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Merge pull request #1460 from jamesagnew/dm-fix-resourcetable-lookups-for-preexpansion-and-code-validation 

Fix ResourceTable lookups for pre-expansion and code validation.
This commit is contained in:
Diederik Muylwyk 2019-09-02 18:17:45 -04:00 committed by GitHub
parent 9ea937d007 c34d8458ef
commit 6b826560c4
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3 changed files with 32 additions and 8 deletions
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30
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -55,6 +55,7 @@ import org.hibernate.search.query.dsl.BooleanJunction;
import org.hibernate.search.query.dsl.QueryBuilder;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.*;
@ -487,7 +488,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
Optional<TermValueSet> optionalTermValueSet;
if (theValueSetToExpand.hasId()) {
Long valueSetResourcePid = IDao.RESOURCE_PID.get(theValueSetToExpand);
Long valueSetResourcePid = getValueSetResourcePid(theValueSetToExpand.getIdElement());
optionalTermValueSet = myValueSetDao.findByResourcePid(valueSetResourcePid);
} else if (theValueSetToExpand.hasUrl()) {
optionalTermValueSet = myValueSetDao.findByUrl(theValueSetToExpand.getUrl());
@ -956,7 +957,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Override
public boolean isValueSetPreExpandedForCodeValidation(ValueSet theValueSet) {
Long valueSetResourcePid = IDao.RESOURCE_PID.get(theValueSet);
Long valueSetResourcePid = getValueSetResourcePid(theValueSet.getIdElement());
Optional<TermValueSet> optionalTermValueSet = myValueSetDao.findByResourcePid(valueSetResourcePid);
if (!optionalTermValueSet.isPresent()) {
@ -980,7 +981,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
ValueSet theValueSet, String theSystem, String theCode, String theDisplay, Coding theCoding, CodeableConcept theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet.hasId(), "ValueSet.id is required");
Long valueSetResourcePid = IDao.RESOURCE_PID.get(theValueSet);
Long valueSetResourcePid = getValueSetResourcePid(theValueSet.getIdElement());
List<TermValueSetConcept> concepts = new ArrayList<>();
if (isNotBlank(theCode)) {
@ -1158,6 +1159,27 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
protected abstract CodeSystem getCodeSystemFromContext(String theSystem);
private Long getCodeSystemResourcePid(IIdType theIdType) {
return getCodeSystemResourcePid(theIdType, null);
}
private Long getCodeSystemResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
return getResourcePid(myCodeSystemResourceDao, theIdType, theRequestDetails);
}
private Long getValueSetResourcePid(IIdType theIdType) {
return getValueSetResourcePid(theIdType, null);
}
private Long getValueSetResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
return getResourcePid(myValueSetResourceDao, theIdType, theRequestDetails);
}
private Long getResourcePid(IFhirResourceDao<? extends IBaseResource> theResourceDao, IIdType theIdType, RequestDetails theRequestDetails) {
ResourceTable resourceTable = (ResourceTable) theResourceDao.readEntity(theIdType, theRequestDetails);
return resourceTable.getId();
}
private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, int theTotalConcepts) {
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
return;
@ -1625,7 +1647,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.COMPLETE || theCodeSystem.getContent() == null || theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", theResourceEntity.getIdDt().getValue(), theCodeSystem.getContentElement().getValueAsString());
Long codeSystemResourcePid = IDao.RESOURCE_PID.get(theCodeSystem);
Long codeSystemResourcePid = getCodeSystemResourcePid(theCodeSystem.getIdElement());
TermCodeSystemVersion persCs = myCodeSystemVersionDao.findCurrentVersionForCodeSystemResourcePid(codeSystemResourcePid);
if (persCs != null) {
ourLog.info("Code system version already exists in database");

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
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@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IDao;
import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
@ -601,7 +600,9 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
TermCodeSystem codeSystem = myTermCodeSystemDao.findByResourcePid(IDao.RESOURCE_PID.get(codeSystemResource));
ResourceTable resourceTable = (ResourceTable) myCodeSystemDao.readEntity(codeSystemResource.getIdElement(), null);
Long codeSystemResourcePid = resourceTable.getId();
TermCodeSystem codeSystem = myTermCodeSystemDao.findByResourcePid(codeSystemResourcePid);
assertEquals(CS_URL, codeSystem.getCodeSystemUri());
assertEquals("SYSTEM NAME", codeSystem.getName());

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
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@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.*;
@ -1591,7 +1590,9 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
TermCodeSystem codeSystem = myTermCodeSystemDao.findByResourcePid(IDao.RESOURCE_PID.get(codeSystemResource));
ResourceTable resourceTable = (ResourceTable) myCodeSystemDao.readEntity(codeSystemResource.getIdElement(), null);
Long codeSystemResourcePid = resourceTable.getId();
TermCodeSystem codeSystem = myTermCodeSystemDao.findByResourcePid(codeSystemResourcePid);
assertEquals(CS_URL, codeSystem.getCodeSystemUri());
assertEquals("SYSTEM NAME", codeSystem.getName());