Merge branch 'master' into 2849_add_new_mdm_param

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
     <parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>5.5.0-PRE8-SNAPSHOT</version>
+		 <version>5.6.0-PRE1-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>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -75,6 +75,7 @@ public enum VersionEnum {
 	V5_4_1,
 	V5_4_2,
 	V5_5_0,
+	V5_6_0
 	;
 
 	public static VersionEnum latestVersion() {

hapi-fhir-bom/pom.xml

@@ -3,14 +3,14 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>ca.uhn.hapi.fhir</groupId>
     <artifactId>hapi-fhir-bom</artifactId>
-    <version>5.5.0-PRE8-SNAPSHOT</version>
+    <version>5.6.0-PRE1-SNAPSHOT</version>
     <packaging>pom</packaging>
 	 <name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
     

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>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -39,8 +39,8 @@ import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.input.CountingInputStream;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.ICompositeType;
-import org.hl7.fhir.r4.model.CodeSystem;
 
 import java.io.ByteArrayOutputStream;
 import java.io.File;
@@ -154,7 +154,7 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
 								throw new ParseException("Could not detect FHIR encoding for file: " + nextDataFile);
 							}
 
-							CodeSystem resource = encoding.newParser(myFhirCtx).parseResource(CodeSystem.class, contents);
+							IBaseResource resource = encoding.newParser(myFhirCtx).parseResource(contents);
 							ParametersUtil.addParameterToParameters(myFhirCtx, inputParameters, TerminologyUploaderProvider.PARAM_CODESYSTEM, resource);
 
 						} else {

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

@@ -0,0 +1,197 @@
+package ca.uhn.fhir.cli;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.term.UploadStatistics;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.test.utilities.JettyUtil;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.ParseException;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.r4.model.IdType;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+import static org.hamcrest.CoreMatchers.hasItems;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyList;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+public class HeaderPassthroughOptionTest {
+	final String FHIR_VERSION = "r4";
+	private FhirContext myCtx = FhirContext.forR4();
+	private Server myServer;
+	private int myPort;
+	private final String headerKey1 = "test-header-key-1";
+	private final String headerValue1 = "test header value-1";
+	private static final String myConceptsFileName = "target/concepts.csv";
+	private static File myConceptsFile = new File(myConceptsFileName);
+	private static final String myHierarchyFileName = "target/hierarchy.csv";
+	private static File myHierarchyFile = new File(myHierarchyFileName);
+	private final CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
+	private final UploadTerminologyCommand testedCommand =
+		new RequestCapturingUploadTerminologyCommand(myCapturingInterceptor);
+
+	@Mock
+	protected ITermLoaderSvc myTermLoaderSvc;
+
+	@BeforeEach
+	public void beforeEach() throws Exception {
+		myServer = new Server(0);
+		TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTermLoaderSvc);
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(myCtx);
+		servlet.registerProvider(provider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		myServer.setHandler(proxyHandler);
+		JettyUtil.startServer(myServer);
+		myPort = JettyUtil.getPortForStartedServer(myServer);
+		writeConceptAndHierarchyFiles();
+		when(myTermLoaderSvc.loadCustom(eq("http://foo"), anyList(), any()))
+			.thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+	}
+
+	@Test
+	public void oneHeader() throws Exception {
+		String[] args = new String[] {
+			"-v", FHIR_VERSION,
+			"-m", "SNAPSHOT",
+			"-t", "http://localhost:" + myPort,
+			"-u", "http://foo",
+			"-d", myConceptsFileName,
+			"-d", myHierarchyFileName,
+			"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\""
+		};
+
+		final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
+		testedCommand.run(commandLine);
+
+		assertNotNull(myCapturingInterceptor.getLastRequest());
+		Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
+		assertFalse(allHeaders.isEmpty());
+
+		assertTrue(allHeaders.containsKey(headerKey1));
+		assertEquals(1, allHeaders.get(headerKey1).size());
+
+		assertThat(allHeaders.get(headerKey1), hasItems(headerValue1));
+	}
+
+	@Test
+	public void twoHeadersSameKey() throws Exception {
+		final String headerValue2 = "test header value-2";
+
+		String[] args = new String[] {
+			"-v", FHIR_VERSION,
+			"-m", "SNAPSHOT",
+			"-t", "http://localhost:" + myPort,
+			"-u", "http://foo",
+			"-d", myConceptsFileName,
+			"-d", myHierarchyFileName,
+			"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\"",
+			"-hp", "\"" + headerKey1 + ":" + headerValue2 + "\""
+		};
+
+		final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
+		testedCommand.run(commandLine);
+
+		assertNotNull(myCapturingInterceptor.getLastRequest());
+		Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
+		assertFalse(allHeaders.isEmpty());
+		assertEquals(2, allHeaders.get(headerKey1).size());
+
+		assertTrue(allHeaders.containsKey(headerKey1));
+		assertEquals(2, allHeaders.get(headerKey1).size());
+
+		assertEquals(headerValue1, allHeaders.get(headerKey1).get(0));
+		assertEquals(headerValue2, allHeaders.get(headerKey1).get(1));
+	}
+
+	@Test
+	public void twoHeadersDifferentKeys() throws Exception {
+		final String headerKey2 = "test-header-key-2";
+		final String headerValue2 = "test header value-2";
+
+		String[] args = new String[] {
+			"-v", FHIR_VERSION,
+			"-m", "SNAPSHOT",
+			"-t", "http://localhost:" + myPort,
+			"-u", "http://foo",
+			"-d", myConceptsFileName,
+			"-d", myHierarchyFileName,
+			"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\"",
+			"-hp", "\"" + headerKey2 + ":" + headerValue2 + "\""
+		};
+
+		final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
+		testedCommand.run(commandLine);
+
+		assertNotNull(myCapturingInterceptor.getLastRequest());
+		Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
+		assertFalse(allHeaders.isEmpty());
+
+		assertTrue(allHeaders.containsKey(headerKey1));
+		assertEquals(1, allHeaders.get(headerKey1).size());
+		assertThat(allHeaders.get(headerKey1), hasItems(headerValue1));
+
+		assertTrue(allHeaders.containsKey(headerKey2));
+		assertEquals(1, allHeaders.get(headerKey2).size());
+		assertThat(allHeaders.get(headerKey2), hasItems(headerValue2));
+	}
+
+	private synchronized void writeConceptAndHierarchyFiles() throws IOException {
+		if (!myConceptsFile.exists()) {
+			try (FileWriter w = new FileWriter(myConceptsFile, false)) {
+				w.append("CODE,DISPLAY\n");
+				w.append("ANIMALS,Animals\n");
+				w.append("CATS,Cats\n");
+				w.append("DOGS,Dogs\n");
+			}
+		}
+
+		if (!myHierarchyFile.exists()) {
+			try (FileWriter w = new FileWriter(myHierarchyFile, false)) {
+				w.append("PARENT,CHILD\n");
+				w.append("ANIMALS,CATS\n");
+				w.append("ANIMALS,DOGS\n");
+			}
+		}
+	}
+
+	private class RequestCapturingUploadTerminologyCommand extends UploadTerminologyCommand {
+		private CapturingInterceptor myCapturingInterceptor;
+
+		public RequestCapturingUploadTerminologyCommand(CapturingInterceptor theCapturingInterceptor) {
+			myCapturingInterceptor = theCapturingInterceptor;
+		}
+
+		@Override
+		protected IGenericClient newClient(CommandLine theCommandLine) throws ParseException {
+			IGenericClient client = super.newClient(theCommandLine);
+			client.getInterceptorService().registerInterceptor(myCapturingInterceptor);
+			return client;
+		}
+	}
+}

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

@@ -4,31 +4,21 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.term.UploadStatistics;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
-import ca.uhn.fhir.rest.client.api.IGenericClient;
-import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
 import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.test.BaseTest;
 import ca.uhn.fhir.test.utilities.JettyUtil;
-import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
 import com.google.common.base.Charsets;
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.DefaultParser;
-import org.apache.commons.cli.ParseException;
 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.hamcrest.Matchers;
-import org.hl7.fhir.r4.model.CodeSystem;
-import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.Patient;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Nested;
+import org.junit.jupiter.api.TestInfo;
-import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
-import org.junit.jupiter.api.extension.RegisterExtension;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.MethodSource;
 import org.mockito.ArgumentCaptor;
 import org.mockito.Captor;
 import org.mockito.Mock;
@@ -41,65 +31,108 @@ import java.io.FileOutputStream;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.util.List;
-import java.util.Map;
+import java.util.stream.Stream;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
 import static org.hamcrest.CoreMatchers.containsString;
-import static org.hamcrest.CoreMatchers.hasItems;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.greaterThan;
 import static org.hamcrest.Matchers.matchesPattern;
 import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyList;
 import static org.mockito.ArgumentMatchers.eq;
-import static org.mockito.Mockito.anyList;
 import static org.mockito.Mockito.times;
 import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
 
 @ExtendWith(MockitoExtension.class)
-public class UploadTerminologyCommandTest extends BaseTest {
+public class UploadTerminologyCommandTest {
+	private static final String FHIR_VERSION_DSTU3 = "DSTU3";
+	private static final String FHIR_VERSION_R4 = "R4";
+	private FhirContext myCtx;
+	private final String myConceptsFileName = "target/concepts.csv";
+	private File myConceptsFile = new File(myConceptsFileName);
+	private final String myHierarchyFileName = "target/hierarchy.csv";
+	private File myHierarchyFile = new File(myHierarchyFileName);
+	private final String myCodeSystemFileName = "target/codesystem.json";
+	private File myCodeSystemFile = new File(myCodeSystemFileName);
+	private final String myTextFileName = "target/hello.txt";
+	private File myTextFile = new File(myTextFileName);
+	private final String myPropertiesFileName = "target/hello.properties";
+	private File myPropertiesFile = new File(myTextFileName);
+	private File myArchiveFile;
+	private String myArchiveFileName;
+	private final String myICD10URL = "http://hl7.org/fhir/sid/icd-10-cm";
+	private final String myICD10FileName = new File("src/test/resources").getAbsolutePath() + "/icd10cm_tabular_2021.xml";
+	private File myICD10File = new File(myICD10FileName);
+	private Server myServer;
+	private int myPort;
+
+	@Mock
+	protected ITermLoaderSvc myTermLoaderSvc;
+
+	@Captor
+	protected ArgumentCaptor<List<ITermLoaderSvc.FileDescriptor>> myDescriptorListCaptor;
 
 	static {
 		System.setProperty("test", "true");
 	}
 
-	private Server myServer;
+	static Stream<String> paramsProvider() {
-	private FhirContext myCtx = FhirContext.forR4();
+		return Stream.of(FHIR_VERSION_DSTU3, FHIR_VERSION_R4);
-	@Mock
+	}
-	private ITermLoaderSvc myTermLoaderSvc;
-	@Captor
-	private ArgumentCaptor<List<ITermLoaderSvc.FileDescriptor>> myDescriptorListCaptor;
-
-	private int myPort;
-	private String myConceptsFileName = "target/concepts.csv";
-	private File myConceptsFile = new File(myConceptsFileName);
-	private String myHierarchyFileName = "target/hierarchy.csv";
-	private File myHierarchyFile = new File(myHierarchyFileName);
-	private String myCodeSystemFileName = "target/codesystem.json";
-	private File myCodeSystemFile = new File(myCodeSystemFileName);
-	private String myTextFileName = "target/hello.txt";
-	private File myTextFile = new File(myTextFileName);
-	private File myArchiveFile;
-	private String myArchiveFileName;
-	private String myPropertiesFileName = "target/hello.properties";
-	private File myPropertiesFile = new File(myTextFileName);
-
-	@Test
-	public void testDeltaAdd() throws IOException {
 
+	@BeforeEach
+	public void beforeEach(TestInfo testInfo) throws Exception {
 		writeConceptAndHierarchyFiles();
+		if (testInfo.getDisplayName().endsWith(FHIR_VERSION_DSTU3)) {
+			myCtx = FhirContext.forDstu3();
+		} else if (testInfo.getDisplayName().endsWith(FHIR_VERSION_R4)) {
+			myCtx = FhirContext.forR4();
+		} else {
+			fail("Unknown FHIR Version param provided: " + testInfo.getDisplayName());
+		}
+		myServer = new Server(0);
+		TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTermLoaderSvc);
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(myCtx);
+		servlet.registerProvider(provider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		myServer.setHandler(proxyHandler);
+		JettyUtil.startServer(myServer);
+		myPort = JettyUtil.getPortForStartedServer(myServer);
+	}
 
-		when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+	@AfterEach
+	public void afterEach() throws Exception {
+		JettyUtil.closeServer(myServer);
+		FileUtils.deleteQuietly(myConceptsFile);
+		FileUtils.deleteQuietly(myHierarchyFile);
+		FileUtils.deleteQuietly(myCodeSystemFile);
+		FileUtils.deleteQuietly(myTextFile);
+		FileUtils.deleteQuietly(myArchiveFile);
+		FileUtils.deleteQuietly(myPropertiesFile);
+		UploadTerminologyCommand.setTransferSizeLimitForUnitTest(-1);
+	}
+
+	@ParameterizedTest
+	@MethodSource("paramsProvider")
+	public void testDeltaAdd(String theFhirVersion) throws IOException {
+		if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
+			when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));
+		} else if (FHIR_VERSION_R4.equals(theFhirVersion)) {
+			when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.r4.model.IdType("CodeSystem/101")));
+		} else {
+			fail("Unknown FHIR Version param provided: " + theFhirVersion);
+		}
 
 		App.main(new String[]{
 			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
-			"-v", "r4",
+			"-v", theFhirVersion,
 			"-m", "ADD",
 			"-t", "http://localhost:" + myPort,
 			"-u", "http://foo",
@@ -115,20 +148,30 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testDeltaAddUsingCodeSystemResource() throws IOException {
+	@MethodSource("paramsProvider")
-
+	public void testDeltaAddUsingCodeSystemResource(String theFhirVersion) throws IOException {
-		try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
+		if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
-			CodeSystem cs = new CodeSystem();
+			try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
-			cs.addConcept().setCode("CODE").setDisplay("Display");
+				org.hl7.fhir.dstu3.model.CodeSystem cs = new org.hl7.fhir.dstu3.model.CodeSystem();
-			myCtx.newJsonParser().encodeResourceToWriter(cs, w);
+				cs.addConcept().setCode("CODE").setDisplay("Display");
+				myCtx.newJsonParser().encodeResourceToWriter(cs, w);
+			}
+		} else if (FHIR_VERSION_R4.equals(theFhirVersion)) {
+			try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
+				org.hl7.fhir.r4.model.CodeSystem cs = new org.hl7.fhir.r4.model.CodeSystem();
+				cs.addConcept().setCode("CODE").setDisplay("Display");
+				myCtx.newJsonParser().encodeResourceToWriter(cs, w);
+			}
+		} else {
+			fail("Unknown FHIR Version param provided: " + theFhirVersion);
 		}
 
