Add support for ICD-10-CM (#2702)
* Add support for ICD-10-CM * Have this working * Fix LGTM issues * Test fix
This commit is contained in:
James Agnew
GitHub
parent
94d6b15db9
commit
62be623cf5
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@ -31,6 +31,7 @@ import org.apache.commons.text.StringEscapeUtils;
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import org.codehaus.stax2.XMLOutputFactory2;
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import org.codehaus.stax2.io.EscapingWriterFactory;
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import org.w3c.dom.Document;
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import org.w3c.dom.Element;
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import org.w3c.dom.Node;
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import org.xml.sax.InputSource;
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import org.xml.sax.SAXException;
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@ -1863,10 +1864,19 @@ public class XmlUtil {
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}
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public static Document parseDocument(String theInput) throws IOException, SAXException {
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StringReader reader = new StringReader(theInput);
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return parseDocument(reader);
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}
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public static Document parseDocument(Reader reader) throws SAXException, IOException {
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return parseDocument(reader, true);
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}
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public static Document parseDocument(Reader theReader, boolean theNamespaceAware) throws SAXException, IOException {
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DocumentBuilder builder;
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try {
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DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory.newInstance();
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docBuilderFactory.setNamespaceAware(true);
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docBuilderFactory.setNamespaceAware(theNamespaceAware);
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docBuilderFactory.setXIncludeAware(false);
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docBuilderFactory.setExpandEntityReferences(false);
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try {
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@ -1885,10 +1895,23 @@ public class XmlUtil {
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throw new ConfigurationException(e);
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}
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InputSource src = new InputSource(new StringReader(theInput));
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InputSource src = new InputSource(theReader);
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return builder.parse(src);
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}
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public static List<Element> getChildrenByTagName(Element theParent, String theName) {
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List<Element> nodeList = new ArrayList<Element>();
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for (Node child = theParent.getFirstChild(); child != null; child = child.getNextSibling()) {
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if (child.getNodeType() == Node.ELEMENT_NODE && theName.equals(child.getNodeName())) {
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nodeList.add((Element) child);
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}
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}
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return nodeList;
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}
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public static String encodeDocument(Node theElement) throws TransformerException {
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return encodeDocument(theElement, false);
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}
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@ -123,6 +123,10 @@ public class UploadTerminologyCommand extends BaseCommand {
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}
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private void invokeOperation(String theTermUrl, String[] theDatafile, IGenericClient theClient, IBaseParameters theInputParameters, String theOperationName) throws ParseException {
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boolean isDeltaOperation =
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theOperationName.equals(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD) ||
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theOperationName.equals(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE);
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ParametersUtil.addParameterToParametersUri(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_SYSTEM, theTermUrl);
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ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
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@ -134,19 +138,37 @@ public class UploadTerminologyCommand extends BaseCommand {
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for (String nextDataFile : theDatafile) {
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try (FileInputStream fileInputStream = new FileInputStream(nextDataFile)) {
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if (nextDataFile.endsWith(".csv") || nextDataFile.endsWith(".properties")) {
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boolean isFhirType = nextDataFile.endsWith(".json") || nextDataFile.endsWith(".xml");
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if (nextDataFile.endsWith(".csv") || nextDataFile.endsWith(".properties") || isFhirType) {
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ourLog.info("Compressing and adding file: {}", nextDataFile);
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ZipEntry nextEntry = new ZipEntry(stripPath(nextDataFile));
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zipOutputStream.putNextEntry(nextEntry);
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if (isDeltaOperation && isFhirType) {
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CountingInputStream countingInputStream = new CountingInputStream(fileInputStream);
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IOUtils.copy(countingInputStream, zipOutputStream);
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haveCompressedContents = true;
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compressedSourceBytesCount += countingInputStream.getCount();
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ourLog.info("Adding CodeSystem resource file: {}", nextDataFile);
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zipOutputStream.flush();
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ourLog.info("Finished compressing {}", nextDataFile);
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String contents = IOUtils.toString(fileInputStream, Charsets.UTF_8);
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EncodingEnum encoding = EncodingEnum.detectEncodingNoDefault(contents);
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if (encoding == null) {
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throw new ParseException("Could not detect FHIR encoding for file: " + nextDataFile);
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}
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CodeSystem resource = encoding.newParser(myFhirCtx).parseResource(CodeSystem.class, contents);
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ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_CODESYSTEM, resource);
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} else {
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ourLog.info("Compressing and adding file: {}", nextDataFile);
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ZipEntry nextEntry = new ZipEntry(stripPath(nextDataFile));
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zipOutputStream.putNextEntry(nextEntry);
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CountingInputStream countingInputStream = new CountingInputStream(fileInputStream);
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IOUtils.copy(countingInputStream, zipOutputStream);
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haveCompressedContents = true;
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compressedSourceBytesCount += countingInputStream.getCount();
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zipOutputStream.flush();
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ourLog.info("Finished compressing {}", nextDataFile);
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}
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} else if (nextDataFile.endsWith(".zip")) {
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@ -154,19 +176,6 @@ public class UploadTerminologyCommand extends BaseCommand {
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String fileName = "file:" + nextDataFile;
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addFileToRequestBundle(theInputParameters, fileName, IOUtils.toByteArray(fileInputStream));
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} else if (nextDataFile.endsWith(".json") || nextDataFile.endsWith(".xml")) {
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ourLog.info("Adding CodeSystem resource file: {}", nextDataFile);
