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Troubleshooting lack of ValueSet pre-expansion when updating a ValueSet via transaction bundle.

This commit is contained in:
Diederik Muylwyk 2019-09-24 15:30:40 -04:00
parent df4b6c798c
commit 46a6b7aaef
2 changed files with 190 additions and 6 deletions
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8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -1870,7 +1870,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Override
@Transactional
public void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap) {
ourLog.info("Storing TermConceptMap {}", theConceptMap.getIdElement().getValue());
ourLog.info("Storing TermConceptMap for {}", theConceptMap.getIdElement().toVersionless().getValueAsString());
ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theConceptMap.getUrl(), "ConceptMap has no value for ConceptMap.url");
@ -1981,7 +1981,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
throw new UnprocessableEntityException(msg);
}
ourLog.info("Done storing TermConceptMap[{}]", termConceptMap.getId());
ourLog.info("Done storing TermConceptMap[{}] for {}", termConceptMap.getId(), theConceptMap.getIdElement().toVersionless().getValueAsString());
}
@Override
@ -2077,7 +2077,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Override
@Transactional
public void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet) {
ourLog.info("Storing TermValueSet {}", theValueSet.getIdElement().getValue());
ourLog.info("Storing TermValueSet for {}", theValueSet.getIdElement().toVersionless().getValueAsString());
ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theValueSet.getUrl(), "ValueSet has no value for ValueSet.url");
@ -2111,7 +2111,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
throw new UnprocessableEntityException(msg);
}
ourLog.info("Done storing TermValueSet[{}]", termValueSet.getId());
ourLog.info("Done storing TermValueSet[{}] for {}", termValueSet.getId(), theValueSet.getIdElement().toVersionless().getValueAsString());
}
@Override

188
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
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@ -3,8 +3,7 @@ package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
@ -36,6 +35,7 @@ import org.springframework.transaction.support.TransactionTemplate;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.Optional;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_VALUE_SET;
@ -57,12 +57,28 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
loadAndPersistValueSet(theVerb);
}
private void loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb theVerb) throws IOException {
loadAndPersistCodeSystemWithDesignations(theVerb);
loadAndPersistValueSet(theVerb);
}
private void loadAndPersistCodeSystemAndValueSetWithDesignationsAndExclude(HttpVerb theVerb) throws IOException {
loadAndPersistCodeSystemWithDesignations(theVerb);
loadAndPersistValueSetWithExclude(theVerb);
}
private void loadAndPersistCodeSystem(HttpVerb theVerb) throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
codeSystem.setId("CodeSystem/cs");
persistCodeSystem(codeSystem, theVerb);
}
private void loadAndPersistCodeSystemWithDesignations(HttpVerb theVerb) throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs-with-designations.xml");
codeSystem.setId("CodeSystem/cs");
persistCodeSystem(codeSystem, theVerb);
}
private void persistCodeSystem(CodeSystem theCodeSystem, HttpVerb theVerb) {
switch (theVerb) {
case POST:
@ -93,6 +109,12 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
persistValueSet(valueSet, theVerb);
}
private void loadAndPersistValueSetWithExclude(HttpVerb theVerb) throws IOException {
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs-with-exclude.xml");
valueSet.setId("ValueSet/vs");
persistValueSet(valueSet, theVerb);
}
private void persistValueSet(ValueSet theValueSet, HttpVerb theVerb) {
switch (theVerb) {
case POST:
@ -687,6 +709,168 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
}
@Test
public void testUpdateValueSetTriggersAnotherPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
String initialValueSetName = valueSet.getName();
validateTermValueSetNotExpanded(initialValueSetName);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildren(initialValueSetName, codeSystem);
ValueSet updatedValueSet = valueSet;
updatedValueSet.setName(valueSet.getName().concat(" - MODIFIED"));
persistValueSet(updatedValueSet, HttpVerb.PUT);
updatedValueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("Updated ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedValueSet));
String updatedValueSetName = valueSet.getName();
validateTermValueSetNotExpanded(updatedValueSetName);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildren(updatedValueSetName, codeSystem);
}
@Test
public void testUpdateValueSetTriggersAnotherPreExpansionUsingTransactionBundle() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
