* Update CLI upload examples for R4. * Fixes #3734 Add support for ICD-10 (International) Include all concept properties in ICD-10 loader. Remove newlines and tabs from ICD Rubrics. * Bump Msg code and use in Term Loader. * Added a changelog entry for this addition. * Update icd10-dummy-test-en.xml * Added a default impl to the new interface method to avoid breaking upstream projects. Co-authored-by: Kevin Dougan <kevin.dougan@smilecdr.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: Kevin SmileCDR <kevinsmilecdr@Kevins-MacBook-Pro-2.local>
This commit is contained in:
Kai Kewley
GitHub
parent
100b8f9190
commit
dd5c49a9ef
|
|
@ -25,7 +25,7 @@ public final class Msg {
|
|||
|
||||
/**
|
||||
* IMPORTANT: Please update the following comment after you add a new code
|
||||
* Last used code value: 2134
|
||||
* Last used code value: 2135
|
||||
*/
|
||||
|
||||
private Msg() {}
|
||||
|
|
|
|||
|
|
@ -1870,10 +1870,10 @@ public class XmlUtil {
|
|||
}
|
||||
|
||||
public static Document parseDocument(Reader reader) throws SAXException, IOException {
|
||||
return parseDocument(reader, true);
|
||||
return parseDocument(reader, true, false);
|
||||
}
|
||||
|
||||
public static Document parseDocument(Reader theReader, boolean theNamespaceAware) throws SAXException, IOException {
|
||||
public static Document parseDocument(Reader theReader, boolean theNamespaceAware, boolean allowDoctypeDeclaration) throws SAXException, IOException {
|
||||
DocumentBuilder builder;
|
||||
try {
|
||||
DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory.newInstance();
|
||||
|
|
@ -1881,7 +1881,7 @@ public class XmlUtil {
|
|||
docBuilderFactory.setXIncludeAware(false);
|
||||
docBuilderFactory.setExpandEntityReferences(false);
|
||||
try {
|
||||
docBuilderFactory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
|
||||
docBuilderFactory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", !allowDoctypeDeclaration);
|
||||
docBuilderFactory.setFeature("http://xml.org/sax/features/external-general-entities", false);
|
||||
docBuilderFactory.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-grammar", false);
|
||||
docBuilderFactory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
|
||||
|
|
|
|||
|
|
@ -0,0 +1,4 @@
|
|||
---
|
||||
type: add
|
||||
issue: 3734
|
||||
title: "Added support for loading the International version of ICD-10. Thanks to kaicode for the contribution!"
|
||||
|
|
@ -74,19 +74,25 @@ Note that the path and exact filename of the terminology files will likely need
|
|||
### SNOMED CT
|
||||
|
||||
```
|
||||
./hapi-fhir-cli upload-terminology -d Downloads/SnomedCT_RF2Release_INT_20160131.zip -f dstu3 -t http://localhost:8080/baseDstu3 -u http://snomed.info/sct
|
||||
./hapi-fhir-cli upload-terminology -d Downloads/SnomedCT_InternationalRF2_PRODUCTION_20220131T120000Z.zip -v r4 -t http://localhost:8080/fhir -u http://snomed.info/sct
|
||||
```
|
||||
|
||||
### LOINC
|
||||
|
||||
```
|
||||
./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
|
||||
./hapi-fhir-cli upload-terminology -d Downloads/LOINC_2.54_MULTI-AXIAL_HIERARCHY.zip -d Downloads/LOINC_2.54_Text.zip -v r4 -t http://localhost:8080/fhir -u http://loinc.org
|
||||
```
|
||||
|
||||
### ICD-10 (International Version)
|
||||
|
||||
```
|
||||
./hapi-fhir-cli upload-terminology -d Downloads/icdClaML2019ens.zip -v r4 -t http://localhost:8080/fhir -u http://hl7.org/fhir/sid/icd-10
|
||||
```
|
||||
|
||||
### 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
|
||||
./hapi-fhir-cli upload-terminology -d Downloads/icd10cm_tabular_2021.xml -v r4 -t http://localhost:8080/fhir -u http://hl7.org/fhir/sid/icd-10-cm
|
||||
```
|
||||
|
||||
# Migrate Database
|
||||
|
|
|
|||
|
|
@ -129,6 +129,9 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
|
|||
|
||||
UploadStatistics stats;
|
||||
switch (codeSystemUrl) {
|
||||
case ITermLoaderSvc.ICD10_URI:
|
||||
stats = myTerminologyLoaderSvc.loadIcd10(localFiles, theRequestDetails);