-		when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+		when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.r4.model.IdType("CodeSystem/101")));
 
 		App.main(new String[]{
 			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
-			"-v", "r4",
+			"-v", theFhirVersion,
 			"-m", "ADD",
 			"-t", "http://localhost:" + myPort,
 			"-u", "http://foo",
@@ -144,19 +187,29 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		assertThat(uploadFile, uploadFile, containsString("\"CODE\",\"Display\""));
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testDeltaAddInvalidResource() throws IOException {
+	@MethodSource("paramsProvider")
-
+	public void testDeltaAddInvalidResource(String theFhirVersion) throws IOException {
-		try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
+		if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
-			Patient patient = new Patient();
+			try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
-			patient.setActive(true);
+				org.hl7.fhir.dstu3.model.Patient patient = new org.hl7.fhir.dstu3.model.Patient();
-			myCtx.newJsonParser().encodeResourceToWriter(patient, w);
+				patient.setActive(true);
+				myCtx.newJsonParser().encodeResourceToWriter(patient, w);
+			}
+		} else if (FHIR_VERSION_R4.equals(theFhirVersion)) {
+			try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
+				org.hl7.fhir.r4.model.Patient patient = new org.hl7.fhir.r4.model.Patient();
+				patient.setActive(true);
+				myCtx.newJsonParser().encodeResourceToWriter(patient, w);
+			}
+		} else {
+			fail("Unknown FHIR Version param provided: " + theFhirVersion);
 		}
 
 		try {
 			App.main(new String[]{
 				UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
-				"-v", "r4",
+				"-v", theFhirVersion,
 				"-m", "ADD",
 				"-t", "http://localhost:" + myPort,
 				"-u", "http://foo",
@@ -164,13 +217,13 @@ public class UploadTerminologyCommandTest extends BaseTest {
 			});
 			fail();
 		} catch (Error e) {
-			assertThat(e.toString(), containsString("Incorrect resource type found, expected \"CodeSystem\" but found \"Patient\""));
+			assertThat(e.toString(), containsString("HTTP 400 Bad Request: Request has parameter codeSystem of type Patient but method expects type CodeSystem"));
 		}
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testDeltaAddInvalidFileType() throws IOException {
+	@MethodSource("paramsProvider")
-
+	public void testDeltaAddInvalidFileType(String theFhirVersion) throws IOException {
 		try (FileWriter w = new FileWriter(myTextFileName, false)) {
 			w.append("Help I'm a Bug");
 		}
@@ -178,7 +231,7 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		try {
 			App.main(new String[]{
 				UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
-				"-v", "r4",
+				"-v", theFhirVersion,
 				"-m", "ADD",
 				"-t", "http://localhost:" + myPort,
 				"-u", "http://foo",
@@ -190,17 +243,16 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		}
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testDeltaAddUsingCompressedFile() throws IOException {
+	@MethodSource("paramsProvider")
-
+	public void testDeltaAddUsingCompressedFile(String theFhirVersion) throws IOException {
-		writeConceptAndHierarchyFiles();
 		writeArchiveFile(myConceptsFile, myHierarchyFile);
 
-		when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+		when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.r4.model.IdType("CodeSystem/101")));
 
 		App.main(new String[]{
 			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
-			"-v", "r4",
+			"-v", theFhirVersion,
 			"-m", "ADD",
 			"-t", "http://localhost:" + myPort,
 			"-u", "http://foo",
@@ -215,15 +267,13 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testDeltaAddInvalidFileName() throws IOException {
+	@MethodSource("paramsProvider")
-
+	public void testDeltaAddInvalidFileName(String theFhirVersion) throws IOException {
-		writeConceptAndHierarchyFiles();
-
 		try {
 			App.main(new String[]{
 				UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
-				"-v", "r4",
+				"-v", theFhirVersion,
 				"-m", "ADD",
 				"-t", "http://localhost:" + myPort,
 				"-u", "http://foo",
@@ -235,15 +285,20 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		}
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testDeltaRemove() throws IOException {
+	@MethodSource("paramsProvider")
-		writeConceptAndHierarchyFiles();
+	public void testDeltaRemove(String theFhirVersion) throws IOException {
-
+		if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
-		when(myTermLoaderSvc.loadDeltaRemove(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+			when(myTermLoaderSvc.loadDeltaRemove(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));
+		} else if (FHIR_VERSION_R4.equals(theFhirVersion)) {
+			when(myTermLoaderSvc.loadDeltaRemove(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.r4.model.IdType("CodeSystem/101")));
+		} else {
+			fail("Unknown FHIR Version param provided: " + theFhirVersion);
+		}
 
 		App.main(new String[]{
 			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
-			"-v", "r4",
+			"-v", theFhirVersion,
 			"-m", "REMOVE",
 			"-t", "http://localhost:" + myPort,
 			"-u", "http://foo",
@@ -257,21 +312,22 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		assertEquals(1, listOfDescriptors.size());
 		assertEquals("file:/files.zip", listOfDescriptors.get(0).getFilename());
 		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
-
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testSnapshot() throws IOException {
+	@MethodSource("paramsProvider")
-
+	public void testSnapshot(String theFhirVersion) throws IOException {
-
+		if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
-
+			when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));
-		writeConceptAndHierarchyFiles();
+		} else if (FHIR_VERSION_R4.equals(theFhirVersion)) {
-
+			when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.r4.model.IdType("CodeSystem/101")));
-		when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+		} else {
+			fail("Unknown FHIR Version param provided: " + theFhirVersion);
+		}
 
 		App.main(new String[]{
 			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
-			"-v", "r4",
+			"-v", theFhirVersion,
 			"-m", "SNAPSHOT",
 			"-t", "http://localhost:" + myPort,
 			"-u", "http://foo",
@@ -287,17 +343,24 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testPropertiesFile() throws IOException {
+	@MethodSource("paramsProvider")
+	public void testPropertiesFile(String theFhirVersion) throws IOException {
 		try (FileWriter w = new FileWriter(myPropertiesFileName, false)) {
 			w.append("a=b\n");
 		}
 
-		when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+		if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
+			when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));
+		} else if (FHIR_VERSION_R4.equals(theFhirVersion)) {
+			when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.r4.model.IdType("CodeSystem/101")));
+		} else {
+			fail("Unknown FHIR Version param provided: " + theFhirVersion);
+		}
 
 		App.main(new String[]{
 			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
-			"-v", "r4",
+			"-v", theFhirVersion,
 			"-m", "SNAPSHOT",
 			"-t", "http://localhost:" + myPort,
 			"-u", "http://foo",
@@ -310,26 +373,24 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		assertEquals(1, listOfDescriptors.size());
 		assertThat(listOfDescriptors.get(0).getFilename(), matchesPattern(".*\\.zip$"));
 		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
-
-
 	}
 
-	/**
+	@ParameterizedTest
-	 * When transferring large files, we use a local file to store the binary instead of
+	@MethodSource("paramsProvider")
-	 * using HTTP to transfer a giant base 64 encoded attachment. Hopefully we can
+	public void testSnapshotLargeFile(String theFhirVersion) throws IOException {
-	 * replace this with a bulk data import at some point when that gets implemented.
-	 */
-	@Test
-	public void testSnapshotLargeFile() throws IOException {
 		UploadTerminologyCommand.setTransferSizeLimitForUnitTest(10);
 
-		writeConceptAndHierarchyFiles();
+		if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
-
+			when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));
-		when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
+		} else if (FHIR_VERSION_R4.equals(theFhirVersion)) {
+			when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.r4.model.IdType("CodeSystem/101")));
+		} else {
+			fail("Unknown FHIR Version param provided: " + theFhirVersion);
+		}
 
 		App.main(new String[]{
 			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
-			"-v", "r4",
+			"-v", theFhirVersion,
 			"-m", "SNAPSHOT",
 			"-t", "http://localhost:" + myPort,
 			"-u", "http://foo",
@@ -345,139 +406,51 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
 	}
 
-	@Nested
+	@ParameterizedTest
-	public class HeaderPassthroughOptionTests {
+	@MethodSource("paramsProvider")
-
+	public void testUploadICD10UsingCompressedFile(String theFhirVersion) throws IOException {
-		@RegisterExtension
+		if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
-		public final RestfulServerExtension myRestfulServerExtension = new RestfulServerExtension(myCtx);
+			when(myTermLoaderSvc.loadIcd10cm(anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));
-
+		} else if (FHIR_VERSION_R4.equals(theFhirVersion)) {
-		private final String headerKey1 = "test-header-key-1";
+			when(myTermLoaderSvc.loadIcd10cm(anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.r4.model.IdType("CodeSystem/101")));
-		private final String headerValue1 = "test header value-1";
+		} else {
-
+			fail("Unknown FHIR Version param provided: " + theFhirVersion);
-		private final CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
-		private final UploadTerminologyCommand testedCommand =
-			new RequestCapturingUploadTerminologyCommand(myCapturingInterceptor);
-
-		@BeforeEach
-		public void before() {
-			when(myTermLoaderSvc.loadCustom(eq("http://foo"), anyList(), any()))
-				.thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
-
-			TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTermLoaderSvc);
-			myRestfulServerExtension.registerProvider(provider);
 		}
 
+		App.main(new String[]{
+			UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
+			"-v", theFhirVersion,
+			"-t", "http://localhost:" + myPort,
+			"-u", myICD10URL,
+			"-d", myICD10FileName
+		});
 
-		@Test
+		verify(myTermLoaderSvc, times(1)).loadIcd10cm(myDescriptorListCaptor.capture(), any());
-		public void oneHeader() throws Exception {
-			String[] args = new String[] {
-				"-v", "r4",
-				"-m", "SNAPSHOT",
-				"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
-				"-u", "http://foo",
-				"-d", myConceptsFileName,
-				"-d", myHierarchyFileName,
-				"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\""
-			};
 
-			writeConceptAndHierarchyFiles();
+		List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
-			final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
+		assertEquals(1, listOfDescriptors.size());
-			testedCommand.run(commandLine);
+		assertThat(listOfDescriptors.get(0).getFilename(), matchesPattern("^file:.*files.*\\.zip$"));
+		assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
+	}
 
-			assertNotNull(myCapturingInterceptor.getLastRequest());
+	private synchronized void writeConceptAndHierarchyFiles() throws IOException {
-			Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
+		if (!myConceptsFile.exists()) {
-			assertFalse(allHeaders.isEmpty());
+			try (FileWriter w = new FileWriter(myConceptsFile, false)) {
-
+				w.append("CODE,DISPLAY\n");
-			assertTrue(allHeaders.containsKey(headerKey1));
+				w.append("ANIMALS,Animals\n");
-			assertEquals(1, allHeaders.get(headerKey1).size());
+				w.append("CATS,Cats\n");
-
+				w.append("DOGS,Dogs\n");
-			assertThat(allHeaders.get(headerKey1), hasItems(headerValue1));
-		}
-
-
-		@Test
-		public void twoHeadersSameKey() throws Exception {
-			final String headerValue2 = "test header value-2";
-
-			String[] args = new String[] {
-				"-v", "r4",
-				"-m", "SNAPSHOT",
-				"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
-				"-u", "http://foo",
-				"-d", myConceptsFileName,
-				"-d", myHierarchyFileName,
-				"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\"",
-				"-hp", "\"" + headerKey1 + ":" + headerValue2 + "\""
-			};
-
-			writeConceptAndHierarchyFiles();
-			final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
-			testedCommand.run(commandLine);
-
-			assertNotNull(myCapturingInterceptor.getLastRequest());
-			Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
-			assertFalse(allHeaders.isEmpty());
-			assertEquals(2, allHeaders.get(headerKey1).size());
-
-			assertTrue(allHeaders.containsKey(headerKey1));
-			assertEquals(2, allHeaders.get(headerKey1).size());
-
-			assertEquals(headerValue1, allHeaders.get(headerKey1).get(0));
-			assertEquals(headerValue2, allHeaders.get(headerKey1).get(1));
-		}
-
-		@Test
-		public void twoHeadersDifferentKeys() throws Exception {
-			final String headerKey2 = "test-header-key-2";
-			final String headerValue2 = "test header value-2";
-
-			String[] args = new String[] {
-				"-v", "r4",
-				"-m", "SNAPSHOT",
-				"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
-				"-u", "http://foo",
-				"-d", myConceptsFileName,
-				"-d", myHierarchyFileName,
-				"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\"",
-				"-hp", "\"" + headerKey2 + ":" + headerValue2 + "\""
-			};
-
-			writeConceptAndHierarchyFiles();
-			final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
-			testedCommand.run(commandLine);
-
-			assertNotNull(myCapturingInterceptor.getLastRequest());
-			Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
-			assertFalse(allHeaders.isEmpty());
-
-			assertTrue(allHeaders.containsKey(headerKey1));
-			assertEquals(1, allHeaders.get(headerKey1).size());
-			assertThat(allHeaders.get(headerKey1), hasItems(headerValue1));
-
-			assertTrue(allHeaders.containsKey(headerKey2));
-			assertEquals(1, allHeaders.get(headerKey2).size());
-			assertThat(allHeaders.get(headerKey2), hasItems(headerValue2));
-		}
-
-
-		private class RequestCapturingUploadTerminologyCommand extends UploadTerminologyCommand {
-			private CapturingInterceptor myCapturingInterceptor;
-
-			public RequestCapturingUploadTerminologyCommand(CapturingInterceptor theCapturingInterceptor) {
-				myCapturingInterceptor = theCapturingInterceptor;
 			}
-
+		}
-			@Override
+		if (!myHierarchyFile.exists()) {
-			protected IGenericClient newClient(CommandLine theCommandLine) throws ParseException {
+			try (FileWriter w = new FileWriter(myHierarchyFile, false)) {
-				IGenericClient client = super.newClient(theCommandLine);
+				w.append("PARENT,CHILD\n");
-				client.getInterceptorService().registerInterceptor(myCapturingInterceptor);
+				w.append("ANIMALS,CATS\n");
-				return client;
+				w.append("ANIMALS,DOGS\n");
 			}
 		}
 	}
 
