,Code 3b,Display 3b,equal,3b This is a comment.
-http://example.com/codesystem/2,Version 2s,http://example.com/codesystem/3,Version 3t,Code 2c,Display 2c,Code 3c,Display 3c,equal,3c This is a comment.
-http://example.com/codesystem/2,Version 2s,http://example.com/codesystem/3,Version 3t,Code 2d,Display 2d,Code 3d,Display 3d,equal,3d This is a comment.
+"SOURCE_CODE_SYSTEM","SOURCE_CODE_SYSTEM_VERSION","TARGET_CODE_SYSTEM","TARGET_CODE_SYSTEM_VERSION","SOURCE_CODE","SOURCE_DISPLAY","TARGET_CODE","TARGET_DISPLAY","EQUIVALENCE","COMMENT"
+"http://example.com/codesystem/1","Version 1s","http://example.com/codesystem/2","Version 2t","Code 1a","Display 1a","Code 2a","Display 2a","equal","2a This is a comment."
+"http://example.com/codesystem/1","Version 1s","http://example.com/codesystem/2","Version 2t","Code 1b","Display 1b","Code 2b","Display 2b","equal","2b This is a comment."
+"http://example.com/codesystem/1","Version 1s","http://example.com/codesystem/2","Version 2t","Code 1c","Display 1c","Code 2c","Display 2c","equal","2c This is a comment."
+"http://example.com/codesystem/1","Version 1s","http://example.com/codesystem/2","Version 2t","Code 1d","Display 1d","Code 2d","Display 2d","equal","2d This is a comment."
+"http://example.com/codesystem/1","Version 1s","http://example.com/codesystem/3","Version 3t","Code 1a","Display 1a","Code 3a","Display 3a","equal","3a This is a comment."
+"http://example.com/codesystem/1","Version 1s","http://example.com/codesystem/3","Version 3t","Code 1b","Display 1b","Code 3b","Display 3b","equal","3b This is a comment."
+"http://example.com/codesystem/1","Version 1s","http://example.com/codesystem/3","Version 3t","Code 1c","Display 1c","Code 3c","Display 3c","equal","3c This is a comment."
+"http://example.com/codesystem/1","Version 1s","http://example.com/codesystem/3","Version 3t","Code 1d","Display 1d","Code 3d","Display 3d","equal","3d This is a comment."
+"http://example.com/codesystem/2","Version 2s","http://example.com/codesystem/3","Version 3t","Code 2a","Display 2a","Code 3a","Display 3a","equal","3a This is a comment."
+"http://example.com/codesystem/2","Version 2s","http://example.com/codesystem/3","Version 3t","Code 2b","Display 2b","Code 3b","Display 3b","equal","3b This is a comment."
+"http://example.com/codesystem/2","Version 2s","http://example.com/codesystem/3","Version 3t","Code 2c","Display 2c","Code 3c","Display 3c","equal","3c This is a comment."
+"http://example.com/codesystem/2","Version 2s","http://example.com/codesystem/3","Version 3t","Code 2d","Display 2d","Code 3d","Display 3d","equal","3d This is a comment."

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -80,23 +80,13 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>org.glassfish.jersey.core</groupId>
-			<artifactId>jersey-server</artifactId>
+			<groupId>org.jboss.resteasy</groupId>
+			<artifactId>resteasy-jaxrs</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>org.glassfish.jersey.containers</groupId>
-			<artifactId>jersey-container-servlet-core</artifactId>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.glassfish.jersey.containers</groupId>
-			<artifactId>jersey-container-jetty-http</artifactId>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.glassfish.jersey.media</groupId>
-			<artifactId>jersey-media-moxy</artifactId>
+			<groupId>org.jboss.resteasy</groupId>
+			<artifactId>resteasy-client</artifactId>
 			<scope>test</scope>
 		</dependency>
 

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -107,6 +107,9 @@ public class LoggingInterceptor implements IClientInterceptor {
 			 * Add response location
 			 */
 			List<String> locationHeaders = theResponse.getHeaders(Constants.HEADER_LOCATION);
+			if (locationHeaders == null || locationHeaders.isEmpty()) {
+				locationHeaders = theResponse.getHeaders(Constants.HEADER_CONTENT_LOCATION);
+			}
 			if (locationHeaders != null && locationHeaders.size() > 0) {
 				String locationValue = locationHeaders.get(0);
 				IdDt locationValueId = new IdDt(locationValue);

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -16,14 +16,14 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-base</artifactId>
-			<version>3.4.0-SNAPSHOT</version>
+			<version>3.5.0-SNAPSHOT</version>
 		</dependency>
 
 		<!-- Server -->
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-server</artifactId>
-			<version>3.4.0-SNAPSHOT</version>
+			<version>3.5.0-SNAPSHOT</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
@@ -35,43 +35,43 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2</artifactId>
-			<version>3.4.0-SNAPSHOT</version>
+			<version>3.5.0-SNAPSHOT</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
-			<version>3.4.0-SNAPSHOT</version>
+			<version>3.5.0-SNAPSHOT</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
-			<version>3.4.0-SNAPSHOT</version>
+			<version>3.5.0-SNAPSHOT</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu3</artifactId>
-			<version>3.4.0-SNAPSHOT</version>
+			<version>3.5.0-SNAPSHOT</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-r4</artifactId>
-			<version>3.4.0-SNAPSHOT</version>
+			<version>3.5.0-SNAPSHOT</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
-			<version>3.4.0-SNAPSHOT</version>
+			<version>3.5.0-SNAPSHOT</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
-			<version>3.4.0-SNAPSHOT</version>
+			<version>3.5.0-SNAPSHOT</version>
 			<optional>true</optional>
 		</dependency>
 

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-igpacks/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<artifactId>hapi-deployable-pom</artifactId>
 		<groupId>ca.uhn.hapi.fhir</groupId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -77,6 +77,21 @@
 			<version>${project.version}</version>
 		</dependency>
 
+      <dependency>
+         <groupId>javax.mail</groupId>
+         <artifactId>javax.mail-api</artifactId>
+      </dependency>
+      <dependency>
+         <groupId>com.sun.mail</groupId>
+         <artifactId>javax.mail</artifactId>
+         <exclusions>
+            <exclusion>
+               <groupId>javax.activation</groupId>
+               <artifactId>activation</artifactId>
+            </exclusion>
+         </exclusions>
+      </dependency>
+
 		<dependency>
 			<groupId>com.helger</groupId>
 			<artifactId>ph-schematron</artifactId>
@@ -330,6 +345,13 @@
 						<sourceDirectory>../hapi-fhir-client-okhttp/src/main/java</sourceDirectory>
 					</sourceDirectories>
 				</configuration>
+				<dependencies>
+					<dependency>
+						<groupId>javax.xml.bind</groupId>
+						<artifactId>jaxb-api</artifactId>
+						<version>2.3.0</version>
+					</dependency>
+				</dependencies>
 			</plugin>
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -88,6 +88,11 @@
 			<scope>provided</scope>
 		</dependency>
 
+		<dependency>
+			<groupId>javax.annotation</groupId>
+			<artifactId>javax.annotation-api</artifactId>
+		</dependency>
+
 		<!-- Unit test dependencies -->
       <dependency>
          <groupId>org.codehaus.woodstox</groupId>
@@ -109,6 +114,20 @@
 			<artifactId>jetty-servlet</artifactId>
 			<scope>test</scope>
 		</dependency>
+
+
+		<dependency>
+			<groupId>org.jboss.resteasy</groupId>
+			<artifactId>resteasy-jaxrs</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.jboss.resteasy</groupId>
+			<artifactId>resteasy-client</artifactId>
+			<scope>test</scope>
+		</dependency>
+
+		<!--
 		<dependency>
 			<groupId>org.glassfish.jersey.core</groupId>
 			<artifactId>jersey-server</artifactId>
@@ -129,6 +148,8 @@
 			<artifactId>jersey-media-moxy</artifactId>
 			<scope>test</scope>
 		</dependency>
+		-->
+
 		<dependency>
 			<groupId>ch.qos.logback</groupId>
 			<artifactId>logback-classic</artifactId>

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsConformanceProvider.java

@@ -69,6 +69,7 @@ public abstract class AbstractJaxRsConformanceProvider extends AbstractJaxRsProv
 	private org.hl7.fhir.dstu2016may.model.Conformance myDstu2_1Conformance;
 	private org.hl7.fhir.instance.model.Conformance myDstu2Hl7OrgConformance;
 	private ca.uhn.fhir.model.dstu2.resource.Conformance myDstu2Conformance;
+	private boolean myInitialized;
 
 	/**
 	 * Constructor allowing the description, servername and server to be set
@@ -112,7 +113,11 @@ public abstract class AbstractJaxRsConformanceProvider extends AbstractJaxRsProv
 	 * conformance
 	 */
 	@PostConstruct
-	protected void setUpPostConstruct() {
+	protected synchronized void setUpPostConstruct() {
+		if (myInitialized) {
+			return;
+		}
+
 		for (Entry<Class<? extends IResourceProvider>, IResourceProvider> provider : getProviders().entrySet()) {
 			addProvider(provider.getValue(), provider.getKey());
 		}
@@ -155,6 +160,8 @@ public abstract class AbstractJaxRsConformanceProvider extends AbstractJaxRsProv
 			default:
 				throw new ConfigurationException("Unsupported Fhir version: " + fhirContextVersion);
 		}
+
+		myInitialized = true;
 	}
 
 	/**
@@ -184,6 +191,8 @@ public abstract class AbstractJaxRsConformanceProvider extends AbstractJaxRsProv
 	@GET
 	@Path("/metadata")
 	public Response conformance() throws IOException {
+		setUpPostConstruct();
+
 		Builder request = getRequest(RequestTypeEnum.OPTIONS, RestOperationTypeEnum.METADATA);
 		IRestfulResponse response = request.build().getResponse();
 		response.addHeader(Constants.HEADER_CORS_ALLOW_ORIGIN, "*");

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsResourceProvider.java

@@ -47,8 +47,8 @@ import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
  * a large amount of the fhir api functionality using JAXRS
  * @author Peter Van Houte | peter.vanhoute@agfa.com | Agfa Healthcare
  */
-@Produces({ MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML, MediaType.TEXT_PLAIN })
-@Consumes({ MediaType.APPLICATION_FORM_URLENCODED, MediaType.APPLICATION_JSON, Constants.CT_FHIR_JSON, Constants.CT_FHIR_XML, Constants.CT_FHIR_JSON_NEW, Constants.CT_FHIR_XML_NEW })
+@Produces({ MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML, MediaType.TEXT_PLAIN, Constants.CT_FHIR_JSON, Constants.CT_FHIR_XML })
+@Consumes({ MediaType.APPLICATION_FORM_URLENCODED, MediaType.APPLICATION_JSON, Constants.CT_FHIR_JSON, Constants.CT_FHIR_XML, Constants.CT_FHIR_JSON_NEW, Constants.CT_FHIR_XML_NEW, "application/octet-stream" })
 @Interceptors(JaxRsExceptionInterceptor.class)
 public abstract class AbstractJaxRsResourceProvider<R extends IBaseResource> extends AbstractJaxRsProvider
 

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/util/JaxRsMethodBindings.java

@@ -118,7 +118,7 @@ public class JaxRsMethodBindings {
      */
     public BaseMethodBinding<?> getBinding(RestOperationTypeEnum operationType, String theBindingKey) {
         String bindingKey = StringUtils.defaultIfBlank(theBindingKey, DEFAULT_METHOD_KEY);
-		ConcurrentHashMap<String, BaseMethodBinding<?>> map = operationBindings.get(operationType);
+		ConcurrentHashMap<String, BaseMethodBinding<?>> map = getMapForOperation(operationType);
         if(map == null || !map.containsKey(bindingKey)) {
             throw new NotImplementedOperationException("Operation not implemented");
         }  else {

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/GenericJaxRsClientDstu2Test.java

@@ -6,6 +6,7 @@ import static org.junit.Assert.*;
 import java.io.IOException;
 import java.util.*;
 
+import javax.annotation.Priority;
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
@@ -81,7 +82,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testAcceptHeaderFetchConformance() throws Exception {
+	public void testAcceptHeaderFetchConformance() {
 		IParser p = ourCtx.newXmlParser();
 
 		Conformance conf = new Conformance();
@@ -115,7 +116,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testAcceptHeaderPreflightConformance() throws Exception {
+	public void testAcceptHeaderPreflightConformance() {
 		final IParser p = ourCtx.newXmlParser();
 
 		final Conformance conf = new Conformance();
@@ -145,7 +146,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testAcceptHeaderPreflightConformancePreferJson() throws Exception {
+	public void testAcceptHeaderPreflightConformancePreferJson() {
 		final IParser p = ourCtx.newXmlParser();
 
 		final Conformance conf = new Conformance();
@@ -175,7 +176,7 @@ public class GenericJaxRsClientDstu2Test {
 
 	@Test
 	@SuppressWarnings("deprecation")
-	public void testConformance() throws Exception {
+	public void testConformance() {
 		IParser p = ourCtx.newXmlParser();
 
 		Conformance conf = new Conformance();
@@ -198,7 +199,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testProviderWhereWeForgotToSetTheContext() throws Exception {		
+	public void testProviderWhereWeForgotToSetTheContext() {
 		JaxRsRestfulClientFactory clientFactory = new JaxRsRestfulClientFactory(); // no ctx
 		clientFactory.setServerValidationMode(ServerValidationModeEnum.NEVER);
 		
@@ -214,7 +215,7 @@ public class GenericJaxRsClientDstu2Test {
 	
 	
 	@Test
-	public void testCreate() throws Exception {		
+	public void testCreate() {
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/fhir");
 
 		
@@ -246,7 +247,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testCreateConditional() throws Exception {
+	public void testCreateConditional() {
 		
 		
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
@@ -290,7 +291,7 @@ public class GenericJaxRsClientDstu2Test {
 
 
 	@Test
-	public void testCreatePrefer() throws Exception {
+	public void testCreatePrefer() {
 		
 		
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
@@ -315,7 +316,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testCreateReturningResourceBody() throws Exception {
+	public void testCreateReturningResourceBody() {
 		Patient p = new Patient();
 		p.setId("123");
 		final String formatted = ourCtx.newXmlParser().encodeResourceToString(p);
@@ -338,7 +339,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testDeleteConditional() throws Exception {
+	public void testDeleteConditional() {
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
 
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/fhir");
@@ -363,7 +364,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testDelete() throws Exception {
+	public void testDelete() {
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
 		
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/fhir");
@@ -377,7 +378,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testHistory() throws Exception {
+	public void testHistory() {
 
 		final String msg = getPatientFeedWithOneResult();
 		