|
||||
break;
|
||||
case ITermLoaderSvc.ICD10CM_URI:
|
||||
stats = myTerminologyLoaderSvc.loadIcd10cm(localFiles, theRequestDetails);
|
||||
break;
|
||||
|
|
|
|||
|
|
@ -10,6 +10,7 @@ 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.icd10.Icd10Loader;
|
||||
import ca.uhn.fhir.jpa.term.icd10cm.Icd10CmLoader;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListHandler;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListLinkHandler;
|
||||
|
|
@ -300,6 +301,39 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public UploadStatistics loadIcd10(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
|
||||
ourLog.info("Beginning ICD-10 processing");
|
||||
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(ICD10_URI);
|
||||
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
|
||||
codeSystem.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
|
||||
TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
|
||||
int count = 0;
|
||||
|
||||
try (LoadedFileDescriptors compressedDescriptors = getLoadedFileDescriptors(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) ) {
|
||||
Icd10Loader loader = new Icd10Loader(codeSystem, codeSystemVersion);
|
||||
loader.load(reader);
|
||||
count += loader.getConceptCount();
|
||||
}
|
||||
}
|
||||
}
|
||||
} catch (IOException | SAXException e) {
|
||||
throw new InternalErrorException(Msg.code(2135) + e);
|
||||
}
|
||||
|
||||
codeSystem.setVersion(codeSystemVersion.getCodeSystemVersionId());
|
||||
|
||||
IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, codeSystem, null, null);
|
||||
return new UploadStatistics(count, target);
|
||||
}
|
||||
|
||||
@Override
|
||||
public UploadStatistics loadIcd10cm(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
|
||||
ourLog.info("Beginning ICD-10-cm processing");
|
||||
|
|
|
|||
|
|
@ -0,0 +1,121 @@
|
|||
package ca.uhn.fhir.jpa.term.icd10;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR JPA Server
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2022 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.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.w3c.dom.Document;
|
||||
import org.w3c.dom.Element;
|
||||
import org.xml.sax.SAXException;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.io.Reader;
|
||||
import java.util.Collection;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
|
||||
import static ca.uhn.fhir.util.XmlUtil.getChildrenByTagName;
|
||||
import static ca.uhn.fhir.util.XmlUtil.parseDocument;
|
||||
|
||||
public class Icd10Loader {
|
||||
|
||||
public static final String EXPECTED_ROOT_NODE = "ClaML";
|
||||
private final CodeSystem codeSystem;
|
||||
private final TermCodeSystemVersion codeSystemVersion;
|
||||
private int conceptCount = 0;
|
||||
|
||||
public Icd10Loader(CodeSystem codeSystem, TermCodeSystemVersion codeSystemVersion) {
|
||||
this.codeSystem = codeSystem;
|
||||
this.codeSystemVersion = codeSystemVersion;
|
||||
}
|
||||
|
||||
public void load(Reader reader) throws IOException, SAXException {
|
||||
Document document = parseDocument(reader, false, true);
|
||||
Element documentElement = document.getDocumentElement();
|
||||
|
||||
String rootNodeName = documentElement.getTagName();
|
||||
if (!EXPECTED_ROOT_NODE.equals(rootNodeName)) {
|
||||
return;
|
||||
}
|
||||
|
||||
for (Element title : getChildrenByTagName(documentElement, "Title")) {
|
||||
String name = title.getAttribute("name");
|
||||
if (!name.isEmpty()) {
|
||||
codeSystem.setName(name);
|
||||
codeSystem.setTitle(name);
|
||||
}
|
||||
String version = title.getAttribute("version");
|
||||
if (!version.isEmpty()) {
|
||||
codeSystemVersion.setCodeSystemVersionId(version);
|
||||
}
|
||||
codeSystem.setDescription(title.getTextContent());
|
||||
}
|
||||
|
||||
Map<String, TermConcept> conceptMap = new HashMap<>();
|
||||
for (Element aClass : getChildrenByTagName(documentElement, "Class")) {
|
||||
String code = aClass.getAttribute("code");
|
||||
