Add support for ICD-10-CM (#2702)

* Add support for ICD-10-CM

* Have this working

* Fix LGTM issues

* Test fix

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

@@ -31,6 +31,7 @@ import org.apache.commons.text.StringEscapeUtils;
 import org.codehaus.stax2.XMLOutputFactory2;
 import org.codehaus.stax2.io.EscapingWriterFactory;
 import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
@@ -1863,10 +1864,19 @@ public class XmlUtil {
 	}
 
 	public static Document parseDocument(String theInput) throws IOException, SAXException {
+		StringReader reader = new StringReader(theInput);
+		return parseDocument(reader);
+	}
+
+	public static Document parseDocument(Reader reader) throws SAXException, IOException {
+		return parseDocument(reader, true);
+	}
+
+	public static Document parseDocument(Reader theReader, boolean theNamespaceAware) throws SAXException, IOException {
 		DocumentBuilder builder;
 		try {
 			DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory.newInstance();
-			docBuilderFactory.setNamespaceAware(true);
+			docBuilderFactory.setNamespaceAware(theNamespaceAware);
 			docBuilderFactory.setXIncludeAware(false);
 			docBuilderFactory.setExpandEntityReferences(false);
 			try {
@@ -1885,10 +1895,23 @@ public class XmlUtil {
 			throw new ConfigurationException(e);
 		}
 
-		InputSource src = new InputSource(new StringReader(theInput));
+		InputSource src = new InputSource(theReader);
 		return builder.parse(src);
 	}
 
+
+	public static List<Element> getChildrenByTagName(Element theParent, String theName) {
+		List<Element> nodeList = new ArrayList<Element>();
+		for (Node child = theParent.getFirstChild(); child != null; child = child.getNextSibling()) {
+			if (child.getNodeType() == Node.ELEMENT_NODE && theName.equals(child.getNodeName())) {
+				nodeList.add((Element) child);
+			}
+		}
+
+		return nodeList;
+	}
+
+
 	public static String encodeDocument(Node theElement) throws TransformerException {
 		return encodeDocument(theElement, false);
 	}

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

@@ -123,6 +123,10 @@ public class UploadTerminologyCommand extends BaseCommand {
 	}
 
 	private void invokeOperation(String theTermUrl, String[] theDatafile, IGenericClient theClient, IBaseParameters theInputParameters, String theOperationName) throws ParseException {
+		boolean isDeltaOperation =
+			theOperationName.equals(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD) ||
+				theOperationName.equals(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE);
+
 		ParametersUtil.addParameterToParametersUri(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_SYSTEM, theTermUrl);
 
 		ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
@@ -134,19 +138,37 @@ public class UploadTerminologyCommand extends BaseCommand {
 			for (String nextDataFile : theDatafile) {
 
 				try (FileInputStream fileInputStream = new FileInputStream(nextDataFile)) {
-					if (nextDataFile.endsWith(".csv") || nextDataFile.endsWith(".properties")) {
+					boolean isFhirType = nextDataFile.endsWith(".json") || nextDataFile.endsWith(".xml");
+					if (nextDataFile.endsWith(".csv") || nextDataFile.endsWith(".properties") || isFhirType) {
 
-						ourLog.info("Compressing and adding file: {}", nextDataFile);
+						if (isDeltaOperation && isFhirType) {
-						ZipEntry nextEntry = new ZipEntry(stripPath(nextDataFile));
-						zipOutputStream.putNextEntry(nextEntry);
 
-						CountingInputStream countingInputStream = new CountingInputStream(fileInputStream);
+							ourLog.info("Adding CodeSystem resource file: {}", nextDataFile);
-						IOUtils.copy(countingInputStream, zipOutputStream);
-						haveCompressedContents = true;
-						compressedSourceBytesCount += countingInputStream.getCount();
 