@@ -474,7 +475,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testMetaAdd() throws Exception {
+	public void testMetaAdd() {
 		IParser p = ourCtx.newXmlParser();
 
 		MetaDt inMeta = new MetaDt().addProfile("urn:profile:in");
@@ -507,7 +508,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testMetaGet() throws Exception {
+	public void testMetaGet() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters inParams = new Parameters();
@@ -563,7 +564,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testOperationAsGetWithInParameters() throws Exception {
+	public void testOperationAsGetWithInParameters() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters inParams = new Parameters();
@@ -642,7 +643,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testOperationAsGetWithNoInParameters() throws Exception {
+	public void testOperationAsGetWithNoInParameters() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters outParams = new Parameters();
@@ -713,7 +714,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testOperationWithBundleResponseJson() throws Exception {
+	public void testOperationWithBundleResponseJson() {
 
 		ourResponseContentType = Constants.CT_FHIR_JSON;
 		final String respString = "{\n" + "    \"resourceType\":\"Bundle\",\n" + "    \"id\":\"8cef5f2a-0ba9-43a5-be26-c8dde9ff0e19\",\n" + "    \"base\":\"http://localhost:" + ourPort + "/fhir\"\n" + "}";
@@ -743,7 +744,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testOperationWithBundleResponseXml() throws Exception {
+	public void testOperationWithBundleResponseXml() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters inParams = new Parameters();
@@ -780,7 +781,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testOperationWithInlineParams() throws Exception {
+	public void testOperationWithInlineParams() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters outParams = new Parameters();
@@ -899,7 +900,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testOperationWithProfiledDatatypeParam() throws IOException, Exception {
+	public void testOperationWithProfiledDatatypeParam() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters outParams = new Parameters();
@@ -948,7 +949,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testOperationWithListOfParameterResponse() throws Exception {
+	public void testOperationWithListOfParameterResponse() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters inParams = new Parameters();
@@ -1023,7 +1024,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testOperationWithNoInParameters() throws Exception {
+	public void testOperationWithNoInParameters() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters inParams = new Parameters();
@@ -1102,7 +1103,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testPageNext() throws Exception {
+	public void testPageNext() {
 		
 		ourResponseContentType = Constants.CT_FHIR_XML + "; charset=UTF-8";
 		ourResponseBody = getPatientFeedWithOneResult();
@@ -1129,7 +1130,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testPageNextNoLink() throws Exception {
+	public void testPageNextNoLink() {
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/fhir");
 
 		ca.uhn.fhir.model.dstu2.resource.Bundle sourceBundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
@@ -1141,7 +1142,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testPagePrev() throws Exception {
+	public void testPagePrev() {
 		
 		
 		
@@ -1187,7 +1188,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testReadByUri() throws Exception {
+	public void testReadByUri() {
 
 		Patient patient = new Patient();
 		patient.addName().addFamily("FAM");
@@ -1207,7 +1208,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testReadFluentByUri() throws Exception {
+	public void testReadFluentByUri() {
 
 		Patient patient = new Patient();
 		patient.addName().addFamily("FAM");
@@ -1220,13 +1221,13 @@ public class GenericJaxRsClientDstu2Test {
 
 		Patient response;
 
-		response = (Patient) client.read().resource(Patient.class).withUrl(new IdDt("http://localhost:" + ourPort + "/AAA/Patient/123")).execute();
+		response = client.read().resource(Patient.class).withUrl(new IdDt("http://localhost:" + ourPort + "/AAA/Patient/123")).execute();
 		assertEquals("http://localhost:" + ourPort + "/AAA/Patient/123", ourRequestUri);
 		assertEquals("FAM", response.getName().get(0).getFamily().get(0).getValue());
 	}
 
 	@Test
-	public void testReadUpdatedHeaderDoesntOverwriteResourceValue() throws Exception {
+	public void testReadUpdatedHeaderDoesntOverwriteResourceValue() {
 
 		
 		final String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" + 
@@ -1264,7 +1265,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testReadWithElementsParam() throws Exception {
+	public void testReadWithElementsParam() {
 		String msg = "{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}";
 
 		
@@ -1287,7 +1288,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testReadWithSummaryInvalid() throws Exception {
+	public void testReadWithSummaryInvalid() {
 		String msg = "<>>>><<<<>";
 
 		
@@ -1313,7 +1314,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testReadWithSummaryParamHtml() throws Exception {
+	public void testReadWithSummaryParamHtml() {
 		String msg = "<div>HELP IM A DIV</div>";
 
 		
@@ -1338,7 +1339,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testSearchByString() throws Exception {
+	public void testSearchByString() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1362,7 +1363,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testSearchByUrl() throws Exception {
+	public void testSearchByUrl() {
 
 		final String msg = getPatientFeedWithOneResult();
 
@@ -1469,7 +1470,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testSearchWithElementsParam() throws Exception {
+	public void testSearchWithElementsParam() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1496,7 +1497,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testSearchByPost() throws Exception {
+	public void testSearchByPost() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1533,7 +1534,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testSearchByPostUseJson() throws Exception {
+	public void testSearchByPostUseJson() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1571,7 +1572,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testSearchWithLastUpdated() throws Exception {
+	public void testSearchWithLastUpdated() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1598,7 +1599,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testSearchWithProfileAndSecurity() throws Exception {
+	public void testSearchWithProfileAndSecurity() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1628,7 +1629,7 @@ public class GenericJaxRsClientDstu2Test {
 
 	@SuppressWarnings("unused")
 	@Test
-	public void testSearchWithReverseInclude() throws Exception {
+	public void testSearchWithReverseInclude() {
 
 		String msg = getPatientFeedWithOneResult();
 
@@ -1655,7 +1656,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testSearchWithSummaryParam() throws Exception {
+	public void testSearchWithSummaryParam() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1682,7 +1683,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testTransactionWithListOfResources() throws Exception {
+	public void testTransactionWithListOfResources() {
 
 		ca.uhn.fhir.model.dstu2.resource.Bundle resp = new ca.uhn.fhir.model.dstu2.resource.Bundle();
 		resp.addEntry().getResponse().setLocation("Patient/1/_history/1");
@@ -1735,7 +1736,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testTransactionWithString() throws Exception {
+	public void testTransactionWithString() {
 
 		ca.uhn.fhir.model.dstu2.resource.Bundle req = new ca.uhn.fhir.model.dstu2.resource.Bundle();
 		Patient patient = new Patient();
@@ -1781,7 +1782,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testTransactionWithTransactionResource() throws Exception {
+	public void testTransactionWithTransactionResource() {
 
 		ca.uhn.fhir.model.dstu2.resource.Bundle resp = new ca.uhn.fhir.model.dstu2.resource.Bundle();
 		resp.addEntry().getResponse().setLocation("Patient/1/_history/1");
@@ -1822,7 +1823,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testUpdateConditional() throws Exception {
+	public void testUpdateConditional() {
 		
 		
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
@@ -1877,7 +1878,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testUpdateNonFluent() throws Exception {
+	public void testUpdateNonFluent() {
 		
 		
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
@@ -1907,7 +1908,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testUpdatePrefer() throws Exception {
+	public void testUpdatePrefer() {
 		
 		
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
@@ -1933,7 +1934,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testUpdateReturningResourceBody() throws Exception {
+	public void testUpdateReturningResourceBody() {
 		Patient p = new Patient();
 		p.setId("123");
 		final String formatted = ourCtx.newXmlParser().encodeResourceToString(p);
@@ -1956,7 +1957,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testValidateFluent() throws Exception {
+	public void testValidateFluent() {
 
 		OperationOutcome oo = new OperationOutcome();
 		oo.addIssue().setDiagnostics("FOOBAR");
@@ -2010,7 +2011,7 @@ public class GenericJaxRsClientDstu2Test {
 	}
 
 	@Test
-	public void testValidateNonFluent() throws Exception {
+	public void testValidateNonFluent() {
 		OperationOutcome oo = new OperationOutcome();
 		oo.addIssue().setDiagnostics("FOOBAR");
 		final String msg = ourCtx.newXmlParser().encodeResourceToString(oo);
@@ -2080,7 +2081,7 @@ public class GenericJaxRsClientDstu2Test {
 		ourServer.setHandler(new AbstractHandler() {
 
 			@Override
-			public void handle(String theArg0, Request theRequest, HttpServletRequest theServletRequest, HttpServletResponse theResp) throws IOException, ServletException {				
+			public void handle(String theArg0, Request theRequest, HttpServletRequest theServletRequest, HttpServletResponse theResp) throws IOException {
 				theRequest.setHandled(true);
 				ourRequestUri = "http:" + theRequest.getHttpURI().toString();
 				ourRequestUriAll.add(ourRequestUri);

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/GenericJaxRsClientDstu3Test.java

@@ -79,7 +79,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testAcceptHeaderFetchConformance() throws Exception {
+	public void testAcceptHeaderFetchConformance() {
 		IParser p = ourCtx.newXmlParser();
 
 		CapabilityStatement conf = new CapabilityStatement();
@@ -113,7 +113,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testAcceptHeaderPreflightConformance() throws Exception {
+	public void testAcceptHeaderPreflightConformance() {
 		final IParser p = ourCtx.newXmlParser();
 
 		final CapabilityStatement conf = new CapabilityStatement();
@@ -143,7 +143,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testAcceptHeaderPreflightConformancePreferJson() throws Exception {
+	public void testAcceptHeaderPreflightConformancePreferJson() {
 		final IParser p = ourCtx.newXmlParser();
 
 		final CapabilityStatement conf = new CapabilityStatement();
@@ -172,7 +172,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testConformance() throws Exception {
+	public void testConformance() {
 		IParser p = ourCtx.newXmlParser();
 
 		CapabilityStatement conf = new CapabilityStatement();
@@ -188,7 +188,7 @@ public class GenericJaxRsClientDstu3Test {
 		
 
 		//@formatter:off
-		CapabilityStatement resp = (CapabilityStatement)client.fetchConformance().ofType(CapabilityStatement.class).execute();
+		CapabilityStatement resp = client.fetchConformance().ofType(CapabilityStatement.class).execute();
 
 		//@formatter:on
 		assertEquals("http://localhost:" + ourPort + "/fhir/metadata", ourRequestUri);
@@ -199,7 +199,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testProviderWhereWeForgotToSetTheContext() throws Exception {		
+	public void testProviderWhereWeForgotToSetTheContext() {
 		JaxRsRestfulClientFactory clientFactory = new JaxRsRestfulClientFactory(); // no ctx
 		clientFactory.setServerValidationMode(ServerValidationModeEnum.NEVER);
 		
@@ -215,7 +215,7 @@ public class GenericJaxRsClientDstu3Test {
 	
 	
 	@Test
-	public void testCreate() throws Exception {		
+	public void testCreate() {
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/fhir");
 
 		
@@ -247,7 +247,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testCreateConditional() throws Exception {
+	public void testCreateConditional() {
 		
 		
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
@@ -289,7 +289,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testCreate2() throws Exception {
+	public void testCreate2() {
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
 
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/fhir");
@@ -310,7 +310,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testCreatePrefer() throws Exception {
+	public void testCreatePrefer() {
 		
 		
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
@@ -335,7 +335,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testCreateReturningResourceBody() throws Exception {
+	public void testCreateReturningResourceBody() {
 		Patient p = new Patient();
 		p.setId("123");
 		final String formatted = ourCtx.newXmlParser().encodeResourceToString(p);
@@ -358,7 +358,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testDeleteConditional() throws Exception {
+	public void testDeleteConditional() {
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
 
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/fhir");
@@ -384,7 +384,7 @@ public class GenericJaxRsClientDstu3Test {
 
 	@SuppressWarnings("deprecation")
 	@Test
-	public void testDeleteNonFluent() throws Exception {
+	public void testDeleteNonFluent() {
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
 		
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/fhir");
@@ -398,7 +398,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testHistory() throws Exception {
+	public void testHistory() {
 
 		final String msg = getPatientFeedWithOneResult();
 		
@@ -494,7 +494,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testMetaAdd() throws Exception {
+	public void testMetaAdd() {
 		IParser p = ourCtx.newXmlParser();
 
 		Meta inMeta = new Meta().addProfile("urn:profile:in");
@@ -527,7 +527,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testMetaGet() throws Exception {
+	public void testMetaGet() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters inParams = new Parameters();
@@ -583,7 +583,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testOperationAsGetWithInParameters() throws Exception {
+	public void testOperationAsGetWithInParameters() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters inParams = new Parameters();
@@ -662,7 +662,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testOperationAsGetWithNoInParameters() throws Exception {
+	public void testOperationAsGetWithNoInParameters() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters outParams = new Parameters();
@@ -733,7 +733,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testOperationWithBundleResponseJson() throws Exception {
+	public void testOperationWithBundleResponseJson() {
 
 		ourResponseContentType = Constants.CT_FHIR_JSON;
 		final String respString = "{\n" + "    \"resourceType\":\"Bundle\",\n" + "    \"id\":\"8cef5f2a-0ba9-43a5-be26-c8dde9ff0e19\",\n" + "    \"base\":\"http://localhost:" + ourPort + "/fhir\"\n" + "}";
@@ -763,7 +763,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testOperationWithBundleResponseXml() throws Exception {
+	public void testOperationWithBundleResponseXml() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters inParams = new Parameters();
@@ -800,7 +800,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testOperationWithInlineParams() throws Exception {
+	public void testOperationWithInlineParams() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters outParams = new Parameters();
@@ -919,7 +919,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testOperationWithProfiledDatatypeParam() throws IOException, Exception {
+	public void testOperationWithProfiledDatatypeParam() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters outParams = new Parameters();
@@ -968,7 +968,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testOperationWithListOfParameterResponse() throws Exception {
+	public void testOperationWithListOfParameterResponse() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters inParams = new Parameters();
@@ -1043,7 +1043,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testOperationWithNoInParameters() throws Exception {
+	public void testOperationWithNoInParameters() {
 		IParser p = ourCtx.newXmlParser();
 
 		Parameters inParams = new Parameters();
@@ -1122,7 +1122,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testPageNext() throws Exception {
+	public void testPageNext() {
 		
 		ourResponseContentType = Constants.CT_FHIR_XML + "; charset=UTF-8";
 		ourResponseBody = getPatientFeedWithOneResult();
@@ -1149,7 +1149,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testPageNextNoLink() throws Exception {
+	public void testPageNextNoLink() {
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/fhir");
 
 		org.hl7.fhir.dstu3.model.Bundle sourceBundle = new org.hl7.fhir.dstu3.model.Bundle();
@@ -1161,7 +1161,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testPagePrev() throws Exception {
+	public void testPagePrev() {
 		