-
-
 	private void writeArchiveFile(File... theFiles) throws IOException {
 		ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
 		ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream, Charsets.UTF_8);
@@ -485,11 +458,9 @@ public class UploadTerminologyCommandTest extends BaseTest {
 		for (File next : theFiles) {
 			ZipEntry nextEntry = new ZipEntry(UploadTerminologyCommand.stripPath(next.getAbsolutePath()));
 			zipOutputStream.putNextEntry(nextEntry);
-
 			try (FileInputStream fileInputStream = new FileInputStream(next)) {
 				IOUtils.copy(fileInputStream, zipOutputStream);
 			}
-
 		}
 
 		zipOutputStream.flush();
@@ -502,54 +473,4 @@ public class UploadTerminologyCommandTest extends BaseTest {
 			fos.write(byteArrayOutputStream.toByteArray());
 		}
 	}
-
-
-	private void writeConceptAndHierarchyFiles() throws IOException {
-		try (FileWriter w = new FileWriter(myConceptsFile, false)) {
-			w.append("CODE,DISPLAY\n");
-			w.append("ANIMALS,Animals\n");
-			w.append("CATS,Cats\n");
-			w.append("DOGS,Dogs\n");
-		}
-
-		try (FileWriter w = new FileWriter(myHierarchyFile, false)) {
-			w.append("PARENT,CHILD\n");
-			w.append("ANIMALS,CATS\n");
-			w.append("ANIMALS,DOGS\n");
-		}
-	}
-
-
-	@AfterEach
-	public void after() throws Exception {
-		JettyUtil.closeServer(myServer);
-
-		FileUtils.deleteQuietly(myConceptsFile);
-		FileUtils.deleteQuietly(myHierarchyFile);
-		FileUtils.deleteQuietly(myArchiveFile);
-		FileUtils.deleteQuietly(myCodeSystemFile);
-		FileUtils.deleteQuietly(myTextFile);
-		FileUtils.deleteQuietly(myPropertiesFile);
-
-		UploadTerminologyCommand.setTransferSizeLimitForUnitTest(-1);
-	}
-
-	@BeforeEach
-	public void before() throws Exception {
-		myServer = new Server(0);
-
-		TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTermLoaderSvc);
-
-		ServletHandler proxyHandler = new ServletHandler();
-		RestfulServer servlet = new RestfulServer(myCtx);
-		servlet.registerProvider(provider);
-		ServletHolder servletHolder = new ServletHolder(servlet);
-		proxyHandler.addServletWithMapping(servletHolder, "/*");
-		myServer.setHandler(proxyHandler);
-		JettyUtil.startServer(myServer);
-		myPort = JettyUtil.getPortForStartedServer(myServer);
-
-	}
-
-
 }

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>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-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-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-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>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2829-fix-upload-terminology-add-dstu3-support.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 2829
+title: "Add DSTU3 Support To UploadTerminologyCommand."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2852-simplify-java-mail-code.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+issue: 2852
+title: "Replace existing email implementation code with SimpleJavaMail library."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2876-resource-util-npe.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 2876
+jira: SMILE-1006
+backport: 5.5.0
+title: "Fixed a bug wherein an NPE could be thrown by the MDM module interceptor if an incoming resource had a tag with no system."

hapi-fhir-docs/src/test/java/ca/uhn/hapi/fhir/docs/ChangelogFilesTest.java

@@ -69,6 +69,9 @@ public class ChangelogFilesTest {
 			// this one is optional
 			fieldNames.remove("backport");
 
+			// this one is optional
+			fieldNames.remove("jira");
+
 			assertThat("Invalid element in " + next + ": " + fieldNames, fieldNames, empty());
 
 			if (haveIssue) {

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-example/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-api/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -410,22 +410,6 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
-		<dependency>
-			<groupId>javax.mail</groupId>
-			<artifactId>javax.mail-api</artifactId>
-			<scope>provided</scope>
-		</dependency>
-		<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>javax.el</groupId>
 			<artifactId>javax.el-api</artifactId>
@@ -533,25 +517,19 @@
 			<artifactId>spring-boot-test</artifactId>
 			<scope>test</scope>
 		</dependency>
-
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-test</artifactId>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>com.icegreen</groupId>
 			<artifactId>greenmail</artifactId>
 			<scope>test</scope>
-			<exclusions>
-				<exclusion>
-					<groupId>com.sun.mail</groupId>
-					<artifactId>javax.mail</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>junit</groupId>
-					<artifactId>junit</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>com.icegreen</groupId>
-			<artifactId>greenmail-spring</artifactId>
+			<artifactId>greenmail-junit5</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>

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

@@ -1056,7 +1056,13 @@ public class SearchBuilder implements ISearchBuilder {
 			for (String nextParamName : comboParamNames) {
 				List<List<IQueryParameterType>> nextValues = theParams.get(nextParamName);
 
-				nextParamName = UrlUtil.escapeUrlParam(nextParamName);
+				// TODO Hack to fix weird IOOB on the next stanza until James comes back and makes sense of this.
+				if (nextValues.isEmpty()) {
+					ourLog.error("query parameter {} is unexpectedly empty. Encountered while considering {} index for {}", nextParamName, comboParam.getName(), theRequest.getCompleteUrl());
+					sb = null;
+					break;
+				}
+
 				if (nextValues.get(0).size() != 1) {
 					sb = null;
 					break;
@@ -1083,14 +1089,15 @@ public class SearchBuilder implements ISearchBuilder {
 					}
 				}
 
-				nextOrValue = UrlUtil.escapeUrlParam(nextOrValue);
-
 				if (first) {
 					first = false;
 				} else {
 					sb.append('&');
 				}
 
+				nextParamName = UrlUtil.escapeUrlParam(nextParamName);
+				nextOrValue = UrlUtil.escapeUrlParam(nextOrValue);
+
 				sb.append(nextParamName).append('=').append(nextOrValue);
 
 			}

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

@@ -473,30 +473,23 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		// defaults to true
 		boolean isMakeVersionCurrent = theRequestDetails == null ||
 			(boolean) theRequestDetails.getUserData().getOrDefault(MAKE_LOADING_VERSION_CURRENT, Boolean.TRUE);
+
 		if (isMakeVersionCurrent) {
-			makeCodeSystemCurrentVersion(codeSystem, codeSystemToStore, conceptsToSave, totalCodeCount);
+			codeSystem.setCurrentVersion(codeSystemToStore);
+			if (codeSystem.getPid() == null) {
+				codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
+			}
 		}
 
-	}
+		ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
-
+		for (TermConcept next : conceptsToSave) {
-
+			populateVersion(next, codeSystemToStore);
-	private void makeCodeSystemCurrentVersion(TermCodeSystem theCodeSystem, TermCodeSystemVersion theCodeSystemToStore,
-			Collection<TermConcept> theConceptsToSave, int theTotalCodeCount) {
-
-		theCodeSystem.setCurrentVersion(theCodeSystemToStore);
-		if (theCodeSystem.getPid() == null) {
-			theCodeSystem = myCodeSystemDao.saveAndFlush(theCodeSystem);
 		}
 
-		ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", theCodeSystem.getPid(), theTotalCodeCount);
+		ourLog.debug("Saving {} concepts...", totalCodeCount);
-		for (TermConcept next : theConceptsToSave) {
-			populateVersion(next, theCodeSystemToStore);
-		}
-
-		ourLog.debug("Saving {} concepts...", theTotalCodeCount);
 		IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
-		for (TermConcept next : theConceptsToSave) {
+		for (TermConcept next : conceptsToSave) {
-			persistChildren(next, theCodeSystemToStore, conceptsStack2, theTotalCodeCount);
+			persistChildren(next, codeSystemToStore, conceptsStack2, totalCodeCount);
 		}
 
 		ourLog.debug("Done saving concepts, flushing to database");

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

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term.loinc;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.trim;
+import static org.apache.commons.lang3.StringUtils.trimToEmpty;
 
 import java.util.Map;
 
@@ -54,18 +55,36 @@ public class LoincLinguisticVariantHandler implements IZipContentsHandlerCsv {
 			return;
 		}
 	
-		addDesignation(theRecord, concept, "COMPONENT");
+		// The following should be created as designations for each term:
-		addDesignation(theRecord, concept, "PROPERTY");
+        // COMPONENT:PROPERTY:TIME_ASPCT:SYSTEM:SCALE_TYP:METHOD_TYP (as colon-separated concatenation - FormalName)
-		addDesignation(theRecord, concept, "TIME_ASPCT");
+        // SHORTNAME
-		addDesignation(theRecord, concept, "SYSTEM");
+        // LONG_COMMON_NAME
-		addDesignation(theRecord, concept, "SCALE_TYP");
+        // LinguisticVariantDisplayName
 			
-		addDesignation(theRecord, concept, "METHOD_TYP");
+		//-- add formalName designation
-		addDesignation(theRecord, concept, "CLASS");
+		StringBuilder fullySpecifiedName = new StringBuilder();
+		fullySpecifiedName.append(trimToEmpty(theRecord.get("COMPONENT") + ":"));
+		fullySpecifiedName.append(trimToEmpty(theRecord.get("PROPERTY") + ":"));
+		fullySpecifiedName.append(trimToEmpty(theRecord.get("TIME_ASPCT") + ":"));
+		fullySpecifiedName.append(trimToEmpty(theRecord.get("SYSTEM") + ":"));
+		fullySpecifiedName.append(trimToEmpty(theRecord.get("SCALE_TYP") + ":"));
+		fullySpecifiedName.append(trimToEmpty(theRecord.get("METHOD_TYP")));
+		
+		String fullySpecifiedNameStr = fullySpecifiedName.toString();
+		
+		// skip if COMPONENT, PROPERTY, TIME_ASPCT, SYSTEM, SCALE_TYP and METHOD_TYP are all empty
+		if (!fullySpecifiedNameStr.equals(":::::")) {
+			concept.addDesignation()
+				.setLanguage(myLanguageCode)
+				.setUseSystem(ITermLoaderSvc.LOINC_URI)
+				.setUseCode("FullySpecifiedName")
+				.setUseDisplay("FullySpecifiedName")
+				.setValue(fullySpecifiedNameStr);
+		}
+		
+		//-- other designations
 		addDesignation(theRecord, concept, "SHORTNAME");
 		addDesignation(theRecord, concept, "LONG_COMMON_NAME");		
-		addDesignation(theRecord, concept, "RELATEDNAMES2");
-		
 		addDesignation(theRecord, concept, "LinguisticVariantDisplayName");
 		
 	}

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

@@ -1,11 +1,12 @@
 package ca.uhn.fhir.jpa.config;
 
 import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
-import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
 import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.rest.server.mail.MailConfig;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
 import org.apache.commons.dbcp2.BasicDataSource;
@@ -132,10 +133,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 
 	@Bean
 	public IEmailSender emailSender() {
-		JavaMailEmailSender retVal = new JavaMailEmailSender();
+		return new EmailSenderImpl(new MailConfig().setSmtpHostname("localhost").setSmtpPort(3025));
-		retVal.setSmtpServerHostname("localhost");
-		retVal.setSmtpServerPort(3025);
-		return retVal;
 	}
 
 	@Override

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

@@ -702,26 +702,6 @@ public abstract class BaseJpaTest extends BaseTest {
 
 	}
 
-	public static void waitForSize(int theTarget, Callable<Number> theCallable) throws Exception {
-		waitForSize(theTarget, 10000, theCallable);
-	}
-
-	@SuppressWarnings("BusyWait")
-	public static void waitForSize(int theTarget, int theTimeout, Callable<Number> theCallable) throws Exception {
-		StopWatch sw = new StopWatch();
-		while (theCallable.call().intValue() != theTarget && sw.getMillis() < theTimeout) {
-			try {
-				Thread.sleep(50);
-			} catch (InterruptedException theE) {
-				throw new Error(theE);
-			}
-		}
-		if (sw.getMillis() >= theTimeout) {
-			fail("Size " + theCallable.call() + " is != target " + theTarget);
-		}
-		Thread.sleep(500);
-	}
-
 	public static void waitForSize(int theTarget, Callable<Number> theCallable, Callable<String> theFailureMessage) throws Exception {
 		waitForSize(theTarget, 10000, theCallable, theFailureMessage);
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/SubscriptionTestUtil.java

@@ -3,14 +3,14 @@ package ca.uhn.fhir.jpa.subscription;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.cache.IResourceChangeListenerCacheRefresher;
 import ca.uhn.fhir.jpa.subscription.channel.impl.LinkedBlockingChannel;
-import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionSubmitInterceptorLoader;
-import ca.uhn.fhir.jpa.subscription.match.registry.ActiveSubscription;
-import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionChannelRegistry;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionChannelWithHandlers;
-import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionMatcherInterceptor;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
-import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.SubscriptionDeliveringEmailSubscriber;
+import ca.uhn.fhir.jpa.subscription.match.registry.ActiveSubscription;
+import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
+import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionMatcherInterceptor;
+import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionSubmitInterceptorLoader;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -18,8 +18,6 @@ import org.springframework.beans.factory.annotation.Autowired;
 public class SubscriptionTestUtil {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SubscriptionTestUtil.class);
 
-	private JavaMailEmailSender myEmailSender;
-
 	@Autowired
 	private DaoConfig myDaoConfig;
 	@Autowired
@@ -77,21 +75,15 @@ public class SubscriptionTestUtil {
 		return getExecutorQueueSize();
 	}
 
