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Merge branch 'master' into 2849_add_new_mdm_param

This commit is contained in:
Nick Goupinets 2021-08-16 13:33:57 -04:00
parent 4be3334f6f c8c0e1080c
commit 4cfe11a221
91 changed files with 234183 additions and 913 deletions
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2
hapi-deployable-pom/pom.xml
View File

@ -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>

2
hapi-fhir-android/pom.xml
View File

@ -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>

2
hapi-fhir-base/pom.xml
View File

@ -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>

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java
View File

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

4
hapi-fhir-bom/pom.xml
View File

@ -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>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -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>

4
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
View File

@ -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 {

197
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HeaderPassthroughOptionTest.java Normal file
View File

@ -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;
}
}
}

495
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java
View File

@ -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.Test;
import org.junit.jupiter.api.TestInfo;
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;
private FhirContext myCtx = FhirContext.forR4();
@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 {
static Stream<String> paramsProvider() {
return Stream.of(FHIR_VERSION_DSTU3, FHIR_VERSION_R4);
}
@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
public void testDeltaAddUsingCodeSystemResource() throws IOException {
try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
CodeSystem cs = new CodeSystem();
cs.addConcept().setCode("CODE").setDisplay("Display");
myCtx.newJsonParser().encodeResourceToWriter(cs, w);
@ParameterizedTest
@MethodSource("paramsProvider")
public void testDeltaAddUsingCodeSystemResource(String theFhirVersion) throws IOException {
if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
org.hl7.fhir.dstu3.model.CodeSystem cs = new org.hl7.fhir.dstu3.model.CodeSystem();
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
public void testDeltaAddInvalidResource() throws IOException {
try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
Patient patient = new Patient();
patient.setActive(true);
myCtx.newJsonParser().encodeResourceToWriter(patient, w);
@ParameterizedTest
@MethodSource("paramsProvider")
public void testDeltaAddInvalidResource(String theFhirVersion) throws IOException {
if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
try (FileWriter w = new FileWriter(myCodeSystemFile, false)) {
org.hl7.fhir.dstu3.model.Patient patient = new org.hl7.fhir.dstu3.model.Patient();
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
public void testDeltaAddInvalidFileType() throws IOException {
@ParameterizedTest
@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
public void testDeltaAddUsingCompressedFile() throws IOException {
writeConceptAndHierarchyFiles();
@ParameterizedTest
@MethodSource("paramsProvider")
public void testDeltaAddUsingCompressedFile(String theFhirVersion) throws IOException {
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
public void testDeltaAddInvalidFileName() throws IOException {
writeConceptAndHierarchyFiles();
@ParameterizedTest
@MethodSource("paramsProvider")
public void testDeltaAddInvalidFileName(String theFhirVersion) throws IOException {
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
public void testDeltaRemove() throws IOException {
writeConceptAndHierarchyFiles();
when(myTermLoaderSvc.loadDeltaRemove(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
@ParameterizedTest
@MethodSource("paramsProvider")
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 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
public void testSnapshot() throws IOException {
writeConceptAndHierarchyFiles();
when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
@ParameterizedTest
@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")));
} 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",
@ -287,17 +343,24 @@ public class UploadTerminologyCommandTest extends BaseTest {
assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
}
@Test
public void testPropertiesFile() throws IOException {
@ParameterizedTest
@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));
}
/**
* When transferring large files, we use a local file to store the binary instead of
* using HTTP to transfer a giant base 64 encoded attachment. Hopefully we can
* replace this with a bulk data import at some point when that gets implemented.
*/
@Test
public void testSnapshotLargeFile() throws IOException {
@ParameterizedTest
@MethodSource("paramsProvider")
public void testSnapshotLargeFile(String theFhirVersion) throws IOException {
UploadTerminologyCommand.setTransferSizeLimitForUnitTest(10);
writeConceptAndHierarchyFiles();
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",
@ -345,139 +406,51 @@ public class UploadTerminologyCommandTest extends BaseTest {
assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
}
@Nested
public class HeaderPassthroughOptionTests {
@RegisterExtension
public final RestfulServerExtension myRestfulServerExtension = new RestfulServerExtension(myCtx);
private final String headerKey1 = "test-header-key-1";
private final String headerValue1 = "test header value-1";
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);
@ParameterizedTest
@MethodSource("paramsProvider")
public void testUploadICD10UsingCompressedFile(String theFhirVersion) throws IOException {
if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
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)) {
when(myTermLoaderSvc.loadIcd10cm(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", theFhirVersion,
"-t", "http://localhost:" + myPort,
"-u", myICD10URL,
"-d", myICD10FileName
});
@Test
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 + "\""
};
verify(myTermLoaderSvc, times(1)).loadIcd10cm(myDescriptorListCaptor.capture(), any());
writeConceptAndHierarchyFiles();
final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
testedCommand.run(commandLine);
List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
assertEquals(1, listOfDescriptors.size());
assertThat(listOfDescriptors.get(0).getFilename(), matchesPattern("^file:.*files.*\\.zip$"));
assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
}
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", "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;
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");
}
@Override
protected IGenericClient newClient(CommandLine theCommandLine) throws ParseException {
IGenericClient client = super.newClient(theCommandLine);
client.getInterceptorService().registerInterceptor(myCapturingInterceptor);
return client;
}
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 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);
}
}