 		
 		
@@ -1207,7 +1207,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testReadByUri() throws Exception {
+	public void testReadByUri() {
 
 		Patient patient = new Patient();
 		patient.addName().setFamily("FAM");
@@ -1227,7 +1227,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testReadFluentByUri() throws Exception {
+	public void testReadFluentByUri() {
 
 		Patient patient = new Patient();
 		patient.addName().setFamily("FAM");
@@ -1240,13 +1240,13 @@ public class GenericJaxRsClientDstu3Test {
 
 		Patient response;
 
-		response = (Patient) client.read().resource(Patient.class).withUrl(new IdType("http://localhost:" + ourPort + "/AAA/Patient/123")).execute();
+		response = client.read().resource(Patient.class).withUrl(new IdType("http://localhost:" + ourPort + "/AAA/Patient/123")).execute();
 		assertEquals("http://localhost:" + ourPort + "/AAA/Patient/123", ourRequestUri);
 		assertEquals("FAM", response.getName().get(0).getFamily());
 	}
 
 	@Test
-	public void testReadUpdatedHeaderDoesntOverwriteResourceValue() throws Exception {
+	public void testReadUpdatedHeaderDoesntOverwriteResourceValue() {
 
 		//@formatter:off
 		final String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" + 
@@ -1286,7 +1286,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testReadWithElementsParam() throws Exception {
+	public void testReadWithElementsParam() {
 		String msg = "{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}";
 
 		
@@ -1311,7 +1311,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testReadWithSummaryInvalid() throws Exception {
+	public void testReadWithSummaryInvalid() {
 		String msg = "<>>>><<<<>";
 
 		
@@ -1338,7 +1338,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testReadWithSummaryParamHtml() throws Exception {
+	public void testReadWithSummaryParamHtml() {
 		String msg = "<div>HELP IM A DIV</div>";
 
 		
@@ -1365,7 +1365,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testSearchByString() throws Exception {
+	public void testSearchByString() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1391,7 +1391,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testSearchByUrl() throws Exception {
+	public void testSearchByUrl() {
 
 		final String msg = getPatientFeedWithOneResult();
 
@@ -1498,7 +1498,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testSearchWithElementsParam() throws Exception {
+	public void testSearchWithElementsParam() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1525,7 +1525,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testSearchByPost() throws Exception {
+	public void testSearchByPost() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1562,7 +1562,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testSearchByPostUseJson() throws Exception {
+	public void testSearchByPostUseJson() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1600,7 +1600,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testSearchWithLastUpdated() throws Exception {
+	public void testSearchWithLastUpdated() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1627,7 +1627,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testSearchWithProfileAndSecurity() throws Exception {
+	public void testSearchWithProfileAndSecurity() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1657,7 +1657,7 @@ public class GenericJaxRsClientDstu3Test {
 
 	@SuppressWarnings("unused")
 	@Test
-	public void testSearchWithReverseInclude() throws Exception {
+	public void testSearchWithReverseInclude() {
 
 		String msg = getPatientFeedWithOneResult();
 
@@ -1684,7 +1684,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testSearchWithSummaryParam() throws Exception {
+	public void testSearchWithSummaryParam() {
 		String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		
@@ -1711,7 +1711,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testTransactionWithListOfResources() throws Exception {
+	public void testTransactionWithListOfResources() {
 
 		org.hl7.fhir.dstu3.model.Bundle resp = new org.hl7.fhir.dstu3.model.Bundle();
 		resp.addEntry().getResponse().setLocation("Patient/1/_history/1");
@@ -1764,7 +1764,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testTransactionWithString() throws Exception {
+	public void testTransactionWithString() {
 
 		org.hl7.fhir.dstu3.model.Bundle req = new org.hl7.fhir.dstu3.model.Bundle();
 		Patient patient = new Patient();
@@ -1810,7 +1810,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testTransactionWithTransactionResource() throws Exception {
+	public void testTransactionWithTransactionResource() {
 
 		org.hl7.fhir.dstu3.model.Bundle resp = new org.hl7.fhir.dstu3.model.Bundle();
 		resp.addEntry().getResponse().setLocation("Patient/1/_history/1");
@@ -1851,7 +1851,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testUpdateConditional() throws Exception {
+	public void testUpdateConditional() {
 		
 		
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
@@ -1906,7 +1906,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testUpdateNonFluent() throws Exception {
+	public void testUpdateNonFluent() {
 		
 		
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
@@ -1936,7 +1936,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testUpdatePrefer() throws Exception {
+	public void testUpdatePrefer() {
 		
 		
 		ourResponseStatus = Constants.STATUS_HTTP_204_NO_CONTENT;
@@ -1962,7 +1962,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testUpdateReturningResourceBody() throws Exception {
+	public void testUpdateReturningResourceBody() {
 		Patient p = new Patient();
 		p.setId("123");
 		final String formatted = ourCtx.newXmlParser().encodeResourceToString(p);
@@ -1985,7 +1985,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testValidateFluent() throws Exception {
+	public void testValidateFluent() {
 
 		OperationOutcome oo = new OperationOutcome();
 		oo.addIssue().setDiagnostics("FOOBAR");
@@ -2039,7 +2039,7 @@ public class GenericJaxRsClientDstu3Test {
 	}
 
 	@Test
-	public void testValidateNonFluent() throws Exception {
+	public void testValidateNonFluent() {
 		OperationOutcome oo = new OperationOutcome();
 		oo.addIssue().setDiagnostics("FOOBAR");
 		final String msg = ourCtx.newXmlParser().encodeResourceToString(oo);
@@ -2109,7 +2109,7 @@ public class GenericJaxRsClientDstu3Test {
 		ourServer.setHandler(new AbstractHandler() {
 
 			@Override
-			public void handle(String theArg0, Request theRequest, HttpServletRequest theServletRequest, HttpServletResponse theResp) throws IOException, ServletException {				
+			public void handle(String theArg0, Request theRequest, HttpServletRequest theServletRequest, HttpServletResponse theResp) throws IOException {
 				theRequest.setHandled(true);
 				ourRequestUri = "http:" + theRequest.getHttpURI().toString();
 				ourRequestUriAll.add(ourRequestUri);

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/JaxRsRestfulClientFactoryTest.java

@@ -3,51 +3,56 @@ package ca.uhn.fhir.jaxrs.client;
 import ca.uhn.fhir.context.FhirContext;
 import org.junit.Before;
 import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.ws.rs.client.Client;
 import java.util.ArrayList;
 import java.util.Arrays;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.hamcrest.CoreMatchers.hasItem;
+import static org.hamcrest.core.IsNot.not;
+import static org.junit.Assert.*;
 
 /**
  * Created by Sebastien Riviere on 31/07/2017.
  */
 public class JaxRsRestfulClientFactoryTest {
 
-    private final FhirContext context = FhirContext.forDstu2();
-    private JaxRsRestfulClientFactory factory;
+	private static final Logger ourLog = LoggerFactory.getLogger(JaxRsRestfulClientFactoryTest.class);
+	private final FhirContext context = FhirContext.forDstu2();
+	private JaxRsRestfulClientFactory factory;
 
-    @Before
-    public void setUp() {
-        factory = new JaxRsRestfulClientFactory(context);
-    }
+	@Test
+	public void emptyConstructorTest() {
+		assertNotNull(new JaxRsRestfulClientFactory());
+	}
 
-    @Test
-    public void emptyConstructorTest() {
-        assertNotNull(new JaxRsRestfulClientFactory());
-    }
+	@Test
+	public void getDefaultNativeClientTest() {
+		assertNotNull(factory.getNativeClientClient());
+	}
 
-    @Test
-    public void getDefaultNativeClientTest() {
-        assertNotNull(factory.getNativeClientClient());
-    }
+	@Test
+	public void getNativeClientEmptyRegisteredComponentListTest() {
+		factory.register(new ArrayList<>());
+		final Client result = factory.getNativeClientClient();
+		assertNotNull(result);
+		ourLog.info("Classes: {}", result.getConfiguration().getClasses());
+		assertThat(result.getConfiguration().getClasses(), not(hasItem(ca.uhn.fhir.jaxrs.client.MyFilter.class)));
+	}
 
-    @Test
-    public void getNativeClientEmptyRegisteredComponentListTest() {
-        factory.register(new ArrayList<Class<?>>());
-        final Client result = factory.getNativeClientClient();
-        assertNotNull(result);
-        assertTrue(result.getConfiguration().getClasses().isEmpty());
-    }
+	@Test
+	public void getNativeClientRegisteredComponentListTest() {
+		factory.register(Arrays.asList(MyFilter.class, String.class));
+		final Client result = factory.getNativeClientClient();
+		assertNotNull(result);
+		ourLog.info("Classes: {}", result.getConfiguration().getClasses());
+		assertThat(result.getConfiguration().getClasses(), hasItem(ca.uhn.fhir.jaxrs.client.MyFilter.class));
+	}
 
-    @Test
-    public void getNativeClientRegisteredComponentListTest() {
-        factory.register(Arrays.asList(MyFilter.class, String.class));
-        final Client result = factory.getNativeClientClient();
-        assertNotNull(result);
-        assertEquals(1, result.getConfiguration().getClasses().size());
-    }
-}
+	@Before
+	public void setUp() {
+		factory = new JaxRsRestfulClientFactory(context);
+	}
+}

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsConformanceProviderDstu2Hl7OrgTest.java

@@ -1,27 +1,24 @@
 package ca.uhn.fhir.jaxrs.server;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProviderDstu2Hl7Org;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProviderDstu2Hl7Org;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import org.jboss.resteasy.specimpl.ResteasyHttpHeaders;
+import org.junit.Before;
+import org.junit.Test;
 
+import javax.ws.rs.core.MultivaluedHashMap;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.core.UriInfo;
 import java.net.URI;
 import java.util.Arrays;
 import java.util.concurrent.ConcurrentHashMap;
 
-import javax.ws.rs.HttpMethod;
-import javax.ws.rs.core.*;
-
-import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProviderDstu2Hl7Org;
-import org.glassfish.jersey.internal.MapPropertiesDelegate;
-import org.glassfish.jersey.server.ContainerRequest;
-import org.junit.Before;
-import org.junit.Test;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProviderDstu2Hl7Org;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.server.IResourceProvider;
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 public class AbstractJaxRsConformanceProviderDstu2Hl7OrgTest {
 
@@ -29,16 +26,17 @@ public class AbstractJaxRsConformanceProviderDstu2Hl7OrgTest {
 	private static final String REQUESTURI = BASEURI + "/metadata";
 	AbstractJaxRsConformanceProvider provider;
 	private ConcurrentHashMap<Class<? extends IResourceProvider>, IResourceProvider> providers;
-	private ContainerRequest headers;
+	private ResteasyHttpHeaders headers;
 	private MultivaluedHashMap<String, String> queryParameters;
 
 	@Before
 	public void setUp() throws Exception {
-		// headers
-		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
-				new MapPropertiesDelegate());
 		// uri info
-		queryParameters = new MultivaluedHashMap<String, String>();
+		queryParameters = new MultivaluedHashMap<>();
+		// headers
+//		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
+//				new MapPropertiesDelegate());
+		headers = new ResteasyHttpHeaders(queryParameters);
 
 
 		providers = new ConcurrentHashMap<Class<? extends IResourceProvider>, IResourceProvider>();

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsConformanceProviderDstu2_1Test.java

@@ -1,27 +1,24 @@
 package ca.uhn.fhir.jaxrs.server;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProviderDstu2_1;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProviderDstu2_1;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import org.jboss.resteasy.specimpl.ResteasyHttpHeaders;
+import org.junit.Before;
+import org.junit.Test;
 
+import javax.ws.rs.core.MultivaluedHashMap;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.core.UriInfo;
 import java.net.URI;
 import java.util.Arrays;
 import java.util.concurrent.ConcurrentHashMap;
 
-import javax.ws.rs.HttpMethod;
-import javax.ws.rs.core.*;
-
-import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProviderDstu2_1;
-import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProviderDstu2_1;
-import org.glassfish.jersey.internal.MapPropertiesDelegate;
-import org.glassfish.jersey.server.ContainerRequest;
-import org.junit.Before;
-import org.junit.Test;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.server.IResourceProvider;
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 public class AbstractJaxRsConformanceProviderDstu2_1Test {
 
@@ -29,19 +26,20 @@ public class AbstractJaxRsConformanceProviderDstu2_1Test {
 	private static final String REQUESTURI = BASEURI + "/metadata";
 	AbstractJaxRsConformanceProvider provider;
 	private ConcurrentHashMap<Class<? extends IResourceProvider>, IResourceProvider> providers;
-	private ContainerRequest headers;
+	private ResteasyHttpHeaders headers;
 	private MultivaluedHashMap<String, String> queryParameters;
 
 	@Before
 	public void setUp() throws Exception {
-		// headers
-		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
-				new MapPropertiesDelegate());
 		// uri info
-		queryParameters = new MultivaluedHashMap<String, String>();
+		queryParameters = new MultivaluedHashMap<>();
+		// headers
+//		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
+//				new MapPropertiesDelegate());
+		headers = new ResteasyHttpHeaders(queryParameters);
 
 
-		providers = new ConcurrentHashMap<Class<? extends IResourceProvider>, IResourceProvider>();
+		providers = new ConcurrentHashMap<>();
 		provider = createConformanceProvider(providers);
 	}
 

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsConformanceProviderDstu3Test.java

@@ -1,27 +1,24 @@
 package ca.uhn.fhir.jaxrs.server;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
-
-import java.net.URI;
-import java.util.Arrays;
-import java.util.concurrent.ConcurrentHashMap;
-
-import javax.ws.rs.HttpMethod;
-import javax.ws.rs.core.*;
-
-import org.glassfish.jersey.internal.MapPropertiesDelegate;
-import org.glassfish.jersey.server.ContainerRequest;
-import org.junit.Before;
-import org.junit.Test;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProvider;
 import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProviderDstu3;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.IResourceProvider;
+import org.jboss.resteasy.specimpl.ResteasyHttpHeaders;
+import org.junit.Before;
+import org.junit.Test;
+
+import javax.ws.rs.core.MultivaluedHashMap;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.core.UriInfo;
+import java.net.URI;
+import java.util.Arrays;
+import java.util.concurrent.ConcurrentHashMap;
+
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 public class AbstractJaxRsConformanceProviderDstu3Test {
 