if (code.isEmpty()) {
|
||||
continue;
|
||||
}
|
||||
|
||||
boolean rootConcept = getChildrenByTagName(aClass, "SuperClass").isEmpty();
|
||||
TermConcept termConcept = rootConcept ? codeSystemVersion.addConcept() : new TermConcept();
|
||||
termConcept.setCode(code);
|
||||
|
||||
// Preferred label and other properties
|
||||
for (Element rubric : getChildrenByTagName(aClass, "Rubric")) {
|
||||
String kind = rubric.getAttribute("kind");
|
||||
Optional<Element> firstLabel = getChildrenByTagName(rubric, "Label").stream().findFirst();
|
||||
if (firstLabel.isPresent()) {
|
||||
String textContent = firstLabel.get().getTextContent();
|
||||
if (textContent != null && !textContent.isEmpty()) {
|
||||
textContent = textContent.replace("\n", "").replace("\r", "").replace("\t", "");
|
||||
if (kind.equals("preferred")) {
|
||||
termConcept.setDisplay(textContent);
|
||||
} else {
|
||||
termConcept.addPropertyString(kind, textContent);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (Element superClass : getChildrenByTagName(aClass, "SuperClass")) {
|
||||
TermConcept parent = conceptMap.get(superClass.getAttribute("code"));
|
||||
if (parent != null) {
|
||||
parent.addChild(termConcept, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
|
||||
}
|
||||
}
|
||||
|
||||
conceptMap.put(code, termConcept);
|
||||
}
|
||||
|
||||
conceptCount = conceptMap.size();
|
||||
}
|
||||
|
||||
public int getConceptCount() {
|
||||
return conceptCount;
|
||||
}
|
||||
}
|
||||
|
|
@ -57,7 +57,7 @@ public class Icd10CmLoader {
|
|||
public void load(Reader theReader) throws IOException, SAXException {
|
||||
myConceptCount = 0;
|
||||
|
||||
Document document = XmlUtil.parseDocument(theReader, false);
|
||||
Document document = XmlUtil.parseDocument(theReader, false, false);
|
||||
Element documentElement = document.getDocumentElement();
|
||||
|
||||
// Extract version: Should only be 1 tag
|
||||
|
|
|
|||
|
|
@ -0,0 +1,78 @@
|
|||
package ca.uhn.fhir.jpa.term.icd10;
|
||||
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
|
||||
import ca.uhn.fhir.util.ClasspathUtil;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
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.Collection;
|
||||
import java.util.List;
|
||||
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
public class Icd10LoaderTest {
|
||||
|
||||
@Test
|
||||
public void testLoadIcd10Cm() throws IOException, SAXException {
|
||||
StringReader reader = new StringReader(ClasspathUtil.loadResource("icd/icd10-dummy-test-en.xml"));
|
||||
TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
Icd10Loader loader = new Icd10Loader(codeSystem, codeSystemVersion);
|
||||
loader.load(reader);
|
||||
|
||||
assertEquals("ICD-10-EN", codeSystem.getTitle());
|
||||
assertEquals("International Statistical Classification of Diseases and Related Health Problems 10th Revision", codeSystem.getDescription());
|
||||
assertEquals("2022-tree-expanded", codeSystemVersion.getCodeSystemVersionId());
|
||||
|
||||
List<TermConcept> rootConcepts = new ArrayList<>(codeSystemVersion.getConcepts());
|
||||
assertEquals(2, rootConcepts.size());
|
||||
TermConcept chapterA = rootConcepts.get(0);
|
||||
assertEquals("A", chapterA.getCode());
|
||||
assertEquals("Fruit", chapterA.getDisplay());
|
||||
Collection<TermConceptProperty> properties = chapterA.getProperties();
|
||||
assertEquals(2, properties.size());
|
||||
assertEquals("Include fruit", chapterA.getStringProperty("inclusion"));
|
||||
assertEquals("Things that are not fruit", chapterA.getStringProperty("exclusion"));
|
||||
|
||||
assertEquals("""
|
||||
A "Fruit"
|
||||
-A1-A3 "A1 to A3 type fruit"
|
||||
--A1 "Apples"
|
||||
--A2 "Pears"
|
||||
--A3 "Bananas"
|
||||
B "Trees"
|
||||
-B1-B2 "A group of trees"
|
||||
--B1 "Oak trees"
|
||||
--B2 "Ash trees"
|
||||
""", toTree(rootConcepts));
|
||||
}
|
||||
|
||||
private String toTree(List<TermConcept> concepts) {
|
||||
StringBuilder buffer = new StringBuilder();
|
||||