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String contents = IOUtils.toString(fileInputStream, Charsets.UTF_8);
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EncodingEnum encoding = EncodingEnum.detectEncodingNoDefault(contents);
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if (encoding == null) {
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throw new ParseException("Could not detect FHIR encoding for file: " + nextDataFile);
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}
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CodeSystem resource = encoding.newParser(myFhirCtx).parseResource(CodeSystem.class, contents);
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ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_CODESYSTEM, resource);
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} else {
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throw new ParseException("Don't know how to handle file: " + nextDataFile);
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@ -96,6 +96,21 @@
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<artifactId>h2</artifactId>
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</dependency>
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<!-- Hibernate search Lucene backend -->
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<dependency>
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<groupId>org.hibernate.search</groupId>
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<artifactId>hibernate-search-backend-lucene</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.lucene</groupId>
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<artifactId>lucene-analyzers-phonetic</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.lucene</groupId>
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<artifactId>lucene-backward-codecs</artifactId>
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</dependency>
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<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
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<dependency>
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<groupId>org.eclipse.jetty</groupId>
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@ -92,14 +92,15 @@ public class CommonConfig {
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extraProperties.put("hibernate.cache.use_second_level_cache", "false");
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extraProperties.put("hibernate.cache.use_structured_entries", "false");
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extraProperties.put("hibernate.cache.use_minimal_puts", "false");
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extraProperties.put("hibernate.search.backend.type", "lucene");
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extraProperties.put(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
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extraProperties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), "local-filesystem");
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extraProperties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
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extraProperties.put(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), "LUCENE_CURRENT");
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if (System.getProperty("lowmem") != null) {
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// extraProperties.put(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
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// extraProperties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), "local-filesystem");
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// extraProperties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
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// extraProperties.put(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), "LUCENE_CURRENT");
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// if (System.getProperty("lowmem") != null) {
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extraProperties.put(HibernateOrmMapperSettings.ENABLED, "false");
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}
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// }
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return extraProperties;
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}
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@ -0,0 +1,5 @@
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---
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type: add
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issue: 2702
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title: "The JPA server terminology uploader now supports uploading ICD-10-CM (US Edition) using the
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native format for that vocabulary."
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@ -83,6 +83,12 @@ Note that the path and exact filename of the terminology files will likely need
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./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
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```
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### ICD-10-CM
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```
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./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
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```
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# Migrate Database
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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.
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@ -127,14 +127,17 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
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UploadStatistics stats;
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switch (codeSystemUrl) {
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case ITermLoaderSvc.SCT_URI:
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stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
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case ITermLoaderSvc.ICD10CM_URI:
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stats = myTerminologyLoaderSvc.loadIcd10cm(localFiles, theRequestDetails);
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break;
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case ITermLoaderSvc.IMGTHLA_URI:
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stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
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break;
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case ITermLoaderSvc.LOINC_URI:
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stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
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break;
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case ITermLoaderSvc.IMGTHLA_URI:
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stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
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case ITermLoaderSvc.SCT_URI:
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stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
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break;
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default:
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stats = myTerminologyLoaderSvc.loadCustom(codeSystemUrl, localFiles, theRequestDetails);
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@ -395,7 +398,7 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
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return retVal;
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}
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private static class FileBackedFileDescriptor implements ITermLoaderSvc.FileDescriptor {
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public static class FileBackedFileDescriptor implements ITermLoaderSvc.FileDescriptor {
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private final File myNextFile;
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public FileBackedFileDescriptor(File theNextFile) {
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@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
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import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
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import ca.uhn.fhir.jpa.term.icd10cm.Icd10CmLoader;
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import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListLinkHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincDocumentOntologyHandler;
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@ -53,6 +54,7 @@ import org.hl7.fhir.r4.model.Enumerations;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.springframework.aop.support.AopUtils;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.xml.sax.SAXException;
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import javax.annotation.Nonnull;
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import javax.validation.constraints.NotNull;
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@ -69,6 +71,7 @@ import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Locale;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Optional;
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@ -260,6 +263,40 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
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}
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}
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@Override
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public UploadStatistics loadIcd10cm(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
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ourLog.info("Beginning ICD-10-cm processing");