@@ -29,16 +26,17 @@ public class AbstractJaxRsConformanceProviderDstu3Test {
 	private static final String REQUESTURI = BASEURI + "/metadata";
 	AbstractJaxRsConformanceProvider provider;
 	private ConcurrentHashMap<Class<? extends IResourceProvider>, IResourceProvider> providers;
-	private ContainerRequest headers;
+	private ResteasyHttpHeaders headers;
 	private MultivaluedHashMap<String, String> queryParameters;
 	
 	@Before
 	public void setUp() throws Exception {
-		// headers
-		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
-				new MapPropertiesDelegate());
 		// uri info
-		queryParameters = new MultivaluedHashMap<String, String>();
+		queryParameters = new MultivaluedHashMap<>();
+		// headers
+//		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
+//				new MapPropertiesDelegate());
+		headers = new ResteasyHttpHeaders(queryParameters);
 		
 		
 		providers = new ConcurrentHashMap<Class<? extends IResourceProvider>, IResourceProvider>();

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsConformanceProviderR4Test.java

@@ -1,27 +1,24 @@
 package ca.uhn.fhir.jaxrs.server;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProviderR4;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProviderR4;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import org.jboss.resteasy.specimpl.ResteasyHttpHeaders;
+import org.junit.Before;
+import org.junit.Test;
 
+import javax.ws.rs.core.MultivaluedHashMap;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.core.UriInfo;
 import java.net.URI;
 import java.util.Arrays;
 import java.util.concurrent.ConcurrentHashMap;
 
-import javax.ws.rs.HttpMethod;
-import javax.ws.rs.core.*;
-
-import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProviderR4;
-import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProviderR4;
-import org.glassfish.jersey.internal.MapPropertiesDelegate;
-import org.glassfish.jersey.server.ContainerRequest;
-import org.junit.Before;
-import org.junit.Test;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.server.IResourceProvider;
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 public class AbstractJaxRsConformanceProviderR4Test {
 
@@ -29,16 +26,17 @@ public class AbstractJaxRsConformanceProviderR4Test {
 	private static final String REQUESTURI = BASEURI + "/metadata";
 	AbstractJaxRsConformanceProvider provider;
 	private ConcurrentHashMap<Class<? extends IResourceProvider>, IResourceProvider> providers;
-	private ContainerRequest headers;
+	private ResteasyHttpHeaders headers;
 	private MultivaluedHashMap<String, String> queryParameters;
 
 	@Before
 	public void setUp() throws Exception {
-		// headers
-		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
-				new MapPropertiesDelegate());
 		// uri info
-		queryParameters = new MultivaluedHashMap<String, String>();
+		queryParameters = new MultivaluedHashMap<>();
+		// headers
+//		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
+//				new MapPropertiesDelegate());
+		headers = new ResteasyHttpHeaders(queryParameters);
 
 
 		providers = new ConcurrentHashMap<Class<? extends IResourceProvider>, IResourceProvider>();

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsConformanceProviderTest.java

@@ -1,26 +1,23 @@
 package ca.uhn.fhir.jaxrs.server;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
-
-import java.net.URI;
-import java.util.Arrays;
-import java.util.concurrent.ConcurrentHashMap;
-
-import javax.ws.rs.HttpMethod;
-import javax.ws.rs.core.*;
-
-import org.glassfish.jersey.internal.MapPropertiesDelegate;
-import org.glassfish.jersey.server.ContainerRequest;
-import org.junit.Before;
-import org.junit.Test;
-
 import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProvider;
 import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProvider;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.IResourceProvider;
+import org.jboss.resteasy.specimpl.ResteasyHttpHeaders;
+import org.junit.Before;
+import org.junit.Test;
+
+import javax.ws.rs.core.MultivaluedHashMap;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.core.UriInfo;
+import java.net.URI;
+import java.util.Arrays;
+import java.util.concurrent.ConcurrentHashMap;
+
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 public class AbstractJaxRsConformanceProviderTest {
 
@@ -28,16 +25,17 @@ public class AbstractJaxRsConformanceProviderTest {
 	private static final String REQUESTURI = BASEURI + "/metadata";
 	AbstractJaxRsConformanceProvider provider;
 	private ConcurrentHashMap<Class<? extends IResourceProvider>, IResourceProvider> providers;
-	private ContainerRequest headers;
+	private ResteasyHttpHeaders headers;
 	private MultivaluedHashMap<String, String> queryParameters;
 	
 	@Before
 	public void setUp() throws Exception {
-		// headers
-		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
-				new MapPropertiesDelegate());
 		// uri info
-		queryParameters = new MultivaluedHashMap<String, String>();
+		queryParameters = new MultivaluedHashMap<>();
+		// headers
+//		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
+//				new MapPropertiesDelegate());
+		headers = new ResteasyHttpHeaders(queryParameters);
 		
 		
 		providers = new ConcurrentHashMap<Class<? extends IResourceProvider>, IResourceProvider>();

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsResourceProviderDstu3Test.java

@@ -1,11 +1,24 @@
 package ca.uhn.fhir.jaxrs.server;
 
-import static org.junit.Assert.*;
-import static org.mockito.Matchers.*;
-import static org.mockito.Mockito.*;
-
-import java.util.*;
-
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jaxrs.client.JaxRsRestfulClientFactory;
+import ca.uhn.fhir.jaxrs.server.interceptor.JaxRsResponseException;
+import ca.uhn.fhir.jaxrs.server.test.RandomServerPortProvider;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsConformanceRestProviderDstu3;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPageProviderDstu3;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProviderDstu3;
+import ca.uhn.fhir.model.primitive.UriDt;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.PreferReturnEnum;
+import ca.uhn.fhir.rest.api.SearchStyleEnum;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.param.StringAndListParam;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.lang3.StringUtils;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletContextHandler;
@@ -16,22 +29,21 @@ import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.junit.*;
 import org.junit.runners.MethodSorters;
-import org.mockito.*;
+import org.mockito.ArgumentCaptor;
+import org.mockito.ArgumentMatcher;
+import org.mockito.ArgumentMatchers;
+import org.mockito.Matchers;
 
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jaxrs.client.JaxRsRestfulClientFactory;
-import ca.uhn.fhir.jaxrs.server.interceptor.JaxRsExceptionInterceptor;
-import ca.uhn.fhir.jaxrs.server.interceptor.JaxRsResponseException;
-import ca.uhn.fhir.jaxrs.server.test.*;
-import ca.uhn.fhir.model.primitive.UriDt;
-import ca.uhn.fhir.rest.api.*;
-import ca.uhn.fhir.rest.client.api.IGenericClient;
-import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
-import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.rest.param.StringAndListParam;
-import ca.uhn.fhir.rest.param.StringParam;
-import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
-import ca.uhn.fhir.util.TestUtil;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.Assert.*;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.argThat;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.ArgumentMatchers.isNull;
+import static org.mockito.Mockito.*;
 
 @FixMethodOrder(MethodSorters.NAME_ASCENDING)
 public class AbstractJaxRsResourceProviderDstu3Test {
@@ -135,7 +147,7 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 	@Test
 	public void testConformance() {
 		final CapabilityStatement conf = client.fetchConformance().ofType(CapabilityStatement.class).execute();
-		assertEquals(conf.getRest().get(0).getResource().get(0).getType().toString(), "Patient");
+		assertEquals(conf.getRest().get(0).getResource().get(0).getType(), "Patient");
 	}
 
 	@Test
@@ -149,7 +161,7 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 		client.setEncoding(EncodingEnum.JSON);
 		final MethodOutcome response = client.create().resource(toCreate).prefer(PreferReturnEnum.REPRESENTATION)
 				.execute();
-		IBaseResource resource = (IBaseResource) response.getResource();
+		IBaseResource resource = response.getResource();
 		compareResultId(1, resource);
 		assertEquals("myIdentifier", patientCaptor.getValue().getIdentifier().get(0).getValue());
 	}
@@ -162,7 +174,7 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 	}
 	
     @Test
-    public void testConditionalDelete() throws Exception {
+    public void testConditionalDelete() {
         when(mock.delete(idCaptor.capture(), conditionalCaptor.capture())).thenReturn(new MethodOutcome());
         client.delete().resourceConditionalByType("Patient").where(Patient.IDENTIFIER.exactly().identifier("2")).execute();
         assertEquals("Patient?identifier=2&_format=json", conditionalCaptor.getValue());
@@ -187,7 +199,7 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 		assertEquals("outputValue", ((StringType)outParams.getParameter().get(0).getValue()).getValueAsString());
 	}
 	
-	class StringTypeMatcher extends ArgumentMatcher<StringType> {
+	class StringTypeMatcher implements ArgumentMatcher<StringType> {
 	    private StringType myStringType;
 	    
 	    public StringTypeMatcher(StringType stringType) {
@@ -195,8 +207,8 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 	    }
 	    
         @Override
-        public boolean matches(Object argument) {
-            return myStringType.getValue().equals(((StringType)argument).getValue());
+        public boolean matches(StringType argument) {
+            return myStringType.getValue().equals(argument.getValue());
         }
 	    
 	}
@@ -214,17 +226,18 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 		inParams.addParameter().setName("dummy").setValue(new StringType("myAwesomeDummyValue"));
 
 		// invoke
-		Parameters outParams = client.operation().onInstance(new IdType("Patient", "1")).named("$someCustomOperation")
-				.withParameters(inParams).useHttpGet().execute();
+		Parameters outParams = client
+			.operation()
+			.onInstance(new IdType("Patient", "1"))
+			.named("$someCustomOperation")
+			.withParameters(inParams)
+			.useHttpGet()
+			.execute();
+
 		// verify
 		assertEquals("outputValue", ((StringType)outParams.getParameter().get(0).getValue()).getValueAsString());
 	}
 
-	/** Search using other query options */
-	public void testOther() {
-		// missing
-	}
-
 	@Test
 	public void testRead() {
 		when(mock.find(idCaptor.capture())).thenReturn(createPatient(1));
@@ -236,7 +249,7 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 
 	/** Search - Compartments */
 	@Test
-	public void testSearchCompartements() {
+	public void testSearchCompartments() {
 		when(mock.searchCompartment(any(IdType.class))).thenReturn(Arrays.asList((IBaseResource) createPatient(1)));
 		org.hl7.fhir.dstu3.model.Bundle response = client.search().forResource(Patient.class).withIdAndCompartment("1", "Condition")
 				.returnBundle(org.hl7.fhir.dstu3.model.Bundle.class).execute();
@@ -248,7 +261,7 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 	/** */
 	@Test
 	public void testSearchPost() {
-		when(mock.search(any(StringParam.class), Matchers.isNull(StringAndListParam.class)))
+		when(mock.search(ArgumentMatchers.isNull(), ArgumentMatchers.isNull()))
 				.thenReturn(createPatients(1, 13));
 		org.hl7.fhir.dstu3.model.Bundle result = client.search().forResource("Patient").usingStyle(SearchStyleEnum.POST)
 				.returnBundle(org.hl7.fhir.dstu3.model.Bundle.class).execute();
@@ -275,12 +288,12 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 	/** Search - Multi-valued Parameters (ANY/OR) */
 	@Test
 	public void testSearchUsingGenericClientBySearchWithMultiValues() {
-		when(mock.search(any(StringParam.class), Matchers.isNotNull(StringAndListParam.class)))
+		when(mock.search(any(StringParam.class), ArgumentMatchers.notNull()))
 				.thenReturn(Arrays.asList(createPatient(1)));
 		final Bundle results = client.search().forResource(Patient.class)
 				.where(Patient.ADDRESS.matches().values("Toronto")).and(Patient.ADDRESS.matches().values("Ontario"))
 				.and(Patient.ADDRESS.matches().values("Canada"))
-				.where(Patient.IDENTIFIER.exactly().systemAndIdentifier("SHORTNAME", "TOYS")).returnBundle(Bundle.class).execute();
+				.where(Patient.NAME.matches().value("SHORTNAME")).returnBundle(Bundle.class).execute();
 		IBaseResource resource = results.getEntry().get(0).getResource();
 
 		compareResultId(1, resource);
@@ -291,7 +304,7 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 	@Test
 	public void testSearchWithPaging() {
 		// Perform a search
-		when(mock.search(any(StringParam.class), Matchers.isNull(StringAndListParam.class)))
+		when(mock.search(ArgumentMatchers.isNull(), ArgumentMatchers.isNull()))
 				.thenReturn(createPatients(1, 13));
 		final org.hl7.fhir.dstu3.model.Bundle results = client.search().forResource(Patient.class).count(8).returnBundle(org.hl7.fhir.dstu3.model.Bundle.class)
 				.execute();
@@ -416,17 +429,17 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 		System.out.println(ourPort);
 		jettyServer = new Server(ourPort);
 		jettyServer.setHandler(context);
-		ServletHolder jerseyServlet = context.addServlet(org.glassfish.jersey.servlet.ServletContainer.class, "/*");
+		ServletHolder jerseyServlet = context.addServlet(org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.class, "/*");
 		jerseyServlet.setInitOrder(0);
 
 		//@formatter:off
-		jerseyServlet.setInitParameter("jersey.config.server.provider.classnames",
+		jerseyServlet.setInitParameter("resteasy.resources",
 				StringUtils.join(Arrays.asList(
 					TestJaxRsMockPatientRestProviderDstu3.class.getCanonicalName(),
-					JaxRsExceptionInterceptor.class.getCanonicalName(),
+//					JaxRsExceptionInterceptor.class.getCanonicalName(),
 					TestJaxRsConformanceRestProviderDstu3.class.getCanonicalName(),
 					TestJaxRsMockPageProviderDstu3.class.getCanonicalName()
-						), ";"));
+						), ","));
 		//@formatter:on
 		
 		jettyServer.start();
@@ -441,7 +454,7 @@ public class AbstractJaxRsResourceProviderDstu3Test {
 	}
 
 	@AfterClass
-	public static void tearDownClass() throws Exception {
+	public static void tearDownClass() {
 		try {
 			jettyServer.destroy();
 		} catch (Exception e) {

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsResourceProviderTest.java

@@ -1,35 +1,23 @@
 package ca.uhn.fhir.jaxrs.server;
 