-						zipOutputStream.flush();
+							String contents = IOUtils.toString(fileInputStream, Charsets.UTF_8);
-						ourLog.info("Finished compressing {}", nextDataFile);
+							EncodingEnum encoding = EncodingEnum.detectEncodingNoDefault(contents);
+							if (encoding == null) {
+								throw new ParseException("Could not detect FHIR encoding for file: " + nextDataFile);
+							}
+
+							CodeSystem resource = encoding.newParser(myFhirCtx).parseResource(CodeSystem.class, contents);
+							ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_CODESYSTEM, resource);
+
+						} else {
+
+							ourLog.info("Compressing and adding file: {}", nextDataFile);
+							ZipEntry nextEntry = new ZipEntry(stripPath(nextDataFile));
+							zipOutputStream.putNextEntry(nextEntry);
+
+							CountingInputStream countingInputStream = new CountingInputStream(fileInputStream);
+							IOUtils.copy(countingInputStream, zipOutputStream);
+							haveCompressedContents = true;
+							compressedSourceBytesCount += countingInputStream.getCount();
+
+							zipOutputStream.flush();
+							ourLog.info("Finished compressing {}", nextDataFile);
+
+						}
 
 					} else if (nextDataFile.endsWith(".zip")) {
 
@@ -154,19 +176,6 @@ public class UploadTerminologyCommand extends BaseCommand {
 						String fileName = "file:" + nextDataFile;
 						addFileToRequestBundle(theInputParameters, fileName, IOUtils.toByteArray(fileInputStream));
 
-					} else if (nextDataFile.endsWith(".json") || nextDataFile.endsWith(".xml")) {
-
-						ourLog.info("Adding CodeSystem resource file: {}", nextDataFile);
-
-						String contents = IOUtils.toString(fileInputStream, Charsets.UTF_8);
-						EncodingEnum encoding = EncodingEnum.detectEncodingNoDefault(contents);
-						if (encoding == null) {
-							throw new ParseException("Could not detect FHIR encoding for file: " + nextDataFile);
-						}
-
-						CodeSystem resource = encoding.newParser(myFhirCtx).parseResource(CodeSystem.class, contents);
-						ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_CODESYSTEM, resource);
-
 					} else {
 
 						throw new ParseException("Don't know how to handle file: " + nextDataFile);

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

@@ -96,6 +96,21 @@
 			<artifactId>h2</artifactId>
 		</dependency>
 
+		<!-- Hibernate search Lucene backend -->
+		<dependency>
+			<groupId>org.hibernate.search</groupId>
+			<artifactId>hibernate-search-backend-lucene</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-analyzers-phonetic</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-backward-codecs</artifactId>
+		</dependency>
+
+
 		<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
 		<dependency>
 			<groupId>org.eclipse.jetty</groupId>

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java

@@ -92,14 +92,15 @@ public class CommonConfig {
 		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
 		extraProperties.put("hibernate.cache.use_structured_entries", "false");
 		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.backend.type", "lucene");
 
-		extraProperties.put(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
+//		extraProperties.put(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
-		extraProperties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), "local-filesystem");
+//		extraProperties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), "local-filesystem");
-		extraProperties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
+//		extraProperties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
-		extraProperties.put(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), "LUCENE_CURRENT");
+//		extraProperties.put(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), "LUCENE_CURRENT");
-		if (System.getProperty("lowmem") != null) {
+//		if (System.getProperty("lowmem") != null) {
 			extraProperties.put(HibernateOrmMapperSettings.ENABLED, "false");
-		}
+//		}
 
 		return extraProperties;
 	}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2702-add-icd10cm-support.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2702
+title: "The JPA server terminology uploader now supports uploading ICD-10-CM (US Edition) using the
+   native format for that vocabulary."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/tools/hapi_fhir_cli.md