232702
hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/icd10cm_tabular_2021.xml Normal file
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File diff suppressed because it is too large Load Diff

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -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>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -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>

2
hapi-fhir-cli/pom.xml
View File

@ -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>

2
hapi-fhir-client-okhttp/pom.xml
View File

@ -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>

2
hapi-fhir-client/pom.xml
View File

@ -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>

2
hapi-fhir-converter/pom.xml
View File

@ -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>

2
hapi-fhir-dist/pom.xml
View File

@ -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>

2
hapi-fhir-docs/pom.xml
View File

@ -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>

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2829-fix-upload-terminology-add-dstu3-support.yaml Normal file
View File

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

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2852-simplify-java-mail-code.yaml Normal file
View File

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

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2876-resource-util-npe.yaml Normal file
View File

@ -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."

3
hapi-fhir-docs/src/test/java/ca/uhn/hapi/fhir/docs/ChangelogFilesTest.java
View File

@ -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) {

2
hapi-fhir-jacoco/pom.xml
View File

@ -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>

2
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -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>

2
hapi-fhir-jaxrsserver-example/pom.xml
View File

@ -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>

2
hapi-fhir-jpaserver-api/pom.xml
View File

@ -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>

36
hapi-fhir-jpaserver-base/pom.xml
View File

@ -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>

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
View File

@ -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);
}

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
View File

@ -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);
}
}
}
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...", codeSystem.getPid(), totalCodeCount);
for (TermConcept next : conceptsToSave) {
populateVersion(next, codeSystemToStore);
}
ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", theCodeSystem.getPid(), theTotalCodeCount);
for (TermConcept next : theConceptsToSave) {
populateVersion(next, theCodeSystemToStore);
}
ourLog.debug("Saving {} concepts...", theTotalCodeCount);
ourLog.debug("Saving {} concepts...", totalCodeCount);
IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
for (TermConcept next : theConceptsToSave) {
persistChildren(next, theCodeSystemToStore, conceptsStack2, theTotalCodeCount);
for (TermConcept next : conceptsToSave) {
persistChildren(next, codeSystemToStore, conceptsStack2, totalCodeCount);
}
ourLog.debug("Done saving concepts, flushing to database");

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincLinguisticVariantHandler.java
View File

@ -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");
addDesignation(theRecord, concept, "PROPERTY");
addDesignation(theRecord, concept, "TIME_ASPCT");
addDesignation(theRecord, concept, "SYSTEM");
addDesignation(theRecord, concept, "SCALE_TYP");
// The following should be created as designations for each term:
// COMPONENT:PROPERTY:TIME_ASPCT:SYSTEM:SCALE_TYP:METHOD_TYP (as colon-separated concatenation - FormalName)
// SHORTNAME
// LONG_COMMON_NAME
// LinguisticVariantDisplayName
//-- add formalName designation
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")));
addDesignation(theRecord, concept, "METHOD_TYP");
addDesignation(theRecord, concept, "CLASS");
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, "LONG_COMMON_NAME");
addDesignation(theRecord, concept, "LinguisticVariantDisplayName");
}

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java
View File

@ -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();
retVal.setSmtpServerHostname("localhost");
retVal.setSmtpServerPort(3025);
return retVal;
return new EmailSenderImpl(new MailConfig().setSmtpHostname("localhost").setSmtpPort(3025));
}
@Override

