Some test fixes

hapi-fhir-jpaserver-base/pom.xml

@@ -398,6 +398,10 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
+		<dependency>
+			<groupId>com.sun.activation</groupId>
+			<artifactId>javax.activation</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>javax.validation</groupId>
 			<artifactId>validation-api</artifactId>

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserHl7OrgDstu2Test.java

@@ -1016,42 +1016,6 @@ public class JsonParserHl7OrgDstu2Test {
 		//@formatter:on
   }
 
-  /*
-   * Narrative generation is disabled for HL7org structs for now
-   */
-  // @Test
-  public void testNarrativeGeneration() throws DataFormatException, IOException {
-
-    Patient patient = new Patient();
-    patient.addName().addFamily("Smith");
-    Organization org = new Organization();
-    patient.getManagingOrganization().setResource(org);
-
-    INarrativeGenerator gen = new INarrativeGenerator() {
-
-      @Override
-      public void generateNarrative(FhirContext theContext, IBaseResource theResource, INarrative theNarrative) {
-        try {
-          theNarrative.setDivAsString("<div>help</div>");
-        } catch (Exception e) {
-          throw new Error(e);
-        }
-        theNarrative.setStatusAsString("generated");
-      }
-
-    };
-
-    FhirContext context = ourCtx;
-    context.setNarrativeGenerator(gen);
-    IParser p = context.newJsonParser();
-    p.encodeResourceToWriter(patient, new OutputStreamWriter(System.out));
-    String str = p.encodeResourceToString(patient);
-
-    ourLog.info(str);
-
-    assertThat(str, StringContains.containsString(",\"text\":{\"status\":\"generated\",\"div\":\"<div>help</div>\"},"));
-  }
-
   @Test
   public void testNestedContainedResources() {
 

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserHl7OrgDstu2Test.java

@@ -1502,37 +1502,6 @@ public class XmlParserHl7OrgDstu2Test {
         "<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
   }
 
-  // Narrative generation not currently supported for HL7org structures
-  public void testNarrativeGeneration() throws DataFormatException, IOException {
-
-    Patient patient = new Patient();
-    patient.addName().addFamily("Smith");
-    Organization org = new Organization();
-    patient.getManagingOrganization().setResource(org);
-
-    INarrativeGenerator gen = new INarrativeGenerator() {
-
-      @Override
-      public void generateNarrative(FhirContext theContext, IBaseResource theResource, INarrative theNarrative) {
-        try {
-          theNarrative.setDivAsString("<div>help</div>");
-        } catch (Exception e) {
-          throw new Error(e);
-        }
-        theNarrative.setStatusAsString("generated");
-      }
-
-    };
-
-    FhirContext context = ourCtx;
-    context.setNarrativeGenerator(gen);
-    IParser p = context.newXmlParser();
-    String str = p.encodeResourceToString(patient);
-
-    ourLog.info(str);
-
-    assertThat(str, StringContains.containsString(",\"text\":{\"status\":\"generated\",\"div\":\"<div>help</div>\"},"));
-  }
 
   @Test
   public void testNestedContainedResources() {

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/rest/server/BinaryHl7OrgDstu2Test.java

@@ -99,23 +99,6 @@ public class BinaryHl7OrgDstu2Test {
 
 	}
 
-	public void testCreateWrongType() throws Exception {
-		Binary res = new Binary();
-		res.setContent(new byte[] { 1, 2, 3, 4 });
-		res.setContentType("text/plain");
-		String stringContent = ourCtx.newJsonParser().encodeResourceToString(res);
-
-		HttpPost http = new HttpPost("http://localhost:" + ourPort + "/Binary");
-		http.setEntity(new StringEntity(stringContent, ContentType.create(Constants.CT_FHIR_JSON, "UTF-8")));
-
-		HttpResponse status = ourClient.execute(http);
-		assertEquals(201, status.getStatusLine().getStatusCode());
-
-		assertEquals("text/plain", ourLast.getContentType());
-		assertArrayEquals(new byte[] { 1, 2, 3, 4 }, ourLast.getContent());
-
-	}
-
 	@Test
 	public void testRead() throws Exception {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Binary/foo");

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/rest/server/IncludeHl7OrgDstu2Test.java

@@ -95,20 +95,6 @@ public class IncludeHl7OrgDstu2Test {
 		assertEquals("foo", p.getName().get(0).getFamily().get(0).getValue());
 	}
 
-	// @Test
-	public void testMixedContainedAndNonContained() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/DiagnosticReport?_query=stitchedInclude&_pretty=true");
-		HttpResponse status = ourClient.execute(httpGet);
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-
-		ourLog.info(responseContent);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		Bundle bundle = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
-		assertEquals(4, bundle.getEntry().size());
-	}
-
 	@Test
 	public void testIIncludedResourcesNonContained() throws Exception {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=normalInclude&_pretty=true");

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

@@ -185,20 +185,6 @@ public class IncludeTest {
 		}
 	}
 
-	// @Test
-	public void testMixedContainedAndNonContained() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/DiagnosticReport?_query=stitchedInclude&_pretty=true");
-		HttpResponse status = ourClient.execute(httpGet);
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-
-		ourLog.info(responseContent);
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		Bundle bundle = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
-		assertEquals(4, bundle.getEntry().size());
-	}
-
 	@Test
 	public void testNoIncludes() throws Exception {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello");

hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/QuestionnaireResponseValidatorDstu3Test.java