@@ -83,6 +83,12 @@ Note that the path and exact filename of the terminology files will likely need
 ./hapi-fhir-cli upload-terminology -d Downloads/LOINC_2.54_MULTI-AXIAL_HIERARCHY.zip -d Downloads/LOINC_2.54_Text.zip -f dstu3 -t http://localhost:8080/baseDstu3 -u http://loinc.org
 ```
 
+### ICD-10-CM
+
+```
+./hapi-fhir-cli upload-terminology -d Downloads/LOINC_2.54_MULTI-AXIAL_HIERARCHY.zip -d icd10cm_tabular_2021.xml -f dstu3 -t http://localhost:8080/baseDstu3 -u http://hl7.org/fhir/sid/icd-10-cm
+```
+
 # Migrate Database
 
 The `migrate-database` command may be used to Migrate a database schema when upgrading a [HAPI FHIR JPA](/docs/server_jpa/introduction.html) project from one version of HAPI	FHIR to another version.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java

@@ -127,14 +127,17 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 
 			UploadStatistics stats;
 			switch (codeSystemUrl) {
-				case ITermLoaderSvc.SCT_URI:
+				case ITermLoaderSvc.ICD10CM_URI:
-					stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
+					stats = myTerminologyLoaderSvc.loadIcd10cm(localFiles, theRequestDetails);
+					break;
+				case ITermLoaderSvc.IMGTHLA_URI:
+					stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
 					break;
 				case ITermLoaderSvc.LOINC_URI:
 					stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
 					break;
-				case ITermLoaderSvc.IMGTHLA_URI:
+				case ITermLoaderSvc.SCT_URI:
-					stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
+					stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
 					break;
 				default:
 					stats = myTerminologyLoaderSvc.loadCustom(codeSystemUrl, localFiles, theRequestDetails);
@@ -395,7 +398,7 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 		return retVal;
 	}
 
-	private static class FileBackedFileDescriptor implements ITermLoaderSvc.FileDescriptor {
+	public static class FileBackedFileDescriptor implements ITermLoaderSvc.FileDescriptor {
 		private final File myNextFile;
 
 		public FileBackedFileDescriptor(File theNextFile) {

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

@@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
+import ca.uhn.fhir.jpa.term.icd10cm.Icd10CmLoader;
 import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListHandler;
 import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListLinkHandler;
 import ca.uhn.fhir.jpa.term.loinc.LoincDocumentOntologyHandler;
@@ -53,6 +54,7 @@ import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.springframework.aop.support.AopUtils;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.xml.sax.SAXException;
 
 import javax.annotation.Nonnull;
 import javax.validation.constraints.NotNull;
@@ -69,6 +71,7 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Optional;
@@ -260,6 +263,40 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
 		}
 	}
 
+	@Override
+	public UploadStatistics loadIcd10cm(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
+		ourLog.info("Beginning ICD-10-cm processing");
+
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl(ICD10CM_URI);
+		cs.setName("ICD-10-CM");
+		cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+
+		TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
+		int count = 0;
+
+		try (LoadedFileDescriptors compressedDescriptors = new LoadedFileDescriptors(theFiles)) {
+			for (FileDescriptor nextDescriptor : compressedDescriptors.getUncompressedFileDescriptors()) {
+				if (nextDescriptor.getFilename().toLowerCase(Locale.US).endsWith(".xml")) {
+					try (InputStream inputStream = nextDescriptor.getInputStream()) {
+						InputStreamReader reader = new InputStreamReader(inputStream, Charsets.UTF_8);
+						Icd10CmLoader loader = new Icd10CmLoader(codeSystemVersion);
+						loader.load(reader);
+						count += loader.getConceptCount();
+					}
+				}
+			}
+		} catch (IOException | SAXException e) {