20
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -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);
}

24
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/SubscriptionTestUtil.java
View File

@ -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.JavaMailEmailSender;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
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) {
myEmailSender = new JavaMailEmailSender();
myEmailSender.setSmtpServerHostname("localhost");
myEmailSender.setSmtpServerPort(theListenerPort);
myEmailSender.start();
}
public void setEmailSender(IIdType theIdElement) {
public void setEmailSender(IIdType theIdElement, EmailSenderImpl theEmailSender) {
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();
}
}

71
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSenderImplTest.java Normal file
View File

@ -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());
}
}

81
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu2Test.java
View File

@ -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 static org.awaitility.Awaitility.await;
import static org.hamcrest.MatcherAssert.assertThat;
import org.junit.jupiter.api.AfterEach;
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 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());
assertEquals(0, Arrays.asList(ourTestSmtp.getReceivedMessages()).size());
mySubscriptionTestUtil.setEmailSender(subscription1.getIdElement(), new EmailSenderImpl(withMailConfig()));
assertEquals(0, Arrays.asList(ourGreenMail.getReceivedMessages()).size());
Observation observation1 = sendObservation(code, "SNOMED-CT");
waitForSize(2, 60000, new Callable<Number>() {
@Override
public Number call() {
int length = ourTestSmtp.getReceivedMessages().length;
ourLog.trace("Have received {}", length);
return length;
}
});
assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
MimeMessage[] messages = ourTestSmtp.getReceivedMessages();
MimeMessage[] messages = ourGreenMail.getReceivedMessages();
assertEquals(2, messages.length);
int msgIdx = 0;
ourLog.info("Received: " + GreenMailUtil.getWholeMessage(messages[msgIdx]));
assertEquals("HAPI FHIR Subscriptions", messages[msgIdx].getSubject());
assertEquals(1, messages[msgIdx].getFrom().length);
assertEquals("noreply@unknown.com", ((InternetAddress) messages[msgIdx].getFrom()[0]).getAddress());
assertEquals(2, messages[msgIdx].getAllRecipients().length);
assertEquals("to1@example.com", ((InternetAddress) messages[msgIdx].getAllRecipients()[0]).getAddress());
assertEquals("to2@example.com", ((InternetAddress) messages[msgIdx].getAllRecipients()[1]).getAddress());
assertEquals(1, messages[msgIdx].getHeader("Content-Type").length);
assertEquals("text/plain; charset=us-ascii", messages[msgIdx].getHeader("Content-Type")[0]);
String foundBody = GreenMailUtil.getBody(messages[msgIdx]);
ourLog.info("Received: " + GreenMailUtil.getWholeMessage(messages[0]));
assertEquals("HAPI FHIR Subscriptions", messages[0].getSubject());
assertEquals(1, messages[0].getFrom().length);
assertEquals("noreply@unknown.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=UTF-8", messages[0].getHeader("Content-Type")[0]);
String foundBody = GreenMailUtil.getBody(messages[0]);
assertEquals("", foundBody);
}
@AfterAll
public static void afterClass() {
ourTestSmtp.stop();
private MailConfig withMailConfig() {
return new MailConfig()
.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);
ourTestSmtp = new GreenMail(smtp);
ourTestSmtp.start();
ourListenerPort = ourTestSmtp.getSmtp().getPort();
}
}

76
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu3Test.java
View File

@ -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.ServerSetup;
import com.icegreen.greenmail.util.ServerSetupTest;
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>() {
@Override
public Number call() {
return ourTestSmtp.getReceivedMessages().length;
}
});
assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
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>() {
@Override
public Number call() throws Exception {
return ourTestSmtp.getReceivedMessages().length;
}
});
assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
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>() {
@Override
public Number call() throws Exception {
return ourTestSmtp.getReceivedMessages().length;
}
});
assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
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
public static void afterClass() {
ourTestSmtp.stop();
private MailConfig withMailConfig() {
return new MailConfig()
.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();
}
}

75
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/email/JavaMailEmailSenderTest.java
View File

@ -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();
}
}

71
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincJpaTest.java
View File

