Merge branch 'java9'

.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

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

@@ -14,6 +14,7 @@
 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 void ActivityDefinitionApplyTest() {
 		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");

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

@@ -72,6 +72,7 @@ public void testParserJson() {
 	 * 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 void testBinaryCreateWithNoContentType() throws Exception {
 	@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 void testClientFailures() throws Exception {
 			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/src/main/java/ca/uhn/fhir/util/XmlUtil.java

@@ -1757,8 +1757,8 @@ static void setThrowExceptionForUnitTest(Throwable theException) {
 
 	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

@@ -166,32 +166,40 @@
 			<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>
 		<dependency>
 			<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-client-okhttp/pom.xml

@@ -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-jacoco/pom.xml

@@ -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

@@ -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 @@ protected AbstractJaxRsConformanceProvider(FhirContext ctx, String implementatio
 	 * 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 @@ protected void setUpPostConstruct() {
 			default:
 				throw new ConfigurationException("Unsupported Fhir version: " + fhirContextVersion);
 		}
+
+		myInitialized = true;
 	}
 
 	/**
@@ -184,6 +191,8 @@ public Response conformanceUsingOptions() throws IOException {
 	@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 @@
  * a large amount of the fhir api functionality using JAXRS
  * @author Peter Van Houte | [email protected] | 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 @@ private ConcurrentHashMap<String, BaseMethodBinding<?>> getMapForOperation(RestO
      */
     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 {