+			throw new InternalErrorException(e);
+		}
+
+		cs.setVersion(codeSystemVersion.getCodeSystemVersionId());
+
+		IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, cs, null, null);
+		return new UploadStatistics(count, target);
+	}
+
 	@Override
 	public UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
 		try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {

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

@@ -36,6 +36,7 @@ public interface ITermLoaderSvc {
 	String IMGTHLA_URI = "http://www.ebi.ac.uk/ipd/imgt/hla";
 	String LOINC_URI = "http://loinc.org";
 	String SCT_URI = "http://snomed.info/sct";
+	String ICD10CM_URI = "http://hl7.org/fhir/sid/icd-10-cm";
 	String IEEE_11073_10101_URI = "urn:iso:std:iso:11073:10101";
 
 	UploadStatistics loadImgthla(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
@@ -44,6 +45,8 @@ public interface ITermLoaderSvc {
 
 	UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
 
+	UploadStatistics loadIcd10cm(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
+
 	UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
 
 	UploadStatistics loadDeltaAdd(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/icd10cm/Icd10CmLoader.java

@@ -0,0 +1,81 @@
+package ca.uhn.fhir.jpa.term.icd10cm;
+
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
+import ca.uhn.fhir.util.XmlUtil;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.xml.sax.SAXException;
+
+import java.io.IOException;
+import java.io.Reader;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class Icd10CmLoader {
+
+	private final TermCodeSystemVersion myCodeSystemVersion;
+	private int myConceptCount;
+
+	/**
+	 * Constructor
+	 */
+	public Icd10CmLoader(TermCodeSystemVersion theCodeSystemVersion) {
+		myCodeSystemVersion = theCodeSystemVersion;
+	}
+
+
+	public void load(Reader theReader) throws IOException, SAXException {
+		myConceptCount = 0;
+
+		Document document = XmlUtil.parseDocument(theReader, false);
+		Element documentElement = document.getDocumentElement();
+
+		// Extract version: Should only be 1 tag
+		for (Element nextVersion : XmlUtil.getChildrenByTagName(documentElement, "version")) {
+			String versionId = nextVersion.getTextContent();
+			if (isNotBlank(versionId)) {
+				myCodeSystemVersion.setCodeSystemVersionId(versionId);
+			}
+		}
+
+		// Extract Diags (codes)
+		for (Element nextChapter : XmlUtil.getChildrenByTagName(documentElement, "chapter")) {
+			for (Element nextSection : XmlUtil.getChildrenByTagName(nextChapter, "section")) {
+				for (Element nextDiag : XmlUtil.getChildrenByTagName(nextSection, "diag")) {
+					extractCode(nextDiag, null);
+				}
+			}
+		}
+
+	}
+
+
+	private void extractCode(Element theDiagElement, TermConcept theParentConcept) {
+		String code = theDiagElement.getElementsByTagName("name").item(0).getTextContent();
+		String display = theDiagElement.getElementsByTagName("desc").item(0).getTextContent();
+
+		TermConcept concept;
+		if (theParentConcept == null) {
+			concept = myCodeSystemVersion.addConcept();
+		} else {
+			concept = theParentConcept.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA);
+		}
+
+		concept.setCode(code);
+		concept.setDisplay(display);
+
+		for (Element nextChildDiag : XmlUtil.getChildrenByTagName(theDiagElement, "diag")) {
+			extractCode(nextChildDiag, concept);
+		}
+
+		myConceptCount++;
+	}
+
+
+	public int getConceptCount() {
+		return myConceptCount;
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java

@@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.ClasspathUtil;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.r4.model.Attachment;
@@ -95,6 +96,25 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
 	}
 
 	@Test
+	public void testUploadIcd10cm() {
+		byte[] packageBytes = ClasspathUtil.loadResourceAsByteArray("/icd/icd10cm_tabular_2021.xml");
+