@ -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
*/

50
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
View File

@ -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 propertyDes = null;
TermConceptDesignation timeAspctDes = null;
TermConceptDesignation systemDes = null;
TermConceptDesignation scaleTypDes = null;
TermConceptDesignation methodTypDes = null;
TermConceptDesignation classDes = null;
TermConceptDesignation formalNameDes = null;
TermConceptDesignation shortNameDes = null;
TermConceptDesignation longCommonNameDes = null;
TermConceptDesignation relatedNames2Des = null;
TermConceptDesignation longCommonNameDes = null;
TermConceptDesignation linguisticVariantDisplayNameDes = null;
for (TermConceptDesignation designation : designationList) {
if (theLanguage.equals(designation.getLanguage())) {
if ("COMPONENT".equals(designation.getUseDisplay()))
componentDes = 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 ("FullySpecifiedName".equals(designation.getUseDisplay()))
formalNameDes = 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(classDes, ITermLoaderSvc.LOINC_URI, "CLASS", theClass);
verifyDesignation(formalNameDes, ITermLoaderSvc.LOINC_URI, "FullySpecifiedName", theComponent+":"+theProperty+":"+theTimeAspct+":"+theSystem+":"+theScaleTyp+":"+methodType);
verifyDesignation(shortNameDes, ITermLoaderSvc.LOINC_URI, "SHORTNAME", theShortName);
verifyDesignation(longCommonNameDes, ITermLoaderSvc.LOINC_URI, "LONG_COMMON_NAME", theLongCommonName);
verifyDesignation(relatedNames2Des, ITermLoaderSvc.LOINC_URI, "RELATEDNAMES2", theRelatedName2);
verifyDesignation(longCommonNameDes, ITermLoaderSvc.LOINC_URI, "LONG_COMMON_NAME", theLongCommonName);
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());

99
hapi-fhir-jpaserver-base/src/test/resources/loinc/v268_curr_false_loincupload.properties Normal file
View File

@ -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

2
hapi-fhir-jpaserver-batch/pom.xml
View File

@ -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>

2
hapi-fhir-jpaserver-cql/pom.xml
View File

@ -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>

2
hapi-fhir-jpaserver-mdm/pom.xml
View File

@ -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>

2
hapi-fhir-jpaserver-migrate/pom.xml
View File

@ -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>

2
hapi-fhir-jpaserver-model/pom.xml
View File

@ -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>

2
hapi-fhir-jpaserver-searchparam/pom.xml
View File

@ -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>

8
hapi-fhir-jpaserver-subscription/pom.xml
View File

@ -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>

67
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/email/EmailDetails.java
View File

@ -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() {
return myBodyTemplate;
public EmailDetails() {
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() {
return mySubjectTemplate;
public String getSubject() {
return myTemplateEngine.process(mySubjectTemplate, myContext);
}
public void setSubjectTemplate(String theSubjectTemplate) {
mySubjectTemplate = theSubjectTemplate;
}
public IIdType getSubscription() {
return mySubscription;
public String getSubscriptionId() {
return mySubscription.toUnqualifiedVersionless().getValue();
}
public void setSubscription(IIdType theSubscription) {
mySubscription = theSubscription;
}
public List<String> getTo() {
return myTo;
public String getTo() {
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;
}
}

64
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/email/EmailSenderImpl.java Normal file
View File

@ -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);
});
}
}

194
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/email/JavaMailEmailSender.java
View File

@ -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, ",");
}
}

7
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/email/SubscriptionDeliveringEmailSubscriber.java
View File

@ -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);

2
hapi-fhir-jpaserver-test-utilities/pom.xml
View File

@ -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>

2
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
View File

@ -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>

2
hapi-fhir-server-mdm/pom.xml
View File

@ -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>

12
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/MdmResourceUtil.java
View File

@ -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) {
return theResource.getMeta().getTag().stream().filter(tag -> tag.getSystem().equalsIgnoreCase(theSystem)).findFirst();
private static Optional<? extends IBaseCoding> getTagWithSystem(IBaseResource theResource, @Nonnull String theSystem) {
return theResource.getMeta().getTag().stream().filter(tag -> theSystem.equalsIgnoreCase(tag.getSystem())).findFirst();
}
public static void removeTagWithSystem(IBaseResource theResource, String theSystem) {
theResource.getMeta().getTag().removeIf(tag -> tag.getSystem().equalsIgnoreCase(theSystem));
public static void removeTagWithSystem(IBaseResource theResource, @Nonnull String theSystem) {
theResource.getMeta().getTag().removeIf(tag -> theSystem.equalsIgnoreCase(tag.getSystem()));
}
/**