-	public void initEmailSender(int theListenerPort) {
+	public void setEmailSender(IIdType theIdElement, EmailSenderImpl theEmailSender) {
-		myEmailSender = new JavaMailEmailSender();
-		myEmailSender.setSmtpServerHostname("localhost");
-		myEmailSender.setSmtpServerPort(theListenerPort);
-		myEmailSender.start();
-	}
-
-	public void setEmailSender(IIdType theIdElement) {
 		ActiveSubscription activeSubscription = mySubscriptionRegistry.get(theIdElement.getIdPart());
 		SubscriptionChannelWithHandlers subscriptionChannelWithHandlers = mySubscriptionChannelRegistry.getDeliveryReceiverChannel(activeSubscription.getChannelName());
 		SubscriptionDeliveringEmailSubscriber subscriber = (SubscriptionDeliveringEmailSubscriber) subscriptionChannelWithHandlers.getDeliveryHandlerForUnitTest();
-		subscriber.setEmailSender(myEmailSender);
+		subscriber.setEmailSender(theEmailSender);
 	}
 
 	public int getActiveSubscriptionCount() {
 		return mySubscriptionRegistry.size();
 	}
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSenderImplTest.java

@@ -0,0 +1,71 @@
+package ca.uhn.fhir.jpa.subscription.email;
+
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailDetails;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
+import ca.uhn.fhir.rest.server.mail.MailConfig;
+import com.icegreen.greenmail.junit5.GreenMailExtension;
+import com.icegreen.greenmail.util.GreenMailUtil;
+import com.icegreen.greenmail.util.ServerSetupTest;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.mail.internet.InternetAddress;
+import javax.mail.internet.MimeMessage;
+import java.util.Arrays;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+public class EmailSenderImplTest {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(EmailSenderImplTest.class);
+
+	@RegisterExtension
+	static GreenMailExtension ourGreenMail = new GreenMailExtension(ServerSetupTest.SMTP);
+
+	private EmailSenderImpl fixture;
+
+	@BeforeEach
+	public void setUp() {
+		fixture = new EmailSenderImpl(withMailConfig());
+	}
+
+	@Test
+	public void testSend() throws Exception {
+		EmailDetails details = new EmailDetails();
+		details.setSubscription(new IdType("Subscription/123"));
+		details.setFrom("foo@example.com ");
+		details.setTo(Arrays.asList(" to1@example.com", "to2@example.com   "));
+		details.setSubjectTemplate("test subject");
+		details.setBodyTemplate("foo");
+		fixture.send(details);
+
+		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
+
+		MimeMessage[] messages = ourGreenMail.getReceivedMessages();
+		assertEquals(2, messages.length);
+		final MimeMessage message = messages[0];
+		ourLog.info("Received: " + GreenMailUtil.getWholeMessage(message));
+		assertEquals("test subject", message.getSubject());
+		assertEquals(1, message.getFrom().length);
+		assertEquals("foo@example.com", ((InternetAddress) message.getFrom()[0]).getAddress());
+		assertEquals(2, message.getAllRecipients().length);
+		assertEquals("to1@example.com", ((InternetAddress) message.getAllRecipients()[0]).getAddress());
+		assertEquals("to2@example.com", ((InternetAddress) message.getAllRecipients()[1]).getAddress());
+		assertEquals(1, message.getHeader("Content-Type").length);
+		assertEquals("text/plain; charset=UTF-8", message.getHeader("Content-Type")[0]);
+		String foundBody = GreenMailUtil.getBody(message);
+		assertEquals("foo", foundBody);
+	}
+
+	private MailConfig withMailConfig() {
+		return new MailConfig()
+			.setSmtpHostname(ServerSetupTest.SMTP.getBindAddress())
+			.setSmtpPort(ServerSetupTest.SMTP.getPort());
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu2Test.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.subscription.email;
 
 import ca.uhn.fhir.jpa.provider.BaseResourceProviderDstu2Test;
 import ca.uhn.fhir.jpa.subscription.SubscriptionTestUtil;
-import ca.uhn.fhir.jpa.subscription.match.registry.ActiveSubscription;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
@@ -11,15 +11,16 @@ import ca.uhn.fhir.model.dstu2.valueset.ObservationStatusEnum;
 import ca.uhn.fhir.model.dstu2.valueset.SubscriptionChannelTypeEnum;
 import ca.uhn.fhir.model.dstu2.valueset.SubscriptionStatusEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
-import com.icegreen.greenmail.util.GreenMail;
+import ca.uhn.fhir.rest.server.mail.MailConfig;
+import com.icegreen.greenmail.junit5.GreenMailExtension;
 import com.icegreen.greenmail.util.GreenMailUtil;
-import com.icegreen.greenmail.util.ServerSetup;
+import com.icegreen.greenmail.util.ServerSetupTest;
 import org.hamcrest.Matchers;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.*;
+import org.junit.jupiter.api.AfterEach;
-
+import org.junit.jupiter.api.BeforeEach;
-import static org.awaitility.Awaitility.await;
+import org.junit.jupiter.api.Test;
-import static org.hamcrest.MatcherAssert.assertThat;
+import org.junit.jupiter.api.extension.RegisterExtension;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -29,16 +30,19 @@ import javax.mail.internet.MimeMessage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.concurrent.Callable;
 
 import static ca.uhn.fhir.jpa.subscription.resthook.RestHookTestDstu3Test.logAllInterceptors;
+import static org.awaitility.Awaitility.await;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class EmailSubscriptionDstu2Test extends BaseResourceProviderDstu2Test {
 
 	private static final Logger ourLog = LoggerFactory.getLogger(EmailSubscriptionDstu2Test.class);
-	private static GreenMail ourTestSmtp;
+
-	private static int ourListenerPort;
+	@RegisterExtension
+	static GreenMailExtension ourGreenMail = new GreenMailExtension(ServerSetupTest.SMTP);
+
 	private List<IIdType> mySubscriptionIds = new ArrayList<>();
 
 	@Autowired
@@ -65,8 +69,6 @@ public class EmailSubscriptionDstu2Test extends BaseResourceProviderDstu2Test {
 		ourLog.info("Before re-registering interceptors");
 		logAllInterceptors(myInterceptorRegistry);
 
-		mySubscriptionTestUtil.initEmailSender(ourListenerPort);
-
 		mySubscriptionTestUtil.registerEmailInterceptor();
 
 		ourLog.info("After re-registering interceptors");
@@ -121,51 +123,32 @@ public class EmailSubscriptionDstu2Test extends BaseResourceProviderDstu2Test {
 		Subscription subscription1 = createSubscription(criteria1, payload, "to1@example.com,to2@example.com");
 		mySubscriptionTestUtil.waitForQueueToDrain();
 		await().until(()->mySubscriptionRegistry.get(subscription1.getIdElement().getIdPart()), Matchers.not(Matchers.nullValue()));
-		mySubscriptionTestUtil.setEmailSender(subscription1.getIdElement());
+		mySubscriptionTestUtil.setEmailSender(subscription1.getIdElement(), new EmailSenderImpl(withMailConfig()));
-		assertEquals(0, Arrays.asList(ourTestSmtp.getReceivedMessages()).size());
+		assertEquals(0, Arrays.asList(ourGreenMail.getReceivedMessages()).size());
 
 		Observation observation1 = sendObservation(code, "SNOMED-CT");
 
-		waitForSize(2, 60000, new Callable<Number>() {
+		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
-			@Override
-			public Number call() {
-				int length = ourTestSmtp.getReceivedMessages().length;
-				ourLog.trace("Have received {}", length);
-				return length;
-			}
-		});
 
-		MimeMessage[] messages = ourTestSmtp.getReceivedMessages();
+		MimeMessage[] messages = ourGreenMail.getReceivedMessages();
 		assertEquals(2, messages.length);
-		int msgIdx = 0;
+		ourLog.info("Received: " + GreenMailUtil.getWholeMessage(messages[0]));
-		ourLog.info("Received: " + GreenMailUtil.getWholeMessage(messages[msgIdx]));
+		assertEquals("HAPI FHIR Subscriptions", messages[0].getSubject());
-		assertEquals("HAPI FHIR Subscriptions", messages[msgIdx].getSubject());
+		assertEquals(1, messages[0].getFrom().length);
-		assertEquals(1, messages[msgIdx].getFrom().length);
+		assertEquals("noreply@unknown.com", ((InternetAddress) messages[0].getFrom()[0]).getAddress());
-		assertEquals("noreply@unknown.com", ((InternetAddress) messages[msgIdx].getFrom()[0]).getAddress());
+		assertEquals(2, messages[0].getAllRecipients().length);
-		assertEquals(2, messages[msgIdx].getAllRecipients().length);
+		assertEquals("to1@example.com", ((InternetAddress) messages[0].getAllRecipients()[0]).getAddress());
-		assertEquals("to1@example.com", ((InternetAddress) messages[msgIdx].getAllRecipients()[0]).getAddress());
+		assertEquals("to2@example.com", ((InternetAddress) messages[0].getAllRecipients()[1]).getAddress());
-		assertEquals("to2@example.com", ((InternetAddress) messages[msgIdx].getAllRecipients()[1]).getAddress());
+		assertEquals(1, messages[0].getHeader("Content-Type").length);
-		assertEquals(1, messages[msgIdx].getHeader("Content-Type").length);
+		assertEquals("text/plain; charset=UTF-8", messages[0].getHeader("Content-Type")[0]);
-		assertEquals("text/plain; charset=us-ascii", messages[msgIdx].getHeader("Content-Type")[0]);
+		String foundBody = GreenMailUtil.getBody(messages[0]);
-		String foundBody = GreenMailUtil.getBody(messages[msgIdx]);
 		assertEquals("", foundBody);
-
 	}
 
-
+	private MailConfig withMailConfig() {
-	@AfterAll
+		return new MailConfig()
-	public static void afterClass() {
+			.setSmtpHostname(ServerSetupTest.SMTP.getBindAddress())
-		ourTestSmtp.stop();
+			.setSmtpPort(ServerSetupTest.SMTP.getPort());
 	}
 
-	@BeforeAll
-	public static void beforeClass() {
-		ServerSetup smtp = new ServerSetup(0, null, ServerSetup.PROTOCOL_SMTP);
-		smtp.setServerStartupTimeout(2000);
-		ourTestSmtp = new GreenMail(smtp);
-		ourTestSmtp.start();
-        ourListenerPort = ourTestSmtp.getSmtp().getPort();
-	}
-
-
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu3Test.java

@@ -3,11 +3,13 @@ package ca.uhn.fhir.jpa.subscription.email;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.provider.dstu3.BaseResourceProviderDstu3Test;
 import ca.uhn.fhir.jpa.subscription.SubscriptionTestUtil;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
 import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.server.mail.MailConfig;
 import ca.uhn.fhir.util.HapiExtensions;
+import com.icegreen.greenmail.junit5.GreenMailExtension;
 import com.icegreen.greenmail.store.FolderException;
-import com.icegreen.greenmail.util.GreenMail;
+import com.icegreen.greenmail.util.ServerSetupTest;
-import com.icegreen.greenmail.util.ServerSetup;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Coding;
@@ -15,11 +17,10 @@ import org.hl7.fhir.dstu3.model.Observation;
 import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.dstu3.model.Subscription;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.mail.internet.InternetAddress;
@@ -27,11 +28,11 @@ import javax.mail.internet.MimeMessage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.concurrent.Callable;
 
 import static ca.uhn.fhir.jpa.subscription.resthook.RestHookTestDstu3Test.logAllInterceptors;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 /**
  * Test the rest-hook subscriptions
@@ -40,11 +41,12 @@ public class EmailSubscriptionDstu3Test extends BaseResourceProviderDstu3Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(EmailSubscriptionDstu3Test.class);
 
+	@RegisterExtension
+	static GreenMailExtension ourGreenMail = new GreenMailExtension(ServerSetupTest.SMTP);
+
 	@Autowired
 	private SubscriptionTestUtil mySubscriptionTestUtil;
 
-	private static int ourListenerPort;
-	private static GreenMail ourTestSmtp;
 	private List<IIdType> mySubscriptionIds = new ArrayList<>();
 
 	@AfterEach
@@ -68,7 +70,7 @@ public class EmailSubscriptionDstu3Test extends BaseResourceProviderDstu3Test {
 
 	@BeforeEach
 	public void beforeRegisterEmailListener() throws FolderException {
-		ourTestSmtp.purgeEmailFromAllMailboxes();
+		ourGreenMail.purgeEmailFromAllMailboxes();
 
 		ourLog.info("Before re-registering interceptors");
 		logAllInterceptors(myInterceptorRegistry);
@@ -78,8 +80,6 @@ public class EmailSubscriptionDstu3Test extends BaseResourceProviderDstu3Test {
 		ourLog.info("After re-registering interceptors");
 		logAllInterceptors(myInterceptorRegistry);
 
-		mySubscriptionTestUtil.initEmailSender(ourListenerPort);
-
 		myDaoConfig.setEmailFromAddress("123@hapifhir.io");
 	}
 
@@ -133,24 +133,19 @@ public class EmailSubscriptionDstu3Test extends BaseResourceProviderDstu3Test {
 		String criteria1 = "Observation?code=SNOMED-CT|" + code + "&_format=xml";
 		Subscription subscription = createSubscription(criteria1, payload);
 		waitForQueueToDrain();
-		mySubscriptionTestUtil.setEmailSender(subscription.getIdElement());
+		mySubscriptionTestUtil.setEmailSender(subscription.getIdElement(), new EmailSenderImpl(withMailConfig()));
 
 		sendObservation(code, "SNOMED-CT");
 		waitForQueueToDrain();
 
-		waitForSize(1, 60000, new Callable<Number>() {
+		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
-			@Override
-			public Number call() {
-				return ourTestSmtp.getReceivedMessages().length;
-			}
-		});
 
-		List<MimeMessage> received = Arrays.asList(ourTestSmtp.getReceivedMessages());
+		List<MimeMessage> received = Arrays.asList(ourGreenMail.getReceivedMessages());
 		assertEquals(1, received.get(0).getFrom().length);
 		assertEquals("123@hapifhir.io", ((InternetAddress) received.get(0).getFrom()[0]).getAddress());
 		assertEquals(1, received.get(0).getAllRecipients().length);
 		assertEquals("foo@example.com", ((InternetAddress) received.get(0).getAllRecipients()[0]).getAddress());
-		assertEquals("text/plain; charset=us-ascii", received.get(0).getContentType());
+		assertEquals("text/plain; charset=UTF-8", received.get(0).getContentType());
 		assertEquals(mySubscriptionIds.get(0).toUnqualifiedVersionless().getValue(), received.get(0).getHeader("X-FHIR-Subscription")[0]);
 