-import static org.junit.Assert.*;
-import static org.mockito.Matchers.*;
-import static org.mockito.Mockito.*;
-
-import java.util.*;
-
-import org.apache.commons.lang3.StringUtils;
-import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.servlet.ServletContextHandler;
-import org.eclipse.jetty.servlet.ServletHolder;
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
-import org.junit.*;
-import org.junit.Test;
-import org.junit.runners.MethodSorters;
-import org.mockito.ArgumentCaptor;
-import org.mockito.Matchers;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jaxrs.client.JaxRsRestfulClientFactory;
-import ca.uhn.fhir.jaxrs.server.interceptor.JaxRsExceptionInterceptor;
 import ca.uhn.fhir.jaxrs.server.interceptor.JaxRsResponseException;
-import ca.uhn.fhir.jaxrs.server.test.*;
+import ca.uhn.fhir.jaxrs.server.test.RandomServerPortProvider;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsConformanceRestProvider;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPageProvider;
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsMockPatientRestProvider;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
 import ca.uhn.fhir.model.dstu2.resource.*;
-import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
-import ca.uhn.fhir.model.primitive.*;
-import ca.uhn.fhir.rest.api.*;
+import ca.uhn.fhir.model.primitive.DateDt;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.model.primitive.UriDt;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.PreferReturnEnum;
+import ca.uhn.fhir.rest.api.SearchStyleEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
@@ -37,6 +25,26 @@ import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.TestUtil;
+import org.apache.commons.lang3.StringUtils;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.junit.*;
+import org.junit.runners.MethodSorters;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Matchers;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.Assert.*;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.argThat;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.ArgumentMatchers.isNull;
+import static org.mockito.Mockito.*;
 
 @FixMethodOrder(MethodSorters.NAME_ASCENDING)
 public class AbstractJaxRsResourceProviderTest {
@@ -127,7 +135,7 @@ public class AbstractJaxRsResourceProviderTest {
 	@Test
 	public void testConformance() {
 		final Conformance conf = client.fetchConformance().ofType(Conformance.class).execute();
-		assertEquals(conf.getRest().get(0).getResource().get(0).getType().toString(), "Patient");
+		assertEquals(conf.getRest().get(0).getResource().get(0).getType(), "Patient");
 	}
 
 	@Test
@@ -154,7 +162,7 @@ public class AbstractJaxRsResourceProviderTest {
 	}
 
 	@Test
-	public void testConditionalDelete() throws Exception {
+	public void testConditionalDelete() {
 		when(mock.delete(idCaptor.capture(), conditionalCaptor.capture())).thenReturn(new MethodOutcome());
 		client.delete().resourceConditionalByType("Patient").where(Patient.IDENTIFIER.exactly().identifier("2")).execute();
 		assertEquals("Patient?identifier=2&_format=json", conditionalCaptor.getValue());
@@ -198,11 +206,6 @@ public class AbstractJaxRsResourceProviderTest {
 		assertEquals("outputValue", ((StringDt) outParams.getParameter().get(0).getValue()).getValueAsString());
 	}
 
-	/** Search using other query options */
-	public void testOther() {
-		// missing
-	}
-
 	@Test
 	public void testRead() {
 		when(mock.find(idCaptor.capture())).thenReturn(createPatient(1));
@@ -226,9 +229,12 @@ public class AbstractJaxRsResourceProviderTest {
 	/** */
 	@Test
 	public void testSearchPost() {
-		when(mock.search(any(StringParam.class), Matchers.isNull(StringAndListParam.class)))
+		when(mock.search(isNull(), isNull()))
 				.thenReturn(createPatients(1, 13));
-		Bundle result = client.search().forResource("Patient").usingStyle(SearchStyleEnum.POST)
+		Bundle result = client
+			.search()
+			.forResource("Patient")
+			.usingStyle(SearchStyleEnum.POST)
 				.returnBundle(Bundle.class).execute();
 		IResource resource = result.getEntry().get(0).getResource();
 		compareResultId(1, resource);
@@ -253,12 +259,12 @@ public class AbstractJaxRsResourceProviderTest {
 	/** Search - Multi-valued Parameters (ANY/OR) */
 	@Test
 	public void testSearchUsingGenericClientBySearchWithMultiValues() {
-		when(mock.search(any(StringParam.class), Matchers.isNotNull(StringAndListParam.class)))
+		when(mock.search(any(StringParam.class), any(StringAndListParam.class)))
 				.thenReturn(Arrays.asList(createPatient(1)));
 		Bundle results = client.search().forResource(Patient.class)
 				.where(Patient.ADDRESS.matches().values("Toronto")).and(Patient.ADDRESS.matches().values("Ontario"))
 				.and(Patient.ADDRESS.matches().values("Canada"))
-				.where(Patient.IDENTIFIER.exactly().systemAndIdentifier("SHORTNAME", "TOYS")).returnBundle(Bundle.class).execute();
+				.where(Patient.NAME.matches().value("SHORTNAME")).returnBundle(Bundle.class).execute();
 		IResource resource = results.getEntry().get(0).getResource();
 
 		compareResultId(1, resource);
@@ -269,7 +275,7 @@ public class AbstractJaxRsResourceProviderTest {
 	@Test
 	public void testSearchWithPaging() {
 		// Perform a search
-		when(mock.search(any(StringParam.class), Matchers.isNull(StringAndListParam.class)))
+		when(mock.search(isNull(), isNull()))
 				.thenReturn(createPatients(1, 13));
 		final Bundle results = client.search().forResource(Patient.class).limitTo(8).returnBundle(Bundle.class)
 				.execute();
@@ -370,24 +376,17 @@ public class AbstractJaxRsResourceProviderTest {
 	}
 
 	private <T> T withId(final T id) {
-		return argThat(new BaseMatcher<T>() {
-			@Override
-			public void describeTo(Description arg0) {
-			}
-
-			@Override
-			public boolean matches(Object other) {
-				IdDt thisId;
-				IdDt otherId;
-				if (id instanceof IdDt) {
-					thisId = (IdDt) id;
-					otherId = (IdDt) other;
-				} else {
-					thisId = ((IResource) id).getId();
-					otherId = ((IResource) other).getId();
-				}
-				return thisId.getIdPartAsLong().equals(otherId.getIdPartAsLong());
+		return argThat(other -> {
+			IdDt thisId;
+			IdDt otherId;
+			if (id instanceof IdDt) {
+				thisId = (IdDt) id;
+				otherId = (IdDt) other;
+			} else {
+				thisId = ((IResource) id).getId();
+				otherId = ((IResource) other).getId();
 			}
+			return thisId.getIdPartAsLong().equals(otherId.getIdPartAsLong());
 		});
 	}
 
@@ -399,17 +398,16 @@ public class AbstractJaxRsResourceProviderTest {
 		System.out.println(ourPort);
 		jettyServer = new Server(ourPort);
 		jettyServer.setHandler(context);
-		ServletHolder jerseyServlet = context.addServlet(org.glassfish.jersey.servlet.ServletContainer.class, "/*");
+		ServletHolder jerseyServlet = context.addServlet(org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.class, "/*");
 		jerseyServlet.setInitOrder(0);
 
 		//@formatter:off
-		jerseyServlet.setInitParameter("jersey.config.server.provider.classnames",
+		jerseyServlet.setInitParameter("resteasy.resources",
 				StringUtils.join(Arrays.asList(
 					TestJaxRsMockPatientRestProvider.class.getCanonicalName(),
-					JaxRsExceptionInterceptor.class.getCanonicalName(),
 					TestJaxRsConformanceRestProvider.class.getCanonicalName(),
 					TestJaxRsMockPageProvider.class.getCanonicalName()
-						), ";"));
+						), ","));
 		//@formatter:on
 
 		jettyServer.start();
@@ -424,7 +422,7 @@ public class AbstractJaxRsResourceProviderTest {
 	}
 
 	@AfterClass
-	public static void tearDownClass() throws Exception {
+	public static void tearDownClass() {
 		try {
 			jettyServer.destroy();
 		} catch (Exception e) {

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/util/JaxRsRequestDstu3Test.java

@@ -1,34 +1,22 @@
 package ca.uhn.fhir.jaxrs.server.util;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.mockito.Mockito.doReturn;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.spy;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.util.Arrays;
-
-import javax.ws.rs.HttpMethod;
-import javax.ws.rs.core.MultivaluedHashMap;
-import javax.ws.rs.core.MultivaluedMap;
-import javax.ws.rs.core.UriInfo;
-
+import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProviderDstu3;
+import ca.uhn.fhir.rest.api.RequestTypeEnum;
+import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import org.apache.commons.lang3.StringUtils;
-import org.glassfish.jersey.internal.MapPropertiesDelegate;
-import org.glassfish.jersey.server.ContainerRequest;
+import org.jboss.resteasy.specimpl.ResteasyHttpHeaders;
 import org.junit.Before;
 import org.junit.Test;
 
-import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProvider;
-import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProviderDstu3;
-import ca.uhn.fhir.jaxrs.server.util.JaxRsRequest;
-import ca.uhn.fhir.jaxrs.server.util.JaxRsResponse;
-import ca.uhn.fhir.rest.api.RequestTypeEnum;
-import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
+import javax.ws.rs.core.MultivaluedHashMap;
+import javax.ws.rs.core.MultivaluedMap;
+import javax.ws.rs.core.UriInfo;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.Arrays;
+
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.*;
 
 public class JaxRsRequestDstu3Test {
 	
@@ -38,7 +26,7 @@ public class JaxRsRequestDstu3Test {
 	
 	private JaxRsRequest details;
 	private MultivaluedMap<String, String> queryParameters = new MultivaluedHashMap<String, String>();
-	private ContainerRequest headers;
+	private ResteasyHttpHeaders headers;
 	private TestJaxRsDummyPatientProviderDstu3 provider;
 	
 	@Before
@@ -52,11 +40,11 @@ public class JaxRsRequestDstu3Test {
 		String headerValue = "location_value";
 		String headerValue2 = "location_value_2";
 		assertTrue(StringUtils.isBlank(details.getHeader(headerKey)));
-		headers.header(headerKey, headerValue);
+		queryParameters.add(headerKey, headerValue);
 		assertEquals(headerValue, details.getHeader(headerKey));
 		assertEquals(Arrays.asList(headerValue), details.getHeaders(headerKey));
 		
-		headers.header(headerKey, headerValue2);
+		queryParameters.add(headerKey, headerValue2);
 		assertEquals(headerValue, details.getHeader(headerKey));
 		assertEquals(Arrays.asList(headerValue, headerValue2), details.getHeaders(headerKey));
 	}
@@ -98,9 +86,9 @@ public class JaxRsRequestDstu3Test {
 		assertEquals(this.provider, details.getServer());
 	}
 
-	public JaxRsRequest createRequestDetails() throws URISyntaxException {
-		//headers
-		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null, new MapPropertiesDelegate());
+	public JaxRsRequest createRequestDetails() {
+		// headers
+		headers = new ResteasyHttpHeaders(queryParameters);
 		
 		//uri info
 		UriInfo uriInfo = mock(UriInfo.class);

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/util/JaxRsRequestTest.java

@@ -1,31 +1,22 @@
 package ca.uhn.fhir.jaxrs.server.util;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.mockito.Mockito.doReturn;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.spy;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.util.Arrays;
-
-import javax.ws.rs.HttpMethod;
-import javax.ws.rs.core.MultivaluedHashMap;
-import javax.ws.rs.core.MultivaluedMap;
-import javax.ws.rs.core.UriInfo;
-
-import org.apache.commons.lang3.StringUtils;
-import org.glassfish.jersey.internal.MapPropertiesDelegate;
-import org.glassfish.jersey.server.ContainerRequest;
-import org.junit.Before;
-import org.junit.Test;
-
 import ca.uhn.fhir.jaxrs.server.test.TestJaxRsDummyPatientProvider;
 import ca.uhn.fhir.rest.api.RequestTypeEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
+import org.apache.commons.lang3.StringUtils;
+import org.jboss.resteasy.specimpl.ResteasyHttpHeaders;
+import org.junit.Before;
+import org.junit.Test;
+
+import javax.ws.rs.core.MultivaluedHashMap;
+import javax.ws.rs.core.MultivaluedMap;
+import javax.ws.rs.core.UriInfo;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.Arrays;
+
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.*;
 
 public class JaxRsRequestTest {
 	
@@ -35,7 +26,7 @@ public class JaxRsRequestTest {
 	
 	private JaxRsRequest details;
 	private MultivaluedMap<String, String> queryParameters = new MultivaluedHashMap<String, String>();
-	private ContainerRequest headers;
+	private ResteasyHttpHeaders headers;
 	private TestJaxRsDummyPatientProvider provider;
 	
 	@Before
@@ -49,11 +40,11 @@ public class JaxRsRequestTest {
 		String headerValue = "location_value";
 		String headerValue2 = "location_value_2";
 		assertTrue(StringUtils.isBlank(details.getHeader(headerKey)));
-		headers.header(headerKey, headerValue);
+		queryParameters.add(headerKey, headerValue);
 		assertEquals(headerValue, details.getHeader(headerKey));
 		assertEquals(Arrays.asList(headerValue), details.getHeaders(headerKey));
 		
-		headers.header(headerKey, headerValue2);
+		queryParameters.add(headerKey, headerValue2);
 		assertEquals(headerValue, details.getHeader(headerKey));
 		assertEquals(Arrays.asList(headerValue, headerValue2), details.getHeaders(headerKey));
 	}
@@ -96,8 +87,10 @@ public class JaxRsRequestTest {
 	}
 
 	public JaxRsRequest createRequestDetails() throws URISyntaxException {
-		//headers
-		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null, new MapPropertiesDelegate());
+		// headers
+//		headers = new ContainerRequest(new URI(BASEURI), new URI(REQUESTURI), HttpMethod.GET, null,
+//				new MapPropertiesDelegate());
+		headers = new ResteasyHttpHeaders(queryParameters);
 		
 		//uri info
 		UriInfo uriInfo = mock(UriInfo.class);

hapi-fhir-jaxrsserver-example/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -58,24 +58,12 @@
 			<version>${jetty_version}</version>
 		</dependency>
 		<dependency>
-			<groupId>org.glassfish.jersey.core</groupId>
-			<artifactId>jersey-server</artifactId>
-			<version>${jersey_version}</version>
+			<groupId>org.jboss.resteasy</groupId>
+			<artifactId>resteasy-jaxrs</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.glassfish.jersey.containers</groupId>
-			<artifactId>jersey-container-servlet-core</artifactId>
-			<version>${jersey_version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.glassfish.jersey.containers</groupId>
-			<artifactId>jersey-container-jetty-http</artifactId>
-			<version>${jersey_version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.glassfish.jersey.media</groupId>
-			<artifactId>jersey-media-moxy</artifactId>
-			<version>${jersey_version}</version>
+			<groupId>org.jboss.resteasy</groupId>
+			<artifactId>resteasy-client</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>ch.qos.logback</groupId>

hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderDstu3Test.java

@@ -43,15 +43,15 @@ public class JaxRsPatientProviderDstu3Test {
 		System.out.println(ourPort);
 		jettyServer = new Server(ourPort);
 		jettyServer.setHandler(context);
-		ServletHolder jerseyServlet = context.addServlet(org.glassfish.jersey.servlet.ServletContainer.class, "/*");
+		ServletHolder jerseyServlet = context.addServlet(org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.class, "/*");
 		jerseyServlet.setInitOrder(0);
 		//@formatter:off
-		jerseyServlet.setInitParameter("jersey.config.server.provider.classnames",
+		jerseyServlet.setInitParameter("resteasy.resources",
 				StringUtils.join(Arrays.asList(
 						JaxRsConformanceProviderDstu3.class.getCanonicalName(),
 						JaxRsPatientRestProviderDstu3.class.getCanonicalName(), 
 						JaxRsPageProviderDstu3.class.getCanonicalName()
-					), ";"));
+					), ","));
 		//@formatter:on
 		jettyServer.start();
 