for (TermConcept concept : concepts) {
|
||||
toTree(concept, 0, buffer);
|
||||
}
|
||||
return buffer.toString();
|
||||
}
|
||||
|
||||
private void toTree(TermConcept concept, int indent, StringBuilder buffer) {
|
||||
buffer.append("-".repeat(indent));
|
||||
buffer.append(concept.getCode());
|
||||
String display = concept.getDisplay();
|
||||
if (display != null) {
|
||||
buffer.append(" \"").append(display).append("\"");
|
||||
}
|
||||
buffer.append("\n");
|
||||
indent++;
|
||||
for (TermConcept childCode : concept.getChildCodes()) {
|
||||
toTree(childCode, indent, buffer);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,66 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<ClaML version="2.0.0">
|
||||
<!-- All dummy data -->
|
||||
<Title date="2022-06-23" name="ICD-10-EN" version="2022-tree-expanded">International Statistical Classification of Diseases and Related Health Problems 10th Revision</Title>
|
||||
<Class code="A" kind="chapter">
|
||||
<Rubric kind="preferred">
|
||||
<Label xml:lang="en" xml:space="default">Fruit</Label>
|
||||
</Rubric>
|
||||
<Rubric id="id-icd10_20190322-1587556953279-585" kind="inclusion">
|
||||
<Label xml:lang="en" xml:space="default">Include fruit</Label>
|
||||
</Rubric>
|
||||
<Rubric id="id-icd10_20190322-1587556953279-587" kind="exclusion">
|
||||
<Label xml:lang="en" xml:space="default">Things that are not fruit</Label>
|
||||
</Rubric>
|
||||
</Class>
|
||||
<Class code="B" kind="chapter">
|
||||
<Rubric kind="preferred">
|
||||
<Label xml:lang="en" xml:space="default">Trees</Label>
|
||||
</Rubric>
|
||||
<Rubric id="id-icd10_20190322-1587556953279-585" kind="inclusion">
|
||||
<Label xml:lang="en" xml:space="default">Anything that we think is a tree</Label>
|
||||
</Rubric>
|
||||
</Class>
|
||||
<Class code="A1-A3" kind="block">
|
||||
<SuperClass code="A"/>
|
||||
<Rubric kind="preferred">
|
||||
<Label xml:lang="en" xml:space="default">A1 to A3 type fruit</Label>
|
||||
</Rubric>
|
||||
</Class>
|
||||
<Class code="A1" kind="category">
|
||||
<SuperClass code="A1-A3"/>
|
||||
<Rubric kind="preferred">
|
||||
<Label xml:lang="en" xml:space="default">Apples</Label>
|
||||
</Rubric>
|
||||
</Class>
|
||||
<Class code="A2" kind="category">
|
||||
<SuperClass code="A1-A3"/>
|
||||
<Rubric kind="preferred">
|
||||
<Label xml:lang="en" xml:space="default">Pears</Label>
|
||||
</Rubric>
|
||||
</Class>
|
||||
<Class code="A3" kind="category">
|
||||
<SuperClass code="A1-A3"/>
|
||||
<Rubric kind="preferred">
|
||||
<Label xml:lang="en" xml:space="default">Bananas</Label>
|
||||
</Rubric>
|
||||
</Class>
|
||||
<Class code="B1-B2" kind="block">
|
||||
<SuperClass code="B"/>
|
||||
<Rubric kind="preferred">
|
||||
<Label xml:lang="en" xml:space="default">A group of trees</Label>
|
||||
</Rubric>
|
||||
</Class>
|
||||
<Class code="B1" kind="category">
|
||||
<SuperClass code="B1-B2"/>
|
||||
<Rubric kind="preferred">
|
||||
<Label xml:lang="en" xml:space="default">Oak trees</Label>
|
||||
</Rubric>
|
||||
</Class>
|
||||
<Class code="B2" kind="category">
|
||||
<SuperClass code="B1-B2"/>
|
||||
<Rubric kind="preferred">
|
||||
<Label xml:lang="en" xml:space="default">Ash trees</Label>
|
||||
</Rubric>
|
||||
</Class>
|
||||
</ClaML>
|
||||
|
|
@ -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 ICD10_URI = "http://hl7.org/fhir/sid/icd-10";
|
||||
String ICD10CM_URI = "http://hl7.org/fhir/sid/icd-10-cm";
|
||||
String IEEE_11073_10101_URI = "urn:iso:std:iso:11073:10101";
|
||||
|
||||
|
|
@ -45,6 +46,10 @@ public interface ITermLoaderSvc {
|
|||
|
||||
UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
|
||||
|
||||
default UploadStatistics loadIcd10(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
|
||||
return null;
|
||||
}
|
||||
|
||||
UploadStatistics loadIcd10cm(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
|
||||
|
||||
UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
|
||||
|
|
|
|||
Loading…
Reference in New Issue