 		// Expect the body of the email subscription to be an Observation formatted as XML
@@ -185,25 +180,20 @@ public class EmailSubscriptionDstu3Test extends BaseResourceProviderDstu3Test {
 
 		ourClient.update().resource(subscriptionTemp).withId(subscriptionTemp.getIdElement()).execute();
 		waitForQueueToDrain();
-		mySubscriptionTestUtil.setEmailSender(subscriptionTemp.getIdElement());
+		mySubscriptionTestUtil.setEmailSender(subscriptionTemp.getIdElement(), new EmailSenderImpl(withMailConfig()));
 
 		sendObservation(code, "SNOMED-CT");
 		waitForQueueToDrain();
 
-		waitForSize(1, 60000, new Callable<Number>() {
+		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
-			@Override
-			public Number call() throws Exception {
-				return ourTestSmtp.getReceivedMessages().length;
-			}
-		});
 
-		List<MimeMessage> received = Arrays.asList(ourTestSmtp.getReceivedMessages());
+		List<MimeMessage> received = Arrays.asList(ourGreenMail.getReceivedMessages());
 		assertEquals(1, received.size());
 		assertEquals(1, received.get(0).getFrom().length);
 		assertEquals("myfrom@from.com", ((InternetAddress) received.get(0).getFrom()[0]).getAddress());
 		assertEquals(1, received.get(0).getAllRecipients().length);
 		assertEquals("foo@example.com", ((InternetAddress) received.get(0).getAllRecipients()[0]).getAddress());
-		assertEquals("text/plain; charset=us-ascii", received.get(0).getContentType());
+		assertEquals("text/plain; charset=UTF-8", received.get(0).getContentType());
 		assertEquals("This is a subject", received.get(0).getSubject().toString().trim());
 		assertEquals(mySubscriptionIds.get(0).toUnqualifiedVersionless().getValue(), received.get(0).getHeader("X-FHIR-Subscription")[0]);
 
@@ -239,25 +229,20 @@ public class EmailSubscriptionDstu3Test extends BaseResourceProviderDstu3Test {
 		ourLog.info("Subscription ID is: {}", id.getValue());
 
 		waitForQueueToDrain();
-		mySubscriptionTestUtil.setEmailSender(subscriptionTemp.getIdElement());
+		mySubscriptionTestUtil.setEmailSender(subscriptionTemp.getIdElement(), new EmailSenderImpl(withMailConfig()));
 
 		sendObservation(code, "SNOMED-CT");
 		waitForQueueToDrain();
 
-		waitForSize(1, 60000, new Callable<Number>() {
+		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
-			@Override
-			public Number call() throws Exception {
-				return ourTestSmtp.getReceivedMessages().length;
-			}
-		});
 
-		List<MimeMessage> received = Arrays.asList(ourTestSmtp.getReceivedMessages());
+		List<MimeMessage> received = Arrays.asList(ourGreenMail.getReceivedMessages());
 		assertEquals(1, received.size());
 		assertEquals(1, received.get(0).getFrom().length);
 		assertEquals("myfrom@from.com", ((InternetAddress) received.get(0).getFrom()[0]).getAddress());
 		assertEquals(1, received.get(0).getAllRecipients().length);
 		assertEquals("foo@example.com", ((InternetAddress) received.get(0).getAllRecipients()[0]).getAddress());
-		assertEquals("text/plain; charset=us-ascii", received.get(0).getContentType());
+		assertEquals("text/plain; charset=UTF-8", received.get(0).getContentType());
 		assertEquals("This is a subject", received.get(0).getSubject().toString().trim());
 		assertEquals("", received.get(0).getContent().toString().trim());
 		assertEquals(mySubscriptionIds.get(0).toUnqualifiedVersionless().getValue(), received.get(0).getHeader("X-FHIR-Subscription")[0]);
@@ -273,20 +258,11 @@ public class EmailSubscriptionDstu3Test extends BaseResourceProviderDstu3Test {
 		mySubscriptionTestUtil.waitForQueueToDrain();
 	}
 
-	@AfterAll
+	private MailConfig withMailConfig() {
-	public static void afterClass() {
+		return new MailConfig()
-		ourTestSmtp.stop();
+			.setSmtpHostname(ServerSetupTest.SMTP.getBindAddress())
+			.setSmtpPort(ServerSetupTest.SMTP.getPort());
 	}
 
-	@BeforeAll
-	public static void beforeClass() {
-		ServerSetup smtp = new ServerSetup(0, null, ServerSetup.PROTOCOL_SMTP);
-		smtp.setServerStartupTimeout(2000);
-		smtp.setReadTimeout(2000);
-		smtp.setConnectionTimeout(2000);
-		ourTestSmtp = new GreenMail(smtp);
-		ourTestSmtp.start();
-        ourListenerPort = ourTestSmtp.getSmtp().getPort();
-	}
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/email/JavaMailEmailSenderTest.java

@@ -1,75 +0,0 @@
-package ca.uhn.fhir.jpa.subscription.email;
-
-import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailDetails;
-import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
-import com.icegreen.greenmail.util.GreenMail;
-import com.icegreen.greenmail.util.GreenMailUtil;
-import com.icegreen.greenmail.util.ServerSetup;
-import org.hl7.fhir.dstu3.model.IdType;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeMessage;
-import java.util.Arrays;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
-public class JavaMailEmailSenderTest {
-
-	private static final Logger ourLog = LoggerFactory.getLogger(JavaMailEmailSenderTest.class);
-	private static GreenMail ourTestSmtp;
-	private static int ourPort;
-
-	@Test
-	public void testSend() throws Exception {
-		JavaMailEmailSender sender = new JavaMailEmailSender();
-		sender.setSmtpServerHostname("localhost");
-		sender.setSmtpServerPort(ourPort);
-		sender.setSmtpServerUsername(null);
-		sender.setSmtpServerPassword(null);
-		sender.start();
-
-		String body = "foo";
-
-		EmailDetails details = new EmailDetails();
-		details.setSubscription(new IdType("Subscription/123"));
-		details.setFrom("foo@example.com ");
-		details.setTo(Arrays.asList(" to1@example.com", "to2@example.com   "));
-		details.setSubjectTemplate("test subject");
-		details.setBodyTemplate(body);
-		sender.send(details);
-
-		MimeMessage[] messages = ourTestSmtp.getReceivedMessages();
-		assertEquals(2, messages.length);
-		ourLog.info("Received: " + GreenMailUtil.getWholeMessage(messages[0]));
-		assertEquals("test subject", messages[0].getSubject());
-		assertEquals(1, messages[0].getFrom().length);
-		assertEquals("foo@example.com", ((InternetAddress)messages[0].getFrom()[0]).getAddress());
-		assertEquals(2, messages[0].getAllRecipients().length);
-		assertEquals("to1@example.com", ((InternetAddress)messages[0].getAllRecipients()[0]).getAddress());
-		assertEquals("to2@example.com", ((InternetAddress)messages[0].getAllRecipients()[1]).getAddress());
-		assertEquals(1, messages[0].getHeader("Content-Type").length);
-		assertEquals("text/plain; charset=us-ascii", messages[0].getHeader("Content-Type")[0]);
-		String foundBody = GreenMailUtil.getBody(messages[0]);
-		assertEquals("foo", foundBody);
-	}
-
-	@AfterAll
-	public static void afterClass() {
-		ourTestSmtp.stop();
-	}
-
-	@BeforeAll
-	public static void beforeClass() {
-		ServerSetup smtp = new ServerSetup(0, null, ServerSetup.PROTOCOL_SMTP);
-		smtp.setServerStartupTimeout(2000);
-		ourTestSmtp = new GreenMail(smtp);
-		ourTestSmtp.start();
-        ourPort = ourTestSmtp.getSmtp().getPort();
-	}
-
-}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincJpaTest.java

@@ -111,6 +111,77 @@ public class TerminologyLoaderSvcLoincJpaTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testLoadLoincVersionNotCurrent() throws IOException {
+
+		// Load LOINC marked as version 2.67
+		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v267_loincupload.properties");
+
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+
+		myTerminologyDeferredStorageSvc.saveAllDeferred();
+
+		// array just to make it final and populate it into following lambda
+		final TermCodeSystemVersion[] currentCodeSystemVersion_before_loading_v2_68 = new TermCodeSystemVersion[1];
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(2, myTermCodeSystemVersionDao.count());
+			assertEquals(24, myTermValueSetDao.count());
+			assertEquals(162, myTermConceptDao.count());
+			assertEquals(12, myTermConceptMapDao.count());
+			assertEquals(38, myResourceTableDao.count());
+			TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
+
+			TermCodeSystemVersion myTermCodeSystemVersion_versioned =
+				myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
+			assertNotEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion_versioned.getPid());
+			assertNotEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion_versioned.getResource().getId());
+
+			TermCodeSystemVersion myTermCodeSystemVersion_nonversioned =
+				myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(myTermCodeSystem.getPid());
+			assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion_nonversioned.getPid());
+			assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion_nonversioned.getResource().getId());
+
+			// current should be null loaded after 2.67
+			currentCodeSystemVersion_before_loading_v2_68[0] =
+				myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(myTermCodeSystem.getPid());
+		});
+
+		// Load LOINC marked as version 2.68 and not making it current (so 2.67 should remain current)
+		myFiles = new ZipCollectionBuilder();
+		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesWithPropertiesFileToZip(
+			myFiles, "v268_curr_false_loincupload.properties");
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+		myTerminologyDeferredStorageSvc.saveAllDeferred();
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(3, myTermCodeSystemVersionDao.count());
+			assertEquals(36, myTermValueSetDao.count());
+			assertEquals(243, myTermConceptDao.count());
+			assertEquals(18, myTermConceptMapDao.count());
+			assertEquals(57, myResourceTableDao.count());
+			TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
+
+			TermCodeSystemVersion currentCodeSystemVersion_after_loading_v2_68 =
+				myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(myTermCodeSystem.getPid());
+
+			// current should be same as before loading 2.68
+			assertEquals(currentCodeSystemVersion_before_loading_v2_68[0].getPid(), currentCodeSystemVersion_after_loading_v2_68.getPid());
+
+			TermCodeSystemVersion termCodeSystemVersion_267 =
+				myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
+			assertNotEquals(myTermCodeSystem.getCurrentVersion().getPid(), termCodeSystemVersion_267.getPid());
+
+			TermCodeSystemVersion termCodeSystemVersion_268 =
+				myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.68");
+			assertNotEquals(myTermCodeSystem.getCurrentVersion().getPid(), termCodeSystemVersion_268.getPid());
+		});
+
+	}
+
+
 	/**
 	 * Loinc distro includes loinc.xml as of 2.70
 	 */

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java

@@ -478,13 +478,13 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		// Consumer Name
 		if (theIncludeConsumerNameAndLinguisticVariants) {
 		    code = concepts.get("61438-8");
-		    assertEquals(28, code.getDesignations().size());
+		    assertEquals(8, code.getDesignations().size());
 		    verifyConsumerName(code.getDesignations(), "Consumer Name 61438-8");
 		    verifyLinguisticVariant(code.getDesignations(), "de-AT", "Entlassungsbrief Ärztlich","Ergebnis","Zeitpunkt","{Setting}","Dokument","Dermatologie","DOC.ONTOLOGY","de shortname","de long common name","de related names 2","de linguistic variant display name");
 		    verifyLinguisticVariant(code.getDesignations(), "fr-CA", "Cellules de Purkinje cytoplasmique type 2 , IgG","Titre","Temps ponctuel","Sérum","Quantitatif","Immunofluorescence","Sérologie","","","","");
 		    verifyLinguisticVariant(code.getDesignations(), "zh-CN", "血流速度.收缩期.最大值","速度","时间点","大脑中动脉","定量型","超声.多普勒","产科学检查与测量指标.超声","","", "Cereb 动态 可用数量表示的;定量性;数值型;数量型;连续数值型标尺 大脑（Cerebral） 时刻;随机;随意;瞬间 术语\"cerebral\"指的是主要由中枢半球（大脑皮质和基底神经节）组成的那部分脑结构 流 流量;流速;流体 血;全血 血流量;血液流量 速度(距离/时间);速率;速率(距离/时间)","");
 		    code = concepts.get("17787-3");
-		    assertEquals(19, code.getDesignations().size());
+		    assertEquals(5, code.getDesignations().size());
 		    verifyConsumerName(code.getDesignations(), "Consumer Name 17787-3");
 		    verifyLinguisticVariant(code.getDesignations(), "de-AT", "","","","","","","","","","CoV OC43 RNA ql/SM P","Coronavirus OC43 RNA ql. /Sondermaterial PCR");
 		    verifyLinguisticVariant(code.getDesignations(), "fr-CA", "Virus respiratoire syncytial bovin","Présence-Seuil","Temps ponctuel","XXX","Ordinal","Culture spécifique à un microorganisme","Microbiologie","","","","");
@@ -958,67 +958,35 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 			String methodType, String theClass, String theShortName, String theLongCommonName, String theRelatedName2,
 			String theLinguisticVariantDisplayName) {
 
-		TermConceptDesignation componentDes = null;
+		TermConceptDesignation formalNameDes = null;
-		TermConceptDesignation propertyDes = null;
-		TermConceptDesignation timeAspctDes = null;
-		TermConceptDesignation systemDes = null;
-		TermConceptDesignation scaleTypDes = null;
-
-		TermConceptDesignation methodTypDes = null;
-		TermConceptDesignation classDes = null;
 		TermConceptDesignation shortNameDes = null;
 		TermConceptDesignation longCommonNameDes = null;	
-		TermConceptDesignation relatedNames2Des = null;
-		
 		TermConceptDesignation linguisticVariantDisplayNameDes = null;
 		
 		for (TermConceptDesignation designation : designationList) {
 			if (theLanguage.equals(designation.getLanguage())) {
 				
-				if ("COMPONENT".equals(designation.getUseDisplay())) 
+				if ("FullySpecifiedName".equals(designation.getUseDisplay())) 
-					componentDes = designation;
+					formalNameDes = designation;
-				if ("PROPERTY".equals(designation.getUseDisplay())) 
-					propertyDes = designation;
-				if ("TIME_ASPCT".equals(designation.getUseDisplay())) 
-					timeAspctDes = designation;
-				if ("SYSTEM".equals(designation.getUseDisplay())) 
-					systemDes = designation;
-				if ("SCALE_TYP".equals(designation.getUseDisplay())) 
-					scaleTypDes = designation;
 				