String initialValueSetName = valueSet.getName();
validateTermValueSetNotExpanded(initialValueSetName);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildren(initialValueSetName, codeSystem);
ValueSet updatedValueSet = valueSet;
updatedValueSet.setName(valueSet.getName().concat(" - MODIFIED"));
String requestUrl = ourClient.getServerBase().concat("/").concat(myExtensionalVsId.getValueAsString());
Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.TRANSACTION);
bundle
.addEntry()
.setFullUrl(updatedValueSet.getUrl())
.setResource(updatedValueSet)
.getRequest()
.setMethod(Bundle.HTTPVerb.PUT)
.setUrl(requestUrl);
ourLog.info("Transaction Bundle:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
ourClient.transaction().withBundle(bundle).execute();
updatedValueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("Updated ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedValueSet));
String updatedValueSetName = valueSet.getName();
validateTermValueSetNotExpanded(updatedValueSetName);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildren(updatedValueSetName, codeSystem);
}
private void validateTermValueSetNotExpanded(String theValueSetName) {
runInTransaction(()->{
Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable);
assertTrue(optionalValueSetByResourcePid.isPresent());
Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
assertTrue(optionalValueSetByUrl.isPresent());
TermValueSet termValueSet = optionalValueSetByUrl.get();
assertSame(optionalValueSetByResourcePid.get(), termValueSet);
ourLog.info("ValueSet:\n" + termValueSet.toString());
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals(theValueSetName, termValueSet.getName());
assertEquals(0, termValueSet.getConcepts().size());
assertEquals(TermValueSetPreExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
});
}
private void validateTermValueSetExpandedAndChildren(String theValueSetName, CodeSystem theCodeSystem) {
runInTransaction(()->{
Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable);
assertTrue(optionalValueSetByResourcePid.isPresent());
Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
assertTrue(optionalValueSetByUrl.isPresent());
TermValueSet termValueSet = optionalValueSetByUrl.get();
assertSame(optionalValueSetByResourcePid.get(), termValueSet);
ourLog.info("ValueSet:\n" + termValueSet.toString());
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals(theValueSetName, termValueSet.getName());
assertEquals(theCodeSystem.getConcept().size(), termValueSet.getConcepts().size());
assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("8450-9", concept.getCode());
assertEquals("Systolic blood pressure--expiration", concept.getDisplay());
assertEquals(2, concept.getDesignations().size());
assertEquals(0, concept.getOrder());
TermValueSetConceptDesignation designation = concept.getDesignations().get(0);
assertEquals("nl", designation.getLanguage());
assertEquals("http://snomed.info/sct", designation.getUseSystem());
assertEquals("900000000000013009", designation.getUseCode());
assertEquals("Synonym", designation.getUseDisplay());
assertEquals("Systolische bloeddruk - expiratie", designation.getValue());
designation = concept.getDesignations().get(1);
assertEquals("sv", designation.getLanguage());
assertEquals("http://snomed.info/sct", designation.getUseSystem());
assertEquals("900000000000013009", designation.getUseCode());
assertEquals("Synonym", designation.getUseDisplay());
assertEquals("Systoliskt blodtryck - utgång", designation.getValue());
concept = termValueSet.getConcepts().get(1);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("11378-7", concept.getCode());
assertEquals("Systolic blood pressure at First encounter", concept.getDisplay());
assertEquals(0, concept.getDesignations().size());
assertEquals(1, concept.getOrder());
// ...
concept = termValueSet.getConcepts().get(22);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("8491-3", concept.getCode());
assertEquals("Systolic blood pressure 1 hour minimum", concept.getDisplay());
assertEquals(1, concept.getDesignations().size());
assertEquals(22, concept.getOrder());
designation = concept.getDesignations().get(0);
assertEquals("nl", designation.getLanguage());
assertEquals("http://snomed.info/sct", designation.getUseSystem());
assertEquals("900000000000013009", designation.getUseCode());
assertEquals("Synonym", designation.getUseDisplay());
assertEquals("Systolische bloeddruk minimaal 1 uur", designation.getValue());
concept = termValueSet.getConcepts().get(23);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("8492-1", concept.getCode());
assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
assertEquals(0, concept.getDesignations().size());
assertEquals(23, concept.getOrder());
});
}
@Test
public void testValidateCodeOperationByCodeAndSystemInstance() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);