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CodeSystem cs = new CodeSystem();
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cs.setUrl(ICD10CM_URI);
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cs.setName("ICD-10-CM");
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cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
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cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
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TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
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int count = 0;
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try (LoadedFileDescriptors compressedDescriptors = new LoadedFileDescriptors(theFiles)) {
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for (FileDescriptor nextDescriptor : compressedDescriptors.getUncompressedFileDescriptors()) {
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if (nextDescriptor.getFilename().toLowerCase(Locale.US).endsWith(".xml")) {
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try (InputStream inputStream = nextDescriptor.getInputStream()) {
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InputStreamReader reader = new InputStreamReader(inputStream, Charsets.UTF_8);
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Icd10CmLoader loader = new Icd10CmLoader(codeSystemVersion);
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loader.load(reader);
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count += loader.getConceptCount();
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}
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}
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}
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} catch (IOException | SAXException e) {
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throw new InternalErrorException(e);
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}
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cs.setVersion(codeSystemVersion.getCodeSystemVersionId());
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IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, cs, null, null);
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return new UploadStatistics(count, target);
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}
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@Override
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public UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
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try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
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@ -36,6 +36,7 @@ public interface ITermLoaderSvc {
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String IMGTHLA_URI = "http://www.ebi.ac.uk/ipd/imgt/hla";
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String LOINC_URI = "http://loinc.org";
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String SCT_URI = "http://snomed.info/sct";
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String ICD10CM_URI = "http://hl7.org/fhir/sid/icd-10-cm";
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String IEEE_11073_10101_URI = "urn:iso:std:iso:11073:10101";
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UploadStatistics loadImgthla(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
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@ -44,6 +45,8 @@ public interface ITermLoaderSvc {
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UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
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UploadStatistics loadIcd10cm(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
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UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
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UploadStatistics loadDeltaAdd(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
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@ -0,0 +1,81 @@
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package ca.uhn.fhir.jpa.term.icd10cm;
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
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import ca.uhn.fhir.util.XmlUtil;
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import org.w3c.dom.Document;
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import org.w3c.dom.Element;
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import org.xml.sax.SAXException;
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import java.io.IOException;
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import java.io.Reader;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public class Icd10CmLoader {
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private final TermCodeSystemVersion myCodeSystemVersion;
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private int myConceptCount;
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/**
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* Constructor
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*/
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public Icd10CmLoader(TermCodeSystemVersion theCodeSystemVersion) {
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myCodeSystemVersion = theCodeSystemVersion;
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}
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public void load(Reader theReader) throws IOException, SAXException {
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myConceptCount = 0;
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Document document = XmlUtil.parseDocument(theReader, false);
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Element documentElement = document.getDocumentElement();
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// Extract version: Should only be 1 tag
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for (Element nextVersion : XmlUtil.getChildrenByTagName(documentElement, "version")) {
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String versionId = nextVersion.getTextContent();
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if (isNotBlank(versionId)) {
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myCodeSystemVersion.setCodeSystemVersionId(versionId);
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}
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}
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// Extract Diags (codes)
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for (Element nextChapter : XmlUtil.getChildrenByTagName(documentElement, "chapter")) {
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for (Element nextSection : XmlUtil.getChildrenByTagName(nextChapter, "section")) {
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for (Element nextDiag : XmlUtil.getChildrenByTagName(nextSection, "diag")) {
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extractCode(nextDiag, null);
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}
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}
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}
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}
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private void extractCode(Element theDiagElement, TermConcept theParentConcept) {
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String code = theDiagElement.getElementsByTagName("name").item(0).getTextContent();
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String display = theDiagElement.getElementsByTagName("desc").item(0).getTextContent();
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TermConcept concept;
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if (theParentConcept == null) {
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concept = myCodeSystemVersion.addConcept();
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} else {
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concept = theParentConcept.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA);
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}
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concept.setCode(code);
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concept.setDisplay(display);
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for (Element nextChildDiag : XmlUtil.getChildrenByTagName(theDiagElement, "diag")) {
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extractCode(nextChildDiag, concept);
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}
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myConceptCount++;
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}
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public int getConceptCount() {
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return myConceptCount;
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}
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}
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@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
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import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
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import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.util.ClasspathUtil;
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import com.google.common.base.Charsets;
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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();
|
||||
|
||||
|
|
|
|||
|
|
@ -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());
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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"));
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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>
|
||||
Loading…
Reference in New Issue