-				if ("METHOD_TYP".equals(designation.getUseDisplay())) 
-					methodTypDes = designation;
-				if ("CLASS".equals(designation.getUseDisplay())) 
-					classDes = designation;
 				if ("SHORTNAME".equals(designation.getUseDisplay())) 
 					shortNameDes = designation;
 				if ("LONG_COMMON_NAME".equals(designation.getUseDisplay())) 
 					longCommonNameDes = designation;
-				if ("RELATEDNAMES2".equals(designation.getUseDisplay())) 
-					relatedNames2Des = designation;
-				
 				if ("LinguisticVariantDisplayName".equals(designation.getUseDisplay())) 
 					linguisticVariantDisplayNameDes = designation;
 			}
 		}
-		verifyDesignation(componentDes, ITermLoaderSvc.LOINC_URI, "COMPONENT", theComponent);
-		verifyDesignation(propertyDes, ITermLoaderSvc.LOINC_URI, "PROPERTY", theProperty);
-		verifyDesignation(timeAspctDes, ITermLoaderSvc.LOINC_URI, "TIME_ASPCT", theTimeAspct);
-		verifyDesignation(systemDes, ITermLoaderSvc.LOINC_URI, "SYSTEM", theSystem);
-		verifyDesignation(scaleTypDes, ITermLoaderSvc.LOINC_URI, "SCALE_TYP", theScaleTyp);
 		
-		verifyDesignation(methodTypDes, ITermLoaderSvc.LOINC_URI, "METHOD_TYP", methodType);
+		verifyDesignation(formalNameDes, ITermLoaderSvc.LOINC_URI, "FullySpecifiedName", theComponent+":"+theProperty+":"+theTimeAspct+":"+theSystem+":"+theScaleTyp+":"+methodType);
-		verifyDesignation(classDes, ITermLoaderSvc.LOINC_URI, "CLASS", theClass);
 		verifyDesignation(shortNameDes, ITermLoaderSvc.LOINC_URI, "SHORTNAME", theShortName);
 		verifyDesignation(longCommonNameDes, ITermLoaderSvc.LOINC_URI, "LONG_COMMON_NAME", theLongCommonName);		
-		verifyDesignation(relatedNames2Des, ITermLoaderSvc.LOINC_URI, "RELATEDNAMES2", theRelatedName2);
-		
 		verifyDesignation(linguisticVariantDisplayNameDes, ITermLoaderSvc.LOINC_URI, "LinguisticVariantDisplayName", theLinguisticVariantDisplayName);
 	}
 	
 	private static void verifyDesignation(TermConceptDesignation theDesignation, String theUseSystem, String theUseCode, String theValue) {
 		if (theDesignation == null)
-			return;
+		   return;
 		assertEquals(theUseSystem, theDesignation.getUseSystem());
 		assertEquals(theUseCode, theDesignation.getUseCode());
 		assertEquals(theValue, theDesignation.getValue());

hapi-fhir-jpaserver-base/src/test/resources/loinc/v268_curr_false_loincupload.properties

@@ -0,0 +1,99 @@
+#################
+### MANDATORY ###
+#################
+
+# Answer lists (ValueSets of potential answers/values for LOINC "questions")
+## File must be present
+loinc.answerlist.file=AccessoryFiles/AnswerFile/AnswerList.csv
+# Answer list links (connects LOINC observation codes to answer list codes)
+## File must be present
+loinc.answerlist.link.file=AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
+
+# Document ontology
+## File must be present
+loinc.document.ontology.file=AccessoryFiles/DocumentOntology/DocumentOntology.csv
+
+# LOINC codes
+## File must be present
+loinc.file=LoincTable/Loinc.csv
+
+# LOINC hierarchy
+## File must be present
+loinc.hierarchy.file=AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
+
+# IEEE medical device codes
+## File must be present
+loinc.ieee.medical.device.code.mapping.table.file=AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
+
+# Imaging document codes
+## File must be present
+loinc.imaging.document.codes.file=AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
+
+# Part
+## File must be present
+loinc.part.file=AccessoryFiles/PartFile/Part.csv
+
+# Part link
+## File must be present
+loinc.part.link.primary.file=AccessoryFiles/PartFile/LoincPartLink_Primary.csv
+loinc.part.link.supplementary.file=AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv
+
+# Part related code mapping
+## File must be present
+loinc.part.related.code.mapping.file=AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
+
+# RSNA playbook
+## File must be present
+loinc.rsna.playbook.file=AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
+
+# Top 2000 codes - SI
+## File must be present
+loinc.top2000.common.lab.results.si.file=AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
+# Top 2000 codes - US
+## File must be present
+loinc.top2000.common.lab.results.us.file=AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
+
+# Universal lab order ValueSet
+## File must be present
+loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
+
+################
+### OPTIONAL ###
+################
+
+# This is the version identifier for the LOINC code system
+## Key may be omitted if only a single version of LOINC is being kept.
+loinc.codesystem.version=2.68
+
+loinc.codesystem.make.current=false
+
+# This is the version identifier for the answer list file
+## Key may be omitted
+loinc.answerlist.version=Beta.1
+
+# This is the version identifier for uploaded ConceptMap resources
+## Key may be omitted
+loinc.conceptmap.version=Beta.1
+
+# Group
+## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv
+## File may be omitted
+loinc.group.file=AccessoryFiles/GroupFile/Group.csv
+# Group terms
+## Default value if key not provided: AccessoryFiles/GroupFile/GroupLoincTerms.csv
+## File may be omitted
+loinc.group.terms.file=AccessoryFiles/GroupFile/GroupLoincTerms.csv
+# Parent group
+## Default value if key not provided: AccessoryFiles/GroupFile/ParentGroup.csv
+## File may be omitted
+loinc.parent.group.file=AccessoryFiles/GroupFile/ParentGroup.csv
+
+# Consumer Names
+## Default value if key not provided: AccessoryFiles/ConsumerName/ConsumerName.csv
+## File may be omitted
+loinc.consumer.name.file=AccessoryFiles/ConsumerName/ConsumerName.csv
+
+# Linguistic Variants
+## Default value if key not provided: AccessoryFiles/LinguisticVariants/LinguisticVariants.csv
+## File may be omitted
+loinc.linguistic.variants.file=AccessoryFiles/LinguisticVariants/LinguisticVariants.csv

hapi-fhir-jpaserver-batch/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-cql/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-mdm/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-migrate/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-subscription/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -65,18 +65,12 @@
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-context-support</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>javax.mail</groupId>
-			<artifactId>javax.mail-api</artifactId>
-			<scope>provided</scope>
-		</dependency>
 		<dependency>
 			<groupId>javax.servlet</groupId>
 			<artifactId>javax.servlet-api</artifactId>
 			<scope>provided</scope>
 		</dependency>
 
-
 		<!-- test dependencies -->
 		<dependency>
 			<groupId>org.springframework</groupId>

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/email/EmailDetails.java

@@ -20,19 +20,38 @@ package ca.uhn.fhir.jpa.subscription.match.deliver.email;
  * #L%
  */
 
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.simplejavamail.api.email.Email;
+import org.simplejavamail.email.EmailBuilder;
+import org.thymeleaf.context.Context;
+import org.thymeleaf.spring5.SpringTemplateEngine;
+import org.thymeleaf.spring5.dialect.SpringStandardDialect;
+import org.thymeleaf.templatemode.TemplateMode;
+import org.thymeleaf.templateresolver.StringTemplateResolver;
 
+import javax.annotation.Nonnull;
 import java.util.List;
+import java.util.stream.Collectors;
 
 public class EmailDetails {
+	private final SpringTemplateEngine myTemplateEngine;
+	private final Context myContext;
+
 	private String mySubjectTemplate;
 	private String myBodyTemplate;
 	private List<String> myTo;
 	private String myFrom;
 	private IIdType mySubscription;
 
-	public String getBodyTemplate() {
+	public EmailDetails() {
-		return myBodyTemplate;
+		myTemplateEngine = makeTemplateEngine();
+		myContext = new Context();
+	}
+
+	public String getBody() {
+		return myTemplateEngine.process(myBodyTemplate, myContext);
 	}
 
 	public void setBodyTemplate(String theBodyTemplate) {
@@ -40,35 +59,65 @@ public class EmailDetails {
 	}
 
 	public String getFrom() {
-		return myFrom;
+		return StringUtils.trim(myFrom);
 	}
 
 	public void setFrom(String theFrom) {
 		myFrom = theFrom;
 	}
 
-	public String getSubjectTemplate() {
+	public String getSubject() {
-		return mySubjectTemplate;
+		return myTemplateEngine.process(mySubjectTemplate, myContext);
 	}
 
 	public void setSubjectTemplate(String theSubjectTemplate) {
 		mySubjectTemplate = theSubjectTemplate;
 	}
 
-	public IIdType getSubscription() {
+	public String getSubscriptionId() {
-		return mySubscription;
+		return mySubscription.toUnqualifiedVersionless().getValue();
 	}
 
 	public void setSubscription(IIdType theSubscription) {
 		mySubscription = theSubscription;
 	}
 
-	public List<String> getTo() {
+	public String getTo() {
-		return myTo;
+		return myTo.stream().filter(StringUtils::isNotBlank).collect(Collectors.joining(","));
 	}
 
 	public void setTo(List<String> theTo) {
 		myTo = theTo;
 	}
 
+	public Email toEmail() {
+		try {
+			return EmailBuilder.startingBlank()
+				.from(getFrom())
+				.to(getTo())
+				.withSubject(getSubject())
+				.withPlainText(getBody())
+				.withHeader("X-FHIR-Subscription", getSubscriptionId())
+				.buildEmail();
+		} catch (IllegalArgumentException e) {
+			throw new InternalErrorException("Failed to create email message", e);
+		}
+	}
+
+	@Nonnull
+	private SpringTemplateEngine makeTemplateEngine() {
+		StringTemplateResolver stringTemplateResolver = new StringTemplateResolver();
+		stringTemplateResolver.setTemplateMode(TemplateMode.TEXT);
+
+		SpringStandardDialect springStandardDialect = new SpringStandardDialect();
+		springStandardDialect.setEnableSpringELCompiler(true);
+
+		SpringTemplateEngine springTemplateEngine = new SpringTemplateEngine();
+		springTemplateEngine.setDialect(springStandardDialect);
+		springTemplateEngine.setEnableSpringELCompiler(true);
+		springTemplateEngine.setTemplateResolver(stringTemplateResolver);
+
+		return springTemplateEngine;
+	}
+
 }

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/email/EmailSenderImpl.java

@@ -0,0 +1,64 @@
+package ca.uhn.fhir.jpa.subscription.match.deliver.email;
+
+/*-
+ * #%L
+ * HAPI FHIR Subscription Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * 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.rest.server.mail.MailConfig;
+import ca.uhn.fhir.rest.server.mail.MailSvc;
+import ca.uhn.fhir.util.StopWatch;
+import org.apache.commons.lang3.Validate;
+import org.simplejavamail.api.email.Email;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.annotation.Nonnull;
+
+public class EmailSenderImpl implements IEmailSender {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(EmailSenderImpl.class);
+	private MailSvc myMailSvc = new MailSvc();
+	private MailConfig myMailConfig;
+
+	public EmailSenderImpl(@Nonnull MailConfig theMailConfig) {
+		Validate.notNull(theMailConfig);
+		myMailConfig = theMailConfig;
+	}
+
+	@Override
+	public void send(EmailDetails theDetails) {
+		Validate.notNull(myMailConfig, "Mail configuration is not set!");
+
+		StopWatch stopWatch = new StopWatch();
+
+		ourLog.info("Sending email for subscription {} from [{}] to recipients: [{}]", theDetails.getSubscriptionId(), theDetails.getFrom(), theDetails.getTo());
+
+		Email email = theDetails.toEmail();
+
+		myMailSvc.sendMail(myMailConfig,	email,
+			() -> ourLog.info("Done sending email for subscription {} from [{}] to recipients: [{}] (took {}ms)",
+				theDetails.getSubscriptionId(), theDetails.getFrom(), theDetails.getTo(), stopWatch.getMillis()),
+			(e) -> {
+				ourLog.error("Error sending email for subscription {} from [{}] to recipients: [{}] (took {}ms)",
+					theDetails.getSubscriptionId(), theDetails.getFrom(), theDetails.getTo(), stopWatch.getMillis());
+				ourLog.error("Error sending email", e);
+		});
+	}
+
+}

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/email/JavaMailEmailSender.java

