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Allow ConceptMap with no explicit group source/target (#1983) 

* Allow ConceptMap with no explicit group source/target

* Add changelog
This commit is contained in:
James Agnew 2020-07-15 12:57:10 -04:00 committed by GitHub
parent 29bf6b8171
commit 063bf4237c
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5 changed files with 75 additions and 7 deletions
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6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1983-allow-conceptmap-with-no-group-source_or_target.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 1983
title: "ConceptMap resources were blocked from uploading into the JPA server if the ConceptMap had a source
and/or target URL defined at the ConceptMap level but not at the group level. This prevented some US Core
resources from being successfully uploaded. This has been corrected."

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
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@ -1504,6 +1504,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return;
}
if (source == null && theConceptMap.hasSourceCanonicalType()) {
source = theConceptMap.getSourceCanonicalType().getValueAsString();
}
if (target == null && theConceptMap.hasTargetCanonicalType()) {
target = theConceptMap.getTargetCanonicalType().getValueAsString();
}
/*
* For now we always delete old versions. At some point, it would be nice to allow configuration to keep old versions.
*/
@ -1531,17 +1538,28 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
if (theConceptMap.hasGroup()) {
TermConceptMapGroup termConceptMapGroup;
for (ConceptMap.ConceptMapGroupComponent group : theConceptMap.getGroup()) {
if (isBlank(group.getSource())) {
String groupSource = group.getSource();
if (isBlank(groupSource)) {
groupSource = source;
}
if (isBlank(groupSource)) {
throw new UnprocessableEntityException("ConceptMap[url='" + theConceptMap.getUrl() + "'] contains at least one group without a value in ConceptMap.group.source");
}
if (isBlank(group.getTarget())) {
String groupTarget = group.getTarget();
if (isBlank(groupTarget)) {
groupTarget = target;
}
if (isBlank(groupTarget)) {
throw new UnprocessableEntityException("ConceptMap[url='" + theConceptMap.getUrl() + "'] contains at least one group without a value in ConceptMap.group.target");
}
termConceptMapGroup = new TermConceptMapGroup();
termConceptMapGroup.setConceptMap(termConceptMap);
termConceptMapGroup.setSource(group.getSource());
termConceptMapGroup.setSource(groupSource);
termConceptMapGroup.setSourceVersion(group.getSourceVersion());
termConceptMapGroup.setTarget(group.getTarget());
termConceptMapGroup.setTarget(groupTarget);
termConceptMapGroup.setTargetVersion(group.getTargetVersion());
myConceptMapGroupDao.save(termConceptMapGroup);

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
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@ -127,7 +127,8 @@ public class TestR4Config extends BaseJavaConfigR4 {
SLF4JLogLevel level = SLF4JLogLevel.INFO;
DataSource dataSource = ProxyDataSourceBuilder
.create(retVal)
.logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
.logQueryBySlf4j(level)
.logSlowQueryBySlf4j(10, TimeUnit.SECONDS, level)
.beforeQuery(new BlockLargeNumbersOfParamsListener())
.afterQuery(captureQueriesListener())
.afterQuery(new CurrentThreadCaptureQueriesListener())

44
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java
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@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.api.model.TranslationResult;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
@ -1042,6 +1043,49 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
});
}
/**
* Some US core ConceptMaps use this style, e.g:
*
* http://hl7.org/fhir/us/core/ConceptMap/ndc-cvx
*/
@Test
public void testUploadConceptMapWithOnlyCanonicalSourceAtConceptMapLevel() {
ConceptMap cm = new ConceptMap();
cm.setUrl("http://foo");
cm.setSource(new CanonicalType("http://source"));
cm.setTarget(new CanonicalType("http://target"));
cm.addGroup().addElement().setCode("source1").addTarget().setCode("target1").setEquivalence(ConceptMapEquivalence.EQUAL);
myConceptMapDao.create(cm);
runInTransaction(()->{
TranslationRequest translationRequest = new TranslationRequest();
translationRequest.getCodeableConcept().addCoding()
.setSystem("http://source")
.setCode("source1");
translationRequest.setTarget(new UriType("http://target"));
ourLog.info("*** About to translate");
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
ourLog.info("*** Done translating");
assertTrue(translationResult.getResult().booleanValue());
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
assertEquals(1, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
assertEquals("equal", translationMatch.getEquivalence().getCode());
Coding concept = translationMatch.getConcept();
assertEquals("target1", concept.getCode());
assertEquals(null, concept.getDisplay());
assertEquals("http://target", concept.getSystem());
});
}
@Test
public void testUploadAndApplyR4DemoConceptMap() throws IOException {

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmTestR4.java
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@ -7,14 +7,12 @@ import ca.uhn.fhir.jpa.dao.data.INpmPackageDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionResourceDao;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.entity.NpmPackageEntity;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionResourceEntity;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.test.utilities.JettyUtil;
@ -96,6 +94,7 @@ public class NpmTestR4 extends BaseJpaR4Test {
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
}
@Test
public void testCacheDstu3Package() throws Exception {
byte[] bytes = loadClasspathBytes("/packages/nictiz.fhir.nl.stu3.questionnaires-1.0.2.tgz");