23
hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/util/MdmResourceUtilTest.java Normal file
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@ -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)));
}
}

2
hapi-fhir-server-openapi/pom.xml
View File

@ -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>

2
hapi-fhir-server-openapi/src/main/java/ca/uhn/fhir/rest/openapi/OpenApiInterceptor.java
View File

@ -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()) {

25
hapi-fhir-server/pom.xml
View File

@ -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>

85
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/mail/MailConfig.java Normal file
View File

@ -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);
}
}

109
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/mail/MailSvc.java Normal file
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@ -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);
}
}
}

108
hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/mail/MailConfigTest.java Normal file
View File

@ -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());
}
}

120
hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/mail/MailSvcIT.java Normal file
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@ -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();
}
}

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml
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@ -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>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml
View File

@ -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>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml
View File

@ -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>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
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@ -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>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml
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@ -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>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml
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@ -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>

2
hapi-fhir-spring-boot/pom.xml
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@ -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>

2
hapi-fhir-structures-dstu2.1/pom.xml
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@ -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>

2
hapi-fhir-structures-dstu2/pom.xml
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@ -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>

2
hapi-fhir-structures-dstu3/pom.xml
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@ -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>

2
hapi-fhir-structures-hl7org-dstu2/pom.xml
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@ -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>

2
hapi-fhir-structures-r4/pom.xml
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@ -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>

2
hapi-fhir-structures-r5/pom.xml
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@ -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>

2
hapi-fhir-test-utilities/pom.xml
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@ -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>

2
hapi-fhir-testpage-overlay/pom.xml
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@ -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>

2
hapi-fhir-validation-resources-dstu2.1/pom.xml
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@ -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>

2
hapi-fhir-validation-resources-dstu2/pom.xml
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@ -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>

2
hapi-fhir-validation-resources-dstu3/pom.xml
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@ -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>

2
hapi-fhir-validation-resources-r4/pom.xml
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@ -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>

2
hapi-fhir-validation-resources-r5/pom.xml
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@ -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>

2
hapi-fhir-validation/pom.xml
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@ -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>

16
hapi-tinder-plugin/pom.xml
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@ -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>

2
hapi-tinder-test/pom.xml
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@ -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>

40
pom.xml
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@ -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>${caffeine_version}</version>
</dependency>
<!-- mail start -->
<dependency>
<groupId>org.simplejavamail</groupId>
<artifactId>simple-java-mail</artifactId>
<version>6.6.1</version>
</dependency>
<dependency>
<groupId>com.icegreen</groupId>
<artifactId>greenmail</artifactId>
<version>1.6.3</version>
<version>1.6.4</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.icegreen</groupId>
<artifactId>greenmail-spring</artifactId>
<version>1.5.10</version>
<artifactId>greenmail-junit5</artifactId>
<version>1.6.4</version>
<scope>test</scope>
</dependency>
<!-- mail end -->
<dependency>
<groupId>com.github.dnault</groupId>
<artifactId>xml-patch</artifactId>
@ -963,11 +973,6 @@
<artifactId>jakarta.activation</artifactId>
<version>2.0.0</version>
</dependency>
<dependency>
<groupId>com.sun.mail</groupId>
<artifactId>javax.mail</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>com.vladsch.flexmark</groupId>
<artifactId>flexmark</artifactId>
@ -1115,11 +1120,6 @@
<artifactId>mssql-jdbc</artifactId>
<version>9.2.1.jre8</version>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
<version>1.6.0</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
@ -1784,17 +1784,7 @@
<artifactId>spring-websocket</artifactId>
<version>${spring_version}</version>
</dependency>
<dependency>
<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>
<dependency>
<groupId>org.springframework.retry</groupId>
<artifactId>spring-retry</artifactId>
<version>${spring_retry_version}</version>

2
restful-server-example/pom.xml
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@ -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>

2
tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml
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@ -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>

2
tests/hapi-fhir-base-test-mindeps-client/pom.xml
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@ -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>

2
tests/hapi-fhir-base-test-mindeps-server/pom.xml
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@ -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>