+		Parameters respParam = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("upload-external-code-system")
+			.withParameter(Parameters.class, TerminologyUploaderProvider.PARAM_SYSTEM, new UriType(ITermLoaderSvc.ICD10CM_URI))
+			.andParameter(TerminologyUploaderProvider.PARAM_FILE, new Attachment().setUrl("icd10cm_tabular_2021.xml").setData(packageBytes))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+
+		assertThat(((IntegerType) respParam.getParameter().get(1).getValue()).getValue(), greaterThan(1));
+		assertThat(((Reference) respParam.getParameter().get(2).getValue()).getReference(), matchesPattern("CodeSystem\\/[a-zA-Z0-9\\.\\-]+"));
+	}
+
+		@Test
 	public void testUploadLoinc() throws Exception {
 		byte[] packageBytes = createLoincZip();
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcIcd10cmJpaTest.java

@@ -0,0 +1,61 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
+import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.util.ClasspathUtil;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import java.io.FileDescriptor;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
+
+public class TerminologyLoaderSvcIcd10cmJpaTest extends BaseJpaR4Test {
+	private TermLoaderSvcImpl mySvc;
+	private ZipCollectionBuilder myFiles;
+
+	@BeforeEach
+	public void before() {
+		mySvc = new TermLoaderSvcImpl(myTerminologyDeferredStorageSvc, myTermCodeSystemStorageSvc);
+
+		myFiles = new ZipCollectionBuilder();
+	}
+
+	@Test
+	public void testLoadIcd10cm() throws IOException {
+		String filename = "icd/icd10cm_tabular_2021.xml";
+
+		String resource = ClasspathUtil.loadResource(filename);
+		List<ITermLoaderSvc.FileDescriptor> descriptors = new ArrayList<>();
+		descriptors.add(new ITermLoaderSvc.ByteArrayFileDescriptor(filename, resource.getBytes(StandardCharsets.UTF_8)));
+		mySvc.loadIcd10cm(descriptors, new SystemRequestDetails());
+
+		myTerminologyDeferredStorageSvc.saveAllDeferred();
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(1, myTermCodeSystemVersionDao.count());
+			assertEquals(0, myTermValueSetDao.count());
+			assertEquals(0, myTermConceptMapDao.count());
+			assertEquals(1, myResourceTableDao.count());
+			assertEquals(17, myTermConceptDao.count());
+			TermCodeSystem codeSystem = myTermCodeSystemDao.findByCodeSystemUri(ITermLoaderSvc.ICD10CM_URI);
+
+			assertEquals("2021", codeSystem.getCurrentVersion().getCodeSystemVersionId());
+
+			TermCodeSystemVersion codeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(codeSystem.getPid(), "2021");
+			assertEquals(codeSystem.getCurrentVersion().getPid(), codeSystemVersion.getPid());
+			assertEquals(codeSystem.getResource().getId(), codeSystemVersion.getResource().getId());
+		});
+
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/icd10cm/Icd10CmLoaderTest.java

@@ -0,0 +1,46 @@
+package ca.uhn.fhir.jpa.term.icd10cm;
+
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.util.ClasspathUtil;
+import org.hamcrest.Matchers;
+import org.junit.jupiter.api.Test;
+import org.xml.sax.SAXException;
+
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class Icd10CmLoaderTest {
+
+	@Test
+	public void testLoadIcd10Cm() throws IOException, SAXException {
+		StringReader reader = new StringReader(ClasspathUtil.loadResource("icd/icd10cm_tabular_2021.xml"));
+		TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
+		Icd10CmLoader loader = new Icd10CmLoader(codeSystemVersion);
+		loader.load(reader);
+
+		assertEquals("2021", codeSystemVersion.getCodeSystemVersionId());
+
+		List<TermConcept> rootConcepts = new ArrayList<>(codeSystemVersion.getConcepts());
+		assertEquals(2, rootConcepts.size());
+		assertEquals("A00", rootConcepts.get(0).getCode());
+		assertEquals("Cholera", rootConcepts.get(0).getDisplay());
+		List<String> conceptNames = rootConcepts.stream().map(t -> t.getCode()).collect(Collectors.toList());