@@ -1,194 +0,0 @@
-package ca.uhn.fhir.jpa.subscription.match.deliver.email;
-
-/*-
- * #%L
- * HAPI FHIR Subscription Server
- * %%
- * Copyright (C) 2014 - 2021 Smile CDR, Inc.
- * %%
- * 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.rest.api.Constants;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.util.StopWatch;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.Validate;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.mail.javamail.JavaMailSenderImpl;
-import org.thymeleaf.context.Context;
-import org.thymeleaf.spring5.SpringTemplateEngine;
-import org.thymeleaf.spring5.dialect.SpringStandardDialect;
-import org.thymeleaf.templatemode.TemplateMode;
-import org.thymeleaf.templateresolver.StringTemplateResolver;
-
-import javax.annotation.PostConstruct;
-import javax.mail.Message;
-import javax.mail.MessagingException;
-import javax.mail.internet.MimeMessage;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.Properties;
-
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import static org.apache.commons.lang3.StringUtils.trim;
-
-public class JavaMailEmailSender implements IEmailSender {
-
-	private static final Logger ourLog = LoggerFactory.getLogger(JavaMailEmailSender.class);
-	private String mySmtpServerHostname;
-	private int mySmtpServerPort = 25;
-	private JavaMailSenderImpl mySender;
-	private String mySmtpServerUsername;
-	private String mySmtpServerPassword;
-	private final Properties myJavaMailProperties = new Properties();
-
-	public String getSmtpServerHostname() {
-		return mySmtpServerHostname;
-	}
-
-	/**
-	 * Set the SMTP server host to use for outbound mail
-	 */
-	public void setSmtpServerHostname(String theSmtpServerHostname) {
-		mySmtpServerHostname = theSmtpServerHostname;
-	}
-
-	public String getSmtpServerPassword() {
-		return mySmtpServerPassword;
-	}
-
-	public void setSmtpServerPassword(String theSmtpServerPassword) {
-		mySmtpServerPassword = theSmtpServerPassword;
-	}
-
-	public int getSmtpServerPort() {
-		return mySmtpServerPort;
-	}
-
-	/**
-	 * Set the SMTP server port to use for outbound mail
-	 */
-	public void setSmtpServerPort(int theSmtpServerPort) {
-		mySmtpServerPort = theSmtpServerPort;
-	}
-
-	public String getSmtpServerUsername() {
-		return mySmtpServerUsername;
-	}
-
-	public void setSmtpServerUsername(String theSmtpServerUsername) {
-		mySmtpServerUsername = theSmtpServerUsername;
-	}
-
-	/**
-	 * Set the "mail.smtp.auth" Java Mail Property
-	 */
-
-	public void setAuth(Boolean theAuth) {
-		myJavaMailProperties.setProperty("mail.smtp.auth", theAuth.toString());
-	}
-
-	/**
-	 * Set the "mail.smtp.starttls.enable" Java Mail Property
-	 */
-
-	public void setStartTlsEnable(Boolean theStartTlsEnable) {
-		myJavaMailProperties.setProperty("mail.smtp.starttls.enable", theStartTlsEnable.toString());
-	}
-
-	/**
-	 * Set the "mail.smtp.starttls.required" Java Mail Property
-	 */
-
-	public void setStartTlsRequired(Boolean theStartTlsRequired) {
-		myJavaMailProperties.setProperty("mail.smtp.starttls.required", theStartTlsRequired.toString());
-	}
-
-	/**
-	 * Set the "mail.smtp.quitwait" Java Mail Property
-	 */
-
-	public void setQuitWait(Boolean theQuitWait) {
-		myJavaMailProperties.setProperty("mail.smtp.quitwait", theQuitWait.toString());
-	}
-
-	@Override
-	public void send(EmailDetails theDetails) {
-		String subscriptionId = theDetails.getSubscription().toUnqualifiedVersionless().getValue();
-		StopWatch sw = new StopWatch();
-
-		StringTemplateResolver templateResolver = new StringTemplateResolver();
-		templateResolver.setTemplateMode(TemplateMode.TEXT);
-
-		SpringStandardDialect dialect = new SpringStandardDialect();
-		dialect.setEnableSpringELCompiler(true);
-
-		SpringTemplateEngine engine = new SpringTemplateEngine();
-		engine.setDialect(dialect);
-		engine.setEnableSpringELCompiler(true);
-		engine.setTemplateResolver(templateResolver);
-
-		Context context = new Context();
-
-		String body = engine.process(theDetails.getBodyTemplate(), context);
-		String subject = engine.process(theDetails.getSubjectTemplate(), context);
-
-		MimeMessage email = mySender.createMimeMessage();
-
-		String from = trim(theDetails.getFrom());
-		ourLog.info("Sending email for subscription {} from [{}] to recipients: [{}]", subscriptionId, from, theDetails.getTo());
-
-		try {
-			email.setFrom(from);
-			email.setRecipients(Message.RecipientType.TO, toTrimmedCommaSeparatedString(theDetails.getTo()));
-			email.setSubject(subject);
-			email.setText(body);
-			email.setSentDate(new Date());
-			email.addHeader("X-FHIR-Subscription", subscriptionId);
-		} catch (MessagingException e) {
-			throw new InternalErrorException("Failed to create email message", e);
-		}
-
-		mySender.send(email);
-
-		ourLog.info("Done sending email (took {}ms)", sw.getMillis());
-	}
-
-	@PostConstruct
-	public void start() {
-		Validate.notBlank(mySmtpServerHostname, "No SMTP host defined");
-
-		mySender = new JavaMailSenderImpl();
-		mySender.setHost(getSmtpServerHostname());
-		mySender.setPort(getSmtpServerPort());
-		mySender.setUsername(getSmtpServerUsername());
-		mySender.setPassword(getSmtpServerPassword());
-		mySender.setDefaultEncoding(Constants.CHARSET_UTF8.name());
-		mySender.setJavaMailProperties(myJavaMailProperties);
-	}
-
-	private static String toTrimmedCommaSeparatedString(List<String> theTo) {
-		List<String> to = new ArrayList<>();
-		for (String next : theTo) {
-			if (isNotBlank(next)) {
-				to.add(next);
-			}
-		}
-
-		return StringUtils.join(to, ",");
-	}
-}

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/email/SubscriptionDeliveringEmailSubscriber.java

@@ -22,20 +22,21 @@ package ca.uhn.fhir.jpa.subscription.match.deliver.email;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
-import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
 import ca.uhn.fhir.jpa.subscription.match.deliver.BaseSubscriptionDeliverySubscriber;
+import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
 import ca.uhn.fhir.jpa.subscription.model.ResourceDeliveryMessage;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.annotation.Scope;
 
 import java.util.ArrayList;
 import java.util.List;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
 
 public class SubscriptionDeliveringEmailSubscriber extends BaseSubscriptionDeliverySubscriber {
 	private Logger ourLog = LoggerFactory.getLogger(SubscriptionDeliveringEmailSubscriber.class);

hapi-fhir-jpaserver-test-utilities/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-server-mdm/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/MdmResourceUtil.java

@@ -76,19 +76,19 @@ public final class MdmResourceUtil {
 		return theBaseResource.getMeta().getTag(theSystem, theCode) != null;
 	}
 
-	private static boolean resourceHasTagWithSystem(IBaseResource theBaseResource, String theSystem) {
+	private static boolean resourceHasTagWithSystem(IBaseResource theBaseResource, @Nonnull String theSystem) {
 		if (theBaseResource == null) {
 			return false;
 		}
-		return theBaseResource.getMeta().getTag().stream().anyMatch(tag -> tag.getSystem().equalsIgnoreCase(theSystem));
+		return theBaseResource.getMeta().getTag().stream().anyMatch(tag -> theSystem.equalsIgnoreCase(tag.getSystem()));
 	}
 
-	private static Optional<? extends IBaseCoding> getTagWithSystem(IBaseResource theResource, String theSystem) {
+	private static Optional<? extends IBaseCoding> getTagWithSystem(IBaseResource theResource, @Nonnull String theSystem) {
-		return theResource.getMeta().getTag().stream().filter(tag -> tag.getSystem().equalsIgnoreCase(theSystem)).findFirst();
+		return theResource.getMeta().getTag().stream().filter(tag -> theSystem.equalsIgnoreCase(tag.getSystem())).findFirst();
 	}
 
-	public static void removeTagWithSystem(IBaseResource theResource, String theSystem) {
+	public static void removeTagWithSystem(IBaseResource theResource, @Nonnull String theSystem) {
-		theResource.getMeta().getTag().removeIf(tag -> tag.getSystem().equalsIgnoreCase(theSystem));
+		theResource.getMeta().getTag().removeIf(tag -> theSystem.equalsIgnoreCase(tag.getSystem()));
 	}
 
 	/**

hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/util/MdmResourceUtilTest.java

@@ -0,0 +1,23 @@
+package ca.uhn.fhir.mdm.util;
+
+import org.hl7.fhir.r4.model.Organization;
+import org.junit.jupiter.api.Test;
+
+import static org.hamcrest.CoreMatchers.equalTo;
+import static org.hamcrest.CoreMatchers.is;
+import static org.hamcrest.MatcherAssert.assertThat;
+
+class MdmResourceUtilTest {
+
+	//See https://github.com/hapifhir/hapi-fhir/issues/2876
+	@Test
+	public void testNoNpeOnTagWithNoSystem() {
+		//Given
+		Organization organization = new Organization();
+		organization.getMeta().addTag(null, "Some Code", "Some Display");
+
+		boolean hasGoldenRecordTag = MdmResourceUtil.hasGoldenRecordSystemTag(organization);
+
+		assertThat(hasGoldenRecordTag, is(equalTo(false)));
+	}
+}

hapi-fhir-server-openapi/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -509,7 +509,7 @@ public class OpenApiInterceptor {
 				Operation operation = getPathItem(paths, "/" + resourceType, PathItem.HttpMethod.GET);
 				operation.addTagsItem(resourceType);
 				operation.setDescription("This is a search type");
-				operation.setSummary("search-type: Update an existing " + resourceType + " instance, or create using a client-assigned ID");
+				operation.setSummary("search-type: Search for " + resourceType + " instances");
 				addFhirResourceResponse(ctx, openApi, operation, null);
 
 				for (CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent nextSearchParam : nextResource.getSearchParam()) {

hapi-fhir-server/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -87,6 +87,29 @@
 			<scope>test</scope>
 		</dependency>
 
+		<!-- mail start -->
+		<dependency>
+			<groupId>org.simplejavamail</groupId>
+			<artifactId>simple-java-mail</artifactId>
+			<exclusions>
+				<exclusion>
+					<groupId>jakarta.annotation</groupId>
+					<artifactId>jakarta.annotation-api</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>com.icegreen</groupId>
+			<artifactId>greenmail</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>com.icegreen</groupId>
+			<artifactId>greenmail-junit5</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<!-- mail end -->
+
 	</dependencies>
 
 	<build>

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

@@ -0,0 +1,85 @@
+package ca.uhn.fhir.rest.server.mail;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+
+public class MailConfig {
+	private String mySmtpHostname;
+	private Integer mySmtpPort;
+	private String mySmtpUsername;
+	private String mySmtpPassword;
+	private boolean mySmtpUseStartTLS;
+
+	public MailConfig() {
+	}
+
+	public String getSmtpHostname() {
+		return mySmtpHostname;
+	}
+
+	public MailConfig setSmtpHostname(String theSmtpHostname) {
+		mySmtpHostname = theSmtpHostname;
+		return this;
+	}
+
+	public Integer getSmtpPort() {
+		return mySmtpPort;
+	}
+
+	public MailConfig setSmtpPort(Integer theSmtpPort) {
+		mySmtpPort = theSmtpPort;
+		return this;
+	}
+
+	public String getSmtpUsername() {
+		return mySmtpUsername;
+	}
+
+	public MailConfig setSmtpUsername(String theSmtpUsername) {
+		// SimpleJavaMail treats empty smtp username as valid username and requires auth
+		mySmtpUsername = StringUtils.isBlank(theSmtpUsername) ? null : theSmtpUsername;
+		return this;
+	}
+
+	public String getSmtpPassword() {
+		return mySmtpPassword;
+	}
+
+	public MailConfig setSmtpPassword(String theSmtpPassword) {
+		// SimpleJavaMail treats empty smtp password as valid password and requires auth
+		mySmtpPassword = StringUtils.isBlank(theSmtpPassword) ? null : theSmtpPassword;
+		return this;
+	}
+
+	public boolean isSmtpUseStartTLS() {
+		return mySmtpUseStartTLS;
+	}
+
+	public MailConfig setSmtpUseStartTLS(boolean theSmtpUseStartTLS) {
+		mySmtpUseStartTLS = theSmtpUseStartTLS;
+		return this;
+	}
+
+	@Override
+	public boolean equals(Object object) {
+		if (this == object) {
+			return true;
+		}
+		if (object == null || getClass() != object.getClass()) {
+			return false;
+		}
+		return EqualsBuilder.reflectionEquals(this, object);
+	}
+
+	@Override
+	public int hashCode() {
+		return HashCodeBuilder.reflectionHashCode(this);
+	}
+
+	@Override
+	public String toString() {
+		return ToStringBuilder.reflectionToString(this);
+	}
+}

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

@@ -0,0 +1,109 @@
+package ca.uhn.fhir.rest.server.mail;
+
+import org.apache.commons.lang3.Validate;
+import org.simplejavamail.MailException;
+import org.simplejavamail.api.email.Email;
+import org.simplejavamail.api.email.Recipient;
+import org.simplejavamail.api.mailer.AsyncResponse;
+import org.simplejavamail.api.mailer.AsyncResponse.ExceptionConsumer;
+import org.simplejavamail.api.mailer.Mailer;
+import org.simplejavamail.api.mailer.config.TransportStrategy;
+import org.simplejavamail.mailer.MailerBuilder;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.annotation.Nonnull;
+import java.util.List;
+import java.util.stream.Collectors;
+
+public class MailSvc {
+	private static final Logger ourLog = LoggerFactory.getLogger(MailSvc.class);
+
+	public void sendMail(@Nonnull MailConfig theMailConfig, @Nonnull List<Email> theEmails) {
+		Validate.notNull(theMailConfig);
+		Validate.notNull(theEmails);
+		final Mailer mailer = makeMailer(theMailConfig);
+		theEmails.forEach(theEmail -> sendMail(mailer, theEmail, new OnSuccess(theEmail), new ErrorHandler(theEmail)));
+	}
+
+	public void sendMail(@Nonnull MailConfig theMailConfig, @Nonnull Email theEmail) {
+		Validate.notNull(theMailConfig);
+		final Mailer mailer = makeMailer(theMailConfig);
+		sendMail(mailer, theEmail, new OnSuccess(theEmail), new ErrorHandler(theEmail));
+	}
+
+	public void sendMail(@Nonnull MailConfig theMailConfig,
+								@Nonnull Email theEmail,
+								@Nonnull Runnable theOnSuccess,
+								@Nonnull ExceptionConsumer theErrorHandler) {
+		Validate.notNull(theMailConfig);
+		final Mailer mailer = makeMailer(theMailConfig);
+		sendMail(mailer, theEmail, theOnSuccess, theErrorHandler);
+	}
+
+	private void sendMail(@Nonnull Mailer theMailer,
+								 @Nonnull Email theEmail,
+								 @Nonnull Runnable theOnSuccess,
+								 @Nonnull ExceptionConsumer theErrorHandler) {
+		Validate.notNull(theMailer);
+		Validate.notNull(theEmail);
+		Validate.notNull(theOnSuccess);
+		Validate.notNull(theErrorHandler);
+		try {
+			final AsyncResponse asyncResponse = theMailer.sendMail(theEmail, true);
+			if (asyncResponse != null) {
+				asyncResponse.onSuccess(theOnSuccess);
+				asyncResponse.onException(theErrorHandler);
+			}
+		} catch (MailException e) {
+			theErrorHandler.accept(e);
+		}
+	}
+
+	@Nonnull
+	private Mailer makeMailer(@Nonnull MailConfig theMailConfig) {
+		ourLog.info("SMTP Mailer config Hostname:[{}] | Port:[{}] | Username:[{}] | TLS:[{}]",
+			theMailConfig.getSmtpHostname(), theMailConfig.getSmtpPort(),
+			theMailConfig.getSmtpUsername(), theMailConfig.isSmtpUseStartTLS());
+		return MailerBuilder
+			.withSMTPServer(
+				theMailConfig.getSmtpHostname(),
+				theMailConfig.getSmtpPort(),
+				theMailConfig.getSmtpUsername(),
+				theMailConfig.getSmtpPassword())
+			.withTransportStrategy(theMailConfig.isSmtpUseStartTLS() ? TransportStrategy.SMTP_TLS : TransportStrategy.SMTP)
+			.buildMailer();
+	}
+
+	@Nonnull
+	private String makeMessage(@Nonnull Email theEmail) {
+		return " with subject [" + theEmail.getSubject() + "] and recipients ["
+			+ theEmail.getRecipients().stream().map(Recipient::getAddress).collect(Collectors.joining(",")) + "]";
+	}
+
+	private class OnSuccess implements Runnable {
+		private final Email myEmail;
+
+		private OnSuccess(@Nonnull Email theEmail) {
+			myEmail = theEmail;
+		}
+
+		@Override
+		public void run() {
+			ourLog.info("Email sent" + makeMessage(myEmail));
+		}
+	}
+
+	private class ErrorHandler implements ExceptionConsumer {
+		private final Email myEmail;
+
+		private ErrorHandler(@Nonnull Email theEmail) {
+			myEmail = theEmail;
+		}
+
+		@Override
+		public void accept(Exception t) {
+			ourLog.error("Email not sent" + makeMessage(myEmail), t);
+		}
+	}
+}

hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/mail/MailConfigTest.java

@@ -0,0 +1,108 @@
+package ca.uhn.fhir.rest.server.mail;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
+import static org.junit.jupiter.api.Assertions.assertNotSame;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertSame;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+public class MailConfigTest {
+
+	private static final String SMTP_HOST_NAME = "SMTP_HOST_NAME";
+	private static final Integer SMTP_PORT = 1025;
+	private static final String SMTP_USERNAME = "SMTP_USERNAME";
+	private static final String SMTP_PASSWORD = "SMTP_PASSWORD";
+
+	private MailConfig fixture;
+
+	@BeforeEach
+	public void setUp() {
+		fixture = withMainConfig();
+	}
+
+	private MailConfig withMainConfig() {
+		return new MailConfig()
+			.setSmtpHostname(SMTP_HOST_NAME)
+			.setSmtpPort(SMTP_PORT)
+			.setSmtpUsername(SMTP_USERNAME)
+			.setSmtpPassword(SMTP_PASSWORD)
+			.setSmtpUseStartTLS(true);
+	}
+
+	@Test
+	public void testGetSmtpHostname() {
+		// execute
+		final String actual = fixture.getSmtpHostname();
+		// validate
+		assertEquals(SMTP_HOST_NAME, actual);
+	}
+
+	@Test
+	public void testGetSmtpPort() {
+		// execute
+		final int actual = fixture.getSmtpPort();
+		// validate
+		assertEquals(SMTP_PORT, actual);
+	}
+
+	@Test
+	public void testGetSmtpUsername() {
+		// execute
+		final String actual = fixture.getSmtpUsername();
+		// validate
+		assertEquals(SMTP_USERNAME, actual);
+	}
+
+	@Test
+	public void testGetSmtpPassword() {
+		// execute
+		final String actual = fixture.getSmtpPassword();
+		// validate
+		assertEquals(SMTP_PASSWORD, actual);
+	}
+
+	@Test
+	public void testIsSmtpUseStartTLS() {
+		// execute
+		final boolean actual = fixture.isSmtpUseStartTLS();
+		// validate
+		assertTrue(actual);
+	}
+
+	@Test
+	public void testEquality() {
+		// setup
+		final MailConfig other = withMainConfig();
+		// execute & validate
+		assertEquals(fixture, fixture);
+		assertSame(fixture, fixture);
+		assertEquals(fixture, other);
+		assertNotSame(fixture, other);
+		assertEquals(fixture.hashCode(), other.hashCode());
+		assertNotEquals(fixture.toString(), other.toString());
+		assertNotEquals(fixture, null);
+	}
+
+	@Test
+	public void testSetSmtpUsername() {
+		// execute & validate
+		assertEquals("xyz", fixture.setSmtpUsername("xyz").getSmtpUsername());
+		assertNull(fixture.setSmtpUsername(null).getSmtpUsername());
+		assertNull(fixture.setSmtpUsername("").getSmtpUsername());
+		assertNull(fixture.setSmtpUsername("  ").getSmtpUsername());
+	}
+
+	@Test
+	public void testSetSmtpPassword() {
+		// execute & validate
+		assertEquals("xyz", fixture.setSmtpPassword("xyz").getSmtpPassword());
+		assertNull(fixture.setSmtpPassword(null).getSmtpPassword());
+		assertNull(fixture.setSmtpPassword("").getSmtpPassword());
+		assertNull(fixture.setSmtpPassword("  ").getSmtpPassword());
+	}
+
+}

hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/mail/MailSvcIT.java

@@ -0,0 +1,120 @@
+package ca.uhn.fhir.rest.server.mail;
+
+import com.icegreen.greenmail.junit5.GreenMailExtension;
+import com.icegreen.greenmail.util.GreenMailUtil;
+import com.icegreen.greenmail.util.ServerSetupTest;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
+import org.simplejavamail.MailException;
+import org.simplejavamail.api.email.Email;
+import org.simplejavamail.email.EmailBuilder;
+
+import javax.annotation.Nonnull;
+import javax.mail.internet.MimeMessage;
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.fail;
+
+public class MailSvcIT {
+	private static final String FROM_ADDRESS = "from_address@email.com";
+	private static final String TO_ADDRESS = "to_address@email.com";
+	private static final String SUBJECT = "Email Subject";
+	private static final String BODY = "Email Body !!!";
+
+	@RegisterExtension
+	static GreenMailExtension ourGreenMail = new GreenMailExtension(ServerSetupTest.SMTP);
+
+	private MailSvc fixture;
+
+	@BeforeEach
+	public void setUp() {
+		fixture = new MailSvc();
+	}
+
+	@Test
+	public void testSendSingleMail() throws Exception {
+		// setup
+		final MailConfig mailConfig = withMailConfig();
+		final Email email = withEmail();
+		// execute
+		fixture.sendMail(mailConfig, email);
+		// validate
+		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
+		final MimeMessage[] receivedMessages = ourGreenMail.getReceivedMessages();
+		assertEquals(1, receivedMessages.length);
+		assertEquals(SUBJECT, receivedMessages[0].getSubject());
+		assertEquals(BODY, GreenMailUtil.getBody(receivedMessages[0]));
+	}
+
+	@Test
+	public void testSendMultipleMail() throws Exception {
+		// setup
+		final MailConfig mailConfig = withMailConfig();
+		final List<Email> emails = Arrays.asList(withEmail(), withEmail(), withEmail());
+		// execute
+		fixture.sendMail(mailConfig, emails);
+		// validate
+		assertTrue(ourGreenMail.waitForIncomingEmail(1000, emails.size()));
+		final MimeMessage[] receivedMessages = ourGreenMail.getReceivedMessages();
+		assertEquals(emails.size(), receivedMessages.length);
+		assertEquals(SUBJECT, receivedMessages[0].getSubject());
+		assertEquals(BODY, GreenMailUtil.getBody(receivedMessages[0]));
+		assertEquals(SUBJECT, receivedMessages[1].getSubject());
+		assertEquals(BODY, GreenMailUtil.getBody(receivedMessages[1]));
+		assertEquals(SUBJECT, receivedMessages[2].getSubject());
+		assertEquals(BODY, GreenMailUtil.getBody(receivedMessages[2]));
+	}
+
+	@Test
+	public void testSendMailWithInvalidToAddress() {
+		// setup
+		final MailConfig mailConfig = withMailConfig();
+		final Email email = withEmail("xyz");
+		// execute
+		fixture.sendMail(mailConfig, email);
+		// validate
+		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 0));
+		final MimeMessage[] receivedMessages = ourGreenMail.getReceivedMessages();
+		assertEquals(0, receivedMessages.length);
+	}
+
+	@Test
+	public void testSendMailWithInvalidToAddressExpectErrorHandler() {
+		// setup
+		final MailConfig mailConfig = withMailConfig();
+		final Email email = withEmail("xyz");
+		// execute
+		fixture.sendMail(mailConfig, email,
+			() -> fail("Should not execute on Success"),
+			(e) -> {
+				assertTrue(e instanceof MailException);
+				assertEquals("Invalid TO address: " + email, e.getMessage());
+			});
+		// validate
+		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 0));
+	}
+
+	private MailConfig withMailConfig() {
+		return new MailConfig()
+			.setSmtpHostname(ServerSetupTest.SMTP.getBindAddress())
+			.setSmtpPort(ServerSetupTest.SMTP.getPort());
+	}
+
+	private Email withEmail() {
+		return withEmail(TO_ADDRESS);
+	}
+
+	private Email withEmail(@Nonnull String toAddress) {
+		return EmailBuilder.startingBlank()
+			.from(FROM_ADDRESS)
+			.to(toAddress)
+			.withSubject(SUBJECT)
+			.withPlainText(BODY)
+			.buildEmail();
+	}
+
+}

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-samples</artifactId>

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

@@ -5,7 +5,7 @@
    <parent>
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-deployable-pom</artifactId>
-      <version>5.5.0-PRE8-SNAPSHOT</version>
+      <version>5.6.0-PRE1-SNAPSHOT</version>
       <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
    </parent>
 

hapi-fhir-spring-boot/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-dstu2/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-dstu3/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-r4/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-structures-r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-test-utilities/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-testpage-overlay/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

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

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-validation-resources-r5/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-validation/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-tinder-plugin/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -58,37 +58,37 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu3</artifactId>
-			<version>5.5.0-PRE8-SNAPSHOT</version>
+			<version>5.6.0-PRE1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
-			<version>5.5.0-PRE8-SNAPSHOT</version>
+			<version>5.6.0-PRE1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-r4</artifactId>
-			<version>5.5.0-PRE8-SNAPSHOT</version>
+			<version>5.6.0-PRE1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-r5</artifactId>
-			<version>5.5.0-PRE8-SNAPSHOT</version>
+			<version>5.6.0-PRE1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
-			<version>5.5.0-PRE8-SNAPSHOT</version>
+			<version>5.6.0-PRE1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
-			<version>5.5.0-PRE8-SNAPSHOT</version>
+			<version>5.6.0-PRE1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-validation-resources-r4</artifactId>
-			<version>5.5.0-PRE8-SNAPSHOT</version>
+			<version>5.6.0-PRE1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.velocity</groupId>

hapi-tinder-test/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

pom.xml

@@ -6,11 +6,12 @@
 	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir</artifactId>
 	<packaging>pom</packaging>
-	<version>5.5.0-PRE8-SNAPSHOT</version>
+	<version>5.6.0-PRE1-SNAPSHOT</version>
 	<name>HAPI-FHIR</name>
 	<description>An open-source implementation of the FHIR specification in Java.</description>
 	<url>https://hapifhir.io</url>
 
+
 	<organization>
 		<name>Smile CDR, Inc.</name>
 		<url>https://smilecdr.com</url>
@@ -893,16 +894,25 @@
 				<artifactId>caffeine</artifactId>
 				<version>${caffeine_version}</version>
 			</dependency>
+			<!-- mail start -->
+			<dependency>
+				<groupId>org.simplejavamail</groupId>
+				<artifactId>simple-java-mail</artifactId>
+				<version>6.6.1</version>
+			</dependency>
 			<dependency>
 				<groupId>com.icegreen</groupId>
 				<artifactId>greenmail</artifactId>
-				<version>1.6.3</version>
+				<version>1.6.4</version>
+				<scope>test</scope>
 			</dependency>
 			<dependency>
 				<groupId>com.icegreen</groupId>
-				<artifactId>greenmail-spring</artifactId>
+				<artifactId>greenmail-junit5</artifactId>
-				<version>1.5.10</version>
+				<version>1.6.4</version>
+				<scope>test</scope>
 			</dependency>
+			<!-- mail end -->
 			<dependency>
 				<groupId>com.github.dnault</groupId>
 				<artifactId>xml-patch</artifactId>
@@ -963,11 +973,6 @@
 				<artifactId>jakarta.activation</artifactId>
 				<version>2.0.0</version>
 			</dependency>
-			<dependency>
-				<groupId>com.sun.mail</groupId>
-				<artifactId>javax.mail</artifactId>
-				<version>1.6.1</version>
-			</dependency>
             <dependency>
                 <groupId>com.vladsch.flexmark</groupId>
                 <artifactId>flexmark</artifactId>
@@ -1115,11 +1120,6 @@
 				<artifactId>mssql-jdbc</artifactId>
 				<version>9.2.1.jre8</version>
 			</dependency>
-			<dependency>
-				<groupId>javax.mail</groupId>
-				<artifactId>javax.mail-api</artifactId>
-				<version>1.6.0</version>
-			</dependency>
 			<dependency>
 				<groupId>javax.servlet</groupId>
 				<artifactId>javax.servlet-api</artifactId>
@@ -1784,17 +1784,7 @@
 				<artifactId>spring-websocket</artifactId>
 				<version>${spring_version}</version>
 			</dependency>
-            <dependency>
+			<dependency>
-                <groupId>org.springframework.batch</groupId>
-                <artifactId>spring-batch-core</artifactId>
-                <version>${spring_batch_version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.springframework.batch</groupId>
-                <artifactId>spring-batch-infrastructure</artifactId>
-                <version>${spring_batch_version}</version>
-            </dependency>
-            <dependency>
 				<groupId>org.springframework.retry</groupId>
 				<artifactId>spring-retry</artifactId>
 				<version>${spring_retry_version}</version>

restful-server-example/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 	

tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 

tests/hapi-fhir-base-test-mindeps-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 

tests/hapi-fhir-base-test-mindeps-server/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.5.0-PRE8-SNAPSHOT</version>
+		<version>5.6.0-PRE1-SNAPSHOT</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>