@@ -108,11 +108,6 @@ public class JaxRsPatientProviderDstu3Test {
         }
     }
     
-    /** Search using other query options */
-    public void testOther() {
-        //missing
-    }
-    
     /** */ 
     @Test
     public void testSearchPost() {

hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderTest.java

@@ -47,15 +47,15 @@ public class JaxRsPatientProviderTest {
 		System.out.println(ourPort);
 		jettyServer = new Server(ourPort);
 		jettyServer.setHandler(context);
-		ServletHolder jerseyServlet = context.addServlet(org.glassfish.jersey.servlet.ServletContainer.class, "/*");
+		ServletHolder jerseyServlet = context.addServlet(org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.class, "/*");
 		jerseyServlet.setInitOrder(0);
 		//@formatter:off
-		jerseyServlet.setInitParameter("jersey.config.server.provider.classnames",
+		jerseyServlet.setInitParameter("resteasy.resources",
 				StringUtils.join(Arrays.asList(
 						JaxRsConformanceProvider.class.getCanonicalName(),
 						JaxRsPatientRestProvider.class.getCanonicalName(), 
 						JaxRsPageProvider.class.getCanonicalName()
-					), ";"));
+					), ","));
 		//@formatter:on
 		jettyServer.start();
 
@@ -119,11 +119,6 @@ public class JaxRsPatientProviderTest {
 		}
 	}
 
-	/** Search using other query options */
-	public void testOther() {
-		// missing
-	}
-
 	/** */
 	@Test
 	public void testSearchPost() {

hapi-fhir-jpaserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.4.0-SNAPSHOT</version>
+		<version>3.5.0-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -205,7 +205,25 @@
 		    <scope>provided</scope>
 		</dependency>
 
-
+		<!--
+		Dependencies that need to be added since JDK9
+		-->
+		<dependency>
+			<groupId>javax.annotation</groupId>
+			<artifactId>javax.annotation-api</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>javax.xml.bind</groupId>
+			<artifactId>jaxb-api</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.sun.xml.bind</groupId>
+			<artifactId>jaxb-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.sun.xml.bind</groupId>
+			<artifactId>jaxb-impl</artifactId>
+		</dependency>
 
 		<!-- Test Database -->
 		<dependency>
@@ -368,11 +386,22 @@
 		<dependency>
 			<groupId>com.sun.mail</groupId>
 			<artifactId>javax.mail</artifactId>
+			<scope>provided</scope>
+			<exclusions>
+				<exclusion>
+					<groupId>javax.activation</groupId>
+					<artifactId>activation</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
+			<groupId>com.sun.activation</groupId>
+			<artifactId>javax.activation</artifactId>
+		</dependency>
+		<!--<dependency>
 			<groupId>javax.validation</groupId>
 			<artifactId>validation-api</artifactId>
-		</dependency>
+		</dependency>-->
 		<dependency>
 			<groupId>javax.el</groupId>
 			<artifactId>javax.el-api</artifactId>
@@ -566,9 +595,19 @@
 					as JDK9 no longer includes them by default
 					-->
 					<dependency>
-						<groupId>org.glassfish.jaxb</groupId>
-						<artifactId>jaxb-runtime</artifactId>
-						<version>${jaxb_runtime_version}</version>
+						<groupId>javax.xml.bind</groupId>
+						<artifactId>jaxb-api</artifactId>
+						<version>${jaxb_api_version}</version>
+					</dependency>
+					<dependency>
+						<groupId>com.sun.xml.bind</groupId>
+						<artifactId>jaxb-core</artifactId>
+						<version>${jaxb_core_version}</version>
+					</dependency>
+					<dependency>
+						<groupId>com.sun.xml.bind</groupId>
+						<artifactId>jaxb-impl</artifactId>
+						<version>${jaxb_core_version}</version>
 					</dependency>
 				</dependencies>
 			</plugin>

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

@@ -58,6 +58,7 @@ import ca.uhn.fhir.util.*;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Charsets;
 import com.google.common.collect.ArrayListMultimap;
+import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
 import com.google.common.hash.HashFunction;
 import com.google.common.hash.Hashing;
@@ -85,6 +86,7 @@ import org.springframework.stereotype.Repository;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import javax.annotation.PostConstruct;
 import javax.persistence.*;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -372,22 +374,22 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	}
 
 	private void expungeCurrentVersionOfResource(Long theResourceId) {
-		ResourceTable resource = myResourceTableDao.findOne(theResourceId);
+		ResourceTable resource = myResourceTableDao.findById(theResourceId).orElseThrow(IllegalStateException::new);
 
 		ResourceHistoryTable currentVersion = myResourceHistoryTableDao.findForIdAndVersion(resource.getId(), resource.getVersion());
 		expungeHistoricalVersion(currentVersion.getId());
 
 		ourLog.info("Deleting current version of resource {}", resource.getIdDt().getValue());
 
-		myResourceIndexedSearchParamUriDao.delete(resource.getParamsUri());
-		myResourceIndexedSearchParamCoordsDao.delete(resource.getParamsCoords());
-		myResourceIndexedSearchParamDateDao.delete(resource.getParamsDate());
-		myResourceIndexedSearchParamNumberDao.delete(resource.getParamsNumber());
-		myResourceIndexedSearchParamQuantityDao.delete(resource.getParamsQuantity());
-		myResourceIndexedSearchParamStringDao.delete(resource.getParamsString());
-		myResourceIndexedSearchParamTokenDao.delete(resource.getParamsToken());
+		myResourceIndexedSearchParamUriDao.deleteAll(resource.getParamsUri());
+		myResourceIndexedSearchParamCoordsDao.deleteAll(resource.getParamsCoords());
+		myResourceIndexedSearchParamDateDao.deleteAll(resource.getParamsDate());
+		myResourceIndexedSearchParamNumberDao.deleteAll(resource.getParamsNumber());
+		myResourceIndexedSearchParamQuantityDao.deleteAll(resource.getParamsQuantity());
+		myResourceIndexedSearchParamStringDao.deleteAll(resource.getParamsString());
+		myResourceIndexedSearchParamTokenDao.deleteAll(resource.getParamsToken());
 
-		myResourceTagDao.delete(resource.getTags());
+		myResourceTagDao.deleteAll(resource.getTags());
 		resource.getTags().clear();
 
 		if (resource.getForcedId() != null) {
@@ -402,15 +404,15 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	}
 
 	protected void expungeHistoricalVersion(Long theNextVersionId) {
-		ResourceHistoryTable version = myResourceHistoryTableDao.findOne(theNextVersionId);
+		ResourceHistoryTable version = myResourceHistoryTableDao.findById(theNextVersionId).orElseThrow(IllegalArgumentException::new);
 		ourLog.info("Deleting resource version {}", version.getIdDt().getValue());
 
-		myResourceHistoryTagDao.delete(version.getTags());
+		myResourceHistoryTagDao.deleteAll(version.getTags());
 		myResourceHistoryTableDao.delete(version);
 	}
 
 	protected void expungeHistoricalVersionsOfId(Long theResourceId, AtomicInteger theRemainingCount) {
-		ResourceTable resource = myResourceTableDao.findOne(theResourceId);
+		ResourceTable resource = myResourceTableDao.findById(theResourceId).orElseThrow(IllegalArgumentException::new);
 
 		Pageable page = new PageRequest(0, theRemainingCount.get());
 
@@ -727,23 +729,32 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 
 	private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> getDaos() {
 		if (myResourceTypeToDao == null) {
-			Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> theResourceTypeToDao = new HashMap<>();
+			Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> resourceTypeToDao = new HashMap<>();
+
 			Map<String, IFhirResourceDao> daos = myApplicationContext.getBeansOfType(IFhirResourceDao.class, false, false);
+
+			String[] beanNames = myApplicationContext.getBeanNamesForType(IFhirResourceDao.class);
+
 			for (IFhirResourceDao<?> next : daos.values()) {
-				theResourceTypeToDao.put(next.getResourceType(), next);
+				resourceTypeToDao.put(next.getResourceType(), next);
 			}
 
 			if (this instanceof IFhirResourceDao<?>) {
 				IFhirResourceDao<?> thiz = (IFhirResourceDao<?>) this;
-				theResourceTypeToDao.put(thiz.getResourceType(), thiz);
+				resourceTypeToDao.put(thiz.getResourceType(), thiz);
 			}
 
-			myResourceTypeToDao = theResourceTypeToDao;
+			myResourceTypeToDao = resourceTypeToDao;
 		}
 
 		return Collections.unmodifiableMap(myResourceTypeToDao);
 	}
 
+	@PostConstruct
+	public void startClearCaches() {
+		myResourceTypeToDao = null;
+	}
+
 
 	protected Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IBaseResource theResource) {
 		return mySearchParamExtractor.extractSearchParamCoords(theEntity, theResource);
@@ -948,7 +959,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 
 	@Override
 	public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
-		myApplicationContext = theApplicationContext;
+		/*
+		 * We do a null check here because Smile's module system tries to
+		 * initialize the application context twice if two modules depend on
+		 * the persistence module. The second time sets the dependency's appctx.
+		 */
+		if (myApplicationContext == null) {
+			myApplicationContext = theApplicationContext;
+		}
 	}
 
 	public void setConfig(DaoConfig theConfig) {

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

@@ -1314,7 +1314,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		if (myDaoConfig.isEnforceReferentialIntegrityOnDelete() == false && !theForValidate) {
 			ourLog.debug("Deleting {} resource dependencies which can no longer be satisfied", resultList.size());
-			myResourceLinkDao.delete(resultList);
+			myResourceLinkDao.deleteAll(resultList);
 			return;
 		}
 
@@ -1336,5 +1336,9 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 	}
 
+	@PostConstruct
+	public void start() {
+		ourLog.debug("Starting resource DAO for type: {}", getResourceName());
+	}
 
 }

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

@@ -257,7 +257,7 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 	@Transactional(propagation = Propagation.NEVER)
 	public Integer performReindexingPass(final Integer theCount) {
 		if (!myReindexLock.tryLock()) {
-			return null;
+			return -1;
 		}
 		try {
 			return doPerformReindexingPass(theCount);
@@ -288,7 +288,7 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 				reindexFailure = txTemplate.execute(new TransactionCallback<Throwable>() {
 					@Override
 					public Throwable doInTransaction(TransactionStatus theStatus) {
-						ResourceTable resourceTable = myResourceTableDao.findOne(myNextId);
+						ResourceTable resourceTable = myResourceTableDao.findById(myNextId).orElseThrow(IllegalStateException::new);
 
 						try {
 							/*
@@ -305,7 +305,7 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 
 							final IBaseResource resource = toResource(resourceTable, false);
 
-							@SuppressWarnings("rawtypes") final IFhirResourceDao dao = getDao(resource.getClass());
+							@SuppressWarnings("rawtypes") final IFhirResourceDao dao = getDaoOrThrowException(resource.getClass());
 							dao.reindex(resource, resourceTable);
 							return null;
 

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

@@ -3,9 +3,11 @@ package ca.uhn.fhir.jpa.dao;
 import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
 import ca.uhn.fhir.jpa.util.JpaConstants;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import com.google.common.collect.Sets;
 import org.apache.commons.lang3.ObjectUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.time.DateUtils;
+import org.hl7.fhir.r4.model.Bundle;
 
 import java.util.*;
 
@@ -62,6 +64,19 @@ public class DaoConfig {
 	 * @see #setMaximumSearchResultCountInTransaction(Integer)
 	 */
 	private static final Integer DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = null;
+	/**
+	 * Default {@link #setBundleTypesAllowedForStorage(Set)} value:
+	 * <ul>
+	 * <li>collection</li>
+	 * <li>document</li>
+	 * <li>message</li>
+	 * </ul>
+	 */
+	private static final Set<String> DEFAULT_BUNDLE_TYPES_ALLOWED_FOR_STORAGE = Collections.unmodifiableSet(new TreeSet<>(Sets.newHashSet(
+		Bundle.BundleType.COLLECTION.toCode(),
+		Bundle.BundleType.DOCUMENT.toCode(),
+		Bundle.BundleType.MESSAGE.toCode()
+	)));
 	private IndexEnabledEnum myIndexMissingFieldsEnabled = IndexEnabledEnum.DISABLED;
 	/**
 	 * update setter javadoc if default changes
@@ -128,6 +143,7 @@ public class DaoConfig {
 	private boolean myMarkResourcesForReindexingUponSearchParameterChange;
 	private boolean myExpungeEnabled;
 	private int myReindexThreadCount;
+	private Set<String> myBundleTypesAllowedForStorage;
 
 	/**
 	 * Constructor
@@ -138,6 +154,7 @@ public class DaoConfig {
 		setSubscriptionPurgeInactiveAfterMillis(Long.MAX_VALUE);
 		setMarkResourcesForReindexingUponSearchParameterChange(true);
 		setReindexThreadCount(Runtime.getRuntime().availableProcessors());
+		setBundleTypesAllowedForStorage(DEFAULT_BUNDLE_TYPES_ALLOWED_FOR_STORAGE);
 	}
 
 	/**
@@ -154,6 +171,27 @@ public class DaoConfig {
 		myTreatReferencesAsLogical.add(theTreatReferencesAsLogical);
 	}
 