+		assertThat(conceptNames.toString(), conceptNames, Matchers.contains("A00", "A01"));
+
+		assertEquals(3, rootConcepts.get(0).getChildCodes().size());
+		TermConcept firstChildCode = rootConcepts.get(0).getChildCodes().get(0);
+		assertEquals("A00.0", firstChildCode.getCode());
+		assertEquals("Cholera due to Vibrio cholerae 01, biovar cholerae", firstChildCode.getDisplay());
+		conceptNames = rootConcepts.get(0).getChildCodes().stream().map(t -> t.getCode()).collect(Collectors.toList());
+		assertThat(conceptNames.toString(), conceptNames, Matchers.contains("A00.0", "A00.1", "A00.9"));
+
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/resources/icd/icd10cm_tabular_2021.xml

@@ -0,0 +1,105 @@
+<?xml version="1.0" encoding="utf-8"?>
+<ICD10CM.tabular>
+  <version>2021</version>
+  <introduction>
+    <introSection type="title">
+      <title>ICD-10-CM TABULAR LIST of DISEASES and INJURIES</title>
+    </introSection>
+  </introduction>
+  <chapter>
+    <name>1</name>
+    <desc>Certain infectious and parasitic diseases (A00-B99)</desc>
+    <sectionIndex>
+      <sectionRef first="A00" last="A09" id="A00-A09">
+         Intestinal infectious diseases
+      </sectionRef>
+    </sectionIndex>
+    <section id="A00-A09">
+      <desc>Intestinal infectious diseases (A00-A09)</desc>
+      <diag>
+        <name>A00</name>
+        <desc>Cholera</desc>
+        <diag>
+          <name>A00.0</name>
+          <desc>Cholera due to Vibrio cholerae 01, biovar cholerae</desc>
+          <inclusionTerm>
+            <note>Classical cholera</note>
+          </inclusionTerm>
+        </diag>
+        <diag>
+          <name>A00.1</name>
+          <desc>Cholera due to Vibrio cholerae 01, biovar eltor</desc>
+          <inclusionTerm>
+            <note>Cholera eltor</note>
+          </inclusionTerm>
+        </diag>
+        <diag>
+          <name>A00.9</name>
+          <desc>Cholera, unspecified</desc>
+        </diag>
+      </diag>
+      <diag>
+        <name>A01</name>
+        <desc>Typhoid and paratyphoid fevers</desc>
+        <diag>
+          <name>A01.0</name>
+          <desc>Typhoid fever</desc>
+          <inclusionTerm>
+            <note>Infection due to Salmonella typhi</note>
+          </inclusionTerm>
+          <diag>
+            <name>A01.00</name>
+            <desc>Typhoid fever, unspecified</desc>
+          </diag>
+          <diag>
+            <name>A01.01</name>
+            <desc>Typhoid meningitis</desc>
+          </diag>
+          <diag>
+            <name>A01.02</name>
+            <desc>Typhoid fever with heart involvement</desc>
+            <inclusionTerm>
+              <note>Typhoid endocarditis</note>
+              <note>Typhoid myocarditis</note>
+            </inclusionTerm>
+          </diag>
+          <diag>
+            <name>A01.03</name>
+            <desc>Typhoid pneumonia</desc>
+          </diag>
+          <diag>
+            <name>A01.04</name>
+            <desc>Typhoid arthritis</desc>
+          </diag>
+          <diag>
+            <name>A01.05</name>
+            <desc>Typhoid osteomyelitis</desc>
+          </diag>
+          <diag>
+            <name>A01.09</name>
+            <desc>Typhoid fever with other complications</desc>
+          </diag>
+        </diag>
+        <diag>
+          <name>A01.1</name>
+          <desc>Paratyphoid fever A</desc>
+        </diag>
+        <diag>
+          <name>A01.2</name>
+          <desc>Paratyphoid fever B</desc>
+        </diag>
+        <diag>
+          <name>A01.3</name>
+          <desc>Paratyphoid fever C</desc>
+        </diag>
+        <diag>
+          <name>A01.4</name>
+          <desc>Paratyphoid fever, unspecified</desc>
+          <inclusionTerm>
+            <note>Infection due to Salmonella paratyphi NOS</note>
+          </inclusionTerm>
+        </diag>
+      </diag>
+    </section>
+  </chapter>
+</ICD10CM.tabular>