@@ -693,41 +693,6 @@ public class QuestionnaireResponseValidatorDstu3Test {
 		assertThat(errors.toString(), containsString("LinkId \"link1\" not found in questionnaire"));
 	}
 
-	// @Test
-	public void validateHealthConnexExample() throws Exception {
-		String input = IOUtils.toString(QuestionnaireResponseValidatorDstu3Test.class.getResourceAsStream("/questionnaireanswers-0f431c50ddbe4fff8e0dd6b7323625fc.xml"));
-
-		QuestionnaireResponse qa = ourCtx.newXmlParser().parseResource(QuestionnaireResponse.class, input);
-		ValidationResult errors = myVal.validateWithResult(qa);
-		assertEquals(errors.toString(), 0, errors.getMessages().size());
-
-		/*
-		 * Now change a coded value
-		 */
-		//@formatter:off
-		input = input.replaceAll(
-			"<answer>\n" +
-				"					<valueCoding>\n" +
-				"						<system value=\"f69573b8-cb63-4d31-85a4-23ac784735ab\"/>\n" +
-				"						<code value=\"2\"/>\n" +
-				"						<display value=\"Once/twice\"/>\n" +
-				"					</valueCoding>\n" +
-				"				</answer>",
-			"<answer>\n" +
-				"					<valueCoding>\n" +
-				"						<system value=\"f69573b8-cb63-4d31-85a4-23ac784735ab\"/>\n" +
-				"						<code value=\"GGG\"/>\n" +
-				"						<display value=\"Once/twice\"/>\n" +
-				"					</valueCoding>\n" +
-				"				</answer>");
-		assertThat(input, containsString("GGG"));
-		//@formatter:on
-
-		qa = ourCtx.newXmlParser().parseResource(QuestionnaireResponse.class, input);
-		errors = myVal.validateWithResult(qa);
-		assertEquals(errors.toString(), 10, errors.getMessages().size());
-	}
-
 	@AfterClass
 	public static void afterClassClearContext() {
 		myDefaultValidationSupport.flush();

pom.xml

@@ -493,13 +493,13 @@
 		<jaxb_api_version>2.3.0</jaxb_api_version>
 		<jaxb_core_version>2.3.0</jaxb_core_version>
 		<jersey_version>2.25.1</jersey_version>
-		<jetty_version>9.4.8.v20171121</jetty_version>
+		<jetty_version>9.4.10.v20180503</jetty_version>
 		<jsr305_version>3.0.2</jsr305_version>
 		<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
-		<hibernate_version>5.2.16.Final</hibernate_version>
+		<hibernate_version>5.3.1.Final</hibernate_version>
 		<hibernate_validator_version>5.4.1.Final</hibernate_validator_version>
 		<!-- Update lucene version when you update hibernate-search version -->
-		<hibernate_search_version>5.7.1.Final</hibernate_search_version>
+		<hibernate_search_version>5.10.1.Final</hibernate_search_version>
 		<httpcore_version>4.4.6</httpcore_version>
 		<httpclient_version>4.5.3</httpclient_version>
 		<lucene_version>5.5.4</lucene_version>
@@ -510,7 +510,7 @@
 		<ph_commons_version>9.1.1</ph_commons_version>
 		<servicemix_saxon_version>9.5.1-5_1</servicemix_saxon_version>
 		<servicemix_xmlresolver_version>1.2_5</servicemix_xmlresolver_version>
-		<spring_version>5.0.3.RELEASE</spring_version>
+		<spring_version>5.0.6.RELEASE</spring_version>
 		<spring-boot.version>1.5.6.RELEASE</spring-boot.version>
 		<stax2_api_version>3.1.4</stax2_api_version>
 		<thymeleaf-version>3.0.9.RELEASE</thymeleaf-version>
@@ -625,6 +625,11 @@
 				<artifactId>okhttp</artifactId>
 				<version>3.8.1</version>
 			</dependency>
+			<dependency>
+				<groupId>com.sun.activation</groupId>
+				<artifactId>javax.activation</artifactId>
+				<version>1.2.0</version>
+			</dependency>
 			<dependency>
 				<groupId>com.sun.mail</groupId>
 				<artifactId>javax.mail</artifactId>

src/changes/changes.xml

@@ -6,6 +6,20 @@
 		<title>HAPI FHIR Changelog</title>
 	</properties>
 	<body>
+		<release version="3.5.0" date="TBD">
+			<action type="add">
+				The version of a few dependencies have been bumped to the
+				latest versions (dependent HAPI modules listed in brackets):
+				<![CDATA[
+					<ul>
+						<li>Spring Framework (JPA): 5.0.3.RELEASE -&gt; 5.0.6.RELEASE</li>
+						<li>Hibernate OR (JPA): 5.2.16.Final -&gt; 5.3.1.Final</li>
+						<li>Hibernate Search (JPA): 5.7.1.Final -&gt; 5.10.1.Final</li>
+						<li>Jetty (CLI): 9.4.8.v20171121 -&gt; 9.4.10.v20180503</li>
+					</ul>
+				]]>
+			</action>
+		</release>
 		<release version="3.4.0" date="2018-05-28">
 			<action type="add">
 				The version of a few dependencies have been bumped to the