+	/**
+	 * This setting specifies the bundle types (<code>Bundle.type</code>) that
+	 * are allowed to be stored as-is on the /Bundle endpoint.
+	 *
+	 * @see #DEFAULT_BUNDLE_TYPES_ALLOWED_FOR_STORAGE
+	 */
+	public Set<String> getBundleTypesAllowedForStorage() {
+		return myBundleTypesAllowedForStorage;
+	}
+
+	/**
+	 * This setting specifies the bundle types (<code>Bundle.type</code>) that
+	 * are allowed to be stored as-is on the /Bundle endpoint.
+	 *
+	 * @see #DEFAULT_BUNDLE_TYPES_ALLOWED_FOR_STORAGE
+	 */
+	public void setBundleTypesAllowedForStorage(Set<String> theBundleTypesAllowedForStorage) {
+		Validate.notNull(theBundleTypesAllowedForStorage, "theBundleTypesAllowedForStorage must not be null");
+		myBundleTypesAllowedForStorage = theBundleTypesAllowedForStorage;
+	}
+
 	/**
 	 * Specifies the highest number that a client is permitted to use in a
 	 * <code>Cache-Control: nostore, max-results=NNN</code>
@@ -418,11 +456,8 @@ public class DaoConfig {
 	/**
 	 * This may be used to optionally register server interceptors directly against the DAOs.
 	 */
-	public void setInterceptors(IServerInterceptor... theInterceptor) {
-		setInterceptors(new ArrayList<IServerInterceptor>());
-		if (theInterceptor != null && theInterceptor.length != 0) {
-			getInterceptors().addAll(Arrays.asList(theInterceptor));
-		}
+	public void setInterceptors(List<IServerInterceptor> theInterceptors) {
+		myInterceptors = theInterceptors;
 	}
 
 	/**
@@ -1164,8 +1199,11 @@ public class DaoConfig {
 	/**
 	 * This may be used to optionally register server interceptors directly against the DAOs.
 	 */
-	public void setInterceptors(List<IServerInterceptor> theInterceptors) {
-		myInterceptors = theInterceptors;
+	public void setInterceptors(IServerInterceptor... theInterceptor) {
+		setInterceptors(new ArrayList<IServerInterceptor>());
+		if (theInterceptor != null && theInterceptor.length != 0) {
+			getInterceptors().addAll(Arrays.asList(theInterceptor));
+		}
 	}
 
 	/**

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoBundleDstu2.java

@@ -25,14 +25,19 @@ import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 
+import java.util.Set;
+
+import static org.apache.commons.lang3.StringUtils.defaultString;
+
 public class FhirResourceDaoBundleDstu2 extends FhirResourceDaoDstu2<Bundle> {
 
 	@Override
 	protected void preProcessResourceForStorage(Bundle theResource) {
 		super.preProcessResourceForStorage(theResource);
 
-		if (theResource.getTypeElement().getValueAsEnum() != BundleTypeEnum.DOCUMENT && theResource.getTypeElement().getValueAsEnum() != BundleTypeEnum.COLLECTION) {
-			String message = "Unable to store a Bundle resource on this server with a Bundle.type of: " + (theResource.getTypeElement().getValueAsEnum() != null ? theResource.getTypeElement().getValueAsEnum().getCode() : "(missing)");
+		Set<String> allowedBundleTypes = getConfig().getBundleTypesAllowedForStorage();
+		if (!allowedBundleTypes.contains(defaultString(theResource.getType()))) {
+			String message = "Unable to store a Bundle resource on this server with a Bundle.type value of: " + (theResource.getType() != null ? theResource.getType() : "(missing)");
 			throw new UnprocessableEntityException(message);
 		}
 

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

@@ -43,7 +43,9 @@ import org.hibernate.search.query.dsl.QueryBuilder;
 import org.hl7.fhir.dstu3.model.BaseResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.annotation.Transactional;
+import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
@@ -57,10 +59,14 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	private EntityManager myEntityManager;
+	@Autowired
+	private PlatformTransactionManager myTxManager;
 
 	@Autowired
 	protected IForcedIdDao myForcedIdDao;
 
+	private Boolean ourDisabled;
+
 	/**
 	 * Constructor
 	 */
@@ -73,7 +79,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 			return;
 		}
 		for (List<? extends IQueryParameterType> nextAnd : theTerms) {
-			Set<String> terms = new HashSet<String>();
+			Set<String> terms = new HashSet<>();
 			for (IQueryParameterType nextOr : nextAnd) {
 				StringParam nextOrString = (StringParam) nextOr;
 				String nextValueTrimmed = StringUtils.defaultString(nextOrString.getValue()).trim();
@@ -229,15 +235,25 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 
 	@Override
 	public boolean isDisabled() {
-		try {
-			FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
-			em.getSearchFactory().buildQueryBuilder().forEntity(ResourceTable.class).get();
-		} catch (Exception e) {
-			ourLog.trace("FullText test failed", e);
-			ourLog.debug("Hibernate Search (Lucene) appears to be disabled on this server, fulltext will be disabled");
-			return true;
+		Boolean retVal = ourDisabled;
+
+		if (retVal == null) {
+			retVal = new TransactionTemplate(myTxManager).execute(t -> {
+				try {
+					FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
+					em.getSearchFactory().buildQueryBuilder().forEntity(ResourceTable.class).get();
+					return Boolean.FALSE;
+				} catch (Exception e) {
+					ourLog.trace("FullText test failed", e);
+					ourLog.debug("Hibernate Search (Lucene) appears to be disabled on this server, fulltext will be disabled");
+					return Boolean.TRUE;
+				}
+			});
+			ourDisabled = retVal;
 		}
-		return false;
+
+		assert retVal != null;
+		return retVal;
 	}
 
 	@Transactional()
@@ -246,6 +262,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 		return doSearch(theResourceName, theParams, null);
 	}
 
+	@Transactional()
 	@Override
 	public List<Suggestion> suggestKeywords(String theContext, String theSearchParam, String theText) {
 		Validate.notBlank(theContext, "theContext must be provided");

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

@@ -144,7 +144,7 @@ import ca.uhn.fhir.util.UrlUtil;
 
 /**
  * The SearchBuilder is responsible for actually forming the SQL query that handles
- * searchs for resources
+ * searches for resources
  */
 public class SearchBuilder implements ISearchBuilder {
 
@@ -152,6 +152,7 @@ public class SearchBuilder implements ISearchBuilder {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchBuilder.class);
 	private static Long NO_MORE = -1L;
 	private static HandlerTypeEnum ourLastHandlerMechanismForUnitTest;
+	private static SearchParameterMap ourLastHandlerParamsForUnitTest;
 	private List<Long> myAlsoIncludePids;
 	private CriteriaBuilder myBuilder;
 	private BaseHapiFhirDao<?> myCallingDao;
@@ -1089,6 +1090,8 @@ public class SearchBuilder implements ISearchBuilder {
 					num = builder.or(lowPred, highPred);
 				}
 				break;
+			case ENDS_BEFORE:
+			case STARTS_AFTER:
 			default:
 				String msg = myContext.getLocalizer().getMessage(SearchBuilder.class, invalidMessageName, thePrefix.getValue(), theParam.getValueAsQueryToken(myContext));
 				throw new InvalidRequestException(msg);
@@ -1374,6 +1377,7 @@ public class SearchBuilder implements ISearchBuilder {
 									}
 
 									Set<String> uniqueQueryStrings = BaseHapiFhirDao.extractCompositeStringUniquesValueChains(myResourceName, params);
+									ourLastHandlerParamsForUnitTest = theParams;
 									ourLastHandlerMechanismForUnitTest = HandlerTypeEnum.UNIQUE_INDEX;
 									return new UniqueIndexIterator(uniqueQueryStrings);
 
@@ -1385,6 +1389,7 @@ public class SearchBuilder implements ISearchBuilder {
 			}
 		}
 
+		ourLastHandlerParamsForUnitTest = theParams;
 		ourLastHandlerMechanismForUnitTest = HandlerTypeEnum.STANDARD_QUERY;
 		return new QueryIterator();
 	}
@@ -1598,6 +1603,8 @@ public class SearchBuilder implements ISearchBuilder {
 				sortAttrName = new String[] {"myValue"};
 				joinType = JoinEnum.QUANTITY;
 				break;
+			case COMPOSITE:
+			case HAS:
 			default:
 				throw new InvalidRequestException("This server does not support _sort specifications of type " + param.getParamType() + " - Can't serve _sort=" + theSort.getParamName());
 		}
@@ -1832,7 +1839,6 @@ public class SearchBuilder implements ISearchBuilder {
 			roundCounts++;
 
 			HashSet<Long> pidsToInclude = new HashSet<>();
-			Set<Long> nextRoundOmit = new HashSet<>();
 
 			for (Iterator<Include> iter = includes.iterator(); iter.hasNext(); ) {
 				Include nextInclude = iter.next();
@@ -1927,8 +1933,6 @@ public class SearchBuilder implements ISearchBuilder {
 				}
 			}
 
-			pidsToInclude.removeAll(nextRoundOmit);
-
 			addedSomeThisRound = allAdded.addAll(pidsToInclude);
 			nextRoundMatches = pidsToInclude;
 		} while (includes.size() > 0 && nextRoundMatches.size() > 0 && addedSomeThisRound);
@@ -2104,6 +2108,8 @@ public class SearchBuilder implements ISearchBuilder {
 			case REFERENCE:
 				qp = new ReferenceParam();
 				break;
+			case URI:
+			case HAS:
 			default:
 				throw new InternalErrorException("Don't know how to convert param type: " + theParam.getParamType());
 		}
@@ -2202,14 +2208,18 @@ public class SearchBuilder implements ISearchBuilder {
 
 	@VisibleForTesting
 	public static HandlerTypeEnum getLastHandlerMechanismForUnitTest() {
-		ourLog.info("Retrieving last handler mechanism: {}", ourLastHandlerMechanismForUnitTest);
 		return ourLastHandlerMechanismForUnitTest;
 	}
 
+	@VisibleForTesting
+	public static SearchParameterMap getLastHandlerParamsForUnitTest() {
+		return ourLastHandlerParamsForUnitTest;
+	}
+
 	@VisibleForTesting
 	public static void resetLastHandlerMechanismForUnitTest() {
-		ourLog.info("Clearing last handler mechanism (was {})", ourLastHandlerMechanismForUnitTest);
 		ourLastHandlerMechanismForUnitTest = null;
+		ourLastHandlerParamsForUnitTest = null;
 	}
 
 	static Predicate[] toArray(List<Predicate> thePredicates) {

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

@@ -27,7 +27,7 @@ import org.springframework.data.repository.query.Param;
  */
 
 public interface ITermConceptMapGroupDao extends JpaRepository<TermConceptMapGroup, Long> {
-	@Query("DELETE FROM TermConceptMapGroup g WHERE g.myConceptMap.myId = :pid")
+	@Query("DELETE FROM TermConceptMapGroup g WHERE g.myId = :pid")
 	@Modifying
 	void deleteTermConceptMapGroupById(@Param("pid") Long theId);
 }

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

@@ -27,7 +27,7 @@ import org.springframework.data.repository.query.Param;
  */
 
 public interface ITermConceptMapGroupElementDao extends JpaRepository<TermConceptMapGroupElement, Long> {
-	@Query("DELETE FROM TermConceptMapGroupElement e WHERE e.myConceptMapGroup.myConceptMap.myId = :pid")
+	@Query("DELETE FROM TermConceptMapGroupElement e WHERE e.myId = :pid")
 	@Modifying
 	void deleteTermConceptMapGroupElementById(@Param("pid") Long theId);
 }

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

@@ -27,7 +27,7 @@ import org.springframework.data.repository.query.Param;
  */
 
 public interface ITermConceptMapGroupElementTargetDao extends JpaRepository<TermConceptMapGroupElementTarget, Long> {
-	@Query("DELETE FROM TermConceptMapGroupElementTarget t WHERE t.myConceptMapGroupElement.myConceptMapGroup.myConceptMap.myId = :pid")
+	@Query("DELETE FROM TermConceptMapGroupElementTarget t WHERE t.myId = :pid")
 	@Modifying
 	void deleteTermConceptMapGroupElementTargetById(@Param("pid") Long theId);
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoBundleDstu3.java

@@ -25,13 +25,18 @@ import org.hl7.fhir.dstu3.model.Bundle.BundleType;
 
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 
+import java.util.Set;
+
+import static org.apache.commons.lang3.StringUtils.defaultString;
+
 public class FhirResourceDaoBundleDstu3 extends FhirResourceDaoDstu3<Bundle> {
 
 	@Override
 	protected void preProcessResourceForStorage(Bundle theResource) {
 		super.preProcessResourceForStorage(theResource);
 
-		if (theResource.getType() != BundleType.DOCUMENT && theResource.getType() != BundleType.COLLECTION) {
+		Set<String> allowedBundleTypes = getConfig().getBundleTypesAllowedForStorage();
+		if (theResource.getType() == null || !allowedBundleTypes.contains(defaultString(theResource.getType().toCode()))) {
 			String message = "Unable to store a Bundle resource on this server with a Bundle.type value of: " + (theResource.getType() != null ? theResource.getType().toCode() : "(missing)");
 			throw new UnprocessableEntityException(message);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoBundleR4.java

@@ -25,19 +25,23 @@ import org.hl7.fhir.r4.model.Bundle.BundleType;
 
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 
+import java.util.Set;
+import java.util.TreeSet;
+
+import static org.apache.commons.lang3.StringUtils.defaultString;
+
 public class FhirResourceDaoBundleR4 extends FhirResourceDaoR4<Bundle> {
 
 	@Override
 	protected void preProcessResourceForStorage(Bundle theResource) {
 		super.preProcessResourceForStorage(theResource);
 
-		if (theResource.getType() != BundleType.DOCUMENT && theResource.getType() != BundleType.COLLECTION) {
+		Set<String> allowedBundleTypes = getConfig().getBundleTypesAllowedForStorage();
+		if (theResource.getType() == null || !allowedBundleTypes.contains(defaultString(theResource.getType().toCode()))) {
 			String message = "Unable to store a Bundle resource on this server with a Bundle.type value of: " + (theResource.getType() != null ? theResource.getType().toCode() : "(missing)");
 			throw new UnprocessableEntityException(message);
 		}
 
 	}
 
-
-
 }

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

@@ -115,11 +115,12 @@ public class TermConceptMap implements Serializable {
 		return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
 			.append("myId", myId)
 			.append("myResource", myResource.toString())
+			.append(myResource != null ? ("myResource=" + myResource.toString()) : ("myResource=(null)"))
 			.append("myResourcePid", myResourcePid)
 			.append("mySource", mySource)
 			.append("myTarget", myTarget)
 			.append("myUrl", myUrl)
-			.append("myConceptMapGroups - size", myConceptMapGroups.size())
+			.append(myConceptMapGroups != null ? ("myConceptMapGroups - size=" + myConceptMapGroups.size()) : ("myConceptMapGroups=(null)"))
 			.toString();
 	}
 }

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

@@ -137,12 +137,12 @@ public class TermConceptMapGroup implements Serializable {
 	public String toString() {
 		return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
 			.append("myId", myId)
-			.append("myConceptMap - id", myConceptMap.getId())
+			.append(myConceptMap != null ? ("myConceptMap - id=" + myConceptMap.getId()) : ("myConceptMap=(null)"))
 			.append("mySource", mySource)
 			.append("mySourceVersion", mySourceVersion)
 			.append("myTarget", myTarget)
 			.append("myTargetVersion", myTargetVersion)
-			.append("myConceptMapGroupElements - size", myConceptMapGroupElements.size())
+			.append(myConceptMapGroupElements != null ? ("myConceptMapGroupElements - size=" + myConceptMapGroupElements.size()) : ("myConceptMapGroupElements=(null)"))
 			.append("myConceptMapUrl", this.getConceptMapUrl())
 			.append("mySourceValueSet", this.getSourceValueSet())
 			.append("myTargetValueSet", this.getTargetValueSet())

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

@@ -151,10 +151,10 @@ public class TermConceptMapGroupElement implements Serializable {
 	public String toString() {
 		return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
 			.append("myId", myId)
-			.append("myConceptMapGroup - id", myConceptMapGroup.getId())
+			.append(myConceptMapGroup != null ? ("myConceptMapGroup - id=" + myConceptMapGroup.getId()) : ("myConceptMapGroup=(null)"))
 			.append("myCode", myCode)
 			.append("myDisplay", myDisplay)
-			.append("myConceptMapGroupElementTargets - size", myConceptMapGroupElementTargets.size())
+			.append(myConceptMapGroupElementTargets != null ? ("myConceptMapGroupElementTargets - size=" + myConceptMapGroupElementTargets.size()) : ("myConceptMapGroupElementTargets=(null)"))
 			.append("myConceptMapUrl", this.getConceptMapUrl())
 			.append("mySystem", this.getSystem())
 			.append("mySystemVersion", this.getSystemVersion())

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

@@ -153,7 +153,7 @@ public class TermConceptMapGroupElementTarget implements Serializable {
 	public String toString() {
 		return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
 			.append("myId", myId)
-			.append("myConceptMapGroupElement - id", myConceptMapGroupElement.getId())
+			.append(myConceptMapGroupElement != null ? ("myConceptMapGroupElement - id=" + myConceptMapGroupElement.getId()) : ("myConceptMapGroupElement=(null)"))
 			.append("myCode", myCode)
 			.append("myDisplay", myDisplay)
 			.append("myEquivalence", myEquivalence.toCode())

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

@@ -75,13 +75,13 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		mySearchEntity = null;
 	}
 
-	protected List<IBaseResource> doHistoryInTransaction(int theFromIndex, int theToIndex) {
+	private List<IBaseResource> doHistoryInTransaction(int theFromIndex, int theToIndex) {
 		List<ResourceHistoryTable> results;
 
 		CriteriaBuilder cb = myEntityManager.getCriteriaBuilder();
 		CriteriaQuery<ResourceHistoryTable> q = cb.createQuery(ResourceHistoryTable.class);
 		Root<ResourceHistoryTable> from = q.from(ResourceHistoryTable.class);
-		List<Predicate> predicates = new ArrayList<Predicate>();
+		List<Predicate> predicates = new ArrayList<>();
 
 		if (mySearchEntity.getResourceType() == null) {
 			// All resource types
@@ -215,6 +215,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		}
 	}
 
+	@Override
 	public String getUuid() {
 		return myUuid;
 	}
@@ -223,7 +224,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		return myCacheHit;
 	}
 
-	public void setCacheHit(boolean theCacheHit) {
+	void setCacheHit(boolean theCacheHit) {
 		myCacheHit = theCacheHit;
 	}
 
@@ -253,7 +254,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		mySearchDao = theSearchDao;
 	}
 
-	protected void setSearchEntity(Search theSearchEntity) {
+	void setSearchEntity(Search theSearchEntity) {
 		mySearchEntity = theSearchEntity;
 	}
 
@@ -269,8 +270,8 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		return Math.max(0, size);
 	}
 
-	protected List<IBaseResource> toResourceList(ISearchBuilder sb, List<Long> pidsSubList) {
-		Set<Long> includedPids = new HashSet<Long>();
+	List<IBaseResource> toResourceList(ISearchBuilder sb, List<Long> pidsSubList) {
+		Set<Long> includedPids = new HashSet<>();
 		if (mySearchEntity.getSearchType() == SearchTypeEnum.SEARCH) {
 			includedPids.addAll(sb.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated()));
 			includedPids.addAll(sb.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated()));

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

@@ -420,7 +420,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			private static final long serialVersionUID = 1L;
 
 			@Override
-			public int getOffset() {
+			public long getOffset() {
 				return theFromIndex;
 			}
 		};
@@ -702,7 +702,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 						nextResult.setOrder(myCountSaved++);
 						resultsToSave.add(nextResult);
 					}
-					mySearchResultDao.save(resultsToSave);
+					mySearchResultDao.saveAll(resultsToSave);
 
 					synchronized (mySyncedPids) {
 						int numSyncedThisPass = myUnsyncedPids.size();

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

@@ -67,13 +67,12 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 	private PlatformTransactionManager myTransactionManager;
 
 	private void deleteSearch(final Long theSearchPid) {
-		Search searchToDelete = mySearchDao.findOne(theSearchPid);
-		if (searchToDelete != null) {
+		mySearchDao.findById(theSearchPid).ifPresent(searchToDelete -> {
 			ourLog.info("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), new InstantType(searchToDelete.getCreated()), new InstantType(searchToDelete.getSearchLastReturned()));
 			mySearchIncludeDao.deleteForSearch(searchToDelete.getId());
 			mySearchResultDao.deleteForSearch(searchToDelete.getId());
 			mySearchDao.delete(searchToDelete);
-		}
+		});
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sp/SearchParamPresenceSvcImpl.java

@@ -104,7 +104,7 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
 		}
 
 		mySearchParamPresentDao.deleteInBatch(entitiesToDelete);
-		mySearchParamPresentDao.save(entitiesToSave);
+		mySearchParamPresentDao.saveAll(entitiesToSave);
 
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java

@@ -243,7 +243,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		ourLog.info(" * Deleting code system {}", theCodeSystem.getPid());
 
 		myEntityManager.flush();
-		TermCodeSystem cs = myCodeSystemDao.findOne(theCodeSystem.getPid());
+		TermCodeSystem cs = myCodeSystemDao.findById(theCodeSystem.getPid()).orElseThrow(IllegalStateException::new);
 		cs.setCurrentVersion(null);
 		myCodeSystemDao.save(cs);
 		myCodeSystemDao.flush();
@@ -252,8 +252,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		for (TermCodeSystemVersion next : myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystem.getPid())) {
 			myConceptParentChildLinkDao.deleteByCodeSystemVersion(next.getPid());
 			for (TermConcept nextConcept : myConceptDao.findByCodeSystemVersion(next.getPid())) {
-				myConceptPropertyDao.delete(nextConcept.getProperties());
-				myConceptDesignationDao.delete(nextConcept.getDesignations());
+				myConceptPropertyDao.deleteAll(nextConcept.getProperties());
+				myConceptDesignationDao.deleteAll(nextConcept.getDesignations());
 				myConceptDao.delete(nextConcept);
 			}
 			if (next.getCodeSystem().getCurrentVersion() == next) {
@@ -639,7 +639,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 			while (relCount < count && myConceptLinksToSaveLater.size() > 0) {
 				TermConceptParentChildLink next = myConceptLinksToSaveLater.remove(0);
 
-				if (myConceptDao.findOne(next.getChild().getId()) == null || myConceptDao.findOne(next.getParent().getId()) == null) {
+				if (!myConceptDao.findById(next.getChild().getId()).isPresent() || !myConceptDao.findById(next.getParent().getId()).isPresent()) {
 					ourLog.warn("Not inserting link from child {} to parent {} because it appears to have been deleted", next.getParent().getCode(), next.getChild().getCode());
 					continue;
 				}
@@ -850,7 +850,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 			ourLog.info(" * Deleting code system version {}", next.getPid());
 			myConceptParentChildLinkDao.deleteByCodeSystemVersion(next.getPid());
 			for (TermConcept nextConcept : myConceptDao.findByCodeSystemVersion(next.getPid())) {
-				myConceptPropertyDao.delete(nextConcept.getProperties());
+				myConceptPropertyDao.deleteAll(nextConcept.getProperties());
 				myConceptDao.delete(nextConcept);
 			}
 		}
@@ -964,20 +964,33 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		termConceptMap.setUrl(theConceptMap.getUrl());
 
 		// Get existing entity so it can be deleted.
-		Optional<TermConceptMap> optionalExistingTermConceptMapById = myConceptMapDao.findTermConceptMapByResourcePid(termConceptMap.getResourcePid());
+		Optional<TermConceptMap> optionalExistingTermConceptMapById = myConceptMapDao.findTermConceptMapByResourcePid(theResourceTable.getId());
 
 		/*
 		 * For now we always delete old versions. At some point, it would be nice to allow configuration to keep old versions.
 		 */
 
 		if (optionalExistingTermConceptMapById.isPresent()) {
-			Long id = optionalExistingTermConceptMapById.get().getId();
-			ourLog.info("Deleting existing TermConceptMap {} and its children...", id);
-			myConceptMapGroupElementTargetDao.deleteTermConceptMapGroupElementTargetById(id);
-			myConceptMapGroupElementDao.deleteTermConceptMapGroupElementById(id);
-			myConceptMapGroupDao.deleteTermConceptMapGroupById(id);
-			myConceptMapDao.deleteTermConceptMapById(id);
-			ourLog.info("Done deleting existing TermConceptMap {} and its children.", id);
+			TermConceptMap existingTermConceptMap = optionalExistingTermConceptMapById.get();
+
+			ourLog.info("Deleting existing TermConceptMap {} and its children...", existingTermConceptMap.getId());
+			for (TermConceptMapGroup group : existingTermConceptMap.getConceptMapGroups()) {
+
+				for (TermConceptMapGroupElement element : group.getConceptMapGroupElements()) {
+
+					for (TermConceptMapGroupElementTarget target : element.getConceptMapGroupElementTargets()) {
+
+						myConceptMapGroupElementTargetDao.deleteTermConceptMapGroupElementTargetById(target.getId());
+					}
+
+					myConceptMapGroupElementDao.deleteTermConceptMapGroupElementById(element.getId());
+				}
+
+				myConceptMapGroupDao.deleteTermConceptMapGroupById(group.getId());
+			}
+
+			myConceptMapDao.deleteTermConceptMapById(existingTermConceptMap.getId());
+			ourLog.info("Done deleting existing TermConceptMap {} and its children.", existingTermConceptMap.getId());
 
 			ourLog.info("Flushing...");
 			myConceptMapGroupElementTargetDao.flush();

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

@@ -21,11 +21,6 @@ public class SearchBuilderTest {
 	}
 
 
-	@Test
-	public void testAA() {
-		assertTrue(123.00004f <= 123.0001f);
-	}
-	
 	@Test
 	public void testCalculateMultiplierEqualNoDecimal() {
 		BigDecimal in = new BigDecimal("200");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java

@@ -14,7 +14,6 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
-import ca.uhn.fhir.jpa.util.SingleItemLoadingCache;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
@@ -42,7 +41,6 @@ import org.springframework.transaction.support.TransactionTemplate;
 import javax.persistence.EntityManager;
 import java.io.IOException;
 import java.io.InputStream;
-import java.util.Map;
 
 import static org.junit.Assert.*;
 import static org.mockito.Mockito.mock;
@@ -181,12 +179,13 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	}
 
 	@Before
-	@Transactional
 	public void beforeFlushFT() {
-		FullTextEntityManager ftem = Search.getFullTextEntityManager(myEntityManager);
-		ftem.purgeAll(ResourceTable.class);
-		ftem.purgeAll(ResourceIndexedSearchParamString.class);
-		ftem.flushToIndexes();
+		runInTransaction(() -> {
+			FullTextEntityManager ftem = Search.getFullTextEntityManager(myEntityManager);
+			ftem.purgeAll(ResourceTable.class);
+			ftem.purgeAll(ResourceIndexedSearchParamString.class);
+			ftem.flushToIndexes();
+		});
 
 		myDaoConfig.setSchedulingDisabled(true);
 		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);

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

@@ -319,7 +319,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 			myBundleDao.create(bundle, mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals("Unable to store a Bundle resource on this server with a Bundle.type of: (missing)", e.getMessage());
+			assertEquals("Unable to store a Bundle resource on this server with a Bundle.type value of: (missing)", e.getMessage());
 		}
 
 		bundle = new Bundle();
@@ -329,7 +329,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 			myBundleDao.create(bundle, mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals("Unable to store a Bundle resource on this server with a Bundle.type of: batch-response", e.getMessage());
+			assertEquals("Unable to store a Bundle resource on this server with a Bundle.type value of: batch-response", e.getMessage());
 		}
 
 		bundle = new Bundle();
@@ -2435,6 +2435,8 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertThat(actual, contains(id3, id2, id1));
 	}
 
+	@Test
+	@Ignore
 	public void testSortByQuantity() {
 		Observation res;
 
@@ -2700,6 +2702,8 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
+	@Test
+	@Ignore
 	public void testSortByUri() {
 		ConceptMap res = new ConceptMap();
 		res.addElement().addTarget().addDependsOn().setElement("http://foo2");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -274,12 +274,13 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	}
 
 	@Before
-	@Transactional
 	public void beforeFlushFT() {
-		FullTextEntityManager ftem = Search.getFullTextEntityManager(myEntityManager);
-		ftem.purgeAll(ResourceTable.class);
-		ftem.purgeAll(ResourceIndexedSearchParamString.class);
-		ftem.flushToIndexes();
+		runInTransaction(() -> {
+			FullTextEntityManager ftem = Search.getFullTextEntityManager(myEntityManager);
+			ftem.purgeAll(ResourceTable.class);
+			ftem.purgeAll(ResourceIndexedSearchParamString.class);
+			ftem.flushToIndexes();
+		});
 
 		myDaoConfig.setSchedulingDisabled(true);
 		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java

@@ -63,7 +63,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
 		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
 
-		ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
+		ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
 
 		TermCodeSystemVersion cs = new TermCodeSystemVersion();
 		cs.setResource(table);
@@ -106,7 +106,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
 		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
 
-		ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
+		ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
 
 		TermCodeSystemVersion cs = new TermCodeSystemVersion();
 		cs.setResource(table);
@@ -143,7 +143,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
 		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
 
-		ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
+		ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
 
 		TermCodeSystemVersion cs = new TermCodeSystemVersion();
 		cs.setResource(table);
@@ -707,7 +707,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
 		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
 
-		ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
+		ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
 
 		TermCodeSystemVersion cs = new TermCodeSystemVersion();
 		cs.setResource(table);